Start: 2024-02-01 22:22:00 GMT [stable] Package: iva Version: 1.0.9+ds-11 Installed-Size: 8765 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: fastaq (>= 1.6), python3-networkx, python3-pysam, python3:any, perl:any, kmc, mummer, smalt, samtools, python3-numpy, default-jre-headless Recommends: r-base-core, bioperl, trimmomatic Description: iterative virus sequence assembler Homepage: https://github.com/sanger-pathogens/iva Description-md5: 698e26411c0dbe5917f816e7b7229be9 Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::python, interface::commandline, role::program, works-with::biological-sequence, works-with::file Section: science Priority: optional Filename: pool/main/i/iva/iva_1.0.9+ds-11_amd64.deb Size: 8578708 MD5sum: 513e2e9c47ca6d1804645c4851efa742 SHA256: 2334df55b94c72173f454c5f4c9c2c87996342ee787ad7f556fc5bbf6ee18b51 [sid] Package: iva Version: 1.0.11+ds-5 Installed-Size: 8770 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: fastaq, python3-networkx, python3-packaging, python3-pysam, python3:any, perl:any, kmc, mummer, smalt, samtools, python3-numpy, default-jre-headless Recommends: r-base-core, bioperl, trimmomatic Description: iterative virus sequence assembler Homepage: https://github.com/sanger-pathogens/iva Description-md5: 698e26411c0dbe5917f816e7b7229be9 Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::python, interface::commandline, role::program, works-with::biological-sequence, works-with::file Section: science Priority: optional Filename: pool/main/i/iva/iva_1.0.11+ds-5_amd64.deb Size: 8581624 MD5sum: 81641314ba9e9e3b5e100a7443802397 SHA256: 07f3c24da91e13d1b175ddb6db6f913e23b26a8f954f47a678ed9ed4b7aa60ef 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/bullseye-merged-usr_amd64.tar.gz -d stable -d sid -B /srv/piuparts.debian.org/slave/refchroot/stable2sid/reference-chroot-metadata.dat --apt iva=1.0.11+ds-5 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 1.3.1~202401311821~1.3-2-g28295102 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/bullseye-merged-usr_amd64.tar.gz -d stable -d sid -B /srv/piuparts.debian.org/slave/refchroot/stable2sid/reference-chroot-metadata.dat --apt iva=1.0.11+ds-5 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/tmpncbapv2j 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpncbapv2j 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m2.1s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m2.1s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpncbapv2j/proc'] 0m2.1s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpncbapv2j/proc'] 0m2.1s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpncbapv2j/dev/pts'] 0m2.1s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpncbapv2j/dev/pts'] 0m2.1s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpncbapv2j/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpncbapv2j/dev/ptmx'] 0m2.1s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpncbapv2j/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpncbapv2j/dev/ptmx'] 0m2.1s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmpncbapv2j/dev/console'] 0m2.1s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmpncbapv2j/dev/console'] 0m2.1s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpncbapv2j/dev/shm'] 0m2.1s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpncbapv2j/dev/shm'] 0m2.1s DEBUG: sources.list: deb http://deb.debian.org/debian/ bullseye main 0m2.2s DEBUG: Created policy-rc.d and chmodded it. 0m2.2s DEBUG: Created resolv.conf. 0m2.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpncbapv2j/tmp/scripts/ 0m2.2s INFO: Running scripts post_chroot_unpack 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'apt-get', 'update'] 0m3.2s DUMP: Hit:1 http://deb.debian.org/debian bullseye InRelease Reading package lists... 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'apt-get', 'update'] 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'apt-get', '-yf', 'dist-upgrade'] 0m3.6s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'apt-get', '-yf', 'dist-upgrade'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.0s DUMP: cd994be14815166bf41ad7cebd6f56fc - 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.0s INFO: Running scripts post_setup 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/post_setup_dummy_users'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/post_setup_dummy_users'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/post_setup_forbid_home'] 0m4.9s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/post_setup_forbid_home'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.0s 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' 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/post_setup_minimize'] 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/post_setup_minimize'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/post_setup_zz_backports'] 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/post_setup_zz_backports'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.0s DUMP: install ok installed adduser adduser 3.118+deb11u1 install ok installed apt apt 2.2.4 install ok installed base-files base-files 11.1+deb11u8 install ok installed base-passwd base-passwd 3.5.51 install ok installed bash bash 5.1-2+deb11u1 install ok installed bsdutils bsdutils 1:2.36.1-8+deb11u1 install ok installed coreutils coreutils 8.32-4+b1 install ok installed dash dash 0.5.11+git20200708+dd9ef66-5 install ok installed debconf debconf 1.5.77 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1+deb11u1 install ok installed debianutils debianutils 4.11.2 install ok installed diffutils diffutils 1:3.7-5 install ok installed dpkg dpkg 1.20.13 install ok installed e2fsprogs e2fsprogs 1.46.2-2 install ok installed findutils findutils 4.8.0-1 install ok installed gcc-10-base:amd64 gcc-10-base 10.2.1-6 install ok installed gcc-9-base:amd64 gcc-9-base 9.3.0-22 install ok installed gpgv gpgv 2.2.27-2+deb11u2 install ok installed grep grep 3.6-1+deb11u1 install ok installed gzip gzip 1.10-4+deb11u1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.60 install ok installed libacl1:amd64 libacl1 2.2.53-10 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.2.4 install ok installed libattr1:amd64 libattr1 1:2.4.48-6 install ok installed libaudit-common libaudit-common 1:3.0-2 install ok installed libaudit1:amd64 libaudit1 1:3.0-2 install ok installed libblkid1:amd64 libblkid1 2.36.1-8+deb11u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4 install ok installed libc-bin libc-bin 2.31-13+deb11u6 install ok installed libc6:amd64 libc6 2.31-13+deb11u6 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2+b1 install ok installed libcom-err2:amd64 libcom-err2 1.46.2-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.18-4 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.8 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.260 install ok installed libext2fs2:amd64 libext2fs2 1.46.2-2 install ok installed libffi7:amd64 libffi7 3.3-6 install ok installed libgcc-s1:amd64 libgcc-s1 10.2.1-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.7-6 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg-1+deb11u1 install ok installed libgnutls30:amd64 libgnutls30 3.7.1-5+deb11u3 install ok installed libgpg-error0:amd64 libgpg-error0 1.38-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.18.3-6+deb11u4 install ok installed libhogweed6:amd64 libhogweed6 3.7.3-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.0-5 install ok installed libk5crypto3:amd64 libk5crypto3 1.18.3-6+deb11u4 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.18.3-6+deb11u4 install ok installed libkrb5support0:amd64 libkrb5support0 1.18.3-6+deb11u4 install ok installed liblz4-1:amd64 liblz4-1 1.9.3-2 install ok installed liblzma5:amd64 liblzma5 5.2.5-2.1~deb11u1 install ok installed libmount1:amd64 libmount1 2.36.1-8+deb11u1 install ok installed libnettle8:amd64 libnettle8 3.7.3-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.22-1 install ok installed libpam-modules:amd64 libpam-modules 1.4.0-9+deb11u1 install ok installed libpam-modules-bin libpam-modules-bin 1.4.0-9+deb11u1 install ok installed libpam-runtime libpam-runtime 1.4.0-9+deb11u1 install ok installed libpam0g:amd64 libpam0g 1.4.0-9+deb11u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.36-2+deb11u1 install ok installed libpcre3:amd64 libpcre3 2:8.39-13 install ok installed libseccomp2:amd64 libseccomp2 2.5.1-1+deb11u1 install ok installed libselinux1:amd64 libselinux1 3.1-3 install ok installed libsemanage-common libsemanage-common 3.1-1 install ok installed libsemanage1:amd64 libsemanage1 3.1-1+b2 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.36.1-8+deb11u1 install ok installed libss2:amd64 libss2 1.46.2-2 install ok installed libssl1.1:amd64 libssl1.1 1.1.1w-0+deb11u1 install ok installed libstdc++6:amd64 libstdc++6 10.2.1-6 install ok installed libsystemd0:amd64 libsystemd0 247.3-7+deb11u4 install ok installed libtasn1-6:amd64 libtasn1-6 4.16.0-2+deb11u1 install ok installed libtinfo6:amd64 libtinfo6 6.2+20201114-2+deb11u2 install ok installed libtirpc-common libtirpc-common 1.3.1-1+deb11u1 install ok installed libtirpc3:amd64 libtirpc3 1.3.1-1+deb11u1 install ok installed libudev1:amd64 libudev1 247.3-7+deb11u4 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed libuuid1:amd64 libuuid1 2.36.1-8+deb11u1 install ok installed libxxhash0:amd64 libxxhash0 0.8.0-2 install ok installed libzstd1:amd64 libzstd1 1.4.8+dfsg-2.1 install ok installed login login 1:4.8.1-1 install ok installed logsave logsave 1.46.2-2 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.4.20200120-2 install ok installed mount mount 2.36.1-8+deb11u1 install ok installed ncurses-base ncurses-base 6.2+20201114-2+deb11u2 install ok installed ncurses-bin ncurses-bin 6.2+20201114-2+deb11u2 install ok installed passwd passwd 1:4.8.1-1 install ok installed perl-base perl-base 5.32.1-4+deb11u2 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.96-7+deb11u1 install ok installed tar tar 1.34+dfsg-1 install ok installed tzdata tzdata 2021a-1+deb11u10 install ok installed util-linux util-linux 2.36.1-8+deb11u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2+deb11u2 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.0s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/stable2sid/reference-chroot-metadata.dat 0m5.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpncbapv2j'] 0m5.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpncbapv2j'] 0m5.5s INFO: Running scripts is_testable 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/is_testable_uninstallable'] 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/is_testable_uninstallable'] 0m5.5s INFO: Running scripts pre_test 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_test_exceptions'] 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_test_exceptions'] 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_test_root_password'] 0m5.6s DUMP: New password: Retype new password: passwd: password updated successfully 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_test_root_password'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'apt-cache', 'show', '--no-all-versions', 'iva'] 0m5.8s DUMP: Package: iva Version: 1.0.9+ds-11 Installed-Size: 8765 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: fastaq (>= 1.6), python3-networkx, python3-pysam, python3:any, perl:any, kmc, mummer, smalt, samtools, python3-numpy, default-jre-headless Recommends: r-base-core, bioperl, trimmomatic Description-en: iterative virus sequence assembler IVA is a de novo assembler designed to assemble virus genomes that have no repeat sequences, using Illumina read pairs sequenced from mixed populations at extremely high depth. . IVA's main algorithm works by iteratively extending contigs using aligned read pairs. Its input can be just read pairs, or additionally you can provide an existing set of contigs to be extended. Alternatively, it can take reads together with a reference sequence. Description-md5: 698e26411c0dbe5917f816e7b7229be9 Homepage: https://github.com/sanger-pathogens/iva Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::python, interface::commandline, role::program, works-with::biological-sequence, works-with::file Section: science Priority: optional Filename: pool/main/i/iva/iva_1.0.9+ds-11_amd64.deb Size: 8578708 MD5sum: 513e2e9c47ca6d1804645c4851efa742 SHA256: 2334df55b94c72173f454c5f4c9c2c87996342ee787ad7f556fc5bbf6ee18b51 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'apt-cache', 'show', '--no-all-versions', 'iva'] 0m5.8s INFO: apt-cache knows about the following packages: iva 0m5.8s INFO: Running scripts pre_install 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_install_database-server'] 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_install_database-server'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_install_exceptions'] 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_install_exceptions'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_install_extras'] 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_install_extras'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'apt-cache', 'policy'] 0m5.