Start: 2024-02-21 17:07:42 GMT [bullseye] Package: shasta Version: 0.7.0-3 Installed-Size: 2324 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libboost-chrono1.74.0 (>= 1.74.0), libboost-program-options1.74.0 (>= 1.74.0), libc6 (>= 2.14), libgcc-s1 (>= 3.0), libstdc++6 (>= 9), python3-shasta (= 0.7.0-3) 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_0.7.0-3_amd64.deb Size: 546876 MD5sum: 55e0f6cafa186ae7f31f9f48cb1ec27c SHA256: 7f2703331d94ebabf4b40e5a3552ffdbdb9ead1dc524420e6b7fdae0f16d3dc2 [bullseye-next] Package: shasta Version: 0.7.0-3 Installed-Size: 2324 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libboost-chrono1.74.0 (>= 1.74.0), libboost-program-options1.74.0 (>= 1.74.0), libc6 (>= 2.14), libgcc-s1 (>= 3.0), libstdc++6 (>= 9), python3-shasta (= 0.7.0-3) 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_0.7.0-3_amd64.deb Size: 546876 MD5sum: 55e0f6cafa186ae7f31f9f48cb1ec27c SHA256: 7f2703331d94ebabf4b40e5a3552ffdbdb9ead1dc524420e6b7fdae0f16d3dc2 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 --warn-on-usr-move fail --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz -d bullseye -d bullseye-next -B /srv/piuparts.debian.org/slave/refchroot/bullseye2next/reference-chroot-metadata.dat --apt shasta=0.7.0-3 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.3.1~202401311821~1.3-2-g28295102 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 --warn-on-usr-move fail --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz -d bullseye -d bullseye-next -B /srv/piuparts.debian.org/slave/refchroot/bullseye2next/reference-chroot-metadata.dat --apt shasta=0.7.0-3 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpa5_fhb1n 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpa5_fhb1n 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m2.1s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m2.1s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n/proc'] 0m2.1s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n/proc'] 0m2.1s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n/dev/pts'] 0m2.1s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n/dev/pts'] 0m2.1s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n/dev/ptmx'] 0m2.1s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n/dev/ptmx'] 0m2.1s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n/dev/console'] 0m2.1s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n/dev/console'] 0m2.1s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n/dev/shm'] 0m2.1s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n/dev/shm'] 0m2.1s DEBUG: sources.list: deb http://deb.debian.org/debian/ bullseye main 0m2.1s DEBUG: Created policy-rc.d and chmodded it. 0m2.1s DEBUG: Created resolv.conf. 0m2.1s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpa5_fhb1n/tmp/scripts/ 0m2.1s INFO: Running scripts post_chroot_unpack 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'apt-get', 'update'] 0m5.9s DUMP: Get:1 http://deb.debian.org/debian bullseye InRelease [116 kB] Get:2 http://deb.debian.org/debian bullseye/main amd64 Packages [8068 kB] Get:3 http://deb.debian.org/debian bullseye/main Translation-en [6236 kB] Fetched 14.4 MB in 3s (4952 kB/s) Reading package lists... 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'apt-get', 'update'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'apt-get', '-yf', 'dist-upgrade'] 0m9.1s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: base-files libc-bin libc6 libgnutls30 perl-base tar tzdata 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 7841 kB of archives. After this operation, 44.0 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main amd64 base-files amd64 11.1+deb11u9 [70.2 kB] Get:2 http://deb.debian.org/debian bullseye/main amd64 perl-base amd64 5.32.1-4+deb11u3 [1628 kB] Get:3 http://deb.debian.org/debian bullseye/main amd64 tar amd64 1.34+dfsg-1+deb11u1 [847 kB] Get:4 http://deb.debian.org/debian bullseye/main amd64 libc6 amd64 2.31-13+deb11u8 [2823 kB] Get:5 http://deb.debian.org/debian bullseye/main amd64 libc-bin amd64 2.31-13+deb11u8 [829 kB] Get:6 http://deb.debian.org/debian bullseye/main amd64 libgnutls30 amd64 3.7.1-5+deb11u4 [1340 kB] Get:7 http://deb.debian.org/debian bullseye/main amd64 tzdata all 2024a-0+deb11u1 [304 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 7841 kB in 0s (48.2 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 ... 6664 files and directories currently installed.) Preparing to unpack .../base-files_11.1+deb11u9_amd64.deb ... Unpacking base-files (11.1+deb11u9) over (11.1+deb11u8) ... Setting up base-files (11.1+deb11u9) ... 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 ... 6664 files and directories currently installed.) Preparing to unpack .../perl-base_5.32.1-4+deb11u3_amd64.deb ... Unpacking perl-base (5.32.1-4+deb11u3) over (5.32.1-4+deb11u2) ... Setting up perl-base (5.32.1-4+deb11u3) ... (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 ... 6664 files and directories currently installed.) Preparing to unpack .../tar_1.34+dfsg-1+deb11u1_amd64.deb ... Unpacking tar (1.34+dfsg-1+deb11u1) over (1.34+dfsg-1) ... Setting up tar (1.34+dfsg-1+deb11u1) ... (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 ... 6664 files and directories currently installed.) Preparing to unpack .../libc6_2.31-13+deb11u8_amd64.deb ... Unpacking libc6:amd64 (2.31-13+deb11u8) over (2.31-13+deb11u6) ... Setting up libc6:amd64 (2.31-13+deb11u8) ... (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 ... 6664 files and directories currently installed.) Preparing to unpack .../libc-bin_2.31-13+deb11u8_amd64.deb ... Unpacking libc-bin (2.31-13+deb11u8) over (2.31-13+deb11u6) ... Setting up libc-bin (2.31-13+deb11u8) ... (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 ... 6664 files and directories currently installed.) Preparing to unpack .../libgnutls30_3.7.1-5+deb11u4_amd64.deb ... Unpacking libgnutls30:amd64 (3.7.1-5+deb11u4) over (3.7.1-5+deb11u3) ... Setting up libgnutls30:amd64 (3.7.1-5+deb11u4) ... (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 ... 6664 files and directories currently installed.) Preparing to unpack .../tzdata_2024a-0+deb11u1_all.deb ... Unpacking tzdata (2024a-0+deb11u1) over (2021a-1+deb11u10) ... Setting up tzdata (2024a-0+deb11u1) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Feb 21 17:07:51 UTC 2024. Universal Time is now: Wed Feb 21 17:07:51 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Processing triggers for libc-bin (2.31-13+deb11u8) ... 