Start: 2023-08-05 21:45:53 GMT [testing] Package: hisat2 Source: hisat2 (2.2.1-4) Version: 2.2.1-4+b2 Installed-Size: 14154 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 (= 0.7.4~rc2-2) Description-md5: 5f7b7bae1f6d1899a67fb91260ec0d0f Section: science Priority: optional Filename: pool/main/h/hisat2/hisat2_2.2.1-4+b2_amd64.deb Size: 3658228 MD5sum: c2465b320da09260bf48cc787ba6f9de SHA256: 350a7f690242019f023a74aad71983563b1381a72fe4eff24e9dabdb509dfb17 [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 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt hisat2=2.2.1-4+b3 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.1.8~202306121314~1.1.7-9-g57dfbde6 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt hisat2=2.2.1-4+b3 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-23-amd64 #1 SMP Debian 5.10.179-3 (2023-07-27) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpgthoocvq 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpgthoocvq 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz'] 0m2.5s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz'] 0m2.5s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpgthoocvq/proc'] 0m2.5s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpgthoocvq/proc'] 0m2.5s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpgthoocvq/dev/pts'] 0m2.5s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpgthoocvq/dev/pts'] 0m2.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpgthoocvq/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpgthoocvq/dev/ptmx'] 0m2.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpgthoocvq/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpgthoocvq/dev/ptmx'] 0m2.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpgthoocvq/dev/console'] 0m2.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpgthoocvq/dev/console'] 0m2.5s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpgthoocvq/dev/shm'] 0m2.5s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpgthoocvq/dev/shm'] 0m2.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m2.5s DEBUG: Created policy-rc.d and chmodded it. 0m2.5s DEBUG: Created resolv.conf. 0m2.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpgthoocvq/tmp/scripts/ 0m2.6s INFO: Running scripts post_chroot_unpack 0m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'apt-get', 'update'] 0m3.8s DUMP: Hit:1 http://deb.debian.org/debian bookworm InRelease Reading package lists... 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'apt-get', 'update'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'apt-get', '-yf', 'dist-upgrade'] 0m4.3s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'apt-get', '-yf', 'dist-upgrade'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.6s DUMP: 06167fd988d2fa1ed9015ed386bb0220 - 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.6s INFO: Running scripts post_setup 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/post_setup_dummy_users'] 0m5.5s 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 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/post_setup_dummy_users'] 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/post_setup_forbid_home'] 0m5.5s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/post_setup_forbid_home'] 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.6s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' dpkg-divert: warning: diverting file '/bin/sync' from an Essential package with rename is dangerous, use --no-rename '/bin/sync' -> 'true' 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/post_setup_minimize'] 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/post_setup_minimize'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/post_setup_zz_backports'] 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/post_setup_zz_backports'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.6s DUMP: install ok installed adduser adduser 3.134 install ok installed apt apt 2.6.1 install ok installed base-files base-files 12.4+deb12u1 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b2 install ok installed bsdutils bsdutils 1:2.38.1-5+b1 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.12-2 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.3 install ok installed debianutils debianutils 5.7-0.4 install ok installed diffutils diffutils 1:3.8-4 install ok installed dpkg dpkg 1.21.22 install ok installed e2fsprogs e2fsprogs 1.47.0-2 install ok installed findutils findutils 4.9.0-4 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-14 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.8-5 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu1 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.6.1 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.0.9-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.9-1 install ok installed libblkid1:amd64 libblkid1 2.38.1-5+b1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-9+deb12u1 install ok installed libc6:amd64 libc6 2.36-9+deb12u1 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3 install ok installed libcap2:amd64 libcap2 1:2.66-4 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.33-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.270 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-14 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-3 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.9-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.1-0.2 install ok installed libmd0:amd64 libmd0 1.0.4-2 install ok installed libmount1:amd64 libmount1 2.38.1-5+b1 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-6 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-6 install ok installed libpam-runtime libpam-runtime 1.5.2-6 install ok installed libpam0g:amd64 libpam0g 1.5.2-6 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-1 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+b3 install ok installed libselinux1:amd64 libselinux1 3.4-1+b6 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b5 install ok installed libsepol2:amd64 libsepol2 3.4-2.1 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-5+b1 install ok installed libss2:amd64 libss2 1.47.0-2 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-14 install ok installed libsystemd0:amd64 libsystemd0 252.12-1~deb12u1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.4-4 install ok installed libudev1:amd64 libudev1 252.12-1~deb12u1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+b1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.4+dfsg2-5 install ok installed login login 1:4.13+dfsg1-1+b1 install ok installed logsave logsave 1.47.0-2 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mount mount 2.38.1-5+b1 install ok installed ncurses-base ncurses-base 6.4-4 install ok installed ncurses-bin ncurses-bin 6.4-4 install ok installed passwd passwd 1:4.13+dfsg1-1+b1 install ok installed perl-base perl-base 5.36.0-7 install ok installed sed sed 4.9-1 install ok installed sysvinit-utils sysvinit-utils 3.06-4 install ok installed tar tar 1.34+dfsg-1.2 install ok installed tzdata tzdata 2023c-5 install ok installed usr-is-merged usr-is-merged 35 install ok installed util-linux util-linux 2.38.1-5+b1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+b1 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.6s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m5.