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.8,o=Debian,a=oldstable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'apt-cache', 'policy'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'apt-cache', 'policy', 'iva'] 0m5.9s DUMP: iva: Installed: (none) Candidate: 1.0.9+ds-11 Version table: 1.0.9+ds-11 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 0m5.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'apt-cache', 'policy', 'iva'] 0m5.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'apt-get', '-y', 'install', 'iva'] 0m29.7s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: ca-certificates ca-certificates-java default-jre-headless fastaq fontconfig-config fonts-dejavu-core gawk java-common kmc libasound2 libasound2-data libavahi-client3 libavahi-common-data libavahi-common3 libbambamc0 libblas3 libbrotli1 libcups2 libcurl3-gnutls libdbus-1-3 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libgdbm-compat4 libgdbm6 libgfortran5 libglib2.0-0 libgraphite2-3 libharfbuzz0b libhts3 libjpeg62-turbo liblapack3 liblcms2-2 libldap-2.4-2 libmpdec3 libmpfr6 libncurses6 libncursesw6 libnghttp2-14 libnspr4 libnss3 libpcsclite1 libperl5.32 libpng16-16 libpsl5 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libquadmath0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsqlite3-0 libssh2-1 media-types mummer openjdk-11-jre-headless openssl perl perl-modules-5.32 python3 python3-decorator python3-minimal python3-networkx python3-numpy python3-pkg-resources python3-pysam python3.9 python3.9-minimal readline-common samtools sensible-utils smalt ucf Suggested packages: default-jre gawk-doc libasound2-plugins alsa-utils cups-common gdbm-l10n liblcms2-utils pcscd libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl python3-doc python3-tk python3-venv python-networkx-doc gcc gfortran python-numpy-doc python3-dev python3-numpy-dbg python3-pytest python3-setuptools python3.9-venv python3.9-doc binutils binfmt-support readline-doc cwltool Recommended packages: r-base-core bioperl trimmomatic alsa-ucm-conf alsa-topology-conf dbus libglib2.0-data shared-mime-info xdg-user-dirs libldap-common libgpm2 publicsuffix libsasl2-modules netbase python3-gdal python3-matplotlib python3-pydot python3-pygraphviz python3-scipy python3-yaml The following NEW packages will be installed: ca-certificates ca-certificates-java default-jre-headless fastaq fontconfig-config fonts-dejavu-core gawk iva java-common kmc libasound2 libasound2-data libavahi-client3 libavahi-common-data libavahi-common3 libbambamc0 libblas3 libbrotli1 libcups2 libcurl3-gnutls libdbus-1-3 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libgdbm-compat4 libgdbm6 libgfortran5 libglib2.0-0 libgraphite2-3 libharfbuzz0b libhts3 libjpeg62-turbo liblapack3 liblcms2-2 libldap-2.4-2 libmpdec3 libmpfr6 libncurses6 libncursesw6 libnghttp2-14 libnspr4 libnss3 libpcsclite1 libperl5.32 libpng16-16 libpsl5 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libquadmath0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsqlite3-0 libssh2-1 media-types mummer openjdk-11-jre-headless openssl perl perl-modules-5.32 python3 python3-decorator python3-minimal python3-networkx python3-numpy python3-pkg-resources python3-pysam python3.9 python3.9-minimal readline-common samtools sensible-utils smalt ucf 0 upgraded, 78 newly installed, 0 to remove and 0 not upgraded. Need to get 85.4 MB of archives. After this operation, 335 MB of additional disk space will be used. 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amd64 3.9.2-1 [801 kB] Get:12 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2+deb11u5 [98.2 kB] Get:13 http://deb.debian.org/debian bullseye/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB] Get:14 http://deb.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get:15 http://deb.debian.org/debian bullseye/main amd64 media-types all 4.0.0 [30.3 kB] Get:16 http://deb.debian.org/debian bullseye/main amd64 libmpdec3 amd64 2.5.1-1 [87.7 kB] Get:17 http://deb.debian.org/debian bullseye/main amd64 libncursesw6 amd64 6.2+20201114-2+deb11u2 [132 kB] Get:18 http://deb.debian.org/debian bullseye/main amd64 libsqlite3-0 amd64 3.34.1-3 [797 kB] Get:19 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB] Get:20 http://deb.debian.org/debian bullseye/main amd64 python3.9 amd64 3.9.2-1 [466 kB] Get:21 http://deb.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get:22 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http://deb.debian.org/debian bullseye/main amd64 libncurses6 amd64 6.2+20201114-2+deb11u2 [102 kB] Get:64 http://deb.debian.org/debian bullseye/main amd64 samtools amd64 1.11-1 [545 kB] Get:65 http://deb.debian.org/debian bullseye/main amd64 fastaq all 3.17.0-3 [47.8 kB] Get:66 http://deb.debian.org/debian bullseye/main amd64 python3-decorator all 4.4.2-2 [15.8 kB] Get:67 http://deb.debian.org/debian bullseye/main amd64 python3-networkx all 2.5+ds-2 [900 kB] Get:68 http://deb.debian.org/debian bullseye/main amd64 python3-pysam amd64 0.15.4+ds-3+b2 [1536 kB] Get:69 http://deb.debian.org/debian bullseye/main amd64 kmc amd64 3.1.1+dfsg-3+b2 [882 kB] Get:70 http://deb.debian.org/debian bullseye/main amd64 mummer amd64 3.23+dfsg-7 [664 kB] Get:71 http://deb.debian.org/debian bullseye/main amd64 libbambamc0 amd64 0.0.50-4 [37.3 kB] Get:72 http://deb.debian.org/debian bullseye/main amd64 smalt amd64 0.7.6-9 [113 kB] Get:73 http://deb.debian.org/debian bullseye/main amd64 libblas3 amd64 3.9.0-3+deb11u1 [153 kB] Get:74 http://deb.debian.org/debian bullseye/main amd64 libquadmath0 amd64 10.2.1-6 [145 kB] Get:75 http://deb.debian.org/debian bullseye/main amd64 libgfortran5 amd64 10.2.1-6 [727 kB] Get:76 http://deb.debian.org/debian bullseye/main amd64 liblapack3 amd64 3.9.0-3+deb11u1 [2166 kB] Get:77 http://deb.debian.org/debian bullseye/main amd64 python3-numpy amd64 1:1.19.5-1 [2693 kB] Get:78 http://deb.debian.org/debian bullseye/main amd64 iva amd64 1.0.9+ds-11 [8579 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 85.4 MB in 1s (114 MB/s) Selecting previously unselected package perl-modules-5.32. (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 ... 6666 files and directories currently installed.) Preparing to unpack .../0-perl-modules-5.32_5.32.1-4+deb11u2_all.deb ... Unpacking perl-modules-5.32 (5.32.1-4+deb11u2) ... Selecting previously unselected package libgdbm6:amd64. Preparing to unpack .../1-libgdbm6_1.19-2_amd64.deb ... Unpacking libgdbm6:amd64 (1.19-2) ... Selecting previously unselected package libgdbm-compat4:amd64. 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9564 files and directories currently installed.) Preparing to unpack .../00-python3_3.9.2-3_amd64.deb ... Unpacking python3 (3.9.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../01-sensible-utils_0.0.14_all.deb ... Unpacking sensible-utils (0.0.14) ... Selecting previously unselected package openssl. Preparing to unpack .../02-openssl_1.1.1w-0+deb11u1_amd64.deb ... Unpacking openssl (1.1.1w-0+deb11u1) ... 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Unpacking libdbus-1-3:amd64 (1.12.28-0+deb11u1) ... Selecting previously unselected package libavahi-client3:amd64. Preparing to unpack .../09-libavahi-client3_0.8-5+deb11u2_amd64.deb ... Unpacking libavahi-client3:amd64 (0.8-5+deb11u2) ... Selecting previously unselected package libcups2:amd64. Preparing to unpack .../10-libcups2_2.3.3op2-3+deb11u6_amd64.deb ... Unpacking libcups2:amd64 (2.3.3op2-3+deb11u6) ... Selecting previously unselected package liblcms2-2:amd64. Preparing to unpack .../11-liblcms2-2_2.12~rc1-2_amd64.deb ... Unpacking liblcms2-2:amd64 (2.12~rc1-2) ... Selecting previously unselected package libjpeg62-turbo:amd64. Preparing to unpack .../12-libjpeg62-turbo_1%3a2.0.6-4_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:2.0.6-4) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../13-libbrotli1_1.0.9-2+b2_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2+b2) ... Selecting previously unselected package libpng16-16:amd64. Preparing to unpack .../14-libpng16-16_1.6.37-3_amd64.deb ... Unpacking libpng16-16:amd64 (1.6.37-3) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../15-libfreetype6_2.10.4+dfsg-1+deb11u1_amd64.deb ... Unpacking libfreetype6:amd64 (2.10.4+dfsg-1+deb11u1) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../16-fonts-dejavu-core_2.37-2_all.deb ... Unpacking fonts-dejavu-core (2.37-2) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../17-fontconfig-config_2.13.1-4.2_all.deb ... Unpacking fontconfig-config (2.13.1-4.2) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../18-libfontconfig1_2.13.1-4.2_amd64.deb ... Unpacking libfontconfig1:amd64 (2.13.1-4.2) ... Selecting previously unselected package libnspr4:amd64. Preparing to unpack .../19-libnspr4_2%3a4.29-1_amd64.deb ... Unpacking libnspr4:amd64 (2:4.29-1) ... 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Unpacking libharfbuzz0b:amd64 (2.7.4-1) ... Selecting previously unselected package libpcsclite1:amd64. Preparing to unpack .../26-libpcsclite1_1.9.1-1_amd64.deb ... Unpacking libpcsclite1:amd64 (1.9.1-1) ... Selecting previously unselected package openjdk-11-jre-headless:amd64. Preparing to unpack .../27-openjdk-11-jre-headless_11.0.20+8-1~deb11u1_amd64.deb ... Unpacking openjdk-11-jre-headless:amd64 (11.0.20+8-1~deb11u1) ... Selecting previously unselected package default-jre-headless. Preparing to unpack .../28-default-jre-headless_2%3a1.11-72_amd64.deb ... Unpacking default-jre-headless (2:1.11-72) ... Selecting previously unselected package ca-certificates-java. Preparing to unpack .../29-ca-certificates-java_20190909+deb11u1_all.deb ... Unpacking ca-certificates-java (20190909+deb11u1) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../30-python3-pkg-resources_52.0.0-4_all.deb ... Unpacking python3-pkg-resources (52.0.0-4) ... 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Preparing to unpack .../54-liblapack3_3.9.0-3+deb11u1_amd64.deb ... Unpacking liblapack3:amd64 (3.9.0-3+deb11u1) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../55-python3-numpy_1%3a1.19.5-1_amd64.deb ... Unpacking python3-numpy (1:1.19.5-1) ... Selecting previously unselected package iva. Preparing to unpack .../56-iva_1.0.9+ds-11_amd64.deb ... Unpacking iva (1.0.9+ds-11) ... Setting up media-types (4.0.0) ... Setting up libgraphite2-3:amd64 (1.3.14-1) ... Setting up liblcms2-2:amd64 (2.12~rc1-2) ... Setting up libpsl5:amd64 (0.21.0-1.2) ... Setting up java-common (0.72) ... Setting up gawk (1:5.1.0-1) ... Setting up libglib2.0-0:amd64 (2.66.8-1) ... No schema files found: doing nothing. Setting up perl-modules-5.32 (5.32.1-4+deb11u2) ... Setting up libbrotli1:amd64 (1.0.9-2+b2) ... Setting up libsqlite3-0:amd64 (3.34.1-3) ... Setting up libnghttp2-14:amd64 (1.43.0-1) ... Setting up libdeflate0:amd64 (1.7-1) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Setting up libasound2-data (1.2.4-1.1) ... Setting up libblas3:amd64 (3.9.0-3+deb11u1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libjpeg62-turbo:amd64 (1:2.0.6-4) ... Setting up libnspr4:amd64 (2:4.29-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libavahi-common-data:amd64 (0.8-5+deb11u2) ... Setting up libncurses6:amd64 (6.2+20201114-2+deb11u2) ... Setting up libdbus-1-3:amd64 (1.12.28-0+deb11u1) ... Setting up libquadmath0:amd64 (10.2.1-6) ... Setting up libbambamc0 (0.0.50-4) ... Setting up libpng16-16:amd64 (1.6.37-3) ... Setting up fonts-dejavu-core (2.37-2) ... Setting up libpcsclite1:amd64 (1.9.1-1) ... Setting up libncursesw6:amd64 (6.2+20201114-2+deb11u2) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Setting up libgfortran5:amd64 (10.2.1-6) ... Setting up sensible-utils (0.0.14) ... Setting up libasound2:amd64 (1.2.4-1.1) ... Setting up libmpdec3:amd64 (2.5.1-1) ... Setting up libssh2-1:amd64 (1.9.0-2) ... Setting up openssl (1.1.1w-0+deb11u1) ... Setting up kmc (3.1.1+dfsg-3+b2) ... Setting up libpython3.9-stdlib:amd64 (3.9.2-1) ... Setting up libpython3-stdlib:amd64 (3.9.2-3) ... Setting up libgdbm6:amd64 (1.19-2) ... Setting up smalt (0.7.6-9) ... Setting up liblapack3:amd64 (3.9.0-3+deb11u1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libavahi-common3:amd64 (0.8-5+deb11u2) ... Setting up libldap-2.4-2:amd64 (2.4.57+dfsg-3+deb11u1) ... Setting up libcurl3-gnutls:amd64 (7.74.0-1.3+deb11u9) ... Setting up libnss3:amd64 (2:3.61-1+deb11u3) ... Setting up ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 129 added, 0 removed; done. Setting up libfreetype6:amd64 (2.10.4+dfsg-1+deb11u1) ... Setting up libgdbm-compat4:amd64 (1.19-2) ... Setting up ucf (3.0043) ... Setting up libperl5.32:amd64 (5.32.1-4+deb11u2) ... Setting up libharfbuzz0b:amd64 (2.7.4-1) ... Setting up libavahi-client3:amd64 (0.8-5+deb11u2) ... Setting up python3.9 (3.9.2-1) ... Setting up libhts3:amd64 (1.11-4) ... Setting up fontconfig-config (2.13.1-4.2) ... Setting up python3 (3.9.2-3) ... Setting up samtools (1.11-1) ... Setting up python3-decorator (4.4.2-2) ... Setting up perl (5.32.1-4+deb11u2) ... Setting up libcups2:amd64 (2.3.3op2-3+deb11u6) ... Setting up mummer (3.23+dfsg-7) ... Setting up libfontconfig1:amd64 (2.13.1-4.2) ... Setting up python3-pkg-resources (52.0.0-4) ... Setting up python3-pysam (0.15.4+ds-3+b2) ... Setting up fastaq (3.17.0-3) ... Setting up python3-networkx (2.5+ds-2) ... Setting up python3-numpy (1:1.19.5-1) ... Setting up openjdk-11-jre-headless:amd64 (11.0.20+8-1~deb11u1) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up ca-certificates-java (20190909+deb11u1) ... head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory Adding debian:emSign_Root_CA_-_G1.