Start: 2025-02-27 20:44:47 GMT [sid] Package: python3-shasta-doc Source: shasta Version: 0.12.0-1 Installed-Size: 269 Maintainer: Debian Med Packaging Team Architecture: all Depends: libjs-sphinxdoc (>= 7.2.2) Recommends: shasta, python3-shasta Description: nanopore whole genome assembly (documentation) Multi-Arch: foreign Homepage: https://github.com/chanzuckerberg/shasta Built-Using: sphinx (= 7.2.6-8) Description-md5: 10ae554fed8f7cd0eb220c1a4845e979 Section: doc Priority: optional Filename: pool/main/s/shasta/python3-shasta-doc_0.12.0-1_all.deb Size: 24028 MD5sum: e46e18b99341ee902b646ed016e499a1 SHA256: 4b1c09fbce6b1737c9b3444fdd1b0d672d6c769a64d6e1babcef5a0f7724ecd0 [experimental] Package: python3-shasta-doc Source: shasta Version: 0.12.0-2 Installed-Size: 270 Maintainer: Debian Med Packaging Team Architecture: all Depends: libjs-sphinxdoc (>= 7.4) Recommends: shasta, python3-shasta Description: nanopore whole genome assembly (documentation) Multi-Arch: foreign Homepage: https://github.com/chanzuckerberg/shasta Built-Using: sphinx (= 7.4.7-4) Description-md5: 10ae554fed8f7cd0eb220c1a4845e979 Section: doc Priority: optional Filename: pool/main/s/shasta/python3-shasta-doc_0.12.0-2_all.deb Size: 24220 MD5sum: 73c95c96b1596e73d09abe00dce95d44 SHA256: c9a7d383da30b5c5bcef98c3af92144a1cf0074cb2867181173a5ec45b93aa1a 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 python3-shasta-doc=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 python3-shasta-doc=0.12.0-2 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-34-amd64 #1 SMP Debian 5.10.234-1 (2025-02-24) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmp63__w87i 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp63__w87i 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp63__w87i', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp63__w87i', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp63__w87i/proc'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp63__w87i/proc'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp63__w87i/dev/pts'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp63__w87i/dev/pts'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp63__w87i/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp63__w87i/dev/ptmx'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp63__w87i/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp63__w87i/dev/ptmx'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmp63__w87i/dev/console'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmp63__w87i/dev/console'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp63__w87i/dev/shm'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp63__w87i/dev/shm'] 0m0.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m0.2s DEBUG: Created policy-rc.d and chmodded it. 0m0.2s DEBUG: Created resolv.conf. 0m0.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp63__w87i/tmp/scripts/ 0m0.2s INFO: Running scripts post_chroot_unpack 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'apt-get', 'update'] 0m2.1s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [205 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.1 MB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7379 kB] Fetched 17.7 MB in 1s (12.4 MB/s) Reading package lists... 0m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'apt-get', 'update'] 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'apt-get', '-yf', 'dist-upgrade'] 0m2.7s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: libaudit1 libcap-ng0 libseccomp2 libsemanage2 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 215 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 libcap-ng0 amd64 0.8.5-4+b1 [17.6 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libaudit1 amd64 1:4.0.2-2+b2 [55.1 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libseccomp2 amd64 2.5.5-2+b1 [48.1 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libsemanage2 amd64 3.8-1+b1 [94.7 kB] Fetched 215 kB in 0s (4196 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 ... 4906 files and directories currently installed.) Preparing to unpack .../libcap-ng0_0.8.5-4+b1_amd64.deb ... Unpacking libcap-ng0:amd64 (0.8.5-4+b1) over (0.8.5-4) ... Setting up libcap-ng0:amd64 (0.8.5-4+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4907 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a4.0.2-2+b2_amd64.deb ... Unpacking libaudit1:amd64 (1:4.0.2-2+b2) over (1:4.0.2-2+b1) ... Setting up libaudit1:amd64 (1:4.0.2-2+b2) ... (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 ... 4907 files and directories currently installed.) Preparing to unpack .../libseccomp2_2.5.5-2+b1_amd64.deb ... Unpacking libseccomp2:amd64 (2.5.5-2+b1) over (2.5.5-2) ... Setting up libseccomp2:amd64 (2.5.5-2+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4908 files and directories currently installed.) Preparing to unpack .../libsemanage2_3.8-1+b1_amd64.deb ... Unpacking libsemanage2:amd64 (3.8-1+b1) over (3.8-1) ... Setting up libsemanage2:amd64 (3.8-1+b1) ... Processing triggers for libc-bin (2.40-7) ... 