Start: 2025-10-02 21:36:37 GMT [testing] Package: libgenomicsdb-java Source: genomicsdb Version: 1.5.5-1 Installed-Size: 493 Maintainer: Debian Med Packaging Team Architecture: all Depends: libcommons-io-java (>= 2.19.0), libgetopt-java, libgoogle-gson-java, libguava-java, libhtsjdk-java (>= 4.1.3), libjson-simple-java, liblog4j2-java (>= 2.19.0), libprotobuf-java, libgenomicsdb-jni (>= 1.5.5-1), libgenomicsdb-jni (<< 1.5.5-1.1~) Description: sparse array storage library for genomics (Java library) Homepage: https://www.genomicsdb.org/ Description-md5: 6a43860137619ae15d009235c0ac2bc5 Section: java Priority: optional Filename: pool/main/g/genomicsdb/libgenomicsdb-java_1.5.5-1_all.deb Size: 409712 MD5sum: c2df8d83f21fa971beba345321195426 SHA256: bda253f13ff35f19fef97259179f890d938e45dc7b1c6a2522d445e8c7c6f98d [sid] Package: libgenomicsdb-java Source: genomicsdb Version: 1.5.5-2 Installed-Size: 493 Maintainer: Debian Med Packaging Team Architecture: all Depends: libcommons-io-java (>= 2.19.0), libgetopt-java, libgoogle-gson-java, libguava-java, libhtsjdk-java (>= 4.1.3), libjson-simple-java, liblog4j2-java (>= 2.19.0), libprotobuf-java, libgenomicsdb-jni (>= 1.5.5-2), libgenomicsdb-jni (<< 1.5.5-2.1~) Description: sparse array storage library for genomics (Java library) Homepage: https://www.genomicsdb.org/ Description-md5: 6a43860137619ae15d009235c0ac2bc5 Section: java Priority: optional Filename: pool/main/g/genomicsdb/libgenomicsdb-java_1.5.5-2_all.deb Size: 409744 MD5sum: 7b092b28958fa56002a798ef943a9348 SHA256: ec2b5be8ba865e38d1373c4867614a96293eece3e1b58594e709285d92094c73 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/bin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/forky-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt libgenomicsdb-java=1.5.5-2 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 1.6.1~202508211856~1.6.0-10-gffba2cce starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/bin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/forky-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt libgenomicsdb-java=1.5.5-2 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 6.1.0-40-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.153-1 (2025-09-20) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmp5ixqmldo 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/forky-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp5ixqmldo 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/forky-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/forky-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo/proc'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo/proc'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo/dev/pts'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo/dev/pts'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo/dev/ptmx'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo/dev/ptmx'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo/dev/console'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo/dev/console'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo/dev/shm'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo/dev/shm'] 0m0.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ forky main 0m0.2s DEBUG: Created policy-rc.d and chmodded it. 0m0.2s DEBUG: Created resolv.conf. 0m0.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp5ixqmldo/tmp/scripts/ 0m0.2s INFO: Running scripts post_chroot_unpack 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'apt-get', 'update'] 0m1.6s DUMP: Get:1 http://deb.debian.org/debian forky InRelease [147 kB] Get:2 http://deb.debian.org/debian forky/main amd64 Packages [9759 kB] Get:3 http://deb.debian.org/debian forky/main Translation-en [6492 kB] Fetched 16.4 MB in 1s (17.8 MB/s) Reading package lists... 0m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'apt-get', 'update'] 0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'apt-get', '-yf', 'dist-upgrade'] 0m4.0s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following NEW packages will be installed: gcc-15-base The following packages will be upgraded: apt base-files bash bsdutils gcc-14-base grep init-system-helpers libapt-pkg7.0 libaudit-common libaudit1 libblkid1 libgcc-s1 libgmp10 libhogweed6t64 liblastlog2-2 liblzma5 libmount1 libnettle8t64 libpcre2-8-0 libsmartcols1 libsqlite3-0 libssl3t64 libstdc++6 libsystemd0 libudev1 libuuid1 libzstd1 login login.defs mount openssl-provider-legacy passwd tzdata util-linux 34 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 16.2 MB of archives. After this operation, 818 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian forky/main amd64 base-files amd64 14 [72.9 kB] Get:2 http://deb.debian.org/debian forky/main amd64 bash amd64 5.3-1 [1556 kB] Get:3 http://deb.debian.org/debian forky/main amd64 grep amd64 3.12-1 [443 kB] Get:4 http://deb.debian.org/debian forky/main amd64 liblastlog2-2 amd64 2.41.2-1 [28.9 kB] Get:5 http://deb.debian.org/debian forky/main amd64 libuuid1 amd64 2.41.2-1 [38.1 kB] Get:6 http://deb.debian.org/debian forky/main amd64 bsdutils amd64 1:2.41.2-1 [93.4 kB] Get:7 http://deb.debian.org/debian forky/main amd64 libblkid1 amd64 2.41.2-1 [173 kB] Get:8 http://deb.debian.org/debian forky/main amd64 libmount1 amd64 2.41.2-1 [211 kB] Get:9 http://deb.debian.org/debian forky/main amd64 libsmartcols1 amd64 2.41.2-1 [144 kB] Get:10 http://deb.debian.org/debian forky/main amd64 util-linux amd64 2.41.2-1 [1257 kB] Get:11 http://deb.debian.org/debian forky/main amd64 mount amd64 2.41.2-1 [162 kB] Get:12 http://deb.debian.org/debian forky/main amd64 libsqlite3-0 amd64 3.46.1-8 [968 kB] Get:13 http://deb.debian.org/debian forky/main amd64 libsystemd0 amd64 258-1 [466 kB] Get:14 http://deb.debian.org/debian forky/main amd64 gcc-15-base amd64 15.2.0-4 [52.8 kB] Get:15 http://deb.debian.org/debian forky/main amd64 libgcc-s1 amd64 15.2.0-4 [71.7 kB] Get:16 http://deb.debian.org/debian forky/main amd64 liblzma5 amd64 5.8.1-1.1 [316 kB] Get:17 http://deb.debian.org/debian forky/main amd64 openssl-provider-legacy amd64 3.5.3-1 [308 kB] Get:18 http://deb.debian.org/debian forky/main amd64 libzstd1 amd64 1.5.7+dfsg-1.1 [320 kB] Get:19 http://deb.debian.org/debian forky/main amd64 libssl3t64 amd64 3.5.3-1 [2445 kB] Get:20 http://deb.debian.org/debian forky/main amd64 libstdc++6 amd64 15.2.0-4 [738 kB] Get:21 http://deb.debian.org/debian forky/main amd64 libudev1 amd64 258-1 [156 kB] Get:22 http://deb.debian.org/debian forky/main amd64 libapt-pkg7.0 amd64 3.1.6 [1205 kB] Get:23 http://deb.debian.org/debian forky/main amd64 apt amd64 3.1.6 [1478 kB] Get:24 http://deb.debian.org/debian forky/main amd64 init-system-helpers all 1.69 [39.3 kB] Get:25 http://deb.debian.org/debian forky/main amd64 libaudit-common all 1:4.1.2-1 [14.3 kB] Get:26 http://deb.debian.org/debian forky/main amd64 libaudit1 amd64 1:4.1.2-1 [60.4 kB] Get:27 http://deb.debian.org/debian forky/main amd64 login amd64 1:4.16.0-2+really2.41.2-1 [105 kB] Get:28 http://deb.debian.org/debian forky/main amd64 libgmp10 amd64 2:6.3.0+dfsg-5 [574 kB] Get:29 http://deb.debian.org/debian forky/main amd64 libnettle8t64 amd64 3.10.2-1 [307 kB] Get:30 http://deb.debian.org/debian forky/main amd64 libhogweed6t64 amd64 3.10.2-1 [336 kB] Get:31 http://deb.debian.org/debian forky/main amd64 libpcre2-8-0 amd64 10.46-1 [298 kB] Get:32 http://deb.debian.org/debian forky/main amd64 login.defs all 1:4.18.0-1 [211 kB] Get:33 http://deb.debian.org/debian forky/main amd64 passwd amd64 1:4.18.0-1 [1284 kB] Get:34 http://deb.debian.org/debian forky/main amd64 tzdata all 2025b-5 [260 kB] Get:35 http://deb.debian.org/debian forky/main amd64 gcc-14-base amd64 14.3.0-8 [52.1 kB] Preconfiguring packages ... Fetched 16.2 MB in 0s (65.0 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 ... 4934 files and directories currently installed.) Preparing to unpack .../base-files_14_amd64.deb ... Unpacking base-files (14) over (13.8) ... Setting up base-files (14) ... Installing new version of config file /etc/debian_version ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4934 files and directories currently installed.) Preparing to unpack .../libuuid1_2.41.2-1_amd64.deb ... Unpacking libuuid1:amd64 (2.41.2-1) over (2.41-5) ... Setting up libuuid1:amd64 (2.41.2-1) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4931 files and directories currently installed.) Preparing to unpack .../util-linux_2.41.2-1_amd64.deb ... Unpacking util-linux (2.41.2-1) over (2.41-5) ... Setting up util-linux (2.41.2-1) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4942 files and directories currently installed.) Preparing to unpack .../libzstd1_1.5.7+dfsg-1.1_amd64.deb ... Unpacking libzstd1:amd64 (1.5.7+dfsg-1.1) over (1.5.7+dfsg-1) ... Setting up libzstd1:amd64 (1.5.7+dfsg-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 ... 4942 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.5.3-1_amd64.deb ... Unpacking libssl3t64:amd64 (3.5.3-1) over (3.5.1-1) ... Setting up libssl3t64:amd64 (3.5.3-1) ... (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 ... 4942 files and directories currently installed.) Preparing to unpack .../libstdc++6_15.2.0-4_amd64.deb ... Unpacking libstdc++6:amd64 (15.2.0-4) over (14.2.0-19) ... Setting up libstdc++6:amd64 (15.2.0-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4942 files and directories currently installed.) Preparing to unpack .../libudev1_258-1_amd64.deb ... Unpacking libudev1:amd64 (258-1) over (257.7-1) ... Setting up libudev1:amd64 (258-1) ... (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 ... 4942 files and directories currently installed.) Preparing to unpack .../libapt-pkg7.0_3.1.6_amd64.deb ... Unpacking libapt-pkg7.0:amd64 (3.1.6) over (3.0.3) ... Setting up libapt-pkg7.0:amd64 (3.1.6) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4942 files and directories currently installed.) Preparing to unpack .../archives/apt_3.1.6_amd64.deb ... Unpacking apt (3.1.6) over (3.0.3) ... Setting up apt (3.1.6) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4940 files and directories currently installed.) Preparing to unpack .../init-system-helpers_1.69_all.deb ... Unpacking init-system-helpers (1.69) over (1.68) ... Setting up init-system-helpers (1.69) ... (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 ... 