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustis_FPS_Root_CA.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:TrustCor_ECA-1.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem Adding debian:Sonera_Class_2_Root_CA.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Secure_Global_CA.pem Adding debian:SecureTrust_CA.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Izenpe.com.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:ISRG_Root_X1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:GTS_Root_R4.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R1.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:EC-ACC.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DST_Root_CA_X3.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certigna.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:ACCVRAIZ1.pem done. Setting up default-jre-headless (2:1.11-72) ... Setting up iva (1.0.9+ds-11) ... Processing triggers for libc-bin (2.31-13+deb11u6) ... Processing triggers for ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. done. 0m29.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'apt-get', '-y', 'install', 'iva'] 0m29.7s INFO: Running scripts post_install 0m29.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/post_install_exceptions'] 0m29.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/post_install_exceptions'] 0m29.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpncbapv2j'] 0m30.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpncbapv2j'] 0m30.6s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpncbapv2j to sid 0m30.6s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m30.6s INFO: Running scripts pre_distupgrade 0m30.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m30.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m30.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_distupgrade_exceptions'] 0m30.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_distupgrade_exceptions'] 0m30.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m30.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m30.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m30.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m30.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m30.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m30.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'apt-get', 'update'] 0m34.8s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [198 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9711 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7130 kB] Fetched 17.0 MB in 3s (5099 kB/s) Reading package lists... 0m34.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'apt-get', 'update'] 0m34.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'apt-get', '-yf', 'dist-upgrade'] 1m25.0s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libldap-2.4-2 libmpdec3 libperl5.32 libpython3.9-minimal libpython3.9-stdlib libquadmath0 openjdk-11-jre-headless perl-modules-5.32 python3-decorator python3.9 python3.9-minimal ucf Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libsemanage1 The following NEW packages will be installed: fonts-dejavu-mono gcc-14-base libcap2 libffi8 libfile-find-rule-perl libhtscodecs2 libldap-2.5-0 libmd0 libnumber-compare-perl libperl5.38 libpython3.11-minimal libpython3.11-stdlib libpython3.12-minimal libpython3.12-stdlib libsemanage2 libsepol2 libssl3 libtext-glob-perl libunistring5 netbase openjdk-17-jre-headless perl-modules-5.38 python3-packaging python3.11 python3.11-minimal python3.12 python3.12-minimal usrmerge The following packages will be upgraded: adduser apt base-files base-passwd bash bsdutils ca-certificates ca-certificates-java coreutils dash debconf debian-archive-keyring debianutils default-jre-headless diffutils dpkg e2fsprogs fastaq findutils fontconfig-config fonts-dejavu-core gawk gcc-10-base gcc-9-base gpgv grep gzip hostname init-system-helpers iva java-common kmc libacl1 libapt-pkg6.0 libasound2 libasound2-data libattr1 libaudit-common libaudit1 libavahi-client3 libavahi-common-data libavahi-common3 libbambamc0 libblas3 libblkid1 libbrotli1 libbz2-1.0 libc-bin libc6 libcap-ng0 libcom-err2 libcrypt1 libcups2 libcurl3-gnutls libdb5.3 libdbus-1-3 libdebconfclient0 libdeflate0 libexpat1 libext2fs2 libfontconfig1 libfreetype6 libgcc-s1 libgcrypt20 libgdbm-compat4 libgdbm6 libgfortran5 libglib2.0-0 libgmp10 libgnutls30 libgpg-error0 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhogweed6 libhts3 libidn2-0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 liblz4-1 liblzma5 libmount1 libmpdec3 libmpfr6 libncurses6 libncursesw6 libnettle8 libnghttp2-14 libnsl2 libnspr4 libnss3 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libpcre3 libpcsclite1 libpng16-16 libpsl5 libpython3-stdlib libquadmath0 libreadline8 libsasl2-2 libsasl2-modules-db libseccomp2 libselinux1 libsemanage-common libsigsegv2 libsmartcols1 libsqlite3-0 libss2 libssh2-1 libstdc++6 libsystemd0 libtasn1-6 libtinfo6 libtirpc-common libtirpc3 libudev1 libuuid1 libxxhash0 libzstd1 login logsave lsb-base mawk media-types mount mummer ncurses-base ncurses-bin openjdk-11-jre-headless openssl passwd perl perl-base python3 python3-decorator python3-minimal python3-networkx python3-numpy python3-pkg-resources python3-pysam readline-common samtools sed sensible-utils smalt sysvinit-utils tar tzdata ucf util-linux zlib1g 161 upgraded, 28 newly installed, 1 to remove and 0 not upgraded. Need to get 178 MB of archives. After this operation, 363 MB 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 libc6 amd64 2.37-15 [2750 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libc-bin amd64 2.37-15 [602 kB] Get:4 http://deb.debian.org/debian sid/main amd64 gcc-14-base amd64 14-20240201-1 [42.3 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 14-20240201-1 [71.6 kB] Get:6 http://deb.debian.org/debian sid/main amd64 debianutils amd64 5.16 [88.9 kB] Get:7 http://deb.debian.org/debian sid/main amd64 bash amd64 5.2.21-2 [1492 kB] Get:8 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.39.3-6 [96.9 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libgmp10 amd64 2:6.3.0+dfsg-2 [557 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libssl3 amd64 3.1.4-2 [2058 kB] Get:11 http://deb.debian.org/debian sid/main amd64 coreutils amd64 9.4-3+b1 [2950 kB] Get:12 http://deb.debian.org/debian sid/main amd64 liblzma5 amd64 5.4.5-0.3 [240 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libmd0 amd64 1.1.0-2 [35.8 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libzstd1 amd64 1.5.5+dfsg2-2 [295 kB] Get:15 http://deb.debian.org/debian sid/main amd64 tar amd64 1.35+dfsg-3 [813 kB] Get:16 http://deb.debian.org/debian sid/main amd64 dpkg amd64 1.22.4 [1509 kB] Get:17 http://deb.debian.org/debian sid/main amd64 dash amd64 0.5.12-6 [92.1 kB] Get:18 http://deb.debian.org/debian sid/main amd64 diffutils amd64 1:3.10-1 [375 kB] Get:19 http://deb.debian.org/debian sid/main amd64 findutils amd64 4.9.0-5 [636 kB] Get:20 http://deb.debian.org/debian sid/main amd64 grep amd64 3.11-4 [431 kB] Get:21 http://deb.debian.org/debian sid/main amd64 gzip amd64 1.12-1 [140 kB] Get:22 http://deb.debian.org/debian sid/main amd64 hostname amd64 3.23+nmu2 [10.6 kB] Get:23 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.13+dfsg1-3+b1 [616 kB] Get:24 http://deb.debian.org/debian sid/main amd64 libncurses6 amd64 6.4+20240113-1 [104 kB] Get:25 http://deb.debian.org/debian sid/main amd64 libncursesw6 amd64 6.4+20240113-1 [135 kB] Get:26 http://deb.debian.org/debian sid/main amd64 libtinfo6 amd64 6.4+20240113-1 [342 kB] Get:27 http://deb.debian.org/debian sid/main amd64 ncurses-bin amd64 6.4+20240113-1 [431 kB] Get:28 http://deb.debian.org/debian sid/main amd64 perl-modules-5.38 all 5.38.2-3 [2899 kB] Get:29 http://deb.debian.org/debian sid/main amd64 libgdbm6 amd64 1.23-5 [72.5 kB] Get:30 http://deb.debian.org/debian sid/main amd64 libperl5.38 amd64 5.38.2-3 [4275 kB] Get:31 http://deb.debian.org/debian sid/main amd64 perl amd64 5.38.2-3 [236 kB] Get:32 http://deb.debian.org/debian sid/main amd64 perl-base amd64 5.38.2-3 [1643 kB] Get:33 http://deb.debian.org/debian sid/main amd64 libbz2-1.0 amd64 1.0.8-5+b2 [38.2 kB] Get:34 http://deb.debian.org/debian sid/main amd64 libaudit-common all 1:3.1.2-2 [11.3 kB] Get:35 http://deb.debian.org/debian sid/main amd64 libcap-ng0 amd64 0.8.4-1 [16.9 kB] Get:36 http://deb.debian.org/debian sid/main amd64 libaudit1 amd64 1:3.1.2-2 [48.4 kB] Get:37 http://deb.debian.org/debian sid/main amd64 debconf all 1.5.85 [119 kB] Get:38 http://deb.debian.org/debian sid/main amd64 libpam0g amd64 1.5.2-9.1+b1 [65.8 kB] Get:39 http://deb.debian.org/debian sid/main amd64 libcrypt1 amd64 1:4.4.36-4 [89.8 kB] Get:40 http://deb.debian.org/debian sid/main amd64 libdb5.3 amd64 5.3.28+dfsg2-4+b1 [697 kB] Get:41 http://deb.debian.org/debian sid/main amd64 libgdbm-compat4 amd64 1.23-5 [48.3 kB] Get:42 http://deb.debian.org/debian sid/main amd64 zlib1g amd64 1:1.3.dfsg-3+b1 [87.8 kB] Get:43 http://deb.debian.org/debian sid/main amd64 sed amd64 4.9-2 [329 kB] Get:44 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.39.3-6 [159 kB] Get:45 http://deb.debian.org/debian sid/main amd64 libpcre2-8-0 amd64 10.42-4 [261 kB] Get:46 http://deb.debian.org/debian sid/main amd64 libselinux1 amd64 3.5-2 [74.8 kB] Get:47 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.39.3-6 [190 kB] Get:48 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.39.3-6 [117 kB] Get:49 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.39.3-6 [1230 kB] Get:50 http://deb.debian.org/debian sid/main amd64 libdebconfclient0 amd64 0.271 [9940 B] Get:51 http://deb.debian.org/debian sid/main amd64 base-passwd amd64 3.6.3 [50.8 kB] Get:52 http://deb.debian.org/debian sid/main amd64 libgpg-error0 amd64 1.47-3 [77.8 kB] Get:53 http://deb.debian.org/debian sid/main amd64 libgcrypt20 amd64 1.10.3-2 [708 kB] Get:54 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 14-20240201-1 [714 kB] Get:55 http://deb.debian.org/debian sid/main amd64 liblz4-1 amd64 1.9.4-1+b2 [61.6 kB] Get:56 http://deb.debian.org/debian sid/main amd64 libcap2 amd64 1:2.66-4+b2 [27.6 kB] Get:57 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 255.3-2 [362 kB] Get:58 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 255.3-2 [124 kB] Get:59 http://deb.debian.org/debian sid/main amd64 libxxhash0 amd64 0.8.2-2 [26.4 kB] Get:60 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0 amd64 2.7.10 [982 kB] Get:61 http://deb.debian.org/debian sid/main amd64 libnettle8 amd64 3.9.1-2 [295 kB] Get:62 http://deb.debian.org/debian sid/main amd64 libffi8 amd64 3.4.4-2 [23.5 kB] Get:63 http://deb.debian.org/debian sid/main amd64 libp11-kit0 amd64 0.25.3-4 [418 kB] Get:64 http://deb.debian.org/debian sid/main amd64 libunistring5 amd64 1.1-2 [421 kB] Get:65 http://deb.debian.org/debian sid/main amd64 libhogweed6 amd64 3.9.1-2 [327 kB] Get:66 http://deb.debian.org/debian sid/main amd64 libidn2-0 amd64 2.3.7-2 [128 kB] Get:67 http://deb.debian.org/debian sid/main amd64 libtasn1-6 amd64 4.19.0-3+b2 [48.9 kB] Get:68 http://deb.debian.org/debian sid/main amd64 libgnutls30 amd64 3.8.3-1 [1425 kB] Get:69 http://deb.debian.org/debian sid/main amd64 libsemanage-common all 3.5-1 [9908 B] Get:70 http://deb.debian.org/debian sid/main amd64 libsepol2 amd64 3.5-2 [277 kB] Get:71 http://deb.debian.org/debian sid/main amd64 libsemanage2 amd64 3.5-1+b2 [90.3 kB] Get:72 http://deb.debian.org/debian sid/main amd64 passwd amd64 1:4.13+dfsg1-3+b1 [973 kB] Get:73 http://deb.debian.org/debian sid/main amd64 libpam-modules-bin amd64 1.5.2-9.1+b1 [50.1 kB] Get:74 http://deb.debian.org/debian sid/main amd64 libpam-modules amd64 1.5.2-9.1+b1 [265 kB] Get:75 http://deb.debian.org/debian sid/main amd64 adduser all 3.137 [140 kB] Get:76 http://deb.debian.org/debian sid/main amd64 gpgv amd64 2.2.40-1.1+b1 [649 kB] Get:77 http://deb.debian.org/debian sid/main amd64 debian-archive-keyring all 2023.4 [161 kB] Get:78 http://deb.debian.org/debian sid/main amd64 libseccomp2 amd64 2.5.5-1 [47.0 kB] Get:79 http://deb.debian.org/debian sid/main amd64 apt amd64 2.7.10 [1363 kB] Get:80 http://deb.debian.org/debian sid/main amd64 libnumber-compare-perl all 0.03-3 [6332 B] Get:81 http://deb.debian.org/debian sid/main amd64 libtext-glob-perl all 0.11-3 [7676 B] Get:82 http://deb.debian.org/debian sid/main amd64 libfile-find-rule-perl all 0.34-3 [26.6 kB] Get:83 http://deb.debian.org/debian sid/main amd64 usrmerge all 39 [13.1 kB] Get:84 