Start: 2021-10-20 04:59:02 GMT [oldstable] Package: iva Version: 1.0.9+ds-6 Installed-Size: 8766 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: fastaq (>= 1.6), python3-networkx, python3-pysam, python3: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-6_amd64.deb Size: 8578172 MD5sum: 31d1c6798ee139eb5f98dc4195e3bb97 SHA256: d3ee51ec2c8816ebe93d9c2aa6e337ebc87f76139120efc534577fd05d5c6894 [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 [testing] Package: iva Version: 1.0.11+ds-1 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-1_amd64.deb Size: 8581916 MD5sum: d959f23643f7b09bba4dade6c9db4733 SHA256: 3332a1bc2771ce3aecd95ac3c7f6a12382b39411379d32eafe84899843a923a3 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 --warn-on-debsums-errors --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/buster_amd64.tar.gz -d oldstable -d stable -d testing -B /srv/piuparts.debian.org/slave/refchroot/oldstable22testing/reference-chroot-metadata.dat --apt iva=1.0.11+ds-1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.1.4 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 --warn-on-debsums-errors --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/buster_amd64.tar.gz -d oldstable -d stable -d testing -B /srv/piuparts.debian.org/slave/refchroot/oldstable22testing/reference-chroot-metadata.dat --apt iva=1.0.11+ds-1 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 4.19.0-18-amd64 #1 SMP Debian 4.19.208-1 (2021-09-29) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpt6l8nlya 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/buster_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpt6l8nlya 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/buster_amd64.tar.gz'] 0m1.8s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/buster_amd64.tar.gz'] 0m1.8s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya/proc'] 0m1.9s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya/proc'] 0m1.9s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya/dev/pts'] 0m1.9s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya/dev/pts'] 0m1.9s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya/dev/ptmx'] 0m1.9s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya/dev/ptmx'] 0m1.9s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya/dev/console'] 0m1.9s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya/dev/console'] 0m1.9s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya/dev/shm'] 0m1.9s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya/dev/shm'] 0m1.9s DEBUG: sources.list: deb http://deb.debian.org/debian/ buster main 0m1.9s DEBUG: Created policy-rc.d and chmodded it. 0m1.9s DEBUG: Created resolv.conf. 0m1.9s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpt6l8nlya/tmp/scripts/ 0m1.9s INFO: Running scripts post_chroot_unpack 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-get', 'update'] 0m5.3s DUMP: Get:1 http://deb.debian.org/debian buster InRelease [122 kB] Get:2 http://deb.debian.org/debian buster/main amd64 Packages [7906 kB] Get:3 http://deb.debian.org/debian buster/main Translation-en [5968 kB] Fetched 14.0 MB in 3s (5243 kB/s) Reading package lists... 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-get', 'update'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-get', '-yf', 'dist-upgrade'] 0m6.7s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: base-files debconf libhogweed4 libnettle6 libsystemd0 libudev1 tzdata 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 1319 kB of archives. After this operation, 0 B of additional disk space will be used. Get:1 http://deb.debian.org/debian buster/main amd64 base-files amd64 10.3+deb10u11 [69.9 kB] Get:2 http://deb.debian.org/debian buster/main amd64 debconf all 1.5.71+deb10u1 [145 kB] Get:3 http://deb.debian.org/debian buster/main amd64 libsystemd0 amd64 241-7~deb10u8 [331 kB] Get:4 http://deb.debian.org/debian buster/main amd64 libnettle6 amd64 3.4.1-1+deb10u1 [215 kB] Get:5 http://deb.debian.org/debian buster/main amd64 libhogweed4 amd64 3.4.1-1+deb10u1 [141 kB] Get:6 http://deb.debian.org/debian buster/main amd64 libudev1 amd64 241-7~deb10u8 [151 kB] Get:7 http://deb.debian.org/debian buster/main amd64 tzdata all 2021a-0+deb10u2 [266 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1319 kB in 0s (29.2 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6460 files and directories currently installed.) Preparing to unpack .../base-files_10.3+deb10u11_amd64.deb ... Unpacking base-files (10.3+deb10u11) over (10.3+deb10u10) ... Setting up base-files (10.3+deb10u11) ... Installing new version of config file /etc/debian_version ... (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 ... 6460 files and directories currently installed.) Preparing to unpack .../debconf_1.5.71+deb10u1_all.deb ... Unpacking debconf (1.5.71+deb10u1) over (1.5.71) ... Setting up debconf (1.5.71+deb10u1) ... (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 ... 6460 files and directories currently installed.) Preparing to unpack .../libsystemd0_241-7~deb10u8_amd64.deb ... Unpacking libsystemd0:amd64 (241-7~deb10u8) over (241-7~deb10u7) ... Setting up libsystemd0:amd64 (241-7~deb10u8) ... (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 ... 6460 files and directories currently installed.) Preparing to unpack .../libnettle6_3.4.1-1+deb10u1_amd64.deb ... Unpacking libnettle6:amd64 (3.4.1-1+deb10u1) over (3.4.1-1) ... Setting up libnettle6:amd64 (3.4.1-1+deb10u1) ... (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 ... 6460 files and directories currently installed.) Preparing to unpack .../libhogweed4_3.4.1-1+deb10u1_amd64.deb ... Unpacking libhogweed4:amd64 (3.4.1-1+deb10u1) over (3.4.1-1) ... Setting up libhogweed4:amd64 (3.4.1-1+deb10u1) ... (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 ... 6460 files and directories currently installed.) Preparing to unpack .../libudev1_241-7~deb10u8_amd64.deb ... Unpacking libudev1:amd64 (241-7~deb10u8) over (241-7~deb10u7) ... Setting up libudev1:amd64 (241-7~deb10u8) ... (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 ... 6460 files and directories currently installed.) Preparing to unpack .../tzdata_2021a-0+deb10u2_all.deb ... Unpacking tzdata (2021a-0+deb10u2) over (2021a-0+deb10u1) ... Setting up tzdata (2021a-0+deb10u2) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Oct 20 04:59:08 UTC 2021. Universal Time is now: Wed Oct 20 04:59:08 UTC 2021. Run 'dpkg-reconfigure tzdata' if you wish to change it. Processing triggers for libc-bin (2.28-10) ... 0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-get', '-yf', 'dist-upgrade'] 0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m7.0s DUMP: c93c23a13c49c4c6c576dd270f29e40e - 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m7.0s INFO: Running scripts post_setup 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_setup_dummy_users'] 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_setup_dummy_users'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_setup_forbid_home'] 0m7.9s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_setup_forbid_home'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_setup_force-unsafe-io'] 0m7.9s 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' 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_setup_force-unsafe-io'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_setup_minimize'] 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_setup_minimize'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_setup_squeeze-backports'] 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_setup_squeeze-backports'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_setup_zz_backports'] 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_setup_zz_backports'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m7.9s DUMP: install ok installed adduser adduser 3.118 install ok installed apt apt 1.8.2.3 install ok installed base-files base-files 10.3+deb10u11 install ok installed base-passwd base-passwd 3.5.46 install ok installed bash bash 5.0-4 install ok installed bsdutils bsdutils 1:2.33.1-0.1 install ok installed coreutils coreutils 8.30-3 install ok installed dash dash 0.5.10.2-5 install ok installed debconf debconf 1.5.71+deb10u1 install ok installed debian-archive-keyring debian-archive-keyring 2019.1+deb10u1 install ok installed debianutils debianutils 4.8.6.1 install ok installed diffutils diffutils 1:3.7-3 install ok installed dpkg dpkg 1.19.7 install ok installed e2fsprogs e2fsprogs 1.44.5-1+deb10u3 install ok installed fdisk fdisk 2.33.1-0.1 install ok installed findutils findutils 4.6.0+git+20190209-2 install ok installed gcc-8-base:amd64 gcc-8-base 8.3.0-6 install ok installed gpgv gpgv 2.2.12-1+deb10u1 install ok installed grep grep 3.3-1 install ok installed gzip gzip 1.9-3 install ok installed hostname hostname 3.21 install ok installed init-system-helpers init-system-helpers 1.56+nmu1 install ok installed libacl1:amd64 libacl1 2.2.53-4 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.8.2.3 install ok installed libattr1:amd64 libattr1 1:2.4.48-4 install ok installed libaudit-common libaudit-common 1:2.8.4-3 install ok installed libaudit1:amd64 libaudit1 1:2.8.4-3 install ok installed libblkid1:amd64 libblkid1 2.33.1-0.1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-9.2~deb10u1 install ok installed libc-bin libc-bin 2.28-10 install ok installed libc6:amd64 libc6 2.28-10 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2 install ok installed libcom-err2:amd64 libcom-err2 1.44.5-1+deb10u3 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.5 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.249 install ok installed libext2fs2:amd64 libext2fs2 1.44.5-1+deb10u3 install ok installed libfdisk1:amd64 libfdisk1 2.33.1-0.1 install ok installed libffi6:amd64 libffi6 3.2.1-9 install ok installed libgcc1:amd64 libgcc1 1:8.3.0-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.4-5+deb10u1 install ok installed libgmp10:amd64 libgmp10 2:6.1.2+dfsg-4 install ok installed libgnutls30:amd64 libgnutls30 3.6.7-4+deb10u7 install ok installed libgpg-error0:amd64 libgpg-error0 1.35-1 install ok installed libhogweed4:amd64 libhogweed4 3.4.1-1+deb10u1 install ok installed libidn2-0:amd64 libidn2-0 2.0.5-1+deb10u1 install ok installed liblz4-1:amd64 liblz4-1 1.8.3-1+deb10u1 install ok installed liblzma5:amd64 liblzma5 5.2.4-1 install ok installed libmount1:amd64 libmount1 2.33.1-0.1 install ok installed libncursesw6:amd64 libncursesw6 6.1+20181013-2+deb10u2 install ok installed libnettle6:amd64 libnettle6 3.4.1-1+deb10u1 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.15-2+deb10u1 install ok installed libpam-modules:amd64 libpam-modules 1.3.1-5 install ok installed libpam-modules-bin libpam-modules-bin 1.3.1-5 install ok installed libpam-runtime libpam-runtime 1.3.1-5 install ok installed libpam0g:amd64 libpam0g 1.3.1-5 install ok installed libpcre3:amd64 libpcre3 2:8.39-12 install ok installed libseccomp2:amd64 libseccomp2 2.3.3-4 install ok installed libselinux1:amd64 libselinux1 2.8-1+b1 install ok installed libsemanage-common libsemanage-common 2.8-2 install ok installed libsemanage1:amd64 libsemanage1 2.8-2 install ok installed libsepol1:amd64 libsepol1 2.8-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.33.1-0.1 install ok installed libss2:amd64 libss2 1.44.5-1+deb10u3 install ok installed libstdc++6:amd64 libstdc++6 8.3.0-6 install ok installed libsystemd0:amd64 libsystemd0 241-7~deb10u8 install ok installed libtasn1-6:amd64 libtasn1-6 4.13-3 install ok installed libtinfo6:amd64 libtinfo6 6.1+20181013-2+deb10u2 install ok installed libudev1:amd64 libudev1 241-7~deb10u8 install ok installed libunistring2:amd64 libunistring2 0.9.10-1 install ok installed libuuid1:amd64 libuuid1 2.33.1-0.1 install ok installed libzstd1:amd64 libzstd1 1.3.8+dfsg-3+deb10u2 install ok installed login login 1:4.5-1.1 install ok installed mawk mawk 1.3.3-17+b3 install ok installed mount mount 2.33.1-0.1 install ok installed ncurses-base ncurses-base 6.1+20181013-2+deb10u2 install ok installed ncurses-bin ncurses-bin 6.1+20181013-2+deb10u2 install ok installed passwd passwd 1:4.5-1.1 install ok installed perl-base perl-base 5.28.1-6+deb10u1 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.93-8 install ok installed tar tar 1.30+dfsg-6 install ok installed tzdata tzdata 2021a-0+deb10u2 install ok installed util-linux util-linux 2.33.1-0.1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-1 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m7.9s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/oldstable22testing/reference-chroot-metadata.dat 0m8.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya'] 0m8.