0m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'apt-get', '-yf', 'dist-upgrade'] 0m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.9s DUMP: ce78c6543ea7d145f8e26b46cb2f24a4 - 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.9s INFO: Running scripts post_setup 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/post_setup_dummy_users'] 0m3.3s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/post_setup_dummy_users'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/post_setup_forbid_home'] 0m3.3s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/post_setup_forbid_home'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.3s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/post_setup_minimize'] 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/post_setup_minimize'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/post_setup_zz_backports'] 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/post_setup_zz_backports'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.4s DUMP: install ok installed apt apt 2.9.30 install ok installed base-files base-files 13.6 install ok installed base-passwd base-passwd 3.6.6 install ok installed bash bash 5.2.37-1.1 install ok installed bsdutils bsdutils 1:2.40.4-5 install ok installed coreutils coreutils 9.5-1+b1 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.89 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.21 install ok installed diffutils diffutils 1:3.10-2 install ok installed dpkg dpkg 1.22.15 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-17 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.13-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.68 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 2.9.30 install ok installed libattr1:amd64 libattr1 1:2.5.2-3 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2+b2 install ok installed libblkid1:amd64 libblkid1 2.40.4-5 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.40-7 install ok installed libc6:amd64 libc6 2.40-7 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1 install ok installed libcap2:amd64 libcap2 1:2.73-4 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.277 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-17 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-3 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 2.40.4-5 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-3 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-3 install ok installed libpam-runtime libpam-runtime 1.7.0-3 install ok installed libpam0g:amd64 libpam0g 1.7.0-3 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.45-1 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-2+b1 install ok installed libselinux1:amd64 libselinux1 3.8-4 install ok installed libsemanage-common libsemanage-common 3.8-1 install ok installed libsemanage2:amd64 libsemanage2 3.8-1+b1 install ok installed libsepol2:amd64 libsepol2 3.8-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.4-5 install ok installed libssl3t64:amd64 libssl3t64 3.4.1-1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-17 install ok installed libsystemd0:amd64 libsystemd0 257.3-1 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-1 install ok installed libudev1:amd64 libudev1 257.3-1 install ok installed libuuid1:amd64 libuuid1 2.40.4-5 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-2 install ok installed login login 1:4.16.0-2+really2.40.4-5 install ok installed login.defs login.defs 1:4.17.3-1 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed mount mount 2.40.4-5 install ok installed ncurses-base ncurses-base 6.5+20250216-1 install ok installed ncurses-bin ncurses-bin 6.5+20250216-1 install ok installed openssl-provider-legacy openssl-provider-legacy 3.4.1-1 install ok installed passwd passwd 1:4.17.3-1 install ok installed perl-base perl-base 5.40.1-2 install ok installed sed sed 4.9-2 install ok installed sqv sqv 1.2.1-6+b1 install ok installed sysvinit-utils sysvinit-utils 3.14-3 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tzdata tzdata 2025a-2 install ok installed usr-is-merged usr-is-merged 39+nmu2 install ok installed util-linux util-linux 2.40.4-5 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.4s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/sid2experimental/reference-chroot-metadata.dat 0m3.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp63__w87i'] 0m3.