Start: 2025-09-28 15:55:16 GMT [stable] Package: berkeley-express Source: berkeley-express (1.5.3+dfsg-3) Version: 1.5.3+dfsg-3+b3 Installed-Size: 759 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libbamtools2.5.2 (>= 2.5.2+dfsg), libboost-filesystem1.83.0 (>= 1.83.0), libboost-program-options1.83.0 (>= 1.83.0), libboost-thread1.83.0 (>= 1.83.0), libc6 (>= 2.34), libgcc-s1 (>= 3.0), libprotobuf32t64 (>= 3.21.12), libstdc++6 (>= 13.1) Recommends: med-config 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_1.5.3+dfsg-3+b3_amd64.deb Size: 232556 MD5sum: 6903d535f401a5862314041023eac835 SHA256: 0c6627b538fd511ac87b37a88828bdb4b5f61ba9080eb0cd7b12649d562944bf [testing] Package: berkeley-express Source: berkeley-express (1.5.3+dfsg-3) Version: 1.5.3+dfsg-3+b3 Installed-Size: 759 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libbamtools2.5.2 (>= 2.5.2+dfsg), libboost-filesystem1.83.0 (>= 1.83.0), libboost-program-options1.83.0 (>= 1.83.0), libboost-thread1.83.0 (>= 1.83.0), libc6 (>= 2.34), libgcc-s1 (>= 3.0), libprotobuf32t64 (>= 3.21.12), libstdc++6 (>= 13.1) Recommends: med-config 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_1.5.3+dfsg-3+b3_amd64.deb Size: 232556 MD5sum: 6903d535f401a5862314041023eac835 SHA256: 0c6627b538fd511ac87b37a88828bdb4b5f61ba9080eb0cd7b12649d562944bf [sid] Package: berkeley-express Source: berkeley-express (1.5.3+dfsg-3) Version: 1.5.3+dfsg-3+b4 Installed-Size: 763 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libbamtools2.5.3 (>= 2.5.3+dfsg), libboost-filesystem1.83.0 (>= 1.83.0), libboost-program-options1.83.0 (>= 1.83.0), libboost-thread1.83.0 (>= 1.83.0), libc6 (>= 2.38), libgcc-s1 (>= 3.0), libprotobuf32t64 (>= 3.21.12), libstdc++6 (>= 14) Recommends: med-config 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_1.5.3+dfsg-3+b4_amd64.deb Size: 236344 MD5sum: 35ac090a0bf0fee288c779c38c61b061 SHA256: 68c0900024a475e88bc3b4873f1298afdf3e98dde2adc27c558978e29fc62dfa Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/bin/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/trixie-merged-usr_amd64.tar.gz -d stable -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/stable22sid/reference-chroot-metadata.dat --apt berkeley-express=1.5.3+dfsg-3+b4 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 1.6.1~202508211856~1.6.0-10-gffba2cce starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/bin/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/trixie-merged-usr_amd64.tar.gz -d stable -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/stable22sid/reference-chroot-metadata.dat --apt berkeley-express=1.5.3+dfsg-3+b4 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 6.1.0-40-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.153-1 (2025-09-20) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpn1thdtbm 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpn1thdtbm 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm/proc'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm/proc'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm/dev/pts'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm/dev/pts'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm/dev/ptmx'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm/dev/ptmx'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm/dev/console'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm/dev/console'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm/dev/shm'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm/dev/shm'] 0m0.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main 0m0.2s DEBUG: Created policy-rc.d and chmodded it. 0m0.2s DEBUG: Created resolv.conf. 0m0.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpn1thdtbm/tmp/scripts/ 0m0.2s INFO: Running scripts post_chroot_unpack 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-get', 'update'] 0m0.7s DUMP: Hit:1 http://deb.debian.org/debian trixie InRelease Reading package lists... 0m0.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-get', 'update'] 0m0.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-get', '-yf', 'dist-upgrade'] 0m1.0s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m1.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-get', '-yf', 'dist-upgrade'] 0m1.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m1.2s DUMP: cc6be03135582e5dd4c9ee869186ad39 - 0m1.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m1.2s INFO: Running scripts post_setup 0m1.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_setup_dummy_users'] 0m1.6s 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 0m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_setup_dummy_users'] 0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_setup_forbid_home'] 0m1.6s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_setup_forbid_home'] 0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_setup_force-unsafe-io'] 0m1.6s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_setup_force-unsafe-io'] 0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_setup_minimize'] 0m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_setup_minimize'] 0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_setup_squeeze-backports'] 0m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_setup_squeeze-backports'] 0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_setup_zz_backports'] 0m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_setup_zz_backports'] 0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m1.6s DUMP: install ok installed apt apt 3.0.3 install ok installed base-files base-files 13.8+deb13u1 install ok installed base-passwd base-passwd 3.6.7 install ok installed bash bash 5.2.37-2+b5 install ok installed bsdutils bsdutils 1:2.41-5 install ok installed coreutils coreutils 9.7-3 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.91 install ok installed debian-archive-keyring debian-archive-keyring 2025.1 install ok installed debianutils debianutils 5.23.2 install ok installed diffutils diffutils 1:3.10-4 install ok installed