Start: 2024-01-23 15:11:59 GMT [sid] Package: python3-hisat2 Source: hisat2 Version: 2.2.1-4 Installed-Size: 80 Maintainer: Debian Med Packaging Team Architecture: all Depends: hisat2, python3 Description: Python scripts accompanying hisat2 Homepage: https://daehwankimlab.github.io/hisat2/ Built-Using: simde (= 0.7.2-6) Description-md5: e4e54f7ce22e56031a8aabf0c8c9a868 Section: python Priority: optional Filename: pool/main/h/hisat2/python3-hisat2_2.2.1-4_all.deb Size: 13932 MD5sum: d05820037d28e745a0bc57687332f3d3 SHA256: 1328e3d46aae3476b059747c2cf4aed62751d2629fda125c72c47e99dea16921 [experimental] Package: python3-hisat2 Source: hisat2 Version: 2.2.1-5~0exp Installed-Size: 80 Maintainer: Debian Med Packaging Team Architecture: all Depends: hisat2, python3 Description: Python scripts accompanying hisat2 Homepage: https://daehwankimlab.github.io/hisat2/ Built-Using: simde (= 0.7.3~0git20230118123246.d1e75cd-1) Description-md5: e4e54f7ce22e56031a8aabf0c8c9a868 Section: python Priority: optional Filename: pool/main/h/hisat2/python3-hisat2_2.2.1-5~0exp_all.deb Size: 14044 MD5sum: 27582815ba5895f58b78c021dbd99019 SHA256: 90d467837ed3a407f727fd9e798eddb94e38e929fbe4108242d54b98d9b6ea0c Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz -d sid -d experimental -B /srv/piuparts.debian.org/slave/refchroot/sid2experimental/reference-chroot-metadata.dat --apt 'python3-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 1.2 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz -d sid -d experimental -B /srv/piuparts.debian.org/slave/refchroot/sid2experimental/reference-chroot-metadata.dat --apt 'python3-hisat2=2.2.1-5~0exp' 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-27-amd64 #1 SMP Debian 5.10.205-2 (2023-12-31) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpi2f6rp0g 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpi2f6rp0g 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m1.6s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m1.6s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g/proc'] 0m1.6s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g/proc'] 0m1.6s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g/dev/pts'] 0m1.6s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g/dev/pts'] 0m1.6s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g/dev/ptmx'] 0m1.7s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g/dev/ptmx'] 0m1.7s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/6', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g/dev/console'] 0m1.7s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/6', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g/dev/console'] 0m1.7s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g/dev/shm'] 0m1.7s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g/dev/shm'] 0m1.7s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m1.7s DEBUG: Created policy-rc.d and chmodded it. 0m1.7s DEBUG: Created resolv.conf. 0m1.7s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpi2f6rp0g/tmp/scripts/ 0m1.7s INFO: Running scripts post_chroot_unpack 0m1.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'apt-get', 'update'] 0m5.3s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [198 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9665 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7108 kB] Fetched 17.0 MB in 3s (6720 kB/s) Reading package lists... 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'apt-get', 'update'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'apt-get', '-yf', 'dist-upgrade'] 0m6.9s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: libc-bin libc6 usr-is-merged 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 3363 kB of archives. After this operation, 0 B of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 libc6 amd64 2.37-14 [2756 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libc-bin amd64 2.37-14 [602 kB] Get:3 http://deb.debian.org/debian sid/main amd64 usr-is-merged all 39 [5572 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 3363 kB in 0s (36.3 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 ... 5230 files and directories currently installed.) Preparing to unpack .../libc6_2.37-14_amd64.deb ... Unpacking libc6:amd64 (2.37-14) over (2.37-13) ... Setting up libc6:amd64 (2.37-14) ... (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 ... 5230 files and directories currently installed.) Preparing to unpack .../libc-bin_2.37-14_amd64.deb ... Unpacking libc-bin (2.37-14) over (2.37-13) ... Setting up libc-bin (2.37-14) ... (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 ... 5230 files and directories currently installed.) Preparing to unpack .../usr-is-merged_39_all.deb ... Unpacking usr-is-merged (39) over (38) ... Setting up usr-is-merged (39) ... 