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp63__w87i'] 0m3.6s INFO: Running scripts is_testable 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/is_testable_uninstallable'] 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/is_testable_uninstallable'] 0m3.6s INFO: Running scripts pre_test 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_test_exceptions'] 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_test_exceptions'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_test_root_password'] 0m3.6s DUMP: New password: Retype new password: passwd: password updated successfully 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_test_root_password'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'apt-cache', 'show', '--no-all-versions', 'python3-shasta-doc'] 0m3.7s DUMP: Package: python3-shasta-doc Source: shasta Version: 0.12.0-1 Installed-Size: 269 Maintainer: Debian Med Packaging Team Architecture: all Depends: libjs-sphinxdoc (>= 7.2.2) Recommends: shasta, python3-shasta Description-en: nanopore whole genome assembly (documentation) 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 documentation for the shasta and python3-shasta packages. Description-md5: 10ae554fed8f7cd0eb220c1a4845e979 Multi-Arch: foreign Homepage: https://github.com/chanzuckerberg/shasta Built-Using: sphinx (= 7.2.6-8) Section: doc Priority: optional Filename: pool/main/s/shasta/python3-shasta-doc_0.12.0-1_all.deb Size: 24028 MD5sum: e46e18b99341ee902b646ed016e499a1 SHA256: 4b1c09fbce6b1737c9b3444fdd1b0d672d6c769a64d6e1babcef5a0f7724ecd0 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'apt-cache', 'show', '--no-all-versions', 'python3-shasta-doc'] 0m3.7s INFO: apt-cache knows about the following packages: python3-shasta-doc 0m3.7s INFO: Running scripts pre_install 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_install_database-server'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_install_database-server'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_install_exceptions'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_install_exceptions'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_install_extras'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_install_extras'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'apt-cache', 'policy'] 0m3.8s 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: 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'apt-cache', 'policy'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'apt-cache', 'policy', 'python3-shasta-doc'] 0m3.8s DUMP: python3-shasta-doc: Installed: (none) Candidate: 0.12.0-1 Version table: 0.12.0-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'apt-cache', 'policy', 'python3-shasta-doc'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'apt-get', '-y', 'install', 'python3-shasta-doc'] 0m4.5s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libjs-jquery libjs-sphinxdoc libjs-underscore Recommended packages: javascript-common shasta python3-shasta The following NEW packages will be installed: libjs-jquery libjs-sphinxdoc libjs-underscore python3-shasta-doc 0 upgraded, 4 newly installed, 0 to remove and 0 not upgraded. Need to get 496 kB of archives. After this operation, 1443 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libjs-sphinxdoc all 8.1.3-5 [30.5 kB] Get:4 http://deb.debian.org/debian sid/main amd64 python3-shasta-doc all 0.12.0-1 [24.0 kB] Fetched 496 kB in 0s (2291 kB/s) Selecting previously unselected package libjs-jquery. (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 ... 4913 files and directories currently installed.) Preparing to unpack .../libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Selecting previously unselected package libjs-underscore. Preparing to unpack .../libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Selecting previously unselected package libjs-sphinxdoc. Preparing to unpack .../libjs-sphinxdoc_8.1.3-5_all.deb ... Unpacking libjs-sphinxdoc (8.1.3-5) ... Selecting previously unselected package python3-shasta-doc. Preparing to unpack .../python3-shasta-doc_0.12.0-1_all.deb ... Unpacking python3-shasta-doc (0.12.0-1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libjs-sphinxdoc (8.1.3-5) ... Setting up python3-shasta-doc (0.12.0-1) ... 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'apt-get', '-y', 'install', 'python3-shasta-doc'] 0m4.5s INFO: Running scripts post_install 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/post_install_exceptions'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/post_install_exceptions'] 0m4.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp63__w87i'] 0m4.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp63__w87i'] 0m4.7s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmp63__w87i to experimental 0m4.7s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main deb http://deb.debian.org/debian/ experimental main 0m4.7s INFO: Running scripts pre_distupgrade 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_distupgrade_exceptions'] 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_distupgrade_exceptions'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'apt-get', 'update'] 0m5.3s 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 [552 kB] Get:4 http://deb.debian.org/debian experimental/main Translation-en [287 kB] Fetched 940 kB in 0s (6149 kB/s) Reading package lists... 