4941 files and directories currently installed.) Preparing to unpack .../libaudit-common_1%3a4.1.2-1_all.deb ... Unpacking libaudit-common (1:4.1.2-1) over (1:4.0.2-2) ... Setting up libaudit-common (1:4.1.2-1) ... (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 ... 4941 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a4.1.2-1_amd64.deb ... Unpacking libaudit1:amd64 (1:4.1.2-1) over (1:4.0.2-2+b2) ... Setting up libaudit1:amd64 (1:4.1.2-1) ... (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 ... 4940 files and directories currently installed.) Preparing to unpack .../login_1%3a4.16.0-2+really2.41.2-1_amd64.deb ... Unpacking login (1:4.16.0-2+really2.41.2-1) over (1:4.16.0-2+really2.41-5) ... Preparing to unpack .../libgmp10_2%3a6.3.0+dfsg-5_amd64.deb ... Unpacking libgmp10:amd64 (2:6.3.0+dfsg-5) over (2:6.3.0+dfsg-3) ... Setting up libgmp10:amd64 (2:6.3.0+dfsg-5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4932 files and directories currently installed.) Preparing to unpack .../libnettle8t64_3.10.2-1_amd64.deb ... Unpacking libnettle8t64:amd64 (3.10.2-1) over (3.10.1-1) ... Setting up libnettle8t64:amd64 (3.10.2-1) ... (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 ... 4932 files and directories currently installed.) Preparing to unpack .../libhogweed6t64_3.10.2-1_amd64.deb ... Unpacking libhogweed6t64:amd64 (3.10.2-1) over (3.10.1-1) ... Setting up libhogweed6t64:amd64 (3.10.2-1) ... (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 ... 4932 files and directories currently installed.) Preparing to unpack .../libpcre2-8-0_10.46-1_amd64.deb ... Unpacking libpcre2-8-0:amd64 (10.46-1) over (10.45-1) ... Setting up libpcre2-8-0:amd64 (10.46-1) ... (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 ... 4932 files and directories currently installed.) Preparing to unpack .../login.defs_1%3a4.18.0-1_all.deb ... Unpacking login.defs (1:4.18.0-1) over (1:4.17.4-2) ... Preparing to unpack .../passwd_1%3a4.18.0-1_amd64.deb ... Unpacking passwd (1:4.18.0-1) over (1:4.17.4-2) ... Preparing to unpack .../tzdata_2025b-5_all.deb ... Unpacking tzdata (2025b-5) over (2025b-4) ... Preparing to unpack .../gcc-14-base_14.3.0-8_amd64.deb ... Unpacking gcc-14-base:amd64 (14.3.0-8) over (14.2.0-19) ... Setting up gcc-14-base:amd64 (14.3.0-8) ... Setting up login.defs (1:4.18.0-1) ... Setting up tzdata (2025b-5) ... Current default time zone: 'Etc/UTC' Local time is now: Thu Oct 2 21:36:40 UTC 2025. Universal Time is now: Thu Oct 2 21:36:40 UTC 2025. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up passwd (1:4.18.0-1) ... Setting up mount (2.41.2-1) ... Setting up login (1:4.16.0-2+really2.41.2-1) ... Processing triggers for debianutils (5.23.2) ... Processing triggers for libc-bin (2.41-12) ... 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'apt-get', '-yf', 'dist-upgrade'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.5s DUMP: 67022dda6fa54a742fe44d0f2c8f8153 - 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.5s INFO: Running scripts post_setup 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/post_setup_dummy_users'] 0m5.0s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/post_setup_dummy_users'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/post_setup_forbid_home'] 0m5.0s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/post_setup_forbid_home'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.0s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/post_setup_minimize'] 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/post_setup_minimize'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/post_setup_zz_backports'] 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/post_setup_zz_backports'] 0m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.0s DUMP: install ok installed apt apt 3.1.6 install ok installed base-files base-files 14 install ok installed base-passwd base-passwd 3.6.7 install ok installed bash bash 5.3-1 install ok installed bsdutils bsdutils 1:2.41.2-1 install ok installed coreutils coreutils 9.7-3 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.91 install ok installed debian-archive-keyring debian-archive-keyring 2025.1 install ok installed debianutils debianutils 5.23.2 install ok installed diffutils diffutils 1:3.10-4 install ok installed dpkg dpkg 1.22.21 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.3.0-8 install ok installed gcc-15-base:amd64 gcc-15-base 15.2.0-4 install ok installed grep grep 3.12-1 install ok installed gzip gzip 1.13-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.69 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.1.6 install ok installed libattr1:amd64 libattr1 1:2.5.2-3 install ok installed libaudit-common libaudit-common 1:4.1.2-1 install ok installed libaudit1:amd64 libaudit1 1:4.1.2-1 install ok installed libblkid1:amd64 libblkid1 2.41.2-1 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.41-12 install ok installed libc6:amd64 libc6 2.41-12 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1 install ok installed libcap2:amd64 libcap2 1:2.75-10+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.280 install ok installed libgcc-s1:amd64 libgcc-s1 15.2.0-4 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-5 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.2-1 install ok installed liblastlog2-2:amd64 liblastlog2-2 2.41.2-1 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-4 install ok installed liblzma5:amd64 liblzma5 5.8.1-1.1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.41.2-1 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.2-1 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-5 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-5 install ok installed libpam-runtime libpam-runtime 1.7.0-5 install ok installed libpam0g:amd64 libpam0g 1.7.0-5 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.46-1 install ok installed libseccomp2:amd64 libseccomp2 2.6.0-2 install ok installed libselinux1:amd64 libselinux1 3.8.1-1 install ok installed libsemanage-common libsemanage-common 3.8.1-1 install ok installed libsemanage2:amd64 libsemanage2 3.8.1-1 install ok installed libsepol2:amd64 libsepol2 3.8.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.41.2-1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-8 install ok installed libssl3t64:amd64 libssl3t64 3.5.3-1 install ok installed libstdc++6:amd64 libstdc++6 15.2.0-4 install ok installed libsystemd0:amd64 libsystemd0 258-1 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2 install ok installed libudev1:amd64 libudev1 258-1 install ok installed libuuid1:amd64 libuuid1 2.41.2-1 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-1.1 install ok installed login login 1:4.16.0-2+really2.41.2-1 install ok installed login.defs login.defs 1:4.18.0-1 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed mount mount 2.41.2-1 install ok installed ncurses-base ncurses-base 6.5+20250216-2 install ok installed ncurses-bin ncurses-bin 6.5+20250216-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.5.3-1 install ok installed passwd passwd 1:4.18.0-1 install ok installed perl-base perl-base 5.40.1-6 install ok installed sed sed 4.9-2 install ok installed sqv sqv 1.3.0-3 install ok installed sysvinit-utils sysvinit-utils 3.14-4 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tzdata tzdata 2025b-5 install ok installed util-linux util-linux 2.41.2-1 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.0s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m5.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo'] 0m5.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo'] 0m5.2s INFO: Running scripts is_testable 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/is_testable_uninstallable'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/is_testable_uninstallable'] 0m5.2s INFO: Running scripts pre_test 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_test_exceptions'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_test_exceptions'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_test_root_password'] 0m5.3s DUMP: New password: Retype new password: passwd: password updated successfully 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_test_root_password'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'apt-cache', 'show', '--no-all-versions', 'libgenomicsdb-java'] 0m5.4s DUMP: Package: libgenomicsdb-java Source: genomicsdb Version: 1.5.5-1 Installed-Size: 493 Maintainer: Debian Med Packaging Team Architecture: all Depends: libcommons-io-java (>= 2.19.0), libgetopt-java, libgoogle-gson-java, libguava-java, libhtsjdk-java (>= 4.1.3), libjson-simple-java, liblog4j2-java (>= 2.19.0), libprotobuf-java, libgenomicsdb-jni (>= 1.5.5-1), libgenomicsdb-jni (<< 1.5.5-1.1~) Description-en: sparse array storage library for genomics (Java library) GenomicsDB is built on top of a htslib fork and an internal array storage system for importing, querying and transforming variant data. Variant data is sparse by nature (sparse relative to the whole genome) and using sparse array data stores is a perfect fit for storing such data. . The GenomicsDB stores variant data in a 2D array where: - Each column corresponds to a genomic position (chromosome + position); - Each row corresponds to a sample in a VCF (or CallSet in the GA4GH terminology); - Each cell contains data for a given sample/CallSet at a given position; data is stored in the form of cell attributes; - Cells are stored in column major order - this makes accessing cells with the same column index (i.e. data for a given genomic position over all samples) fast. - Variant interval/gVCF interval data is stored in a cell at the start of the interval. The END is stored as a cell attribute. For variant intervals (such as deletions and gVCF REF blocks), an additional cell is stored at the END value of the variant interval. When queried for a given