0m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'apt-get', '-yf', 'dist-upgrade'] 0m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m7.2s DUMP: f6d5c590b167b2f62dfa524041564b40 - 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m7.2s INFO: Running scripts post_setup 0m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/post_setup_dummy_users'] 0m8.1s 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 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/post_setup_dummy_users'] 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/post_setup_forbid_home'] 0m8.1s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/post_setup_forbid_home'] 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/post_setup_force-unsafe-io'] 0m8.2s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' dpkg-divert: warning: diverting file '/bin/sync' from an Essential package with rename is dangerous, use --no-rename '/bin/sync' -> 'true' 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/post_setup_force-unsafe-io'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/post_setup_minimize'] 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/post_setup_minimize'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/post_setup_squeeze-backports'] 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/post_setup_squeeze-backports'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/post_setup_zz_backports'] 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/post_setup_zz_backports'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m8.2s DUMP: install ok installed apt apt 2.7.10 install ok installed base-files base-files 13 install ok installed base-passwd base-passwd 3.6.3 install ok installed bash bash 5.2.21-2 install ok installed bsdutils bsdutils 1:2.39.3-6 install ok installed coreutils coreutils 9.4-3+b1 install ok installed dash dash 0.5.12-6 install ok installed debconf debconf 1.5.83 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.16 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.2 install ok installed e2fsprogs e2fsprogs 1.47.0-2+b1 install ok installed findutils findutils 4.9.0-5 install ok installed gcc-13-base:amd64 gcc-13-base 13.2.0-10 install ok installed gpgv gpgv 2.2.40-1.1+b1 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1 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 2.3.1-6 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.7.10 install ok installed libattr1:amd64 libattr1 1:2.5.1-5 install ok installed libaudit-common libaudit-common 1:3.1.2-1 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-1 install ok installed libblkid1:amd64 libblkid1 2.39.3-6 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b2 install ok installed libc-bin libc-bin 2.37-14 install ok installed libc6:amd64 libc6 2.37-14 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.4-1 install ok installed libcap2:amd64 libcap2 1:2.66-4+b2 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-4 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-4+b1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.271 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2+b1 install ok installed libffi8:amd64 libffi8 3.4.4-2 install ok installed libgcc-s1:amd64 libgcc-s1 13.2.0-10 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.3-2 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2 install ok installed libgnutls30:amd64 libgnutls30 3.8.3-1 install ok installed libgpg-error0:amd64 libgpg-error0 1.47-3 install ok installed libhogweed6:amd64 libhogweed6 3.9.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.4-1+b2 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1+b2 install ok installed liblzma5:amd64 liblzma5 5.4.5-0.3 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.39.3-6 install ok installed libnettle8:amd64 libnettle8 3.9.1-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.3-4 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-9.1+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-9.1+b1 install ok installed libpam-runtime libpam-runtime 1.5.2-9.1 install ok installed libpam0g:amd64 libpam0g 1.5.2-9.1+b1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1 install ok installed libselinux1:amd64 libselinux1 3.5-1+b2 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b2 install ok installed libsepol2:amd64 libsepol2 3.5-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.39.3-6 install ok installed libss2:amd64 libss2 1.47.0-2+b1 install ok installed libssl3:amd64 libssl3 3.1.4-2 install ok installed libstdc++6:amd64 libstdc++6 13.2.0-10 install ok installed libsystemd0:amd64 libsystemd0 255.2-4 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtinfo6:amd64 libtinfo6 6.4+20240113-1 install ok installed libudev1:amd64 libudev1 255.2-4 install ok installed libunistring5:amd64 libunistring5 1.1-2 install ok installed libuuid1:amd64 libuuid1 2.39.3-6 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-2 install ok installed login login 1:4.13+dfsg1-3+b1 install ok installed logsave logsave 1.47.0-2+b1 install ok installed mawk mawk 1.3.4.20231126-1 install ok installed mount mount 2.39.3-6 install ok installed ncurses-base ncurses-base 6.4+20240113-1 install ok installed ncurses-bin ncurses-bin 6.4+20240113-1 install ok installed passwd passwd 1:4.13+dfsg1-3+b1 install ok installed perl-base perl-base 5.38.2-3 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.08-5 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2023d-1 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.39.3-6 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg-3+b1 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m8.2s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/sid2experimental/reference-chroot-metadata.dat 0m8.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g'] 0m8.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g'] 0m8.7s INFO: Running scripts is_testable 0m8.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/is_testable_uninstallable'] 0m8.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/is_testable_uninstallable'] 0m8.7s INFO: Running scripts pre_test 0m8.