Start: 2024-04-24 20:38:53 GMT [sid] Package: hisat2 Source: hisat2 (2.2.1-4) Version: 2.2.1-4+b3 Installed-Size: 14302 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.0), libstdc++6 (>= 13.1), perl:any, python3 Recommends: python3-hisat2, bcftools, samtools Description: graph-based alignment of short nucleotide reads to many genomes Homepage: https://daehwankimlab.github.io/hisat2/ Built-Using: simde (= 0.7.6-1) Description-md5: 5f7b7bae1f6d1899a67fb91260ec0d0f Section: science Priority: optional Filename: pool/main/h/hisat2/hisat2_2.2.1-4+b3_amd64.deb Size: 3699976 MD5sum: db17b1a9f183db41914de8c2a6740be3 SHA256: c2a8ca5efa43dacd350379b05a14539cb1cf552bed2ebc098bb36575eead30b2 [experimental] Package: hisat2 Version: 2.2.1-5~0exp Installed-Size: 14153 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.0), libstdc++6 (>= 11), perl:any, python3 Recommends: python3-hisat2, bcftools, samtools Description: graph-based alignment of short nucleotide reads to many genomes Homepage: https://daehwankimlab.github.io/hisat2/ Built-Using: simde (= 0.7.3~0git20230118123246.d1e75cd-2) Description-md5: 5f7b7bae1f6d1899a67fb91260ec0d0f Section: science Priority: optional Filename: pool/main/h/hisat2/hisat2_2.2.1-5~0exp_amd64.deb Size: 3658064 MD5sum: b99f016dd13c1345ddf2e4850168334f SHA256: 8a8539868ff05b2a7833f265f01c728f25dd54293c217bc3b3709370493d10c7 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz -d sid -d experimental -B /srv/piuparts.debian.org/slave/refchroot/sid2experimental/reference-chroot-metadata.dat --apt 'hisat2=2.2.1-5~0exp' 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.4.1~202403190841~1.4-4-g85045c69 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz -d sid -d experimental -B /srv/piuparts.debian.org/slave/refchroot/sid2experimental/reference-chroot-metadata.dat --apt 'hisat2=2.2.1-5~0exp' 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmparm64hbw 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmparm64hbw 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmparm64hbw', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmparm64hbw', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmparm64hbw/proc'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmparm64hbw/proc'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmparm64hbw/dev/pts'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmparm64hbw/dev/pts'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmparm64hbw/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmparm64hbw/dev/ptmx'] 0m0.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmparm64hbw/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmparm64hbw/dev/ptmx'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmparm64hbw/dev/console'] 0m0.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmparm64hbw/dev/console'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmparm64hbw/dev/shm'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmparm64hbw/dev/shm'] 0m0.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m0.5s DEBUG: Created policy-rc.d and chmodded it. 0m0.5s DEBUG: Created resolv.conf. 0m0.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmparm64hbw/tmp/scripts/ 0m0.5s INFO: Running scripts post_chroot_unpack 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'apt-get', 'update'] 0m4.3s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [198 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9872 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7196 kB] Fetched 17.3 MB in 3s (5578 kB/s) Reading package lists... 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'apt-get', 'update'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'apt-get', '-yf', 'dist-upgrade'] 0m5.9s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: apt libapt-pkg6.0t64 2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 2385 kB of archives. After this operation, 31.7 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0t64 amd64 2.9.2 [989 kB] Get:2 http://deb.debian.org/debian sid/main amd64 apt amd64 2.9.2 [1396 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 2385 kB in 0s (41.3 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 ... 5200 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0t64_2.9.2_amd64.deb ... Unpacking libapt-pkg6.0t64:amd64 (2.9.2) over (2.9.1) ... Setting up libapt-pkg6.0t64:amd64 (2.9.2) ... (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 ... 5200 files and directories currently installed.) Preparing to unpack .../archives/apt_2.9.2_amd64.deb ... Unpacking apt (2.9.2) over (2.9.1) ... Setting up apt (2.9.2) ... Processing triggers for libc-bin (2.37-18) ... 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'apt-get', '-yf', 'dist-upgrade'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m7.4s DUMP: 5e5ffeed94e287a1c014496e3a7dba00 - 0m7.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m7.4s INFO: Running scripts post_setup 0m7.