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya'] 0m8.3s INFO: Running scripts is_testable 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/is_testable_uninstallable'] 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/is_testable_uninstallable'] 0m8.3s INFO: Running scripts pre_test 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_test_exceptions'] 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_test_exceptions'] 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_test_root_password'] 0m8.3s DUMP: New password: Retype new password: passwd: password updated successfully 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_test_root_password'] 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-cache', 'show', '--no-all-versions', 'iva'] 0m8.5s DUMP: Package: iva Version: 1.0.9+ds-6 Installed-Size: 8766 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: fastaq (>= 1.6), python3-networkx, python3-pysam, python3: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-6_amd64.deb Size: 8578172 MD5sum: 31d1c6798ee139eb5f98dc4195e3bb97 SHA256: d3ee51ec2c8816ebe93d9c2aa6e337ebc87f76139120efc534577fd05d5c6894 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-cache', 'show', '--no-all-versions', 'iva'] 0m8.5s INFO: apt-cache knows about the following packages: iva 0m8.5s INFO: Running scripts pre_install 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_install_database-server'] 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_install_database-server'] 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_install_exceptions'] 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_install_exceptions'] 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_install_extras'] 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_install_extras'] 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_install_foreign_architecture'] 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_install_foreign_architecture'] 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-cache', 'policy'] 0m8.6s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian buster/main amd64 Packages release v=10.11,o=Debian,a=oldstable,n=buster,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-cache', 'policy'] 0m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-cache', 'policy', 'iva'] 0m8.6s DUMP: iva: Installed: (none) Candidate: 1.0.9+ds-6 Version table: 1.0.9+ds-6 500 500 http://deb.debian.org/debian buster/main amd64 Packages 0m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-cache', 'policy', 'iva'] 0m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-get', '-y', 'install', 'iva'] 0m29.2s DUMP: Reading package lists... Building dependency tree... Reading state information... 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 libcups2 libcurl3-gnutls libdbus-1-3 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libgdbm-compat4 libgdbm6 libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts2 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 libldap-common libmpdec2 libmpfr6 libncurses6 libnghttp2-14 libnspr4 libnss3 libpcsclite1 libperl5.28 libpng16-16 libpsl5 libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libquadmath0 libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsqlite3-0 libssh2-1 libssl1.1 mime-support mummer openjdk-11-jre-headless openssl perl perl-modules-5.28 python3 python3-decorator python3-minimal python3-networkx python3-numpy python3-pkg-resources python3-pysam python3.7 python3.7-minimal readline-common samtools sensible-utils smalt ucf Suggested packages: default-jre gawk-doc libasound2-plugins alsa-utils cups-common gdbm-l10n krb5-doc krb5-user 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 libb-debug-perl liblocale-codes-perl python3-doc python3-tk python3-venv python-networkx-doc gcc gfortran python-numpy-doc python3-dev python3-pytest python3-numpy-dbg python3-setuptools python3.7-venv python3.7-doc binutils binfmt-support readline-doc Recommended packages: r-base-core bioperl trimmomatic dbus libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales libgpm2 publicsuffix libsasl2-modules bzip2 file xz-utils netbase python3-gdal python3-scipy python3-yaml python cwltool 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 libcups2 libcurl3-gnutls libdbus-1-3 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libgdbm-compat4 libgdbm6 libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts2 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 libldap-common libmpdec2 libmpfr6 libncurses6 libnghttp2-14 libnspr4 libnss3 libpcsclite1 libperl5.28 libpng16-16 libpsl5 libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libquadmath0 libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsqlite3-0 libssh2-1 libssl1.1 mime-support mummer openjdk-11-jre-headless openssl perl perl-modules-5.28 python3 python3-decorator python3-minimal python3-networkx python3-numpy python3-pkg-resources python3-pysam python3.7 python3.7-minimal readline-common samtools sensible-utils smalt ucf 0 upgraded, 84 newly installed, 0 to remove and 0 not upgraded. Need to get 82.4 MB of archives. After this operation, 328 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian buster/main amd64 perl-modules-5.28 all 5.28.1-6+deb10u1 [2873 kB] Get:2 http://deb.debian.org/debian buster/main amd64 libgdbm6 amd64 1.18.1-4 [64.7 kB] Get:3 http://deb.debian.org/debian buster/main amd64 libgdbm-compat4 amd64 1.18.1-4 [44.1 kB] Get:4 http://deb.debian.org/debian buster/main amd64 libperl5.28 amd64 5.28.1-6+deb10u1 [3894 kB] Get:5 http://deb.debian.org/debian buster/main amd64 perl amd64 5.28.1-6+deb10u1 [204 kB] Get:6 http://deb.debian.org/debian buster/main amd64 libmpfr6 amd64 4.0.2-1 [775 kB] Get:7 http://deb.debian.org/debian buster/main amd64 readline-common all 7.0-5 [70.6 kB] Get:8 http://deb.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get:9 http://deb.debian.org/debian buster/main amd64 libsigsegv2 amd64 2.12-2 [32.8 kB] Get:10 http://deb.debian.org/debian buster/main amd64 gawk amd64 1:4.2.1+dfsg-1 [660 kB] Get:11 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1d-0+deb10u7 [1539 kB] Get:12 http://deb.debian.org/debian buster/main amd64 libpython3.7-minimal amd64 3.7.3-2+deb10u3 [589 kB] Get:13 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u1 [106 kB] Get:14 http://deb.debian.org/debian buster/main amd64 python3.7-minimal amd64 3.7.3-2+deb10u3 [1737 kB] Get:15 http://deb.debian.org/debian buster/main amd64 python3-minimal amd64 3.7.3-1 [36.6 kB] Get:16 http://deb.debian.org/debian buster/main amd64 mime-support all 3.62 [37.2 kB] Get:17 http://deb.debian.org/debian buster/main amd64 libmpdec2 amd64 2.4.2-2 [87.2 kB] Get:18 http://deb.debian.org/debian buster/main amd64 libsqlite3-0 amd64 3.27.2-3+deb10u1 [641 kB] Get:19 http://deb.debian.org/debian buster/main amd64 libpython3.7-stdlib amd64 3.7.3-2+deb10u3 [1734 kB] Get:20 http://deb.debian.org/debian buster/main amd64 python3.7 amd64 3.7.3-2+deb10u3 [330 kB] Get:21 http://deb.debian.org/debian buster/main amd64 libpython3-stdlib amd64 3.7.3-1 [20.0 kB] Get:22 http://deb.debian.org/debian buster/main amd64 python3 amd64 3.7.3-1 [61.5 kB] Get:23 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get:24 http://deb.debian.org/debian buster/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get:25 http://deb.debian.org/debian buster/main amd64 openssl amd64 1.1.1d-0+deb10u7 [845 kB] Get:26 http://deb.debian.org/debian buster/main amd64 ca-certificates all 20200601~deb10u2 [166 kB] Get:27 http://deb.debian.org/debian buster/main amd64 java-common all 0.71 [14.4 kB] Get:28 http://deb.debian.org/debian buster/main amd64 libavahi-common-data amd64 0.7-4+deb10u1 [122 kB] Get:29 http://deb.debian.org/debian buster/main amd64 libavahi-common3 amd64 0.7-4+deb10u1 [54.4 kB] Get:30 http://deb.debian.org/debian buster/main amd64 libdbus-1-3 amd64 1.12.20-0+deb10u1 [215 kB] Get:31 http://deb.debian.org/debian buster/main amd64 libavahi-client3 amd64 0.7-4+deb10u1 [58.2 kB] Get:32 http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get:33 http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u3 [65.8 kB] Get:34 http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u3 [122 kB] Get:35 http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u3 [370 kB] Get:36 http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u3 [158 kB] Get:37 http://deb.debian.org/debian buster/main amd64 libcups2 amd64 2.2.10-6+deb10u4 [324 kB] Get:38 http://deb.debian.org/debian buster/main amd64 liblcms2-2 amd64 2.9-3 [145 kB] Get:39 http://deb.debian.org/debian buster/main amd64 libjpeg62-turbo amd64 1:1.5.2-2+deb10u1 [133 kB] Get:40 http://deb.debian.org/debian buster/main amd64 libpng16-16 amd64 1.6.36-6 [292 kB] Get:41 http://deb.debian.org/debian buster/main amd64 libfreetype6 amd64 2.9.1-3+deb10u2 [380 kB] Get:42 http://deb.debian.org/debian buster/main amd64 fonts-dejavu-core all 2.37-1 [1068 kB] Get:43 http://deb.debian.org/debian buster/main amd64 fontconfig-config all 2.13.1-2 [280 kB] Get:44 http://deb.debian.org/debian buster/main amd64 libfontconfig1 amd64 2.13.1-2 [346 kB] Get:45 http://deb.debian.org/debian buster/main amd64 libnspr4 amd64 2:4.20-1 [112 kB] Get:46 http://deb.debian.org/debian buster/main amd64 libnss3 amd64 2:3.42.1-1+deb10u3 [1159 kB] Get:47 http://deb.debian.org/debian buster/main amd64 libasound2-data all 1.1.8-1 [59.6 kB] Get:48 http://deb.debian.org/debian buster/main amd64 libasound2 amd64 1.1.8-1 [361 kB] Get:49 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u3 [1259 kB] Get:50 http://deb.debian.org/debian buster/main amd64 libgraphite2-3 amd64 1.3.13-7 [80.7 kB] Get:51 http://deb.debian.org/debian buster/main amd64 libharfbuzz0b amd64 2.3.1-1 [1187 kB] Get:52 http://deb.debian.org/debian buster/main amd64 libpcsclite1 amd64 1.8.24-1 [58.5 kB] Get:53 http://deb.debian.org/debian buster/main amd64 openjdk-11-jre-headless amd64 11.0.12+7-2~deb10u1 [37.2 MB] Get:54 http://deb.debian.org/debian buster/main amd64 default-jre-headless amd64 2:1.11-71 [10.9 kB] Get:55 http://deb.debian.org/debian buster/main amd64 ca-certificates-java all 20190405 [15.7 kB] Get:56 http://deb.debian.org/debian buster/main amd64 python3-pkg-resources all 40.8.0-1 [153 kB] Get:57 http://deb.debian.org/debian buster/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-1+deb10u1 [69.1 kB] Get:58 http://deb.debian.org/debian buster/main amd64 libsasl2-2 amd64 2.1.27+dfsg-1+deb10u1 [106 kB] Get:59 http://deb.debian.org/debian buster/main amd64 libldap-common all 2.4.47+dfsg-3+deb10u6 [90.0 kB] Get:60 http://deb.debian.org/debian buster/main amd64 libldap-2.4-2 amd64 2.4.47+dfsg-3+deb10u6 [224 kB] Get:61 http://deb.debian.org/debian buster/main amd64 libnghttp2-14 amd64 1.36.0-2+deb10u1 [85.0 kB] Get:62 http://deb.debian.org/debian buster/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get:63 http://deb.debian.org/debian buster/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [60.5 kB] Get:64 http://deb.debian.org/debian buster/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get:65 http://deb.debian.org/debian buster/main amd64 libcurl3-gnutls amd64 7.64.0-4+deb10u2 [330 kB] Get:66 http://deb.debian.org/debian buster/main amd64 libdeflate0 amd64 1.2-1 [55.4 kB] Get:67 http://deb.debian.org/debian buster/main amd64 libhts2 amd64 1.9-12~deb10u1 [305 kB] Get:68 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get:69 http://deb.debian.org/debian buster/main amd64 samtools amd64 1.9-4 [443 kB] Get:70 http://deb.debian.org/debian buster/main amd64 fastaq all 3.17.0-2 [47.8 kB] Get:71 http://deb.debian.org/debian buster/main amd64 python3-decorator all 4.3.0-1.1 [14.5 kB] Get:72 http://deb.debian.org/debian buster/main amd64 python3-networkx all 2.2-1 [818 kB] Get:73 http://deb.debian.org/debian buster/main amd64 python3-pysam amd64 0.15.2+ds-2 [1661 kB] Get:74 http://deb.debian.org/debian buster/main amd64 libgomp1 amd64 8.3.0-6 [75.8 kB] Get:75 http://deb.debian.org/debian buster/main amd64 kmc amd64 2.3+dfsg-7 [466 kB] Get:76 http://deb.debian.org/debian buster/main amd64 mummer amd64 3.23+dfsg-4 [809 kB] Get:77 http://deb.debian.org/debian buster/main amd64 libbambamc0 amd64 0.0.50-3 [37.9 kB] Get:78 http://deb.debian.org/debian buster/main amd64 smalt amd64 0.7.6-8 [113 kB] Get:79 http://deb.debian.org/debian buster/main amd64 libquadmath0 amd64 8.3.0-6 [133 kB] Get:80 http://deb.debian.org/debian buster/main amd64 libgfortran5 amd64 8.3.0-6 [581 kB] Get:81 http://deb.debian.org/debian buster/main amd64 libblas3 amd64 3.8.0-2 [148 kB] Get:82 http://deb.debian.org/debian buster/main amd64 liblapack3 amd64 3.8.0-2 [2110 kB] Get:83 http://deb.debian.org/debian buster/main amd64 python3-numpy amd64 1:1.16.2-1 [2119 kB] Get:84 http://deb.debian.org/debian buster/main amd64 iva amd64 1.0.9+ds-6 [8578 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 82.4 MB in 2s (49.1 MB/s) Selecting previously unselected package perl-modules-5.28. 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No schema files found: doing nothing. Setting up libsqlite3-0:amd64 (3.27.2-3+deb10u1) ... Setting up libnghttp2-14:amd64 (1.36.0-2+deb10u1) ... Setting up libdeflate0:amd64 (1.2-1) ... Setting up libgomp1:amd64 (8.3.0-6) ... Setting up libldap-common (2.4.47+dfsg-3+deb10u6) ... Setting up libkrb5support0:amd64 (1.17-3+deb10u3) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-1+deb10u1) ... Setting up libasound2-data (1.1.8-1) ... Setting up libjpeg62-turbo:amd64 (1:1.5.2-2+deb10u1) ... Setting up libnspr4:amd64 (2:4.20-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Setting up libavahi-common-data:amd64 (0.7-4+deb10u1) ... Setting up libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Setting up libdbus-1-3:amd64 (1.12.20-0+deb10u1) ... Setting up libquadmath0:amd64 (8.3.0-6) ... Setting up libbambamc0 (0.0.50-3) ... Setting up libpng16-16:amd64 (1.6.36-6) ... Setting up fonts-dejavu-core (2.37-1) ... Setting up libpcsclite1:amd64 (1.8.24-1) ... Setting up libk5crypto3:amd64 (1.17-3+deb10u3) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-1+deb10u1) ... Setting up libgfortran5:amd64 (8.3.0-6) ... Setting up sensible-utils (0.0.12) ... Setting up libasound2:amd64 (1.1.8-1) ... Setting up libssh2-1:amd64 (1.8.0-2.1) ... Setting up libkrb5-3:amd64 (1.17-3+deb10u3) ... Setting up libmpdec2:amd64 (2.4.2-2) ... Setting up openssl (1.1.1d-0+deb10u7) ... Setting up kmc (2.3+dfsg-7) ... Setting up libgdbm6:amd64 (1.18.1-4) ... Setting up smalt (0.7.6-8) ... Setting up libpython3.7-stdlib:amd64 (3.7.3-2+deb10u3) ... Setting up libavahi-common3:amd64 (0.7-4+deb10u1) ... Setting up libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u6) ... Setting up libnss3:amd64 (2:3.42.1-1+deb10u3) ... Setting up ca-certificates (20200601~deb10u2) ... Updating certificates in /etc/ssl/certs... 137 added, 0 removed; done. Setting up libblas3:amd64 (3.8.0-2) ... 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 libfreetype6:amd64 (2.9.1-3+deb10u2) ... Setting up libgssapi-krb5-2:amd64 (1.17-3+deb10u3) ... Setting up libgdbm-compat4:amd64 (1.18.1-4) ... Setting up ucf (3.0038+nmu1) ... Setting up libperl5.28:amd64 (5.28.1-6+deb10u1) ... Setting up libharfbuzz0b:amd64 (2.3.1-1) ... Setting up libavahi-client3:amd64 (0.7-4+deb10u1) ... Setting up libpython3-stdlib:amd64 (3.7.3-1) ... Setting up python3.7 (3.7.3-2+deb10u3) ... Setting up liblapack3:amd64 (3.8.0-2) ... 