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_test_exceptions'] 0m8.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_test_exceptions'] 0m8.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', '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/tmpi2f6rp0g', 'tmp/scripts/pre_test_root_password'] 0m8.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'apt-cache', 'show', '--no-all-versions', 'python3-hisat2'] 0m9.0s DUMP: Package: python3-hisat2 Source: hisat2 Version: 2.2.1-4 Installed-Size: 80 Maintainer: Debian Med Packaging Team Architecture: all Depends: hisat2, python3 Description-en: Python scripts accompanying hisat2 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). . This package provides a serires of platform-independent scripts that are typically expected to be co-installed with the hisat2 binary. Description-md5: e4e54f7ce22e56031a8aabf0c8c9a868 Homepage: https://daehwankimlab.github.io/hisat2/ Built-Using: simde (= 0.7.2-6) Section: python Priority: optional Filename: pool/main/h/hisat2/python3-hisat2_2.2.1-4_all.deb Size: 13932 MD5sum: d05820037d28e745a0bc57687332f3d3 SHA256: 1328e3d46aae3476b059747c2cf4aed62751d2629fda125c72c47e99dea16921 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'apt-cache', 'show', '--no-all-versions', 'python3-hisat2'] 0m9.0s INFO: apt-cache knows about the following packages: python3-hisat2 0m9.0s INFO: Running scripts pre_install 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_install_database-server'] 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_install_database-server'] 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_install_exceptions'] 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_install_exceptions'] 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_install_extras'] 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_install_extras'] 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_install_foreign_architecture'] 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_install_foreign_architecture'] 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'apt-cache', 'policy'] 0m9.1s 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: 0m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'apt-cache', 'policy'] 0m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'apt-cache', 'policy', 'python3-hisat2'] 0m9.1s DUMP: python3-hisat2: Installed: (none) Candidate: 2.2.1-4 Version table: 2.2.1-4 500 500 http://deb.debian.org/debian sid/main amd64 Packages 0m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'apt-cache', 'policy', 'python3-hisat2'] 0m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'apt-get', '-y', 'install', 'python3-hisat2'] 0m15.6s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: hisat2 libexpat1 libgdbm-compat4 libgdbm6 libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libncursesw6 libnsl2 libperl5.38 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libreadline8 libsqlite3-0 libtirpc-common libtirpc3 media-types netbase perl perl-modules-5.38 python3 python3-minimal python3.11 python3.11-minimal readline-common Suggested packages: gdbm-l10n krb5-doc krb5-user 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: bcftools samtools krb5-locales libgpm2 ca-certificates The following NEW packages will be installed: hisat2 libexpat1 libgdbm-compat4 libgdbm6 libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libncursesw6 libnsl2 libperl5.38 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libreadline8 libsqlite3-0 libtirpc-common libtirpc3 media-types netbase perl perl-modules-5.38 python3 python3-hisat2 python3-minimal python3.11 python3.11-minimal readline-common 0 upgraded, 29 newly installed, 0 to remove and 0 not upgraded. Need to get 18.7 MB of archives. After this operation, 92.8 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 [2899 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libgdbm6 amd64 1.23-5 [72.5 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libgdbm-compat4 amd64 1.23-5 [48.3 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libperl5.38 amd64 5.38.2-3 [4275 kB] Get:5 http://deb.debian.org/debian sid/main amd64 perl amd64 5.38.2-3 [236 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libpython3.11-minimal amd64 3.11.7-2 [816 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.5.0-2+b2 [99.4 kB] Get:8 http://deb.debian.org/debian sid/main amd64 python3.11-minimal amd64 3.11.7-2 [2035 kB] Get:9 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.11.6-1 [26.2 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+20240113-1 [135 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libkrb5support0 amd64 1.20.1-5 [32.9 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libk5crypto3 amd64 1.20.1-5 [79.6 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libkeyutils1 amd64 1.6.3-2+b2 [9140 B] Get:16 http://deb.debian.org/debian sid/main amd64 libkrb5-3 amd64 1.20.1-5 [332 kB] Get:17 http://deb.debian.org/debian sid/main amd64 libgssapi-krb5-2 amd64 1.20.1-5 [135 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libtirpc-common all 1.3.4+ds-1 [10.7 kB] Get:19 http://deb.debian.org/debian sid/main amd64 libtirpc3 amd64 1.3.4+ds-1 [82.1 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libnsl2 amd64 1.3.0-3 [40.0 kB] Get:21 http://deb.debian.org/debian sid/main amd64 readline-common all 8.2-3 [69.1 kB] Get:22 http://deb.debian.org/debian sid/main amd64 libreadline8 amd64 8.2-3 [167 kB] Get:23 http://deb.debian.org/debian sid/main amd64 libsqlite3-0 amd64 3.45.0-1 [894 kB] Get:24 http://deb.debian.org/debian sid/main amd64 libpython3.11-stdlib amd64 3.11.7-2 [1822 kB] Get:25 http://deb.debian.org/debian sid/main amd64 python3.11 amd64 3.11.7-2 [590 kB] Get:26 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.11.6-1 [9224 B] Get:27 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.11.6-1 [26.2 kB] Get:28 http://deb.debian.org/debian sid/main amd64 hisat2 amd64 2.2.1-4+b3 [3700 kB] Get:29 http://deb.debian.org/debian sid/main amd64 python3-hisat2 all 2.2.1-4 [13.