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/post_setup_dummy_users'] 0m8.2s 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 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/post_setup_dummy_users'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/post_setup_forbid_home'] 0m8.2s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/post_setup_forbid_home'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/post_setup_force-unsafe-io'] 0m8.2s 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' 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/post_setup_force-unsafe-io'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/post_setup_minimize'] 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/post_setup_minimize'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/post_setup_squeeze-backports'] 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/post_setup_squeeze-backports'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/post_setup_zz_backports'] 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/post_setup_zz_backports'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m8.3s DUMP: install ok installed apt apt 2.9.2 install ok installed base-files base-files 13.1 install ok installed base-passwd base-passwd 3.6.3 install ok installed bash bash 5.2.21-2 install ok installed bsdutils bsdutils 1:2.40-6 install ok installed coreutils coreutils 9.4-3.1 install ok installed dash dash 0.5.12-6 install ok installed debconf debconf 1.5.86 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.17 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.6 install ok installed e2fsprogs e2fsprogs 1.47.0-2.4 install ok installed findutils findutils 4.9.0-5 install ok installed gcc-14-base:amd64 gcc-14-base 14-20240330-1 install ok installed gpgv gpgv 2.2.40-3 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.23+nmu2 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed libacl1:amd64 libacl1 2.3.2-1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.2 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:3.1.2-2.1 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-2.1 install ok installed libblkid1:amd64 libblkid1 2.40-6 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5.1 install ok installed libc-bin libc-bin 2.37-18 install ok installed libc6:amd64 libc6 2.37-18 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-1 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2.4 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-4 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-7 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.271+b3 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.0-2.4 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14-20240330-1 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.3-2 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.5-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.47-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.9.1-2.2 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-2 install ok installed liblzma5:amd64 liblzma5 5.6.1+really5.4.5-1 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.40-6 install ok installed libnettle8t64:amd64 libnettle8t64 3.9.1-2.2 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.3-4 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b1 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1 install ok installed libselinux1:amd64 libselinux1 3.5-2+b2 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b3 install ok installed libsepol2:amd64 libsepol2 3.5-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.40-6 install ok installed libss2:amd64 libss2 1.47.0-2.4 install ok installed libssl3t64:amd64 libssl3t64 3.2.1-3 install ok installed libstdc++6:amd64 libstdc++6 14-20240330-1 install ok installed libsystemd0:amd64 libsystemd0 255.4-1+b1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtinfo6:amd64 libtinfo6 6.4+20240414-1 install ok installed libudev1:amd64 libudev1 255.4-1+b1 install ok installed libunistring5:amd64 libunistring5 1.2-1 install ok installed libuuid1:amd64 libuuid1 2.40-6 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-2 install ok installed login login 1:4.13+dfsg1-4 install ok installed logsave logsave 1.47.0-2.4 install ok installed mawk mawk 1.3.4.20240123-1 install ok installed mount mount 2.40-6 install ok installed ncurses-base ncurses-base 6.4+20240414-1 install ok installed ncurses-bin ncurses-bin 6.4+20240414-1 install ok installed passwd passwd 1:4.13+dfsg1-4 install ok installed perl-base perl-base 5.38.2-3.2+b2 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.09-1 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024a-3 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40-6 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg-3.1 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m8.3s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/sid2experimental/reference-chroot-metadata.dat 0m8.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmparm64hbw'] 0m8.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmparm64hbw'] 0m8.7s INFO: Running scripts is_testable 0m8.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/is_testable_uninstallable'] 0m8.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/is_testable_uninstallable'] 0m8.7s INFO: Running scripts pre_test 0m8.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_test_exceptions'] 0m8.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_test_exceptions'] 0m8.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_test_root_password'] 0m8.7s DUMP: New password: Retype new password: passwd: password updated successfully 0m8.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_test_root_password'] 0m8.