Start: 2023-04-12 14:58:39 GMT [testing] Package: kallisto-examples Source: kallisto Version: 0.48.0+dfsg-3 Installed-Size: 1495 Maintainer: Debian Med Packaging Team Architecture: all Recommends: kallisto Suggests: snakemake Description: near-optimal RNA-Seq quantification (example data) Multi-Arch: foreign Homepage: https://pachterlab.github.io/kallisto Description-md5: 26f735b25852358e202670077e2510b5 Section: science Priority: optional Filename: pool/main/k/kallisto/kallisto-examples_0.48.0+dfsg-3_all.deb Size: 1302728 MD5sum: 794fff89009e5dec6d1900b1ec3bb4ed SHA256: 24b80a5a03ac60e6e6b610a9d614a0e0a0396170db5f1259ac8f52495ba0a6dc [sid] Package: kallisto-examples Source: kallisto Version: 0.48.0+dfsg-4 Installed-Size: 1494 Maintainer: Debian Med Packaging Team Architecture: all Recommends: kallisto Suggests: snakemake Description: near-optimal RNA-Seq quantification (example data) Multi-Arch: foreign Homepage: https://pachterlab.github.io/kallisto Description-md5: 26f735b25852358e202670077e2510b5 Section: science Priority: optional Filename: pool/main/k/kallisto/kallisto-examples_0.48.0+dfsg-4_all.deb Size: 1302540 MD5sum: 95f988414c9b1adfafbed0bab82ed408 SHA256: 376837ad47ed58027407d654d5121894f28c0187501b19a23d6464354877bf6a Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt kallisto-examples=0.48.0+dfsg-4 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 1.1.5 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt kallisto-examples=0.48.0+dfsg-4 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmp11d4045x 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp11d4045x 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp11d4045x', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz'] 0m2.4s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp11d4045x', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz'] 0m2.4s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp11d4045x/proc'] 0m2.4s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp11d4045x/proc'] 0m2.4s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp11d4045x/dev/pts'] 0m2.4s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp11d4045x/dev/pts'] 0m2.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp11d4045x/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp11d4045x/dev/ptmx'] 0m2.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp11d4045x/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp11d4045x/dev/ptmx'] 0m2.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmp11d4045x/dev/console'] 0m2.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmp11d4045x/dev/console'] 0m2.4s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp11d4045x/dev/shm'] 0m2.4s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp11d4045x/dev/shm'] 0m2.4s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m2.5s DEBUG: Created policy-rc.d and chmodded it. 0m2.5s DEBUG: Created resolv.conf. 0m2.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp11d4045x/tmp/scripts/ 0m2.5s INFO: Running scripts post_chroot_unpack 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'apt-get', 'update'] 0m7.1s DUMP: Get:1 http://deb.debian.org/debian bookworm InRelease [181 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 Packages [8915 kB] Get:3 http://deb.debian.org/debian bookworm/main Translation-en [6089 kB] Fetched 15.2 MB in 4s (4084 kB/s) Reading package lists... 0m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'apt-get', 'update'] 0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'apt-get', '-yf', 'dist-upgrade'] 0m7.7s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'apt-get', '-yf', 'dist-upgrade'] 0m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m8.0s DUMP: b1e3f93156d00dfead581e7311ea9c94 - 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m8.0s INFO: Running scripts post_setup 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/post_setup_dummy_users'] 0m9.0s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/post_setup_dummy_users'] 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/post_setup_forbid_home'] 0m9.0s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/post_setup_forbid_home'] 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/post_setup_force-unsafe-io'] 0m9.0s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' dpkg-divert: warning: diverting file '/bin/sync' from an Essential package with rename is dangerous, use --no-rename '/bin/sync' -> 'true' 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/post_setup_force-unsafe-io'] 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/post_setup_minimize'] 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/post_setup_minimize'] 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/post_setup_squeeze-backports'] 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/post_setup_squeeze-backports'] 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/post_setup_zz_backports'] 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/post_setup_zz_backports'] 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m9.0s DUMP: install ok installed apt apt 2.6.0 install ok installed base-files base-files 12.4 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b1 install ok installed bsdutils bsdutils 1:2.38.1-5+b1 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.12-2 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.2 install ok installed debianutils debianutils 5.7-0.4 install ok installed diffutils diffutils 1:3.8-4 install ok installed dpkg dpkg 1.21.21 install ok installed e2fsprogs e2fsprogs 1.47.0-2 install ok installed findutils findutils 4.9.0-4 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-14 