Start: 2023-07-04 15:39:33 GMT [buster] Package: berkeley-express Source: berkeley-express (1.5.2+dfsg-1) Version: 1.5.2+dfsg-1+b2 Installed-Size: 838 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libbamtools2.5.1, libboost-atomic1.67.0, libboost-chrono1.67.0, libboost-date-time1.67.0, libboost-filesystem1.67.0, libboost-program-options1.67.0, libboost-system1.67.0, libboost-thread1.67.0, libc6 (>= 2.27), libgcc1 (>= 1:3.0), libprotobuf17, libstdc++6 (>= 5.2) Recommends: med-config (>= 2.1) Description: Streaming quantification for high-throughput sequencing Homepage: http://bio.math.berkeley.edu/eXpress/index.html Description-md5: 4d4c6aaf75f2e0fff660b1816f1f13c6 Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::c++, interface::commandline, role::program, works-with::biological-sequence Section: science Priority: optional Filename: pool/main/b/berkeley-express/berkeley-express_1.5.2+dfsg-1+b2_amd64.deb Size: 236832 MD5sum: b797ce4b0c44f86aea4a79b104204186 SHA256: 4759353194a7659acf06eb0bc8e4d4dec728d05cd4dc0e225715c5f6c09c74ad [buster-next] Package: berkeley-express Source: berkeley-express (1.5.2+dfsg-1) Version: 1.5.2+dfsg-1+b2 Installed-Size: 838 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libbamtools2.5.1, libboost-atomic1.67.0, libboost-chrono1.67.0, libboost-date-time1.67.0, libboost-filesystem1.67.0, libboost-program-options1.67.0, libboost-system1.67.0, libboost-thread1.67.0, libc6 (>= 2.27), libgcc1 (>= 1:3.0), libprotobuf17, libstdc++6 (>= 5.2) Recommends: med-config (>= 2.1) Description: Streaming quantification for high-throughput sequencing Homepage: http://bio.math.berkeley.edu/eXpress/index.html Description-md5: 4d4c6aaf75f2e0fff660b1816f1f13c6 Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::c++, interface::commandline, role::program, works-with::biological-sequence Section: science Priority: optional Filename: pool/main/b/berkeley-express/berkeley-express_1.5.2+dfsg-1+b2_amd64.deb Size: 236832 MD5sum: b797ce4b0c44f86aea4a79b104204186 SHA256: 4759353194a7659acf06eb0bc8e4d4dec728d05cd4dc0e225715c5f6c09c74ad Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --warn-on-debsums-errors --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/buster_amd64.tar.gz -d buster -d buster-next -B /srv/piuparts.debian.org/slave/refchroot/buster2next/reference-chroot-metadata.dat --apt berkeley-express=1.5.2+dfsg-1+b2 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 1.1.8~202306121314~1.1.7-9-g57dfbde6 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --warn-on-debsums-errors --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/buster_amd64.tar.gz -d buster -d buster-next -B /srv/piuparts.debian.org/slave/refchroot/buster2next/reference-chroot-metadata.dat --apt berkeley-express=1.5.2+dfsg-1+b2 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-23-amd64 #1 SMP Debian 5.10.179-1 (2023-05-12) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpl0zukkwr 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/buster_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpl0zukkwr 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/buster_amd64.tar.gz'] 0m2.0s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/buster_amd64.tar.gz'] 0m2.0s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr/proc'] 0m2.0s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr/proc'] 0m2.0s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr/dev/pts'] 0m2.0s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr/dev/pts'] 0m2.0s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr/dev/ptmx'] 0m2.0s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr/dev/ptmx'] 0m2.1s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr/dev/console'] 0m2.1s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr/dev/console'] 0m2.1s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr/dev/shm'] 0m2.1s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr/dev/shm'] 0m2.1s DEBUG: sources.list: deb http://deb.debian.org/debian/ buster main 0m2.1s DEBUG: Created policy-rc.d and chmodded it. 0m2.1s DEBUG: Created resolv.conf. 0m2.1s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpl0zukkwr/tmp/scripts/ 0m2.1s INFO: Running scripts post_chroot_unpack 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'apt-get', 'update'] 0m3.3s DUMP: Get:1 http://deb.debian.org/debian buster InRelease [122 kB] Fetched 122 kB in 0s (557 kB/s) Reading package lists... 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'apt-get', 'update'] 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'apt-get', '-yf', 'dist-upgrade'] 0m3.8s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'apt-get', '-yf', 'dist-upgrade'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.2s DUMP: f6fc0f2636004ef589309651dfd778f4 - 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.2s INFO: Running scripts post_setup 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/post_setup_dummy_users'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/post_setup_dummy_users'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/post_setup_forbid_home'] 0m5.2s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/post_setup_forbid_home'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.2s 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' 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/post_setup_minimize'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/post_setup_minimize'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/post_setup_zz_backports'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/post_setup_zz_backports'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.2s DUMP: install ok installed adduser adduser 3.118 install ok installed apt apt 1.8.2.3 install ok installed base-files base-files 10.3+deb10u13 install ok installed base-passwd base-passwd 3.5.46 install ok installed bash bash 5.0-4 install ok installed bsdutils bsdutils 1:2.33.1-0.1 install ok installed coreutils coreutils 8.30-3 install ok installed dash dash 0.5.10.2-5 install ok installed debconf debconf 1.5.71+deb10u1 install ok installed debian-archive-keyring debian-archive-keyring 2019.1+deb10u1 install ok installed debianutils debianutils 4.8.6.1 install ok installed diffutils diffutils 1:3.7-3 install ok installed dpkg dpkg 1.19.8 install ok installed e2fsprogs e2fsprogs 1.44.5-1+deb10u3 