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'apt-cache', 'show', '--no-all-versions', 'hisat2'] 0m9.1s DUMP: Package: hisat2 Source: hisat2 (2.2.1-4) Version: 2.2.1-4+b3 Installed-Size: 14302 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.0), libstdc++6 (>= 13.1), perl:any, python3 Recommends: python3-hisat2, bcftools, samtools Description-en: graph-based alignment of short nucleotide reads to many genomes HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as against a single reference genome). Based on an extension of BWT for graphs a graph FM index (GFM) was designed and implementd. In addition to using one global GFM index that represents a population of human genomes, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome (each index representing a genomic region of 56 Kbp, with 55,000 indexes needed to cover the human population). These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is called a Hierarchical Graph FM index (HGFM). Description-md5: 5f7b7bae1f6d1899a67fb91260ec0d0f Homepage: https://daehwankimlab.github.io/hisat2/ Built-Using: simde (= 0.7.6-1) Section: science Priority: optional Filename: pool/main/h/hisat2/hisat2_2.2.1-4+b3_amd64.deb Size: 3699976 MD5sum: db17b1a9f183db41914de8c2a6740be3 SHA256: c2a8ca5efa43dacd350379b05a14539cb1cf552bed2ebc098bb36575eead30b2 0m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'apt-cache', 'show', '--no-all-versions', 'hisat2'] 0m9.1s INFO: apt-cache knows about the following packages: hisat2 0m9.1s INFO: Running scripts pre_install 0m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_install_database-server'] 0m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_install_database-server'] 0m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_install_exceptions'] 0m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_install_exceptions'] 0m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_install_extras'] 0m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_install_extras'] 0m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_install_foreign_architecture'] 0m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_install_foreign_architecture'] 0m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'apt-cache', 'policy'] 0m9.2s 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: 0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'apt-cache', 'policy'] 0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'apt-cache', 'policy', 'hisat2'] 0m9.2s DUMP: hisat2: Installed: (none) Candidate: 2.2.1-4+b3 Version table: 2.2.1-4+b3 500 500 http://deb.debian.org/debian sid/main amd64 Packages 0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'apt-cache', 'policy', 'hisat2'] 0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'apt-get', '-y', 'install', 'hisat2'] 0m15.9s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libexpat1 libgdbm-compat4t64 libgdbm6t64 libncursesw6 libperl5.38t64 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libreadline8t64 libsqlite3-0 media-types netbase perl perl-modules-5.38 python3 python3-minimal python3.11 python3.11-minimal readline-common Suggested packages: gdbm-l10n sensible-utils perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl python3-doc python3-tk python3-venv python3.11-venv python3.11-doc binutils binfmt-support readline-doc Recommended packages: python3-hisat2 bcftools samtools libgpm2 ca-certificates The following NEW packages will be installed: hisat2 libexpat1 libgdbm-compat4t64 libgdbm6t64 libncursesw6 libperl5.38t64 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libreadline8t64 libsqlite3-0 media-types netbase perl perl-modules-5.38 python3 python3-minimal python3.11 python3.11-minimal readline-common 0 upgraded, 20 newly installed, 0 to remove and 0 not upgraded. Need to get 17.8 MB of archives. After this operation, 90.5 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 perl-modules-5.38 all 5.38.2-3.2 [2899 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libgdbm6t64 amd64 1.23-5.1+b1 [73.0 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libgdbm-compat4t64 amd64 1.23-5.1+b1 [48.8 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libperl5.38t64 amd64 5.38.2-3.2+b2 [4279 kB] Get:5 http://deb.debian.org/debian sid/main amd64 perl amd64 5.38.2-3.2+b2 [236 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get:8 http://deb.debian.org/debian sid/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get:9 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get:10 http://deb.debian.org/debian sid/main amd64 media-types all 10.1.0 [26.9 kB] Get:11 http://deb.debian.org/debian sid/main amd64 netbase all 6.4 [12.8 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libncursesw6 amd64 6.4+20240414-1 [135 kB] Get:13 http://deb.debian.org/debian sid/main amd64 readline-common all 8.2-4 [69.3 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libsqlite3-0 amd64 3.45.3-1 [896 kB] Get:16 http://deb.debian.org/debian sid/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get:17 http://deb.debian.org/debian sid/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get:19 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get:20 http://deb.debian.org/debian sid/main amd64 hisat2 amd64 2.2.1-4+b3 [3700 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 17.8 MB in 0s (104 MB/s) Selecting previously unselected package perl-modules-5.38. (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 ... 