dpkg dpkg 1.22.21 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-19 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.13-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.69~deb13u1 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.0.3 install ok installed libattr1:amd64 libattr1 1:2.5.2-3 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2+b2 install ok installed libblkid1:amd64 libblkid1 2.41-5 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.41-12 install ok installed libc6:amd64 libc6 2.41-12 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1 install ok installed libcap2:amd64 libcap2 1:2.75-10+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.280 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-19 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1 install ok installed liblastlog2-2:amd64 liblastlog2-2 2.41-5 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-4 install ok installed liblzma5:amd64 liblzma5 5.8.1-1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.41-5 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-5 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-5 install ok installed libpam-runtime libpam-runtime 1.7.0-5 install ok installed libpam0g:amd64 libpam0g 1.7.0-5 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.46-1~deb13u1 install ok installed libseccomp2:amd64 libseccomp2 2.6.0-2 install ok installed libselinux1:amd64 libselinux1 3.8.1-1 install ok installed libsemanage-common libsemanage-common 3.8.1-1 install ok installed libsemanage2:amd64 libsemanage2 3.8.1-1 install ok installed libsepol2:amd64 libsepol2 3.8.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.41-5 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-7 install ok installed libssl3t64:amd64 libssl3t64 3.5.1-1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-19 install ok installed libsystemd0:amd64 libsystemd0 257.8-1~deb13u1 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2 install ok installed libudev1:amd64 libudev1 257.8-1~deb13u1 install ok installed libuuid1:amd64 libuuid1 2.41-5 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-1 install ok installed login login 1:4.16.0-2+really2.41-5 install ok installed login.defs login.defs 1:4.17.4-2 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed mount mount 2.41-5 install ok installed ncurses-base ncurses-base 6.5+20250216-2 install ok installed ncurses-bin ncurses-bin 6.5+20250216-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.5.1-1 install ok installed passwd passwd 1:4.17.4-2 install ok installed perl-base perl-base 5.40.1-6 install ok installed sed sed 4.9-2 install ok installed sqv sqv 1.3.0-3 install ok installed sysvinit-utils sysvinit-utils 3.14-4 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tzdata tzdata 2025b-4+deb13u1 install ok installed util-linux util-linux 2.41-5 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m1.6s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/stable22sid/reference-chroot-metadata.dat 0m1.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm'] 0m1.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm'] 0m1.9s INFO: Running scripts is_testable 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/is_testable_uninstallable'] 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/is_testable_uninstallable'] 0m1.9s INFO: Running scripts pre_test 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_test_exceptions'] 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_test_exceptions'] 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_test_root_password'] 0m1.9s DUMP: New password: Retype new password: passwd: password updated successfully 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_test_root_password'] 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-cache', 'show', '--no-all-versions', 'berkeley-express'] 0m2.0s DUMP: Package: berkeley-express Source: berkeley-express (1.5.3+dfsg-3) Version: 1.5.3+dfsg-3+b3 Installed-Size: 759 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libbamtools2.5.2 (>= 2.5.2+dfsg), libboost-filesystem1.83.0 (>= 1.83.0), libboost-program-options1.83.0 (>= 1.83.0), libboost-thread1.83.0 (>= 1.83.0), libc6 (>= 2.34), libgcc-s1 (>= 3.0), libprotobuf32t64 (>= 3.21.12), libstdc++6 (>= 13.1) Recommends: med-config 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_1.5.3+dfsg-3+b3_amd64.deb Size: 232556 MD5sum: 6903d535f401a5862314041023eac835 SHA256: 0c6627b538fd511ac87b37a88828bdb4b5f61ba9080eb0cd7b12649d562944bf 0m2.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-cache', 'show', '--no-all-versions', 'berkeley-express'] 0m2.0s INFO: apt-cache knows about the following packages: berkeley-express 0m2.0s INFO: Running scripts pre_install 0m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_install_database-server'] 0m2.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_install_database-server'] 0m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_install_exceptions'] 0m2.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_install_exceptions'] 0m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_install_extras'] 0m2.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_install_extras'] 0m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_install_foreign_architecture'] 0m2.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_install_foreign_architecture'] 0m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m2.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-cache', 'policy'] 0m2.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie/main amd64 Packages release v=13.1,o=Debian,a=stable,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m2.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-cache', 'policy'] 0m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-cache', 'policy', 'berkeley-express'] 0m2.0s DUMP: berkeley-express: Installed: (none) Candidate: 1.5.3+dfsg-3+b3 Version table: 1.5.3+dfsg-3+b3 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m2.