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.8-5 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu1 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.6.0 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.0.9-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.9-1 install ok installed libblkid1:amd64 libblkid1 2.38.1-5+b1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-8 install ok installed libc6:amd64 libc6 2.36-8 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3 install ok installed libcap2:amd64 libcap2 1:2.66-3 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.33-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.268 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libfile-find-rule-perl libfile-find-rule-perl 0.34-3 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-14 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-3 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.23-3 install ok installed libgdbm6:amd64 libgdbm6 1.23-3 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.9-1 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.1-0.2 install ok installed libmd0:amd64 libmd0 1.0.4-2 install ok installed libmount1:amd64 libmount1 2.38.1-5+b1 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libnumber-compare-perl libnumber-compare-perl 0.03-3 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-6 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-6 install ok installed libpam-runtime libpam-runtime 1.5.2-6 install ok installed libpam0g:amd64 libpam0g 1.5.2-6 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-1 install ok installed libperl5.36:amd64 libperl5.36 5.36.0-7 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+b3 install ok installed libselinux1:amd64 libselinux1 3.4-1+b5 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b5 install ok installed libsepol2:amd64 libsepol2 3.4-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-5+b1 install ok installed libss2:amd64 libss2 1.47.0-2 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-14 install ok installed libsystemd0:amd64 libsystemd0 252.6-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtext-glob-perl libtext-glob-perl 0.11-3 install ok installed libtinfo6:amd64 libtinfo6 6.4-2 install ok installed libudev1:amd64 libudev1 252.6-1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+b1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.4+dfsg2-5 install ok installed login login 1:4.13+dfsg1-1+b1 install ok installed logsave logsave 1.47.0-2 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mount mount 2.38.1-5+b1 install ok installed ncurses-base ncurses-base 6.4-2 install ok installed ncurses-bin ncurses-bin 6.4-2 install ok installed passwd passwd 1:4.13+dfsg1-1+b1 install ok installed perl perl 5.36.0-7 install ok installed perl-base perl-base 5.36.0-7 install ok installed perl-modules-5.36 perl-modules-5.36 5.36.0-7 install ok installed sed sed 4.9-1 install ok installed sysvinit-utils sysvinit-utils 3.06-2 install ok installed tar tar 1.34+dfsg-1 install ok installed tzdata tzdata 2023c-2 install ok installed usr-is-merged usr-is-merged 35 install ok installed usrmerge usrmerge 35 install ok installed util-linux util-linux 2.38.1-5+b1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+b1 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m9.0s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m9.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp11d4045x'] 0m9.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp11d4045x'] 0m9.5s INFO: Running scripts is_testable 0m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/is_testable_uninstallable'] 0m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/is_testable_uninstallable'] 0m9.5s INFO: Running scripts pre_test 0m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_test_exceptions'] 0m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_test_exceptions'] 0m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_test_root_password'] 0m9.5s DUMP: New password: Retype new password: passwd: password updated successfully 0m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_test_root_password'] 0m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'apt-cache', 'show', '--no-all-versions', 'kallisto-examples'] 0m9.8s DUMP: Package: kallisto-examples Source: kallisto Version: 0.48.0+dfsg-3 Installed-Size: 1495 Maintainer: Debian Med Packaging Team Architecture: all Recommends: kallisto Suggests: snakemake Description-en: near-optimal RNA-Seq quantification (example data) Kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. On benchmarks with standard RNA-Seq data, kallisto can quantify 30 million human reads in less than 3 minutes on a Mac desktop computer using only the read sequences and a transcriptome index that itself takes less than 10 minutes to build. Pseudoalignment of reads preserves the key information needed for quantification, and kallisto is therefore not only fast, but also as accurate than existing quantification tools. In fact, because the pseudoalignment procedure is robust to errors in the reads, in many benchmarks kallisto significantly outperforms existing tools. . This package contains usage examples which are used in autopkgtest. Description-md5: 26f735b25852358e202670077e2510b5 Multi-Arch: foreign Homepage: https://pachterlab.github.io/kallisto Section: science Priority: optional Filename: pool/main/k/kallisto/kallisto-examples_0.48.0+dfsg-3_all.deb Size: 1302728 MD5sum: 794fff89009e5dec6d1900b1ec3bb4ed SHA256: 24b80a5a03ac60e6e6b610a9d614a0e0a0396170db5f1259ac8f52495ba0a6dc 0m9.