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgthoocvq'] 0m6.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgthoocvq'] 0m6.1s INFO: Running scripts is_testable 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/is_testable_uninstallable'] 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/is_testable_uninstallable'] 0m6.1s INFO: Running scripts pre_test 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_test_exceptions'] 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_test_exceptions'] 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_test_root_password'] 0m6.1s DUMP: New password: Retype new password: passwd: password updated successfully 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_test_root_password'] 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'apt-cache', 'show', '--no-all-versions', 'hisat2'] 0m6.4s DUMP: Package: hisat2 Source: hisat2 (2.2.1-4) Version: 2.2.1-4+b2 Installed-Size: 14154 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-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 (= 0.7.4~rc2-2) Section: science Priority: optional Filename: pool/main/h/hisat2/hisat2_2.2.1-4+b2_amd64.deb Size: 3658228 MD5sum: c2465b320da09260bf48cc787ba6f9de SHA256: 350a7f690242019f023a74aad71983563b1381a72fe4eff24e9dabdb509dfb17 0m6.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'apt-cache', 'show', '--no-all-versions', 'hisat2'] 0m6.4s INFO: apt-cache knows about the following packages: hisat2 0m6.4s INFO: Running scripts pre_install 0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_install_database-server'] 0m6.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_install_database-server'] 0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_install_exceptions'] 0m6.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_install_exceptions'] 0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_install_extras'] 0m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_install_extras'] 0m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'apt-cache', 'policy'] 0m6.5s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.1,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'apt-cache', 'policy'] 0m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'apt-cache', 'policy', 'hisat2'] 0m6.6s DUMP: hisat2: Installed: (none) Candidate: 2.2.1-4+b2 Version table: 2.2.1-4+b2 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'apt-cache', 'policy', 'hisat2'] 0m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'apt-get', '-y', 'install', 'hisat2'] 0m13.5s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: libexpat1 libgdbm-compat4 libgdbm6 libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libncursesw6 libnsl2 libperl5.36 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libreadline8 libsqlite3-0 libssl3 libtirpc-common libtirpc3 media-types perl perl-modules-5.36 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: python3-hisat2 bcftools samtools krb5-locales libgpm2 netbase ca-certificates The following NEW packages will be installed: hisat2 libexpat1 libgdbm-compat4 libgdbm6 libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libncursesw6 libnsl2 libperl5.36 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libreadline8 libsqlite3-0 libssl3 libtirpc-common libtirpc3 media-types perl perl-modules-5.36 python3 python3-minimal python3.11 python3.11-minimal readline-common 0 upgraded, 28 newly installed, 0 to remove and 0 not upgraded. Need to get 20.4 MB of archives. After this operation, 96.6 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 perl-modules-5.36 all 5.36.0-7 [2815 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 libgdbm6 amd64 1.23-3 [72.2 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libgdbm-compat4 amd64 1.23-3 [48.2 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 libperl5.36 amd64 5.36.0-7 [4218 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 perl amd64 5.36.0-7 [239 kB] Get:6 http://deb.debian.org/debian bookworm/main amd64 libssl3 amd64 3.0.9-1 [2016 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get:8 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get:9 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get:10 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get:11 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get:12 http://deb.debian.org/debian bookworm/main amd64 libncursesw6 amd64 6.4-4 [134 kB] Get:13 http://deb.debian.org/debian bookworm/main amd64 libkrb5support0 amd64 1.20.1-2 [32.3 kB] Get:14 http://deb.debian.org/debian bookworm/main amd64 libk5crypto3 amd64 1.20.1-2 [79.0 kB] Get:15 http://deb.debian.org/debian bookworm/main amd64 libkeyutils1 amd64 1.6.3-2 [8808 B] Get:16 http://deb.debian.org/debian bookworm/main amd64 libkrb5-3 amd64 1.20.1-2 [331 kB] Get:17 http://deb.debian.org/debian bookworm/main amd64 libgssapi-krb5-2 amd64 1.20.1-2 [134 kB] Get:18 http://deb.debian.org/debian bookworm/main amd64 libtirpc-common all 1.3.3+ds-1 [14.0 kB] Get:19 http://deb.debian.org/debian bookworm/main amd64 libtirpc3 amd64 1.3.3+ds-1 [85.2 kB] Get:20 http://deb.debian.org/debian bookworm/main amd64 libnsl2 amd64 1.3.0-2 [39.5 kB] Get:21 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get:22 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get:23 http://deb.debian.org/debian bookworm/main amd64 libsqlite3-0 amd64 3.40.1-2 [837 kB] Get:24 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get:25 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get:26 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get:27 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get:28 http://deb.debian.org/debian bookworm/main amd64 hisat2 amd64 2.2.1-4+b2 [3658 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 20.4 MB in 0s (92.5 MB/s) Selecting previously unselected package perl-modules-5.36. (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 ... 