genomic position, the query library performs an efficient sweep to determine all intervals that intersect with the queried position. . This package contains the Java library. Description-md5: 6a43860137619ae15d009235c0ac2bc5 Homepage: https://www.genomicsdb.org/ Section: java Priority: optional Filename: pool/main/g/genomicsdb/libgenomicsdb-java_1.5.5-1_all.deb Size: 409712 MD5sum: c2df8d83f21fa971beba345321195426 SHA256: bda253f13ff35f19fef97259179f890d938e45dc7b1c6a2522d445e8c7c6f98d 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'apt-cache', 'show', '--no-all-versions', 'libgenomicsdb-java'] 0m5.4s INFO: apt-cache knows about the following packages: libgenomicsdb-java 0m5.4s INFO: Running scripts pre_install 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_install_database-server'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_install_database-server'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_install_exceptions'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_install_exceptions'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_install_extras'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_install_extras'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'apt-cache', 'policy'] 0m5.4s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian forky/main amd64 Packages release o=Debian,a=testing,n=forky,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'apt-cache', 'policy'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'apt-cache', 'policy', 'libgenomicsdb-java'] 0m5.4s DUMP: libgenomicsdb-java: Installed: (none) Candidate: 1.5.5-1 Version table: 1.5.5-1 500 500 http://deb.debian.org/debian forky/main amd64 Packages 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'apt-cache', 'policy', 'libgenomicsdb-java'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'apt-get', '-y', 'install', 'libgenomicsdb-java'] 0m14.3s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: adduser ca-certificates ca-certificates-java default-jre-headless ibverbs-providers java-common junit4 libamd-comgr2 libamdhip64-5 libapache-pom-java libatinject-jsr330-api-java libbrotli1 libcbor0.10 libcom-err2 libcommons-beanutils-java libcommons-codec-java libcommons-collections3-java libcommons-collections4-java libcommons-compress-java libcommons-io-java libcommons-jexl2-java libcommons-lang3-java libcommons-logging-java libcommons-parent-java libcurl4t64 libdrm-amdgpu1 libdrm-common libdrm2 libedit2 libelf1t64 liberror-prone-java libevent-core-2.1-7t64 libevent-pthreads-2.1-7t64 libezmorph-java libfabric1 libffi8 libfido2-1 libfmt10 libfuse3-4 libgenomicsdb-jni libgenomicsdb1 libgetopt-java libgnutls30t64 libgomp1 libgoogle-gson-java libgssapi-krb5-2 libguava-java libhamcrest-java libhsa-runtime64-1 libhsakmt1 libhtsjdk-java libhttpclient-java libhttpcore-java libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs1 libidn2-0 libjaxen-java libjpeg62-turbo libjson-java libjson-simple-java libjsr305-java libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblcms2-2 libldap2 liblightcouch-java libllvm17t64 liblog4j2-java libmbedcrypto16 libmbedtls21 libmbedx509-7 libmongodb-java libmunge2 libmuparserx4.0.12 libncbi-ngs3 libncbi-vdb3 libnghttp2-14 libnghttp3-9 libngs-java libngs-jni libnl-3-200 libnl-route-3-200 libnspr4 libnss3 libnuma1 libopenmpi40 libp11-kit0 libpciaccess0 libpcsclite1 libpmix2t64 libprotobuf-java libprotobuf32t64 libpsl5t64 libpsm2-2 librdmacm1t64 librhino-java librtmp1 libsasl2-2 libsasl2-modules-db libslf4j-java libsnappy-java libsnappy-jni libsnappy1v5 libssh2-1t64 libtasn1-6 libucx0 libunistring5 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxerces2-java libxext6 libxml-commons-external-java libxml-commons-resolver1.1-java libxml2-16 libxnvctrl0 libxom-java libz3-4 libze1 mpi-default-bin ncbi-vdb-data ocl-icd-libopencl1 openjdk-21-jre-headless openmpi-bin openmpi-common openssh-client openssl Suggested packages: liblocale-gettext-perl perl cron quota default-jre libatinject-jsr330-api-java-doc libcommons-collections3-java-doc libcommons-collections4-java-doc libasm-java libxz-java libavalon-framework-java libexcalibur-logkit-java liblog4j1.2-java fuse3 gnutls-bin libgoogle-gson-java-doc krb5-doc krb5-user picard-tools python3 libhwloc-contrib-plugins libdom4j-java libjdom1-java libjson-simple-doc libjsr305-java-doc liblcms2-utils libactivation-java libcommons-csv-java libconversant-disruptor-java libdisruptor-java libgeronimo-jms-1.1-spec-java libjackson2-dataformat-xml-java libjackson2-dataformat-yaml libjansi-java libjctools-java libjeromq-java libmail-java libwoodstox-java libngs-java-doc pciutils pcscd rhino libxerces2-java-doc libxml-commons-resolver1.1-java-doc libxom-java-doc opencl-icd libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic gfortran | fortran-compiler keychain libpam-ssh monkeysphere ssh-askpass Recommended packages: krb5-locales libldap-common publicsuffix libsasl2-modules python3:any libcups2t64 libfontconfig1 libfreetype6 libharfbuzz0b libasound2t64 xauth The following NEW packages will be installed: adduser ca-certificates ca-certificates-java default-jre-headless ibverbs-providers java-common junit4 libamd-comgr2 libamdhip64-5 libapache-pom-java libatinject-jsr330-api-java libbrotli1 libcbor0.10 libcom-err2 libcommons-beanutils-java libcommons-codec-java libcommons-collections3-java libcommons-collections4-java libcommons-compress-java libcommons-io-java libcommons-jexl2-java libcommons-lang3-java libcommons-logging-java libcommons-parent-java libcurl4t64 libdrm-amdgpu1 libdrm-common libdrm2 libedit2 libelf1t64 liberror-prone-java libevent-core-2.1-7t64 libevent-pthreads-2.1-7t64 libezmorph-java libfabric1 libffi8 libfido2-1 libfmt10 libfuse3-4 libgenomicsdb-java libgenomicsdb-jni libgenomicsdb1 libgetopt-java libgnutls30t64 libgomp1 libgoogle-gson-java libgssapi-krb5-2 libguava-java libhamcrest-java libhsa-runtime64-1 libhsakmt1 libhtsjdk-java libhttpclient-java libhttpcore-java libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs1 libidn2-0 libjaxen-java libjpeg62-turbo libjson-java libjson-simple-java libjsr305-java libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblcms2-2 libldap2 liblightcouch-java libllvm17t64 liblog4j2-java libmbedcrypto16 libmbedtls21 libmbedx509-7 libmongodb-java libmunge2 libmuparserx4.0.12 libncbi-ngs3 libncbi-vdb3 libnghttp2-14 libnghttp3-9 libngs-java libngs-jni libnl-3-200 libnl-route-3-200 libnspr4 libnss3 libnuma1 libopenmpi40 libp11-kit0 libpciaccess0 libpcsclite1 libpmix2t64 libprotobuf-java libprotobuf32t64 libpsl5t64 libpsm2-2 librdmacm1t64 librhino-java librtmp1 libsasl2-2 libsasl2-modules-db libslf4j-java libsnappy-java libsnappy-jni libsnappy1v5 libssh2-1t64 libtasn1-6 libucx0 libunistring5 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxerces2-java libxext6 libxml-commons-external-java libxml-commons-resolver1.1-java libxml2-16 libxnvctrl0 libxom-java libz3-4 libze1 mpi-default-bin ncbi-vdb-data ocl-icd-libopencl1 openjdk-21-jre-headless openmpi-bin openmpi-common openssh-client openssl 0 upgraded, 135 newly installed, 0 to remove and 0 not upgraded. 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libxml-commons-resolver1.1-java all 1.2-11 [98.3 kB] Get:86 http://deb.debian.org/debian forky/main amd64 libxerces2-java all 2.12.2-1 [1440 kB] Get:87 http://deb.debian.org/debian forky/main amd64 libxom-java all 1.3.9-1 [174 kB] Get:88 http://deb.debian.org/debian forky/main amd64 libjson-java all 3.1.0+dfsg-2 [142 kB] Get:89 http://deb.debian.org/debian forky/main amd64 libmbedcrypto16 amd64 3.6.4-2 [360 kB] Get:90 http://deb.debian.org/debian forky/main amd64 libmbedx509-7 amd64 3.6.4-2 [151 kB] Get:91 http://deb.debian.org/debian forky/main amd64 libmbedtls21 amd64 3.6.4-2 [242 kB] Get:92 http://deb.debian.org/debian forky/main amd64 ncbi-vdb-data all 3.2.1+dfsg-2 [88.5 kB] Get:93 http://deb.debian.org/debian forky/main amd64 libncbi-vdb3 amd64 3.2.1+dfsg-2 [1164 kB] Get:94 http://deb.debian.org/debian forky/main amd64 libncbi-ngs3 amd64 3.2.1+dfsg-5 [159 kB] Get:95 http://deb.debian.org/debian forky/main amd64 libngs-jni amd64 3.2.1+dfsg-5 [27.8 kB] Get:96 http://deb.debian.org/debian forky/main amd64 libngs-java amd64 3.2.1+dfsg-5 [114 kB] Get:97 http://deb.debian.org/debian forky/main amd64 librhino-java all 1.7.15-1 [1382 kB] Get:98 http://deb.debian.org/debian forky/main amd64 libsnappy1v5 amd64 1.2.2-2 [30.7 kB] Get:99 http://deb.debian.org/debian forky/main amd64 libsnappy-jni amd64 1.1.10.8-1 [6548 B] Get:100 http://deb.debian.org/debian forky/main amd64 libsnappy-java all 1.1.10.8-1 [87.8 kB] Get:101 http://deb.debian.org/debian forky/main amd64 libhtsjdk-java all 4.1.3+dfsg-2 [1841 kB] Get:102 http://deb.debian.org/debian forky/main amd64 libjson-simple-java all 2.3.0-2 [61.7 kB] Get:103 http://deb.debian.org/debian forky/main amd64 libhttpcore-java all 4.4.16-1 [636 kB] Get:104 http://deb.debian.org/debian forky/main amd64 libhttpclient-java all 4.5.14-1 [1247 kB] Get:105 http://deb.debian.org/debian forky/main amd64 liblightcouch-java all 0.2.0-1 [75.0 kB] Get:106 http://deb.debian.org/debian forky/main amd64 libmongodb-java all 3.6.3-2 [1901 kB] Get:107 http://deb.debian.org/debian forky/main amd64 liblog4j2-java all 2.19.0-2 [2310 kB] Get:108 http://deb.debian.org/debian forky/main amd64 libprotobuf-java all 3.21.12-14 [1268 kB] Get:109 http://deb.debian.org/debian forky/main amd64 libgomp1 amd64 15.2.0-4 [140 kB] Get:110 http://deb.debian.org/debian forky/main amd64 libmuparserx4.0.12 amd64 4.0.12-2 [198 kB] Get:111 http://deb.debian.org/debian forky/main amd64 libprotobuf32t64 amd64 3.21.12-14 [988 kB] Get:112 http://deb.debian.org/debian forky/main amd64 libhwloc15 amd64 2.12.2-1 [164 kB] Get:113 http://deb.debian.org/debian forky/main amd64 libmunge2 amd64 0.5.16-1 [19.7 kB] Get:114 http://deb.debian.org/debian forky/main amd64 libpciaccess0 amd64 0.17-3+b3 [51.9 kB] Get:115 http://deb.debian.org/debian forky/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get:116 http://deb.debian.org/debian forky/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get:117 