0m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'apt-get', '-yf', 'dist-upgrade'] 0m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m9.5s DUMP: 29fcf27583012b383113cec2bf757015 - 0m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m9.5s INFO: Running scripts post_setup 0m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/post_setup_dummy_users'] 0m10.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/post_setup_dummy_users'] 0m10.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/post_setup_forbid_home'] 0m10.6s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/post_setup_forbid_home'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/post_setup_force-unsafe-io'] 0m10.6s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' dpkg-divert: warning: diverting file '/bin/sync' from an Essential package with rename is dangerous, use --no-rename '/bin/sync' -> 'true' 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/post_setup_force-unsafe-io'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/post_setup_minimize'] 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/post_setup_minimize'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/post_setup_squeeze-backports'] 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/post_setup_squeeze-backports'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/post_setup_zz_backports'] 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/post_setup_zz_backports'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m10.6s DUMP: install ok installed adduser adduser 3.118+deb11u1 install ok installed apt apt 2.2.4 install ok installed base-files base-files 11.1+deb11u9 install ok installed base-passwd base-passwd 3.5.51 install ok installed bash bash 5.1-2+deb11u1 install ok installed bsdutils bsdutils 1:2.36.1-8+deb11u1 install ok installed coreutils coreutils 8.32-4+b1 install ok installed dash dash 0.5.11+git20200708+dd9ef66-5 install ok installed debconf debconf 1.5.77 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1+deb11u1 install ok installed debianutils debianutils 4.11.2 install ok installed diffutils diffutils 1:3.7-5 install ok installed dpkg dpkg 1.20.13 install ok installed e2fsprogs e2fsprogs 1.46.2-2 install ok installed findutils findutils 4.8.0-1 install ok installed gcc-10-base:amd64 gcc-10-base 10.2.1-6 install ok installed gcc-9-base:amd64 gcc-9-base 9.3.0-22 install ok installed gpgv gpgv 2.2.27-2+deb11u2 install ok installed grep grep 3.6-1+deb11u1 install ok installed gzip gzip 1.10-4+deb11u1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.60 install ok installed libacl1:amd64 libacl1 2.2.53-10 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.2.4 install ok installed libattr1:amd64 libattr1 1:2.4.48-6 install ok installed libaudit-common libaudit-common 1:3.0-2 install ok installed libaudit1:amd64 libaudit1 1:3.0-2 install ok installed libblkid1:amd64 libblkid1 2.36.1-8+deb11u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4 install ok installed libc-bin libc-bin 2.31-13+deb11u8 install ok installed libc6:amd64 libc6 2.31-13+deb11u8 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2+b1 install ok installed libcom-err2:amd64 libcom-err2 1.46.2-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.18-4 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.8 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.260 install ok installed libext2fs2:amd64 libext2fs2 1.46.2-2 install ok installed libffi7:amd64 libffi7 3.3-6 install ok installed libgcc-s1:amd64 libgcc-s1 10.2.1-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.7-6 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg-1+deb11u1 install ok installed libgnutls30:amd64 libgnutls30 3.7.1-5+deb11u4 install ok installed libgpg-error0:amd64 libgpg-error0 1.38-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.18.3-6+deb11u4 install ok installed libhogweed6:amd64 libhogweed6 3.7.3-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.0-5 install ok installed libk5crypto3:amd64 libk5crypto3 1.18.3-6+deb11u4 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.18.3-6+deb11u4 install ok installed libkrb5support0:amd64 libkrb5support0 1.18.3-6+deb11u4 install ok installed liblz4-1:amd64 liblz4-1 1.9.3-2 install ok installed liblzma5:amd64 liblzma5 5.2.5-2.1~deb11u1 install ok installed libmount1:amd64 libmount1 2.36.1-8+deb11u1 install ok installed libnettle8:amd64 libnettle8 3.7.3-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.22-1 install ok installed libpam-modules:amd64 libpam-modules 1.4.0-9+deb11u1 install ok installed libpam-modules-bin libpam-modules-bin 1.4.0-9+deb11u1 install ok installed libpam-runtime libpam-runtime 1.4.0-9+deb11u1 install ok installed libpam0g:amd64 libpam0g 1.4.0-9+deb11u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.36-2+deb11u1 install ok installed libpcre3:amd64 libpcre3 2:8.39-13 install ok installed libseccomp2:amd64 libseccomp2 2.5.1-1+deb11u1 install ok installed libselinux1:amd64 libselinux1 3.1-3 install ok installed libsemanage-common libsemanage-common 3.1-1 install ok installed libsemanage1:amd64 libsemanage1 3.1-1+b2 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.36.1-8+deb11u1 install ok installed libss2:amd64 libss2 1.46.2-2 install ok installed libssl1.1:amd64 libssl1.1 1.1.1w-0+deb11u1 install ok installed libstdc++6:amd64 libstdc++6 10.2.1-6 install ok installed libsystemd0:amd64 libsystemd0 247.3-7+deb11u4 install ok installed libtasn1-6:amd64 libtasn1-6 4.16.0-2+deb11u1 install ok installed libtinfo6:amd64 libtinfo6 6.2+20201114-2+deb11u2 install ok installed libtirpc-common libtirpc-common 1.3.1-1+deb11u1 install ok installed libtirpc3:amd64 libtirpc3 1.3.1-1+deb11u1 install ok installed libudev1:amd64 libudev1 247.3-7+deb11u4 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed libuuid1:amd64 libuuid1 2.36.1-8+deb11u1 install ok installed libxxhash0:amd64 libxxhash0 0.8.0-2 install ok installed libzstd1:amd64 libzstd1 1.4.8+dfsg-2.1 install ok installed login login 1:4.8.1-1 install ok installed logsave logsave 1.46.2-2 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.4.20200120-2 install ok installed mount mount 2.36.1-8+deb11u1 install ok installed ncurses-base ncurses-base 6.2+20201114-2+deb11u2 install ok installed ncurses-bin ncurses-bin 6.2+20201114-2+deb11u2 install ok installed passwd passwd 1:4.8.1-1 install ok installed perl-base perl-base 5.32.1-4+deb11u3 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.96-7+deb11u1 install ok installed tar tar 1.34+dfsg-1+deb11u1 install ok installed tzdata tzdata 2024a-0+deb11u1 install ok installed util-linux util-linux 2.36.1-8+deb11u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2+deb11u2 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m10.6s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/bullseye2next/reference-chroot-metadata.dat 0m10.