6100 files and directories currently installed.) Preparing to unpack .../0-perl-modules-5.36_5.36.0-7_all.deb ... Unpacking perl-modules-5.36 (5.36.0-7) ... Selecting previously unselected package libgdbm6:amd64. Preparing to unpack .../1-libgdbm6_1.23-3_amd64.deb ... Unpacking libgdbm6:amd64 (1.23-3) ... Selecting previously unselected package libgdbm-compat4:amd64. Preparing to unpack .../2-libgdbm-compat4_1.23-3_amd64.deb ... Unpacking libgdbm-compat4:amd64 (1.23-3) ... Selecting previously unselected package libperl5.36:amd64. Preparing to unpack .../3-libperl5.36_5.36.0-7_amd64.deb ... Unpacking libperl5.36:amd64 (5.36.0-7) ... Selecting previously unselected package perl. Preparing to unpack .../4-perl_5.36.0-7_amd64.deb ... Unpacking perl (5.36.0-7) ... Selecting previously unselected package libssl3:amd64. Preparing to unpack .../5-libssl3_3.0.9-1_amd64.deb ... Unpacking libssl3:amd64 (3.0.9-1) ... Selecting previously unselected package libpython3.11-minimal:amd64. Preparing to unpack .../6-libpython3.11-minimal_3.11.2-6_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../7-libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../8-python3.11-minimal_3.11.2-6_amd64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libssl3:amd64 (3.0.9-1) ... Setting up libpython3.11-minimal:amd64 (3.11.2-6) ... Setting up libexpat1:amd64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... 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 ... 8432 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.11.2-1+b1_amd64.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package libncursesw6:amd64. Preparing to unpack .../02-libncursesw6_6.4-4_amd64.deb ... Unpacking libncursesw6:amd64 (6.4-4) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../03-libkrb5support0_1.20.1-2_amd64.deb ... Unpacking libkrb5support0:amd64 (1.20.1-2) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../04-libk5crypto3_1.20.1-2_amd64.deb ... Unpacking libk5crypto3:amd64 (1.20.1-2) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../05-libkeyutils1_1.6.3-2_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-2) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../06-libkrb5-3_1.20.1-2_amd64.deb ... Unpacking libkrb5-3:amd64 (1.20.1-2) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../07-libgssapi-krb5-2_1.20.1-2_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.20.1-2) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../08-libtirpc-common_1.3.3+ds-1_all.deb ... Unpacking libtirpc-common (1.3.3+ds-1) ... Selecting previously unselected package libtirpc3:amd64. Preparing to unpack .../09-libtirpc3_1.3.3+ds-1_amd64.deb ... Unpacking libtirpc3:amd64 (1.3.3+ds-1) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../10-libnsl2_1.3.0-2_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-2) ... Selecting previously unselected package readline-common. Preparing to unpack .../11-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:amd64. Preparing to unpack .../12-libreadline8_8.2-1.3_amd64.deb ... Unpacking libreadline8:amd64 (8.2-1.3) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../13-libsqlite3-0_3.40.1-2_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.40.1-2) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../14-libpython3.11-stdlib_3.11.2-6_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../15-python3.11_3.11.2-6_amd64.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../16-libpython3-stdlib_3.11.2-1+b1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package python3. (Reading database ... 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Setting up libkrb5support0:amd64 (1.20.1-2) ... Setting up perl-modules-5.36 (5.36.0-7) ... Setting up libncursesw6:amd64 (6.4-4) ... Setting up libk5crypto3:amd64 (1.20.1-2) ... Setting up libkrb5-3:amd64 (1.20.1-2) ... Setting up readline-common (8.2-1.3) ... Setting up libgdbm6:amd64 (1.23-3) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-2) ... Setting up libgdbm-compat4:amd64 (1.23-3) ... Setting up libperl5.36:amd64 (5.36.0-7) ... Setting up libtirpc3:amd64 (1.3.3+ds-1) ... Setting up perl (5.36.0-7) ... Setting up libnsl2:amd64 (1.3.0-2) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6) ... Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6) ... Setting up python3 (3.11.2-1+b1) ... Setting up hisat2 (2.2.1-4+b2) ... Processing triggers for libc-bin (2.36-9+deb12u1) ... 0m13.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'apt-get', '-y', 'install', 'hisat2'] 0m13.5s INFO: Running scripts post_install 0m13.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/post_install_exceptions'] 0m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/post_install_exceptions'] 0m13.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgthoocvq'] 0m14.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgthoocvq'] 0m14.2s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpgthoocvq to sid 0m14.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m14.2s INFO: Running scripts pre_distupgrade 0m14.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m14.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m14.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_distupgrade_exceptions'] 0m14.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_distupgrade_exceptions'] 0m14.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m14.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m14.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m14.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m14.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m14.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m14.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'apt-get', 'update'] 0m19.3s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [210 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9575 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7010 kB] Fetched 16.8 MB in 4s (4162 kB/s) Reading package lists... 