http://deb.debian.org/debian sid/main amd64 init-system-helpers all 1.66 [39.0 kB] Get:85 http://deb.debian.org/debian sid/main amd64 ncurses-base all 6.4+20240113-1 [268 kB] Get:86 http://deb.debian.org/debian sid/main amd64 sysvinit-utils amd64 3.08-6 [32.1 kB] Get:87 http://deb.debian.org/debian sid/main amd64 lsb-base all 11.6 [4584 B] Get:88 http://deb.debian.org/debian sid/main amd64 logsave amd64 1.47.0-2+b1 [19.9 kB] Get:89 http://deb.debian.org/debian sid/main amd64 libext2fs2 amd64 1.47.0-2+b1 [205 kB] Get:90 http://deb.debian.org/debian sid/main amd64 e2fsprogs amd64 1.47.0-2+b1 [572 kB] Get:91 http://deb.debian.org/debian sid/main amd64 mount amd64 2.39.3-6 [143 kB] Get:92 http://deb.debian.org/debian sid/main amd64 gawk amd64 1:5.2.1-2 [673 kB] Get:93 http://deb.debian.org/debian sid/main amd64 libpython3.11-minimal amd64 3.11.7-2 [816 kB] Get:94 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.5.0-2+b2 [99.4 kB] Get:95 http://deb.debian.org/debian sid/main amd64 python3.11-minimal amd64 3.11.7-2 [2035 kB] Get:96 http://deb.debian.org/debian sid/main amd64 samtools amd64 1.19-1 [644 kB] Get:97 http://deb.debian.org/debian sid/main amd64 libhts3 amd64 1.18+ds-1 [441 kB] Get:98 http://deb.debian.org/debian sid/main amd64 python3-pysam amd64 0.22.0+ds-1+b1 [4110 kB] Get:99 http://deb.debian.org/debian sid/main amd64 python3-numpy amd64 1:1.24.2-2 [6299 kB] Get:100 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.11.6-1 [26.2 kB] Get:101 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.11.6-1 [26.2 kB] Get:102 http://deb.debian.org/debian sid/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get:103 http://deb.debian.org/debian sid/main amd64 libgssapi-krb5-2 amd64 1.20.1-5 [135 kB] Get:104 http://deb.debian.org/debian sid/main amd64 libkrb5-3 amd64 1.20.1-5 [332 kB] Get:105 http://deb.debian.org/debian sid/main amd64 libk5crypto3 amd64 1.20.1-5 [79.6 kB] Get:106 http://deb.debian.org/debian sid/main amd64 libkrb5support0 amd64 1.20.1-5 [32.9 kB] Get:107 http://deb.debian.org/debian sid/main amd64 libcom-err2 amd64 1.47.0-2+b1 [20.1 kB] Get:108 http://deb.debian.org/debian sid/main amd64 libkeyutils1 amd64 1.6.3-2+b2 [9140 B] Get:109 http://deb.debian.org/debian sid/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-4+b1 [19.7 kB] Get:110 http://deb.debian.org/debian sid/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-4+b1 [57.0 kB] Get:111 http://deb.debian.org/debian sid/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5+b3 [184 kB] Get:112 http://deb.debian.org/debian sid/main amd64 libnghttp2-14 amd64 1.58.0-1 [74.1 kB] Get:113 http://deb.debian.org/debian sid/main amd64 libpsl5 amd64 0.21.2-1+b1 [59.1 kB] Get:114 http://deb.debian.org/debian sid/main amd64 libssh2-1 amd64 1.11.0-4 [215 kB] Get:115 http://deb.debian.org/debian sid/main amd64 libcurl3-gnutls amd64 8.6.0-1 [421 kB] Get:116 http://deb.debian.org/debian sid/main amd64 libdeflate0 amd64 1.19-1 [41.4 kB] Get:117 http://deb.debian.org/debian sid/main amd64 libhtscodecs2 amd64 1.6.0-1 [92.8 kB] Get:118 http://deb.debian.org/debian sid/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get:119 http://deb.debian.org/debian sid/main amd64 media-types all 10.1.0 [26.9 kB] Get:120 http://deb.debian.org/debian sid/main amd64 netbase all 6.4 [12.8 kB] Get:121 http://deb.debian.org/debian sid/main amd64 tzdata all 2023d-1 [257 kB] Get:122 http://deb.debian.org/debian sid/main amd64 libtirpc-common all 1.3.4+ds-1 [10.7 kB] Get:123 http://deb.debian.org/debian sid/main amd64 libtirpc3 amd64 1.3.4+ds-1 [82.1 kB] Get:124 http://deb.debian.org/debian sid/main amd64 libnsl2 amd64 1.3.0-3 [40.0 kB] Get:125 http://deb.debian.org/debian sid/main amd64 readline-common all 8.2-3 [69.1 kB] Get:126 http://deb.debian.org/debian sid/main amd64 libreadline8 amd64 8.2-3 [167 kB] Get:127 http://deb.debian.org/debian sid/main amd64 libsqlite3-0 amd64 3.45.0-1 [894 kB] Get:128 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.39.3-6 [29.7 kB] Get:129 http://deb.debian.org/debian sid/main amd64 libpython3.11-stdlib amd64 3.11.7-2 [1822 kB] Get:130 http://deb.debian.org/debian sid/main amd64 python3.11 amd64 3.11.7-2 [590 kB] Get:131 http://deb.debian.org/debian sid/main amd64 libpython3.12-minimal amd64 3.12.1-2 [807 kB] Get:132 http://deb.debian.org/debian sid/main amd64 python3.12-minimal amd64 3.12.1-2 [2185 kB] Get:133 http://deb.debian.org/debian sid/main amd64 libpython3.12-stdlib amd64 3.12.1-2 [1919 kB] Get:134 http://deb.debian.org/debian sid/main amd64 python3.12 amd64 3.12.1-2 [646 kB] Get:135 http://deb.debian.org/debian sid/main amd64 libblas3 amd64 3.12.0-2 [148 kB] Get:136 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14-20240201-1 [836 kB] Get:137 http://deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.12.0-2 [2407 kB] Get:138 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.11.6-1 [9224 B] Get:139 http://deb.debian.org/debian sid/main amd64 libpam-runtime all 1.5.2-9.1 [134 kB] Get:140 http://deb.debian.org/debian sid/main amd64 libacl1 amd64 2.3.2-1 [32.4 kB] Get:141 http://deb.debian.org/debian sid/main amd64 libattr1 amd64 1:2.5.2-1 [22.5 kB] Get:142 http://deb.debian.org/debian sid/main amd64 libpcre3 amd64 2:8.39-15 [341 kB] Get:143 http://deb.debian.org/debian sid/main amd64 mawk amd64 1.3.4.20240123-1 [136 kB] Get:144 http://deb.debian.org/debian sid/main amd64 sensible-utils all 0.0.20 [19.3 kB] Get:145 http://deb.debian.org/debian sid/main amd64 openssl amd64 3.1.4-2 [1426 kB] Get:146 http://deb.debian.org/debian sid/main amd64 ca-certificates all 20230311 [153 kB] Get:147 http://deb.debian.org/debian sid/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:148 http://deb.debian.org/debian sid/main amd64 ca-certificates-java all 20240118 [11.6 kB] Get:149 http://deb.debian.org/debian sid/main amd64 java-common all 0.75 [6640 B] Get:150 http://deb.debian.org/debian sid/main amd64 libavahi-client3 amd64 0.8-13+b1 [47.1 kB] Get:151 http://deb.debian.org/debian sid/main amd64 libavahi-common3 amd64 0.8-13+b1 [43.3 kB] Get:152 http://deb.debian.org/debian sid/main amd64 libavahi-common-data amd64 0.8-13+b1 [111 kB] Get:153 http://deb.debian.org/debian sid/main amd64 libdbus-1-3 amd64 1.14.10-4 [203 kB] Get:154 http://deb.debian.org/debian sid/main amd64 libcups2 amd64 2.4.7-1+b1 [247 kB] Get:155 http://deb.debian.org/debian sid/main amd64 liblcms2-2 amd64 2.14-2 [154 kB] Get:156 http://deb.debian.org/debian sid/main amd64 libjpeg62-turbo amd64 1:2.1.5-2+b2 [167 kB] Get:157 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:158 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:159 http://deb.debian.org/debian sid/main amd64 fontconfig-config amd64 2.14.2-6+b1 [316 kB] Get:160 http://deb.debian.org/debian sid/main amd64 libpng16-16 amd64 1.6.42-1 [277 kB] Get:161 http://deb.debian.org/debian sid/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b1 [439 kB] Get:162 http://deb.debian.org/debian sid/main amd64 libfontconfig1 amd64 2.14.2-6+b1 [388 kB] Get:163 http://deb.debian.org/debian sid/main amd64 libnspr4 amd64 2:4.35-1.1 [108 kB] Get:164 http://deb.debian.org/debian sid/main amd64 libnss3 amd64 2:3.96.1-1 [1365 kB] Get:165 http://deb.debian.org/debian sid/main amd64 libasound2 amd64 1.2.10-3 [368 kB] Get:166 http://deb.debian.org/debian sid/main amd64 libasound2-data all 1.2.10-3 [20.7 kB] Get:167 http://deb.debian.org/debian sid/main amd64 libglib2.0-0 amd64 2.78.3-2 [1452 kB] Get:168 http://deb.debian.org/debian sid/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get:169 http://deb.debian.org/debian sid/main amd64 libharfbuzz0b amd64 8.3.0-2 [2213 kB] Get:170 http://deb.debian.org/debian sid/main amd64 libpcsclite1 amd64 2.0.1-1 [50.8 kB] Get:171 http://deb.debian.org/debian sid/main amd64 openjdk-17-jre-headless amd64 17.0.10+7-1 [43.7 MB] Get:172 http://deb.debian.org/debian sid/main amd64 default-jre-headless amd64 2:1.17-75 [3068 B] Get:173 http://deb.debian.org/debian sid/main amd64 fastaq all 3.17.0-6 [47.5 kB] Get:174 http://deb.debian.org/debian sid/main amd64 libquadmath0 amd64 14-20240201-1 [147 kB] Get:175 http://deb.debian.org/debian sid/main amd64 gcc-10-base amd64 10.5.0-2 [36.4 kB] Get:176 http://deb.debian.org/debian sid/main amd64 gcc-9-base amd64 9.5.0-4 [28.7 kB] Get:177 http://deb.debian.org/debian sid/main amd64 python3-networkx all 2.8.8-1 [1425 kB] Get:178 http://deb.debian.org/debian sid/main amd64 python3-packaging all 23.2-1 [44.8 kB] Get:179 http://deb.debian.org/debian sid/main amd64 kmc amd64 3.2.3+dfsg-1 [1007 kB] Get:180 http://deb.debian.org/debian sid/main amd64 mummer amd64 3.23+dfsg-8 [662 kB] Get:181 http://deb.debian.org/debian sid/main amd64 libbambamc0 amd64 0.0.50-6+b1 [39.1 kB] Get:182 http://deb.debian.org/debian sid/main amd64 smalt amd64 0.7.6-13 [115 kB] Get:183 http://deb.debian.org/debian sid/main amd64 iva amd64 1.0.11+ds-5 [8582 kB] Get:184 http://deb.debian.org/debian sid/main amd64 libmpdec3 amd64 2.5.1-2 [87.8 kB] Get:185 http://deb.debian.org/debian sid/main amd64 libmpfr6 amd64 4.2.1-1 [713 kB] Get:186 http://deb.debian.org/debian sid/main amd64 libsigsegv2 amd64 2.14-1 [37.2 kB] Get:187 http://deb.debian.org/debian sid/main amd64 libss2 amd64 1.47.0-2+b1 [24.8 kB] Get:188 http://deb.debian.org/debian sid/main amd64 openjdk-11-jre-headless amd64 11.0.22+7-2 [38.3 MB] Get:189 http://deb.debian.org/debian sid/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 178 MB in 2s (101 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 ... 12460 files and directories currently installed.) Preparing to unpack .../base-files_13_amd64.deb ... Unpacking base-files (13) over (11.1+deb11u8) ... Setting up base-files (13) ... Installing new version of config file /etc/debian_version ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... (Reading database ... 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(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 ... 12468 files and directories currently installed.) Preparing to unpack .../dash_0.5.12-6_amd64.deb ... Unpacking dash (0.5.12-6) over (0.5.11+git20200708+dd9ef66-5) ... Setting up dash (0.5.12-6) ... Removing 'diversion of /bin/sh to /bin/sh.distrib by dash' Removing 'diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash' (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12469 files and directories currently installed.) Preparing to unpack .../findutils_4.9.0-5_amd64.deb ... Unpacking findutils (4.9.0-5) over (4.8.0-1) ... Setting up findutils (4.9.0-5) ... (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 ... 12469 files and directories currently installed.) Preparing to unpack .../archives/grep_3.11-4_amd64.deb ... Unpacking grep (3.11-4) over (3.6-1+deb11u1) ... Setting up grep (3.11-4) ... (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 ... 12471 files and directories currently installed.) Preparing to unpack .../archives/gzip_1.12-1_amd64.deb ... Unpacking gzip (1.12-1) over (1.10-4+deb11u1) ... Setting up gzip (1.12-1) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12485 files and directories currently installed.) Preparing to unpack .../libncurses6_6.4+20240113-1_amd64.deb ... Unpacking libncurses6:amd64 (6.4+20240113-1) over (6.2+20201114-2+deb11u2) ... Preparing to unpack .../libncursesw6_6.4+20240113-1_amd64.deb ... Unpacking libncursesw6:amd64 (6.4+20240113-1) over (6.2+20201114-2+deb11u2) ... Preparing to unpack .../libtinfo6_6.4+20240113-1_amd64.deb ... Unpacking libtinfo6:amd64 (6.4+20240113-1) over (6.2+20201114-2+deb11u2) ... Setting up libtinfo6:amd64 (6.4+20240113-1) ... (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 ... 12483 files and directories currently installed.) Preparing to unpack .../ncurses-bin_6.4+20240113-1_amd64.deb ... Unpacking ncurses-bin (6.4+20240113-1) over (6.2+20201114-2+deb11u2) ... Setting up ncurses-bin (6.4+20240113-1) ... (Reading database ... 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Selecting previously unselected package libperl5.38:amd64. Preparing to unpack .../libperl5.38_5.38.2-3_amd64.deb ... Unpacking libperl5.38:amd64 (5.38.2-3) ... Preparing to unpack .../perl-base_5.38.2-3_amd64.deb ... Unpacking perl-base (5.38.2-3) over (5.32.1-4+deb11u2) ... Setting up perl-base (5.38.2-3) ... (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 ... 14422 files and directories currently installed.) Preparing to unpack .../libbz2-1.0_1.0.8-5+b2_amd64.deb ... Unpacking libbz2-1.0:amd64 (1.0.8-5+b2) over (1.0.8-4) ... Setting up libbz2-1.0:amd64 (1.0.8-5+b2) ... (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 ... 14423 files and directories currently installed.) Preparing to unpack .../libaudit-common_1%3a3.1.2-2_all.deb ... Unpacking libaudit-common (1:3.1.2-2) over (1:3.0-2) ... Setting up libaudit-common (1:3.1.2-2) ... (Reading database ... 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Unpacking util-linux (2.39.3-6) over (2.36.1-8+deb11u1) ... dpkg: warning: unable to delete old directory '/usr/lib/udev/rules.d': Directory not empty dpkg: warning: unable to delete old directory '/usr/lib/udev': Directory not empty dpkg: warning: unable to delete old directory '/etc/init.d': Directory not empty Setting up util-linux (2.39.3-6) ... (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 ... 