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 fontconfig-config (2.13.1-2) ... Setting up libcurl3-gnutls:amd64 (7.64.0-4+deb10u2) ... Setting up python3 (3.7.3-1) ... Setting up python3-decorator (4.3.0-1.1) ... Setting up perl (5.28.1-6+deb10u1) ... Setting up libcups2:amd64 (2.2.10-6+deb10u4) ... Setting up mummer (3.23+dfsg-4) ... Setting up libfontconfig1:amd64 (2.13.1-2) ... Setting up python3-pkg-resources (40.8.0-1) ... Setting up libhts2:amd64 (1.9-12~deb10u1) ... Setting up python3-networkx (2.2-1) ... Setting up samtools (1.9-4) ... Setting up python3-numpy (1:1.16.2-1) ... Setting up python3-pysam (0.15.2+ds-2) ... Setting up fastaq (3.17.0-2) ... Setting up default-jre-headless (2:1.11-71) ... Setting up iva (1.0.9+ds-6) ... Setting up openjdk-11-jre-headless:amd64 (11.0.12+7-2~deb10u1) ... 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 (20190405) ... head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory Adding debian:thawte_Primary_Root_CA_-_G3.pem Adding debian:thawte_Primary_Root_CA_-_G2.pem Adding debian:thawte_Primary_Root_CA.pem 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:certSIGN_ROOT_CA.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.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: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:Taiwan_GRCA.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_Root_CA_-_G2.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:OISTE_WISeKey_Global_Root_GA_CA.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:LuxTrust_Global_Root_2.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_Universal_CA_2.pem Adding debian:GeoTrust_Universal_CA.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:GeoTrust_Primary_Certification_Authority.pem Adding debian:GeoTrust_Global_CA.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:EE_Certification_Centre_Root_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. Processing triggers for libc-bin (2.28-10) ... Processing triggers for ca-certificates (20200601~deb10u2) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. done. 0m29.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-get', '-y', 'install', 'iva'] 0m29.2s INFO: Running scripts post_install 0m29.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_install_exceptions'] 0m29.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_install_exceptions'] 0m29.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya'] 0m29.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya'] 0m29.6s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpt6l8nlya to stable 0m29.6s DEBUG: sources.list: deb http://deb.debian.org/debian/ bullseye main 0m29.6s INFO: Running scripts pre_distupgrade 0m29.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m29.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m29.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_distupgrade_exceptions'] 0m29.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_distupgrade_exceptions'] 0m29.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m29.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m29.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m29.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m29.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m29.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m29.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-get', 'update'] 0m33.3s DUMP: Get:1 http://deb.debian.org/debian bullseye InRelease [116 kB] Get:2 http://deb.debian.org/debian bullseye/main amd64 Packages [8180 kB] Get:3 http://deb.debian.org/debian bullseye/main Translation-en [6241 kB] Fetched 14.5 MB in 3s (5029 kB/s) Reading package lists... 0m33.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-get', 'update'] 0m33.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-get', '-yf', 'dist-upgrade'] 1m5.6s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libgomp1 libhts2 libmpdec2 libperl5.28 libpython3.7-minimal libpython3.7-stdlib libreadline7 perl-modules-5.28 python3.7 python3.7-minimal Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: gcc-10-base libapt-pkg6.0 libbrotli1 libcrypt1 libffi7 libgcc-s1 libhogweed6 libhts3 libmpdec3 libnettle8 libnsl2 libpcre2-8-0 libperl5.32 libpython3.9-minimal libpython3.9-stdlib libreadline8 libtirpc-common libtirpc3 libxxhash0 logsave lsb-base mailcap media-types perl-modules-5.32 python3.9 python3.9-minimal The following packages will be upgraded: 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 fdisk findutils fontconfig-config fonts-dejavu-core gawk gpgv grep gzip hostname init-system-helpers iva java-common kmc libacl1 libasound2 libasound2-data libattr1 libaudit-common libaudit1 libavahi-client3 libavahi-common-data libavahi-common3 libbambamc0 libblas3 libblkid1 libbz2-1.0 libc-bin libc6 libcap-ng0 libcom-err2 libcups2 libcurl3-gnutls libdb5.3 libdbus-1-3 libdebconfclient0 libdeflate0 libexpat1 libext2fs2 libfdisk1 libfontconfig1 libfreetype6 libgcrypt20 libgdbm-compat4 libgdbm6 libgfortran5 libglib2.0-0 libgmp10 libgnutls30 libgomp1 libgpg-error0 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libidn2-0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 libldap-common liblz4-1 liblzma5 libmount1 libmpfr6 libncurses6 libncursesw6 libnghttp2-14 libnspr4 libnss3 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre3 libpcsclite1 libpng16-16 libpsl5 libpython3-stdlib libquadmath0 librtmp1 libsasl2-2 libsasl2-modules-db libseccomp2 libselinux1 libsemanage-common libsemanage1 libsepol1 libsigsegv2 libsmartcols1 libsqlite3-0 libss2 libssh2-1 libssl1.1 libstdc++6 libsystemd0 libtasn1-6 libtinfo6 libudev1 libunistring2 libuuid1 libzstd1 login mawk mime-support 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 sensible-utils smalt sysvinit-utils tar tzdata ucf util-linux zlib1g 151 upgraded, 26 newly installed, 0 to remove and 0 not upgraded. Need to get 121 MB of archives. After this operation, 88.4 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main amd64 base-files amd64 11.1+deb11u1 [70.0 kB] Get:2 http://deb.debian.org/debian bullseye/main amd64 debianutils amd64 4.11.2 [101 kB] Get:3 http://deb.debian.org/debian bullseye/main amd64 bash amd64 5.1-2+b3 [1416 kB] Get:4 http://deb.debian.org/debian bullseye/main amd64 bsdutils amd64 1:2.36.1-8 [148 kB] Get:5 http://deb.debian.org/debian bullseye/main amd64 gcc-10-base amd64 10.2.1-6 [201 kB] Get:6 http://deb.debian.org/debian bullseye/main amd64 libgcc-s1 amd64 10.2.1-6 [41.4 kB] Get:7 http://deb.debian.org/debian bullseye/main amd64 libcrypt1 amd64 1:4.4.18-4 [87.5 kB] Get:8 http://deb.debian.org/debian bullseye/main amd64 libc6 amd64 2.31-13+deb11u2 [2814 kB] Get:9 http://deb.debian.org/debian bullseye/main amd64 libc-bin amd64 2.31-13+deb11u2 [817 kB] Get:10 http://deb.debian.org/debian bullseye/main amd64 libpcre2-8-0 amd64 10.36-2 [247 kB] Get:11 http://deb.debian.org/debian bullseye/main amd64 libselinux1 amd64 3.1-3 [88.1 kB] Get:12 http://deb.debian.org/debian bullseye/main amd64 coreutils amd64 8.32-4+b1 [2867 kB] Get:13 http://deb.debian.org/debian bullseye/main amd64 tar amd64 1.34+dfsg-1 [847 kB] Get:14 http://deb.debian.org/debian bullseye/main amd64 dpkg amd64 1.20.9 [2472 kB] Get:15 http://deb.debian.org/debian bullseye/main amd64 perl-modules-5.32 all 5.32.1-4+deb11u2 [2823 kB] Get:16 http://deb.debian.org/debian bullseye/main amd64 libperl5.32 amd64 5.32.1-4+deb11u2 [4106 kB] Get:17 http://deb.debian.org/debian bullseye/main amd64 perl amd64 5.32.1-4+deb11u2 [293 kB] Get:18 http://deb.debian.org/debian bullseye/main amd64 perl-base amd64 5.32.1-4+deb11u2 [1628 kB] Get:19 http://deb.debian.org/debian bullseye/main amd64 libbz2-1.0 amd64 1.0.8-4 [45.8 kB] Get:20 http://deb.debian.org/debian bullseye/main amd64 libdb5.3 amd64 5.3.28+dfsg1-0.8 [687 kB] Get:21 http://deb.debian.org/debian bullseye/main amd64 libgdbm6 amd64 1.19-2 [64.9 kB] Get:22 http://deb.debian.org/debian bullseye/main amd64 libgdbm-compat4 amd64 1.19-2 [44.7 kB] Get:23 http://deb.debian.org/debian bullseye/main amd64 zlib1g amd64 1:1.2.11.dfsg-2 [90.4 kB] Get:24 http://deb.debian.org/debian bullseye/main amd64 debconf all 1.5.77 [144 kB] Get:25 http://deb.debian.org/debian bullseye/main amd64 dash amd64 0.5.11+git20200708+dd9ef66-5 [115 kB] Get:26 http://deb.debian.org/debian bullseye/main amd64 diffutils amd64 1:3.7-5 [373 kB] Get:27 http://deb.debian.org/debian bullseye/main amd64 findutils amd64 4.8.0-1 [697 kB] Get:28 http://deb.debian.org/debian bullseye/main amd64 grep amd64 3.6-1 [398 kB] Get:29 http://deb.debian.org/debian bullseye/main amd64 gzip amd64 1.10-4 [132 kB] Get:30 http://deb.debian.org/debian bullseye/main amd64 hostname amd64 3.23 [14.9 kB] Get:31 http://deb.debian.org/debian bullseye/main amd64 login amd64 1:4.8.1-1 [655 kB] Get:32 http://deb.debian.org/debian bullseye/main amd64 libncurses6 amd64 6.2+20201114-2 [102 kB] Get:33 http://deb.debian.org/debian bullseye/main amd64 libtinfo6 amd64 6.2+20201114-2 [341 kB] Get:34 http://deb.debian.org/debian bullseye/main amd64 libncursesw6 amd64 6.2+20201114-2 [132 kB] Get:35 http://deb.debian.org/debian bullseye/main amd64 ncurses-bin amd64 6.2+20201114-2 [428 kB] Get:36 http://deb.debian.org/debian bullseye/main amd64 libblkid1 amd64 2.36.1-8 [193 kB] Get:37 http://deb.debian.org/debian bullseye/main amd64 libmount1 amd64 2.36.1-8 [211 kB] Get:38 http://deb.debian.org/debian bullseye/main amd64 libsmartcols1 amd64 2.36.1-8 [157 kB] Get:39 http://deb.debian.org/debian bullseye/main amd64 libuuid1 amd64 2.36.1-8 [83.7 kB] Get:40 http://deb.debian.org/debian bullseye/main amd64 libfdisk1 amd64 2.36.1-8 [237 kB] Get:41 http://deb.debian.org/debian bullseye/main amd64 fdisk amd64 2.36.1-8 [192 kB] Get:42 http://deb.debian.org/debian bullseye/main amd64 util-linux amd64 2.36.1-8 [1139 kB] Get:43 http://deb.debian.org/debian bullseye/main amd64 libstdc++6 amd64 10.2.1-6 [493 kB] Get:44 http://deb.debian.org/debian bullseye/main amd64 libxxhash0 amd64 0.8.0-2 [26.9 kB] Get:45 http://deb.debian.org/debian bullseye/main amd64 libzstd1 amd64 1.4.8+dfsg-2.1 [319 kB] Get:46 http://deb.debian.org/debian bullseye/main amd64 libgpg-error0 amd64 1.38-2 [77.5 kB] Get:47 http://deb.debian.org/debian bullseye/main amd64 libgcrypt20 amd64 1.8.7-6 [563 kB] Get:48 http://deb.debian.org/debian bullseye/main amd64 liblz4-1 amd64 1.9.3-2 [57.5 kB] Get:49 http://deb.debian.org/debian bullseye/main amd64 liblzma5 amd64 5.2.5-2 [168 kB] Get:50 http://deb.debian.org/debian bullseye/main amd64 libsystemd0 amd64 247.3-6 [376 kB] Get:51 http://deb.debian.org/debian bullseye/main amd64 libudev1 amd64 247.3-6 [168 kB] Get:52 http://deb.debian.org/debian bullseye/main amd64 libapt-pkg6.0 amd64 2.2.4 [1013 kB] Get:53 http://deb.debian.org/debian bullseye/main amd64 libnettle8 amd64 3.7.3-1 [270 kB] Get:54 http://deb.debian.org/debian bullseye/main amd64 libgmp10 amd64 2:6.2.1+dfsg-1 [564 kB] Get:55 http://deb.debian.org/debian bullseye/main amd64 libhogweed6 amd64 3.7.3-1 [320 kB] Get:56 http://deb.debian.org/debian bullseye/main amd64 libffi7 amd64 3.3-6 [23.1 kB] Get:57 http://deb.debian.org/debian bullseye/main amd64 libp11-kit0 amd64 0.23.22-1 [337 kB] Get:58 http://deb.debian.org/debian bullseye/main amd64 libtasn1-6 amd64 4.16.0-2 [55.0 kB] Get:59 http://deb.debian.org/debian bullseye/main amd64 libunistring2 amd64 0.9.10-4 [379 kB] Get:60 http://deb.debian.org/debian bullseye/main amd64 libidn2-0 amd64 2.3.0-5 [86.1 kB] Get:61 http://deb.debian.org/debian bullseye/main amd64 libgnutls30 amd64 3.7.1-5 [1340 kB] Get:62 http://deb.debian.org/debian bullseye/main amd64 libseccomp2 amd64 2.5.1-1 [48.4 kB] Get:63 http://deb.debian.org/debian bullseye/main amd64 gpgv amd64 2.2.27-2 [626 kB] Get:64 http://deb.debian.org/debian bullseye/main amd64 debian-archive-keyring all 2021.1.1 [93.6 kB] Get:65 http://deb.debian.org/debian bullseye/main amd64 apt amd64 2.2.4 [1491 kB] Get:66 http://deb.debian.org/debian bullseye/main amd64 libdebconfclient0 amd64 0.260 [50.6 kB] Get:67 http://deb.debian.org/debian bullseye/main amd64 base-passwd amd64 3.5.51 [58.1 kB] Get:68 http://deb.debian.org/debian bullseye/main amd64 init-system-helpers all 1.60 [47.1 kB] Get:69 http://deb.debian.org/debian bullseye/main amd64 ncurses-base all 6.2+20201114-2 [271 kB] Get:70 http://deb.debian.org/debian bullseye/main amd64 lsb-base all 11.1.0 [28.7 kB] Get:71 http://deb.debian.org/debian bullseye/main amd64 sysvinit-utils amd64 2.96-7 [25.3 kB] Get:72 http://deb.debian.org/debian bullseye/main amd64 libtirpc-common all 1.3.1-1 [13.4 kB] Get:73 http://deb.debian.org/debian bullseye/main amd64 libgssapi-krb5-2 amd64 1.18.3-6+deb11u1 [165 kB] Get:74 http://deb.debian.org/debian bullseye/main amd64 libkrb5-3 amd64 1.18.3-6+deb11u1 [363 kB] Get:75 http://deb.debian.org/debian bullseye/main amd64 libk5crypto3 amd64 1.18.3-6+deb11u1 [114 kB] Get:76 http://deb.debian.org/debian bullseye/main amd64 libkrb5support0 amd64 1.18.3-6+deb11u1 [65.4 kB] Get:77 http://deb.debian.org/debian bullseye/main amd64 libcom-err2 amd64 1.46.2-2 [74.2 kB] Get:78 http://deb.debian.org/debian bullseye/main amd64 libkeyutils1 amd64 1.6.1-2 [15.4 kB] Get:79 http://deb.debian.org/debian bullseye/main amd64 libssl1.1 amd64 1.1.1k-1+deb11u1 [1554 kB] Get:80 http://deb.debian.org/debian bullseye/main amd64 libtirpc3 amd64 1.3.1-1 [83.6 kB] Get:81 http://deb.debian.org/debian bullseye/main amd64 libnsl2 amd64 1.3.0-2 [39.5 kB] Get:82 http://deb.debian.org/debian bullseye/main amd64 libaudit-common all 1:3.0-2 [14.8 kB] Get:83 http://deb.debian.org/debian bullseye/main amd64 libcap-ng0 amd64 0.7.9-2.2+b1 [14.8 kB] Get:84 http://deb.debian.org/debian bullseye/main amd64 libaudit1 amd64 1:3.0-2 [50.4 kB] Get:85 http://deb.debian.org/debian bullseye/main amd64 libpam0g amd64 1.4.0-9+deb11u1 [129 kB] Get:86 http://deb.debian.org/debian bullseye/main amd64 libpam-modules-bin amd64 1.4.0-9+deb11u1 [108 kB] Get:87 http://deb.debian.org/debian bullseye/main amd64 libpam-modules amd64 1.4.0-9+deb11u1 [326 kB] Get:88 http://deb.debian.org/debian bullseye/main amd64 libext2fs2 amd64 1.46.2-2 [257 kB] Get:89 http://deb.debian.org/debian bullseye/main amd64 e2fsprogs amd64 1.46.2-2 [615 kB] Get:90 http://deb.debian.org/debian bullseye/main amd64 logsave amd64 1.46.2-2 [74.9 kB] Get:91 http://deb.debian.org/debian bullseye/main amd64 mount amd64 2.36.1-8 [185 kB] Get:92 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get:93 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get:94 http://deb.debian.org/debian bullseye/main amd64 gawk amd64 1:5.1.0-1 [605 kB] Get:95 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-minimal amd64 3.9.2-1 [801 kB] Get:96 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2 [96.9 kB] Get:97 http://deb.debian.org/debian bullseye/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB] Get:98 http://deb.debian.org/debian bullseye/main amd64 python3-pysam amd64 0.15.4+ds-3+b2 [1536 kB] Get:99 http://deb.debian.org/debian bullseye/main amd64 python3-numpy amd64 1:1.19.5-1 [2693 kB] Get:100 http://deb.