0m19.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'apt-get', 'update'] 0m19.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'apt-get', '-yf', 'dist-upgrade'] 0m32.1s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: gcc-13-base The following packages will be upgraded: adduser apt base-files bash bsdutils dash debian-archive-keyring debianutils findutils gcc-12-base grep hisat2 libapt-pkg6.0 libaudit-common libaudit1 libblkid1 libc-bin libc6 libcrypt1 libexpat1 libgcc-s1 libgcrypt20 libgmp10 libhogweed6 libidn2-0 libmd0 libmount1 libncursesw6 libnettle8 libp11-kit0 libpcre2-8-0 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libselinux1 libsemanage-common libsemanage2 libsepol2 libsmartcols1 libsqlite3-0 libssl3 libstdc++6 libsystemd0 libtasn1-6 libtinfo6 libudev1 libuuid1 libzstd1 mawk media-types mount ncurses-base ncurses-bin python3 python3-minimal python3.11 python3.11-minimal sysvinit-utils tzdata util-linux util-linux-extra 61 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 29.5 MB of archives. After this operation, 1006 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 base-files amd64 13 [70.6 kB] Get:2 http://deb.debian.org/debian sid/main amd64 debianutils amd64 5.8-1 [103 kB] Get:3 http://deb.debian.org/debian sid/main amd64 bash amd64 5.2.15-2+b4 [1490 kB] Get:4 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.39.1-3 [95.9 kB] Get:5 http://deb.debian.org/debian sid/main amd64 dash amd64 0.5.12-6 [92.1 kB] Get:6 http://deb.debian.org/debian sid/main amd64 findutils amd64 4.9.0-5 [636 kB] Get:7 http://deb.debian.org/debian sid/main amd64 grep amd64 3.11-2 [431 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libc6 amd64 2.37-7 [2754 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libc-bin amd64 2.37-7 [600 kB] Get:10 http://deb.debian.org/debian sid/main amd64 gcc-13-base amd64 13.2.0-1 [39.1 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 13.2.0-1 [57.7 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libncursesw6 amd64 6.4+20230625-2 [134 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libtinfo6 amd64 6.4+20230625-2 [339 kB] Get:14 http://deb.debian.org/debian sid/main amd64 ncurses-bin amd64 6.4+20230625-2 [426 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.39.1-3 [158 kB] Get:16 http://deb.debian.org/debian sid/main amd64 libpcre2-8-0 amd64 10.42-2 [261 kB] Get:17 http://deb.debian.org/debian sid/main amd64 libselinux1 amd64 3.5-1 [73.9 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.39.1-3 [189 kB] Get:19 http://deb.debian.org/debian sid/main amd64 libaudit-common all 1:3.1.1-1 [10.8 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libaudit1 amd64 1:3.1.1-1 [47.3 kB] Get:21 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.39.1-3 [115 kB] Get:22 http://deb.debian.org/debian sid/main amd64 util-linux-extra amd64 2.39.1-3 [156 kB] Get:23 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.39.1-3 [1223 kB] Get:24 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 13.2.0-1 [695 kB] Get:25 http://deb.debian.org/debian sid/main amd64 libzstd1 amd64 1.5.5+dfsg2-1 [293 kB] Get:26 http://deb.debian.org/debian sid/main amd64 libgcrypt20 amd64 1.10.2-2 [704 kB] Get:27 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 254-1 [355 kB] Get:28 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 254-1 [117 kB] Get:29 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0 amd64 2.7.3 [945 kB] Get:30 http://deb.debian.org/debian sid/main amd64 adduser all 3.137 [140 kB] Get:31 http://deb.debian.org/debian sid/main amd64 debian-archive-keyring all 2023.4 [161 kB] Get:32 http://deb.debian.org/debian sid/main amd64 apt amd64 2.7.3 [1361 kB] Get:33 http://deb.debian.org/debian sid/main amd64 ncurses-base all 6.4+20230625-2 [265 kB] Get:34 http://deb.debian.org/debian sid/main amd64 sysvinit-utils amd64 3.07-1 [31.3 kB] Get:35 http://deb.debian.org/debian sid/main amd64 mount amd64 2.39.1-3 [142 kB] Get:36 http://deb.debian.org/debian sid/main amd64 media-types all 10.1.0 [26.9 kB] Get:37 http://deb.debian.org/debian sid/main amd64 python3.11 amd64 3.11.4-1 [579 kB] Get:38 http://deb.debian.org/debian sid/main amd64 libcrypt1 amd64 1:4.4.36-2 [89.7 kB] Get:39 http://deb.debian.org/debian sid/main amd64 libsqlite3-0 amd64 3.42.0-1 [859 kB] Get:40 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.39.1-3 [29.0 kB] Get:41 http://deb.debian.org/debian sid/main amd64 libpython3.11-stdlib amd64 3.11.4-1 [1803 kB] Get:42 http://deb.debian.org/debian sid/main amd64 libssl3 amd64 3.0.10-1 [2014 kB] Get:43 http://deb.debian.org/debian sid/main amd64 python3.11-minimal amd64 3.11.4-1 [2060 kB] Get:44 http://deb.debian.org/debian sid/main amd64 libpython3.11-minimal amd64 3.11.4-1 [815 kB] Get:45 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.5.0-2 [99.0 kB] Get:46 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.11.4-5 [26.2 kB] Get:47 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.11.4-5 [26.2 kB] Get:48 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.11.4-5 [9200 B] Get:49 http://deb.debian.org/debian sid/main amd64 libgmp10 amd64 2:6.3.0+dfsg-2 [557 kB] Get:50 http://deb.debian.org/debian sid/main amd64 libnettle8 amd64 3.9.1-2 [295 kB] Get:51 http://deb.debian.org/debian sid/main amd64 libhogweed6 amd64 3.9.1-2 [327 kB] Get:52 http://deb.debian.org/debian sid/main amd64 libidn2-0 amd64 2.3.4-1 [143 kB] Get:53 http://deb.debian.org/debian sid/main amd64 libmd0 amd64 1.1.0-1 [35.5 kB] Get:54 http://deb.debian.org/debian sid/main amd64 libp11-kit0 amd64 0.25.0-4 [413 kB] Get:55 http://deb.debian.org/debian sid/main amd64 libsemanage-common all 3.5-1 [9908 B] Get:56 http://deb.debian.org/debian sid/main amd64 libsepol2 amd64 3.5-1 [276 kB] Get:57 http://deb.debian.org/debian sid/main amd64 libsemanage2 amd64 3.5-1 [89.7 kB] Get:58 http://deb.debian.org/debian sid/main amd64 libtasn1-6 amd64 4.19.0-3 [48.3 kB] Get:59 http://deb.debian.org/debian sid/main amd64 mawk amd64 1.3.4.20230730-1 [134 kB] Get:60 http://deb.debian.org/debian sid/main amd64 tzdata all 2023c-7 [254 kB] Get:61 http://deb.debian.org/debian sid/main amd64 gcc-12-base amd64 12.3.0-7 [39.9 kB] Get:62 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 29.5 MB in 0s (124 MB/s) (Reading database ... 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Unpacking libcrypt1:amd64 (1:4.4.36-2) over (1:4.4.33-2) ... Setting up libcrypt1:amd64 (1:4.4.36-2) ... (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 ... 