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 18.7 MB in 1s (35.6 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 ... 5232 files and directories currently installed.) Preparing to unpack .../0-perl-modules-5.38_5.38.2-3_all.deb ... Unpacking perl-modules-5.38 (5.38.2-3) ... Selecting previously unselected package libgdbm6:amd64. Preparing to unpack .../1-libgdbm6_1.23-5_amd64.deb ... Unpacking libgdbm6:amd64 (1.23-5) ... Selecting previously unselected package libgdbm-compat4:amd64. Preparing to unpack .../2-libgdbm-compat4_1.23-5_amd64.deb ... 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Setting up media-types (10.1.0) ... Setting up libkeyutils1:amd64 (1.6.3-2+b2) ... Setting up libtirpc-common (1.3.4+ds-1) ... Setting up libsqlite3-0:amd64 (3.45.0-1) ... Setting up libkrb5support0:amd64 (1.20.1-5) ... Setting up perl-modules-5.38 (5.38.2-3) ... Setting up libncursesw6:amd64 (6.4+20240113-1) ... Setting up libk5crypto3:amd64 (1.20.1-5) ... Setting up netbase (6.4) ... Setting up libkrb5-3:amd64 (1.20.1-5) ... Setting up readline-common (8.2-3) ... Setting up libgdbm6:amd64 (1.23-5) ... Setting up libreadline8:amd64 (8.2-3) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-5) ... Setting up libgdbm-compat4:amd64 (1.23-5) ... Setting up libtirpc3:amd64 (1.3.4+ds-1) ... Setting up libperl5.38:amd64 (5.38.2-3) ... Setting up perl (5.38.2-3) ... Setting up libnsl2:amd64 (1.3.0-3) ... Setting up libpython3.11-stdlib:amd64 (3.11.7-2) ... Setting up libpython3-stdlib:amd64 (3.11.6-1) ... Setting up python3.11 (3.11.7-2) ... Setting up python3 (3.11.6-1) ... Setting up hisat2 (2.2.1-4+b3) ... Setting up python3-hisat2 (2.2.1-4) ... Processing triggers for libc-bin (2.37-14) ... 0m15.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'apt-get', '-y', 'install', 'python3-hisat2'] 0m15.6s INFO: Running scripts post_install 0m15.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/post_install_exceptions'] 0m15.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/post_install_exceptions'] 0m15.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g'] 0m16.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g'] 0m16.3s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpi2f6rp0g to experimental 0m16.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main deb http://deb.debian.org/debian/ experimental main 0m16.3s INFO: Running scripts pre_distupgrade 0m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_distupgrade_exceptions'] 0m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_distupgrade_exceptions'] 0m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m16.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m16.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m16.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m16.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m16.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m16.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'apt-get', 'update'] 0m17.9s 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 [514 kB] Get:4 http://deb.debian.org/debian experimental/main Translation-en [302 kB] Fetched 917 kB in 1s (1518 kB/s) Reading package lists... 0m17.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'apt-get', 'update'] 0m17.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'apt-get', '-yf', 'dist-upgrade'] 0m18.4s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m18.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'apt-get', '-yf', 'dist-upgrade'] 0m18.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m19.0s DUMP: 200a6a17ea09caa30c89ce8e391d31df - 0m19.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m19.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'apt-cache', 'show', '--no-all-versions', 'python3-hisat2'] 0m19.2s DUMP: Package: python3-hisat2 Source: hisat2 Version: 2.2.1-4 Installed-Size: 80 Maintainer: Debian Med Packaging Team Architecture: all Depends: hisat2, python3 Description-en: Python scripts accompanying hisat2 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). . This package provides a serires of platform-independent scripts that are typically expected to be co-installed with the hisat2 binary. Description-md5: e4e54f7ce22e56031a8aabf0c8c9a868 Homepage: https://daehwankimlab.github.io/hisat2/ Built-Using: simde (= 0.7.2-6) Section: python Priority: optional Filename: pool/main/h/hisat2/python3-hisat2_2.2.1-4_all.deb Size: 13932 MD5sum: d05820037d28e745a0bc57687332f3d3 SHA256: 1328e3d46aae3476b059747c2cf4aed62751d2629fda125c72c47e99dea16921 0m19.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'apt-cache', 'show', '--no-all-versions', 'python3-hisat2'] 0m19.2s INFO: apt-cache knows about the following packages: python3-hisat2 0m19.2s INFO: Running scripts pre_install 0m19.