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get:101 http://deb.debian.org/debian bullseye/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get:102 http://deb.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get:103 http://deb.debian.org/debian bullseye/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2.1 [69.1 kB] Get:104 http://deb.debian.org/debian bullseye/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2.1 [106 kB] Get:105 http://deb.debian.org/debian bullseye/main amd64 libldap-2.4-2 amd64 2.4.57+dfsg-3 [232 kB] Get:106 http://deb.debian.org/debian bullseye/main amd64 libnghttp2-14 amd64 1.43.0-1 [77.1 kB] Get:107 http://deb.debian.org/debian bullseye/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get:108 http://deb.debian.org/debian bullseye/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:109 http://deb.debian.org/debian bullseye/main amd64 libssh2-1 amd64 1.9.0-2 [156 kB] Get:110 http://deb.debian.org/debian bullseye/main amd64 libcurl3-gnutls amd64 7.74.0-1.3+b1 [338 kB] Get:111 http://deb.debian.org/debian bullseye/main amd64 libdeflate0 amd64 1.7-1 [53.1 kB] Get:112 http://deb.debian.org/debian bullseye/main amd64 libhts3 amd64 1.11-4 [378 kB] Get:113 http://deb.debian.org/debian bullseye/main amd64 python3-pkg-resources all 52.0.0-4 [190 kB] Get:114 http://deb.debian.org/debian bullseye/main amd64 mime-support all 3.66 [10.9 kB] Get:115 http://deb.debian.org/debian bullseye/main amd64 mailcap all 3.69 [31.7 kB] Get:116 http://deb.debian.org/debian bullseye/main amd64 media-types all 4.0.0 [30.3 kB] Get:117 http://deb.debian.org/debian bullseye/main amd64 tzdata all 2021a-1+deb11u1 [284 kB] Get:118 http://deb.debian.org/debian bullseye/main amd64 libmpdec3 amd64 2.5.1-1 [87.7 kB] Get:119 http://deb.debian.org/debian bullseye/main amd64 libsqlite3-0 amd64 3.34.1-3 [797 kB] Get:120 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB] Get:121 http://deb.debian.org/debian bullseye/main amd64 python3.9 amd64 3.9.2-1 [466 kB] Get:122 http://deb.debian.org/debian bullseye/main amd64 libblas3 amd64 3.9.0-3 [153 kB] Get:123 http://deb.debian.org/debian bullseye/main amd64 libquadmath0 amd64 10.2.1-6 [145 kB] Get:124 http://deb.debian.org/debian bullseye/main amd64 libgfortran5 amd64 10.2.1-6 [727 kB] Get:125 http://deb.debian.org/debian bullseye/main amd64 liblapack3 amd64 3.9.0-3 [2166 kB] Get:126 http://deb.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get:127 http://deb.debian.org/debian bullseye/main amd64 libpam-runtime all 1.4.0-9+deb11u1 [207 kB] Get:128 http://deb.debian.org/debian bullseye/main amd64 libsepol1 amd64 3.1-1 [265 kB] Get:129 http://deb.debian.org/debian bullseye/main amd64 libsemanage-common all 3.1-1 [21.3 kB] Get:130 http://deb.debian.org/debian bullseye/main amd64 libsemanage1 amd64 3.1-1+b2 [99.3 kB] Get:131 http://deb.debian.org/debian bullseye/main amd64 passwd amd64 1:4.8.1-1 [990 kB] Get:132 http://deb.debian.org/debian bullseye/main amd64 libacl1 amd64 2.2.53-10 [31.1 kB] Get:133 http://deb.debian.org/debian bullseye/main amd64 libattr1 amd64 1:2.4.48-6 [21.6 kB] Get:134 http://deb.debian.org/debian bullseye/main amd64 libpcre3 amd64 2:8.39-13 [343 kB] Get:135 http://deb.debian.org/debian bullseye/main amd64 mawk amd64 1.3.4.20200120-2 [112 kB] Get:136 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get:137 http://deb.debian.org/debian bullseye/main amd64 openssl amd64 1.1.1k-1+deb11u1 [851 kB] Get:138 http://deb.debian.org/debian bullseye/main amd64 ca-certificates all 20210119 [158 kB] Get:139 http://deb.debian.org/debian bullseye/main amd64 ucf all 3.0043 [74.0 kB] Get:140 http://deb.debian.org/debian bullseye/main amd64 java-common all 0.72 [14.5 kB] Get:141 http://deb.debian.org/debian bullseye/main amd64 libavahi-common-data amd64 0.8-5 [124 kB] Get:142 http://deb.debian.org/debian bullseye/main amd64 libavahi-common3 amd64 0.8-5 [58.4 kB] Get:143 http://deb.debian.org/debian bullseye/main amd64 libdbus-1-3 amd64 1.12.20-2 [219 kB] Get:144 http://deb.debian.org/debian bullseye/main amd64 libavahi-client3 amd64 0.8-5 [62.1 kB] Get:145 http://deb.debian.org/debian bullseye/main amd64 libcups2 amd64 2.3.3op2-3+deb11u1 [350 kB] Get:146 http://deb.debian.org/debian bullseye/main amd64 liblcms2-2 amd64 2.12~rc1-2 [150 kB] Get:147 http://deb.debian.org/debian bullseye/main amd64 libjpeg62-turbo amd64 1:2.0.6-4 [151 kB] Get:148 http://deb.debian.org/debian bullseye/main amd64 fonts-dejavu-core all 2.37-2 [1069 kB] Get:149 http://deb.debian.org/debian bullseye/main amd64 fontconfig-config all 2.13.1-4.2 [281 kB] Get:150 http://deb.debian.org/debian bullseye/main amd64 libpng16-16 amd64 1.6.37-3 [294 kB] Get:151 http://deb.debian.org/debian bullseye/main amd64 libfreetype6 amd64 2.10.4+dfsg-1 [418 kB] Get:152 http://deb.debian.org/debian bullseye/main amd64 libfontconfig1 amd64 2.13.1-4.2 [347 kB] Get:153 http://deb.debian.org/debian bullseye/main amd64 libnspr4 amd64 2:4.29-1 [112 kB] Get:154 http://deb.debian.org/debian bullseye/main amd64 libnss3 amd64 2:3.61-1 [1304 kB] Get:155 http://deb.debian.org/debian bullseye/main amd64 libasound2 amd64 1.2.4-1.1 [356 kB] Get:156 http://deb.debian.org/debian bullseye/main amd64 libasound2-data all 1.2.4-1.1 [38.2 kB] Get:157 http://deb.debian.org/debian bullseye/main amd64 libglib2.0-0 amd64 2.66.8-1 [1370 kB] Get:158 http://deb.debian.org/debian bullseye/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get:159 http://deb.debian.org/debian bullseye/main amd64 libharfbuzz0b amd64 2.7.4-1 [1471 kB] Get:160 http://deb.debian.org/debian bullseye/main amd64 libpcsclite1 amd64 1.9.1-1 [60.2 kB] Get:161 http://deb.debian.org/debian bullseye/main amd64 openjdk-11-jre-headless amd64 11.0.12+7-2 [37.3 MB] Get:162 http://deb.debian.org/debian bullseye/main amd64 default-jre-headless amd64 2:1.11-72 [10.9 kB] Get:163 http://deb.debian.org/debian bullseye/main amd64 ca-certificates-java all 20190909 [15.7 kB] Get:164 http://deb.debian.org/debian bullseye/main amd64 python3-decorator all 4.4.2-2 [15.8 kB] Get:165 http://deb.debian.org/debian bullseye/main amd64 python3-networkx all 2.5+ds-2 [900 kB] Get:166 http://deb.debian.org/debian bullseye/main amd64 kmc amd64 3.1.1+dfsg-3+b2 [882 kB] Get:167 http://deb.debian.org/debian bullseye/main amd64 mummer amd64 3.23+dfsg-7 [664 kB] Get:168 http://deb.debian.org/debian bullseye/main amd64 libbambamc0 amd64 0.0.50-4 [37.3 kB] Get:169 http://deb.debian.org/debian bullseye/main amd64 smalt amd64 0.7.6-9 [113 kB] Get:170 http://deb.debian.org/debian bullseye/main amd64 iva amd64 1.0.9+ds-11 [8579 kB] Get:171 http://deb.debian.org/debian bullseye/main amd64 samtools amd64 1.11-1 [545 kB] Get:172 http://deb.debian.org/debian bullseye/main amd64 fastaq all 3.17.0-3 [47.8 kB] Get:173 http://deb.debian.org/debian bullseye/main amd64 libgomp1 amd64 10.2.1-6 [99.9 kB] Get:174 http://deb.debian.org/debian bullseye/main amd64 libldap-common all 2.4.57+dfsg-3 [95.9 kB] Get:175 http://deb.debian.org/debian bullseye/main amd64 libmpfr6 amd64 4.1.0-3 [2012 kB] Get:176 http://deb.debian.org/debian bullseye/main amd64 libsigsegv2 amd64 2.13-1 [34.8 kB] Get:177 http://deb.debian.org/debian bullseye/main amd64 libss2 amd64 1.46.2-2 [78.8 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 121 MB in 2s (52.4 MB/s) (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 ... 14403 files and directories currently installed.) Preparing to unpack .../debconf_1.5.77_all.deb ... Unpacking debconf (1.5.77) over (1.5.71+deb10u1) ... Setting up debconf (1.5.77) ... (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 ... 14408 files and directories currently installed.) Preparing to unpack .../libsystemd0_247.3-6_amd64.deb ... Unpacking libsystemd0:amd64 (247.3-6) over (241-7~deb10u8) ... Setting up libsystemd0:amd64 (247.3-6) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 14496 files and directories currently installed.) Preparing to unpack .../sysvinit-utils_2.96-7_amd64.deb ... Unpacking sysvinit-utils (2.96-7) over (2.93-8) ... Setting up sysvinit-utils (2.96-7) ... Selecting previously unselected package libtirpc-common. (Reading database ... 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Preparing to unpack .../10-libaudit-common_1%3a3.0-2_all.deb ... Unpacking libaudit-common (1:3.0-2) over (1:2.8.4-3) ... Setting up libaudit-common (1:3.0-2) ... (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 ... 14507 files and directories currently installed.) Preparing to unpack .../libcap-ng0_0.7.9-2.2+b1_amd64.deb ... Unpacking libcap-ng0:amd64 (0.7.9-2.2+b1) over (0.7.9-2) ... Setting up libcap-ng0:amd64 (0.7.9-2.2+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 ... 14508 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a3.0-2_amd64.deb ... Unpacking libaudit1:amd64 (1:3.0-2) over (1:2.8.4-3) ... Setting up libaudit1:amd64 (1:3.0-2) ... (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 ... 14508 files and directories currently installed.) Preparing to unpack .../libpam0g_1.4.0-9+deb11u1_amd64.deb ... Unpacking libpam0g:amd64 (1.4.0-9+deb11u1) over (1.3.1-5) ... Setting up libpam0g:amd64 (1.4.0-9+deb11u1) ... Checking for services that may need to be restarted...Checking init scripts... Nothing to restart. (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 ... 14508 files and directories currently installed.) Preparing to unpack .../libpam-modules-bin_1.4.0-9+deb11u1_amd64.deb ... Unpacking libpam-modules-bin (1.4.0-9+deb11u1) over (1.3.1-5) ... Setting up libpam-modules-bin (1.4.0-9+deb11u1) ... Setting up libcom-err2:amd64 (1.46.2-2) ... Setting up libkrb5support0:amd64 (1.18.3-6+deb11u1) ... Setting up libk5crypto3:amd64 (1.18.3-6+deb11u1) ... Setting up libkeyutils1:amd64 (1.6.1-2) ... Setting up libssl1.1:amd64 (1.1.1k-1+deb11u1) ... Setting up libkrb5-3:amd64 (1.18.3-6+deb11u1) ... Setting up libgssapi-krb5-2:amd64 (1.18.3-6+deb11u1) ... Setting up libtirpc-common (1.3.1-1) ... Setting up libtirpc3:amd64 (1.3.1-1) ... Setting up libnsl2:amd64 (1.3.0-2) ... (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 ... 14508 files and directories currently installed.) Preparing to unpack .../libpam-modules_1.4.0-9+deb11u1_amd64.deb ... Unpacking libpam-modules:amd64 (1.4.0-9+deb11u1) over (1.3.1-5) ... Setting up libpam-modules:amd64 (1.4.0-9+deb11u1) ... Installing new version of config file /etc/security/namespace.conf ... Installing new version of config file /etc/security/pam_env.conf ... (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 ... 14513 files and directories currently installed.) Preparing to unpack .../libext2fs2_1.46.2-2_amd64.deb ... Unpacking libext2fs2:amd64 (1.46.2-2) over (1.44.5-1+deb10u3) ... Setting up libext2fs2:amd64 (1.46.2-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 14513 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.46.2-2_amd64.deb ... Unpacking e2fsprogs (1.46.2-2) over (1.44.5-1+deb10u3) ... Selecting previously unselected package logsave. Preparing to unpack .../logsave_1.46.2-2_amd64.deb ... Unpacking logsave (1.46.2-2) ... Preparing to unpack .../mount_2.36.1-8_amd64.deb ... 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Current default time zone: 'Etc/UTC' Local time is now: Wed Oct 20 04:59:57 UTC 2021. Universal Time is now: Wed Oct 20 04:59:57 UTC 2021. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libasound2-data (1.2.4-1.1) ... Setting up libblas3:amd64 (3.9.0-3) ... Setting up libjpeg62-turbo:amd64 (1:2.0.6-4) ... Setting up libmpfr6:amd64 (4.1.0-3) ... 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) ... Setting up libncurses6:amd64 (6.2+20201114-2) ... Setting up libdbus-1-3:amd64 (1.12.20-2) ... Setting up libsigsegv2:amd64 (2.13-1) ... 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 libss2:amd64 (1.46.2-2) ... Setting up fonts-dejavu-core (2.37-2) ... Installing new version of config file /etc/fonts/conf.avail/57-dejavu-sans-mono.conf ... Installing new version of config file /etc/fonts/conf.avail/57-dejavu-sans.conf ... Installing new version of config file /etc/fonts/conf.avail/57-dejavu-serif.conf ... Setting up libpcsclite1:amd64 (1.9.1-1) ... Setting up logsave (1.46.2-2) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-2.1) ... Setting up libgfortran5:amd64 (10.2.1-6) ... Setting up mount (2.36.1-8) ... 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 mawk (1.3.4.20200120-2) ... Setting up openssl (1.1.1k-1+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) ... Setting up gawk (1:5.1.0-1) ... Setting up libavahi-common3:amd64 (0.8-5) ... Setting up libldap-2.4-2:amd64 (2.4.57+dfsg-3) ... Setting up e2fsprogs (1.46.2-2) ... Setting up libcurl3-gnutls:amd64 (7.74.0-1.3+b1) ... Setting up libnss3:amd64 (2:3.61-1) ... Setting up ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 8 added, 16 removed; done. Setting up libfreetype6:amd64 (2.10.4+dfsg-1) ... 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) ... Setting up python3.9 (3.9.2-1) ... Setting up libhts3:amd64 (1.11-4) ... Setting up fontconfig-config (2.13.1-4.2) ... Installing new version of config file /etc/fonts/fonts.conf ... 