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-cache', 'policy', 'berkeley-express'] 0m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-get', '-y', 'install', 'berkeley-express'] 0m2.7s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: libbamtools2.5.2 libboost-filesystem1.83.0 libboost-program-options1.83.0 libboost-thread1.83.0 libprotobuf32t64 Recommended packages: med-config The following NEW packages will be installed: berkeley-express libbamtools2.5.2 libboost-filesystem1.83.0 libboost-program-options1.83.0 libboost-thread1.83.0 libprotobuf32t64 0 upgraded, 6 newly installed, 0 to remove and 0 not upgraded. Need to get 2275 kB of archives. After this operation, 12.2 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 libbamtools2.5.2 amd64 2.5.2+dfsg-6+b1 [161 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 libboost-filesystem1.83.0 amd64 1.83.0-4.2 [282 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 libboost-program-options1.83.0 amd64 1.83.0-4.2 [347 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 libboost-thread1.83.0 amd64 1.83.0-4.2 [270 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 libprotobuf32t64 amd64 3.21.12-11 [983 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 berkeley-express amd64 1.5.3+dfsg-3+b3 [233 kB] Fetched 2275 kB in 0s (15.0 MB/s) Selecting previously unselected package libbamtools2.5.2: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 ... 4939 files and directories currently installed.) Preparing to unpack .../0-libbamtools2.5.2_2.5.2+dfsg-6+b1_amd64.deb ... Unpacking libbamtools2.5.2:amd64 (2.5.2+dfsg-6+b1) ... Selecting previously unselected package libboost-filesystem1.83.0:amd64. Preparing to unpack .../1-libboost-filesystem1.83.0_1.83.0-4.2_amd64.deb ... Unpacking libboost-filesystem1.83.0:amd64 (1.83.0-4.2) ... Selecting previously unselected package libboost-program-options1.83.0:amd64. Preparing to unpack .../2-libboost-program-options1.83.0_1.83.0-4.2_amd64.deb ... Unpacking libboost-program-options1.83.0:amd64 (1.83.0-4.2) ... Selecting previously unselected package libboost-thread1.83.0:amd64. Preparing to unpack .../3-libboost-thread1.83.0_1.83.0-4.2_amd64.deb ... Unpacking libboost-thread1.83.0:amd64 (1.83.0-4.2) ... Selecting previously unselected package libprotobuf32t64:amd64. Preparing to unpack .../4-libprotobuf32t64_3.21.12-11_amd64.deb ... Unpacking libprotobuf32t64:amd64 (3.21.12-11) ... Selecting previously unselected package berkeley-express. Preparing to unpack .../5-berkeley-express_1.5.3+dfsg-3+b3_amd64.deb ... Unpacking berkeley-express (1.5.3+dfsg-3+b3) ... Setting up libboost-program-options1.83.0:amd64 (1.83.0-4.2) ... Setting up libprotobuf32t64:amd64 (3.21.12-11) ... Setting up libboost-thread1.83.0:amd64 (1.83.0-4.2) ... Setting up libboost-filesystem1.83.0:amd64 (1.83.0-4.2) ... Setting up libbamtools2.5.2:amd64 (2.5.2+dfsg-6+b1) ... Setting up berkeley-express (1.5.3+dfsg-3+b3) ... Processing triggers for libc-bin (2.41-12) ... 0m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-get', '-y', 'install', 'berkeley-express'] 0m2.7s INFO: Running scripts post_install 0m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_install_exceptions'] 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_install_exceptions'] 0m2.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm'] 0m3.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm'] 0m3.0s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpn1thdtbm to testing 0m3.0s DEBUG: sources.list: deb http://deb.debian.org/debian/ forky main 0m3.0s INFO: Running scripts pre_distupgrade 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_distupgrade_exceptions'] 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_distupgrade_exceptions'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-get', 'update'] 0m4.4s DUMP: Get:1 http://deb.debian.org/debian forky InRelease [147 kB] Get:2 http://deb.debian.org/debian forky/main amd64 Packages [9742 kB] Get:3 http://deb.debian.org/debian forky/main Translation-en [6480 kB] Fetched 16.4 MB in 1s (17.2 MB/s) Reading package lists... 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-get', 'update'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-get', '-yf', 'dist-upgrade'] 0m6.8s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: gcc-15-base The following packages will be upgraded: apt base-files bash bsdutils gcc-14-base init-system-helpers libapt-pkg7.0 libaudit-common libaudit1 libblkid1 libboost-filesystem1.83.0 libboost-program-options1.83.0 libboost-thread1.83.0 libgcc-s1 libgmp10 liblastlog2-2 liblzma5 libmount1 libpcre2-8-0 libprotobuf32t64 libsmartcols1 libsqlite3-0 libssl3t64 libstdc++6 libsystemd0 libudev1 libuuid1 libzstd1 login login.defs mount openssl-provider-legacy passwd tzdata util-linux 35 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 17.0 MB of archives. After this operation, 816 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian forky/main amd64 base-files amd64 14 [72.9 kB] Get:2 http://deb.debian.org/debian forky/main amd64 bash amd64 5.3-1 [1556 kB] Get:3 http://deb.debian.org/debian forky/main amd64 liblastlog2-2 amd64 2.41.2-1 [28.9 kB] Get:4 http://deb.debian.org/debian forky/main amd64 libuuid1 amd64 2.41.2-1 [38.1 kB] Get:5 http://deb.debian.org/debian forky/main amd64 bsdutils amd64 1:2.41.2-1 [93.4 kB] Get:6 http://deb.debian.org/debian forky/main amd64 libblkid1 amd64 2.41.2-1 [173 kB] Get:7 http://deb.debian.org/debian forky/main amd64 libmount1 amd64 2.41.2-1 [211 kB] Get:8 http://deb.debian.org/debian forky/main amd64 libsmartcols1 amd64 2.41.2-1 [144 kB] Get:9 http://deb.debian.org/debian forky/main amd64 util-linux amd64 2.41.2-1 [1257 kB] Get:10 http://deb.debian.org/debian forky/main amd64 mount amd64 2.41.2-1 [162 kB] Get:11 http://deb.debian.org/debian forky/main amd64 libsqlite3-0 amd64 3.46.1-8 [968 kB] Get:12 http://deb.debian.org/debian forky/main amd64 libsystemd0 amd64 258-1 [466 kB] Get:13 http://deb.debian.org/debian forky/main amd64 gcc-15-base amd64 15.2.0-4 [52.8 kB] Get:14 http://deb.debian.org/debian forky/main