http://deb.debian.org/debian forky/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get:118 http://deb.debian.org/debian forky/main amd64 libx11-data all 2:1.8.12-1 [343 kB] Get:119 http://deb.debian.org/debian forky/main amd64 libx11-6 amd64 2:1.8.12-1 [815 kB] Get:120 http://deb.debian.org/debian forky/main amd64 libxext6 amd64 2:1.3.4-1+b3 [50.4 kB] Get:121 http://deb.debian.org/debian forky/main amd64 libxnvctrl0 amd64 535.171.04-1+b2 [14.2 kB] Get:122 http://deb.debian.org/debian forky/main amd64 libze1 amd64 1.24.1-2 [514 kB] Get:123 http://deb.debian.org/debian forky/main amd64 ocl-icd-libopencl1 amd64 2.3.3-1 [42.9 kB] Get:124 http://deb.debian.org/debian forky/main amd64 libhwloc-plugins amd64 2.12.2-1 [23.5 kB] Get:125 http://deb.debian.org/debian forky/main amd64 libpmix2t64 amd64 6.0.0+really5.0.8-1 [668 kB] Get:126 http://deb.debian.org/debian forky/main amd64 libibumad3 amd64 56.1-1+b1 [30.1 kB] Get:127 http://deb.debian.org/debian forky/main amd64 libibmad5 amd64 56.1-1+b1 [44.9 kB] Get:128 http://deb.debian.org/debian forky/main amd64 libucx0 amd64 1.19.0+ds-1 [1336 kB] Get:129 http://deb.debian.org/debian forky/main amd64 libopenmpi40 amd64 5.0.8-10+b1 [2414 kB] Get:130 http://deb.debian.org/debian forky/main amd64 openmpi-common all 5.0.8-10 [97.5 kB] Get:131 http://deb.debian.org/debian forky/main amd64 openmpi-bin amd64 5.0.8-10+b1 [190 kB] Get:132 http://deb.debian.org/debian forky/main amd64 mpi-default-bin amd64 1.19 [2640 B] Get:133 http://deb.debian.org/debian forky/main amd64 libgenomicsdb1 amd64 1.5.5-1 [1628 kB] Get:134 http://deb.debian.org/debian forky/main amd64 libgenomicsdb-jni amd64 1.5.5-1 [84.8 kB] Get:135 http://deb.debian.org/debian forky/main amd64 libgenomicsdb-java all 1.5.5-1 [410 kB] Preconfiguring packages ... Fetched 143 MB in 2s (81.9 MB/s) Selecting previously unselected package adduser. (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 ... 4936 files and directories currently installed.) Preparing to unpack .../archives/adduser_3.153_all.deb ... Unpacking adduser (3.153) ... Setting up adduser (3.153) ... Selecting previously unselected package openssl. (Reading database ... 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Setting up openssl (3.5.3-1) ... Setting up libdrm-common (2.4.125-2) ... Setting up libsnappy-jni (1.1.10.8-1) ... Setting up libezmorph-java (1.0.6-4) ... Setting up libldap2:amd64 (2.6.10+dfsg-1) ... Setting up libfmt10:amd64 (10.1.1+ds1-4) ... Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libcommons-parent-java (56-1) ... Setting up libcommons-logging-java (1.3.0-2) ... Setting up libxext6:amd64 (2:1.3.4-1+b3) ... Setting up libidn2-0:amd64 (2.3.8-4) ... Setting up libnss3:amd64 (2:3.116-1) ... Setting up libxom-java (1.3.9-1) ... Setting up libnl-route-3-200:amd64 (3.11.0-2) ... Setting up libxnvctrl0:amd64 (535.171.04-1+b2) ... Setting up libcommons-jexl2-java (2.1.1-6) ... Setting up ca-certificates (20250419) ... Updating certificates in /etc/ssl/certs... 150 added, 0 removed; done. Setting up libmbedx509-7:amd64 (3.6.4-2) ... Setting up libllvm17t64:amd64 (1:17.0.6-22+b3) ... Setting up libp11-kit0:amd64 (0.25.9-2) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-5) ... Setting up libcommons-collections4-java (4.4-2) ... Setting up libcommons-lang3-java (3.17.0-2) ... Setting up libmbedtls21:amd64 (3.6.4-2) ... Setting up libdrm2:amd64 (2.4.125-2) ... Setting up libcommons-beanutils-java (1.10.1-1.1) ... Setting up libsnappy-java (1.1.10.8-1) ... Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3+b2) ... Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up libcommons-codec-java (1.18.0-1) ... Setting up libdrm-amdgpu1:amd64 (2.4.125-2) ... Setting up libgnutls30t64:amd64 (3.8.10-2) ... Setting up libibverbs1:amd64 (56.1-1+b1) ... Setting up openjdk-21-jre-headless:amd64 (21.0.9~8ea-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up ibverbs-providers:amd64 (56.1-1+b1) ... Setting up libcommons-io-java (2.19.0-1) ... Setting up openssh-client (1:10.0p1-8) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libncbi-vdb3:amd64 (3.2.1+dfsg-2) ... Setting up libhwloc-plugins:amd64 (2.12.2-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-3) ... Setting up libpmix2t64:amd64 (6.0.0+really5.0.8-1) ... Setting up libhttpclient-java (4.5.14-1) ... Setting up librdmacm1t64:amd64 (56.1-1+b1) ... Setting up liblightcouch-java (0.2.0-1) ... Setting up libhsakmt1:amd64 (6.2.4+ds-1) ... Setting up libncbi-ngs3:amd64 (3.2.1+dfsg-5) ... Setting up libfabric1:amd64 (2.1.0-1.1) ... Setting up libngs-jni:amd64 (3.2.1+dfsg-5) ... Setting up libcommons-compress-java (1.27.1-2) ... Setting up libcurl4t64:amd64 (8.16.0-1) ... Setting up liblog4j2-java (2.19.0-2) ... Setting up libhsa-runtime64-1:amd64 (6.1.2-3) ... Setting up libngs-java:amd64 (3.2.1+dfsg-5) ... Setting up libamdhip64-5:amd64 (5.7.1-6) ... Setting up libucx0:amd64 (1.19.0+ds-1) ... Setting up libopenmpi40:amd64 (5.0.8-10+b1) ... Setting up openmpi-bin (5.0.8-10+b1) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/mpiexec.1.gz because associated file /usr/share/man/man1/mpiexec.openmpi.1.gz (of link group mpirun) doesn't exist update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up mpi-default-bin (1.19) ... Setting up libgenomicsdb1 (1.5.5-1) ... Setting up libgenomicsdb-jni (1.5.5-1) ... Setting up liberror-prone-java (2.18.0-1) ... Setting up libguava-java (32.0.1-1) ... Setting up libprotobuf-java (3.21.12-14) ... Processing triggers for libc-bin (2.41-12) ... Processing triggers for ca-certificates-java (20240118) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:BJCA_Global_Root_CA1.pem Adding debian:BJCA_Global_Root_CA2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:CommScope_Public_Trust_ECC_Root-01.pem Adding debian:CommScope_Public_Trust_ECC_Root-02.pem Adding debian:CommScope_Public_Trust_RSA_Root-01.pem Adding debian:CommScope_Public_Trust_RSA_Root-02.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_BR_Root_CA_2_2023.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_2_2023.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:FIRMAPROFESIONAL_CA_ROOT-A_WEB.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem Adding debian:SecureSign_Root_CA12.pem Adding debian:SecureSign_Root_CA14.pem Adding debian:SecureSign_Root_CA15.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_CYBER_Root_CA.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:Telekom_Security_TLS_ECC_Root_2020.pem Adding debian:Telekom_Security_TLS_RSA_Root_2023.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustAsia_Global_Root_CA_G3.pem Adding debian:TrustAsia_Global_Root_CA_G4.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up junit4 (4.13.2-5) ... Setting up default-jre-headless (2:1.21-76) ... Setting up libjson-java (3.1.0+dfsg-2) ... Setting up libhtsjdk-java (4.1.3+dfsg-2) ... Setting up libgenomicsdb-java (1.5.5-1) ... Processing triggers for ca-certificates (20250419) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for ca-certificates-java (20240118) ... done. 0m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'apt-get', '-y', 'install', 'libgenomicsdb-java'] 0m14.3s INFO: Running scripts post_install 0m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/post_install_exceptions'] 0m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/post_install_exceptions'] 0m14.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo'] 0m14.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo'] 0m14.6s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmp5ixqmldo to sid 0m14.6s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m14.6s INFO: Running scripts pre_distupgrade 0m14.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m14.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m14.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_distupgrade_exceptions'] 0m14.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_distupgrade_exceptions'] 0m14.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m14.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m14.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m14.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m14.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m14.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m14.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'apt-get', 'update'] 0m16.6s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [207 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.2 MB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7441 kB] Fetched 17.8 MB in 2s (11.4 MB/s) Reading package lists... 0m16.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'apt-get', 'update'] 0m16.