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'apt-get', 'update'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'apt-get', '-yf', 'dist-upgrade'] 0m5.6s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'apt-get', '-yf', 'dist-upgrade'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m5.8s DUMP: 9aace3eb2fe7a720aee3deee4b8a82dc - 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'apt-cache', 'show', '--no-all-versions', 'python3-shasta-doc'] 0m5.9s DUMP: Package: python3-shasta-doc Source: shasta Version: 0.12.0-1 Installed-Size: 269 Maintainer: Debian Med Packaging Team Architecture: all Depends: libjs-sphinxdoc (>= 7.2.2) Recommends: shasta, python3-shasta Description-en: nanopore whole genome assembly (documentation) 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 documentation for the shasta and python3-shasta packages. Description-md5: 10ae554fed8f7cd0eb220c1a4845e979 Multi-Arch: foreign Homepage: https://github.com/chanzuckerberg/shasta Built-Using: sphinx (= 7.2.6-8) Section: doc Priority: optional Filename: pool/main/s/shasta/python3-shasta-doc_0.12.0-1_all.deb Size: 24028 MD5sum: e46e18b99341ee902b646ed016e499a1 SHA256: 4b1c09fbce6b1737c9b3444fdd1b0d672d6c769a64d6e1babcef5a0f7724ecd0 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'apt-cache', 'show', '--no-all-versions', 'python3-shasta-doc'] 0m5.9s INFO: apt-cache knows about the following packages: python3-shasta-doc 0m5.9s INFO: Running scripts pre_install 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_install_database-server'] 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_install_database-server'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_install_exceptions'] 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_install_exceptions'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_install_extras'] 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_install_extras'] 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'apt-cache', 'policy'] 0m6.0s 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: 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'apt-cache', 'policy'] 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'apt-cache', 'policy', 'python3-shasta-doc'] 0m6.0s DUMP: python3-shasta-doc: Installed: 0.12.0-1 Candidate: 0.12.0-1 Version table: 0.12.0-2 1 1 http://deb.debian.org/debian experimental/main amd64 Packages *** 0.12.0-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'apt-cache', 'policy', 'python3-shasta-doc'] 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'apt-get', '-y', '-t', 'experimental', 'install', 'python3-shasta-doc'] 0m6.7s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: python3-shasta-doc 1 upgraded, 0 newly installed, 0 to remove and 16 not upgraded. Need to get 24.2 kB of archives. After this operation, 1024 B of additional disk space will be used. Get:1 http://deb.debian.org/debian experimental/main amd64 python3-shasta-doc all 0.12.0-2 [24.2 kB] Fetched 24.2 kB in 0s (137 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 ... 4981 files and directories currently installed.) Preparing to unpack .../python3-shasta-doc_0.12.0-2_all.deb ... Unpacking python3-shasta-doc (0.12.0-2) over (0.12.0-1) ... Setting up python3-shasta-doc (0.12.0-2) ... 0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'apt-get', '-y', '-t', 'experimental', 'install', 'python3-shasta-doc'] 0m6.7s INFO: Running scripts post_install 0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/post_install_exceptions'] 0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/post_install_exceptions'] 0m6.7s INFO: Running scripts post_distupgrade 0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/post_distupgrade_exceptions'] 0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/post_distupgrade_exceptions'] 0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/post_distupgrade_zz_backports'] 0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/post_distupgrade_zz_backports'] 0m6.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp63__w87i'] 0m6.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp63__w87i'] 0m6.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp63__w87i'] 0m7.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp63__w87i'] 0m7.2s INFO: Running scripts pre_install 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_install_database-server'] 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_install_database-server'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_install_exceptions'] 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_install_exceptions'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_install_extras'] 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_install_extras'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_install_foreign_architecture'] 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_install_foreign_architecture'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'apt-cache', 'policy'] 0m7.2s 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: 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'apt-cache', 'policy'] 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'apt-cache', 'policy', 'python3-shasta-doc'] 0m7.3s DUMP: python3-shasta-doc: 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 0.12.0-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 0m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'apt-cache', 'policy', 'python3-shasta-doc'] 0m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'apt-get', '-y', '-t', 'experimental', 'install', 'python3-shasta-doc=0.12.0-2'] 0m7.5s DUMP: Reading package lists... Building dependency tree... Reading state information... python3-shasta-doc is already the newest version (0.12.0-2). 