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'apt-cache', 'show', '--no-all-versions', 'kallisto-examples'] 0m9.8s INFO: apt-cache knows about the following packages: kallisto-examples 0m9.8s INFO: Running scripts pre_install 0m9.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_install_database-server'] 0m9.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_install_database-server'] 0m9.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_install_exceptions'] 0m9.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_install_exceptions'] 0m9.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_install_extras'] 0m9.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_install_extras'] 0m9.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_install_foreign_architecture'] 0m9.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_install_foreign_architecture'] 0m9.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m9.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m9.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'apt-cache', 'policy'] 0m9.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release o=Debian,a=testing,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'apt-cache', 'policy'] 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'apt-cache', 'policy', 'kallisto-examples'] 0m9.9s DUMP: kallisto-examples: Installed: (none) Candidate: 0.48.0+dfsg-3 Version table: 0.48.0+dfsg-3 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'apt-cache', 'policy', 'kallisto-examples'] 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'apt-get', '-y', 'install', 'kallisto-examples'] 0m11.9s DUMP: Reading package lists... Building dependency tree... Suggested packages: snakemake Recommended packages: kallisto The following NEW packages will be installed: kallisto-examples 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 1303 kB of archives. After this operation, 1531 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 kallisto-examples all 0.48.0+dfsg-3 [1303 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1303 kB in 1s (1421 kB/s) Selecting previously unselected package kallisto-examples. (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 ... 8066 files and directories currently installed.) Preparing to unpack .../kallisto-examples_0.48.0+dfsg-3_all.deb ... Unpacking kallisto-examples (0.48.0+dfsg-3) ... Setting up kallisto-examples (0.48.0+dfsg-3) ... 0m11.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'apt-get', '-y', 'install', 'kallisto-examples'] 0m11.9s INFO: Running scripts post_install 0m11.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/post_install_exceptions'] 0m11.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/post_install_exceptions'] 0m11.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp11d4045x'] 0m12.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp11d4045x'] 0m12.4s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmp11d4045x to sid 0m12.4s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m12.4s INFO: Running scripts pre_distupgrade 0m12.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m12.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m12.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_distupgrade_exceptions'] 0m12.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_distupgrade_exceptions'] 0m12.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m12.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m12.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m12.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m12.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m12.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m12.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'apt-get', 'update'] 0m16.6s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [184 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9433 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [6986 kB] Fetched 16.6 MB in 3s (5000 kB/s) Reading package lists... 0m16.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'apt-get', 'update'] 0m16.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'apt-get', '-yf', 'dist-upgrade'] 0m20.5s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: debian-archive-keyring kallisto-examples libc-bin libc6 sysvinit-utils tar 6 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 5689 kB of archives. After this operation, 1024 B disk space will be freed. Get:1 http://deb.debian.org/debian sid/main amd64 tar amd64 1.34+dfsg-1.2 [836 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libc6 amd64 2.36-9 [2753 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libc-bin amd64 2.36-9 [606 kB] Get:4 http://deb.debian.org/debian sid/main amd64 sysvinit-utils amd64 3.06-4 [31.0 kB] Get:5 http://deb.debian.org/debian sid/main amd64 debian-archive-keyring all 2023.3 [161 kB] Get:6 http://deb.debian.org/debian sid/main amd64 kallisto-examples all 0.48.0+dfsg-4 [1303 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 5689 kB in 1s (5573 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 ... 8087 files and directories currently installed.) Preparing to unpack .../tar_1.34+dfsg-1.2_amd64.deb ... Unpacking tar (1.34+dfsg-1.2) over (1.34+dfsg-1) ... Setting up tar (1.34+dfsg-1.2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8087 files and directories currently installed.) Preparing to unpack .../libc6_2.36-9_amd64.deb ... Unpacking libc6:amd64 (2.36-9) over (2.36-8) ... Setting up libc6:amd64 (2.36-9) ... (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 ... 8087 files and directories currently installed.) Preparing to unpack .../libc-bin_2.36-9_amd64.deb ... Unpacking libc-bin (2.36-9) over (2.36-8) ... Setting up libc-bin (2.36-9) ... (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 ... 