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'apt-get', '-yf', 'dist-upgrade'] 0m18.2s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: bsdutils libblkid1 libgenomicsdb-java libgenomicsdb-jni libgenomicsdb1 liblastlog2-2 libmount1 libnspr4 libsmartcols1 libssl3t64 libuuid1 login mount openssl openssl-provider-legacy util-linux 16 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 8619 kB of archives. After this operation, 674 kB disk space will be freed. Get:1 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.41.2-3 [38.4 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.41.2-3 [174 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.41.2-3 [211 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.41.2-3 [145 kB] Get:5 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.41.2-3 [1164 kB] Get:6 http://deb.debian.org/debian sid/main amd64 mount amd64 2.41.2-3 [163 kB] Get:7 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.16.0-2+really2.41.2-3 [105 kB] Get:8 http://deb.debian.org/debian sid/main amd64 liblastlog2-2 amd64 2.41.2-3 [29.3 kB] Get:9 http://deb.debian.org/debian sid/main amd64 openssl-provider-legacy amd64 3.5.4-1 [308 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libssl3t64 amd64 3.5.4-1 [2446 kB] Get:11 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.41.2-3 [93.5 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libgenomicsdb-java all 1.5.5-2 [410 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libgenomicsdb-jni amd64 1.5.5-2 [86.8 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libgenomicsdb1 amd64 1.5.5-2 [1640 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libnspr4 amd64 2:4.37-1 [111 kB] Get:16 http://deb.debian.org/debian sid/main amd64 openssl amd64 3.5.4-1 [1496 kB] Fetched 8619 kB in 0s (25.3 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8297 files and directories currently installed.) Preparing to unpack .../libuuid1_2.41.2-3_amd64.deb ... Unpacking libuuid1:amd64 (2.41.2-3) over (2.41.2-1) ... Setting up libuuid1:amd64 (2.41.2-3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8297 files and directories currently installed.) Preparing to unpack .../libblkid1_2.41.2-3_amd64.deb ... Unpacking libblkid1:amd64 (2.41.2-3) over (2.41.2-1) ... Setting up libblkid1:amd64 (2.41.2-3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8297 files and directories currently installed.) Preparing to unpack .../libmount1_2.41.2-3_amd64.deb ... Unpacking libmount1:amd64 (2.41.2-3) over (2.41.2-1) ... Setting up libmount1:amd64 (2.41.2-3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8297 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.41.2-3_amd64.deb ... Unpacking libsmartcols1:amd64 (2.41.2-3) over (2.41.2-1) ... Setting up libsmartcols1:amd64 (2.41.2-3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8297 files and directories currently installed.) Preparing to unpack .../util-linux_2.41.2-3_amd64.deb ... Unpacking util-linux (2.41.2-3) over (2.41.2-1) ... Setting up util-linux (2.41.2-3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8262 files and directories currently installed.) Preparing to unpack .../mount_2.41.2-3_amd64.deb ... Unpacking mount (2.41.2-3) over (2.41.2-1) ... Preparing to unpack .../login_1%3a4.16.0-2+really2.41.2-3_amd64.deb ... Unpacking login (1:4.16.0-2+really2.41.2-3) over (1:4.16.0-2+really2.41.2-1) ... Preparing to unpack .../liblastlog2-2_2.41.2-3_amd64.deb ... Unpacking liblastlog2-2:amd64 (2.41.2-3) over (2.41.2-1) ... Setting up liblastlog2-2:amd64 (2.41.2-3) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8262 files and directories currently installed.) Preparing to unpack .../openssl-provider-legacy_3.5.4-1_amd64.deb ... Unpacking openssl-provider-legacy (3.5.4-1) over (3.5.3-1) ... Setting up openssl-provider-legacy (3.5.4-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8262 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.5.4-1_amd64.deb ... Unpacking libssl3t64:amd64 (3.5.4-1) over (3.5.3-1) ... Setting up libssl3t64:amd64 (3.5.4-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 8262 files and directories currently installed.) Preparing to unpack .../0-bsdutils_1%3a2.41.2-3_amd64.deb ... Unpacking bsdutils (1:2.41.2-3) over (1:2.41.2-1) ... Preparing to unpack .../1-libgenomicsdb-java_1.5.5-2_all.deb ... Unpacking libgenomicsdb-java (1.5.5-2) over (1.5.5-1) ... Preparing to unpack .../2-libgenomicsdb-jni_1.5.5-2_amd64.deb ... Unpacking libgenomicsdb-jni (1.5.5-2) over (1.5.5-1) ... Preparing to unpack .../3-libgenomicsdb1_1.5.5-2_amd64.deb ... Unpacking libgenomicsdb1 (1.5.5-2) over (1.5.5-1) ... Preparing to unpack .../4-libnspr4_2%3a4.37-1_amd64.deb ... Unpacking libnspr4:amd64 (2:4.37-1) over (2:4.36-1) ... Preparing to unpack .../5-openssl_3.5.4-1_amd64.deb ... Unpacking openssl (3.5.4-1) over (3.5.3-1) ... Setting up bsdutils (1:2.41.2-3) ... Setting up libnspr4:amd64 (2:4.37-1) ... Setting up libgenomicsdb1 (1.5.5-2) ... Setting up mount (2.41.2-3) ... Setting up openssl (3.5.4-1) ... Setting up login (1:4.16.0-2+really2.41.2-3) ... Setting up libgenomicsdb-jni (1.5.5-2) ... Setting up libgenomicsdb-java (1.5.5-2) ... Processing triggers for libc-bin (2.41-12) ... 0m18.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'apt-get', '-yf', 'dist-upgrade'] 0m18.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m18.4s DUMP: 2752a99edbeec4012d0ed1a2edc9fd60 - 0m18.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m18.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'apt-cache', 'show', '--no-all-versions', 'libgenomicsdb-java'] 0m18.5s DUMP: Package: libgenomicsdb-java Source: genomicsdb Version: 1.5.5-2 Installed-Size: 493 Maintainer: Debian Med Packaging Team Architecture: all Depends: libcommons-io-java (>= 2.19.0), libgetopt-java, libgoogle-gson-java, libguava-java, libhtsjdk-java (>= 4.1.3), libjson-simple-java, liblog4j2-java (>= 2.19.0), libprotobuf-java, libgenomicsdb-jni (>= 1.5.5-2), libgenomicsdb-jni (<< 1.5.5-2.1~) Description-en: sparse array storage library for genomics (Java library) GenomicsDB is built on top of a htslib fork and an internal array storage system for importing, querying and transforming variant data. Variant data is sparse by nature (sparse relative to the whole genome) and using sparse array data stores is a perfect fit for storing such data. . The GenomicsDB stores variant data in a 2D array where: - Each column corresponds to a genomic position (chromosome + position); - Each row corresponds to a sample in a VCF (or CallSet in the GA4GH terminology); - Each cell contains data for a given sample/CallSet at a given position; data is stored in the form of cell attributes; - Cells are stored in column major order - this makes accessing cells with the same column index (i.e. data for a given genomic position over all samples) fast. - Variant interval/gVCF interval data is stored in a cell at the start of the interval. The END is stored as a cell attribute. For variant intervals (such as deletions and gVCF REF blocks), an additional cell is stored at the END value of the variant interval. When queried for a given genomic position, the query library performs an efficient sweep to determine all intervals that intersect with the queried position. . This package contains the Java library. Description-md5: 6a43860137619ae15d009235c0ac2bc5 Homepage: https://www.genomicsdb.org/ Section: java Priority: optional Filename: pool/main/g/genomicsdb/libgenomicsdb-java_1.5.5-2_all.deb Size: 409744 MD5sum: 7b092b28958fa56002a798ef943a9348 SHA256: ec2b5be8ba865e38d1373c4867614a96293eece3e1b58594e709285d92094c73 0m18.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'apt-cache', 'show', '--no-all-versions', 'libgenomicsdb-java'] 0m18.5s INFO: apt-cache knows about the following packages: libgenomicsdb-java 0m18.5s INFO: Running scripts pre_install 0m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_install_database-server'] 0m18.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_install_database-server'] 0m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_install_exceptions'] 0m18.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_install_exceptions'] 0m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_install_extras'] 0m18.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_install_extras'] 0m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_install_foreign_architecture'] 0m18.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_install_foreign_architecture'] 0m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m18.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'apt-cache', 'policy'] 0m18.6s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m18.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'apt-cache', 'policy'] 0m18.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'apt-cache', 'policy', 'libgenomicsdb-java'] 0m18.6s DUMP: libgenomicsdb-java: Installed: 1.5.5-2 Candidate: 1.5.5-2 Version table: *** 1.5.5-2 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m18.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'apt-cache', 'policy', 'libgenomicsdb-java'] 0m18.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'apt-get', '-y', 'install', 'libgenomicsdb-java'] 0m18.9s DUMP: Reading package lists... Building dependency tree... Reading state information... libgenomicsdb-java is already the newest version (1.5.5-2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m18.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'apt-get', '-y', 'install', 'libgenomicsdb-java'] 0m18.9s INFO: Running scripts post_install 0m18.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/post_install_exceptions'] 0m18.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/post_install_exceptions'] 0m18.9s INFO: Running scripts post_distupgrade 0m18.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m18.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m18.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/post_distupgrade_exceptions'] 0m18.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/post_distupgrade_exceptions'] 0m18.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m18.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m18.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m18.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m18.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/post_distupgrade_zz_backports'] 0m18.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/post_distupgrade_zz_backports'] 0m18.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo'] 0m19.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo'] 0m19.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo'] 0m19.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo'] 0m19.5s INFO: Running scripts pre_install 0m19.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_install_database-server'] 0m19.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_install_database-server'] 0m19.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_install_exceptions'] 0m19.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_install_exceptions'] 0m19.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_install_extras'] 0m19.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_install_extras'] 0m19.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_install_foreign_architecture'] 0m19.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_install_foreign_architecture'] 0m19.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m19.