5204 files and directories currently installed.) Preparing to unpack .../0-perl-modules-5.38_5.38.2-3.2_all.deb ... Unpacking perl-modules-5.38 (5.38.2-3.2) ... Selecting previously unselected package libgdbm6t64:amd64. Preparing to unpack .../1-libgdbm6t64_1.23-5.1+b1_amd64.deb ... Unpacking libgdbm6t64:amd64 (1.23-5.1+b1) ... Selecting previously unselected package libgdbm-compat4t64:amd64. Preparing to unpack .../2-libgdbm-compat4t64_1.23-5.1+b1_amd64.deb ... Unpacking libgdbm-compat4t64:amd64 (1.23-5.1+b1) ... Selecting previously unselected package libperl5.38t64:amd64. Preparing to unpack .../3-libperl5.38t64_5.38.2-3.2+b2_amd64.deb ... Unpacking libperl5.38t64:amd64 (5.38.2-3.2+b2) ... Selecting previously unselected package perl. Preparing to unpack .../4-perl_5.38.2-3.2+b2_amd64.deb ... Unpacking perl (5.38.2-3.2+b2) ... Selecting previously unselected package libpython3.11-minimal:amd64. Preparing to unpack .../5-libpython3.11-minimal_3.11.9-1_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.9-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../6-libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../7-python3.11-minimal_3.11.9-1_amd64.deb ... Unpacking python3.11-minimal (3.11.9-1) ... Setting up libpython3.11-minimal:amd64 (3.11.9-1) ... Setting up libexpat1:amd64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.9-1) ... Selecting previously unselected package python3-minimal. (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 ... 7538 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.8-1_amd64.deb ... Unpacking python3-minimal (3.11.8-1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../2-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package libncursesw6:amd64. Preparing to unpack .../3-libncursesw6_6.4+20240414-1_amd64.deb ... Unpacking libncursesw6:amd64 (6.4+20240414-1) ... Selecting previously unselected package readline-common. Preparing to unpack .../4-readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../5-libreadline8t64_8.2-4_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../6-libsqlite3-0_3.45.3-1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.45.3-1) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../7-libpython3.11-stdlib_3.11.9-1_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.9-1) ... Selecting previously unselected package python3.11. Preparing to unpack .../8-python3.11_3.11.9-1_amd64.deb ... Unpacking python3.11 (3.11.9-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../9-libpython3-stdlib_3.11.8-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3-minimal (3.11.8-1) ... Selecting previously unselected package python3. (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 ... 8020 files and directories currently installed.) Preparing to unpack .../python3_3.11.8-1_amd64.deb ... Unpacking python3 (3.11.8-1) ... Selecting previously unselected package hisat2. Preparing to unpack .../hisat2_2.2.1-4+b3_amd64.deb ... Unpacking hisat2 (2.2.1-4+b3) ... Setting up media-types (10.1.0) ... Setting up libgdbm6t64:amd64 (1.23-5.1+b1) ... Setting up libgdbm-compat4t64:amd64 (1.23-5.1+b1) ... Setting up libsqlite3-0:amd64 (3.45.3-1) ... Setting up perl-modules-5.38 (5.38.2-3.2) ... Setting up libncursesw6:amd64 (6.4+20240414-1) ... Setting up netbase (6.4) ... Setting up libperl5.38t64:amd64 (5.38.2-3.2+b2) ... Setting up readline-common (8.2-4) ... Setting up perl (5.38.2-3.2+b2) ... Setting up libreadline8t64:amd64 (8.2-4) ... Setting up libpython3.11-stdlib:amd64 (3.11.9-1) ... Setting up libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3.11 (3.11.9-1) ... Setting up python3 (3.11.8-1) ... Setting up hisat2 (2.2.1-4+b3) ... Processing triggers for libc-bin (2.37-18) ... 0m15.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'apt-get', '-y', 'install', 'hisat2'] 0m15.9s INFO: Running scripts post_install 0m15.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/post_install_exceptions'] 0m15.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/post_install_exceptions'] 0m15.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmparm64hbw'] 0m16.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmparm64hbw'] 0m16.5s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmparm64hbw to experimental 0m16.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main deb http://deb.debian.org/debian/ experimental main 0m16.5s INFO: Running scripts pre_distupgrade 0m16.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m16.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m16.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_distupgrade_exceptions'] 0m16.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_distupgrade_exceptions'] 0m16.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m16.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m16.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m16.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m16.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m16.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m16.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'apt-get', 'update'] 0m18.5s DUMP: Hit:1 http://deb.debian.org/debian sid InRelease Get:2 http://deb.debian.org/debian experimental InRelease [101 kB] Get:3 http://deb.debian.org/debian experimental/main amd64 Packages [743 kB] Get:4 http://deb.debian.org/debian experimental/main Translation-en [464 kB] Fetched 1309 kB in 1s (1823 kB/s) Reading package lists... 0m18.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'apt-get', 'update'] 0m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'apt-get', '-yf', 'dist-upgrade'] 0m19.3s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m19.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'apt-get', '-yf', 'dist-upgrade'] 0m19.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m19.8s DUMP: 47daf7a66ed6cb10db30547b3606b2c0 - 0m19.