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_install_database-server'] 0m19.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_install_database-server'] 0m19.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_install_exceptions'] 0m19.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_install_exceptions'] 0m19.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_install_extras'] 0m19.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_install_extras'] 0m19.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_install_foreign_architecture'] 0m19.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_install_foreign_architecture'] 0m19.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m19.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m19.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'apt-cache', 'policy'] 0m19.4s 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: 0m19.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'apt-cache', 'policy'] 0m19.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'apt-cache', 'policy', 'python3-hisat2'] 0m19.4s DUMP: python3-hisat2: Installed: 2.2.1-4 Candidate: 2.2.1-4 Version table: 2.2.1-5~0exp 1 1 http://deb.debian.org/debian experimental/main amd64 Packages *** 2.2.1-4 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m19.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'apt-cache', 'policy', 'python3-hisat2'] 0m19.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'apt-get', '-y', '-t', 'experimental', 'install', 'python3-hisat2'] 0m21.1s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: hisat2 Recommended packages: bcftools samtools The following packages will be upgraded: hisat2 python3-hisat2 2 upgraded, 0 newly installed, 0 to remove and 14 not upgraded. Need to get 3672 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] Get:2 http://deb.debian.org/debian experimental/main amd64 python3-hisat2 all 2.2.1-5~0exp [14.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 3672 kB in 0s (18.1 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 ... 8163 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) ... Preparing to unpack .../python3-hisat2_2.2.1-5~0exp_all.deb ... Unpacking python3-hisat2 (2.2.1-5~0exp) over (2.2.1-4) ... Setting up hisat2 (2.2.1-5~0exp) ... Setting up python3-hisat2 (2.2.1-5~0exp) ... 0m21.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'apt-get', '-y', '-t', 'experimental', 'install', 'python3-hisat2'] 0m21.1s INFO: Running scripts post_install 0m21.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/post_install_exceptions'] 0m21.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/post_install_exceptions'] 0m21.1s INFO: Running scripts post_distupgrade 0m21.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m21.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m21.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/post_distupgrade_exceptions'] 0m21.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/post_distupgrade_exceptions'] 0m21.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m21.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m21.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m21.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m21.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/post_distupgrade_zz_backports'] 0m21.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/post_distupgrade_zz_backports'] 0m21.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g'] 0m21.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g'] 0m21.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g'] 0m22.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g'] 0m22.1s INFO: Running scripts pre_install 0m22.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_install_database-server'] 0m22.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_install_database-server'] 0m22.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_install_exceptions'] 0m22.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_install_exceptions'] 0m22.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_install_extras'] 0m22.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_install_extras'] 0m22.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_install_foreign_architecture'] 0m22.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_install_foreign_architecture'] 0m22.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m22.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m22.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'apt-cache', 'policy'] 0m22.2s 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: 0m22.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'apt-cache', 'policy'] 0m22.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'apt-cache', 'policy', 'python3-hisat2'] 0m22.2s DUMP: python3-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 2.2.1-4 500 500 http://deb.debian.org/debian sid/main amd64 Packages 0m22.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'apt-cache', 'policy', 'python3-hisat2'] 0m22.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'apt-get', '-y', '-t', 'experimental', 'install', 'python3-hisat2=2.2.1-5~0exp'] 0m22.8s DUMP: Reading package lists... Building dependency tree... Reading state information... python3-hisat2 is already the newest version (2.2.1-5~0exp). 