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n'] 0m11.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n'] 0m11.2s INFO: Running scripts is_testable 0m11.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/is_testable_uninstallable'] 0m11.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/is_testable_uninstallable'] 0m11.2s INFO: Running scripts pre_test 0m11.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_test_exceptions'] 0m11.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_test_exceptions'] 0m11.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_test_root_password'] 0m11.2s DUMP: New password: Retype new password: passwd: password updated successfully 0m11.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_test_root_password'] 0m11.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'apt-cache', 'show', '--no-all-versions', 'shasta'] 0m11.4s DUMP: Package: shasta Version: 0.7.0-3 Installed-Size: 2324 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libboost-chrono1.74.0 (>= 1.74.0), libboost-program-options1.74.0 (>= 1.74.0), libc6 (>= 2.14), libgcc-s1 (>= 3.0), libstdc++6 (>= 9), python3-shasta (= 0.7.0-3) 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_0.7.0-3_amd64.deb Size: 546876 MD5sum: 55e0f6cafa186ae7f31f9f48cb1ec27c SHA256: 7f2703331d94ebabf4b40e5a3552ffdbdb9ead1dc524420e6b7fdae0f16d3dc2 0m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'apt-cache', 'show', '--no-all-versions', 'shasta'] 0m11.4s INFO: apt-cache knows about the following packages: shasta 0m11.4s INFO: Running scripts pre_install 0m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_install_database-server'] 0m11.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_install_database-server'] 0m11.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_install_exceptions'] 0m11.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_install_exceptions'] 0m11.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_install_extras'] 0m11.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_install_extras'] 0m11.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_install_foreign_architecture'] 0m11.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_install_foreign_architecture'] 0m11.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m11.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m11.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'apt-cache', 'policy'] 0m11.5s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.9,o=Debian,a=oldstable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m11.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'apt-cache', 'policy'] 0m11.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'apt-cache', 'policy', 'shasta'] 0m11.6s DUMP: shasta: Installed: (none) Candidate: 0.7.0-3 Version table: 0.7.0-3 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 0m11.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'apt-cache', 'policy', 'shasta'] 0m11.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'apt-get', '-y', 'install', 'shasta'] 0m21.0s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libboost-chrono1.74.0 libboost-program-options1.74.0 libexpat1 libgdbm-compat4 libgdbm6 libgomp1 liblmdb0 libmbedcrypto3 libmbedtls12 libmbedx509-0 libmpdec3 libncursesw6 libperl5.32 libpng16-16 libpython3-stdlib libpython3.9 libpython3.9-minimal libpython3.9-stdlib libreadline8 libspoa7.0.0 libsqlite3-0 media-types ncbi-blast+ ncbi-data perl perl-modules-5.32 python3 python3-minimal python3-shasta python3.9 python3.9-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 python3.9-venv python3.9-doc binutils binfmt-support readline-doc Recommended packages: libgpm2 ca-certificates netbase The following NEW packages will be installed: libboost-chrono1.74.0 libboost-program-options1.74.0 libexpat1 libgdbm-compat4 libgdbm6 libgomp1 liblmdb0 libmbedcrypto3 libmbedtls12 libmbedx509-0 libmpdec3 libncursesw6 libperl5.32 libpng16-16 libpython3-stdlib libpython3.9 libpython3.9-minimal libpython3.9-stdlib libreadline8 libspoa7.0.0 libsqlite3-0 media-types ncbi-blast+ ncbi-data perl perl-modules-5.32 python3 python3-minimal python3-shasta python3.9 python3.9-minimal readline-common shasta 0 upgraded, 33 newly installed, 0 to remove and 0 not upgraded. Need to get 33.9 MB of archives. After this operation, 167 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main amd64 perl-modules-5.32 all 5.32.1-4+deb11u3 [2823 kB] Get:2 http://deb.debian.org/debian bullseye/main amd64 libgdbm6 amd64 1.19-2 [64.9 kB] Get:3 http://deb.debian.org/debian bullseye/main amd64 libgdbm-compat4 amd64 1.19-2 [44.7 kB] Get:4 http://deb.debian.org/debian bullseye/main amd64 libperl5.32 amd64 5.32.1-4+deb11u3 [4121 kB] Get:5 http://deb.debian.org/debian bullseye/main amd64 perl amd64 5.32.1-4+deb11u3 [293 kB] Get:6 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-minimal amd64 3.9.2-1 [801 kB] Get:7 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2+deb11u5 [98.2 kB] Get:8 http://deb.debian.org/debian bullseye/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB] Get:9 http://deb.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get:10 http://deb.debian.org/debian bullseye/main amd64 media-types all 4.0.0 [30.3 kB] Get:11 http://deb.debian.org/debian bullseye/main amd64 libmpdec3 amd64 2.5.1-1 [87.7 kB] Get:12 http://deb.debian.org/debian bullseye/main amd64 libncursesw6 amd64 6.2+20201114-2+deb11u2 [132 kB] Get:13 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get:14 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get:15 http://deb.debian.org/debian bullseye/main amd64 libsqlite3-0 amd64 3.34.1-3 [797 kB] Get:16 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB] Get:17 http://deb.debian.org/debian bullseye/main amd64 python3.9 amd64 3.9.2-1 [466 kB] Get:18 http://deb.