14421 files and directories currently installed.) 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 14440 files and directories currently installed.) Preparing to unpack .../libp11-kit0_0.25.3-4_amd64.deb ... Unpacking libp11-kit0:amd64 (0.25.3-4) over (0.23.22-1) ... Setting up libp11-kit0:amd64 (0.25.3-4) ... Selecting previously unselected package libunistring5:amd64. (Reading database ... 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Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-buster-stable.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bullseye-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bullseye-security-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bullseye-stable.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bookworm-stable.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bookworm-security-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bookworm-automatic.gpg ... (Reading database ... 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(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 ... 14451 files and directories currently installed.) Preparing to unpack .../libnumber-compare-perl_0.03-3_all.deb ... Unpacking libnumber-compare-perl (0.03-3) ... Setting up libnumber-compare-perl (0.03-3) ... Selecting previously unselected package libtext-glob-perl. (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 14465 files and directories currently installed.) Preparing to unpack .../libfile-find-rule-perl_0.34-3_all.deb ... Unpacking libfile-find-rule-perl (0.34-3) ... Setting up perl-modules-5.38 (5.38.2-3) ... Setting up libgdbm6:amd64 (1.23-5) ... Setting up libgdbm-compat4:amd64 (1.23-5) ... Setting up libperl5.38:amd64 (5.38.2-3) ... Setting up perl (5.38.2-3) ... Setting up libfile-find-rule-perl (0.34-3) ... Selecting previously unselected package usrmerge. (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 ... 14480 files and directories currently installed.) Preparing to unpack .../archives/usrmerge_39_all.deb ... Unpacking usrmerge (39) ... Setting up usrmerge (39) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 14486 files and directories currently installed.) Preparing to unpack .../logsave_1.47.0-2+b1_amd64.deb ... Unpacking logsave (1.47.0-2+b1) over (1.46.2-2) ... Preparing to unpack .../libext2fs2_1.47.0-2+b1_amd64.deb ... Unpacking libext2fs2:amd64 (1.47.0-2+b1) over (1.46.2-2) ... Setting up libext2fs2:amd64 (1.47.0-2+b1) ... (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 ... 14488 files and directories currently installed.) Preparing to unpack .../0-e2fsprogs_1.47.0-2+b1_amd64.deb ... Unpacking e2fsprogs (1.47.0-2+b1) over (1.46.2-2) ... Preparing to unpack .../1-mount_2.39.3-6_amd64.deb ... Unpacking mount (2.39.3-6) over (2.36.1-8+deb11u1) ... Preparing to unpack .../2-gawk_1%3a5.2.1-2_amd64.deb ... Unpacking gawk (1:5.2.1-2) over (1:5.1.0-1) ... Selecting previously unselected package libpython3.11-minimal:amd64. Preparing to unpack .../3-libpython3.11-minimal_3.11.7-2_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.7-2) ... Preparing to unpack .../4-libexpat1_2.5.0-2+b2_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-2+b2) over (2.2.10-2+deb11u5) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../5-python3.11-minimal_3.11.7-2_amd64.deb ... Unpacking python3.11-minimal (3.11.7-2) ... Preparing to unpack .../6-samtools_1.19-1_amd64.deb ... Unpacking samtools (1.19-1) over (1.11-1) ... Preparing to unpack .../7-libhts3_1.18+ds-1_amd64.deb ... Unpacking libhts3:amd64 (1.18+ds-1) over (1.11-4) ... Preparing to unpack .../8-python3-pysam_0.22.0+ds-1+b1_amd64.deb ... Unpacking python3-pysam (0.22.0+ds-1+b1) over (0.15.4+ds-3+b2) ... Preparing to unpack .../9-python3-numpy_1%3a1.24.2-2_amd64.deb ... Unpacking python3-numpy (1:1.24.2-2) over (1:1.19.5-1) ... Setting up libpython3.11-minimal:amd64 (3.11.7-2) ... Setting up libexpat1:amd64 (2.5.0-2+b2) ... Setting up python3.11-minimal (3.11.7-2) ... (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 ... 15632 files and directories currently installed.) Preparing to unpack .../python3-minimal_3.11.6-1_amd64.deb ... Unpacking python3-minimal (3.11.6-1) over (3.9.2-3) ... Setting up python3-minimal (3.11.6-1) ... (Reading database ... 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Setting up fontconfig-config (2.14.2-6+b1) ... Installing new version of config file /etc/fonts/conf.d/README ... Installing new version of config file /etc/fonts/fonts.conf ... Setting up libreadline8:amd64 (8.2-3) ... Setting up libavahi-common3:amd64 (0.8-13+b1) ... Setting up e2fsprogs (1.47.0-2+b1) ... Installing new version of config file /etc/mke2fs.conf ... Setting up libnss3:amd64 (2:3.96.1-1) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5+b3) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 26 added, 15 removed; done. Setting up libfreetype6:amd64 (2.13.2+dfsg-1+b1) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-5) ... Setting up ucf (3.0043+nmu1) ... Setting up libharfbuzz0b:amd64 (8.3.0-2) ... Setting up libfontconfig1:amd64 (2.14.2-6+b1) ... Setting up ca-certificates-java (20240118) ... Installing new version of config file /etc/ca-certificates/update.d/jks-keystore ... Removing debian:chambers_of_commerce_root_-_2008.pem Removing debian:cybertrust_global_root.pem Removing debian:dst_root_ca_x3.pem Removing debian:ec-acc.pem Removing debian:geotrust_primary_certification_authority_-_g2.pem Removing debian:global_chambersign_root_-_2008.pem Removing debian:globalsign_root_ca_-_r2.pem Removing debian:hellenic_academic_and_research_institutions_rootca_2011.pem Removing debian:network_solutions_certificate_authority.pem Removing debian:quovadis_root_ca.pem Removing debian:sonera_class_2_root_ca.pem Removing debian:staat_der_nederlanden_ev_root_ca.pem Removing debian:staat_der_nederlanden_root_ca_-_g3.pem Removing debian:trustis_fps_root_ca.pem Removing debian:verisign_universal_root_certification_authority.pem Replacing debian:ACCVRAIZ1.pem Replacing debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Replacing debian:Actalis_Authentication_Root_CA.pem Replacing debian:AffirmTrust_Commercial.pem Replacing debian:AffirmTrust_Networking.pem Replacing debian:AffirmTrust_Premium.pem Replacing debian:AffirmTrust_Premium_ECC.pem Replacing debian:Amazon_Root_CA_1.pem Replacing debian:Amazon_Root_CA_2.pem Replacing debian:Amazon_Root_CA_3.pem Replacing debian:Amazon_Root_CA_4.pem Replacing debian:Atos_TrustedRoot_2011.pem Replacing debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068_2.pem Replacing debian:Baltimore_CyberTrust_Root.pem Replacing debian:Buypass_Class_2_Root_CA.pem Replacing debian:Buypass_Class_3_Root_CA.pem Replacing debian:CA_Disig_Root_R2.pem Replacing debian:CFCA_EV_ROOT.pem Replacing debian:COMODO_Certification_Authority.pem Replacing debian:COMODO_ECC_Certification_Authority.pem Replacing debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Replacing debian:Certigna.pem Replacing debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Replacing debian:Certum_Trusted_Network_CA.pem Replacing debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Replacing debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Replacing debian:D-TRUST_Root_Class_3_CA_2_2009.pem Replacing debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Replacing debian:DigiCert_Assured_ID_Root_CA.pem Replacing debian:DigiCert_Assured_ID_Root_G2.pem Replacing debian:DigiCert_Assured_ID_Root_G3.pem Replacing debian:DigiCert_Global_Root_CA.pem Replacing debian:DigiCert_Global_Root_G2.pem Replacing debian:DigiCert_Global_Root_G3.pem Replacing debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Replacing debian:DigiCert_Trusted_Root_G4.pem Replacing debian:E-Tugra_Certification_Authority.pem Adding debian:E-Tugra_Global_Root_CA_ECC_v3.pem Adding debian:E-Tugra_Global_Root_CA_RSA_v3.pem Replacing debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Replacing debian:Entrust_Root_Certification_Authority.pem Replacing debian:Entrust_Root_Certification_Authority_-_EC1.pem Replacing debian:Entrust_Root_Certification_Authority_-_G2.pem Replacing debian:Entrust_Root_Certification_Authority_-_G4.pem Replacing debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Replacing debian:GTS_Root_R1.pem Replacing debian:GTS_Root_R2.pem Replacing debian:GTS_Root_R3.pem Replacing debian:GTS_Root_R4.pem Replacing debian:GlobalSign_ECC_Root_CA_-_R4.pem Replacing debian:GlobalSign_ECC_Root_CA_-_R5.pem Replacing debian:GlobalSign_Root_CA.pem Replacing debian:GlobalSign_Root_CA_-_R3.pem Replacing debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Replacing debian:Go_Daddy_Class_2_CA.pem Replacing debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Replacing debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Replacing debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Replacing debian:Hongkong_Post_Root_CA_1.pem Replacing debian:Hongkong_Post_Root_CA_3.pem Replacing debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Replacing debian:IdenTrust_Commercial_Root_CA_1.pem Replacing debian:IdenTrust_Public_Sector_Root_CA_1.pem Replacing debian:Izenpe.com.pem Replacing debian:Microsec_e-Szigno_Root_CA_2009.pem Replacing debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Replacing debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Replacing debian:NAVER_Global_Root_Certification_Authority.pem Replacing debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Replacing debian:OISTE_WISeKey_Global_Root_GB_CA.pem Replacing debian:OISTE_WISeKey_Global_Root_GC_CA.pem Replacing debian:QuoVadis_Root_CA_1_G3.pem Replacing debian:QuoVadis_Root_CA_2.pem Replacing debian:QuoVadis_Root_CA_2_G3.pem Replacing debian:QuoVadis_Root_CA_3.pem Replacing debian:QuoVadis_Root_CA_3_G3.pem Replacing debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Replacing debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Replacing debian:SSL.com_Root_Certification_Authority_ECC.pem Replacing debian:SSL.com_Root_Certification_Authority_RSA.pem Replacing debian:SZAFIR_ROOT_CA2.pem Replacing debian:SecureSign_RootCA11.pem Replacing debian:SecureTrust_CA.pem Replacing debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Replacing debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Replacing debian:Security_Communication_Root_CA.pem Replacing debian:Starfield_Class_2_CA.pem Replacing debian:Starfield_Root_Certificate_Authority_-_G2.pem Replacing debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Replacing debian:SwissSign_Gold_CA_-_G2.pem Replacing debian:SwissSign_Silver_CA_-_G2.pem Replacing debian:T-TeleSec_GlobalRoot_Class_2.pem Replacing debian:T-TeleSec_GlobalRoot_Class_3.pem Replacing debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Replacing debian:TWCA_Global_Root_CA.pem Replacing debian:TWCA_Root_Certification_Authority.pem Replacing debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Replacing debian:TrustCor_ECA-1.pem Replacing debian:TrustCor_RootCert_CA-1.pem Replacing debian:TrustCor_RootCert_CA-2.pem Replacing debian:Trustwave_Global_Certification_Authority.pem Replacing debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Replacing debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Replacing debian:UCA_Extended_Validation_Root.pem Replacing debian:UCA_Global_G2_Root.pem Replacing debian:USERTrust_ECC_Certification_Authority.pem Replacing debian:USERTrust_RSA_Certification_Authority.pem Replacing debian:XRamp_Global_CA_Root.pem Replacing debian:certSIGN_ROOT_CA.pem Replacing debian:certSIGN_Root_CA_G2.pem Replacing debian:e-Szigno_Root_CA_2017.pem Replacing debian:ePKI_Root_Certification_Authority.pem Replacing debian:emSign_ECC_Root_CA_-_C3.pem Replacing debian:emSign_ECC_Root_CA_-_G3.pem Replacing debian:emSign_Root_CA_-_C1.pem Replacing debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up libavahi-client3:amd64 (0.8-13+b1) ... Setting up libtirpc3:amd64 (1.3.4+ds-1) ... Setting up gawk (1:5.2.1-2) ... Setting up libcurl3-gnutls:amd64 (8.6.0-1) ... Setting up libcups2:amd64 (2.4.7-1+b1) ... Setting up libnsl2:amd64 (1.3.0-3) ... Setting up mummer (3.23+dfsg-8) ... Setting up libhts3:amd64 (1.18+ds-1) ... Setting up libpython3.12-stdlib:amd64 (3.12.1-2) ... Setting up libpython3.11-stdlib:amd64 (3.11.7-2) ... Setting up python3.12 (3.12.1-2) ... Setting up openjdk-11-jre-headless:amd64 (11.0.22+7-2) ... Installing new version of config file /etc/java-11-openjdk/jfr/default.jfc ... Installing new version of config file /etc/java-11-openjdk/jfr/profile.jfc ... Installing new version of config file /etc/java-11-openjdk/security/java.security ... Installing new version of config file /etc/java-11-openjdk/security/public_suffix_list.dat ... Setting up samtools (1.19-1) ... Setting up openjdk-17-jre-headless:amd64 (17.0.10+7-1) ... update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-17-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode 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 python3-decorator (5.1.1-5) ... Setting up python3-packaging (23.2-1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-pysam (0.22.0+ds-1+b1) ... Setting up fastaq (3.17.0-6) ... /usr/lib/python3/dist-packages/pyfastaq/sequences.py:37: SyntaxWarning: invalid escape sequence '\s' phylip_regex = re.compile('^\s*[0-9]+\s+[0-9]+$') /usr/lib/python3/dist-packages/pyfastaq/sequences.py:38: SyntaxWarning: invalid escape sequence '\s' gbk_regex = re.compile('^LOCUS\s+\S') Setting up python3-networkx (2.8.8-1) ... /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:556: SyntaxWarning: invalid octal escape sequence '\420' "graph [edge [ source u'u\4200' target u'u\4200' ] " /usr/lib/python3/dist-packages/networkx/readwrite/tests/test_gml.py:557: SyntaxWarning: invalid octal escape sequence '\420' + "node [ id u'u\4200' label b ] ]" Setting up python3-numpy (1:1.24.2-2) ... Processing triggers for libc-bin (2.37-15) ... Processing triggers for debianutils (5.16) ... Processing triggers for ca-certificates-java (20240118) ... done. Setting up default-jre-headless (2:1.17-75) ... Setting up iva (1.0.11+ds-5) ... /usr/lib/python3/dist-packages/iva/external_progs.py:33: SyntaxWarning: invalid escape sequence '\(' 'kmc': ('kmc', re.compile('^K-Mer Counter \(KMC\) ver\. (.