amd64 libgcc-s1 amd64 15.2.0-4 [71.7 kB] Get:15 http://deb.debian.org/debian forky/main amd64 liblzma5 amd64 5.8.1-1.1 [316 kB] Get:16 http://deb.debian.org/debian forky/main amd64 openssl-provider-legacy amd64 3.5.3-1 [308 kB] Get:17 http://deb.debian.org/debian forky/main amd64 libzstd1 amd64 1.5.7+dfsg-1.1 [320 kB] Get:18 http://deb.debian.org/debian forky/main amd64 libssl3t64 amd64 3.5.3-1 [2445 kB] Get:19 http://deb.debian.org/debian forky/main amd64 libstdc++6 amd64 15.2.0-4 [738 kB] Get:20 http://deb.debian.org/debian forky/main amd64 libudev1 amd64 258-1 [156 kB] Get:21 http://deb.debian.org/debian forky/main amd64 libapt-pkg7.0 amd64 3.1.5 [1182 kB] Get:22 http://deb.debian.org/debian forky/main amd64 apt amd64 3.1.5 [1479 kB] Get:23 http://deb.debian.org/debian forky/main amd64 init-system-helpers all 1.69 [39.3 kB] Get:24 http://deb.debian.org/debian forky/main amd64 libaudit-common all 1:4.1.2-1 [14.3 kB] Get:25 http://deb.debian.org/debian forky/main amd64 libaudit1 amd64 1:4.1.2-1 [60.4 kB] Get:26 http://deb.debian.org/debian forky/main amd64 login amd64 1:4.16.0-2+really2.41.2-1 [105 kB] Get:27 http://deb.debian.org/debian forky/main amd64 libgmp10 amd64 2:6.3.0+dfsg-5 [574 kB] Get:28 http://deb.debian.org/debian forky/main amd64 libpcre2-8-0 amd64 10.46-1 [298 kB] Get:29 http://deb.debian.org/debian forky/main amd64 login.defs all 1:4.18.0-1 [211 kB] Get:30 http://deb.debian.org/debian forky/main amd64 passwd amd64 1:4.18.0-1 [1284 kB] Get:31 http://deb.debian.org/debian forky/main amd64 tzdata all 2025b-5 [260 kB] Get:32 http://deb.debian.org/debian forky/main amd64 gcc-14-base amd64 14.3.0-8 [52.1 kB] Get:33 http://deb.debian.org/debian forky/main amd64 libboost-filesystem1.83.0 amd64 1.83.0-5 [286 kB] Get:34 http://deb.debian.org/debian forky/main amd64 libboost-program-options1.83.0 amd64 1.83.0-5 [355 kB] Get:35 http://deb.debian.org/debian forky/main amd64 libboost-thread1.83.0 amd64 1.83.0-5 [273 kB] Get:36 http://deb.debian.org/debian forky/main amd64 libprotobuf32t64 amd64 3.21.12-13 [988 kB] Preconfiguring packages ... Fetched 17.0 MB in 0s (68.2 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4977 files and directories currently installed.) Preparing to unpack .../base-files_14_amd64.deb ... Unpacking base-files (14) over (13.8+deb13u1) ... Setting up base-files (14) ... Installing new version of config file /etc/debian_version ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... (Reading database ... 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Unpacking gcc-14-base:amd64 (14.3.0-8) over (14.2.0-19) ... Preparing to unpack .../4-libboost-filesystem1.83.0_1.83.0-5_amd64.deb ... Unpacking libboost-filesystem1.83.0:amd64 (1.83.0-5) over (1.83.0-4.2) ... Preparing to unpack .../5-libboost-program-options1.83.0_1.83.0-5_amd64.deb ... Unpacking libboost-program-options1.83.0:amd64 (1.83.0-5) over (1.83.0-4.2) ... Preparing to unpack .../6-libboost-thread1.83.0_1.83.0-5_amd64.deb ... Unpacking libboost-thread1.83.0:amd64 (1.83.0-5) over (1.83.0-4.2) ... Preparing to unpack .../7-libprotobuf32t64_3.21.12-13_amd64.deb ... Unpacking libprotobuf32t64:amd64 (3.21.12-13) over (3.21.12-11) ... Setting up libboost-program-options1.83.0:amd64 (1.83.0-5) ... Setting up libprotobuf32t64:amd64 (3.21.12-13) ... Setting up gcc-14-base:amd64 (14.3.0-8) ... Setting up login.defs (1:4.18.0-1) ... Setting up libboost-thread1.83.0:amd64 (1.83.0-5) ... Setting up libboost-filesystem1.83.0:amd64 (1.83.0-5) ... Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' Local time is now: Sun Sep 28 15:55:23 UTC 2025. Universal Time is now: Sun Sep 28 15:55:23 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up passwd (1:4.18.0-1) ... Setting up mount (2.41.2-1) ... Setting up login (1:4.16.0-2+really2.41.2-1) ... Processing triggers for debianutils (5.23.2) ... Processing triggers for libc-bin (2.41-12) ... 0m6.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-get', '-yf', 'dist-upgrade'] 0m6.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m7.4s DUMP: aa3af1869e0ecb3dbaf71c3997683bc0 - 0m7.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m7.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-cache', 'show', '--no-all-versions', 'berkeley-express'] 0m7.5s DUMP: Package: berkeley-express Source: berkeley-express (1.5.3+dfsg-3) Version: 1.5.3+dfsg-3+b3 Installed-Size: 759 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libbamtools2.5.2 (>= 2.5.2+dfsg), libboost-filesystem1.83.0 (>= 1.83.0), libboost-program-options1.83.0 (>= 1.83.0), libboost-thread1.83.0 (>= 1.83.0), libc6 (>= 2.34), libgcc-s1 (>= 3.0), libprotobuf32t64 (>= 3.21.12), libstdc++6 (>= 13.1) Recommends: med-config 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_1.5.3+dfsg-3+b3_amd64.deb Size: 232556 MD5sum: 6903d535f401a5862314041023eac835 SHA256: 0c6627b538fd511ac87b37a88828bdb4b5f61ba9080eb0cd7b12649d562944bf 0m7.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-cache', 'show', '--no-all-versions', 'berkeley-express'] 0m7.5s INFO: apt-cache knows about the following packages: berkeley-express 0m7.5s INFO: Running scripts pre_install 0m7.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_install_database-server'] 0m7.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_install_database-server'] 0m7.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_install_exceptions'] 0m7.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_install_exceptions'] 0m7.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_install_extras'] 0m7.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_install_extras'] 0m7.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_install_foreign_architecture'] 0m7.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_install_foreign_architecture'] 0m7.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m7.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m7.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-cache', 'policy'] 0m7.5s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian forky/main amd64 Packages release o=Debian,a=testing,n=forky,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m7.