8087 files and directories currently installed.) Preparing to unpack .../sysvinit-utils_3.06-4_amd64.deb ... Unpacking sysvinit-utils (3.06-4) over (3.06-2) ... Setting up sysvinit-utils (3.06-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8087 files and directories currently installed.) Preparing to unpack .../debian-archive-keyring_2023.3_all.deb ... Unpacking debian-archive-keyring (2023.3) over (2023.2) ... Setting up debian-archive-keyring (2023.3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8087 files and directories currently installed.) Preparing to unpack .../kallisto-examples_0.48.0+dfsg-4_all.deb ... Unpacking kallisto-examples (0.48.0+dfsg-4) over (0.48.0+dfsg-3) ... Setting up kallisto-examples (0.48.0+dfsg-4) ... 0m20.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'apt-get', '-yf', 'dist-upgrade'] 0m20.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m20.8s DUMP: 620430f1c07891068143ead938dff140 - 0m20.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m20.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'apt-cache', 'show', '--no-all-versions', 'kallisto-examples'] 0m21.0s DUMP: Package: kallisto-examples Source: kallisto Version: 0.48.0+dfsg-4 Installed-Size: 1494 Maintainer: Debian Med Packaging Team Architecture: all Recommends: kallisto Suggests: snakemake Description-en: near-optimal RNA-Seq quantification (example data) Kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. On benchmarks with standard RNA-Seq data, kallisto can quantify 30 million human reads in less than 3 minutes on a Mac desktop computer using only the read sequences and a transcriptome index that itself takes less than 10 minutes to build. Pseudoalignment of reads preserves the key information needed for quantification, and kallisto is therefore not only fast, but also as accurate than existing quantification tools. In fact, because the pseudoalignment procedure is robust to errors in the reads, in many benchmarks kallisto significantly outperforms existing tools. . This package contains usage examples which are used in autopkgtest. Description-md5: 26f735b25852358e202670077e2510b5 Multi-Arch: foreign Homepage: https://pachterlab.github.io/kallisto Section: science Priority: optional Filename: pool/main/k/kallisto/kallisto-examples_0.48.0+dfsg-4_all.deb Size: 1302540 MD5sum: 95f988414c9b1adfafbed0bab82ed408 SHA256: 376837ad47ed58027407d654d5121894f28c0187501b19a23d6464354877bf6a 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'apt-cache', 'show', '--no-all-versions', 'kallisto-examples'] 0m21.0s INFO: apt-cache knows about the following packages: kallisto-examples 0m21.0s INFO: Running scripts pre_install 0m21.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_install_database-server'] 0m21.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_install_database-server'] 0m21.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_install_exceptions'] 0m21.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_install_exceptions'] 0m21.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_install_extras'] 0m21.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_install_extras'] 0m21.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_install_foreign_architecture'] 0m21.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_install_foreign_architecture'] 0m21.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m21.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m21.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'apt-cache', 'policy'] 0m21.2s 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: 0m21.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'apt-cache', 'policy'] 0m21.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'apt-cache', 'policy', 'kallisto-examples'] 0m21.2s DUMP: kallisto-examples: Installed: 0.48.0+dfsg-4 Candidate: 0.48.0+dfsg-4 Version table: *** 0.48.0+dfsg-4 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m21.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'apt-cache', 'policy', 'kallisto-examples'] 0m21.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'apt-get', '-y', 'install', 'kallisto-examples'] 0m21.7s DUMP: Reading package lists... Building dependency tree... Reading state information... kallisto-examples is already the newest version (0.48.0+dfsg-4). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m21.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'apt-get', '-y', 'install', 'kallisto-examples'] 0m21.7s INFO: Running scripts post_install 0m21.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/post_install_exceptions'] 0m21.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/post_install_exceptions'] 0m21.7s INFO: Running scripts post_distupgrade 0m21.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m21.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m21.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/post_distupgrade_exceptions'] 0m21.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/post_distupgrade_exceptions'] 0m21.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m21.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m21.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m21.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m21.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/post_distupgrade_zz_backports'] 0m21.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/post_distupgrade_zz_backports'] 0m21.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp11d4045x'] 0m22.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp11d4045x'] 0m22.