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+deb11u1) ... Setting up mummer (3.23+dfsg-7) ... Setting up libfontconfig1:amd64 (2.13.1-4.2) ... Setting up mailcap (3.69) ... Setting up python3-pkg-resources (52.0.0-4) ... Setting up python3-pysam (0.15.4+ds-3+b2) ... Setting up mime-support (3.66) ... 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 (11.0.12+7-2) ... Setting up ca-certificates-java (20190909) ... 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+deb11u2) ... 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. 1m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-get', '-yf', 'dist-upgrade'] 1m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m6.6s DUMP: 3520393b289b1162db47ce3355d1ee05 - 1m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-cache', 'show', '--no-all-versions', 'iva'] 1m6.8s 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 1m6.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-cache', 'show', '--no-all-versions', 'iva'] 1m6.8s INFO: apt-cache knows about the following packages: iva 1m6.8s INFO: Running scripts pre_install 1m6.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_install_database-server'] 1m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_install_database-server'] 1m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_install_exceptions'] 1m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_install_exceptions'] 1m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_install_extras'] 1m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_install_extras'] 1m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_install_foreign_architecture'] 1m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_install_foreign_architecture'] 1m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-cache', 'policy'] 1m7.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.1,o=Debian,a=stable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 1m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-cache', 'policy'] 1m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-cache', 'policy', 'iva'] 1m7.0s DUMP: iva: Installed: 1.0.9+ds-11 Candidate: 1.0.9+ds-11 Version table: *** 1.0.9+ds-11 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 100 /var/lib/dpkg/status 1m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-cache', 'policy', 'iva'] 1m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-get', '-y', 'install', 'iva'] 1m7.4s DUMP: Reading package lists... Building dependency tree... Reading state information... iva is already the newest version (1.0.9+ds-11). The following packages were automatically installed and are no longer required: libgomp1 libhts2 libmpdec2 libperl5.28 libpython3.7-minimal libpython3.7-stdlib libreadline7 perl-modules-5.28 python3.7 python3.7-minimal Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m7.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-get', '-y', 'install', 'iva'] 1m7.4s INFO: Running scripts post_install 1m7.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_install_exceptions'] 1m7.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_install_exceptions'] 1m7.4s INFO: Running scripts post_distupgrade 1m7.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m7.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m7.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_distupgrade_exceptions'] 1m7.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_distupgrade_exceptions'] 1m7.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m7.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m7.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m7.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m7.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_distupgrade_zz_backports'] 1m7.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_distupgrade_zz_backports'] 1m7.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya'] 1m8.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya'] 1m8.1s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpt6l8nlya to testing 1m8.1s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 1m8.1s INFO: Running scripts pre_distupgrade 1m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 1m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 1m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_distupgrade_exceptions'] 1m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_distupgrade_exceptions'] 1m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 1m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 1m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_distupgrade_zz_database-server'] 1m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_distupgrade_zz_database-server'] 1m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 1m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 1m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-get', 'update'] 1m10.7s DUMP: Get:1 http://deb.debian.org/debian bookworm InRelease [128 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 Packages [8286 kB] Get:3 http://deb.debian.org/debian bookworm/main Translation-en [5697 kB] Fetched 14.1 MB in 2s (7336 kB/s) Reading package lists... 1m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-get', 'update'] 1m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-get', '-yf', 'dist-upgrade'] 1m27.1s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libffi7 libgomp1 libhts2 libmpdec2 libperl5.28 libpython3.7-minimal libpython3.7-stdlib libreadline7 perl-modules-5.28 python3.7 python3.7-minimal Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: gcc-11-base libcap2 libffi8 libhtscodecs2 python3-packaging python3-pyparsing The following packages will be upgraded: apt base-files base-passwd bash bsdutils dash e2fsprogs fastaq fdisk gcc-10-base grep iva kmc libacl1 libapt-pkg6.0 libasound2 libasound2-data libattr1 libaudit-common libaudit1 libbambamc0 libblas3 libblkid1 libc-bin libc6 libcom-err2 libcrypt1 libcups2 libdeflate0 libexpat1 libext2fs2 libfdisk1 libgcc-s1 libgcrypt20 libgdbm-compat4 libgdbm6 libgfortran5 libglib2.0-0 libgmp10 libgnutls30 libgomp1 libgpg-error0 libgssapi-krb5-2 libhts3 libidn2-0 libk5crypto3 libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2 libldap-common libmount1 libmpdec3 libncurses6 libncursesw6 libnspr4 libnss3 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcsclite1 libperl5.32 libpython3.9-minimal libpython3.9-stdlib libquadmath0 libreadline8 libseccomp2 libsmartcols1 libsqlite3-0 libss2 libssh2-1 libssl1.1 libstdc++6 libsystemd0 libtasn1-6 libtinfo6 libtirpc-common libtirpc3 libudev1 libunistring2 libuuid1 libzstd1 logsave mailcap mount ncurses-base ncurses-bin openssl perl perl-base perl-modules-5.32 python3-pkg-resources python3-pysam python3.9 python3.9-minimal readline-common samtools sed sensible-utils sysvinit-utils tzdata util-linux 104 upgraded, 6 newly installed, 0 to remove and 0 not upgraded. Need to get 58.9 MB of archives. After this operation, 2900 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 base-files amd64 12 [70.0 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 bash amd64 5.1-3+b2 [1415 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 bsdutils amd64 1:2.37.2-3 [150 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 dash amd64 0.5.11+git20210120+802ebd4-1 [116 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 grep amd64 3.7-1 [404 kB] Get:6 http://deb.debian.org/debian bookworm/main amd64 ncurses-bin amd64 6.2+20201114-4 [428 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 libc6 amd64 2.32-4 [2820 kB] Get:8 http://deb.debian.org/debian bookworm/main amd64 libc-bin amd64 2.32-4 [822 kB] Get:9 http://deb.debian.org/debian bookworm/main amd64 libperl5.32 amd64 5.32.1-6 [4106 kB] Get:10 http://deb.debian.org/debian bookworm/main amd64 perl amd64 5.32.1-6 [293 kB] Get:11 http://deb.debian.org/debian bookworm/main amd64 perl-base amd64 5.32.1-6 [1626 kB] Get:12 http://deb.debian.org/debian bookworm/main amd64 perl-modules-5.32 all 5.32.1-6 [2824 kB] Get:13 http://deb.debian.org/debian bookworm/main amd64 gcc-11-base amd64 11.2.0-9 [205 kB] Get:14 http://deb.debian.org/debian bookworm/main amd64 libgcc-s1 amd64 11.2.0-9 [42.0 kB] Get:15 http://deb.debian.org/debian bookworm/main amd64 libaudit-common all 1:3.0.6-1 [15.8 kB] Get:16 http://deb.debian.org/debian bookworm/main amd64 libaudit1 amd64 1:3.0.6-1 [52.0 kB] Get:17 http://deb.debian.org/debian bookworm/main amd64 libpam0g amd64 1.4.0-10 [130 kB] Get:18 http://deb.debian.org/debian bookworm/main amd64 libcrypt1 amd64 1:4.4.25-2 [89.2 kB] Get:19 http://deb.debian.org/debian bookworm/main amd64 libgdbm6 amd64 1.21-1 [77.7 kB] Get:20 http://deb.debian.org/debian bookworm/main amd64 libgdbm-compat4 amd64 1.21-1 [52.1 kB] Get:21 http://deb.debian.org/debian bookworm/main amd64 sed amd64 4.8-1 [316 kB] Get:22 http://deb.debian.org/debian bookworm/main amd64 libblkid1 amd64 2.37.2-3 [201 kB] Get:23 http://deb.debian.org/debian bookworm/main amd64 libmount1 amd64 2.37.2-3 [218 kB] Get:24 http://deb.debian.org/debian bookworm/main amd64 libuuid1 amd64 2.37.2-3 [84.6 kB] Get:25 http://deb.debian.org/debian bookworm/main amd64 libfdisk1 amd64 2.37.2-3 [241 kB] Get:26 http://deb.debian.org/debian bookworm/main amd64 libncurses6 amd64 6.2+20201114-4 [102 kB] Get:27 http://deb.debian.org/debian bookworm/main amd64 libncursesw6 amd64 6.2+20201114-4 [132 kB] Get:28 http://deb.debian.org/debian bookworm/main amd64 libtinfo6 amd64 6.2+20201114-4 [341 kB] Get:29 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.1-2 [73.8 kB] Get:30 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.1-2 [168 kB] Get:31 http://deb.debian.org/debian bookworm/main amd64 libsmartcols1 amd64 2.37.2-3 [161 kB] Get:32 http://deb.debian.org/debian bookworm/main amd64 fdisk amd64 2.37.2-3 [196 kB] Get:33 http://deb.debian.org/debian bookworm/main amd64 util-linux amd64 2.37.2-3 [1196 kB] Get:34 http://deb.debian.org/debian bookworm/main amd64 libgpg-error0 amd64 1.42-3 [79.0 kB] Get:35 http://deb.debian.org/debian bookworm/main amd64 libgcrypt20 amd64 1.9.4-3+b1 [664 kB] Get:36 http://deb.debian.org/debian bookworm/main amd64 libstdc++6 amd64 11.2.0-9 [576 kB] Get:37 http://deb.debian.org/debian bookworm/main amd64 libcap2 amd64 1:2.44-1 [23.6 kB] Get:38 http://deb.debian.org/debian bookworm/main amd64 libsystemd0 amd64 249.5-1 [393 kB] Get:39 http://deb.debian.org/debian bookworm/main amd64 libudev1 amd64 249.5-1 [173 kB] Get:40 http://deb.debian.org/debian bookworm/main amd64 libzstd1 amd64 1.4.8+dfsg-3 [319 kB] Get:41 http://deb.debian.org/debian bookworm/main amd64 libapt-pkg6.0 amd64 2.3.9 [1021 kB] Get:42 http://deb.debian.org/debian bookworm/main amd64 libgmp10 amd64 2:6.2.1+dfsg-2 [561 kB] Get:43 http://deb.debian.org/debian bookworm/main amd64 libunistring2 amd64 0.9.10-6 [384 kB] Get:44 http://deb.debian.org/debian bookworm/main amd64 libidn2-0 amd64 2.3.2-2 [95.3 kB] Get:45 http://deb.debian.org/debian bookworm/main amd64 libffi8 amd64 3.4.2-3 [24.8 kB] Get:46 http://deb.debian.org/debian bookworm/main amd64 libp11-kit0 amd64 0.24.0-5 [346 kB] Get:47 http://deb.debian.org/debian bookworm/main amd64 libtasn1-6 amd64 4.17.0-2 [55.2 kB] Get:48 http://deb.debian.org/debian bookworm/main amd64 libgnutls30 amd64 3.7.2-2 [1350 kB] Get:49 http://deb.debian.org/debian bookworm/main amd64 libseccomp2 amd64 2.5.2-2 [48.9 kB] Get:50 http://deb.debian.org/debian bookworm/main amd64 apt amd64 2.3.9 [1499 kB] Get:51 http://deb.debian.org/debian bookworm/main amd64 base-passwd amd64 3.5.52 [58.7 kB] Get:52 http://deb.debian.org/debian bookworm/main amd64 ncurses-base all 6.2+20201114-4 [272 kB] Get:53 http://deb.debian.org/debian bookworm/main amd64 sysvinit-utils amd64 3.00-1 [26.4 kB] Get:54 http://deb.debian.org/debian bookworm/main amd64 libpam-modules-bin amd64 1.4.0-10 [108 kB] Get:55 http://deb.debian.org/debian bookworm/main amd64 libpam-modules amd64 1.4.0-10 [326 kB] Get:56 http://deb.debian.org/debian bookworm/main amd64 logsave amd64 1.46.4-1 [75.9 kB] Get:57 http://deb.debian.org/debian bookworm/main amd64 libext2fs2 amd64 1.46.4-1 [258 kB] Get:58 http://deb.debian.org/debian bookworm/main amd64 e2fsprogs amd64 1.46.4-1 [619 kB] Get:59 http://deb.debian.org/debian bookworm/main amd64 mount amd64 2.37.2-3 [190 kB] Get:60 http://deb.debian.org/debian bookworm/main amd64 libssl1.1 amd64 1.1.1l-1 [1555 kB] Get:61 http://deb.debian.org/debian bookworm/main amd64 python3.9 amd64 3.9.7-4 [480 kB] Get:62 http://deb.debian.org/debian bookworm/main amd64 python3.9-minimal amd64 3.9.7-4 [1963 kB] Get:63 http://deb.debian.org/debian bookworm/main amd64 libpython3.9-stdlib amd64 3.9.7-4 [1688 kB] Get:64 http://deb.debian.org/debian bookworm/main amd64 libpython3.9-minimal amd64 3.9.7-4 [804 kB] Get:65 http://deb.debian.org/debian bookworm/main amd64 tzdata all 2021c-2 [287 kB] Get:66 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samtools amd64 1.13-2 [568 kB] Get:88 http://deb.debian.org/debian bookworm/main amd64 libhts3 amd64 1.13+ds-2 [395 kB] Get:89 http://deb.debian.org/debian bookworm/main amd64 fastaq all 3.17.0-4 [48.2 kB] Get:90 http://deb.debian.org/debian bookworm/main amd64 python3-pyparsing all 2.4.7-1 [109 kB] Get:91 http://deb.debian.org/debian bookworm/main amd64 python3-packaging all 21.0-1 [33.5 kB] Get:92 http://deb.debian.org/debian bookworm/main amd64 python3-pysam amd64 0.17.0+ds-2 [1627 kB] Get:93 http://deb.debian.org/debian bookworm/main amd64 kmc amd64 3.1.1+dfsg-4 [882 kB] Get:94 http://deb.debian.org/debian bookworm/main amd64 iva amd64 1.0.11+ds-1 [8582 kB] Get:95 http://deb.debian.org/debian bookworm/main amd64 libasound2 amd64 1.2.5.1-1 [373 kB] Get:96 http://deb.debian.org/debian bookworm/main amd64 libasound2-data all 1.2.5.1-1 [38.6 kB] Get:97 http://deb.debian.org/debian bookworm/main amd64 libbambamc0 amd64 0.0.50-5 [37.4 kB] Get:98 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.10.0-1 [156 kB] Get:99 http://deb.debian.org/debian bookworm/main amd64 libcups2 amd64 2.3.3op2-7 [349 kB] Get:100 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.70.0-1+b1 [1402 kB] Get:101 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.10.0-1 [2213 kB] Get:102 http://deb.debian.org/debian bookworm/main amd64 libldap-2.4-2 amd64 2.4.59+dfsg-1 [232 kB] Get:103 http://deb.debian.org/debian bookworm/main amd64 libldap-common all 2.4.59+dfsg-1 [96.2 kB] Get:104 http://deb.debian.org/debian bookworm/main amd64 libnspr4 amd64 2:4.32-1 [112 kB] Get:105 http://deb.debian.org/debian bookworm/main amd64 libnss3 amd64 2:3.70-1 [1319 kB] Get:106 http://deb.debian.org/debian bookworm/main amd64 libpcsclite1 amd64 1.9.4-1 [60.0 kB] Get:107 http://deb.debian.org/debian bookworm/main amd64 libss2 amd64 1.46.4-1 [79.9 kB] Get:108 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-2 [178 kB] Get:109 http://deb.debian.org/debian bookworm/main amd64 mailcap all 3.70 [31.8 kB] Get:110 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 1.1.1l-1 [851 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 58.9 MB in 1s (93.5 MB/s) (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 ... 