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-cache', 'policy'] 0m7.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-cache', 'policy', 'berkeley-express'] 0m7.5s DUMP: berkeley-express: Installed: 1.5.3+dfsg-3+b3 Candidate: 1.5.3+dfsg-3+b3 Version table: *** 1.5.3+dfsg-3+b3 500 500 http://deb.debian.org/debian forky/main amd64 Packages 100 /var/lib/dpkg/status 0m7.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-cache', 'policy', 'berkeley-express'] 0m7.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-get', '-y', 'install', 'berkeley-express'] 0m7.8s DUMP: Reading package lists... Building dependency tree... Reading state information... berkeley-express is already the newest version (1.5.3+dfsg-3+b3). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-get', '-y', 'install', 'berkeley-express'] 0m7.8s INFO: Running scripts post_install 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_install_exceptions'] 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_install_exceptions'] 0m7.8s INFO: Running scripts post_distupgrade 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_distupgrade_exceptions'] 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_distupgrade_exceptions'] 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m7.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_distupgrade_zz_backports'] 0m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_distupgrade_zz_backports'] 0m7.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm'] 0m8.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm'] 0m8.0s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpn1thdtbm to sid 0m8.0s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m8.0s INFO: Running scripts pre_distupgrade 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_distupgrade_exceptions'] 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_distupgrade_exceptions'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-get', 'update'] 0m10.0s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [207 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.2 MB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7445 kB] Fetched 17.9 MB in 2s (11.7 MB/s) Reading package lists... 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-get', 'update'] 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-get', '-yf', 'dist-upgrade'] 0m11.4s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following package was automatically installed and is no longer required: libbamtools2.5.2 Use 'sudo apt autoremove' to remove it. The following NEW packages will be installed: libbamtools2.5.3 The following packages will be upgraded: apt berkeley-express bsdutils grep libapt-pkg7.0 libblkid1 libhogweed6t64 liblastlog2-2 libmount1 libnettle8t64 libsmartcols1 libuuid1 login mount util-linux 15 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 6290 kB of archives. After this operation, 97.3 kB disk space will be freed. Get:1 http://deb.debian.org/debian sid/main amd64 grep amd64 3.12-1 [443 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.41.2-2 [38.4 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.41.2-2 [174 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.41.2-2 [211 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.41.2-2 [145 kB] Get:6 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.41.2-2 [1165 kB] Get:7 http://deb.debian.org/debian sid/main amd64 mount amd64 2.41.2-2 [163 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libapt-pkg7.0 amd64 3.1.6 [1205 kB] Get:9 http://deb.debian.org/debian sid/main amd64 apt amd64 3.1.6 [1478 kB] Get:10 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.16.0-2+really2.41.2-2 [105 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libnettle8t64 amd64 3.10.2-1 [307 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libhogweed6t64 amd64 3.10.2-1 [336 kB] Get:13 http://deb.debian.org/debian sid/main amd64 liblastlog2-2 amd64 2.41.2-2 [29.3 kB] Get:14 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.41.2-2 [93.4 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libbamtools2.5.3 amd64 2.5.3+dfsg-1 [161 kB] Get:16 http://deb.debian.org/debian sid/main amd64 berkeley-express amd64 1.5.3+dfsg-3+b4 [236 kB] Fetched 6290 kB in 0s (27.3 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4974 files and directories currently installed.) Preparing to unpack .../archives/grep_3.12-1_amd64.deb ... Unpacking grep (3.12-1) over (3.11-4) ... Setting up grep (3.12-1) ... (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 ... 4939 files and directories currently installed.) Preparing to unpack .../mount_2.41.2-2_amd64.deb ... Unpacking mount (2.41.2-2) over (2.41.2-1) ... Preparing to unpack .../libapt-pkg7.0_3.1.6_amd64.deb ... Unpacking libapt-pkg7.0:amd64 (3.1.6) over (3.1.5) ... Setting up libapt-pkg7.0:amd64 (3.1.6) ... (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 ... 4939 files and directories currently installed.) Preparing to unpack .../libhogweed6t64_3.10.2-1_amd64.deb ... Unpacking libhogweed6t64:amd64 (3.10.2-1) over (3.10.1-1) ... Setting up libhogweed6t64:amd64 (3.10.2-1) ... (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 ... 4939 files and directories currently installed.) Preparing to unpack .../liblastlog2-2_2.41.2-2_amd64.deb ... Unpacking liblastlog2-2:amd64 (2.41.2-2) over (2.41.2-1) ... Setting up liblastlog2-2:amd64 (2.41.2-2) ... (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 ... 4939 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.41.2-2_amd64.deb ... Unpacking bsdutils (1:2.41.2-2) over (1:2.41.2-1) ... Selecting previously unselected package libbamtools2.5.3:amd64. Preparing to unpack .../libbamtools2.5.3_2.5.3+dfsg-1_amd64.deb ... Unpacking libbamtools2.5.3:amd64 (2.5.3+dfsg-1) ... Preparing to unpack .../berkeley-express_1.5.3+dfsg-3+b4_amd64.deb ... Unpacking berkeley-express (1.5.3+dfsg-3+b4) over (1.5.3+dfsg-3+b3) ... Setting up bsdutils (1:2.41.2-2) ... Setting up libbamtools2.5.3:amd64 (2.5.3+dfsg-1) ... Setting up mount (2.41.2-2) ... Setting up login (1:4.16.0-2+really2.41.2-2) ... Setting up berkeley-express (1.5.3+dfsg-3+b4) ... Processing triggers for libc-bin (2.41-12) ... 