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m19.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'apt-cache', 'show', '--no-all-versions', 'hisat2'] 0m20.1s DUMP: Package: hisat2 Source: hisat2 (2.2.1-4) Version: 2.2.1-4+b3 Installed-Size: 14302 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.0), libstdc++6 (>= 13.1), perl:any, python3 Recommends: python3-hisat2, bcftools, samtools Description-en: graph-based alignment of short nucleotide reads to many genomes HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as against a single reference genome). Based on an extension of BWT for graphs a graph FM index (GFM) was designed and implementd. In addition to using one global GFM index that represents a population of human genomes, HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome (each index representing a genomic region of 56 Kbp, with 55,000 indexes needed to cover the human population). These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. This new indexing scheme is called a Hierarchical Graph FM index (HGFM). Description-md5: 5f7b7bae1f6d1899a67fb91260ec0d0f Homepage: https://daehwankimlab.github.io/hisat2/ Built-Using: simde (= 0.7.6-1) Section: science Priority: optional Filename: pool/main/h/hisat2/hisat2_2.2.1-4+b3_amd64.deb Size: 3699976 MD5sum: db17b1a9f183db41914de8c2a6740be3 SHA256: c2a8ca5efa43dacd350379b05a14539cb1cf552bed2ebc098bb36575eead30b2 0m20.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'apt-cache', 'show', '--no-all-versions', 'hisat2'] 0m20.1s INFO: apt-cache knows about the following packages: hisat2 0m20.1s INFO: Running scripts pre_install 0m20.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_install_database-server'] 0m20.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_install_database-server'] 0m20.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_install_exceptions'] 0m20.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_install_exceptions'] 0m20.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_install_extras'] 0m20.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_install_extras'] 0m20.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_install_foreign_architecture'] 0m20.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_install_foreign_architecture'] 0m20.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m20.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m20.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'apt-cache', 'policy'] 0m20.2s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 1 http://deb.debian.org/debian experimental/main amd64 Packages release o=Debian,a=experimental,n=rc-buggy,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m20.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'apt-cache', 'policy'] 0m20.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'apt-cache', 'policy', 'hisat2'] 0m20.2s DUMP: hisat2: Installed: 2.2.1-4+b3 Candidate: 2.2.1-4+b3 Version table: 2.2.1-5~0exp 1 1 http://deb.debian.org/debian experimental/main amd64 Packages *** 2.2.1-4+b3 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m20.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'apt-cache', 'policy', 'hisat2'] 0m20.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'apt-get', '-y', '-t', 'experimental', 'install', 'hisat2'] 0m22.0s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be upgraded: hisat2 1 upgraded, 0 newly installed, 0 to remove and 9 not upgraded. Need to get 3658 kB of archives. After this operation, 153 kB disk space will be freed. Get:1 http://deb.debian.org/debian experimental/main amd64 hisat2 amd64 2.2.1-5~0exp [3658 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 3658 kB in 0s (59.2 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 ... 8080 files and directories currently installed.) Preparing to unpack .../hisat2_2.2.1-5~0exp_amd64.deb ... Unpacking hisat2 (2.2.1-5~0exp) over (2.2.1-4+b3) ... Setting up hisat2 (2.2.1-5~0exp) ... 0m22.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'apt-get', '-y', '-t', 'experimental', 'install', 'hisat2'] 0m22.0s INFO: Running scripts post_install 0m22.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/post_install_exceptions'] 0m22.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/post_install_exceptions'] 0m22.0s INFO: Running scripts post_distupgrade 0m22.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m22.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m22.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/post_distupgrade_exceptions'] 0m22.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/post_distupgrade_exceptions'] 0m22.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m22.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m22.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m22.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m22.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/post_distupgrade_zz_backports'] 0m22.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/post_distupgrade_zz_backports'] 0m22.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmparm64hbw'] 0m22.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmparm64hbw'] 0m22.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmparm64hbw'] 0m23.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmparm64hbw'] 0m23.2s INFO: Running scripts pre_install 0m23.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_install_database-server'] 0m23.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_install_database-server'] 0m23.