8996 files and directories currently installed.) Preparing to unpack .../libsqlite3-0_3.42.0-1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.42.0-1) over (3.40.1-2) ... Preparing to unpack .../libuuid1_2.39.1-3_amd64.deb ... Unpacking libuuid1:amd64 (2.39.1-3) over (2.38.1-5+b1) ... Setting up libuuid1:amd64 (2.39.1-3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8995 files and directories currently installed.) Preparing to unpack .../libpython3.11-stdlib_3.11.4-1_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.4-1) over (3.11.2-6) ... Preparing to unpack .../libssl3_3.0.10-1_amd64.deb ... Unpacking libssl3:amd64 (3.0.10-1) over (3.0.9-1) ... Preparing to unpack .../python3.11-minimal_3.11.4-1_amd64.deb ... Unpacking python3.11-minimal (3.11.4-1) over (3.11.2-6) ... Preparing to unpack .../libpython3.11-minimal_3.11.4-1_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.4-1) over (3.11.2-6) ... Preparing to unpack .../libexpat1_2.5.0-2_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-2) over (2.5.0-1) ... Setting up libssl3:amd64 (3.0.10-1) ... Setting up libpython3.11-minimal:amd64 (3.11.4-1) ... Setting up libexpat1:amd64 (2.5.0-2) ... Setting up python3.11-minimal (3.11.4-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8995 files and directories currently installed.) Preparing to unpack .../python3-minimal_3.11.4-5_amd64.deb ... Unpacking python3-minimal (3.11.4-5) over (3.11.2-1+b1) ... Setting up python3-minimal (3.11.4-5) ... (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 ... 8994 files and directories currently installed.) Preparing to unpack .../python3_3.11.4-5_amd64.deb ... Unpacking python3 (3.11.4-5) over (3.11.2-1+b1) ... Preparing to unpack .../libpython3-stdlib_3.11.4-5_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.4-5) over (3.11.2-1+b1) ... Preparing to unpack .../libgmp10_2%3a6.3.0+dfsg-2_amd64.deb ... Unpacking libgmp10:amd64 (2:6.3.0+dfsg-2) over (2:6.2.1+dfsg1-1.1) ... Setting up libgmp10:amd64 (2:6.3.0+dfsg-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 ... 8992 files and directories currently installed.) Preparing to unpack .../libnettle8_3.9.1-2_amd64.deb ... Unpacking libnettle8:amd64 (3.9.1-2) over (3.8.1-2) ... Setting up libnettle8:amd64 (3.9.1-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8992 files and directories currently installed.) Preparing to unpack .../libhogweed6_3.9.1-2_amd64.deb ... Unpacking libhogweed6:amd64 (3.9.1-2) over (3.8.1-2) ... Setting up libhogweed6:amd64 (3.9.1-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8992 files and directories currently installed.) Preparing to unpack .../libidn2-0_2.3.4-1_amd64.deb ... Unpacking libidn2-0:amd64 (2.3.4-1) over (2.3.3-1+b1) ... Setting up libidn2-0:amd64 (2.3.4-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8992 files and directories currently installed.) Preparing to unpack .../libmd0_1.1.0-1_amd64.deb ... Unpacking libmd0:amd64 (1.1.0-1) over (1.0.4-2) ... Setting up libmd0:amd64 (1.1.0-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8992 files and directories currently installed.) Preparing to unpack .../libp11-kit0_0.25.0-4_amd64.deb ... Unpacking libp11-kit0:amd64 (0.25.0-4) over (0.24.1-2) ... Setting up libp11-kit0:amd64 (0.25.0-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8992 files and directories currently installed.) Preparing to unpack .../libsemanage-common_3.5-1_all.deb ... Unpacking libsemanage-common (3.5-1) over (3.4-1) ... Setting up libsemanage-common (3.5-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8992 files and directories currently installed.) Preparing to unpack .../libsepol2_3.5-1_amd64.deb ... Unpacking libsepol2:amd64 (3.5-1) over (3.4-2.1) ... Setting up libsepol2:amd64 (3.5-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8992 files and directories currently installed.) Preparing to unpack .../libsemanage2_3.5-1_amd64.deb ... Unpacking libsemanage2:amd64 (3.5-1) over (3.4-1+b5) ... Setting up libsemanage2:amd64 (3.5-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8991 files and directories currently installed.) Preparing to unpack .../libtasn1-6_4.19.0-3_amd64.deb ... Unpacking libtasn1-6:amd64 (4.19.0-3) over (4.19.0-2) ... Setting up libtasn1-6:amd64 (4.19.0-3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8991 files and directories currently installed.) Preparing to unpack .../mawk_1.3.4.20230730-1_amd64.deb ... Unpacking mawk (1.3.4.20230730-1) over (1.3.4.20200120-3.1) ... Preparing to unpack .../tzdata_2023c-7_all.deb ... Unpacking tzdata (2023c-7) over (2023c-5) ... Preparing to unpack .../gcc-12-base_12.3.0-7_amd64.deb ... Unpacking gcc-12-base:amd64 (12.3.0-7) over (12.2.0-14) ... Preparing to unpack .../hisat2_2.2.1-4+b3_amd64.deb ... Unpacking hisat2 (2.2.1-4+b3) over (2.2.1-4+b2) ... Setting up media-types (10.1.0) ... Installing new version of config file /etc/mime.types ... Setting up libsqlite3-0:amd64 (3.42.0-1) ... Setting up gcc-12-base:amd64 (12.3.0-7) ... Setting up tzdata (2023c-7) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Aug 5 21:46:24 UTC 2023. Universal Time is now: Sat Aug 5 21:46:24 UTC 2023. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libncursesw6:amd64 (6.4+20230625-2) ... Setting up mount (2.39.1-3) ... Setting up mawk (1.3.4.20230730-1) ... Setting up libpython3.11-stdlib:amd64 (3.11.4-1) ... Setting up libpython3-stdlib:amd64 (3.11.4-5) ... Setting up python3.11 (3.11.4-1) ... Setting up python3 (3.11.4-5) ... Setting up hisat2 (2.2.1-4+b3) ... Processing triggers for libc-bin (2.37-7) ... Processing triggers for debianutils (5.8-1) ... 0m32.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'apt-get', '-yf', 'dist-upgrade'] 0m32.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m33.4s DUMP: 1cf056ae86862e92c7408518092c61cc - 0m33.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m33.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'apt-cache', 'show', '--no-all-versions', 'hisat2'] 0m33.6s 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 0m33.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'apt-cache', 'show', '--no-all-versions', 'hisat2'] 0m33.6s INFO: apt-cache knows about the following packages: hisat2 0m33.6s INFO: Running scripts pre_install 0m33.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_install_database-server'] 0m33.