*) \(.*\)$')), /usr/lib/python3/dist-packages/iva/external_progs.py:34: SyntaxWarning: invalid escape sequence '\(' 'kmc_dump': ('kmc_dump', re.compile('^KMC dump ver. (.*) \(.*\)$')), /usr/lib/python3/dist-packages/iva/external_progs.py:37: SyntaxWarning: invalid escape sequence '\(' 'nucmer': ('nucmer --version', re.compile('^NUCmer \(NUCleotide MUMmer\) version (.*)$')), /usr/lib/python3/dist-packages/iva/external_progs.py:38: SyntaxWarning: invalid escape sequence '\(' 'R': ('R --version', re.compile('^R version (.*) \(.*\) --')), /usr/lib/python3/dist-packages/iva/external_progs.py:40: SyntaxWarning: invalid escape sequence '\d' 'samtools': ('samtools', re.compile('(\d+\.\d+[\.\d]*)')), /usr/lib/python3/dist-packages/iva/kraken.py:360: SyntaxWarning: invalid escape sequence '\.' self._genbank2embl(fname, re.sub('\.gbk$', '', fname) + '.embl') /usr/lib/python3/dist-packages/iva/kraken.py:415: SyntaxWarning: invalid escape sequence '\W' return re.sub('\W', '_', s).strip('_') /usr/lib/python3/dist-packages/iva/mapping.py:161: SyntaxWarning: invalid escape sequence '\^' s = re.sub('\^.', '', s) Processing triggers for ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for ca-certificates-java (20240118) ... done. 1m25.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'apt-get', '-yf', 'dist-upgrade'] 1m25.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m26.4s DUMP: 170bc12a17196aae5ff1d0978130f677 - 1m26.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m26.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'apt-cache', 'show', '--no-all-versions', 'iva'] 1m26.7s DUMP: Package: iva Version: 1.0.11+ds-5 Installed-Size: 8770 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: fastaq, python3-networkx, python3-packaging, python3-pysam, python3:any, perl:any, kmc, mummer, smalt, samtools, python3-numpy, default-jre-headless Recommends: r-base-core, bioperl, trimmomatic Description-en: iterative virus sequence assembler IVA is a de novo assembler designed to assemble virus genomes that have no repeat sequences, using Illumina read pairs sequenced from mixed populations at extremely high depth. . IVA's main algorithm works by iteratively extending contigs using aligned read pairs. Its input can be just read pairs, or additionally you can provide an existing set of contigs to be extended. Alternatively, it can take reads together with a reference sequence. Description-md5: 698e26411c0dbe5917f816e7b7229be9 Homepage: https://github.com/sanger-pathogens/iva Tag: biology::nucleic-acids, field::biology, field::biology:bioinformatics, implemented-in::python, interface::commandline, role::program, works-with::biological-sequence, works-with::file Section: science Priority: optional Filename: pool/main/i/iva/iva_1.0.11+ds-5_amd64.deb Size: 8581624 MD5sum: 81641314ba9e9e3b5e100a7443802397 SHA256: 07f3c24da91e13d1b175ddb6db6f913e23b26a8f954f47a678ed9ed4b7aa60ef 1m26.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'apt-cache', 'show', '--no-all-versions', 'iva'] 1m26.7s INFO: apt-cache knows about the following packages: iva 1m26.7s INFO: Running scripts pre_install 1m26.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_install_database-server'] 1m26.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_install_database-server'] 1m26.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_install_exceptions'] 1m26.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_install_exceptions'] 1m26.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_install_extras'] 1m26.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_install_extras'] 1m26.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_install_foreign_architecture'] 1m26.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_install_foreign_architecture'] 1m26.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m26.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m26.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'apt-cache', 'policy'] 1m26.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 1m26.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'apt-cache', 'policy'] 1m26.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'apt-cache', 'policy', 'iva'] 1m26.9s DUMP: iva: Installed: 1.0.11+ds-5 Candidate: 1.0.11+ds-5 Version table: *** 1.0.11+ds-5 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 1m26.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'apt-cache', 'policy', 'iva'] 1m26.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'apt-get', '-y', 'install', 'iva'] 1m27.5s DUMP: Reading package lists... Building dependency tree... Reading state information... iva is already the newest version (1.0.11+ds-5). The following packages were automatically installed and are no longer required: libldap-2.4-2 libmpdec3 libperl5.32 libpython3.9-minimal libpython3.9-stdlib libquadmath0 openjdk-11-jre-headless perl-modules-5.32 python3-decorator python3.9 python3.9-minimal ucf Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m27.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'apt-get', '-y', 'install', 'iva'] 1m27.5s INFO: Running scripts post_install 1m27.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/post_install_exceptions'] 1m27.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/post_install_exceptions'] 1m27.6s INFO: Running scripts post_distupgrade 1m27.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m27.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m27.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/post_distupgrade_exceptions'] 1m27.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/post_distupgrade_exceptions'] 1m27.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m27.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m27.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m27.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m27.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/post_distupgrade_zz_backports'] 1m27.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/post_distupgrade_zz_backports'] 1m27.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpncbapv2j'] 1m28.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpncbapv2j'] 1m28.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpncbapv2j'] 1m30.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpncbapv2j'] 1m30.1s INFO: Running scripts pre_install 1m30.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_install_database-server'] 1m30.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_install_database-server'] 1m30.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_install_exceptions'] 1m30.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_install_exceptions'] 1m30.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_install_extras'] 1m30.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_install_extras'] 1m30.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_install_foreign_architecture'] 1m30.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_install_foreign_architecture'] 1m30.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m30.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m30.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'apt-cache', 'policy'] 1m30.2s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 1m30.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'apt-cache', 'policy'] 1m30.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'apt-cache', 'policy', 'iva'] 1m30.2s DUMP: iva: Installed: 1.0.11+ds-5 Candidate: 1.0.11+ds-5 Version table: *** 1.0.11+ds-5 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 1m30.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'apt-cache', 'policy', 'iva'] 1m30.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'apt-get', '-y', 'install', 'iva=1.0.11+ds-5'] 1m30.8s DUMP: Reading package lists... Building dependency tree... Reading state information... iva is already the newest version (1.0.11+ds-5). The following packages were automatically installed and are no longer required: libldap-2.4-2 libmpdec3 libperl5.32 libpython3.9-minimal libpython3.9-stdlib libquadmath0 openjdk-11-jre-headless perl-modules-5.32 python3-decorator python3.9 python3.9-minimal ucf Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m30.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'apt-get', '-y', 'install', 'iva=1.0.11+ds-5'] 1m30.8s INFO: Running scripts post_install 1m30.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/post_install_exceptions'] 1m30.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/post_install_exceptions'] 1m30.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpncbapv2j'] 1m32.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpncbapv2j'] 1m32.1s INFO: /bin converted to /usr/bin by /usr merge 1m32.1s INFO: /lib converted to /usr/lib by /usr merge 1m32.1s INFO: /lib/init converted to /usr/lib/init by /usr merge 1m32.1s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 1m32.1s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 1m32.1s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 1m32.1s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 1m32.1s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 1m32.1s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 1m32.1s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 1m32.1s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 1m32.1s INFO: /lib64 converted to /usr/lib64 by /usr merge 1m32.1s INFO: /sbin converted to /usr/sbin by /usr merge 1m33.5s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', '-ac', '--ignore-obsolete'] 1m36.4s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', '-ac', '--ignore-obsolete'] 1m36.4s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m36.4s DUMP: 0.15.6 1m36.4s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m36.4s INFO: Running adequate version 0.15.6 now. 1m36.4s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'iva'] 1m36.6s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'iva'] 1m36.6s INFO: Running scripts pre_remove 1m36.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m36.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m36.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m36.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m36.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m39.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m39.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m39.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m39.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m39.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m39.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_remove_exceptions'] 1m39.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/pre_remove_exceptions'] 1m39.