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_install_exceptions'] 0m23.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_install_exceptions'] 0m23.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_install_extras'] 0m23.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_install_extras'] 0m23.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_install_foreign_architecture'] 0m23.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_install_foreign_architecture'] 0m23.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m23.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m23.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'apt-cache', 'policy'] 0m23.3s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 1 http://deb.debian.org/debian experimental/main amd64 Packages release o=Debian,a=experimental,n=rc-buggy,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m23.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'apt-cache', 'policy'] 0m23.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'apt-cache', 'policy', 'hisat2'] 0m23.3s DUMP: hisat2: Installed: 2.2.1-5~0exp Candidate: 2.2.1-5~0exp Version table: *** 2.2.1-5~0exp 100 1 http://deb.debian.org/debian experimental/main amd64 Packages 100 /var/lib/dpkg/status 2.2.1-4+b3 500 500 http://deb.debian.org/debian sid/main amd64 Packages 0m23.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'apt-cache', 'policy', 'hisat2'] 0m23.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'apt-get', '-y', '-t', 'experimental', 'install', 'hisat2=2.2.1-5~0exp'] 0m24.0s DUMP: Reading package lists... Building dependency tree... Reading state information... hisat2 is already the newest version (2.2.1-5~0exp). 0 upgraded, 0 newly installed, 0 to remove and 9 not upgraded. 0m24.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'apt-get', '-y', '-t', 'experimental', 'install', 'hisat2=2.2.1-5~0exp'] 0m24.0s INFO: Running scripts post_install 0m24.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/post_install_exceptions'] 0m24.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/post_install_exceptions'] 0m24.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmparm64hbw'] 0m24.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmparm64hbw'] 0m24.6s INFO: /bin converted to /usr/bin by /usr merge 0m24.7s INFO: /lib converted to /usr/lib by /usr merge 0m24.7s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 0m24.7s INFO: /lib64 converted to /usr/lib64 by /usr merge 0m24.7s INFO: /sbin converted to /usr/sbin by /usr merge 0m25.4s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmparm64hbw', '-ac', '--ignore-obsolete'] 0m26.8s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmparm64hbw', '-ac', '--ignore-obsolete'] 0m26.8s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m26.8s DUMP: 0.15.6 0m26.8s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m26.8s INFO: Running adequate version 0.15.6 now. 0m26.8s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'hisat2'] 0m27.0s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'hisat2'] 0m27.0s INFO: Running scripts pre_remove 0m27.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m27.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m27.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m27.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m27.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m27.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m27.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m27.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m27.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m27.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m27.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_remove_exceptions'] 0m28.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/pre_remove_exceptions'] 0m28.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m28.0s DUMP: install ok installed apt apt 2.9.2 install ok installed base-files base-files 13.1 install ok installed base-passwd base-passwd 3.6.3 install ok installed bash bash 5.2.21-2 install ok installed bsdutils bsdutils 1:2.40-6 install ok installed coreutils coreutils 9.4-3.1 install ok installed dash dash 0.5.12-6 install ok installed debconf debconf 1.5.86 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.17 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.6 install ok installed e2fsprogs e2fsprogs 1.47.0-2.4 install ok installed findutils findutils 4.9.0-5 install ok installed gcc-14-base:amd64 gcc-14-base 14-20240330-1 install ok installed gpgv gpgv 2.2.40-3 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hisat2 hisat2 2.2.1-5~0exp install ok installed hostname hostname 3.23+nmu2 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed libacl1:amd64 libacl1 2.3.2-1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.2 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:3.1.2-2.1 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-2.1 install ok installed libblkid1:amd64 libblkid1 2.40-6 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5.1 install ok installed libc-bin libc-bin 2.37-18 install ok installed libc6:amd64 libc6 2.37-18 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-1 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2.4 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-4 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-7 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.271+b3 install ok installed