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m19.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'apt-cache', 'policy'] 0m19.5s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m19.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'apt-cache', 'policy'] 0m19.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'apt-cache', 'policy', 'libgenomicsdb-java'] 0m19.5s DUMP: libgenomicsdb-java: Installed: 1.5.5-2 Candidate: 1.5.5-2 Version table: *** 1.5.5-2 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m19.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'apt-cache', 'policy', 'libgenomicsdb-java'] 0m19.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'apt-get', '-y', 'install', 'libgenomicsdb-java=1.5.5-2'] 0m19.8s DUMP: Reading package lists... Building dependency tree... Reading state information... libgenomicsdb-java is already the newest version (1.5.5-2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m19.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'apt-get', '-y', 'install', 'libgenomicsdb-java=1.5.5-2'] 0m19.8s INFO: Running scripts post_install 0m19.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/post_install_exceptions'] 0m19.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/post_install_exceptions'] 0m19.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo'] 0m20.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo'] 0m20.3s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', '-ac', '--ignore-obsolete'] 0m21.6s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', '-ac', '--ignore-obsolete'] 0m21.6s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m21.6s DUMP: 0.15.9~deb12u1 0m21.6s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m21.6s INFO: Running adequate version 0.15.9~deb12u1 now. 0m21.6s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'libgenomicsdb-java'] 0m21.7s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'libgenomicsdb-java'] 0m21.7s INFO: Running scripts pre_remove 0m21.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m21.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m21.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m21.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m21.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m22.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m22.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m22.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m22.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m22.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m22.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_remove_exceptions'] 0m22.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/pre_remove_exceptions'] 0m22.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m22.9s DUMP: install ok installed adduser adduser 3.153 install ok installed apt apt 3.1.6 install ok installed base-files base-files 14 install ok installed base-passwd base-passwd 3.6.7 install ok installed bash bash 5.3-1 install ok installed bsdutils bsdutils 1:2.41.2-3 install ok installed ca-certificates ca-certificates 20250419 install ok installed ca-certificates-java ca-certificates-java 20240118 install ok installed coreutils coreutils 9.7-3 install ok installed dash dash 0.5.12-12 install ok installed debconf debconf 1.5.91 install ok installed debian-archive-keyring debian-archive-keyring 2025.1 install ok installed debianutils debianutils 5.23.2 install ok installed default-jre-headless default-jre-headless 2:1.21-76 install ok installed diffutils diffutils 1:3.10-4 install ok installed dpkg dpkg 1.22.21 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.3.0-8 install ok installed gcc-15-base:amd64 gcc-15-base 15.2.0-4 install ok installed grep grep 3.12-1 install ok installed gzip gzip 1.13-1 install ok installed hostname hostname 3.25 install ok installed ibverbs-providers:amd64 ibverbs-providers 56.1-1+b1 install ok installed init-system-helpers init-system-helpers 1.69 install ok installed java-common java-common 0.76 install ok installed junit4 junit4 4.13.2-5 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libamd-comgr2:amd64 libamd-comgr2 6.0+git20231212.4510c28+dfsg-3+b2 install ok installed libamdhip64-5:amd64 libamdhip64-5 5.7.1-6 install ok installed libapache-pom-java libapache-pom-java 33-2 install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.1.6 install ok installed libatinject-jsr330-api-java libatinject-jsr330-api-java 1.0+ds1-6 install ok installed libattr1:amd64 libattr1 1:2.5.2-3 install ok installed libaudit-common libaudit-common 1:4.1.2-1 install ok installed libaudit1:amd64 libaudit1 1:4.1.2-1 install ok installed libblkid1:amd64 libblkid1 2.41.2-3 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b7 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.41-12 install ok installed libc6:amd64 libc6 2.41-12 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1 install ok installed libcap2:amd64 libcap2 1:2.75-10+b1 install ok installed libcbor0.10:amd64 libcbor0.10 0.10.2-2 install ok installed libcom-err2:amd64 libcom-err2 1.47.2-3+b3 install ok installed libcommons-beanutils-java libcommons-beanutils-java 1.10.1-1.1 install ok installed libcommons-codec-java libcommons-codec-java 1.18.0-1 install ok installed libcommons-collections3-java libcommons-collections3-java 3.2.2-3 install ok installed libcommons-collections4-java libcommons-collections4-java 4.4-2 install ok installed libcommons-compress-java libcommons-compress-java 1.27.1-2 install ok installed libcommons-io-java libcommons-io-java 2.19.0-1 install ok installed libcommons-jexl2-java libcommons-jexl2-java 2.1.1-6 install ok installed libcommons-lang3-java libcommons-lang3-java 3.17.0-2 install ok installed libcommons-logging-java libcommons-logging-java 1.3.0-2 install ok installed libcommons-parent-java libcommons-parent-java 56-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1 install ok installed libcurl4t64:amd64 libcurl4t64 8.16.0-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.280 install ok installed libdrm-amdgpu1:amd64 libdrm-amdgpu1 2.4.125-2 install ok installed libdrm-common libdrm-common 2.4.125-2 install ok installed libdrm2:amd64 libdrm2 2.4.125-2 install ok installed libedit2:amd64 libedit2 3.1-20250104-1 install ok installed libelf1t64:amd64 libelf1t64 0.193-3 install ok installed liberror-prone-java liberror-prone-java 2.18.0-1 install ok installed libevent-core-2.1-7t64:amd64 libevent-core-2.1-7t64 2.1.12-stable-10+b1 install ok installed libevent-pthreads-2.1-7t64:amd64 libevent-pthreads-2.1-7t64 2.1.12-stable-10+b1 install ok installed libezmorph-java libezmorph-java 1.0.6-4 install ok installed libfabric1:amd64 libfabric1 2.1.0-1.1 install ok installed libffi8:amd64 libffi8 3.5.2-2 install ok installed libfido2-1:amd64 libfido2-1 1.16.0-2 install ok installed libfmt10:amd64 libfmt10 10.1.1+ds1-4 install ok installed libfuse3-4:amd64 libfuse3-4 3.17.4-1 install ok installed libgcc-s1:amd64 libgcc-s1 15.2.0-4 install ok installed libgenomicsdb-java libgenomicsdb-java 1.5.5-2 install ok installed libgenomicsdb-jni libgenomicsdb-jni 1.5.5-2 install ok installed libgenomicsdb1 libgenomicsdb1 1.5.5-2 install ok installed libgetopt-java libgetopt-java 1.0.14+dfsg-6 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-5 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.10-2 install ok installed libgomp1:amd64 libgomp1 15.2.0-4 install ok installed libgoogle-gson-java libgoogle-gson-java 2.10.1-1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.21.3-5 install ok installed libguava-java libguava-java 32.0.1-1 install ok installed libhamcrest-java libhamcrest-java 2.2-2 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.2-1 install ok installed libhsa-runtime64-1:amd64 libhsa-runtime64-1 6.1.2-3 install ok installed libhsakmt1:amd64 libhsakmt1 6.2.4+ds-1 install ok installed libhtsjdk-java libhtsjdk-java 4.1.3+dfsg-2 install ok installed libhttpclient-java libhttpclient-java 4.5.14-1 install ok installed libhttpcore-java libhttpcore-java 4.4.16-1 install ok installed libhwloc-plugins:amd64 libhwloc-plugins 2.12.2-1 install ok installed libhwloc15:amd64 libhwloc15 2.12.2-1 install ok installed libibmad5:amd64 libibmad5 56.1-1+b1 install ok installed libibumad3:amd64 libibumad3 56.1-1+b1 install ok installed libibverbs1:amd64 libibverbs1 56.1-1+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.8-4 install ok installed libjaxen-java libjaxen-java 1.2.0-1 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-4 install ok installed libjson-java libjson-java 3.1.0+dfsg-2 install ok installed libjson-simple-java libjson-simple-java 2.3.0-2 install ok installed libjsr305-java libjsr305-java 0.1~+svn49-12 install ok installed libk5crypto3:amd64 libk5crypto3 1.21.3-5 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-6 install ok installed libkrb5-3:amd64 libkrb5-3 1.21.3-5 install ok installed libkrb5support0:amd64 libkrb5support0 1.21.3-5 install ok installed liblastlog2-2:amd64 liblastlog2-2 2.41.2-3 install ok installed liblcms2-2:amd64 liblcms2-2 2.16-2 install ok installed libldap2:amd64 libldap2 2.6.10+dfsg-1 install ok installed liblightcouch-java liblightcouch-java 0.2.0-1 install ok installed libllvm17t64:amd64 libllvm17t64 1:17.0.6-22+b3 install ok installed liblog4j2-java liblog4j2-java 2.19.0-2 install ok installed liblz4-1:amd64 liblz4-1 1.10.0-4 install ok installed liblzma5:amd64 liblzma5 5.8.1-1.1 install ok installed libmbedcrypto16:amd64 libmbedcrypto16 3.6.4-2 install ok installed libmbedtls21:amd64 libmbedtls21 3.6.4-2 install ok installed libmbedx509-7:amd64 libmbedx509-7 3.6.4-2 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmongodb-java libmongodb-java 3.6.3-2 install ok installed libmount1:amd64 libmount1 2.41.2-3 install ok installed libmunge2:amd64 libmunge2 0.5.16-1 install ok installed libmuparserx4.0.12:amd64 libmuparserx4.0.12 4.0.12-2 install ok installed libncbi-ngs3:amd64 libncbi-ngs3 3.2.1+dfsg-5 install ok installed libncbi-vdb3:amd64 libncbi-vdb3 3.2.1+dfsg-2 install ok installed libnettle8t64:amd64 libnettle8t64 