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp11d4045x'] 0m22.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp11d4045x'] 0m22.6s INFO: Running scripts pre_install 0m22.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_install_database-server'] 0m22.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_install_database-server'] 0m22.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_install_exceptions'] 0m22.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_install_exceptions'] 0m22.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_install_extras'] 0m22.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_install_extras'] 0m22.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_install_foreign_architecture'] 0m22.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_install_foreign_architecture'] 0m22.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m22.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m22.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'apt-cache', 'policy'] 0m22.7s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m22.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'apt-cache', 'policy'] 0m22.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'apt-cache', 'policy', 'kallisto-examples'] 0m22.7s DUMP: kallisto-examples: Installed: 0.48.0+dfsg-4 Candidate: 0.48.0+dfsg-4 Version table: *** 0.48.0+dfsg-4 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m22.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'apt-cache', 'policy', 'kallisto-examples'] 0m22.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'apt-get', '-y', 'install', 'kallisto-examples=0.48.0+dfsg-4'] 0m23.3s DUMP: Reading package lists... Building dependency tree... Reading state information... kallisto-examples is already the newest version (0.48.0+dfsg-4). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m23.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'apt-get', '-y', 'install', 'kallisto-examples=0.48.0+dfsg-4'] 0m23.3s INFO: Running scripts post_install 0m23.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/post_install_exceptions'] 0m23.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/post_install_exceptions'] 0m23.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp11d4045x'] 0m23.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp11d4045x'] 0m24.2s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp11d4045x', '-ac', '--ignore-obsolete'] 0m25.2s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp11d4045x', '-ac', '--ignore-obsolete'] 0m25.2s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m25.2s DUMP: 0.15.6 0m25.2s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m25.2s INFO: Running adequate version 0.15.6 now. 0m25.2s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'kallisto-examples'] 0m25.3s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'kallisto-examples'] 0m25.3s INFO: Running scripts pre_remove 0m25.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m25.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m25.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m25.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m25.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m26.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m26.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m26.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m26.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m26.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m26.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_remove_exceptions'] 0m26.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/pre_remove_exceptions'] 0m26.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m26.4s DUMP: install ok installed apt apt 2.6.0 install ok installed base-files base-files 12.4 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b1 install ok installed bsdutils bsdutils 1:2.38.1-5+b1 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.12-2 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.3 install ok installed debianutils debianutils 5.7-0.4 install ok installed diffutils diffutils 1:3.8-4 install ok installed dpkg dpkg 1.21.21 install ok installed e2fsprogs e2fsprogs 1.47.0-2 install ok installed findutils findutils 4.9.0-4 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-14 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.8-5 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu1 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed kallisto-examples kallisto-examples 0.48.0+dfsg-4 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.6.0 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.0.9-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.9-1 install ok installed libblkid1:amd64 libblkid1 2.38.1-5+b1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-9 install ok installed libc6:amd64 libc6 2.36-9 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3 install ok installed libcap2:amd64 libcap2 1:2.66-3 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.33-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.268 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libfile-find-rule-perl libfile-find-rule-perl 0.34-3 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-14 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-3 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.23-3 install ok installed libgdbm6:amd64 libgdbm6 1.23-3 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.9-1 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.1-0.2 install ok installed libmd0:amd64 libmd0 1.0.4-2 install ok installed libmount1:amd64 libmount1 2.38.1-5+b1 