0 upgraded, 0 newly installed, 0 to remove and 14 not upgraded. 0m22.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'apt-get', '-y', '-t', 'experimental', 'install', 'python3-hisat2=2.2.1-5~0exp'] 0m22.8s INFO: Running scripts post_install 0m22.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/post_install_exceptions'] 0m22.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/post_install_exceptions'] 0m22.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g'] 0m23.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g'] 0m23.3s INFO: /bin converted to /usr/bin by /usr merge 0m23.4s INFO: /lib converted to /usr/lib by /usr merge 0m23.4s INFO: /lib/init converted to /usr/lib/init by /usr merge 0m23.4s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 0m23.4s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 0m23.4s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 0m23.4s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 0m23.4s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 0m23.4s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 0m23.4s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 0m23.4s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 0m23.4s INFO: /lib64 converted to /usr/lib64 by /usr merge 0m23.4s INFO: /sbin converted to /usr/sbin by /usr merge 0m23.9s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', '-ac', '--ignore-obsolete'] 0m24.9s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', '-ac', '--ignore-obsolete'] 0m24.9s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m24.9s DUMP: 0.15.6 0m24.9s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m24.9s INFO: Running adequate version 0.15.6 now. 0m24.9s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'python3-hisat2'] 0m25.0s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'python3-hisat2'] 0m25.0s INFO: Running scripts pre_remove 0m25.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m25.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m25.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m25.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m25.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m26.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m26.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m26.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m26.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m26.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m26.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_remove_exceptions'] 0m26.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/pre_remove_exceptions'] 0m26.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m26.2s DUMP: install ok installed apt apt 2.7.10 install ok installed base-files base-files 13 install ok installed base-passwd base-passwd 3.6.3 install ok installed bash bash 5.2.21-2 install ok installed bsdutils bsdutils 1:2.39.3-6 install ok installed coreutils coreutils 9.4-3+b1 install ok installed dash dash 0.5.12-6 install ok installed debconf debconf 1.5.83 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.16 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.2 install ok installed e2fsprogs e2fsprogs 1.47.0-2+b1 install ok installed findutils findutils 4.9.0-5 install ok installed gcc-13-base:amd64 gcc-13-base 13.2.0-10 install ok installed gpgv gpgv 2.2.40-1.1+b1 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1 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 2.3.1-6 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.7.10 install ok installed libattr1:amd64 libattr1 1:2.5.1-5 install ok installed libaudit-common libaudit-common 1:3.1.2-1 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-1 install ok installed libblkid1:amd64 libblkid1 2.39.3-6 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b2 install ok installed libc-bin libc-bin 2.37-14 install ok installed libc6:amd64 libc6 2.37-14 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.4-1 install ok installed libcap2:amd64 libcap2 1:2.66-4+b2 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-4 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-4+b1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.271 install ok installed libexpat1:amd64 libexpat1 2.5.0-2+b2 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2+b1 install ok installed libffi8:amd64 libffi8 3.4.4-2 install ok installed libgcc-s1:amd64 libgcc-s1 13.2.0-10 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.3-2 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.23-5 install ok installed libgdbm6:amd64 libgdbm6 1.23-5 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2 install ok installed libgnutls30:amd64 libgnutls30 3.8.3-1 install ok installed libgpg-error0:amd64 libgpg-error0 1.47-3 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.20.1-5 install ok installed libhogweed6:amd64 libhogweed6 3.9.