libexpat1:amd64 libexpat1 2.6.2-1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.0-2.4 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14-20240330-1 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.3-2 install ok installed libgdbm-compat4t64:amd64 libgdbm-compat4t64 1.23-5.1+b1 install ok installed libgdbm6t64:amd64 libgdbm6t64 1.23-5.1+b1 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.5-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.47-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.9.1-2.2 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-2 install ok installed liblzma5:amd64 liblzma5 5.6.1+really5.4.5-1 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.40-6 install ok installed libncursesw6:amd64 libncursesw6 6.4+20240414-1 install ok installed libnettle8t64:amd64 libnettle8t64 3.9.1-2.2 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.3-4 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b1 install ok installed libperl5.38t64:amd64 libperl5.38t64 5.38.2-3.2+b2 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.11.8-1 install ok installed libpython3.11-minimal:amd64 libpython3.11-minimal 3.11.9-1 install ok installed libpython3.11-stdlib:amd64 libpython3.11-stdlib 3.11.9-1 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-4 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1 install ok installed libselinux1:amd64 libselinux1 3.5-2+b2 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b3 install ok installed libsepol2:amd64 libsepol2 3.5-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.40-6 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.45.3-1 install ok installed libss2:amd64 libss2 1.47.0-2.4 install ok installed libssl3t64:amd64 libssl3t64 3.2.1-3 install ok installed libstdc++6:amd64 libstdc++6 14-20240330-1 install ok installed libsystemd0:amd64 libsystemd0 255.4-1+b1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtinfo6:amd64 libtinfo6 6.4+20240414-1 install ok installed libudev1:amd64 libudev1 255.4-1+b1 install ok installed libunistring5:amd64 libunistring5 1.2-1 install ok installed libuuid1:amd64 libuuid1 2.40-6 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-2 install ok installed login login 1:4.13+dfsg1-4 install ok installed logsave logsave 1.47.0-2.4 install ok installed mawk mawk 1.3.4.20240123-1 install ok installed media-types media-types 10.1.0 install ok installed mount mount 2.40-6 install ok installed ncurses-base ncurses-base 6.4+20240414-1 install ok installed ncurses-bin ncurses-bin 6.4+20240414-1 install ok installed netbase netbase 6.4 install ok installed passwd passwd 1:4.13+dfsg1-4 install ok installed perl perl 5.38.2-3.2+b2 install ok installed perl-base perl-base 5.38.2-3.2+b2 install ok installed perl-modules-5.38 perl-modules-5.38 5.38.2-3.2 install ok installed python3 python3 3.11.8-1 install ok installed python3-minimal python3-minimal 3.11.8-1 install ok installed python3.11 python3.11 3.11.9-1 install ok installed python3.11-minimal python3.11-minimal 3.11.9-1 install ok installed readline-common readline-common 8.2-4 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.09-1 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024a-3 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40-6 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg-3.1 0m28.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m28.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'apt-get', 'remove', 'libexpat1:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libncursesw6:amd64', 'libperl5.38t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libreadline8t64:amd64', 'libsqlite3-0:amd64', 'media-types', 'netbase', 'perl', 'perl-modules-5.38', 'python3', 'python3-minimal', 'python3.11', 'python3.11-minimal', 'readline-common', 'hisat2'] 0m29.6s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: hisat2 libexpat1 libgdbm-compat4t64 libgdbm6t64 libncursesw6 libperl5.38t64 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libreadline8t64 libsqlite3-0 media-types netbase perl perl-modules-5.38 python3 python3-minimal python3.11 python3.11-minimal readline-common 0 upgraded, 0 newly installed, 20 to remove and 0 not upgraded. After this operation, 90.3 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 ... 8079 files and directories currently installed.) Removing hisat2 (2.2.1-5~0exp) ... Removing python3 (3.11.8-1) ... Removing python3.11 (3.11.9-1) ... Removing python3-minimal (3.11.8-1) ... Removing python3.11-minimal (3.11.9-1) ... Removing libexpat1:amd64 (2.6.2-1) ... Removing perl (5.38.2-3.2+b2) ... Removing libperl5.38t64:amd64 (5.38.2-3.2+b2) ... Removing libgdbm-compat4t64:amd64 (1.23-5.1+b1) ... Removing libgdbm6t64:amd64 (1.23-5.1+b1) ... Removing libpython3-stdlib:amd64 (3.11.8-1) ... Removing libpython3.11-stdlib:amd64 (3.11.9-1) ... find: '/usr/lib/python3': No such file or directory Removing libncursesw6:amd64 (6.4+20240414-1) ... Removing libpython3.11-minimal:amd64 (3.11.9-1) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8t64:amd64 (8.2-4) ... Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Removing libsqlite3-0:amd64 (3.45.3-1) ... Removing media-types (10.1.0) ... Removing netbase (6.4) ... Removing perl-modules-5.38 (5.38.2-3.2) ... Removing readline-common (8.2-4) ... Processing triggers for libc-bin (2.37-18) ... 0m29.