install ok installed fdisk fdisk 2.33.1-0.1 install ok installed findutils findutils 4.6.0+git+20190209-2 install ok installed gcc-8-base:amd64 gcc-8-base 8.3.0-6 install ok installed gpgv gpgv 2.2.12-1+deb10u2 install ok installed grep grep 3.3-1 install ok installed gzip gzip 1.9-3+deb10u1 install ok installed hostname hostname 3.21 install ok installed init-system-helpers init-system-helpers 1.56+nmu1 install ok installed libacl1:amd64 libacl1 2.2.53-4 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.8.2.3 install ok installed libattr1:amd64 libattr1 1:2.4.48-4 install ok installed libaudit-common libaudit-common 1:2.8.4-3 install ok installed libaudit1:amd64 libaudit1 1:2.8.4-3 install ok installed libblkid1:amd64 libblkid1 2.33.1-0.1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-9.2~deb10u1 install ok installed libc-bin libc-bin 2.28-10+deb10u1 install ok installed libc6:amd64 libc6 2.28-10+deb10u1 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2 install ok installed libcom-err2:amd64 libcom-err2 1.44.5-1+deb10u3 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.5 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.249 install ok installed libext2fs2:amd64 libext2fs2 1.44.5-1+deb10u3 install ok installed libfdisk1:amd64 libfdisk1 2.33.1-0.1 install ok installed libffi6:amd64 libffi6 3.2.1-9 install ok installed libgcc1:amd64 libgcc1 1:8.3.0-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.4-5+deb10u1 install ok installed libgmp10:amd64 libgmp10 2:6.1.2+dfsg-4+deb10u1 install ok installed libgnutls30:amd64 libgnutls30 3.6.7-4+deb10u8 install ok installed libgpg-error0:amd64 libgpg-error0 1.35-1 install ok installed libhogweed4:amd64 libhogweed4 3.4.1-1+deb10u1 install ok installed libidn2-0:amd64 libidn2-0 2.0.5-1+deb10u1 install ok installed liblz4-1:amd64 liblz4-1 1.8.3-1+deb10u1 install ok installed liblzma5:amd64 liblzma5 5.2.4-1+deb10u1 install ok installed libmount1:amd64 libmount1 2.33.1-0.1 install ok installed libncursesw6:amd64 libncursesw6 6.1+20181013-2+deb10u2 install ok installed libnettle6:amd64 libnettle6 3.4.1-1+deb10u1 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.15-2+deb10u1 install ok installed libpam-modules:amd64 libpam-modules 1.3.1-5 install ok installed libpam-modules-bin libpam-modules-bin 1.3.1-5 install ok installed libpam-runtime libpam-runtime 1.3.1-5 install ok installed libpam0g:amd64 libpam0g 1.3.1-5 install ok installed libpcre3:amd64 libpcre3 2:8.39-12 install ok installed libseccomp2:amd64 libseccomp2 2.3.3-4 install ok installed libselinux1:amd64 libselinux1 2.8-1+b1 install ok installed libsemanage-common libsemanage-common 2.8-2 install ok installed libsemanage1:amd64 libsemanage1 2.8-2 install ok installed libsepol1:amd64 libsepol1 2.8-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.33.1-0.1 install ok installed libss2:amd64 libss2 1.44.5-1+deb10u3 install ok installed libstdc++6:amd64 libstdc++6 8.3.0-6 install ok installed libsystemd0:amd64 libsystemd0 241-7~deb10u8 install ok installed libtasn1-6:amd64 libtasn1-6 4.13-3 install ok installed libtinfo6:amd64 libtinfo6 6.1+20181013-2+deb10u2 install ok installed libudev1:amd64 libudev1 241-7~deb10u8 install ok installed libunistring2:amd64 libunistring2 0.9.10-1 install ok installed libuuid1:amd64 libuuid1 2.33.1-0.1 install ok installed libzstd1:amd64 libzstd1 1.3.8+dfsg-3+deb10u2 install ok installed login login 1:4.5-1.1 install ok installed mawk mawk 1.3.3-17+b3 install ok installed mount mount 2.33.1-0.1 install ok installed ncurses-base ncurses-base 6.1+20181013-2+deb10u2 install ok installed ncurses-bin ncurses-bin 6.1+20181013-2+deb10u2 install ok installed passwd passwd 1:4.5-1.1 install ok installed perl-base perl-base 5.28.1-6+deb10u1 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.93-8 install ok installed tar tar 1.30+dfsg-6 install ok installed tzdata tzdata 2021a-0+deb10u6 install ok installed util-linux util-linux 2.33.1-0.1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-1+deb10u1 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.2s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/buster2next/reference-chroot-metadata.dat 0m5.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr'] 0m5.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr'] 0m5.8s INFO: Running scripts is_testable 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/is_testable_uninstallable'] 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/is_testable_uninstallable'] 0m5.8s INFO: Running scripts pre_test 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_test_exceptions'] 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_test_exceptions'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_test_root_password'] 0m5.8s DUMP: New password: Retype new password: passwd: password updated successfully 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_test_root_password'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'apt-cache', 'show', '--no-all-versions', 'berkeley-express'] 0m6.1s DUMP: Package: berkeley-express Source: berkeley-express (1.5.2+dfsg-1) Version: 1.5.2+dfsg-1+b2 Installed-Size: 838 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libbamtools2.5.1, libboost-atomic1.67.0, libboost-chrono1.67.0, libboost-date-time1.67.0, libboost-filesystem1.67.0, libboost-program-options1.67.0, libboost-system1.67.0, libboost-thread1.67.0, libc6 (>= 2.27), libgcc1 (>= 1:3.0), libprotobuf17, libstdc++6 (>= 5.2) Recommends: med-config (>= 2.1) Description-en: Streaming quantification for high-throughput sequencing eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences. Example applications include transcript-level RNA-Seq quantification, allele-specific/haplotype expression analysis (from RNA-Seq), transcription factor binding quantification in ChIP-Seq, and analysis of metagenomic data. It is based on an online-EM algorithm that results in space (memory) requirements proportional to the total size of the target sequences and time requirements that are proportional to the number of sampled fragments. Thus, in applications such as RNA-Seq, eXpress can accurately quantify much larger samples than other currently available tools greatly reducing computing infrastructure requirements. eXpress can be used to build lightweight high-throughput sequencing processing pipelines when coupled with a streaming