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.4-1+b2 install ok installed libk5crypto3:amd64 libk5crypto3 1.20.1-5 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-2+b2 install ok installed libkrb5-3:amd64 libkrb5-3 1.20.1-5 install ok installed libkrb5support0:amd64 libkrb5support0 1.20.1-5 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1+b2 install ok installed liblzma5:amd64 liblzma5 5.4.5-0.3 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.39.3-6 install ok installed libncursesw6:amd64 libncursesw6 6.4+20240113-1 install ok installed libnettle8:amd64 libnettle8 3.9.1-2 install ok installed libnsl2:amd64 libnsl2 1.3.0-3 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.3-4 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-9.1+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-9.1+b1 install ok installed libpam-runtime libpam-runtime 1.5.2-9.1 install ok installed libpam0g:amd64 libpam0g 1.5.2-9.1+b1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4 install ok installed libperl5.38:amd64 libperl5.38 5.38.2-3 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.11.6-1 install ok installed libpython3.11-minimal:amd64 libpython3.11-minimal 3.11.7-2 install ok installed libpython3.11-stdlib:amd64 libpython3.11-stdlib 3.11.7-2 install ok installed libreadline8:amd64 libreadline8 8.2-3 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1 install ok installed libselinux1:amd64 libselinux1 3.5-1+b2 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b2 install ok installed libsepol2:amd64 libsepol2 3.5-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.39.3-6 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.45.0-1 install ok installed libss2:amd64 libss2 1.47.0-2+b1 install ok installed libssl3:amd64 libssl3 3.1.4-2 install ok installed libstdc++6:amd64 libstdc++6 13.2.0-10 install ok installed libsystemd0:amd64 libsystemd0 255.2-4 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtinfo6:amd64 libtinfo6 6.4+20240113-1 install ok installed libtirpc-common libtirpc-common 1.3.4+ds-1 install ok installed libtirpc3:amd64 libtirpc3 1.3.4+ds-1 install ok installed libudev1:amd64 libudev1 255.2-4 install ok installed libunistring5:amd64 libunistring5 1.1-2 install ok installed libuuid1:amd64 libuuid1 2.39.3-6 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-2 install ok installed login login 1:4.13+dfsg1-3+b1 install ok installed logsave logsave 1.47.0-2+b1 install ok installed mawk mawk 1.3.4.20231126-1 install ok installed media-types media-types 10.1.0 install ok installed mount mount 2.39.3-6 install ok installed ncurses-base ncurses-base 6.4+20240113-1 install ok installed ncurses-bin ncurses-bin 6.4+20240113-1 install ok installed netbase netbase 6.4 install ok installed passwd passwd 1:4.13+dfsg1-3+b1 install ok installed perl perl 5.38.2-3 install ok installed perl-base perl-base 5.38.2-3 install ok installed perl-modules-5.38 perl-modules-5.38 5.38.2-3 install ok installed python3 python3 3.11.6-1 install ok installed python3-hisat2 python3-hisat2 2.2.1-5~0exp install ok installed python3-minimal python3-minimal 3.11.6-1 install ok installed python3.11 python3.11 3.11.7-2 install ok installed python3.11-minimal python3.11-minimal 3.11.7-2 install ok installed readline-common readline-common 8.2-3 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.08-5 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2023d-1 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.39.3-6 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg-3+b1 0m26.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m26.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'apt-get', 'remove', 'hisat2', 'libexpat1:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgssapi-krb5-2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libperl5.38:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'media-types', 'netbase', 'perl', 'perl-modules-5.38', 'python3', 'python3-minimal', 'python3.11', 'python3.11-minimal', 'readline-common', 'python3-hisat2'] 0m27.5s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: hisat2 libexpat1 libgdbm-compat4 libgdbm6 libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libncursesw6 libnsl2 libperl5.38 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libreadline8 libsqlite3-0 libtirpc-common libtirpc3 media-types netbase perl perl-modules-5.38 python3 python3-hisat2 python3-minimal python3.11 python3.11-minimal readline-common 0 upgraded, 0 newly installed, 29 to remove and 0 not upgraded. After this operation, 92.6 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 ... 8162 files and directories currently installed.) Removing python3-hisat2 (2.2.1-5~0exp) ... Removing hisat2 (2.2.1-5~0exp) ... Removing python3 (3.11.6-1) ... Removing python3-minimal (3.11.6-1) ... Removing python3.11 (3.11.7-2) ... Removing python3.11-minimal (3.11.7-2) ... Removing libexpat1:amd64 (2.5.0-2+b2) ... Removing perl (5.38.2-3) ... Removing libperl5.38:amd64 (5.38.2-3) ... Removing libgdbm-compat4:amd64 (1.23-5) ... Removing libgdbm6:amd64 (1.23-5) ... Removing libpython3-stdlib:amd64 (3.11.6-1) ... Removing libpython3.11-stdlib:amd64 (3.11.7-2) ... find: '/usr/lib/python3': No such file or directory Removing libnsl2:amd64 (1.3.0-3) ... Removing libtirpc3:amd64 (1.3.4+ds-1) ... Removing libgssapi-krb5-2:amd64 (1.20.1-5) ... Removing libkrb5-3:amd64 (1.20.1-5) ... Removing libk5crypto3:amd64 (1.20.1-5) ... Removing libkeyutils1:amd64 (1.6.3-2+b2) ... Removing libkrb5support0:amd64 (1.20.1-5) ... Removing libncursesw6:amd64 (6.4+20240113-1) ... Removing libpython3.11-minimal:amd64 (3.11.7-2) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8:amd64 (8.2-3) ... Removing libsqlite3-0:amd64 (3.45.0-1) ... Removing libtirpc-common (1.3.4+ds-1) ... Removing media-types (10.1.0) ... Removing netbase (6.4) ... Removing perl-modules-5.38 (5.38.2-3) ... Removing readline-common (8.2-3) ... Processing triggers for libc-bin (2.37-14) ... 0m27.