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_install_database-server'] 0m33.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_install_exceptions'] 0m33.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_install_exceptions'] 0m33.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_install_extras'] 0m33.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_install_extras'] 0m33.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_install_foreign_architecture'] 0m33.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_install_foreign_architecture'] 0m33.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m33.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m33.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'apt-cache', 'policy'] 0m33.7s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m33.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'apt-cache', 'policy'] 0m33.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'apt-cache', 'policy', 'hisat2'] 0m33.7s DUMP: hisat2: Installed: 2.2.1-4+b3 Candidate: 2.2.1-4+b3 Version table: *** 2.2.1-4+b3 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m33.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'apt-cache', 'policy', 'hisat2'] 0m33.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'apt-get', '-y', 'install', 'hisat2'] 0m34.3s DUMP: Reading package lists... Building dependency tree... Reading state information... hisat2 is already the newest version (2.2.1-4+b3). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m34.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'apt-get', '-y', 'install', 'hisat2'] 0m34.3s INFO: Running scripts post_install 0m34.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/post_install_exceptions'] 0m34.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/post_install_exceptions'] 0m34.3s INFO: Running scripts post_distupgrade 0m34.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m34.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m34.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/post_distupgrade_exceptions'] 0m34.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/post_distupgrade_exceptions'] 0m34.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m34.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m34.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m34.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m34.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/post_distupgrade_zz_backports'] 0m34.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/post_distupgrade_zz_backports'] 0m34.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgthoocvq'] 0m34.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgthoocvq'] 0m34.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgthoocvq'] 0m35.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgthoocvq'] 0m35.5s INFO: Running scripts pre_install 0m35.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_install_database-server'] 0m35.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_install_database-server'] 0m35.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_install_exceptions'] 0m35.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_install_exceptions'] 0m35.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_install_extras'] 0m35.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_install_extras'] 0m35.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_install_foreign_architecture'] 0m35.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_install_foreign_architecture'] 0m35.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m35.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m35.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'apt-cache', 'policy'] 0m35.6s 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: 0m35.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'apt-cache', 'policy'] 0m35.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'apt-cache', 'policy', 'hisat2'] 0m35.6s DUMP: hisat2: Installed: 2.2.1-4+b3 Candidate: 2.2.1-4+b3 Version table: *** 2.2.1-4+b3 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m35.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'apt-cache', 'policy', 'hisat2'] 0m35.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'apt-get', '-y', 'install', 'hisat2=2.2.1-4+b3'] 0m36.2s DUMP: Reading package lists... Building dependency tree... Reading state information... hisat2 is already the newest version (2.2.1-4+b3). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m36.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'apt-get', '-y', 'install', 'hisat2=2.2.1-4+b3'] 0m36.2s INFO: Running scripts post_install 0m36.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/post_install_exceptions'] 0m36.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/post_install_exceptions'] 0m36.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgthoocvq'] 0m36.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgthoocvq'] 0m37.7s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', '-ac', '--ignore-obsolete'] 0m38.7s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', '-ac', '--ignore-obsolete'] 0m38.8s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m38.8s DUMP: 0.15.6 0m38.8s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m38.8s INFO: Running adequate version 0.15.6 now. 0m38.8s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'hisat2'] 0m39.0s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'hisat2'] 0m39.0s INFO: Running scripts pre_remove 0m39.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m39.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m39.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m39.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m39.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m39.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m39.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m40.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m40.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m40.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m40.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_remove_exceptions'] 0m40.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/pre_remove_exceptions'] 0m40.