15104 files and directories currently installed.) Preparing to unpack .../libacl1_2.3.1-1_amd64.deb ... Unpacking libacl1:amd64 (2.3.1-1) over (2.2.53-10) ... Setting up libacl1:amd64 (2.3.1-1) ... (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 ... 15104 files and directories currently installed.) Preparing to unpack .../libattr1_1%3a2.5.1-1_amd64.deb ... Unpacking libattr1:amd64 (1:2.5.1-1) over (1:2.4.48-6) ... Setting up libattr1:amd64 (1:2.5.1-1) ... Installing new version of config file /etc/xattr.conf ... (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 ... 15104 files and directories currently installed.) Preparing to unpack .../00-libquadmath0_11.2.0-9_amd64.deb ... Unpacking libquadmath0:amd64 (11.2.0-9) over (10.2.1-6) ... Preparing to unpack .../01-libgomp1_11.2.0-9_amd64.deb ... Unpacking libgomp1:amd64 (11.2.0-9) over (10.2.1-6) ... Preparing to unpack .../02-libgfortran5_11.2.0-9_amd64.deb ... Unpacking libgfortran5:amd64 (11.2.0-9) over (10.2.1-6) ... 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Selecting previously unselected package python3-pyparsing. Preparing to unpack .../11-python3-pyparsing_2.4.7-1_all.deb ... Unpacking python3-pyparsing (2.4.7-1) ... Selecting previously unselected package python3-packaging. Preparing to unpack .../12-python3-packaging_21.0-1_all.deb ... Unpacking python3-packaging (21.0-1) ... Preparing to unpack .../13-python3-pysam_0.17.0+ds-2_amd64.deb ... Unpacking python3-pysam (0.17.0+ds-2) over (0.15.4+ds-3+b2) ... Preparing to unpack .../14-kmc_3.1.1+dfsg-4_amd64.deb ... Unpacking kmc (3.1.1+dfsg-4) over (3.1.1+dfsg-3+b2) ... Preparing to unpack .../15-iva_1.0.11+ds-1_amd64.deb ... Unpacking iva (1.0.11+ds-1) over (1.0.9+ds-11) ... Preparing to unpack .../16-libasound2_1.2.5.1-1_amd64.deb ... Unpacking libasound2:amd64 (1.2.5.1-1) over (1.2.4-1.1) ... Preparing to unpack .../17-libasound2-data_1.2.5.1-1_all.deb ... Unpacking libasound2-data (1.2.5.1-1) over (1.2.4-1.1) ... Preparing to unpack .../18-libbambamc0_0.0.50-5_amd64.deb ... Unpacking libbambamc0:amd64 (0.0.50-5) over (0.0.50-4) ... Preparing to unpack .../19-libblas3_3.10.0-1_amd64.deb ... Unpacking libblas3:amd64 (3.10.0-1) over (3.9.0-3) ... Preparing to unpack .../20-libcups2_2.3.3op2-7_amd64.deb ... Unpacking libcups2:amd64 (2.3.3op2-7) over (2.3.3op2-3+deb11u1) ... Preparing to unpack .../21-libglib2.0-0_2.70.0-1+b1_amd64.deb ... Unpacking libglib2.0-0:amd64 (2.70.0-1+b1) over (2.66.8-1) ... Preparing to unpack .../22-liblapack3_3.10.0-1_amd64.deb ... Unpacking liblapack3:amd64 (3.10.0-1) over (3.9.0-3) ... Preparing to unpack .../23-libldap-2.4-2_2.4.59+dfsg-1_amd64.deb ... Unpacking libldap-2.4-2:amd64 (2.4.59+dfsg-1) over (2.4.57+dfsg-3) ... Preparing to unpack .../24-libldap-common_2.4.59+dfsg-1_all.deb ... Unpacking libldap-common (2.4.59+dfsg-1) over (2.4.57+dfsg-3) ... Preparing to unpack .../25-libnspr4_2%3a4.32-1_amd64.deb ... Unpacking libnspr4:amd64 (2:4.32-1) over (2:4.29-1) ... Preparing to unpack .../26-libnss3_2%3a3.70-1_amd64.deb ... Unpacking libnss3:amd64 (2:3.70-1) over (2:3.61-1) ... Preparing to unpack .../27-libpcsclite1_1.9.4-1_amd64.deb ... Unpacking libpcsclite1:amd64 (1.9.4-1) over (1.9.1-1) ... Preparing to unpack .../28-libss2_1.46.4-1_amd64.deb ... Unpacking libss2:amd64 (1.46.4-1) over (1.46.2-2) ... Preparing to unpack .../29-libssh2-1_1.10.0-2_amd64.deb ... Unpacking libssh2-1:amd64 (1.10.0-2) over (1.9.0-2) ... Preparing to unpack .../30-mailcap_3.70_all.deb ... Unpacking mailcap (3.70) over (3.69) ... Preparing to unpack .../31-openssl_1.1.1l-1_amd64.deb ... Unpacking openssl (1.1.1l-1) over (1.1.1k-1+deb11u1) ... Setting up python3-pkg-resources (58.2.0-1) ... Setting up libhtscodecs2:amd64 (1.1.1-3+b1) ... Setting up libexpat1:amd64 (2.4.1-2+b1) ... Setting up libglib2.0-0:amd64 (2.70.0-1+b1) ... No schema files found: doing nothing. Setting up libpython3.9-minimal:amd64 (3.9.7-4) ... Setting up perl-modules-5.32 (5.32.1-6) ... Setting up libsqlite3-0:amd64 (3.36.0-2) ... Setting up libdeflate0:amd64 (1.8-1) ... Setting up libldap-2.4-2:amd64 (2.4.59+dfsg-1) ... Setting up libgomp1:amd64 (11.2.0-9) ... Setting up libldap-common (2.4.59+dfsg-1) ... Setting up tzdata (2021c-2) ... Current default time zone: 'Etc/UTC' Local time is now: Wed Oct 20 05:00:26 UTC 2021. Universal Time is now: Wed Oct 20 05:00:26 UTC 2021. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libasound2-data (1.2.5.1-1) ... Setting up gcc-10-base:amd64 (10.3.0-11) ... Setting up libblas3:amd64 (3.10.0-1) ... Setting up python3-pyparsing (2.4.7-1) ... Setting up libnspr4:amd64 (2:4.32-1) ... Setting up libncurses6:amd64 (6.2+20201114-4) ... Setting up libquadmath0:amd64 (11.2.0-9) ... Setting up libbambamc0:amd64 (0.0.50-5) ... Setting up libss2:amd64 (1.46.4-1) ... Setting up libpcsclite1:amd64 (1.9.4-1) ... Setting up libncursesw6:amd64 (6.2+20201114-4) ... Setting up logsave (1.46.4-1) ... Setting up libgfortran5:amd64 (11.2.0-9) ... Setting up libfdisk1:amd64 (2.37.2-3) ... Setting up libcups2:amd64 (2.3.3op2-7) ... Setting up mount (2.37.2-3) ... Setting up sensible-utils (0.0.17) ... Setting up libasound2:amd64 (1.2.5.1-1) ... Setting up libmpdec3:amd64 (2.5.1-2) ... Setting up libssh2-1:amd64 (1.10.0-2) ... Setting up python3.9-minimal (3.9.7-4) ... Setting up openssl (1.1.1l-1) ... Setting up kmc (3.1.1+dfsg-4) ... Setting up readline-common (8.1-2) ... Setting up libgdbm6:amd64 (1.21-1) ... Setting up liblapack3:amd64 (3.10.0-1) ... Setting up libhts3:amd64 (1.13+ds-2) ... Setting up python3-pysam (0.17.0+ds-2) ... Setting up libreadline8:amd64 (8.1-2) ... Setting up e2fsprogs (1.46.4-1) ... Installing new version of config file /etc/mke2fs.conf ... Setting up libnss3:amd64 (2:3.70-1) ... Setting up fdisk (2.37.2-3) ... Setting up samtools (1.13-2) ... Setting up python3-packaging (21.0-1) ... Setting up libgdbm-compat4:amd64 (1.21-1) ... Setting up libperl5.32:amd64 (5.32.1-6) ... Setting up libpython3.9-stdlib:amd64 (3.9.7-4) ... Setting up fastaq (3.17.0-4) ... Setting up perl (5.32.1-6) ... Setting up mailcap (3.70) ... Setting up python3.9 (3.9.7-4) ... Setting up iva (1.0.11+ds-1) ... Processing triggers for libc-bin (2.32-4) ... 1m27.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-get', '-yf', 'dist-upgrade'] 1m27.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m28.1s DUMP: 656af3ca4846adeec52dafc61d69fc1d - 1m28.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m28.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-cache', 'show', '--no-all-versions', 'iva'] 1m28.3s DUMP: Package: iva Version: 1.0.11+ds-1 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-1_amd64.deb Size: 8581916 MD5sum: d959f23643f7b09bba4dade6c9db4733 SHA256: 3332a1bc2771ce3aecd95ac3c7f6a12382b39411379d32eafe84899843a923a3 1m28.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-cache', 'show', '--no-all-versions', 'iva'] 1m28.3s INFO: apt-cache knows about the following packages: iva 1m28.3s INFO: Running scripts pre_install 1m28.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_install_database-server'] 1m28.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_install_database-server'] 1m28.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_install_exceptions'] 1m28.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_install_exceptions'] 1m28.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_install_extras'] 1m28.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_install_extras'] 1m28.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_install_foreign_architecture'] 1m28.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_install_foreign_architecture'] 1m28.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m28.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m28.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-cache', 'policy'] 1m28.4s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release o=Debian,a=testing,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 1m28.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-cache', 'policy'] 1m28.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-cache', 'policy', 'iva'] 1m28.5s DUMP: iva: Installed: 1.0.11+ds-1 Candidate: 1.0.11+ds-1 Version table: *** 1.0.11+ds-1 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 100 /var/lib/dpkg/status 1m28.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-cache', 'policy', 'iva'] 1m28.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-get', '-y', 'install', 'iva'] 1m28.8s DUMP: Reading package lists... Building dependency tree... Reading state information... iva is already the newest version (1.0.11+ds-1). The following packages were automatically installed and are no longer required: libffi7 libgomp1 libhts2 libmpdec2 libperl5.28 libpython3.7-minimal libpython3.7-stdlib libreadline7 perl-modules-5.28 python3.7 python3.7-minimal Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m28.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-get', '-y', 'install', 'iva'] 1m28.8s INFO: Running scripts post_install 1m28.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_install_exceptions'] 1m28.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_install_exceptions'] 1m28.8s INFO: Running scripts post_distupgrade 1m28.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m28.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m28.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_distupgrade_exceptions'] 1m28.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_distupgrade_exceptions'] 1m28.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m28.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m28.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m28.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m28.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_distupgrade_zz_backports'] 1m28.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_distupgrade_zz_backports'] 1m28.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya'] 1m29.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya'] 1m29.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya'] 1m29.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya'] 1m29.9s INFO: Running scripts pre_install 1m29.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_install_database-server'] 1m29.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_install_database-server'] 1m29.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_install_exceptions'] 1m29.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_install_exceptions'] 1m29.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_install_extras'] 1m30.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_install_extras'] 1m30.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_install_foreign_architecture'] 1m30.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_install_foreign_architecture'] 1m30.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m30.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m30.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-cache', 'policy'] 1m30.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release o=Debian,a=testing,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 1m30.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-cache', 'policy'] 1m30.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-cache', 'policy', 'iva'] 1m30.0s DUMP: iva: Installed: 1.0.11+ds-1 Candidate: 1.0.11+ds-1 Version table: *** 1.0.11+ds-1 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 100 /var/lib/dpkg/status 1m30.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-cache', 'policy', 'iva'] 1m30.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-get', '-y', 'install', 'iva=1.0.11+ds-1'] 1m30.5s DUMP: Reading package lists... Building dependency tree... Reading state information... iva is already the newest version (1.0.11+ds-1). The following packages were automatically installed and are no longer required: libffi7 libgomp1 libhts2 libmpdec2 libperl5.28 libpython3.7-minimal libpython3.7-stdlib libreadline7 perl-modules-5.28 python3.7 python3.7-minimal Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m30.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-get', '-y', 'install', 'iva=1.0.11+ds-1'] 1m30.5s INFO: Running scripts post_install 1m30.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_install_exceptions'] 1m30.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_install_exceptions'] 1m30.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya'] 1m31.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya'] 1m31.9s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', '-ac', '--ignore-obsolete'] 1m33.6s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', '-ac', '--ignore-obsolete'] 1m33.6s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m33.7s DUMP: 0.15.2 1m33.7s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m33.7s INFO: Running adequate version 0.15.2 now. 1m33.7s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'iva'] 1m33.8s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'iva'] 1m33.8s INFO: Running scripts pre_remove 1m33.