aligner (such as Bowtie), as output can be piped directly into eXpress, effectively eliminating the need to store read alignments in memory or on disk. . In an analysis of the performance of eXpress for RNA-Seq data, it was observed that this efficiency does not come at a cost of accuracy. eXpress is more accurate than other available tools, even when limited to smaller datasets that do not require such efficiency. Moreover, like the Cufflinks program, eXpress can be used to estimate transcript abundances in multi-isoform genes. eXpress is also able to resolve multi-mappings of reads across gene families, and does not require a reference genome so that it can be used in conjunction with de novo assemblers such as Trinity, Oases, or Trans-ABySS. The underlying model is based on previously described probabilistic models developed for RNA-Seq but is applicable to other settings where target sequences are sampled, and includes parameters for fragment length distributions, errors in reads, and sequence-specific fragment bias. . eXpress can be used to resolve ambiguous mappings in other high-throughput sequencing based applications. The only required inputs to eXpress are a set of target sequences and a set of sequenced fragments multiply-aligned to them. While these target sequences will often be gene isoforms, they need not be. Haplotypes can be used as the reference for allele-specific expression analysis, binding regions for ChIP-Seq, or target genomes in metagenomics experiments. eXpress is useful in any analysis where reads multi-map to sequences that differ in abundance. Description-md5: 4d4c6aaf75f2e0fff660b1816f1f13c6 Homepage: http://bio.math.berkeley.edu/eXpress/index.html Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::c++, interface::commandline, role::program, works-with::biological-sequence Section: science Priority: optional Filename: pool/main/b/berkeley-express/berkeley-express_1.5.2+dfsg-1+b2_amd64.deb Size: 236832 MD5sum: b797ce4b0c44f86aea4a79b104204186 SHA256: 4759353194a7659acf06eb0bc8e4d4dec728d05cd4dc0e225715c5f6c09c74ad 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'apt-cache', 'show', '--no-all-versions', 'berkeley-express'] 0m6.1s INFO: apt-cache knows about the following packages: berkeley-express 0m6.1s INFO: Running scripts pre_install 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_install_database-server'] 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_install_database-server'] 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_install_exceptions'] 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_install_exceptions'] 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_install_extras'] 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_install_extras'] 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'apt-cache', 'policy'] 0m6.2s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian buster/main amd64 Packages release v=10.13,o=Debian,a=oldoldstable,n=buster,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'apt-cache', 'policy'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'apt-cache', 'policy', 'berkeley-express'] 0m6.2s DUMP: berkeley-express: Installed: (none) Candidate: 1.5.2+dfsg-1+b2 Version table: 1.5.2+dfsg-1+b2 500 500 http://deb.debian.org/debian buster/main amd64 Packages 0m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'apt-cache', 'policy', 'berkeley-express'] 0m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'apt-get', '-y', 'install', 'berkeley-express'] 0m7.8s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: libbamtools2.5.1 libboost-atomic1.67.0 libboost-chrono1.67.0 libboost-date-time1.67.0 libboost-filesystem1.67.0 libboost-program-options1.67.0 libboost-system1.67.0 libboost-thread1.67.0 libprotobuf17 Recommended packages: med-config The following NEW packages will be installed: berkeley-express libbamtools2.5.1 libboost-atomic1.67.0 libboost-chrono1.67.0 libboost-date-time1.67.0 libboost-filesystem1.67.0 libboost-program-options1.67.0 libboost-system1.67.0 libboost-thread1.67.0 libprotobuf17 0 upgraded, 10 newly installed, 0 to remove and 0 not upgraded. Need to get 3018 kB of archives. After this operation, 19.8 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian buster/main amd64 libbamtools2.5.1 amd64 2.5.1+dfsg-3 [154 kB] Get:2 http://deb.debian.org/debian buster/main amd64 libboost-atomic1.67.0 amd64 1.67.0-13+deb10u1 [226 kB] Get:3 http://deb.debian.org/debian buster/main amd64 libboost-system1.67.0 amd64 1.67.0-13+deb10u1 [229 kB] Get:4 http://deb.debian.org/debian buster/main amd64 libboost-chrono1.67.0 amd64 1.67.0-13+deb10u1 [234 kB] Get:5 http://deb.debian.org/debian buster/main amd64 libboost-date-time1.67.0 amd64 1.67.0-13+deb10u1 [239 kB] Get:6 http://deb.debian.org/debian buster/main amd64 libboost-filesystem1.67.0 amd64 1.67.0-13+deb10u1 [261 kB] Get:7 http://deb.debian.org/debian buster/main amd64 libboost-program-options1.67.0 amd64 1.67.0-13+deb10u1 [357 kB] Get:8 http://deb.debian.org/debian buster/main amd64 libboost-thread1.67.0 amd64 1.67.0-13+deb10u1 [268 kB] Get:9 http://deb.debian.org/debian buster/main amd64 libprotobuf17 amd64 3.6.1.3-2 [814 kB] Get:10 http://deb.debian.org/debian buster/main amd64 berkeley-express amd64 1.5.2+dfsg-1+b2 [237 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 3018 kB in 0s (12.5 MB/s) Selecting previously unselected package libbamtools2.5.1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6462 files and directories currently installed.) Preparing to unpack .../0-libbamtools2.5.1_2.5.1+dfsg-3_amd64.deb ... Unpacking libbamtools2.5.1:amd64 (2.5.1+dfsg-3) ... Selecting previously unselected package libboost-atomic1.67.0:amd64. Preparing to unpack .../1-libboost-atomic1.67.0_1.67.0-13+deb10u1_amd64.deb ... Unpacking libboost-atomic1.67.0:amd64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-system1.67.0:amd64. Preparing to unpack .../2-libboost-system1.67.0_1.67.0-13+deb10u1_amd64.deb ... Unpacking libboost-system1.67.0:amd64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-chrono1.67.0:amd64. Preparing to unpack .../3-libboost-chrono1.67.0_1.67.0-13+deb10u1_amd64.deb ... Unpacking libboost-chrono1.67.0:amd64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-date-time1.67.0:amd64. Preparing to unpack .../4-libboost-date-time1.67.0_1.67.0-13+deb10u1_amd64.deb ... Unpacking libboost-date-time1.67.0:amd64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-filesystem1.67.0:amd64. Preparing to unpack .../5-libboost-filesystem1.67.0_1.67.0-13+deb10u1_amd64.deb ... Unpacking libboost-filesystem1.67.0:amd64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-program-options1.67.0:amd64. Preparing to unpack .../6-libboost-program-options1.67.0_1.67.0-13+deb10u1_amd64.deb ... Unpacking libboost-program-options1.67.0:amd64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libboost-thread1.67.0:amd64. Preparing to unpack .../7-libboost-thread1.67.0_1.67.0-13+deb10u1_amd64.deb ... Unpacking libboost-thread1.67.0:amd64 (1.67.0-13+deb10u1) ... Selecting previously unselected package libprotobuf17:amd64. Preparing to unpack .../8-libprotobuf17_3.6.1.3-2_amd64.deb ... Unpacking libprotobuf17:amd64 (3.6.1.3-2) ... Selecting previously unselected package berkeley-express. Preparing to unpack .../9-berkeley-express_1.5.2+dfsg-1+b2_amd64.deb ... Unpacking berkeley-express (1.5.2+dfsg-1+b2) ... Setting up libboost-program-options1.67.0:amd64 (1.67.0-13+deb10u1) ... Setting up libboost-date-time1.67.0:amd64 (1.67.0-13+deb10u1) ... Setting up libbamtools2.5.1:amd64 (2.5.1+dfsg-3) ... Setting up libboost-atomic1.67.0:amd64 (1.67.0-13+deb10u1) ... Setting up libprotobuf17:amd64 (3.6.1.3-2) ... Setting up libboost-system1.67.0:amd64 (1.67.0-13+deb10u1) ... Setting up libboost-chrono1.67.0:amd64 (1.67.0-13+deb10u1) ... Setting up libboost-thread1.67.0:amd64 (1.67.0-13+deb10u1) ... Setting up libboost-filesystem1.67.0:amd64 (1.67.0-13+deb10u1) ... Setting up berkeley-express (1.5.2+dfsg-1+b2) ... Processing triggers for libc-bin (2.28-10+deb10u1) ... 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'apt-get', '-y', 'install', 'berkeley-express'] 0m7.8s INFO: Running scripts post_install 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/post_install_exceptions'] 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/post_install_exceptions'] 0m7.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr'] 0m8.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr'] 0m8.3s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpl0zukkwr to buster-next 0m8.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ buster main deb http://security.debian.org buster/updates main deb http://deb.debian.org/debian/ buster-updates main deb http://deb.debian.org/debian/ buster-proposed-updates main 0m8.3s INFO: Running scripts pre_distupgrade 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_distupgrade_exceptions'] 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_distupgrade_exceptions'] 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'apt-get', 'update'] 0m10.2s DUMP: Get:1 http://security.debian.org buster/updates InRelease [34.8 kB] Hit:2 http://deb.debian.org/debian buster InRelease Get:3 http://deb.debian.org/debian buster-updates InRelease [56.6 kB] Get:4 http://deb.debian.org/debian buster-proposed-updates InRelease [59.2 kB] Get:5 http://security.debian.org buster/updates/main amd64 Packages [522 kB] Get:6 http://security.debian.org buster/updates/main Translation-en [282 kB] Get:7 http://deb.debian.org/debian buster-updates/main amd64 Packages [8788 B] Get:8 http://deb.debian.org/debian buster-updates/main Translation-en [6915 B] Get:9 http://deb.debian.org/debian buster-proposed-updates/main amd64 Packages [728 B] Get:10 http://deb.debian.org/debian buster-proposed-updates/main Translation-en [859 B] Fetched 972 kB in 1s (1275 kB/s) Reading package lists... 0m10.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'apt-get', 'update'] 0m10.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'apt-get', '-yf', 'dist-upgrade'] 0m13.5s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: libbz2-1.0 libc-bin libc6 libgnutls30 libncursesw6 libprotobuf17 libsystemd0 libtasn1-6 libtinfo6 libudev1 ncurses-base ncurses-bin tzdata zlib1g 14 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 7663 kB of archives. After this operation, 0 B of additional disk space will be used. Get:1 http://security.debian.org buster/updates/main amd64 ncurses-bin amd64 6.1+20181013-2+deb10u3 [407 kB] Get:2 http://security.debian.org buster/updates/main amd64 libc6 amd64 2.28-10+deb10u2 [2869 kB] Get:3 http://security.debian.org buster/updates/main amd64 libc-bin amd64 2.28-10+deb10u2 [793 kB] Get:4 http://security.debian.org buster/updates/main amd64 ncurses-base all 6.1+20181013-2+deb10u3 [259 kB] Get:5 http://security.debian.org buster/updates/main amd64 libsystemd0 amd64 241-7~deb10u10 [332 kB] Get:6 http://security.debian.org buster/updates/main amd64 zlib1g amd64 1:1.2.11.dfsg-1+deb10u2 [90.9 kB] Get:7 http://security.debian.org buster/updates/main amd64 libbz2-1.0 amd64 1.0.6-9.2~deb10u2 [45.4 kB] Get:8 http://security.debian.org buster/updates/main amd64 libudev1 amd64 241-7~deb10u10 [151 kB] Get:9 http://security.debian.org buster/updates/main amd64 libtasn1-6 amd64 4.13-3+deb10u1 [52.0 kB] Get:10 http://security.debian.org buster/updates/main amd64 libgnutls30 amd64 3.6.7-4+deb10u10 [1126 kB] Get:11 http://security.debian.org buster/updates/main amd64 libtinfo6 amd64 6.1+20181013-2+deb10u3 [326 kB] Get:12 http://security.debian.org buster/updates/main amd64 libncursesw6 amd64 6.1+20181013-2+deb10u3 [132 kB] Get:13 http://security.debian.org buster/updates/main amd64 tzdata all 2021a-0+deb10u11 [267 kB] Get:14 http://security.debian.org buster/updates/main amd64 libprotobuf17 amd64 3.6.1.3-2+deb10u1 [814 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 7663 kB in 0s (50.2 MB/s) (Reading database ... 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(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 ... 6518 files and directories currently installed.) Preparing to unpack .../ncurses-base_6.1+20181013-2+deb10u3_all.deb ... Unpacking ncurses-base (6.1+20181013-2+deb10u3) over (6.1+20181013-2+deb10u2) ... Setting up ncurses-base (6.1+20181013-2+deb10u3) ... (Reading database ... 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(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 ... 6518 files and directories currently installed.) Preparing to unpack .../libudev1_241-7~deb10u10_amd64.deb ... Unpacking libudev1:amd64 (241-7~deb10u10) over (241-7~deb10u8) ... Setting up libudev1:amd64 (241-7~deb10u10) ... (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 ... 