3.10.2-1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.64.0-1.1+b1 install ok installed libnghttp3-9:amd64 libnghttp3-9 1.11.0-1 install ok installed libngs-java:amd64 libngs-java 3.2.1+dfsg-5 install ok installed libngs-jni:amd64 libngs-jni 3.2.1+dfsg-5 install ok installed libnl-3-200:amd64 libnl-3-200 3.11.0-2 install ok installed libnl-route-3-200:amd64 libnl-route-3-200 3.11.0-2 install ok installed libnspr4:amd64 libnspr4 2:4.37-1 install ok installed libnss3:amd64 libnss3 2:3.116-1 install ok installed libnuma1:amd64 libnuma1 2.0.19-1 install ok installed libopenmpi40:amd64 libopenmpi40 5.0.8-10+b1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.9-2 install ok installed libpam-modules:amd64 libpam-modules 1.7.0-5 install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-5 install ok installed libpam-runtime libpam-runtime 1.7.0-5 install ok installed libpam0g:amd64 libpam0g 1.7.0-5 install ok installed libpciaccess0:amd64 libpciaccess0 0.17-3+b3 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.46-1 install ok installed libpcsclite1:amd64 libpcsclite1 2.3.3-1 install ok installed libpmix2t64:amd64 libpmix2t64 6.0.0+really5.0.8-1 install ok installed libprotobuf-java libprotobuf-java 3.21.12-14 install ok installed libprotobuf32t64:amd64 libprotobuf32t64 3.21.12-14 install ok installed libpsl5t64:amd64 libpsl5t64 0.21.2-1.1+b1 install ok installed libpsm2-2 libpsm2-2 11.2.185-2.1 install ok installed librdmacm1t64:amd64 librdmacm1t64 56.1-1+b1 install ok installed librhino-java librhino-java 1.7.15-1 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-3 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-9 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-9 install ok installed libseccomp2:amd64 libseccomp2 2.6.0-2 install ok installed libselinux1:amd64 libselinux1 3.8.1-1 install ok installed libsemanage-common libsemanage-common 3.8.1-1 install ok installed libsemanage2:amd64 libsemanage2 3.8.1-1 install ok installed libsepol2:amd64 libsepol2 3.8.1-1 install ok installed libslf4j-java libslf4j-java 1.7.32-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.41.2-3 install ok installed libsnappy-java libsnappy-java 1.1.10.8-1 install ok installed libsnappy-jni libsnappy-jni 1.1.10.8-1 install ok installed libsnappy1v5:amd64 libsnappy1v5 1.2.2-2 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-8 install ok installed libssh2-1t64:amd64 libssh2-1t64 1.11.1-1 install ok installed libssl3t64:amd64 libssl3t64 3.5.4-1 install ok installed libstdc++6:amd64 libstdc++6 15.2.0-4 install ok installed libsystemd0:amd64 libsystemd0 258-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.20.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2 install ok installed libucx0:amd64 libucx0 1.19.0+ds-1 install ok installed libudev1:amd64 libudev1 258-1 install ok installed libunistring5:amd64 libunistring5 1.3-2 install ok installed libuuid1:amd64 libuuid1 2.41.2-3 install ok installed libx11-6:amd64 libx11-6 2:1.8.12-1 install ok installed libx11-data libx11-data 2:1.8.12-1 install ok installed libxau6:amd64 libxau6 1:1.0.11-1 install ok installed libxcb1:amd64 libxcb1 1.17.0-2+b1 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.5-1 install ok installed libxerces2-java libxerces2-java 2.12.2-1 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b3 install ok installed libxml-commons-external-java libxml-commons-external-java 1.4.01-6 install ok installed libxml-commons-resolver1.1-java libxml-commons-resolver1.1-java 1.2-11 install ok installed libxml2-16:amd64 libxml2-16 2.14.5+dfsg-0.2 install ok installed libxnvctrl0:amd64 libxnvctrl0 535.171.04-1+b2 install ok installed libxom-java libxom-java 1.3.9-1 install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2 install ok installed libz3-4:amd64 libz3-4 4.13.3-1 install ok installed libze1:amd64 libze1 1.24.1-2 install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-1.1 install ok installed login login 1:4.16.0-2+really2.41.2-3 install ok installed login.defs login.defs 1:4.18.0-1 install ok installed mawk mawk 1.3.4.20250131-1 install ok installed mount mount 2.41.2-3 install ok installed mpi-default-bin mpi-default-bin 1.19 install ok installed ncbi-vdb-data ncbi-vdb-data 3.2.1+dfsg-2 install ok installed ncurses-base ncurses-base 6.5+20250216-2 install ok installed ncurses-bin ncurses-bin 6.5+20250216-2 install ok installed ocl-icd-libopencl1:amd64 ocl-icd-libopencl1 2.3.3-1 install ok installed openjdk-21-jre-headless:amd64 openjdk-21-jre-headless 21.0.9~8ea-1 install ok installed openmpi-bin openmpi-bin 5.0.8-10+b1 install ok installed openmpi-common openmpi-common 5.0.8-10 install ok installed openssh-client openssh-client 1:10.0p1-8 install ok installed openssl openssl 3.5.4-1 install ok installed openssl-provider-legacy openssl-provider-legacy 3.5.4-1 install ok installed passwd passwd 1:4.18.0-1 install ok installed perl-base perl-base 5.40.1-6 install ok installed sed sed 4.9-2 install ok installed sqv sqv 1.3.0-3 install ok installed sysvinit-utils sysvinit-utils 3.14-4 install ok installed tar tar 1.35+dfsg-3.1 install ok installed tzdata tzdata 2025b-5 install ok installed util-linux util-linux 2.41.2-3 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m22.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m22.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'apt-get', 'remove', '--allow-remove-essential', 'adduser', 'ca-certificates', 'ca-certificates-java', 'default-jre-headless', 'ibverbs-providers:amd64', 'java-common', 'junit4', 'libamd-comgr2:amd64', 'libamdhip64-5:amd64', 'libapache-pom-java', 'libatinject-jsr330-api-java', 'libbrotli1:amd64', 'libcbor0.10:amd64', 'libcom-err2:amd64', 'libcommons-beanutils-java', 'libcommons-codec-java', 'libcommons-collections3-java', 'libcommons-collections4-java', 'libcommons-compress-java', 'libcommons-io-java', 'libcommons-jexl2-java', 'libcommons-lang3-java', 'libcommons-logging-java', 'libcommons-parent-java', 'libcurl4t64:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1t64:amd64', 'liberror-prone-java', 'libevent-core-2.1-7t64:amd64', 'libevent-pthreads-2.1-7t64:amd64', 'libezmorph-java', 'libfabric1:amd64', 'libffi8:amd64', 'libfido2-1:amd64', 'libfmt10:amd64', 'libfuse3-4:amd64', 'libgenomicsdb-jni', 'libgenomicsdb1', 'libgetopt-java', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgoogle-gson-java', 'libgssapi-krb5-2:amd64', 'libguava-java', 'libhamcrest-java', 'libhsa-runtime64-1:amd64', 'libhsakmt1:amd64', 'libhtsjdk-java', 'libhttpclient-java', 'libhttpcore-java', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibmad5:amd64', 'libibumad3:amd64', 'libibverbs1:amd64', 'libidn2-0:amd64', 'libjaxen-java', 'libjpeg62-turbo:amd64', 'libjson-java', 'libjson-simple-java', 'libjsr305-java', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblcms2-2:amd64', 'libldap2:amd64', 'liblightcouch-java', 'libllvm17t64:amd64', 'liblog4j2-java', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libmongodb-java', 'libmunge2:amd64', 'libmuparserx4.0.12:amd64', 'libncbi-ngs3:amd64', 'libncbi-vdb3:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngs-java:amd64', 'libngs-jni:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libnuma1:amd64', 'libopenmpi40:amd64', 'libp11-kit0:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libpmix2t64:amd64', 'libprotobuf-java', 'libprotobuf32t64:amd64', 'libpsl5t64:amd64', 'libpsm2-2', 'librdmacm1t64:amd64', 'librhino-java', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libslf4j-java', 'libsnappy-java', 'libsnappy-jni', 'libsnappy1v5:amd64', 'libssh2-1t64:amd64', 'libtasn1-6:amd64', 'libucx0:amd64', 'libunistring5:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxerces2-java', 'libxext6:amd64', 'libxml-commons-external-java', 'libxml-commons-resolver1.1-java', 'libxml2-16:amd64', 'libxnvctrl0:amd64', 'libxom-java', 'libz3-4:amd64', 'libze1:amd64', 'mpi-default-bin', 'ncbi-vdb-data', 'ocl-icd-libopencl1:amd64', 'openjdk-21-jre-headless:amd64', 'openmpi-bin', 'openmpi-common', 'openssh-client', 'openssl', 'libgenomicsdb-java'] 0m23.9s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: adduser ca-certificates ca-certificates-java default-jre-headless ibverbs-providers java-common junit4 libamd-comgr2 libamdhip64-5 libapache-pom-java libatinject-jsr330-api-java libbrotli1 libcbor0.10 libcom-err2 libcommons-beanutils-java libcommons-codec-java libcommons-collections3-java libcommons-collections4-java libcommons-compress-java libcommons-io-java libcommons-jexl2-java libcommons-lang3-java libcommons-logging-java libcommons-parent-java libcurl4t64 libdrm-amdgpu1 libdrm-common libdrm2 libedit2 libelf1t64 liberror-prone-java libevent-core-2.1-7t64 libevent-pthreads-2.1-7t64 libezmorph-java libfabric1 libffi8 libfido2-1 libfmt10 libfuse3-4 libgenomicsdb-java libgenomicsdb-jni libgenomicsdb1 libgetopt-java libgnutls30t64 libgomp1 libgoogle-gson-java libgssapi-krb5-2 libguava-java libhamcrest-java libhsa-runtime64-1 libhsakmt1 libhtsjdk-java libhttpclient-java libhttpcore-java libhwloc-plugins libhwloc15 libibmad5 libibumad3 libibverbs1 libidn2-0 libjaxen-java libjpeg62-turbo libjson-java libjson-simple-java libjsr305-java libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblcms2-2 libldap2 liblightcouch-java libllvm17t64 liblog4j2-java libmbedcrypto16 libmbedtls21 libmbedx509-7 libmongodb-java libmunge2 libmuparserx4.0.12 libncbi-ngs3 libncbi-vdb3 libnghttp2-14 libnghttp3-9 libngs-java libngs-jni libnl-3-200 libnl-route-3-200 libnspr4 libnss3 libnuma1 libopenmpi40 libp11-kit0 libpciaccess0 libpcsclite1 libpmix2t64 libprotobuf-java libprotobuf32t64 libpsl5t64 libpsm2-2 librdmacm1t64 librhino-java librtmp1 libsasl2-2 libsasl2-modules-db libslf4j-java libsnappy-java libsnappy-jni libsnappy1v5 libssh2-1t64 libtasn1-6 libucx0 libunistring5 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxerces2-java libxext6 libxml-commons-external-java libxml-commons-resolver1.1-java libxml2-16 libxnvctrl0 libxom-java libz3-4 libze1 mpi-default-bin ncbi-vdb-data ocl-icd-libopencl1 openjdk-21-jre-headless openmpi-bin openmpi-common openssh-client openssl 0 upgraded, 0 newly installed, 135 to remove and 0 not upgraded. After this operation, 561 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 ... 