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libnumber-compare-perl libnumber-compare-perl 0.03-3 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-6 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-6 install ok installed libpam-runtime libpam-runtime 1.5.2-6 install ok installed libpam0g:amd64 libpam0g 1.5.2-6 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-1 install ok installed libperl5.36:amd64 libperl5.36 5.36.0-7 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+b3 install ok installed libselinux1:amd64 libselinux1 3.4-1+b5 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b5 install ok installed libsepol2:amd64 libsepol2 3.4-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-5+b1 install ok installed libss2:amd64 libss2 1.47.0-2 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-14 install ok installed libsystemd0:amd64 libsystemd0 252.6-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtext-glob-perl libtext-glob-perl 0.11-3 install ok installed libtinfo6:amd64 libtinfo6 6.4-2 install ok installed libudev1:amd64 libudev1 252.6-1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+b1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.4+dfsg2-5 install ok installed login login 1:4.13+dfsg1-1+b1 install ok installed logsave logsave 1.47.0-2 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mount mount 2.38.1-5+b1 install ok installed ncurses-base ncurses-base 6.4-2 install ok installed ncurses-bin ncurses-bin 6.4-2 install ok installed passwd passwd 1:4.13+dfsg1-1+b1 install ok installed perl perl 5.36.0-7 install ok installed perl-base perl-base 5.36.0-7 install ok installed perl-modules-5.36 perl-modules-5.36 5.36.0-7 install ok installed sed sed 4.9-1 install ok installed sysvinit-utils sysvinit-utils 3.06-4 install ok installed tar tar 1.34+dfsg-1.2 install ok installed tzdata tzdata 2023c-2 install ok installed usr-is-merged usr-is-merged 35 install ok installed usrmerge usrmerge 35 install ok installed util-linux util-linux 2.38.1-5+b1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+b1 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m26.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m26.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'apt-get', 'remove', 'kallisto-examples'] 0m27.3s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: kallisto-examples 0 upgraded, 0 newly installed, 1 to remove and 0 not upgraded. After this operation, 1530 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 ... 8086 files and directories currently installed.) Removing kallisto-examples (0.48.0+dfsg-4) ... 0m27.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'apt-get', 'remove', 'kallisto-examples'] 0m27.3s INFO: Running scripts post_remove 0m27.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/post_remove_exceptions'] 0m27.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/post_remove_exceptions'] 0m27.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'dpkg', '--purge', 'kallisto-examples'] 0m27.4s DUMP: dpkg: warning: ignoring request to remove kallisto-examples which isn't installed 0m27.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'dpkg', '--purge', 'kallisto-examples'] 0m27.4s INFO: Running scripts post_purge 0m27.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/post_purge_exceptions'] 0m27.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/post_purge_exceptions'] 0m27.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'dpkg', '--purge', '--pending'] 0m27.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'dpkg', '--purge', '--pending'] 0m27.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'dpkg', '--remove', '--pending'] 0m27.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'dpkg', '--remove', '--pending'] 0m27.4s INFO: Running scripts post_test 0m27.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/post_test_exceptions'] 0m27.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'tmp/scripts/post_test_exceptions'] 0m27.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp11d4045x'] 0m27.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp11d4045x'] 0m27.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'dpkg-divert', '--list'] 0m27.8s 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 0m27.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'dpkg-divert', '--list'] 0m27.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'apt-get', 'clean'] 0m27.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp11d4045x', 'apt-get', 'clean'] 0m27.8s DEBUG: Recording chroot state 0m28.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp11d4045x/dev/shm'] 0m28.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp11d4045x/dev/shm'] 0m28.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp11d4045x/dev/console'] 0m28.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp11d4045x/dev/console'] 0m28.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp11d4045x/dev/ptmx'] 0m28.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp11d4045x/dev/ptmx'] 0m28.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp11d4045x/dev/pts'] 0m28.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp11d4045x/dev/pts'] 0m28.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp11d4045x/proc'] 0m28.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp11d4045x/proc'] 0m28.8s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp11d4045x'] 0m28.9s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp11d4045x'] 0m28.9s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp11d4045x 0m28.9s INFO: PASS: Upgrading between Debian distributions. 0m28.9s INFO: PASS: All tests. 0m28.9s INFO: piuparts run ends. ret=0 End: 2023-04-12 14:59:08 GMT