6518 files and directories currently installed.) Preparing to unpack .../libtasn1-6_4.13-3+deb10u1_amd64.deb ... Unpacking libtasn1-6:amd64 (4.13-3+deb10u1) over (4.13-3) ... Setting up libtasn1-6:amd64 (4.13-3+deb10u1) ... (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 ... 6518 files and directories currently installed.) Preparing to unpack .../libgnutls30_3.6.7-4+deb10u10_amd64.deb ... Unpacking libgnutls30:amd64 (3.6.7-4+deb10u10) over (3.6.7-4+deb10u8) ... Setting up libgnutls30:amd64 (3.6.7-4+deb10u10) ... (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 ... 6518 files and directories currently installed.) Preparing to unpack .../libtinfo6_6.1+20181013-2+deb10u3_amd64.deb ... Unpacking libtinfo6:amd64 (6.1+20181013-2+deb10u3) over (6.1+20181013-2+deb10u2) ... Setting up libtinfo6:amd64 (6.1+20181013-2+deb10u3) ... (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 ... 6518 files and directories currently installed.) Preparing to unpack .../libncursesw6_6.1+20181013-2+deb10u3_amd64.deb ... Unpacking libncursesw6:amd64 (6.1+20181013-2+deb10u3) over (6.1+20181013-2+deb10u2) ... Setting up libncursesw6:amd64 (6.1+20181013-2+deb10u3) ... (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 ... 6518 files and directories currently installed.) Preparing to unpack .../tzdata_2021a-0+deb10u11_all.deb ... Unpacking tzdata (2021a-0+deb10u11) over (2021a-0+deb10u6) ... Preparing to unpack .../libprotobuf17_3.6.1.3-2+deb10u1_amd64.deb ... Unpacking libprotobuf17:amd64 (3.6.1.3-2+deb10u1) over (3.6.1.3-2) ... Setting up tzdata (2021a-0+deb10u11) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Jul 4 15:39:46 UTC 2023. Universal Time is now: Tue Jul 4 15:39:46 UTC 2023. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libprotobuf17:amd64 (3.6.1.3-2+deb10u1) ... Processing triggers for libc-bin (2.28-10+deb10u2) ... 0m13.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'apt-get', '-yf', 'dist-upgrade'] 0m13.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m13.9s DUMP: 6f75ae48b0907c2ef9e2b072ff7d4963 - 0m13.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m13.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'apt-cache', 'show', '--no-all-versions', 'berkeley-express'] 0m14.2s DUMP: Package: berkeley-express Source: berkeley-express (1.5.2+dfsg-1) Version: 1.5.2+dfsg-1+b2 Installed-Size: 838 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libbamtools2.5.1, libboost-atomic1.67.0, libboost-chrono1.67.0, libboost-date-time1.67.0, libboost-filesystem1.67.0, libboost-program-options1.67.0, libboost-system1.67.0, libboost-thread1.67.0, libc6 (>= 2.27), libgcc1 (>= 1:3.0), libprotobuf17, libstdc++6 (>= 5.2) Recommends: med-config (>= 2.1) Description-en: Streaming quantification for high-throughput sequencing eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences. Example applications include transcript-level RNA-Seq quantification, allele-specific/haplotype expression analysis (from RNA-Seq), transcription factor binding quantification in ChIP-Seq, and analysis of metagenomic data. It is based on an online-EM algorithm that results in space (memory) requirements proportional to the total size of the target sequences and time requirements that are proportional to the number of sampled fragments. Thus, in applications such as RNA-Seq, eXpress can accurately quantify much larger samples than other currently available tools greatly reducing computing infrastructure requirements. eXpress can be used to build lightweight high-throughput sequencing processing pipelines when coupled with a streaming aligner (such as Bowtie), as output can be piped directly into eXpress, effectively eliminating the need to store read alignments in memory or on disk. . In an analysis of the performance of eXpress for RNA-Seq data, it was observed that this efficiency does not come at a cost of accuracy. eXpress is more accurate than other available tools, even when limited to smaller datasets that do not require such efficiency. Moreover, like the Cufflinks program, eXpress can be used to estimate transcript abundances in multi-isoform genes. eXpress is also able to resolve multi-mappings of reads across gene families, and does not require a reference genome so that it can be used in conjunction with de novo assemblers such as Trinity, Oases, or Trans-ABySS. The underlying model is based on previously described probabilistic models developed for RNA-Seq but is applicable to other settings where target sequences are sampled, and includes parameters for fragment length distributions, errors in reads, and sequence-specific fragment bias. . eXpress can be used to resolve ambiguous mappings in other high-throughput sequencing based applications. The only required inputs to eXpress are a set of target sequences and a set of sequenced fragments multiply-aligned to them. While these target sequences will often be gene isoforms, they need not be. Haplotypes can be used as the reference for allele-specific expression analysis, binding regions for ChIP-Seq, or target genomes in metagenomics experiments. eXpress is useful in any analysis where reads multi-map to sequences that differ in abundance. Description-md5: 4d4c6aaf75f2e0fff660b1816f1f13c6 Homepage: http://bio.math.berkeley.edu/eXpress/index.html Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::c++, interface::commandline, role::program, works-with::biological-sequence Section: science Priority: optional Filename: pool/main/b/berkeley-express/berkeley-express_1.5.2+dfsg-1+b2_amd64.deb Size: 236832 MD5sum: b797ce4b0c44f86aea4a79b104204186 SHA256: 4759353194a7659acf06eb0bc8e4d4dec728d05cd4dc0e225715c5f6c09c74ad 0m14.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'apt-cache', 'show', '--no-all-versions', 'berkeley-express'] 0m14.2s INFO: apt-cache knows about the following packages: berkeley-express 0m14.2s INFO: Running scripts pre_install 0m14.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_install_database-server'] 0m14.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_install_database-server'] 0m14.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_install_exceptions'] 0m14.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_install_exceptions'] 0m14.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_install_extras'] 0m14.