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'apt-get', 'remove', 'libexpat1:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libncursesw6:amd64', 'libperl5.38t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libreadline8t64:amd64', 'libsqlite3-0:amd64', 'media-types', 'netbase', 'perl', 'perl-modules-5.38', 'python3', 'python3-minimal', 'python3.11', 'python3.11-minimal', 'readline-common', 'hisat2'] 0m29.6s INFO: Running scripts post_remove 0m29.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/post_remove_exceptions'] 0m29.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/post_remove_exceptions'] 0m29.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'dpkg', '--purge', 'libexpat1:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libncursesw6:amd64', 'libperl5.38t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libreadline8t64:amd64', 'libsqlite3-0:amd64', 'media-types', 'netbase', 'perl', 'perl-modules-5.38', 'python3', 'python3-minimal', 'python3.11', 'python3.11-minimal', 'readline-common'] 0m29.7s DUMP: dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libgdbm-compat4t64 which isn't installed dpkg: warning: ignoring request to remove libgdbm6t64 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libperl5.38t64 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed (Reading database ... 5214 files and directories currently installed.) Purging configuration files for libpython3.11-minimal:amd64 (3.11.9-1) ... dpkg: warning: ignoring request to remove libpython3.11-stdlib which isn't installed Purging configuration files for libreadline8t64:amd64 (8.2-4) ... dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed Purging configuration files for media-types (10.1.0) ... Purging configuration files for netbase (6.4) ... Purging configuration files for perl (5.38.2-3.2+b2) ... dpkg: warning: ignoring request to remove perl-modules-5.38 which isn't installed Purging configuration files for python3 (3.11.8-1) ... dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3.11 which isn't installed Purging configuration files for python3.11-minimal (3.11.9-1) ... Purging configuration files for readline-common (8.2-4) ... 0m29.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'dpkg', '--purge', 'libexpat1:amd64', 'libgdbm-compat4t64:amd64', 'libgdbm6t64:amd64', 'libncursesw6:amd64', 'libperl5.38t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libreadline8t64:amd64', 'libsqlite3-0:amd64', 'media-types', 'netbase', 'perl', 'perl-modules-5.38', 'python3', 'python3-minimal', 'python3.11', 'python3.11-minimal', 'readline-common'] 0m29.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'dpkg', '--purge', 'hisat2'] 0m29.7s DUMP: dpkg: warning: ignoring request to remove hisat2 which isn't installed 0m29.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'dpkg', '--purge', 'hisat2'] 0m29.7s INFO: Running scripts post_purge 0m29.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/post_purge_exceptions'] 0m29.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/post_purge_exceptions'] 0m29.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'dpkg', '--purge', '--pending'] 0m29.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'dpkg', '--purge', '--pending'] 0m29.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'dpkg', '--remove', '--pending'] 0m29.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'dpkg', '--remove', '--pending'] 0m29.7s INFO: Running scripts post_test 0m29.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/post_test_exceptions'] 0m29.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'tmp/scripts/post_test_exceptions'] 0m29.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmparm64hbw'] 0m30.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmparm64hbw'] 0m30.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'dpkg-divert', '--list'] 0m30.1s DUMP: diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64 local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64 local diversion of /home to /home.distrib diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64 diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64 local diversion of /usr/bin/sync to /usr/bin/sync.distrib 0m30.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'dpkg-divert', '--list'] 0m30.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'apt-get', 'clean'] 0m30.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmparm64hbw', 'apt-get', 'clean'] 0m30.2s DEBUG: Recording chroot state 0m31.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmparm64hbw/dev/shm'] 0m31.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmparm64hbw/dev/shm'] 0m31.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmparm64hbw/dev/console'] 0m31.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmparm64hbw/dev/console'] 0m31.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmparm64hbw/dev/ptmx'] 0m31.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmparm64hbw/dev/ptmx'] 0m31.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmparm64hbw/dev/pts'] 0m31.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmparm64hbw/dev/pts'] 0m31.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmparm64hbw/proc'] 0m31.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmparm64hbw/proc'] 0m31.4s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmparm64hbw'] 0m31.5s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmparm64hbw'] 0m31.5s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmparm64hbw 0m31.5s INFO: PASS: Upgrading between Debian distributions. 0m31.5s INFO: PASS: All tests. 0m31.5s INFO: piuparts run ends. ret=0 End: 2024-04-24 20:39:25 GMT