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get:19 http://deb.debian.org/debian bullseye/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get:20 http://deb.debian.org/debian bullseye/main amd64 libboost-chrono1.74.0 amd64 1.74.0-9 [252 kB] Get:21 http://deb.debian.org/debian bullseye/main amd64 libboost-program-options1.74.0 amd64 1.74.0-9 [356 kB] Get:22 http://deb.debian.org/debian bullseye/main amd64 libgomp1 amd64 10.2.1-6 [99.9 kB] Get:23 http://deb.debian.org/debian bullseye/main amd64 liblmdb0 amd64 0.9.24-1 [45.0 kB] Get:24 http://deb.debian.org/debian bullseye/main amd64 libmbedcrypto3 amd64 2.16.9-0.1 [219 kB] Get:25 http://deb.debian.org/debian bullseye/main amd64 libmbedx509-0 amd64 2.16.9-0.1 [109 kB] Get:26 http://deb.debian.org/debian bullseye/main amd64 libmbedtls12 amd64 2.16.9-0.1 [139 kB] Get:27 http://deb.debian.org/debian bullseye/main amd64 libpng16-16 amd64 1.6.37-3 [294 kB] Get:28 http://deb.debian.org/debian bullseye/main amd64 libpython3.9 amd64 3.9.2-1 [1691 kB] Get:29 http://deb.debian.org/debian bullseye/main amd64 libspoa7.0.0 amd64 4.0.7+ds-1+b1 [66.8 kB] Get:30 http://deb.debian.org/debian bullseye/main amd64 ncbi-data all 6.1.20170106+dfsg1-9 [3556 kB] Get:31 http://deb.debian.org/debian bullseye/main amd64 ncbi-blast+ amd64 2.11.0+ds-1 [11.3 MB] Get:32 http://deb.debian.org/debian bullseye/main amd64 python3-shasta amd64 0.7.0-3 [1499 kB] Get:33 http://deb.debian.org/debian bullseye/main amd64 shasta amd64 0.7.0-3 [547 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 33.9 MB in 0s (92.1 MB/s) Selecting previously unselected package perl-modules-5.32. (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 ... 6672 files and directories currently installed.) Preparing to unpack .../0-perl-modules-5.32_5.32.1-4+deb11u3_all.deb ... Unpacking perl-modules-5.32 (5.32.1-4+deb11u3) ... Selecting previously unselected package libgdbm6:amd64. Preparing to unpack .../1-libgdbm6_1.19-2_amd64.deb ... Unpacking libgdbm6:amd64 (1.19-2) ... Selecting previously unselected package libgdbm-compat4:amd64. 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Selecting previously unselected package shasta. Preparing to unpack .../14-shasta_0.7.0-3_amd64.deb ... Unpacking shasta (0.7.0-3) ... Setting up libboost-chrono1.74.0:amd64 (1.74.0-9) ... Setting up media-types (4.0.0) ... Setting up liblmdb0:amd64 (0.9.24-1) ... Setting up ncbi-data (6.1.20170106+dfsg1-9) ... Setting up libboost-program-options1.74.0:amd64 (1.74.0-9) ... Setting up perl-modules-5.32 (5.32.1-4+deb11u3) ... Setting up libsqlite3-0:amd64 (3.34.1-3) ... Setting up libgomp1:amd64 (10.2.1-6) ... Setting up libpng16-16:amd64 (1.6.37-3) ... Setting up libspoa7.0.0:amd64 (4.0.7+ds-1+b1) ... Setting up libncursesw6:amd64 (6.2+20201114-2+deb11u2) ... Setting up libmpdec3:amd64 (2.5.1-1) ... Setting up libmbedcrypto3:amd64 (2.16.9-0.1) ... Setting up readline-common (8.1-1) ... Setting up libgdbm6:amd64 (1.19-2) ... Setting up libmbedx509-0:amd64 (2.16.9-0.1) ... Setting up libreadline8:amd64 (8.1-1) ... Setting up libmbedtls12:amd64 (2.16.9-0.1) ... Setting up libgdbm-compat4:amd64 (1.19-2) ... Setting up libperl5.32:amd64 (5.32.1-4+deb11u3) ... Setting up libpython3.9-stdlib:amd64 (3.9.2-1) ... Setting up libpython3-stdlib:amd64 (3.9.2-3) ... Setting up perl (5.32.1-4+deb11u3) ... Setting up libpython3.9:amd64 (3.9.2-1) ... Setting up python3.9 (3.9.2-1) ... Setting up python3 (3.9.2-3) ... Setting up ncbi-blast+ (2.11.0+ds-1) ... Setting up python3-shasta (0.7.0-3) ... Setting up shasta (0.7.0-3) ... Processing triggers for libc-bin (2.31-13+deb11u8) ... 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'apt-get', '-y', 'install', 'shasta'] 0m21.0s INFO: Running scripts post_install 0m21.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/post_install_exceptions'] 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/post_install_exceptions'] 0m21.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n'] 0m21.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n'] 0m21.7s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpa5_fhb1n to bullseye-next 0m21.7s DEBUG: sources.list: deb http://deb.debian.org/debian/ bullseye main deb http://security.debian.org bullseye-security main deb http://deb.debian.org/debian/ bullseye-updates main deb http://deb.debian.org/debian/ bullseye-proposed-updates main 0m21.7s INFO: Running scripts pre_distupgrade 0m21.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m21.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m21.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_distupgrade_exceptions'] 0m21.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_distupgrade_exceptions'] 0m21.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m21.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m21.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m21.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m21.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m21.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m21.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'apt-get', 'update'] 0m23.4s DUMP: Get:1 http://security.debian.org bullseye-security InRelease [48.4 kB] Hit:2 http://deb.debian.org/debian bullseye InRelease Get:3 http://deb.debian.org/debian bullseye-updates InRelease [44.1 kB] Get:4 http://deb.debian.org/debian bullseye-proposed-updates InRelease [54.0 kB] Get:5 http://deb.debian.org/debian bullseye-updates/main amd64 Packages [18.8 kB] Get:6 http://deb.debian.org/debian bullseye-updates/main Translation-en [10.9 kB] Get:7 http://security.debian.org bullseye-security/main amd64 Packages [268 kB] Get:8 http://security.debian.org bullseye-security/main Translation-en [173 kB] Get:9 http://deb.debian.org/debian bullseye-proposed-updates/main amd64 Packages [10.9 kB] Get:10 http://deb.debian.org/debian bullseye-proposed-updates/main Translation-en [8278 B] Fetched 637 kB in 1s (877 kB/s) Reading package lists... 0m23.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'apt-get', 'update'] 0m23.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'apt-get', '-yf', 'dist-upgrade'] 0m23.8s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m23.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'apt-get', '-yf', 'dist-upgrade'] 0m23.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m24.2s DUMP: 3dbdfaeffa7a00cc3fa3ebdbe8870147 - 0m24.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m24.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'apt-cache', 'show', '--no-all-versions', 'shasta'] 0m24.5s DUMP: Package: shasta Version: 0.7.0-3 Installed-Size: 2324 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libboost-chrono1.74.0 (>= 1.74.0), libboost-program-options1.74.0 (>= 1.74.0), libc6 (>= 2.14), libgcc-s1 (>= 3.0), libstdc++6 (>= 9), python3-shasta (= 0.7.0-3) 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_0.7.0-3_amd64.deb Size: 546876 MD5sum: 55e0f6cafa186ae7f31f9f48cb1ec27c SHA256: 7f2703331d94ebabf4b40e5a3552ffdbdb9ead1dc524420e6b7fdae0f16d3dc2 0m24.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'apt-cache', 'show', '--no-all-versions', 'shasta'] 0m24.5s INFO: apt-cache knows about the following packages: shasta 0m24.5s INFO: Running scripts pre_install 0m24.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_install_database-server'] 0m24.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_install_database-server'] 0m24.