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_install_extras'] 0m14.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_install_foreign_architecture'] 0m14.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_install_foreign_architecture'] 0m14.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m14.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m14.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'apt-cache', 'policy'] 0m14.3s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian buster-proposed-updates/main amd64 Packages release v=10-updates,o=Debian,a=oldoldstable-proposed-updates,n=buster-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian buster-updates/main amd64 Packages release o=Debian,a=oldoldstable-updates,n=buster-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org buster/updates/main amd64 Packages release v=10,o=Debian,a=oldoldstable,n=buster,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian buster/main amd64 Packages release v=10.13,o=Debian,a=oldoldstable,n=buster,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'apt-cache', 'policy'] 0m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'apt-cache', 'policy', 'berkeley-express'] 0m14.3s DUMP: berkeley-express: Installed: 1.5.2+dfsg-1+b2 Candidate: 1.5.2+dfsg-1+b2 Version table: *** 1.5.2+dfsg-1+b2 500 500 http://deb.debian.org/debian buster/main amd64 Packages 100 /var/lib/dpkg/status 0m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'apt-cache', 'policy', 'berkeley-express'] 0m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'apt-get', '-y', 'install', 'berkeley-express'] 0m14.7s DUMP: Reading package lists... Building dependency tree... Reading state information... berkeley-express is already the newest version (1.5.2+dfsg-1+b2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m14.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'apt-get', '-y', 'install', 'berkeley-express'] 0m14.7s INFO: Running scripts post_install 0m14.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/post_install_exceptions'] 0m14.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/post_install_exceptions'] 0m14.8s INFO: Running scripts post_distupgrade 0m14.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m14.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m14.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/post_distupgrade_exceptions'] 0m14.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/post_distupgrade_exceptions'] 0m14.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m14.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m14.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m14.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m14.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/post_distupgrade_zz_backports'] 0m14.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/post_distupgrade_zz_backports'] 0m14.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr'] 0m15.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr'] 0m15.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr'] 0m15.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr'] 0m15.7s INFO: Running scripts pre_install 0m15.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_install_database-server'] 0m15.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_install_database-server'] 0m15.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_install_exceptions'] 0m15.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_install_exceptions'] 0m15.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_install_extras'] 0m15.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_install_extras'] 0m15.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_install_foreign_architecture'] 0m15.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_install_foreign_architecture'] 0m15.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m15.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m15.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'apt-cache', 'policy'] 0m15.8s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian buster-proposed-updates/main amd64 Packages release v=10-updates,o=Debian,a=oldoldstable-proposed-updates,n=buster-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian buster-updates/main amd64 Packages release o=Debian,a=oldoldstable-updates,n=buster-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org buster/updates/main amd64 Packages release v=10,o=Debian,a=oldoldstable,n=buster,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian buster/main amd64 Packages release v=10.13,o=Debian,a=oldoldstable,n=buster,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m15.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'apt-cache', 'policy'] 0m15.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'apt-cache', 'policy', 'berkeley-express'] 0m15.9s DUMP: berkeley-express: Installed: 1.5.2+dfsg-1+b2 Candidate: 1.5.2+dfsg-1+b2 Version table: *** 1.5.2+dfsg-1+b2 500 500 http://deb.debian.org/debian buster/main amd64 Packages 100 /var/lib/dpkg/status 0m15.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'apt-cache', 'policy', 'berkeley-express'] 0m15.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'apt-get', '-y', 'install', 'berkeley-express=1.5.2+dfsg-1+b2'] 0m16.3s DUMP: Reading package lists... Building dependency tree... Reading state information... berkeley-express is already the newest version (1.5.2+dfsg-1+b2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'apt-get', '-y', 'install', 'berkeley-express=1.5.2+dfsg-1+b2'] 0m16.3s INFO: Running scripts post_install 0m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/post_install_exceptions'] 0m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/post_install_exceptions'] 0m16.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr'] 0m16.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr'] 0m17.4s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', '-ac', '--ignore-obsolete'] 0m18.3s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', '-ac', '--ignore-obsolete'] 0m18.3s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m18.3s DUMP: 0.15.6 0m18.3s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m18.3s INFO: Running adequate version 0.15.6 now. 0m18.3s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'berkeley-express'] 0m18.5s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'berkeley-express'] 0m18.5s INFO: Running scripts pre_remove 0m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m18.