0 upgraded, 0 newly installed, 0 to remove and 16 not upgraded. 0m7.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'apt-get', '-y', '-t', 'experimental', 'install', 'python3-shasta-doc=0.12.0-2'] 0m7.5s INFO: Running scripts post_install 0m7.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/post_install_exceptions'] 0m7.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/post_install_exceptions'] 0m7.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp63__w87i'] 0m7.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp63__w87i'] 0m7.8s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp63__w87i', '-ac', '--ignore-obsolete'] 0m8.2s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp63__w87i', '-ac', '--ignore-obsolete'] 0m8.2s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m8.2s DUMP: 0.15.6 0m8.2s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m8.2s INFO: Running adequate version 0.15.6 now. 0m8.2s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'python3-shasta-doc'] 0m8.2s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'python3-shasta-doc'] 0m8.2s INFO: Running scripts pre_remove 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_remove_exceptions'] 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/pre_remove_exceptions'] 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m8.5s DUMP: install ok installed apt apt 2.9.30 install ok installed base-files base-files 13.6 install ok installed base-passwd base-passwd 3.6.6 install ok installed bash bash 5.2.37-1.1 install ok installed bsdutils bsdutils 1:2.40.4-5 install ok installed coreutils coreutils 9.5-1+b1 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.89 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.21 install ok installed diffutils diffutils 1:3.10-2 install ok installed dpkg dpkg 1.22.15 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-17 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.13-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.68 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 2.9.30 install ok installed libattr1:amd64 libattr1 1:2.5.2-3 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2+b2 install ok installed libblkid1:amd64 libblkid1 2.40.4-5 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.40-7 install ok installed libc6:amd64 libc6 2.40-7 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1 install ok installed libcap2:amd64 libcap2 1:2.73-4 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.277 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-17 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1 install ok installed libjs-jquery libjs-jquery 3.6.1+dfsg+~3.5.14-1 install ok installed libjs-sphinxdoc libjs-sphinxdoc 8.1.3-5 install ok installed libjs-underscore libjs-underscore 1.13.4~dfsg+~1.11.4-3 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-3 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 2.40.4-5 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-3 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-3 install ok installed libpam-runtime libpam-runtime 1.7.0-3 install ok installed libpam0g:amd64 libpam0g 1.7.0-3 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.45-1 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-2+b1 install ok installed libselinux1:amd64 libselinux1 3.8-4 install ok installed libsemanage-common libsemanage-common 3.8-1 install ok installed libsemanage2:amd64 libsemanage2 3.8-1+b1 install ok installed libsepol2:amd64 libsepol2 3.8-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.4-5 install ok installed libssl3t64:amd64 libssl3t64 3.4.1-1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-17 install ok installed libsystemd0:amd64 libsystemd0 257.3-1 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-1 install ok installed libudev1:amd64 libudev1 257.3-1 install ok installed libuuid1:amd64 libuuid1 2.40.4-5 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-2 install ok installed login login 1:4.16.0-2+really2.40.4-5 install ok installed login.defs login.defs 1:4.17.3-1 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed mount mount 2.40.4-5 install ok installed ncurses-base ncurses-base 6.5+20250216-1 install ok installed ncurses-bin ncurses-bin 6.5+20250216-1 install ok installed openssl-provider-legacy openssl-provider-legacy 3.4.1-1 install ok installed passwd passwd 1:4.17.3-1 install ok installed perl-base perl-base 5.40.1-2 install