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m39.6s DUMP: install ok installed adduser adduser 3.137 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 ca-certificates ca-certificates 20230311 install ok installed ca-certificates-java ca-certificates-java 20240118 install ok installed coreutils coreutils 9.4-3+b1 install ok installed dash dash 0.5.12-6 install ok installed debconf debconf 1.5.85 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.16 install ok installed default-jre-headless default-jre-headless 2:1.17-75 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.4 install ok installed e2fsprogs e2fsprogs 1.47.0-2+b1 install ok installed fastaq fastaq 3.17.0-6 install ok installed findutils findutils 4.9.0-5 install ok installed fontconfig-config fontconfig-config 2.14.2-6+b1 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-8 install ok installed fonts-dejavu-mono fonts-dejavu-mono 2.37-8 install ok installed gawk gawk 1:5.2.1-2 install ok installed gcc-10-base:amd64 gcc-10-base 10.5.0-2 install ok installed gcc-14-base:amd64 gcc-14-base 14-20240201-1 install ok installed gcc-9-base:amd64 gcc-9-base 9.5.0-4 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 iva iva 1.0.11+ds-5 install ok installed java-common java-common 0.75 install ok installed kmc kmc 3.2.3+dfsg-1 install ok installed libacl1:amd64 libacl1 2.3.2-1 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.7.10 install ok installed libasound2:amd64 libasound2 1.2.10-3 install ok installed libasound2-data libasound2-data 1.2.10-3 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:3.1.2-2 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-2 install ok installed libavahi-client3:amd64 libavahi-client3 0.8-13+b1 install ok installed libavahi-common-data:amd64 libavahi-common-data 0.8-13+b1 install ok installed libavahi-common3:amd64 libavahi-common3 0.8-13+b1 install ok installed libbambamc0:amd64 libbambamc0 0.0.50-6+b1 install ok installed libblas3:amd64 libblas3 3.12.0-2 install ok installed libblkid1:amd64 libblkid1 2.39.3-6 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b3 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b2 install ok installed libc-bin libc-bin 2.37-15 install ok installed libc6:amd64 libc6 2.37-15 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 libcups2:amd64 libcups2 2.4.7-1+b1 install ok installed libcurl3-gnutls:amd64 libcurl3-gnutls 8.6.0-1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-4+b1 install ok installed libdbus-1-3:amd64 libdbus-1-3 1.14.10-4 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.271 install ok installed libdeflate0:amd64 libdeflate0 1.19-1 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 libffi7:amd64 libffi7 3.3-6 install ok installed libffi8:amd64 libffi8 3.4.4-2 install ok installed libfile-find-rule-perl libfile-find-rule-perl 0.34-3 install ok installed libfontconfig1:amd64 libfontconfig1 2.14.2-6+b1 install ok installed libfreetype6:amd64 libfreetype6 2.13.2+dfsg-1+b1 install ok installed libgcc-s1:amd64 libgcc-s1 14-20240201-1 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 libgfortran5:amd64 libgfortran5 14-20240201-1 install ok installed libglib2.0-0:amd64 libglib2.0-0 2.78.3-2 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 libgraphite2-3:amd64 libgraphite2-3 1.3.14-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.20.1-5 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 8.3.0-2 install ok installed libhogweed6:amd64 libhogweed6 3.9.1-2 install ok installed libhts3:amd64 libhts3 1.18+ds-1 install ok installed libhtscodecs2:amd64 libhtscodecs2 1.6.0-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-2+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 liblapack3:amd64 liblapack3 3.12.0-2 install ok installed liblcms2-2:amd64 liblcms2-2 2.14-2 install ok installed libldap-2.4-2:amd64 libldap-2.4-2 2.4.57+dfsg-3+deb11u1 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.13+dfsg-5+b3 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 libmpdec3:amd64 libmpdec3 2.5.1-2 install ok installed libmpfr6:amd64 libmpfr6 4.2.1-1 install ok installed libncurses6:amd64 libncurses6 6.4+20240113-1 install ok installed libncursesw6:amd64 libncursesw6 6.4+20240113-1 install ok installed libnettle8:amd64 libnettle8 3.9.1-2 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.58.0-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-3 install ok installed libnspr4:amd64 libnspr4 2:4.35-1.1 install ok installed libnss3:amd64 libnss3 2:3.96.1-1 install ok installed libnumber-compare-perl libnumber-compare-perl 0.03-3 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 libpcre3:amd64 libpcre3 2:8.39-15 install ok installed libpcsclite1:amd64 libpcsclite1 2.0.1-1 install ok installed libperl5.32:amd64 libperl5.32 5.32.1-4+deb11u2 install ok installed libperl5.38:amd64 libperl5.38 5.38.2-3 install ok installed libpng16-16:amd64 libpng16-16 1.6.42-1 install ok installed libpsl5:amd64 libpsl5 0.21.2-1+b1 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 libpython3.12-minimal:amd64 libpython3.12-minimal 3.12.1-2 install ok installed libpython3.12-stdlib:amd64 libpython3.12-stdlib 3.12.1-2 install ok installed libpython3.9-minimal:amd64 libpython3.9-minimal 3.9.2-1 install ok installed libpython3.9-stdlib:amd64 libpython3.9-stdlib 3.9.2-1 install ok installed libquadmath0:amd64 libquadmath0 14-20240201-1 install ok installed libreadline8:amd64 libreadline8 8.2-3 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b2 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-4+b1 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-4+b1 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1 install ok installed libselinux1:amd64 libselinux1 3.5-2 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b2 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsepol2:amd64 libsepol2 3.5-2 install ok installed libsigsegv2:amd64 libsigsegv2 2.14-1 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 libssh2-1:amd64 libssh2-1 1.11.0-4 install ok installed libssl1.1:amd64 libssl1.1 1.1.1w-0+deb11u1 install ok installed libssl3:amd64 libssl3 3.1.4-2 install ok installed libstdc++6:amd64 libstdc++6 14-20240201-1 install ok installed libsystemd0:amd64 libsystemd0 255.3-2 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtext-glob-perl libtext-glob-perl 0.11-3 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 255.3-2 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 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 lsb-base lsb-base 11.6 install ok installed mawk mawk 1.3.4.20240123-1 install ok installed media-types media-types 10.1.0 install ok installed mount mount 2.39.3-6 install ok installed mummer mummer 3.23+dfsg-8 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 openjdk-11-jre-headless:amd64 openjdk-11-jre-headless 11.0.22+7-2 install ok installed openjdk-17-jre-headless:amd64 openjdk-17-jre-headless 17.0.10+7-1 install ok installed openssl openssl 3.1.4-2 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-5.32 perl-modules-5.32 5.32.1-4+deb11u2 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-decorator python3-decorator 5.1.1-5 install ok installed python3-minimal python3-minimal 3.11.6-1 install ok installed python3-networkx python3-networkx 2.8.8-1 install ok installed python3-numpy python3-numpy 1:1.24.2-2 install ok installed python3-packaging python3-packaging 23.2-1 install ok installed python3-pkg-resources python3-pkg-resources 68.1.2-2 install ok installed python3-pysam python3-pysam 0.22.0+ds-1+b1 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 python3.12 python3.12 3.12.1-2 install ok installed python3.12-minimal python3.12-minimal 3.12.1-2 install ok installed python3.9 python3.9 3.9.2-1 install ok installed python3.9-minimal python3.9-minimal 3.9.2-1 install ok installed readline-common readline-common 8.2-3 install ok installed samtools samtools 1.19-1 install ok installed sed sed 4.9-2 install ok installed sensible-utils sensible-utils 0.0.20 install ok installed smalt smalt 0.7.6-13 install ok installed sysvinit-utils sysvinit-utils 3.08-6 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2023d-1 install ok installed ucf ucf 3.0043+nmu1 install ok installed usrmerge usrmerge 39 install ok installed util-linux util-linux 2.39.3-6 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg-3+b1 1m39.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m39.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'apt-get', 'remove', 'ca-certificates', 'ca-certificates-java', 'default-jre-headless', 'fastaq', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'gawk', 'java-common', 'kmc', 'libasound2:amd64', 'libasound2-data', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbambamc0:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libdbus-1-3:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgraphite2-3:amd64', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libjpeg62-turbo:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-2.5-0:amd64', 'libmpdec3:amd64', 'libmpfr6:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libpcsclite1:amd64', 'libperl5.32:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsigsegv2:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'media-types', 'mummer', 'netbase', 'openjdk-11-jre-headless:amd64', 'openjdk-17-jre-headless:amd64', 'openssl', 'perl-modules-5.32', 'python3', 'python3-decorator', 'python3-minimal', 'python3-networkx', 'python3-numpy', 'python3-packaging', 'python3-pkg-resources', 'python3-pysam', 'python3.11', 'python3.11-minimal', 'python3.12', 'python3.12-minimal', 'python3.9', 'python3.9-minimal', 'readline-common', 'samtools', 'sensible-utils', 'smalt', 'ucf', 'iva'] 1m44.2s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: ca-certificates ca-certificates-java default-jre-headless fastaq fontconfig-config fonts-dejavu-core fonts-dejavu-mono gawk iva java-common kmc libasound2 libasound2-data libavahi-client3 libavahi-common-data libavahi-common3 libbambamc0 libblas3 libbrotli1 libcups2 libcurl3-gnutls libdbus-1-3 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libgfortran5 libglib2.0-0 libgraphite2-3 libharfbuzz0b libhts3 libhtscodecs2 libjpeg62-turbo liblapack3 liblcms2-2 libldap-2.4-2 libldap-2.5-0 libmpdec3 libmpfr6 libncurses6 libncursesw6 libnghttp2-14 libnspr4 libnss3 libpcsclite1 libperl5.32 libpng16-16 libpsl5 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libpython3.12-minimal libpython3.12-stdlib libpython3.9-minimal libpython3.9-stdlib libquadmath0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsqlite3-0 libssh2-1 media-types mummer netbase openjdk-11-jre-headless openjdk-17-jre-headless openssl perl-modules-5.32 python3 python3-decorator python3-minimal python3-networkx python3-numpy python3-packaging python3-pkg-resources python3-pysam python3.11 python3.11-minimal python3.12 python3.12-minimal python3.9 python3.9-minimal readline-common samtools sensible-utils smalt ucf 0 upgraded, 0 newly installed, 89 to remove and 0 not upgraded. After this operation, 637 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 ... 16203 files and directories currently installed.) Removing openjdk-11-jre-headless:amd64 (11.0.22+7-2) ... Removing iva (1.0.11+ds-5) ... Removing default-jre-headless (2:1.17-75) ... Removing openjdk-17-jre-headless:amd64 (17.0.10+7-1) ... Removing ca-certificates-java (20240118) ... Removing ca-certificates (20230311) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing fastaq (3.17.0-6) ... Removing libfontconfig1:amd64 (2.14.2-6+b1) ... Removing fontconfig-config (2.14.2-6+b1) ... Removing fonts-dejavu-core (2.37-8) ... Removing fonts-dejavu-mono (2.37-8) ... Removing mummer (3.23+dfsg-8) ... Removing gawk (1:5.2.1-2) ... update-alternatives: using /usr/bin/mawk to provide /usr/bin/awk (awk) in auto mode Removing java-common (0.75) ... Removing kmc (3.2.3+dfsg-1) ... Removing libasound2:amd64 (1.2.10-3) ... Removing libasound2-data (1.2.10-3) ... Removing libcups2:amd64 (2.4.7-1+b1) ... Removing libavahi-client3:amd64 (0.8-13+b1) ... Removing libavahi-common3:amd64 (0.8-13+b1) ... Removing libavahi-common-data:amd64 (0.8-13+b1) ... Removing smalt (0.7.6-13) ... Removing libbambamc0:amd64 (0.0.50-6+b1) ... Removing python3-numpy (1:1.24.2-2) ... Removing liblapack3:amd64 (3.12.0-2) ... Removing libblas3:amd64 (3.12.0-2) ... Removing libharfbuzz0b:amd64 (8.3.0-2) ... Removing libfreetype6:amd64 (2.13.2+dfsg-1+b1) ... Removing samtools (1.19-1) ... Removing libdbus-1-3:amd64 (1.14.10-4) ... Removing python3.9 (3.9.2-1) ... Removing python3.9-minimal (3.9.2-1) ... Removing python3.12 (3.12.1-2) ... Removing python3.12-minimal (3.12.1-2) ... Removing libgfortran5:amd64 (14-20240201-1) ... Removing libglib2.0-0:amd64 (2.78.3-2) ... Removing libgraphite2-3:amd64 (1.3.14-2) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-2+b2) ... Removing liblcms2-2:amd64 (2.14-2) ... Removing libldap-2.4-2:amd64 (2.4.57+dfsg-3+deb11u1) ... Removing libpython3.9-stdlib:amd64 (3.9.2-1) ... Removing libmpdec3:amd64 (2.5.1-2) ... Removing libmpfr6:amd64 (4.2.1-1) ... Removing libncurses6:amd64 (6.4+20240113-1) ... Removing libpython3.12-stdlib:amd64 (3.12.1-2) ... Removing python3-pysam (0.22.0+ds-1+b1) ... Removing python3-networkx (2.8.8-1) ... Removing python3-pkg-resources (68.1.2-2) ... Removing libnss3:amd64 (2:3.96.1-1) ... Removing libnspr4:amd64 (2:4.35-1.1) ... Removing libpcsclite1:amd64 (2.0.1-1) ... Removing libperl5.32:amd64 (5.32.1-4+deb11u2) ... Removing libpng16-16:amd64 (1.6.42-1) ... Removing libpython3.12-minimal:amd64 (3.12.1-2) ... Removing libpython3.9-minimal:amd64 (3.9.2-1) ... Removing libquadmath0:amd64 (14-20240201-1) ... Removing libsigsegv2:amd64 (2.14-1) ... Removing openssl (3.1.4-2) ... Removing perl-modules-5.32 (5.32.1-4+deb11u2) ... Removing python3-decorator (5.1.1-5) ... Removing python3-packaging (23.2-1) ... Removing ucf (3.0043+nmu1) ... Removing sensible-utils (0.0.20) ... Removing libhts3:amd64 (1.18+ds-1) ... Removing libcurl3-gnutls:amd64 (8.6.0-1) ... Removing libbrotli1:amd64 (1.1.0-2+b3) ... Removing libdeflate0:amd64 (1.19-1) ... Removing libhtscodecs2:amd64 (1.6.0-1) ... Removing libldap-2.5-0:amd64 (2.5.13+dfsg-5+b3) ... Removing python3 (3.11.6-1) ... Removing libpython3-stdlib:amd64 (3.11.6-1) ... Removing libnghttp2-14:amd64 (1.58.0-1) ... Removing libpsl5:amd64 (0.21.2-1+b1) ... Removing python3.11 (3.11.7-2) ... Removing python3-minimal (3.11.6-1) ... Removing python3.11-minimal (3.11.7-2) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-4+b1) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-4+b1) ... Removing libssh2-1:amd64 (1.11.0-4) ... Removing libexpat1:amd64 (2.5.0-2+b2) ... Removing libpython3.11-stdlib:amd64 (3.11.7-2) ... find: '/usr/lib/python3': No such file or directory 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 media-types (10.1.0) ... Removing netbase (6.4) ... Removing readline-common (8.2-3) ... Processing triggers for libc-bin (2.37-15) ... 