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m18.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m19.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m19.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m19.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m19.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m19.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m19.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_remove_exceptions'] 0m19.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/pre_remove_exceptions'] 0m19.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m19.6s DUMP: install ok installed adduser adduser 3.118 install ok installed apt apt 1.8.2.3 install ok installed base-files base-files 10.3+deb10u13 install ok installed base-passwd base-passwd 3.5.46 install ok installed bash bash 5.0-4 install ok installed berkeley-express berkeley-express 1.5.2+dfsg-1+b2 install ok installed bsdutils bsdutils 1:2.33.1-0.1 install ok installed coreutils coreutils 8.30-3 install ok installed dash dash 0.5.10.2-5 install ok installed debconf debconf 1.5.71+deb10u1 install ok installed debian-archive-keyring debian-archive-keyring 2019.1+deb10u1 install ok installed debianutils debianutils 4.8.6.1 install ok installed diffutils diffutils 1:3.7-3 install ok installed dpkg dpkg 1.19.8 install ok installed e2fsprogs e2fsprogs 1.44.5-1+deb10u3 install ok installed fdisk fdisk 2.33.1-0.1 install ok installed findutils findutils 4.6.0+git+20190209-2 install ok installed gcc-8-base:amd64 gcc-8-base 8.3.0-6 install ok installed gpgv gpgv 2.2.12-1+deb10u2 install ok installed grep grep 3.3-1 install ok installed gzip gzip 1.9-3+deb10u1 install ok installed hostname hostname 3.21 install ok installed init-system-helpers init-system-helpers 1.56+nmu1 install ok installed libacl1:amd64 libacl1 2.2.53-4 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.8.2.3 install ok installed libattr1:amd64 libattr1 1:2.4.48-4 install ok installed libaudit-common libaudit-common 1:2.8.4-3 install ok installed libaudit1:amd64 libaudit1 1:2.8.4-3 install ok installed libbamtools2.5.1:amd64 libbamtools2.5.1 2.5.1+dfsg-3 install ok installed libblkid1:amd64 libblkid1 2.33.1-0.1 install ok installed libboost-atomic1.67.0:amd64 libboost-atomic1.67.0 1.67.0-13+deb10u1 install ok installed libboost-chrono1.67.0:amd64 libboost-chrono1.67.0 1.67.0-13+deb10u1 install ok installed libboost-date-time1.67.0:amd64 libboost-date-time1.67.0 1.67.0-13+deb10u1 install ok installed libboost-filesystem1.67.0:amd64 libboost-filesystem1.67.0 1.67.0-13+deb10u1 install ok installed libboost-program-options1.67.0:amd64 libboost-program-options1.67.0 1.67.0-13+deb10u1 install ok installed libboost-system1.67.0:amd64 libboost-system1.67.0 1.67.0-13+deb10u1 install ok installed libboost-thread1.67.0:amd64 libboost-thread1.67.0 1.67.0-13+deb10u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-9.2~deb10u2 install ok installed libc-bin libc-bin 2.28-10+deb10u2 install ok installed libc6:amd64 libc6 2.28-10+deb10u2 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2 install ok installed libcom-err2:amd64 libcom-err2 1.44.5-1+deb10u3 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.5 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.249 install ok installed libext2fs2:amd64 libext2fs2 1.44.5-1+deb10u3 install ok installed libfdisk1:amd64 libfdisk1 2.33.1-0.1 install ok installed libffi6:amd64 libffi6 3.2.1-9 install ok installed libgcc1:amd64 libgcc1 1:8.3.0-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.4-5+deb10u1 install ok installed libgmp10:amd64 libgmp10 2:6.1.2+dfsg-4+deb10u1 install ok installed libgnutls30:amd64 libgnutls30 3.6.7-4+deb10u10 install ok installed libgpg-error0:amd64 libgpg-error0 1.35-1 install ok installed libhogweed4:amd64 libhogweed4 3.4.1-1+deb10u1 install ok installed libidn2-0:amd64 libidn2-0 2.0.5-1+deb10u1 install ok installed liblz4-1:amd64 liblz4-1 1.8.3-1+deb10u1 install ok installed liblzma5:amd64 liblzma5 5.2.4-1+deb10u1 install ok installed libmount1:amd64 libmount1 2.33.1-0.1 install ok installed libncursesw6:amd64 libncursesw6 6.1+20181013-2+deb10u3 install ok installed libnettle6:amd64 libnettle6 3.4.1-1+deb10u1 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.15-2+deb10u1 install ok installed libpam-modules:amd64 libpam-modules 1.3.1-5 install ok installed libpam-modules-bin libpam-modules-bin 1.3.1-5 install ok installed libpam-runtime libpam-runtime 1.3.1-5 install ok installed libpam0g:amd64 libpam0g 1.3.1-5 install ok installed libpcre3:amd64 libpcre3 2:8.39-12 install ok installed libprotobuf17:amd64 libprotobuf17 3.6.1.3-2+deb10u1 install ok installed libseccomp2:amd64 libseccomp2 2.3.3-4 install ok installed libselinux1:amd64 libselinux1 2.8-1+b1 install ok installed libsemanage-common libsemanage-common 2.8-2 install ok installed libsemanage1:amd64 libsemanage1 2.8-2 install ok installed libsepol1:amd64 libsepol1 2.8-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.33.1-0.1 install ok installed libss2:amd64 libss2 1.44.5-1+deb10u3 install ok installed libstdc++6:amd64 libstdc++6 8.3.0-6 install ok installed libsystemd0:amd64 libsystemd0 241-7~deb10u10 install ok installed libtasn1-6:amd64 libtasn1-6 4.13-3+deb10u1 install ok installed libtinfo6:amd64 libtinfo6 6.1+20181013-2+deb10u3 install ok installed libudev1:amd64 libudev1 241-7~deb10u10 install ok installed libunistring2:amd64 libunistring2 0.9.10-1 install ok installed libuuid1:amd64 libuuid1 2.33.1-0.1 install ok installed libzstd1:amd64 libzstd1 1.3.8+dfsg-3+deb10u2 install ok installed login login 1:4.5-1.1 install ok installed mawk mawk 1.3.3-17+b3 install ok installed mount mount 2.33.1-0.1 install ok installed ncurses-base ncurses-base 6.1+20181013-2+deb10u3 install ok installed ncurses-bin ncurses-bin 6.1+20181013-2+deb10u3 install ok installed passwd passwd 1:4.5-1.1 install ok installed perl-base perl-base 5.28.1-6+deb10u1 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.93-8 install ok installed tar tar 1.30+dfsg-6 install ok installed tzdata tzdata 2021a-0+deb10u11 install ok installed util-linux util-linux 2.33.1-0.1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-1+deb10u2 0m19.