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m40.2s DUMP: install ok installed adduser adduser 3.137 install ok installed apt apt 2.7.3 install ok installed base-files base-files 13 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b4 install ok installed bsdutils bsdutils 1:2.39.1-3 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.12-6 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.8-1 install ok installed diffutils diffutils 1:3.8-4 install ok installed dpkg dpkg 1.21.22 install ok installed e2fsprogs e2fsprogs 1.47.0-2 install ok installed findutils findutils 4.9.0-5 install ok installed gcc-12-base:amd64 gcc-12-base 12.3.0-7 install ok installed gcc-13-base:amd64 gcc-13-base 13.2.0-1 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.11-2 install ok installed gzip gzip 1.12-1 install ok installed hisat2 hisat2 2.2.1-4+b3 install ok installed hostname hostname 3.23+nmu1 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.7.3 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.1.1-1 install ok installed libaudit1:amd64 libaudit1 1:3.1.1-1 install ok installed libblkid1:amd64 libblkid1 2.39.1-3 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.37-7 install ok installed libc6:amd64 libc6 2.37-7 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3 install ok installed libcap2:amd64 libcap2 1:2.66-4 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.270 install ok installed libexpat1:amd64 libexpat1 2.5.0-2 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libgcc-s1:amd64 libgcc-s1 13.2.0-1 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.2-2 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.23-3 install ok installed libgdbm6:amd64 libgdbm6 1.23-3 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2 install ok installed libgnutls30:amd64 libgnutls30 3.7.9-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.20.1-2 install ok installed libhogweed6:amd64 libhogweed6 3.9.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.4-1 install ok installed libk5crypto3:amd64 libk5crypto3 1.20.1-2 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.20.1-2 install ok installed libkrb5support0:amd64 libkrb5support0 1.20.1-2 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.1-0.2 install ok installed libmd0:amd64 libmd0 1.1.0-1 install ok installed libmount1:amd64 libmount1 2.39.1-3 install ok installed libncursesw6:amd64 libncursesw6 6.4+20230625-2 install ok installed libnettle8:amd64 libnettle8 3.9.1-2 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.0-4 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-6 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-6 install ok installed libpam-runtime libpam-runtime 1.5.2-6 install ok installed libpam0g:amd64 libpam0g 1.5.2-6 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-2 install ok installed libperl5.36:amd64 libperl5.36 5.36.0-7 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.11.4-5 install ok installed libpython3.11-minimal:amd64 libpython3.11-minimal 3.11.4-1 install ok installed libpython3.11-stdlib:amd64 libpython3.11-stdlib 3.11.4-1 install ok installed libreadline8:amd64 libreadline8 8.2-1.3 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+b3 install ok installed libselinux1:amd64 libselinux1 3.5-1 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1 install ok installed libsepol2:amd64 libsepol2 3.5-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.39.1-3 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.42.0-1 install ok installed libss2:amd64 libss2 1.47.0-2 install ok installed libssl3:amd64 libssl3 3.0.10-1 install ok installed libstdc++6:amd64 libstdc++6 13.2.0-1 install ok installed libsystemd0:amd64 libsystemd0 254-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3 install ok installed libtinfo6:amd64 libtinfo6 6.4+20230625-2 install ok installed libtirpc-common libtirpc-common 1.3.3+ds-1 install ok installed libtirpc3:amd64 libtirpc3 1.3.3+ds-1 install ok installed libudev1:amd64 libudev1 254-1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.39.1-3 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-1 install ok installed login login 1:4.13+dfsg1-1+b1 install ok installed logsave logsave 1.47.0-2 install ok installed mawk mawk 1.3.4.20230730-1 install ok installed media-types media-types 10.1.0 install ok installed mount mount 2.39.1-3 install ok installed ncurses-base ncurses-base 6.4+20230625-2 install ok installed ncurses-bin ncurses-bin 6.4+20230625-2 install ok installed passwd passwd 1:4.13+dfsg1-1+b1 install ok installed perl perl 5.36.0-7 install ok installed perl-base perl-base 5.36.0-7 install ok installed perl-modules-5.36 perl-modules-5.36 5.36.0-7 install ok installed python3 python3 3.11.4-5 install ok installed python3-minimal python3-minimal 3.11.4-5 install ok installed python3.11 python3.11 3.11.4-1 install ok installed python3.11-minimal python3.11-minimal 3.11.4-1 install ok installed readline-common readline-common 8.2-1.3 install ok installed sed sed 4.9-1 install ok installed sysvinit-utils sysvinit-utils 3.07-1 install ok installed tar tar 1.34+dfsg-1.2 install ok installed tzdata tzdata 2023c-7 install ok installed usr-is-merged usr-is-merged 35 install ok installed util-linux util-linux 2.39.1-3 install ok installed util-linux-extra util-linux-extra 2.39.1-3 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m40.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m40.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'apt-get', 'remove', 'libexpat1:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgssapi-krb5-2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libperl5.36:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libssl3:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'media-types', 'perl', 'perl-modules-5.36', 'python3', 'python3-minimal', 'python3.11', 'python3.11-minimal', 'readline-common', 'hisat2'] 0m41.6s 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 libperl5.36 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libreadline8 libsqlite3-0 libssl3 libtirpc-common libtirpc3 media-types perl perl-modules-5.36 python3 python3-minimal python3.11 python3.11-minimal readline-common 0 upgraded, 0 newly installed, 28 to remove and 0 not upgraded. After this operation, 96.8 MB disk space will be freed. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8313 files and directories currently installed.) Removing hisat2 (2.2.1-4+b3) ... Removing python3 (3.11.4-5) ... Removing python3.11 (3.11.4-1) ... Removing python3-minimal (3.11.4-5) ... Removing python3.11-minimal (3.11.4-1) ... Removing libexpat1:amd64 (2.5.0-2) ... Removing perl (5.36.0-7) ... Removing libperl5.36:amd64 (5.36.0-7) ... Removing libgdbm-compat4:amd64 (1.23-3) ... Removing libgdbm6:amd64 (1.23-3) ... Removing libpython3-stdlib:amd64 (3.11.4-5) ... Removing libpython3.11-stdlib:amd64 (3.11.4-1) ... find: '/usr/lib/python3': No such file or directory Removing libnsl2:amd64 (1.3.0-2) ... Removing libtirpc3:amd64 (1.3.3+ds-1) ... Removing libgssapi-krb5-2:amd64 (1.20.1-2) ... Removing libkrb5-3:amd64 (1.20.1-2) ... Removing libk5crypto3:amd64 (1.20.1-2) ... Removing libkeyutils1:amd64 (1.6.3-2) ... Removing libkrb5support0:amd64 (1.20.1-2) ... Removing libncursesw6:amd64 (6.4+20230625-2) ... Removing libpython3.11-minimal:amd64 (3.11.4-1) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8:amd64 (8.2-1.3) ... Removing libsqlite3-0:amd64 (3.42.0-1) ... Removing libssl3:amd64 (3.0.10-1) ... Removing libtirpc-common (1.3.3+ds-1) ... Removing media-types (10.1.0) ... Removing perl-modules-5.36 (5.36.0-7) ... Removing readline-common (8.2-1.3) ... Processing triggers for libc-bin (2.37-7) ... 0m41.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'apt-get', 'remove', 'libexpat1:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgssapi-krb5-2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libperl5.36:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libssl3:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'media-types', 'perl', 'perl-modules-5.36', 'python3', 'python3-minimal', 'python3.11', 'python3.11-minimal', 'readline-common', 'hisat2'] 0m41.6s INFO: Running scripts post_remove 0m41.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/post_remove_exceptions'] 0m41.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/post_remove_exceptions'] 0m41.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'dpkg', '--purge', 'libexpat1:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgssapi-krb5-2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libperl5.36:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libssl3:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'media-types', 'perl', 'perl-modules-5.36', 'python3', 'python3-minimal', 'python3.11', 'python3.11-minimal', 'readline-common'] 0m41.6s DUMP: 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 ... 5422 files and directories currently installed.) Purging configuration files for libgssapi-krb5-2:amd64 (1.20.1-2) ... 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 libperl5.36 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.11-minimal:amd64 (3.11.4-1) ... 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 dpkg: warning: ignoring request to remove libssl3 which isn't installed Purging configuration files for libtirpc-common (1.3.3+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 perl (5.36.0-7) ... dpkg: warning: ignoring request to remove perl-modules-5.36 which isn't installed Purging configuration files for python3 (3.11.4-5) ... 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 (3.11.4-1) ... Purging configuration files for readline-common (8.2-1.3) ... 0m41.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'dpkg', '--purge', 'libexpat1:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgssapi-krb5-2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libperl5.36:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libssl3:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'media-types', 'perl', 'perl-modules-5.36', 'python3', 'python3-minimal', 'python3.11', 'python3.11-minimal', 'readline-common'] 0m41.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'dpkg', '--purge', 'hisat2'] 0m41.6s DUMP: dpkg: warning: ignoring request to remove hisat2 which isn't installed 0m41.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'dpkg', '--purge', 'hisat2'] 0m41.6s INFO: Running scripts post_purge 0m41.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/post_purge_exceptions'] 0m41.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/post_purge_exceptions'] 0m41.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'dpkg', '--purge', '--pending'] 0m41.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'dpkg', '--purge', '--pending'] 0m41.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'dpkg', '--remove', '--pending'] 0m41.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'dpkg', '--remove', '--pending'] 0m41.7s INFO: Running scripts post_test 0m41.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/post_test_exceptions'] 0m41.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'tmp/scripts/post_test_exceptions'] 0m41.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgthoocvq'] 0m42.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgthoocvq'] 0m42.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'dpkg-divert', '--list'] 0m42.1s DUMP: local diversion of /bin/sync to /bin/sync.distrib local diversion of /home to /home.distrib 0m42.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'dpkg-divert', '--list'] 0m42.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'apt-get', 'clean'] 0m42.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgthoocvq', 'apt-get', 'clean'] 0m42.1s DEBUG: Recording chroot state 0m43.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpgthoocvq/dev/shm'] 0m43.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpgthoocvq/dev/shm'] 0m43.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpgthoocvq/dev/console'] 0m43.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpgthoocvq/dev/console'] 0m43.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpgthoocvq/dev/ptmx'] 0m43.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpgthoocvq/dev/ptmx'] 0m43.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpgthoocvq/dev/pts'] 0m43.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpgthoocvq/dev/pts'] 0m43.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpgthoocvq/proc'] 0m43.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpgthoocvq/proc'] 0m43.4s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpgthoocvq'] 0m43.6s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpgthoocvq'] 0m43.6s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpgthoocvq 0m43.6s INFO: PASS: Upgrading between Debian distributions. 0m43.6s INFO: PASS: All tests. 0m43.6s INFO: piuparts run ends. ret=0 End: 2023-08-05 21:46:37 GMT