ok installed python3-shasta-doc python3-shasta-doc 0.12.0-2 install ok installed sed sed 4.9-2 install ok installed sqv sqv 1.2.1-6+b1 install ok installed sysvinit-utils sysvinit-utils 3.14-3 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tzdata tzdata 2025a-2 install ok installed usr-is-merged usr-is-merged 39+nmu2 install ok installed util-linux util-linux 2.40.4-5 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'apt-get', 'remove', 'libjs-jquery', 'libjs-sphinxdoc', 'libjs-underscore', 'python3-shasta-doc'] 0m9.0s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: libjs-jquery libjs-sphinxdoc libjs-underscore python3-shasta-doc 0 upgraded, 0 newly installed, 4 to remove and 0 not upgraded. After this operation, 1444 kB 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 ... 4981 files and directories currently installed.) Removing python3-shasta-doc (0.12.0-2) ... Removing libjs-sphinxdoc (8.1.3-5) ... Removing libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Removing libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'apt-get', 'remove', 'libjs-jquery', 'libjs-sphinxdoc', 'libjs-underscore', 'python3-shasta-doc'] 0m9.0s INFO: Running scripts post_remove 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/post_remove_exceptions'] 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/post_remove_exceptions'] 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'dpkg', '--purge', 'libjs-jquery', 'libjs-sphinxdoc', 'libjs-underscore'] 0m9.0s DUMP: (Reading database ... 4913 files and directories currently installed.) Purging configuration files for libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... dpkg: warning: ignoring request to remove libjs-sphinxdoc which isn't installed dpkg: warning: ignoring request to remove libjs-underscore which isn't installed 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'dpkg', '--purge', 'libjs-jquery', 'libjs-sphinxdoc', 'libjs-underscore'] 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'dpkg', '--purge', 'python3-shasta-doc'] 0m9.0s DUMP: dpkg: warning: ignoring request to remove python3-shasta-doc which isn't installed 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'dpkg', '--purge', 'python3-shasta-doc'] 0m9.0s INFO: Running scripts post_purge 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/post_purge_exceptions'] 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/post_purge_exceptions'] 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'dpkg', '--purge', '--pending'] 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'dpkg', '--purge', '--pending'] 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'dpkg', '--remove', '--pending'] 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'dpkg', '--remove', '--pending'] 0m9.0s INFO: Running scripts post_test 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/post_test_exceptions'] 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'tmp/scripts/post_test_exceptions'] 0m9.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp63__w87i'] 0m9.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp63__w87i'] 0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'dpkg-divert', '--list'] 0m9.2s DUMP: local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged local diversion of /home to /home.distrib diversion of /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6 diversion of /libx32 to /.libx32.usr-is-merged by base-files local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /lib32 to /.lib32.usr-is-merged by base-files diversion of /libo32 to /.libo32.usr-is-merged by base-files 0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'dpkg-divert', '--list'] 0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'apt-get', 'clean'] 0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp63__w87i', 'apt-get', 'clean'] 0m9.2s DEBUG: Recording chroot state 0m9.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp63__w87i/dev/shm'] 0m9.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp63__w87i/dev/shm'] 0m9.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp63__w87i/dev/console'] 0m9.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp63__w87i/dev/console'] 0m9.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp63__w87i/dev/ptmx'] 0m9.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp63__w87i/dev/ptmx'] 0m9.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp63__w87i/dev/pts'] 0m9.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp63__w87i/dev/pts'] 0m9.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp63__w87i/proc'] 0m9.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp63__w87i/proc'] 0m9.7s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp63__w87i'] 0m9.8s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp63__w87i'] 0m9.8s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp63__w87i 0m9.8s INFO: PASS: Upgrading between Debian distributions. 0m9.8s INFO: PASS: All tests. 0m9.8s INFO: piuparts run ends. ret=0 End: 2025-02-27 20:44:57 GMT