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_install_exceptions'] 0m24.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_install_exceptions'] 0m24.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_install_extras'] 0m24.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_install_extras'] 0m24.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_install_foreign_architecture'] 0m24.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_install_foreign_architecture'] 0m24.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m24.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m24.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'apt-cache', 'policy'] 0m24.6s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye-proposed-updates/main amd64 Packages release v=11-updates,o=Debian,a=oldstable-proposed-updates,n=bullseye-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian bullseye-updates/main amd64 Packages release v=11-updates,o=Debian,a=oldstable-updates,n=bullseye-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org bullseye-security/main amd64 Packages release v=11,o=Debian,a=oldstable-security,n=bullseye-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.9,o=Debian,a=oldstable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m24.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'apt-cache', 'policy'] 0m24.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'apt-cache', 'policy', 'shasta'] 0m24.6s DUMP: shasta: Installed: 0.7.0-3 Candidate: 0.7.0-3 Version table: *** 0.7.0-3 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 100 /var/lib/dpkg/status 0m24.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'apt-cache', 'policy', 'shasta'] 0m24.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'apt-get', '-y', 'install', 'shasta'] 0m25.1s DUMP: Reading package lists... Building dependency tree... Reading state information... shasta is already the newest version (0.7.0-3). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m25.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'apt-get', '-y', 'install', 'shasta'] 0m25.1s INFO: Running scripts post_install 0m25.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/post_install_exceptions'] 0m25.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/post_install_exceptions'] 0m25.1s INFO: Running scripts post_distupgrade 0m25.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m25.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m25.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/post_distupgrade_exceptions'] 0m25.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/post_distupgrade_exceptions'] 0m25.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m25.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m25.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m25.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m25.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/post_distupgrade_zz_backports'] 0m25.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/post_distupgrade_zz_backports'] 0m25.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n'] 0m25.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n'] 0m25.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n'] 0m26.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n'] 0m26.4s INFO: Running scripts pre_install 0m26.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_install_database-server'] 0m26.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_install_database-server'] 0m26.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_install_exceptions'] 0m26.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_install_exceptions'] 0m26.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_install_extras'] 0m26.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_install_extras'] 0m26.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_install_foreign_architecture'] 0m26.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_install_foreign_architecture'] 0m26.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m26.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m26.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'apt-cache', 'policy'] 0m26.5s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye-proposed-updates/main amd64 Packages release v=11-updates,o=Debian,a=oldstable-proposed-updates,n=bullseye-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian bullseye-updates/main amd64 Packages release v=11-updates,o=Debian,a=oldstable-updates,n=bullseye-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org bullseye-security/main amd64 Packages release v=11,o=Debian,a=oldstable-security,n=bullseye-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.9,o=Debian,a=oldstable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m26.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'apt-cache', 'policy'] 0m26.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'apt-cache', 'policy', 'shasta'] 0m26.5s DUMP: shasta: Installed: 0.7.0-3 Candidate: 0.7.0-3 Version table: *** 0.7.0-3 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 100 /var/lib/dpkg/status 0m26.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'apt-cache', 'policy', 'shasta'] 0m26.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'apt-get', '-y', 'install', 'shasta=0.7.0-3'] 0m27.0s DUMP: Reading package lists... Building dependency tree... Reading state information... shasta is already the newest version (0.7.0-3). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m27.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'apt-get', '-y', 'install', 'shasta=0.7.0-3'] 0m27.0s INFO: Running scripts post_install 0m27.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/post_install_exceptions'] 0m27.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/post_install_exceptions'] 0m27.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n'] 0m27.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n'] 0m27.8s DEBUG: No file moved between /{bin|sbin|lib*} and /usr/{bin|sbin|lib*}. 