1m44.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'apt-get', 'remove', 'ca-certificates', 'ca-certificates-java', 'default-jre-headless', 'fastaq', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'gawk', 'java-common', 'kmc', 'libasound2:amd64', 'libasound2-data', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbambamc0:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libdbus-1-3:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgraphite2-3:amd64', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libjpeg62-turbo:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-2.5-0:amd64', 'libmpdec3:amd64', 'libmpfr6:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libpcsclite1:amd64', 'libperl5.32:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsigsegv2:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'media-types', 'mummer', 'netbase', 'openjdk-11-jre-headless:amd64', 'openjdk-17-jre-headless:amd64', 'openssl', 'perl-modules-5.32', 'python3', 'python3-decorator', 'python3-minimal', 'python3-networkx', 'python3-numpy', 'python3-packaging', 'python3-pkg-resources', 'python3-pysam', 'python3.11', 'python3.11-minimal', 'python3.12', 'python3.12-minimal', 'python3.9', 'python3.9-minimal', 'readline-common', 'samtools', 'sensible-utils', 'smalt', 'ucf', 'iva'] 1m44.2s INFO: Running scripts post_remove 1m44.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/post_remove_exceptions'] 1m44.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/post_remove_exceptions'] 1m44.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'dpkg', '--purge', 'ca-certificates', 'ca-certificates-java', 'default-jre-headless', 'fastaq', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'gawk', 'java-common', 'kmc', 'libasound2:amd64', 'libasound2-data', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbambamc0:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libdbus-1-3:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgraphite2-3:amd64', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libjpeg62-turbo:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-2.5-0:amd64', 'libmpdec3:amd64', 'libmpfr6:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libpcsclite1:amd64', 'libperl5.32:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsigsegv2:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'media-types', 'mummer', 'netbase', 'openjdk-11-jre-headless:amd64', 'openjdk-17-jre-headless:amd64', 'openssl', 'perl-modules-5.32', 'python3', 'python3-decorator', 'python3-minimal', 'python3-networkx', 'python3-numpy', 'python3-packaging', 'python3-pkg-resources', 'python3-pysam', 'python3.11', 'python3.11-minimal', 'python3.12', 'python3.12-minimal', 'python3.9', 'python3.9-minimal', 'readline-common', 'samtools', 'sensible-utils', 'smalt', 'ucf'] 1m44.8s DUMP: (Reading database ... 7555 files and directories currently installed.) Purging configuration files for ca-certificates (20230311) ... Removing dangling symlinks from /etc/ssl/certs... done. Purging configuration files for ca-certificates-java (20240118) ... dpkg: warning: ignoring request to remove default-jre-headless which isn't installed dpkg: warning: ignoring request to remove fastaq which isn't installed Purging configuration files for fontconfig-config (2.14.2-6+b1) ... Purging configuration files for fonts-dejavu-core (2.37-8) ... Purging configuration files for fonts-dejavu-mono (2.37-8) ... Purging configuration files for gawk (1:5.2.1-2) ... Purging configuration files for java-common (0.75) ... dpkg: warning: ignoring request to remove kmc which isn't installed dpkg: warning: ignoring request to remove libasound2 which isn't installed dpkg: warning: ignoring request to remove libasound2-data which isn't installed dpkg: warning: ignoring request to remove libavahi-client3 which isn't installed dpkg: warning: ignoring request to remove libavahi-common-data which isn't installed dpkg: warning: ignoring request to remove libavahi-common3 which isn't installed dpkg: warning: ignoring request to remove libbambamc0 which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libcups2 which isn't installed dpkg: warning: ignoring request to remove libcurl3-gnutls which isn't installed dpkg: warning: ignoring request to remove libdbus-1-3 which isn't installed dpkg: warning: ignoring request to remove libdeflate0 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libfontconfig1 which isn't installed dpkg: warning: ignoring request to remove libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed Purging configuration files for libglib2.0-0:amd64 (2.78.3-2) ... dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed dpkg: warning: ignoring request to remove libhts3 which isn't installed dpkg: warning: ignoring request to remove libhtscodecs2 which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove liblcms2-2 which isn't installed dpkg: warning: ignoring request to remove libldap-2.4-2 which isn't installed dpkg: warning: ignoring request to remove libldap-2.5-0 which isn't installed dpkg: warning: ignoring request to remove libmpdec3 which isn't installed dpkg: warning: ignoring request to remove libmpfr6 which isn't installed dpkg: warning: ignoring request to remove libncurses6 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libnspr4 which isn't installed dpkg: warning: ignoring request to remove libnss3 which isn't installed dpkg: warning: ignoring request to remove libpcsclite1 which isn't installed dpkg: warning: ignoring request to remove libperl5.32 which isn't installed dpkg: warning: ignoring request to remove libpng16-16 which isn't installed dpkg: warning: ignoring request to remove libpsl5 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 Purging configuration files for libpython3.12-minimal:amd64 (3.12.1-2) ... dpkg: warning: ignoring request to remove libpython3.12-stdlib which isn't installed Purging configuration files for libpython3.9-minimal:amd64 (3.9.2-1) ... dpkg: warning: ignoring request to remove libpython3.9-stdlib which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed dpkg: warning: ignoring request to remove libreadline8 which isn't installed dpkg: warning: ignoring request to remove librtmp1 which isn't installed dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed dpkg: warning: ignoring request to remove libsasl2-modules-db which isn't installed dpkg: warning: ignoring request to remove libsigsegv2 which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libssh2-1 which isn't installed Purging configuration files for media-types (10.1.0) ... dpkg: warning: ignoring request to remove mummer which isn't installed Purging configuration files for netbase (6.4) ... Purging configuration files for openjdk-11-jre-headless:amd64 (11.0.22+7-2) ... Purging configuration files for openjdk-17-jre-headless:amd64 (17.0.10+7-1) ... Purging configuration files for openssl (3.1.4-2) ... dpkg: warning: ignoring request to remove perl-modules-5.32 which isn't installed Purging configuration files for python3 (3.11.6-1) ... dpkg: warning: ignoring request to remove python3-decorator which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-networkx which isn't installed dpkg: warning: ignoring request to remove python3-numpy which isn't installed dpkg: warning: ignoring request to remove python3-packaging which isn't installed dpkg: warning: ignoring request to remove python3-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python3-pysam 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) ... dpkg: warning: ignoring request to remove python3.12 which isn't installed Purging configuration files for python3.12-minimal (3.12.1-2) ... dpkg: warning: ignoring request to remove python3.9 which isn't installed Purging configuration files for python3.9-minimal (3.9.2-1) ... Purging configuration files for readline-common (8.2-3) ... dpkg: warning: ignoring request to remove samtools which isn't installed dpkg: warning: ignoring request to remove sensible-utils which isn't installed dpkg: warning: ignoring request to remove smalt which isn't installed Purging configuration files for ucf (3.0043+nmu1) ... 1m44.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'dpkg', '--purge', 'ca-certificates', 'ca-certificates-java', 'default-jre-headless', 'fastaq', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'gawk', 'java-common', 'kmc', 'libasound2:amd64', 'libasound2-data', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbambamc0:amd64', 'libblas3:amd64', 'libbrotli1:amd64', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libdbus-1-3:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgraphite2-3:amd64', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libjpeg62-turbo:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-2.5-0:amd64', 'libmpdec3:amd64', 'libmpfr6:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libpcsclite1:amd64', 'libperl5.32:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsigsegv2:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'media-types', 'mummer', 'netbase', 'openjdk-11-jre-headless:amd64', 'openjdk-17-jre-headless:amd64', 'openssl', 'perl-modules-5.32', 'python3', 'python3-decorator', 'python3-minimal', 'python3-networkx', 'python3-numpy', 'python3-packaging', 'python3-pkg-resources', 'python3-pysam', 'python3.11', 'python3.11-minimal', 'python3.12', 'python3.12-minimal', 'python3.9', 'python3.9-minimal', 'readline-common', 'samtools', 'sensible-utils', 'smalt', 'ucf'] 1m44.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'dpkg', '--purge', 'iva'] 1m44.8s DUMP: dpkg: warning: ignoring request to remove iva which isn't installed 1m44.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'dpkg', '--purge', 'iva'] 1m44.8s INFO: Running scripts post_purge 1m44.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/post_purge_exceptions'] 1m44.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/post_purge_exceptions'] 1m44.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'dpkg', '--purge', '--pending'] 1m44.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'dpkg', '--purge', '--pending'] 1m44.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'dpkg', '--remove', '--pending'] 1m44.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'dpkg', '--remove', '--pending'] 1m44.8s INFO: Running scripts post_test 1m44.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/post_test_exceptions'] 1m44.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'tmp/scripts/post_test_exceptions'] 1m44.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpncbapv2j'] 1m45.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpncbapv2j'] 1m45.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'dpkg-divert', '--list'] 1m45.4s DUMP: local diversion of /bin/sync to /bin/sync.distrib local diversion of /home to /home.distrib 1m45.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'dpkg-divert', '--list'] 1m45.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'apt-get', 'clean'] 1m45.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpncbapv2j', 'apt-get', 'clean'] 1m45.5s DEBUG: Recording chroot state 1m46.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpncbapv2j/dev/shm'] 1m46.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpncbapv2j/dev/shm'] 1m46.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpncbapv2j/dev/console'] 1m46.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpncbapv2j/dev/console'] 1m46.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpncbapv2j/dev/ptmx'] 1m46.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpncbapv2j/dev/ptmx'] 1m46.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpncbapv2j/dev/pts'] 1m46.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpncbapv2j/dev/pts'] 1m46.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpncbapv2j/proc'] 1m47.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpncbapv2j/proc'] 1m47.0s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpncbapv2j'] 1m47.1s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpncbapv2j'] 1m47.1s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpncbapv2j 1m47.1s INFO: PASS: Upgrading between Debian distributions. 1m47.1s INFO: PASS: All tests. 1m47.1s INFO: piuparts run ends. ret=0 End: 2024-02-01 22:23:47 GMT