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m33.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m33.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m33.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m33.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m35.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m35.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m35.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m35.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m35.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m35.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_remove_exceptions'] 1m35.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/pre_remove_exceptions'] 1m35.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m35.9s DUMP: install ok installed adduser adduser 3.118 install ok installed apt apt 2.3.9 install ok installed base-files base-files 12 install ok installed base-passwd base-passwd 3.5.52 install ok installed bash bash 5.1-3+b2 install ok installed bsdutils bsdutils 1:2.37.2-3 install ok installed ca-certificates ca-certificates 20210119 install ok installed ca-certificates-java ca-certificates-java 20190909 install ok installed coreutils coreutils 8.32-4+b1 install ok installed dash dash 0.5.11+git20210120+802ebd4-1 install ok installed debconf debconf 1.5.77 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1 install ok installed debianutils debianutils 4.11.2 install ok installed default-jre-headless default-jre-headless 2:1.11-72 install ok installed diffutils diffutils 1:3.7-5 install ok installed dpkg dpkg 1.20.9 install ok installed e2fsprogs e2fsprogs 1.46.4-1 install ok installed fastaq fastaq 3.17.0-4 install ok installed fdisk fdisk 2.37.2-3 install ok installed findutils findutils 4.8.0-1 install ok installed fontconfig-config fontconfig-config 2.13.1-4.2 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-2 install ok installed gawk gawk 1:5.1.0-1 install ok installed gcc-10-base:amd64 gcc-10-base 10.3.0-11 install ok installed gcc-11-base:amd64 gcc-11-base 11.2.0-9 install ok installed gcc-8-base:amd64 gcc-8-base 8.3.0-6 install ok installed gpgv gpgv 2.2.27-2 install ok installed grep grep 3.7-1 install ok installed gzip gzip 1.10-4 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.60 install ok installed iva iva 1.0.11+ds-1 install ok installed java-common java-common 0.72 install ok installed kmc kmc 3.1.1+dfsg-4 install ok installed libacl1:amd64 libacl1 2.3.1-1 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.8.2.3 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.3.9 install ok installed libasound2:amd64 libasound2 1.2.5.1-1 install ok installed libasound2-data libasound2-data 1.2.5.1-1 install ok installed libattr1:amd64 libattr1 1:2.5.1-1 install ok installed libaudit-common libaudit-common 1:3.0.6-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.6-1 install ok installed libavahi-client3:amd64 libavahi-client3 0.8-5 install ok installed libavahi-common-data:amd64 libavahi-common-data 0.8-5 install ok installed libavahi-common3:amd64 libavahi-common3 0.8-5 install ok installed libbambamc0:amd64 libbambamc0 0.0.50-5 install ok installed libblas3:amd64 libblas3 3.10.0-1 install ok installed libblkid1:amd64 libblkid1 2.37.2-3 install ok installed libbrotli1:amd64 libbrotli1 1.0.9-2+b2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4 install ok installed libc-bin libc-bin 2.32-4 install ok installed libc6:amd64 libc6 2.32-4 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2+b1 install ok installed libcap2:amd64 libcap2 1:2.44-1 install ok installed libcom-err2:amd64 libcom-err2 1.46.4-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.25-2 install ok installed libcups2:amd64 libcups2 2.3.3op2-7 install ok installed libcurl3-gnutls:amd64 libcurl3-gnutls 7.74.0-1.3+b1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.8 install ok installed libdbus-1-3:amd64 libdbus-1-3 1.12.20-2 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.260 install ok installed libdeflate0:amd64 libdeflate0 1.8-1 install ok installed libexpat1:amd64 libexpat1 2.4.1-2+b1 install ok installed libext2fs2:amd64 libext2fs2 1.46.4-1 install ok installed libfdisk1:amd64 libfdisk1 2.37.2-3 install ok installed libffi6:amd64 libffi6 3.2.1-9 install ok installed libffi7:amd64 libffi7 3.3-6 install ok installed libffi8:amd64 libffi8 3.4.2-3 install ok installed libfontconfig1:amd64 libfontconfig1 2.13.1-4.2 install ok installed libfreetype6:amd64 libfreetype6 2.10.4+dfsg-1 install ok installed libgcc-s1:amd64 libgcc-s1 11.2.0-9 install ok installed libgcc1:amd64 libgcc1 1:8.3.0-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.9.4-3+b1 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.21-1 install ok installed libgdbm6:amd64 libgdbm6 1.21-1 install ok installed libgfortran5:amd64 libgfortran5 11.2.0-9 install ok installed libglib2.0-0:amd64 libglib2.0-0 2.70.0-1+b1 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg-2 install ok installed libgnutls30:amd64 libgnutls30 3.7.2-2 install ok installed libgomp1:amd64 libgomp1 11.2.0-9 install ok installed libgpg-error0:amd64 libgpg-error0 1.42-3 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.18.3-7 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 2.7.4-1 install ok installed libhogweed4:amd64 libhogweed4 3.4.1-1+deb10u1 install ok installed libhogweed6:amd64 libhogweed6 3.7.3-1 install ok installed libhts2:amd64 libhts2 1.9-12~deb10u1 install ok installed libhts3:amd64 libhts3 1.13+ds-2 install ok installed libhtscodecs2:amd64 libhtscodecs2 1.1.1-3+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.2-2 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.0.6-4 install ok installed libk5crypto3:amd64 libk5crypto3 1.18.3-7 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.18.3-7 install ok installed libkrb5support0:amd64 libkrb5support0 1.18.3-7 install ok installed liblapack3:amd64 liblapack3 3.10.0-1 install ok installed liblcms2-2:amd64 liblcms2-2 2.12~rc1-2 install ok installed libldap-2.4-2:amd64 libldap-2.4-2 2.4.59+dfsg-1 install ok installed libldap-common libldap-common 2.4.59+dfsg-1 install ok installed liblz4-1:amd64 liblz4-1 1.9.3-2 install ok installed liblzma5:amd64 liblzma5 5.2.5-2 install ok installed libmount1:amd64 libmount1 2.37.2-3 install ok installed libmpdec2:amd64 libmpdec2 2.4.2-2 install ok installed libmpdec3:amd64 libmpdec3 2.5.1-2 install ok installed libmpfr6:amd64 libmpfr6 4.1.0-3 install ok installed libncurses6:amd64 libncurses6 6.2+20201114-4 install ok installed libncursesw6:amd64 libncursesw6 6.2+20201114-4 install ok installed libnettle6:amd64 libnettle6 3.4.1-1+deb10u1 install ok installed libnettle8:amd64 libnettle8 3.7.3-1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.43.0-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libnspr4:amd64 libnspr4 2:4.32-1 install ok installed libnss3:amd64 libnss3 2:3.70-1 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.0-5 install ok installed libpam-modules:amd64 libpam-modules 1.4.0-10 install ok installed libpam-modules-bin libpam-modules-bin 1.4.0-10 install ok installed libpam-runtime libpam-runtime 1.4.0-10 install ok installed libpam0g:amd64 libpam0g 1.4.0-10 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.36-2 install ok installed libpcre3:amd64 libpcre3 2:8.39-13 install ok installed libpcsclite1:amd64 libpcsclite1 1.9.4-1 install ok installed libperl5.28:amd64 libperl5.28 5.28.1-6+deb10u1 install ok installed libperl5.32:amd64 libperl5.32 5.32.1-6 install ok installed libpng16-16:amd64 libpng16-16 1.6.37-3 install ok installed libpsl5:amd64 libpsl5 0.21.0-1.2 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.9.2-3 install ok installed libpython3.7-minimal:amd64 libpython3.7-minimal 3.7.3-2+deb10u3 install ok installed libpython3.7-stdlib:amd64 libpython3.7-stdlib 3.7.3-2+deb10u3 install ok installed libpython3.9-minimal:amd64 libpython3.9-minimal 3.9.7-4 install ok installed libpython3.9-stdlib:amd64 libpython3.9-stdlib 3.9.7-4 install ok installed libquadmath0:amd64 libquadmath0 11.2.0-9 install ok installed libreadline7:amd64 libreadline7 7.0-5 install ok installed libreadline8:amd64 libreadline8 8.1-2 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b2 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.27+dfsg-2.1 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.27+dfsg-2.1 install ok installed libseccomp2:amd64 libseccomp2 2.5.2-2 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 libsigsegv2:amd64 libsigsegv2 2.13-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.37.2-3 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.36.0-2 install ok installed libss2:amd64 libss2 1.46.4-1 install ok installed libssh2-1:amd64 libssh2-1 1.10.0-2 install ok installed libssl1.1:amd64 libssl1.1 1.1.1l-1 install ok installed libstdc++6:amd64 libstdc++6 11.2.0-9 install ok installed libsystemd0:amd64 libsystemd0 249.5-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.17.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.2+20201114-4 install ok installed libtirpc-common libtirpc-common 1.3.2-2 install ok installed libtirpc3:amd64 libtirpc3 1.3.2-2 install ok installed libudev1:amd64 libudev1 249.5-1 install ok installed libunistring2:amd64 libunistring2 0.9.10-6 install ok installed libuuid1:amd64 libuuid1 2.37.2-3 install ok installed libxxhash0:amd64 libxxhash0 0.8.0-2 install ok installed libzstd1:amd64 libzstd1 1.4.8+dfsg-3 install ok installed login login 1:4.8.1-1 install ok installed logsave logsave 1.46.4-1 install ok installed lsb-base lsb-base 11.1.0 install ok installed mailcap mailcap 3.70 install ok installed mawk mawk 1.3.4.20200120-2 install ok installed media-types media-types 4.0.0 install ok installed mime-support mime-support 3.66 install ok installed mount mount 2.37.2-3 install ok installed mummer mummer 3.23+dfsg-7 install ok installed ncurses-base ncurses-base 6.2+20201114-4 install ok installed ncurses-bin ncurses-bin 6.2+20201114-4 install ok installed openjdk-11-jre-headless:amd64 openjdk-11-jre-headless 11.0.12+7-2 install ok installed openssl openssl 1.1.1l-1 install ok installed passwd passwd 1:4.8.1-1 install ok installed perl perl 5.32.1-6 install ok installed perl-base perl-base 5.32.1-6 install ok installed perl-modules-5.28 perl-modules-5.28 5.28.1-6+deb10u1 install ok installed perl-modules-5.32 perl-modules-5.32 5.32.1-6 install ok installed python3 python3 3.9.2-3 install ok installed python3-decorator python3-decorator 4.4.2-2 install ok installed python3-minimal python3-minimal 3.9.2-3 install ok installed python3-networkx python3-networkx 2.5+ds-2 install ok installed python3-numpy python3-numpy 1:1.19.5-1 install ok installed python3-packaging python3-packaging 21.0-1 install ok installed python3-pkg-resources python3-pkg-resources 58.2.0-1 install ok installed python3-pyparsing python3-pyparsing 2.4.7-1 install ok installed python3-pysam python3-pysam 0.17.0+ds-2 install ok installed python3.7 python3.7 3.7.3-2+deb10u3 install ok installed python3.7-minimal python3.7-minimal 3.7.3-2+deb10u3 install ok installed python3.9 python3.9 3.9.7-4 install ok installed python3.9-minimal python3.9-minimal 3.9.7-4 install ok installed readline-common readline-common 8.1-2 install ok installed samtools samtools 1.13-2 install ok installed sed sed 4.8-1 install ok installed sensible-utils sensible-utils 0.0.17 install ok installed smalt smalt 0.7.6-9 install ok installed sysvinit-utils sysvinit-utils 3.00-1 install ok installed tar tar 1.34+dfsg-1 install ok installed tzdata tzdata 2021c-2 install ok installed ucf ucf 3.0043 install ok installed util-linux util-linux 2.37.2-3 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2 1m35.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m35.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-get', 'remove', 'ca-certificates', 'ca-certificates-java', 'default-jre-headless', 'fastaq', 'fontconfig-config', 'fonts-dejavu-core', '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', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libharfbuzz0b:amd64', 'libhts2:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libjpeg62-turbo:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libmpdec2:amd64', 'libmpdec3:amd64', 'libmpfr6:amd64', 'libncurses6:amd64', 'libnghttp2-14:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libpcsclite1:amd64', 'libperl5.28:amd64', 'libperl5.32:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.7-minimal:amd64', 'libpython3.7-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsigsegv2:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'mailcap', 'media-types', 'mime-support', 'mummer', 'openjdk-11-jre-headless:amd64', 'openssl', 'perl', 'perl-modules-5.28', 'perl-modules-5.32', 'python3', 'python3-decorator', 'python3-minimal', 'python3-networkx', 'python3-numpy', 'python3-packaging', 'python3-pkg-resources', 'python3-pyparsing', 'python3-pysam', 'python3.7', 'python3.7-minimal', 'python3.9', 'python3.9-minimal', 'samtools', 'sensible-utils', 'smalt', 'ucf', 'iva'] 1m39.2s DUMP: Reading package lists... Building dependency tree... Reading state information... The following package was automatically installed and is no longer required: libffi7 Use 'sudo apt autoremove' to remove it. The following packages will be REMOVED: 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 libgomp1 libgraphite2-3 libharfbuzz0b libhts2 libhts3 libhtscodecs2 libjpeg62-turbo liblapack3 liblcms2-2 libldap-2.4-2 libldap-common libmpdec2 libmpdec3 libmpfr6 libncurses6 libnghttp2-14 libnspr4 libnss3 libpcsclite1 libperl5.28 libperl5.32 libpng16-16 libpsl5 libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libpython3.9-minimal libpython3.9-stdlib libquadmath0 libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsigsegv2 libsqlite3-0 libssh2-1 mailcap media-types mime-support mummer openjdk-11-jre-headless openssl perl perl-modules-5.28 perl-modules-5.32 python3 python3-decorator python3-minimal python3-networkx python3-numpy python3-packaging python3-pkg-resources python3-pyparsing python3-pysam python3.7 python3.7-minimal python3.9 python3.9-minimal samtools sensible-utils smalt ucf 0 upgraded, 0 newly installed, 91 to remove and 0 not upgraded. After this operation, 401 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 ... 