0m27.9s INFO: /bin converted to /usr/bin by /usr merge 0m27.9s INFO: /lib converted to /usr/lib by /usr merge 0m27.9s INFO: /lib/init converted to /usr/lib/init by /usr merge 0m27.9s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 0m27.9s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 0m27.9s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 0m27.9s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 0m27.9s INFO: /lib/terminfo converted to /usr/lib/terminfo by /usr merge 0m27.9s INFO: /lib/terminfo/E converted to /usr/lib/terminfo/E by /usr merge 0m27.9s INFO: /lib/terminfo/a converted to /usr/lib/terminfo/a by /usr merge 0m27.9s INFO: /lib/terminfo/c converted to /usr/lib/terminfo/c by /usr merge 0m27.9s INFO: /lib/terminfo/d converted to /usr/lib/terminfo/d by /usr merge 0m27.9s INFO: /lib/terminfo/h converted to /usr/lib/terminfo/h by /usr merge 0m27.9s INFO: /lib/terminfo/l converted to /usr/lib/terminfo/l by /usr merge 0m27.9s INFO: /lib/terminfo/m converted to /usr/lib/terminfo/m by /usr merge 0m27.9s INFO: /lib/terminfo/p converted to /usr/lib/terminfo/p by /usr merge 0m27.9s INFO: /lib/terminfo/r converted to /usr/lib/terminfo/r by /usr merge 0m27.9s INFO: /lib/terminfo/s converted to /usr/lib/terminfo/s by /usr merge 0m27.9s INFO: /lib/terminfo/t converted to /usr/lib/terminfo/t by /usr merge 0m27.9s INFO: /lib/terminfo/v converted to /usr/lib/terminfo/v by /usr merge 0m27.9s INFO: /lib/terminfo/w converted to /usr/lib/terminfo/w by /usr merge 0m27.9s INFO: /lib/terminfo/x converted to /usr/lib/terminfo/x by /usr merge 0m27.9s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 0m27.9s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 0m27.9s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 0m27.9s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 0m27.9s INFO: /lib64 converted to /usr/lib64 by /usr merge 0m27.9s INFO: /sbin converted to /usr/sbin by /usr merge 0m28.8s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', '-ac', '--ignore-obsolete'] 0m30.6s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', '-ac', '--ignore-obsolete'] 0m30.6s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m30.6s DUMP: 0.15.6 0m30.6s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m30.6s INFO: Running adequate version 0.15.6 now. 0m30.6s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'shasta'] 0m30.7s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'shasta'] 0m30.7s INFO: Running scripts pre_remove 0m30.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m30.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m30.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m30.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m30.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m32.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m32.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m32.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m32.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m32.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m32.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_remove_exceptions'] 0m32.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/pre_remove_exceptions'] 0m32.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m32.8s DUMP: install ok installed adduser adduser 3.118+deb11u1 install ok installed apt apt 2.2.4 install ok installed base-files base-files 11.1+deb11u9 install ok installed base-passwd base-passwd 3.5.51 install ok installed bash bash 5.1-2+deb11u1 install ok installed bsdutils bsdutils 1:2.36.1-8+deb11u1 install ok installed coreutils coreutils 8.32-4+b1 install ok installed dash dash 0.5.11+git20200708+dd9ef66-5 install ok installed debconf debconf 1.5.77 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1+deb11u1 install ok installed debianutils debianutils 4.11.2 install ok installed diffutils diffutils 1:3.7-5 install ok installed dpkg dpkg 1.20.13 install ok installed e2fsprogs e2fsprogs 1.46.2-2 install ok installed findutils findutils 4.8.0-1 install ok installed gcc-10-base:amd64 gcc-10-base 10.2.1-6 install ok installed gcc-9-base:amd64 gcc-9-base 9.3.0-22 install ok installed gpgv gpgv 2.2.27-2+deb11u2 install ok installed grep grep 3.6-1+deb11u1 install ok installed gzip gzip 1.10-4+deb11u1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.60 install ok installed libacl1:amd64 libacl1 2.2.53-10 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.2.4 install ok installed libattr1:amd64 libattr1 1:2.4.48-6 install ok installed libaudit-common libaudit-common 1:3.0-2 install ok installed libaudit1:amd64 libaudit1 1:3.0-2 install ok installed libblkid1:amd64 libblkid1 2.36.1-8+deb11u1 install ok installed libboost-chrono1.74.0:amd64 libboost-chrono1.74.0 1.74.0-9 install ok installed libboost-program-options1.74.0:amd64 libboost-program-options1.74.0 1.74.0-9 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4 install ok installed libc-bin libc-bin 2.31-13+deb11u8 install ok installed libc6:amd64 libc6 2.31-13+deb11u8 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2+b1 install ok installed libcom-err2:amd64 libcom-err2 1.46.2-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.18-4 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.8 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.260 install ok installed libexpat1:amd64 libexpat1 2.2.10-2+deb11u5 install ok installed libext2fs2:amd64 libext2fs2 1.46.2-2 install ok installed libffi7:amd64 libffi7 3.3-6 install ok installed libgcc-s1:amd64 libgcc-s1 10.2.1-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.7-6 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.19-2 install ok installed libgdbm6:amd64 libgdbm6 1.19-2 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg-1+deb11u1 install ok installed libgnutls30:amd64 libgnutls30 3.7.1-5+deb11u4 install ok installed libgomp1:amd64 libgomp1 10.2.1-6 install ok installed libgpg-error0:amd64 libgpg-error0 1.38-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.18.3-6+deb11u4 install ok installed libhogweed6:amd64 libhogweed6 3.7.3-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.0-5 install ok installed libk5crypto3:amd64 libk5crypto3 1.18.3-6+deb11u4 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.18.3-6+deb11u4 install ok installed libkrb5support0:amd64 libkrb5support0 1.18.3-6+deb11u4 install ok installed liblmdb0:amd64 liblmdb0 0.9.24-1 install ok installed liblz4-1:amd64 liblz4-1 1.9.3-2 install ok installed liblzma5:amd64 liblzma5 5.2.5-2.1~deb11u1 install ok installed libmbedcrypto3:amd64 libmbedcrypto3 2.16.9-0.1 install ok installed libmbedtls12:amd64 libmbedtls12 2.16.9-0.1 install ok installed libmbedx509-0:amd64 libmbedx509-0 2.16.9-0.1 install ok installed libmount1:amd64 libmount1 2.36.1-8+deb11u1 install ok installed libmpdec3:amd64 libmpdec3 2.5.1-1 install ok installed libncursesw6:amd64 libncursesw6 6.2+20201114-2+deb11u2 install ok installed libnettle8:amd64 libnettle8 3.7.3-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.22-1 install ok installed libpam-modules:amd64 libpam-modules 1.4.0-9+deb11u1 install ok installed libpam-modules-bin libpam-modules-bin 1.4.0-9+deb11u1 install ok installed libpam-runtime libpam-runtime 1.4.0-9+deb11u1 install ok installed libpam0g:amd64 libpam0g 