0m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-get', '-yf', 'dist-upgrade'] 0m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m12.0s DUMP: 582e95a659a066919c49ec21ece11f52 - 0m12.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m12.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-cache', 'show', '--no-all-versions', 'berkeley-express'] 0m12.2s DUMP: Package: berkeley-express Source: berkeley-express (1.5.3+dfsg-3) Version: 1.5.3+dfsg-3+b4 Installed-Size: 763 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libbamtools2.5.3 (>= 2.5.3+dfsg), libboost-filesystem1.83.0 (>= 1.83.0), libboost-program-options1.83.0 (>= 1.83.0), libboost-thread1.83.0 (>= 1.83.0), libc6 (>= 2.38), libgcc-s1 (>= 3.0), libprotobuf32t64 (>= 3.21.12), libstdc++6 (>= 14) Recommends: med-config 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_1.5.3+dfsg-3+b4_amd64.deb Size: 236344 MD5sum: 35ac090a0bf0fee288c779c38c61b061 SHA256: 68c0900024a475e88bc3b4873f1298afdf3e98dde2adc27c558978e29fc62dfa 0m12.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-cache', 'show', '--no-all-versions', 'berkeley-express'] 0m12.2s INFO: apt-cache knows about the following packages: berkeley-express 0m12.2s INFO: Running scripts pre_install 0m12.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_install_database-server'] 0m12.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_install_database-server'] 0m12.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_install_exceptions'] 0m12.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_install_exceptions'] 0m12.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_install_extras'] 0m12.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_install_extras'] 0m12.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_install_foreign_architecture'] 0m12.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_install_foreign_architecture'] 0m12.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m12.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m12.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-cache', 'policy'] 0m12.2s 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: 0m12.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-cache', 'policy'] 0m12.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-cache', 'policy', 'berkeley-express'] 0m12.2s DUMP: berkeley-express: Installed: 1.5.3+dfsg-3+b4 Candidate: 1.5.3+dfsg-3+b4 Version table: *** 1.5.3+dfsg-3+b4 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m12.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-cache', 'policy', 'berkeley-express'] 0m12.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-get', '-y', 'install', 'berkeley-express'] 0m12.5s DUMP: Reading package lists... Building dependency tree... Reading state information... berkeley-express is already the newest version (1.5.3+dfsg-3+b4). The following package was automatically installed and is no longer required: libbamtools2.5.2 Use 'sudo apt autoremove' to remove it. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m12.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-get', '-y', 'install', 'berkeley-express'] 0m12.5s INFO: Running scripts post_install 0m12.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_install_exceptions'] 0m12.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_install_exceptions'] 0m12.5s INFO: Running scripts post_distupgrade 0m12.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m12.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m12.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_distupgrade_exceptions'] 0m12.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_distupgrade_exceptions'] 0m12.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m12.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m12.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m12.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m12.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_distupgrade_zz_backports'] 0m12.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_distupgrade_zz_backports'] 0m12.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm'] 0m12.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm'] 0m12.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm'] 0m12.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm'] 0m12.9s INFO: Running scripts pre_install 0m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_install_database-server'] 0m12.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_install_database-server'] 0m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_install_exceptions'] 0m12.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_install_exceptions'] 0m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_install_extras'] 0m12.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_install_extras'] 0m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_install_foreign_architecture'] 0m12.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_install_foreign_architecture'] 0m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m12.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-cache', 'policy'] 0m12.9s 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: 0m12.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-cache', 'policy'] 0m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-cache', 'policy', 'berkeley-express'] 0m12.9s DUMP: berkeley-express: Installed: 1.5.3+dfsg-3+b4 Candidate: 1.5.3+dfsg-3+b4 Version table: *** 1.5.3+dfsg-3+b4 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m12.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-cache', 'policy', 'berkeley-express'] 0m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-get', '-y', 'install', 'berkeley-express=1.5.3+dfsg-3+b4'] 0m13.2s DUMP: Reading package lists... Building dependency tree... Reading state information... berkeley-express is already the newest version (1.5.3+dfsg-3+b4). The following package was automatically installed and is no longer required: libbamtools2.5.2 Use 'sudo apt autoremove' to remove it. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m13.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-get', '-y', 'install', 'berkeley-express=1.5.3+dfsg-3+b4'] 0m13.2s INFO: Running scripts post_install 0m13.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_install_exceptions'] 0m13.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_install_exceptions'] 0m13.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm'] 0m13.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm'] 0m13.5s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', '-ac', '--ignore-obsolete'] 0m13.9s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', '-ac', '--ignore-obsolete'] 0m13.9s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m13.9s DUMP: 0.15.9~deb12u1 0m13.9s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m13.9s INFO: Running adequate version 0.15.9~deb12u1 now. 0m13.9s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'berkeley-express'] 0m13.9s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'berkeley-express'] 0m13.9s INFO: Running scripts pre_remove 0m13.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m13.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m13.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m13.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m13.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m14.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m14.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m14.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m14.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m14.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m14.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_remove_exceptions'] 0m14.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/pre_remove_exceptions'] 0m14.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m14.2s DUMP: install ok installed apt apt 3.1.6 install ok installed base-files base-files 14 install ok installed base-passwd base-passwd 3.6.7 install ok installed bash bash 5.3-1 install ok installed berkeley-express berkeley-express 1.5.3+dfsg-3+b4 install ok installed bsdutils bsdutils 1:2.41.2-2 install ok installed coreutils coreutils 9.7-3 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.91 install ok installed debian-archive-keyring debian-archive-keyring 2025.1 install ok installed debianutils debianutils 5.23.2 install ok installed diffutils diffutils 1:3.10-4 install ok installed dpkg dpkg 1.22.21 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.3.0-8 install ok installed gcc-15-base:amd64 gcc-15-base 15.2.0-4 install ok installed grep grep 3.12-1 install ok installed gzip gzip 1.13-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.69 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.1.6 install ok installed libattr1:amd64 libattr1 1:2.5.2-3 install ok installed libaudit-common libaudit-common 1:4.1.2-1 install ok installed libaudit1:amd64 libaudit1 1:4.1.2-1 install ok installed libbamtools2.5.2:amd64 libbamtools2.5.2 2.5.2+dfsg-6+b1 install ok installed libbamtools2.5.3:amd64 libbamtools2.5.3 2.5.3+dfsg-1 install ok installed libblkid1:amd64 libblkid1 2.41.2-2 install ok installed libboost-filesystem1.83.0:amd64 libboost-filesystem1.83.0 1.83.0-5 install ok installed libboost-program-options1.83.0:amd64 libboost-program-options1.83.0 1.83.0-5 install ok installed libboost-thread1.83.0:amd64 libboost-thread1.83.0 1.83.0-5 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.41-12 install ok installed libc6:amd64 libc6 2.41-12 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1 install ok installed libcap2:amd64 libcap2 1:2.75-10+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.280 install ok installed libgcc-s1:amd64 libgcc-s1 15.2.0-4 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-5 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.2-1 install ok installed liblastlog2-2:amd64 liblastlog2-2 2.41.2-2 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-4 install ok installed liblzma5:amd64 liblzma5 5.8.1-1.1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.41.2-2 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.2-1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-5 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-5 install ok installed libpam-runtime libpam-runtime 1.7.0-5 install ok installed libpam0g:amd64 libpam0g 1.7.0-5 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.46-1 install ok installed libprotobuf32t64:amd64 libprotobuf32t64 3.21.12-13 install ok installed libseccomp2:amd64 libseccomp2 2.6.0-2 install ok installed libselinux1:amd64 libselinux1 3.8.1-1 install ok installed libsemanage-common libsemanage-common 3.8.1-1 install ok installed libsemanage2:amd64 libsemanage2 3.8.1-1 install ok installed libsepol2:amd64 libsepol2 3.8.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.41.2-2 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-8 install ok installed libssl3t64:amd64 libssl3t64 3.5.3-1 install ok installed libstdc++6:amd64 libstdc++6 15.2.0-4 install ok installed libsystemd0:amd64 libsystemd0 258-1 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2 install ok installed libudev1:amd64 libudev1 258-1 install ok installed libuuid1:amd64 libuuid1 2.41.2-2 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-1.1 install ok installed login login 1:4.16.0-2+really2.41.2-2 install ok installed login.defs login.defs 1:4.18.0-1 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed mount mount 2.41.2-2 install ok installed ncurses-base ncurses-base 6.5+20250216-2 install ok installed ncurses-bin ncurses-bin 6.5+20250216-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.5.3-1 install ok installed passwd passwd 1:4.18.0-1 install ok installed perl-base perl-base 5.40.1-6 install ok installed sed sed 4.9-2 install ok installed sqv sqv 1.3.0-3 install ok installed sysvinit-utils sysvinit-utils 3.14-4 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tzdata tzdata 2025b-5 install ok installed util-linux util-linux 2.41.2-2 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m14.