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m19.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'apt-get', 'remove', 'libbamtools2.5.1:amd64', 'libboost-atomic1.67.0:amd64', 'libboost-chrono1.67.0:amd64', 'libboost-date-time1.67.0:amd64', 'libboost-filesystem1.67.0:amd64', 'libboost-program-options1.67.0:amd64', 'libboost-system1.67.0:amd64', 'libboost-thread1.67.0:amd64', 'libprotobuf17:amd64', 'berkeley-express'] 0m20.4s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: berkeley-express libbamtools2.5.1 libboost-atomic1.67.0 libboost-chrono1.67.0 libboost-date-time1.67.0 libboost-filesystem1.67.0 libboost-program-options1.67.0 libboost-system1.67.0 libboost-thread1.67.0 libprotobuf17 0 upgraded, 0 newly installed, 10 to remove and 0 not upgraded. After this operation, 19.8 MB disk space will be freed. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6521 files and directories currently installed.) Removing berkeley-express (1.5.2+dfsg-1+b2) ... Removing libbamtools2.5.1:amd64 (2.5.1+dfsg-3) ... Removing libboost-thread1.67.0:amd64 (1.67.0-13+deb10u1) ... Removing libboost-atomic1.67.0:amd64 (1.67.0-13+deb10u1) ... Removing libboost-chrono1.67.0:amd64 (1.67.0-13+deb10u1) ... Removing libboost-date-time1.67.0:amd64 (1.67.0-13+deb10u1) ... Removing libboost-filesystem1.67.0:amd64 (1.67.0-13+deb10u1) ... Removing libboost-program-options1.67.0:amd64 (1.67.0-13+deb10u1) ... Removing libboost-system1.67.0:amd64 (1.67.0-13+deb10u1) ... Removing libprotobuf17:amd64 (3.6.1.3-2+deb10u1) ... Processing triggers for libc-bin (2.28-10+deb10u2) ... 0m20.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'apt-get', 'remove', 'libbamtools2.5.1:amd64', 'libboost-atomic1.67.0:amd64', 'libboost-chrono1.67.0:amd64', 'libboost-date-time1.67.0:amd64', 'libboost-filesystem1.67.0:amd64', 'libboost-program-options1.67.0:amd64', 'libboost-system1.67.0:amd64', 'libboost-thread1.67.0:amd64', 'libprotobuf17:amd64', 'berkeley-express'] 0m20.4s INFO: Running scripts post_remove 0m20.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/post_remove_exceptions'] 0m20.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/post_remove_exceptions'] 0m20.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'dpkg', '--purge', 'libbamtools2.5.1:amd64', 'libboost-atomic1.67.0:amd64', 'libboost-chrono1.67.0:amd64', 'libboost-date-time1.67.0:amd64', 'libboost-filesystem1.67.0:amd64', 'libboost-program-options1.67.0:amd64', 'libboost-system1.67.0:amd64', 'libboost-thread1.67.0:amd64', 'libprotobuf17:amd64'] 0m20.4s DUMP: dpkg: warning: ignoring request to remove libbamtools2.5.1 which isn't installed dpkg: warning: ignoring request to remove libboost-atomic1.67.0 which isn't installed dpkg: warning: ignoring request to remove libboost-chrono1.67.0 which isn't installed dpkg: warning: ignoring request to remove libboost-date-time1.67.0 which isn't installed dpkg: warning: ignoring request to remove libboost-filesystem1.67.0 which isn't installed dpkg: warning: ignoring request to remove libboost-program-options1.67.0 which isn't installed dpkg: warning: ignoring request to remove libboost-system1.67.0 which isn't installed dpkg: warning: ignoring request to remove libboost-thread1.67.0 which isn't installed dpkg: warning: ignoring request to remove libprotobuf17 which isn't installed 0m20.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'dpkg', '--purge', 'libbamtools2.5.1:amd64', 'libboost-atomic1.67.0:amd64', 'libboost-chrono1.67.0:amd64', 'libboost-date-time1.67.0:amd64', 'libboost-filesystem1.67.0:amd64', 'libboost-program-options1.67.0:amd64', 'libboost-system1.67.0:amd64', 'libboost-thread1.67.0:amd64', 'libprotobuf17:amd64'] 0m20.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'dpkg', '--purge', 'berkeley-express'] 0m20.4s DUMP: dpkg: warning: ignoring request to remove berkeley-express which isn't installed 0m20.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'dpkg', '--purge', 'berkeley-express'] 0m20.4s INFO: Running scripts post_purge 0m20.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/post_purge_exceptions'] 0m20.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/post_purge_exceptions'] 0m20.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'dpkg', '--purge', '--pending'] 0m20.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'dpkg', '--purge', '--pending'] 0m20.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'dpkg', '--remove', '--pending'] 0m20.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'dpkg', '--remove', '--pending'] 0m20.4s INFO: Running scripts post_test 0m20.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/post_test_exceptions'] 0m20.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'tmp/scripts/post_test_exceptions'] 0m20.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr'] 0m20.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr'] 0m20.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'dpkg-divert', '--list'] 0m20.9s 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 0m20.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'dpkg-divert', '--list'] 0m20.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'apt-get', 'clean'] 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr', 'apt-get', 'clean'] 0m21.0s DEBUG: Recording chroot state 0m22.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr/dev/shm'] 0m22.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr/dev/shm'] 0m22.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr/dev/console'] 0m22.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr/dev/console'] 0m22.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr/dev/ptmx'] 0m22.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr/dev/ptmx'] 0m22.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr/dev/pts'] 0m22.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr/dev/pts'] 0m22.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr/proc'] 0m22.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr/proc'] 0m22.5s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr'] 0m22.6s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpl0zukkwr'] 0m22.6s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpl0zukkwr 0m22.6s INFO: PASS: Upgrading between Debian distributions. 0m22.6s INFO: PASS: All tests. 0m22.6s INFO: piuparts run ends. ret=0 End: 2023-07-04 15:39:56 GMT