1.4.0-9+deb11u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.36-2+deb11u1 install ok installed libpcre3:amd64 libpcre3 2:8.39-13 install ok installed libperl5.32:amd64 libperl5.32 5.32.1-4+deb11u3 install ok installed libpng16-16:amd64 libpng16-16 1.6.37-3 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.9.2-3 install ok installed libpython3.9:amd64 libpython3.9 3.9.2-1 install ok installed libpython3.9-minimal:amd64 libpython3.9-minimal 3.9.2-1 install ok installed libpython3.9-stdlib:amd64 libpython3.9-stdlib 3.9.2-1 install ok installed libreadline8:amd64 libreadline8 8.1-1 install ok installed libseccomp2:amd64 libseccomp2 2.5.1-1+deb11u1 install ok installed libselinux1:amd64 libselinux1 3.1-3 install ok installed libsemanage-common libsemanage-common 3.1-1 install ok installed libsemanage1:amd64 libsemanage1 3.1-1+b2 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.36.1-8+deb11u1 install ok installed libspoa7.0.0:amd64 libspoa7.0.0 4.0.7+ds-1+b1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.34.1-3 install ok installed libss2:amd64 libss2 1.46.2-2 install ok installed libssl1.1:amd64 libssl1.1 1.1.1w-0+deb11u1 install ok installed libstdc++6:amd64 libstdc++6 10.2.1-6 install ok installed libsystemd0:amd64 libsystemd0 247.3-7+deb11u4 install ok installed libtasn1-6:amd64 libtasn1-6 4.16.0-2+deb11u1 install ok installed libtinfo6:amd64 libtinfo6 6.2+20201114-2+deb11u2 install ok installed libtirpc-common libtirpc-common 1.3.1-1+deb11u1 install ok installed libtirpc3:amd64 libtirpc3 1.3.1-1+deb11u1 install ok installed libudev1:amd64 libudev1 247.3-7+deb11u4 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed libuuid1:amd64 libuuid1 2.36.1-8+deb11u1 install ok installed libxxhash0:amd64 libxxhash0 0.8.0-2 install ok installed libzstd1:amd64 libzstd1 1.4.8+dfsg-2.1 install ok installed login login 1:4.8.1-1 install ok installed logsave logsave 1.46.2-2 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.4.20200120-2 install ok installed media-types media-types 4.0.0 install ok installed mount mount 2.36.1-8+deb11u1 install ok installed ncbi-blast+ ncbi-blast+ 2.11.0+ds-1 install ok installed ncbi-data ncbi-data 6.1.20170106+dfsg1-9 install ok installed ncurses-base ncurses-base 6.2+20201114-2+deb11u2 install ok installed ncurses-bin ncurses-bin 6.2+20201114-2+deb11u2 install ok installed passwd passwd 1:4.8.1-1 install ok installed perl perl 5.32.1-4+deb11u3 install ok installed perl-base perl-base 5.32.1-4+deb11u3 install ok installed perl-modules-5.32 perl-modules-5.32 5.32.1-4+deb11u3 install ok installed python3 python3 3.9.2-3 install ok installed python3-minimal python3-minimal 3.9.2-3 install ok installed python3-shasta python3-shasta 0.7.0-3 install ok installed python3.9 python3.9 3.9.2-1 install ok installed python3.9-minimal python3.9-minimal 3.9.2-1 install ok installed readline-common readline-common 8.1-1 install ok installed sed sed 4.7-1 install ok installed shasta shasta 0.7.0-3 install ok installed sysvinit-utils sysvinit-utils 2.96-7+deb11u1 install ok installed tar tar 1.34+dfsg-1+deb11u1 install ok installed tzdata tzdata 2024a-0+deb11u1 install ok installed util-linux util-linux 2.36.1-8+deb11u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2+deb11u2 0m32.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m32.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'apt-get', 'remove', 'libboost-chrono1.74.0:amd64', 'libboost-program-options1.74.0:amd64', 'libexpat1:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgomp1:amd64', 'liblmdb0:amd64', 'libmbedcrypto3:amd64', 'libmbedtls12:amd64', 'libmbedx509-0:amd64', 'libmpdec3:amd64', 'libncursesw6:amd64', 'libperl5.32:amd64', 'libpng16-16:amd64', 'libpython3-stdlib:amd64', 'libpython3.9:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libreadline8:amd64', 'libspoa7.0.0:amd64', 'libsqlite3-0:amd64', 'media-types', 'ncbi-blast+-', 'ncbi-data', 'perl', 'perl-modules-5.32', 'python3', 'python3-minimal', 'python3-shasta', 'python3.9', 'python3.9-minimal', 'readline-common', 'shasta'] 0m34.1s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: libboost-chrono1.74.0 libboost-program-options1.74.0 libexpat1 libgdbm-compat4 libgdbm6 libgomp1 liblmdb0 libmbedcrypto3 libmbedtls12 libmbedx509-0 libmpdec3 libncursesw6 libperl5.32 libpng16-16 libpython3-stdlib libpython3.9 libpython3.9-minimal libpython3.9-stdlib libreadline8 libspoa7.0.0 libsqlite3-0 media-types ncbi-blast+ ncbi-data perl perl-modules-5.32 python3 python3-minimal python3-shasta python3.9 python3.9-minimal readline-common shasta 0 upgraded, 0 newly installed, 33 to remove and 0 not upgraded. After this operation, 167 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 ... 9807 files and directories currently installed.) Removing shasta (0.7.0-3) ... Removing libboost-chrono1.74.0:amd64 (1.74.0-9) ... Removing python3-shasta (0.7.0-3) ... Removing libboost-program-options1.74.0:amd64 (1.74.0-9) ... Removing ncbi-blast+ (2.11.0+ds-1) ... Removing python3 (3.9.2-3) ... Removing python3-minimal (3.9.2-3) ... Removing python3.9 (3.9.2-1) ... Removing python3.9-minimal (3.9.2-1) ... Removing libpython3.9:amd64 (3.9.2-1) ... Removing libexpat1:amd64 (2.2.10-2+deb11u5) ... Removing perl (5.32.1-4+deb11u3) ... Removing libperl5.32:amd64 (5.32.1-4+deb11u3) ... Removing libgdbm-compat4:amd64 (1.19-2) ... Removing libgdbm6:amd64 (1.19-2) ... Removing libgomp1:amd64 (10.2.1-6) ... Removing liblmdb0:amd64 (0.9.24-1) ... Removing libmbedtls12:amd64 (2.16.9-0.1) ... Removing libmbedx509-0:amd64 (2.16.9-0.1) ... Removing libmbedcrypto3:amd64 (2.16.9-0.1) ... Removing libpython3-stdlib:amd64 (3.9.2-3) ... Removing libpython3.9-stdlib:amd64 (3.9.2-1) ... find: '/usr/lib/python3': No such file or directory Removing libmpdec3:amd64 (2.5.1-1) ... Removing libncursesw6:amd64 (6.2+20201114-2+deb11u2) ... Removing libpng16-16:amd64 (1.6.37-3) ... Removing libpython3.9-minimal:amd64 (3.9.2-1) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8:amd64 (8.1-1) ... Removing libspoa7.0.0:amd64 (4.0.7+ds-1+b1) ... Removing libsqlite3-0:amd64 (3.34.1-3) ... Removing media-types (4.0.0) ... Removing ncbi-data (6.1.20170106+dfsg1-9) ... Removing perl-modules-5.32 (5.32.1-4+deb11u3) ... Removing readline-common (8.1-1) ... Processing triggers for libc-bin (2.31-13+deb11u8) ... 0m34.