15159 files and directories currently installed.) Removing iva (1.0.11+ds-1) ... Removing default-jre-headless (2:1.11-72) ... Removing fastaq (3.17.0-4) ... Removing mummer (3.23+dfsg-7) ... Removing gawk (1:5.1.0-1) ... update-alternatives: using /usr/bin/mawk to provide /usr/bin/awk (awk) in auto mode Removing kmc (3.1.1+dfsg-4) ... Removing smalt (0.7.6-9) ... Removing libbambamc0:amd64 (0.0.50-5) ... Removing python3-numpy (1:1.19.5-1) ... Removing liblapack3:amd64 (3.10.0-1) ... Removing libblas3:amd64 (3.10.0-1) ... Removing libhts2:amd64 (1.9-12~deb10u1) ... Removing samtools (1.13-2) ... Removing python3-pysam (0.17.0+ds-2) ... Removing libhts3:amd64 (1.13+ds-2) ... Removing libdeflate0:amd64 (1.8-1) ... Removing python3.7 (3.7.3-2+deb10u3) ... Removing python3.7-minimal (3.7.3-2+deb10u3) ... Removing python3-networkx (2.5+ds-2) ... Removing python3-pkg-resources (58.2.0-1) ... Removing libperl5.28:amd64 (5.28.1-6+deb10u1) ... Removing libpython3.7-stdlib:amd64 (3.7.3-2+deb10u3) ... Removing mime-support (3.66) ... Removing mailcap (3.70) ... Removing perl (5.32.1-6) ... Removing libperl5.32:amd64 (5.32.1-6) ... Removing libgdbm-compat4:amd64 (1.21-1) ... Removing libgdbm6:amd64 (1.21-1) ... Removing libgfortran5:amd64 (11.2.0-9) ... Removing libgomp1:amd64 (11.2.0-9) ... Removing libhtscodecs2:amd64 (1.1.1-3+b1) ... Removing libldap-common (2.4.59+dfsg-1) ... Removing libmpdec2:amd64 (2.4.2-2) ... Removing libmpfr6:amd64 (4.1.0-3) ... Removing libncurses6:amd64 (6.2+20201114-4) ... Removing libpython3.7-minimal:amd64 (3.7.3-2+deb10u3) ... Removing libquadmath0:amd64 (11.2.0-9) ... Removing libreadline7:amd64 (7.0-5) ... Removing libsigsegv2:amd64 (2.13-1) ... Removing perl-modules-5.28 (5.28.1-6+deb10u1) ... Removing perl-modules-5.32 (5.32.1-6) ... Removing python3-decorator (4.4.2-2) ... Removing python3-packaging (21.0-1) ... Removing python3-pyparsing (2.4.7-1) ... Removing libcurl3-gnutls:amd64 (7.74.0-1.3+b1) ... Removing python3 (3.9.2-3) ... Removing python3.9 (3.9.7-4) ... Removing libldap-2.4-2:amd64 (2.4.59+dfsg-1) ... Removing libpython3-stdlib:amd64 (3.9.2-3) ... Removing libpython3.9-stdlib:amd64 (3.9.7-4) ... find: '/usr/lib/python3': No such file or directory Removing libmpdec3:amd64 (2.5.1-2) ... Removing libnghttp2-14:amd64 (1.43.0-1) ... Removing libpsl5:amd64 (0.21.0-1.2) ... Removing python3-minimal (3.9.2-3) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Removing libsasl2-2:amd64 (2.1.27+dfsg-2.1) ... Removing libsasl2-modules-db:amd64 (2.1.27+dfsg-2.1) ... Removing libssh2-1:amd64 (1.10.0-2) ... Removing media-types (4.0.0) ... Removing python3.9-minimal (3.9.7-4) ... Removing libpython3.9-minimal:amd64 (3.9.7-4) ... find: '/usr/lib/python3': No such file or directory Removing ca-certificates-java (20190909) ... Removing ca-certificates (20210119) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing openssl (1.1.1l-1) ... Removing openjdk-11-jre-headless:amd64 (11.0.12+7-2) ... Removing libfontconfig1:amd64 (2.13.1-4.2) ... Removing fontconfig-config (2.13.1-4.2) ... Removing fonts-dejavu-core (2.37-2) ... Removing java-common (0.72) ... Removing libasound2:amd64 (1.2.5.1-1) ... Removing libasound2-data (1.2.5.1-1) ... Removing libcups2:amd64 (2.3.3op2-7) ... Removing libavahi-client3:amd64 (0.8-5) ... Removing libavahi-common3:amd64 (0.8-5) ... Removing libavahi-common-data:amd64 (0.8-5) ... Removing libharfbuzz0b:amd64 (2.7.4-1) ... Removing libfreetype6:amd64 (2.10.4+dfsg-1) ... Removing libbrotli1:amd64 (1.0.9-2+b2) ... Removing libdbus-1-3:amd64 (1.12.20-2) ... Removing libexpat1:amd64 (2.4.1-2+b1) ... Removing libglib2.0-0:amd64 (2.70.0-1+b1) ... Removing libgraphite2-3:amd64 (1.3.14-1) ... Removing libjpeg62-turbo:amd64 (1:2.0.6-4) ... Removing liblcms2-2:amd64 (2.12~rc1-2) ... Removing libnss3:amd64 (2:3.70-1) ... Removing libnspr4:amd64 (2:4.32-1) ... Removing libpcsclite1:amd64 (1.9.4-1) ... Removing libpng16-16:amd64 (1.6.37-3) ... Removing libsqlite3-0:amd64 (3.36.0-2) ... Removing ucf (3.0043) ... Removing sensible-utils (0.0.17) ... Processing triggers for libc-bin (2.32-4) ... 1m39.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-get', 'remove', 'ca-certificates', 'ca-certificates-java', 'default-jre-headless', 'fastaq', 'fontconfig-config', 'fonts-dejavu-core', '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', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libharfbuzz0b:amd64', 'libhts2:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libjpeg62-turbo:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libmpdec2:amd64', 'libmpdec3:amd64', 'libmpfr6:amd64', 'libncurses6:amd64', 'libnghttp2-14:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libpcsclite1:amd64', 'libperl5.28:amd64', 'libperl5.32:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.7-minimal:amd64', 'libpython3.7-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsigsegv2:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'mailcap', 'media-types', 'mime-support', 'mummer', 'openjdk-11-jre-headless:amd64', 'openssl', 'perl', 'perl-modules-5.28', 'perl-modules-5.32', 'python3', 'python3-decorator', 'python3-minimal', 'python3-networkx', 'python3-numpy', 'python3-packaging', 'python3-pkg-resources', 'python3-pyparsing', 'python3-pysam', 'python3.7', 'python3.7-minimal', 'python3.9', 'python3.9-minimal', 'samtools', 'sensible-utils', 'smalt', 'ucf', 'iva'] 1m39.2s INFO: Running scripts post_remove 1m39.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_remove_exceptions'] 1m39.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_remove_exceptions'] 1m39.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'dpkg', '--purge', 'ca-certificates', 'ca-certificates-java', 'default-jre-headless', 'fastaq', 'fontconfig-config', 'fonts-dejavu-core', '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', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libharfbuzz0b:amd64', 'libhts2:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libjpeg62-turbo:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libmpdec2:amd64', 'libmpdec3:amd64', 'libmpfr6:amd64', 'libncurses6:amd64', 'libnghttp2-14:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libpcsclite1:amd64', 'libperl5.28:amd64', 'libperl5.32:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.7-minimal:amd64', 'libpython3.7-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsigsegv2:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'mailcap', 'media-types', 'mime-support', 'mummer', 'openjdk-11-jre-headless:amd64', 'openssl', 'perl', 'perl-modules-5.28', 'perl-modules-5.32', 'python3', 'python3-decorator', 'python3-minimal', 'python3-networkx', 'python3-numpy', 'python3-packaging', 'python3-pkg-resources', 'python3-pyparsing', 'python3-pysam', 'python3.7', 'python3.7-minimal', 'python3.9', 'python3.9-minimal', 'samtools', 'sensible-utils', 'smalt', 'ucf'] 1m39.7s DUMP: (Reading database ... 6865 files and directories currently installed.) Purging configuration files for ca-certificates (20210119) ... Removing dangling symlinks from /etc/ssl/certs... done. Purging configuration files for ca-certificates-java (20190909) ... 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 (2.13.1-4.2) ... Purging configuration files for fonts-dejavu-core (2.37-2) ... Purging configuration files for gawk (1:5.1.0-1) ... Purging configuration files for java-common (0.72) ... 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 libgdbm-compat4 which isn't installed dpkg: warning: ignoring request to remove libgdbm6 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed Purging configuration files for libglib2.0-0:amd64 (2.70.0-1+b1) ... dpkg: warning: ignoring request to remove libgomp1 which isn't installed 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 libhts2 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 Purging configuration files for libldap-common (2.4.59+dfsg-1) ... dpkg: warning: ignoring request to remove libmpdec2 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 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 libperl5.28 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 libpython3.7-minimal:amd64 (3.7.3-2+deb10u3) ... dpkg: warning: ignoring request to remove libpython3.7-stdlib which isn't installed Purging configuration files for libpython3.9-minimal:amd64 (3.9.7-4) ... 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 libreadline7 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 mailcap (3.70) ... Purging configuration files for media-types (4.0.0) ... Purging configuration files for mime-support (3.66) ... dpkg: warning: ignoring request to remove mummer which isn't installed Purging configuration files for openjdk-11-jre-headless:amd64 (11.0.12+7-2) ... Purging configuration files for openssl (1.1.1l-1) ... Purging configuration files for perl (5.32.1-6) ... dpkg: warning: ignoring request to remove perl-modules-5.28 which isn't installed dpkg: warning: ignoring request to remove perl-modules-5.32 which isn't installed Purging configuration files for python3 (3.9.2-3) ... 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-pyparsing which isn't installed dpkg: warning: ignoring request to remove python3-pysam which isn't installed dpkg: warning: ignoring request to remove python3.7 which isn't installed Purging configuration files for python3.7-minimal (3.7.3-2+deb10u3) ... dpkg: warning: ignoring request to remove python3.9 which isn't installed Purging configuration files for python3.9-minimal (3.9.7-4) ... 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) ... 1m39.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'dpkg', '--purge', 'ca-certificates', 'ca-certificates-java', 'default-jre-headless', 'fastaq', 'fontconfig-config', 'fonts-dejavu-core', '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', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libharfbuzz0b:amd64', 'libhts2:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libjpeg62-turbo:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libmpdec2:amd64', 'libmpdec3:amd64', 'libmpfr6:amd64', 'libncurses6:amd64', 'libnghttp2-14:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libpcsclite1:amd64', 'libperl5.28:amd64', 'libperl5.32:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.7-minimal:amd64', 'libpython3.7-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsigsegv2:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'mailcap', 'media-types', 'mime-support', 'mummer', 'openjdk-11-jre-headless:amd64', 'openssl', 'perl', 'perl-modules-5.28', 'perl-modules-5.32', 'python3', 'python3-decorator', 'python3-minimal', 'python3-networkx', 'python3-numpy', 'python3-packaging', 'python3-pkg-resources', 'python3-pyparsing', 'python3-pysam', 'python3.7', 'python3.7-minimal', 'python3.9', 'python3.9-minimal', 'samtools', 'sensible-utils', 'smalt', 'ucf'] 1m39.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'dpkg', '--purge', 'iva'] 1m39.7s DUMP: dpkg: warning: ignoring request to remove iva which isn't installed 1m39.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'dpkg', '--purge', 'iva'] 1m39.7s INFO: Running scripts post_purge 1m39.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_purge_exceptions'] 1m39.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_purge_exceptions'] 1m39.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'dpkg', '--purge', '--pending'] 1m39.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'dpkg', '--purge', '--pending'] 1m39.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'dpkg', '--remove', '--pending'] 1m39.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'dpkg', '--remove', '--pending'] 1m39.8s INFO: Running scripts post_test 1m39.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_test_exceptions'] 1m39.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'tmp/scripts/post_test_exceptions'] 1m39.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya'] 1m40.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya'] 1m40.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'dpkg-divert', '--list'] 1m40.1s DUMP: local diversion of /bin/sync to /bin/sync.distrib diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 1m40.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'dpkg-divert', '--list'] 1m40.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-get', 'clean'] 1m40.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya', 'apt-get', 'clean'] 1m40.2s DEBUG: Recording chroot state 1m40.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya/dev/shm'] 1m40.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya/dev/shm'] 1m40.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya/dev/console'] 1m41.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya/dev/console'] 1m41.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya/dev/ptmx'] 1m41.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya/dev/ptmx'] 1m41.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya/dev/pts'] 1m41.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya/dev/pts'] 1m41.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya/proc'] 1m41.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya/proc'] 1m41.1s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya'] 1m41.2s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpt6l8nlya'] 1m41.2s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpt6l8nlya 1m41.2s INFO: PASS: Upgrading between Debian distributions. 1m41.2s INFO: PASS: All tests. 1m41.2s INFO: piuparts run ends. ret=0 End: 2021-10-20 05:00:43 GMT