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m14.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-get', 'remove', '--allow-remove-essential', 'libbamtools2.5.2:amd64', 'libbamtools2.5.3:amd64', 'libboost-filesystem1.83.0:amd64', 'libboost-program-options1.83.0:amd64', 'libboost-thread1.83.0:amd64', 'libprotobuf32t64:amd64', 'berkeley-express'] 0m14.6s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: berkeley-express libbamtools2.5.2 libbamtools2.5.3 libboost-filesystem1.83.0 libboost-program-options1.83.0 libboost-thread1.83.0 libprotobuf32t64 0 upgraded, 0 newly installed, 7 to remove and 0 not upgraded. After this operation, 12.8 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 ... 4943 files and directories currently installed.) Removing berkeley-express (1.5.3+dfsg-3+b4) ... Removing libbamtools2.5.2:amd64 (2.5.2+dfsg-6+b1) ... Removing libbamtools2.5.3:amd64 (2.5.3+dfsg-1) ... Removing libboost-filesystem1.83.0:amd64 (1.83.0-5) ... Removing libboost-program-options1.83.0:amd64 (1.83.0-5) ... Removing libboost-thread1.83.0:amd64 (1.83.0-5) ... Removing libprotobuf32t64:amd64 (3.21.12-13) ... Processing triggers for libc-bin (2.41-12) ... 0m14.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-get', 'remove', '--allow-remove-essential', 'libbamtools2.5.2:amd64', 'libbamtools2.5.3:amd64', 'libboost-filesystem1.83.0:amd64', 'libboost-program-options1.83.0:amd64', 'libboost-thread1.83.0:amd64', 'libprotobuf32t64:amd64', 'berkeley-express'] 0m14.6s INFO: Running scripts post_remove 0m14.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_remove_exceptions'] 0m14.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_remove_exceptions'] 0m14.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'dpkg', '--purge', 'libbamtools2.5.2:amd64', 'libbamtools2.5.3:amd64', 'libboost-filesystem1.83.0:amd64', 'libboost-program-options1.83.0:amd64', 'libboost-thread1.83.0:amd64', 'libprotobuf32t64:amd64'] 0m14.6s DUMP: dpkg: warning: ignoring request to remove libbamtools2.5.2 which isn't installed dpkg: warning: ignoring request to remove libbamtools2.5.3 which isn't installed dpkg: warning: ignoring request to remove libboost-filesystem1.83.0 which isn't installed dpkg: warning: ignoring request to remove libboost-program-options1.83.0 which isn't installed dpkg: warning: ignoring request to remove libboost-thread1.83.0 which isn't installed dpkg: warning: ignoring request to remove libprotobuf32t64 which isn't installed 0m14.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'dpkg', '--purge', 'libbamtools2.5.2:amd64', 'libbamtools2.5.3:amd64', 'libboost-filesystem1.83.0:amd64', 'libboost-program-options1.83.0:amd64', 'libboost-thread1.83.0:amd64', 'libprotobuf32t64:amd64'] 0m14.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'dpkg', '--purge', 'berkeley-express'] 0m14.7s DUMP: dpkg: warning: ignoring request to remove berkeley-express which isn't installed 0m14.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'dpkg', '--purge', 'berkeley-express'] 0m14.7s INFO: Running scripts post_purge 0m14.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_purge_exceptions'] 0m14.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_purge_exceptions'] 0m14.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'dpkg', '--purge', '--pending'] 0m14.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'dpkg', '--purge', '--pending'] 0m14.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'dpkg', '--remove', '--pending'] 0m14.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'dpkg', '--remove', '--pending'] 0m14.7s INFO: Running scripts post_test 0m14.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_test_exceptions'] 0m14.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'tmp/scripts/post_test_exceptions'] 0m14.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm'] 0m14.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm'] 0m14.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'dpkg-divert', '--list'] 0m14.9s DUMP: local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged local diversion of /home to /home.distrib diversion of /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6 diversion of /libx32 to /.libx32.usr-is-merged by base-files local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /lib32 to /.lib32.usr-is-merged by base-files diversion of /libo32 to /.libo32.usr-is-merged by base-files 0m14.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'dpkg-divert', '--list'] 0m14.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-get', 'clean'] 0m14.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm', 'apt-get', 'clean'] 0m14.9s DEBUG: Recording chroot state 0m15.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm/dev/shm'] 0m15.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm/dev/shm'] 0m15.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm/dev/console'] 0m15.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm/dev/console'] 0m15.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm/dev/ptmx'] 0m15.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm/dev/ptmx'] 0m15.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm/dev/pts'] 0m15.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm/dev/pts'] 0m15.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm/proc'] 0m15.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm/proc'] 0m15.6s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm'] 0m15.6s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpn1thdtbm'] 0m15.6s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpn1thdtbm 0m15.6s INFO: PASS: Upgrading between Debian distributions. 0m15.6s INFO: PASS: All tests. 0m15.6s INFO: piuparts run ends. ret=0 End: 2025-09-28 15:55:32 GMT