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'apt-get', 'remove', 'libboost-chrono1.74.0:amd64', 'libboost-program-options1.74.0:amd64', 'libexpat1:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgomp1:amd64', 'liblmdb0:amd64', 'libmbedcrypto3:amd64', 'libmbedtls12:amd64', 'libmbedx509-0:amd64', 'libmpdec3:amd64', 'libncursesw6:amd64', 'libperl5.32:amd64', 'libpng16-16:amd64', 'libpython3-stdlib:amd64', 'libpython3.9:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libreadline8:amd64', 'libspoa7.0.0:amd64', 'libsqlite3-0:amd64', 'media-types', 'ncbi-blast+-', 'ncbi-data', 'perl', 'perl-modules-5.32', 'python3', 'python3-minimal', 'python3-shasta', 'python3.9', 'python3.9-minimal', 'readline-common', 'shasta'] 0m34.1s INFO: Running scripts post_remove 0m34.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/post_remove_exceptions'] 0m34.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/post_remove_exceptions'] 0m34.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'dpkg', '--purge', 'libboost-chrono1.74.0:amd64', 'libboost-program-options1.74.0:amd64', 'libexpat1:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgomp1:amd64', 'liblmdb0:amd64', 'libmbedcrypto3:amd64', 'libmbedtls12:amd64', 'libmbedx509-0:amd64', 'libmpdec3:amd64', 'libncursesw6:amd64', 'libperl5.32:amd64', 'libpng16-16:amd64', 'libpython3-stdlib:amd64', 'libpython3.9:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libreadline8:amd64', 'libspoa7.0.0:amd64', 'libsqlite3-0:amd64', 'media-types', 'ncbi-blast+', 'ncbi-data', 'perl', 'perl-modules-5.32', 'python3', 'python3-minimal', 'python3-shasta', 'python3.9', 'python3.9-minimal', 'readline-common'] 0m34.2s DUMP: dpkg: warning: ignoring request to remove libboost-chrono1.74.0 which isn't installed dpkg: warning: ignoring request to remove libboost-program-options1.74.0 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libgdbm-compat4 which isn't installed dpkg: warning: ignoring request to remove libgdbm6 which isn't installed dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove liblmdb0 which isn't installed dpkg: warning: ignoring request to remove libmbedcrypto3 which isn't installed dpkg: warning: ignoring request to remove libmbedtls12 which isn't installed dpkg: warning: ignoring request to remove libmbedx509-0 which isn't installed dpkg: warning: ignoring request to remove libmpdec3 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libperl5.32 which isn't installed dpkg: warning: ignoring request to remove libpng16-16 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed dpkg: warning: ignoring request to remove libpython3.9 which isn't installed (Reading database ... 6681 files and directories currently installed.) Purging configuration files for libpython3.9-minimal:amd64 (3.9.2-1) ... dpkg: warning: ignoring request to remove libpython3.9-stdlib which isn't installed dpkg: warning: ignoring request to remove libreadline8 which isn't installed 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 media-types (4.0.0) ... dpkg: warning: ignoring request to remove ncbi-blast+ which isn't installed Purging configuration files for ncbi-data (6.1.20170106+dfsg1-9) ... Purging configuration files for perl (5.32.1-4+deb11u3) ... dpkg: warning: ignoring request to remove perl-modules-5.32 which isn't installed Purging configuration files for python3 (3.9.2-3) ... 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 python3.9 which isn't installed Purging configuration files for python3.9-minimal (3.9.2-1) ... Purging configuration files for readline-common (8.1-1) ... 0m34.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'dpkg', '--purge', 'libboost-chrono1.74.0:amd64', 'libboost-program-options1.74.0:amd64', 'libexpat1:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgomp1:amd64', 'liblmdb0:amd64', 'libmbedcrypto3:amd64', 'libmbedtls12:amd64', 'libmbedx509-0:amd64', 'libmpdec3:amd64', 'libncursesw6:amd64', 'libperl5.32:amd64', 'libpng16-16:amd64', 'libpython3-stdlib:amd64', 'libpython3.9:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libreadline8:amd64', 'libspoa7.0.0:amd64', 'libsqlite3-0:amd64', 'media-types', 'ncbi-blast+', 'ncbi-data', 'perl', 'perl-modules-5.32', 'python3', 'python3-minimal', 'python3-shasta', 'python3.9', 'python3.9-minimal', 'readline-common'] 0m34.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'dpkg', '--purge', 'shasta'] 0m34.2s DUMP: dpkg: warning: ignoring request to remove shasta which isn't installed 0m34.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'dpkg', '--purge', 'shasta'] 0m34.2s INFO: Running scripts post_purge 0m34.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/post_purge_exceptions'] 0m34.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/post_purge_exceptions'] 0m34.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'dpkg', '--purge', '--pending'] 0m34.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'dpkg', '--purge', '--pending'] 0m34.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'dpkg', '--remove', '--pending'] 0m34.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'dpkg', '--remove', '--pending'] 0m34.2s INFO: Running scripts post_test 0m34.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/post_test_exceptions'] 0m34.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'tmp/scripts/post_test_exceptions'] 0m34.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n'] 0m34.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n'] 0m34.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'dpkg-divert', '--list'] 0m34.8s DUMP: local diversion of /bin/sync to /bin/sync.distrib diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m34.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'dpkg-divert', '--list'] 0m34.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'apt-get', 'clean'] 0m34.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n', 'apt-get', 'clean'] 0m34.8s DEBUG: Recording chroot state 0m36.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n/dev/shm'] 0m36.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n/dev/shm'] 0m36.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n/dev/console'] 0m36.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n/dev/console'] 0m36.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n/dev/ptmx'] 0m36.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n/dev/ptmx'] 0m36.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n/dev/pts'] 0m36.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n/dev/pts'] 0m36.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n/proc'] 0m36.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n/proc'] 0m36.3s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n'] 0m36.4s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpa5_fhb1n'] 0m36.4s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpa5_fhb1n 0m36.4s INFO: PASS: Upgrading between Debian distributions. 0m36.4s INFO: PASS: All tests. 0m36.4s INFO: piuparts run ends. ret=0 End: 2024-02-21 17:08:19 GMT