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'apt-get', 'remove', 'hisat2', 'libexpat1:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgssapi-krb5-2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libperl5.38:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'media-types', 'netbase', 'perl', 'perl-modules-5.38', 'python3', 'python3-minimal', 'python3.11', 'python3.11-minimal', 'readline-common', 'python3-hisat2'] 0m27.5s INFO: Running scripts post_remove 0m27.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/post_remove_exceptions'] 0m27.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/post_remove_exceptions'] 0m27.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'dpkg', '--purge', 'hisat2', 'libexpat1:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgssapi-krb5-2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libperl5.38:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'media-types', 'netbase', 'perl', 'perl-modules-5.38', 'python3', 'python3-minimal', 'python3.11', 'python3.11-minimal', 'readline-common'] 0m27.6s DUMP: dpkg: warning: ignoring request to remove hisat2 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libgdbm-compat4 which isn't installed dpkg: warning: ignoring request to remove libgdbm6 which isn't installed (Reading database ... 5243 files and directories currently installed.) Purging configuration files for libgssapi-krb5-2:amd64 (1.20.1-5) ... dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libnsl2 which isn't installed dpkg: warning: ignoring request to remove libperl5.38 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.11-minimal:amd64 (3.11.7-2) ... dpkg: warning: ignoring request to remove libpython3.11-stdlib which isn't installed dpkg: warning: ignoring request to remove libreadline8 which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed Purging configuration files for libtirpc-common (1.3.4+ds-1) ... dpkg: warning: ignoring request to remove libtirpc3 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) ... dpkg: warning: ignoring request to remove perl-modules-5.38 which isn't installed Purging configuration files for python3 (3.11.6-1) ... 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 (3.11.7-2) ... Purging configuration files for readline-common (8.2-3) ... 0m27.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'dpkg', '--purge', 'hisat2', 'libexpat1:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgssapi-krb5-2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libperl5.38:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'media-types', 'netbase', 'perl', 'perl-modules-5.38', 'python3', 'python3-minimal', 'python3.11', 'python3.11-minimal', 'readline-common'] 0m27.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'dpkg', '--purge', 'python3-hisat2'] 0m27.6s DUMP: dpkg: warning: ignoring request to remove python3-hisat2 which isn't installed 0m27.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'dpkg', '--purge', 'python3-hisat2'] 0m27.6s INFO: Running scripts post_purge 0m27.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/post_purge_exceptions'] 0m27.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/post_purge_exceptions'] 0m27.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'dpkg', '--purge', '--pending'] 0m27.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'dpkg', '--purge', '--pending'] 0m27.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'dpkg', '--remove', '--pending'] 0m27.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'dpkg', '--remove', '--pending'] 0m27.6s INFO: Running scripts post_test 0m27.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/post_test_exceptions'] 0m27.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'tmp/scripts/post_test_exceptions'] 0m27.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g'] 0m28.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g'] 0m28.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'dpkg-divert', '--list'] 0m28.1s DUMP: local diversion of /bin/sync to /bin/sync.distrib local diversion of /home to /home.distrib 0m28.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'dpkg-divert', '--list'] 0m28.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'apt-get', 'clean'] 0m28.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g', 'apt-get', 'clean'] 0m28.1s DEBUG: Recording chroot state 0m29.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g/dev/shm'] 0m29.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g/dev/shm'] 0m29.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g/dev/console'] 0m29.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g/dev/console'] 0m29.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g/dev/ptmx'] 0m29.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g/dev/ptmx'] 0m29.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g/dev/pts'] 0m29.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g/dev/pts'] 0m29.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g/proc'] 0m29.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g/proc'] 0m29.1s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g'] 0m29.3s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpi2f6rp0g'] 0m29.3s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpi2f6rp0g 0m29.3s INFO: PASS: Upgrading between Debian distributions. 0m29.3s INFO: PASS: All tests. 0m29.3s INFO: piuparts run ends. ret=0 End: 2024-01-23 15:12:28 GMT