8262 files and directories currently installed.) Removing libgenomicsdb-java (1.5.5-2) ... Removing libgenomicsdb-jni (1.5.5-2) ... Removing libgenomicsdb1 (1.5.5-2) ... Removing mpi-default-bin (1.19) ... Removing openmpi-bin (5.0.8-10+b1) ... Removing libopenmpi40:amd64 (5.0.8-10+b1) ... Removing libucx0:amd64 (1.19.0+ds-1) ... Removing libfabric1:amd64 (2.1.0-1.1) ... Removing ibverbs-providers:amd64 (56.1-1+b1) ... Removing librdmacm1t64:amd64 (56.1-1+b1) ... Removing libibverbs1:amd64 (56.1-1+b1) ... Removing openssh-client (1:10.0p1-8) ... Removing adduser (3.153) ... Removing libhtsjdk-java (4.1.3+dfsg-2) ... Removing libjson-java (3.1.0+dfsg-2) ... Removing junit4 (4.13.2-5) ... Removing default-jre-headless (2:1.21-76) ... Removing openjdk-21-jre-headless:amd64 (21.0.9~8ea-1) ... Removing ca-certificates-java (20240118) ... Removing ca-certificates (20250419) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing java-common (0.76) ... Removing libamdhip64-5:amd64 (5.7.1-6) ... Removing libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3+b2) ... Removing libcommons-jexl2-java (2.1.1-6) ... Removing liblog4j2-java (2.19.0-2) ... Removing liblightcouch-java (0.2.0-1) ... Removing libhttpclient-java (4.5.14-1) ... Removing libcommons-lang3-java (3.17.0-2) ... Removing libprotobuf-java (3.21.12-14) ... Removing libcurl4t64:amd64 (8.16.0-1) ... Removing libbrotli1:amd64 (1.1.0-2+b7) ... Removing libfido2-1:amd64 (1.16.0-2) ... Removing libcbor0.10:amd64 (0.10.2-2) ... Removing libgssapi-krb5-2:amd64 (1.21.3-5) ... Removing libkrb5-3:amd64 (1.21.3-5) ... Removing libcom-err2:amd64 (1.47.2-3+b3) ... Removing libcommons-beanutils-java (1.10.1-1.1) ... Removing libcommons-compress-java (1.27.1-2) ... Removing libcommons-codec-java (1.18.0-1) ... Removing libcommons-collections3-java (3.2.2-3) ... Removing libcommons-collections4-java (4.4-2) ... Removing libcommons-io-java (2.19.0-1) ... Removing libhsa-runtime64-1:amd64 (6.1.2-3) ... Removing libhsakmt1:amd64 (6.2.4+ds-1) ... Removing libdrm-amdgpu1:amd64 (2.4.125-2) ... Removing libdrm2:amd64 (2.4.125-2) ... Removing libdrm-common (2.4.125-2) ... Removing libllvm17t64:amd64 (1:17.0.6-22+b3) ... Removing libedit2:amd64 (3.1-20250104-1) ... Removing libelf1t64:amd64 (0.193-3) ... Removing libpmix2t64:amd64 (6.0.0+really5.0.8-1) ... Removing libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Removing libevent-core-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Removing libezmorph-java (1.0.6-4) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-3) ... Removing libgnutls30t64:amd64 (3.8.10-2) ... Removing libp11-kit0:amd64 (0.25.9-2) ... Removing libffi8:amd64 (3.5.2-2) ... Removing libfmt10:amd64 (10.1.1+ds1-4) ... Removing libfuse3-4:amd64 (3.17.4-1) ... Removing libgetopt-java (1.0.14+dfsg-6) ... Removing libgomp1:amd64 (15.2.0-4) ... Removing libgoogle-gson-java (2.10.1-1) ... Removing libhamcrest-java (2.2-2) ... Removing libhttpcore-java (4.4.16-1) ... Removing libhwloc-plugins:amd64 (2.12.2-1) ... Removing libhwloc15:amd64 (2.12.2-1) ... Removing libibmad5:amd64 (56.1-1+b1) ... Removing libibumad3:amd64 (56.1-1+b1) ... Removing libpsl5t64:amd64 (0.21.2-1.1+b1) ... Removing libidn2-0:amd64 (2.3.8-4) ... Removing libxom-java (1.3.9-1) ... Removing libjaxen-java (1.2.0-1) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-4) ... Removing libjson-simple-java (2.3.0-2) ... Removing libk5crypto3:amd64 (1.21.3-5) ... Removing libkeyutils1:amd64 (1.6.3-6) ... Removing libkrb5support0:amd64 (1.21.3-5) ... Removing liblcms2-2:amd64 (2.16-2) ... Removing libldap2:amd64 (2.6.10+dfsg-1) ... Removing libngs-java:amd64 (3.2.1+dfsg-5) ... Removing libngs-jni:amd64 (3.2.1+dfsg-5) ... Removing libncbi-ngs3:amd64 (3.2.1+dfsg-5) ... Removing libncbi-vdb3:amd64 (3.2.1+dfsg-2) ... Removing libmbedtls21:amd64 (3.6.4-2) ... Removing libmbedx509-7:amd64 (3.6.4-2) ... Removing libmbedcrypto16:amd64 (3.6.4-2) ... Removing libmongodb-java (3.6.3-2) ... Removing libmunge2:amd64 (0.5.16-1) ... Removing libmuparserx4.0.12:amd64 (4.0.12-2) ... Removing libnghttp2-14:amd64 (1.64.0-1.1+b1) ... Removing libnghttp3-9:amd64 (1.11.0-1) ... Removing libnl-route-3-200:amd64 (3.11.0-2) ... Removing libnl-3-200:amd64 (3.11.0-2) ... Removing libnss3:amd64 (2:3.116-1) ... Removing libnspr4:amd64 (2:4.37-1) ... Removing libpsm2-2 (11.2.185-2.1) ... Removing libnuma1:amd64 (2.0.19-1) ... Removing libpciaccess0:amd64 (0.17-3+b3) ... Removing libpcsclite1:amd64 (2.3.3-1) ... Removing libprotobuf32t64:amd64 (3.21.12-14) ... Removing librhino-java (1.7.15-1) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-9) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-9) ... Removing libslf4j-java (1.7.32-2) ... Removing libsnappy-java (1.1.10.8-1) ... Removing libsnappy-jni (1.1.10.8-1) ... Removing libsnappy1v5:amd64 (1.2.2-2) ... Removing libssh2-1t64:amd64 (1.11.1-1) ... Removing libtasn1-6:amd64 (4.20.0-2) ... Removing libunistring5:amd64 (1.3-2) ... Removing libxnvctrl0:amd64 (535.171.04-1+b2) ... Removing libxext6:amd64 (2:1.3.4-1+b3) ... Removing libx11-6:amd64 (2:1.8.12-1) ... Removing libx11-data (2:1.8.12-1) ... Removing libxcb1:amd64 (1.17.0-2+b1) ... Removing libxau6:amd64 (1:1.0.11-1) ... Removing libxdmcp6:amd64 (1:1.1.5-1) ... Removing libxerces2-java (2.12.2-1) ... Removing libxml-commons-external-java (1.4.01-6) ... Removing libxml-commons-resolver1.1-java (1.2-11) ... Removing libxml2-16:amd64 (2.14.5+dfsg-0.2) ... Removing libz3-4:amd64 (4.13.3-1) ... Removing libze1:amd64 (1.24.1-2) ... Removing ncbi-vdb-data (3.2.1+dfsg-2) ... rm: cannot remove '/usr/lib/python3/dist-packages/__pycache__/vdb.*': No such file or directory Removing ocl-icd-libopencl1:amd64 (2.3.3-1) ... Removing openmpi-common (5.0.8-10) ... Removing openssl (3.5.4-1) ... Removing libcommons-logging-java (1.3.0-2) ... Removing libcommons-parent-java (56-1) ... Removing libapache-pom-java (33-2) ... Removing liberror-prone-java (2.18.0-1) ... Removing libguava-java (32.0.1-1) ... Removing libatinject-jsr330-api-java (1.0+ds1-6) ... Removing libjsr305-java (0.1~+svn49-12) ... Processing triggers for libc-bin (2.41-12) ... 0m23.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'apt-get', 'remove', '--allow-remove-essential', 'adduser', 'ca-certificates', 'ca-certificates-java', 'default-jre-headless', 'ibverbs-providers:amd64', 'java-common', 'junit4', 'libamd-comgr2:amd64', 'libamdhip64-5:amd64', 'libapache-pom-java', 'libatinject-jsr330-api-java', 'libbrotli1:amd64', 'libcbor0.10:amd64', 'libcom-err2:amd64', 'libcommons-beanutils-java', 'libcommons-codec-java', 'libcommons-collections3-java', 'libcommons-collections4-java', 'libcommons-compress-java', 'libcommons-io-java', 'libcommons-jexl2-java', 'libcommons-lang3-java', 'libcommons-logging-java', 'libcommons-parent-java', 'libcurl4t64:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1t64:amd64', 'liberror-prone-java', 'libevent-core-2.1-7t64:amd64', 'libevent-pthreads-2.1-7t64:amd64', 'libezmorph-java', 'libfabric1:amd64', 'libffi8:amd64', 'libfido2-1:amd64', 'libfmt10:amd64', 'libfuse3-4:amd64', 'libgenomicsdb-jni', 'libgenomicsdb1', 'libgetopt-java', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgoogle-gson-java', 'libgssapi-krb5-2:amd64', 'libguava-java', 'libhamcrest-java', 'libhsa-runtime64-1:amd64', 'libhsakmt1:amd64', 'libhtsjdk-java', 'libhttpclient-java', 'libhttpcore-java', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibmad5:amd64', 'libibumad3:amd64', 'libibverbs1:amd64', 'libidn2-0:amd64', 'libjaxen-java', 'libjpeg62-turbo:amd64', 'libjson-java', 'libjson-simple-java', 'libjsr305-java', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblcms2-2:amd64', 'libldap2:amd64', 'liblightcouch-java', 'libllvm17t64:amd64', 'liblog4j2-java', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libmongodb-java', 'libmunge2:amd64', 'libmuparserx4.0.12:amd64', 'libncbi-ngs3:amd64', 'libncbi-vdb3:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngs-java:amd64', 'libngs-jni:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libnuma1:amd64', 'libopenmpi40:amd64', 'libp11-kit0:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libpmix2t64:amd64', 'libprotobuf-java', 'libprotobuf32t64:amd64', 'libpsl5t64:amd64', 'libpsm2-2', 'librdmacm1t64:amd64', 'librhino-java', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libslf4j-java', 'libsnappy-java', 'libsnappy-jni', 'libsnappy1v5:amd64', 'libssh2-1t64:amd64', 'libtasn1-6:amd64', 'libucx0:amd64', 'libunistring5:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxerces2-java', 'libxext6:amd64', 'libxml-commons-external-java', 'libxml-commons-resolver1.1-java', 'libxml2-16:amd64', 'libxnvctrl0:amd64', 'libxom-java', 'libz3-4:amd64', 'libze1:amd64', 'mpi-default-bin', 'ncbi-vdb-data', 'ocl-icd-libopencl1:amd64', 'openjdk-21-jre-headless:amd64', 'openmpi-bin', 'openmpi-common', 'openssh-client', 'openssl', 'libgenomicsdb-java'] 0m23.9s INFO: Running scripts post_remove 0m23.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/post_remove_exceptions'] 0m23.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/post_remove_exceptions'] 0m23.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'dpkg', '--purge', 'adduser', 'ca-certificates', 'ca-certificates-java', 'default-jre-headless', 'ibverbs-providers:amd64', 'java-common', 'junit4', 'libamd-comgr2:amd64', 'libamdhip64-5:amd64', 'libapache-pom-java', 'libatinject-jsr330-api-java', 'libbrotli1:amd64', 'libcbor0.10:amd64', 'libcom-err2:amd64', 'libcommons-beanutils-java', 'libcommons-codec-java', 'libcommons-collections3-java', 'libcommons-collections4-java', 'libcommons-compress-java', 'libcommons-io-java', 'libcommons-jexl2-java', 'libcommons-lang3-java', 'libcommons-logging-java', 'libcommons-parent-java', 'libcurl4t64:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1t64:amd64', 'liberror-prone-java', 'libevent-core-2.1-7t64:amd64', 'libevent-pthreads-2.1-7t64:amd64', 'libezmorph-java', 'libfabric1:amd64', 'libffi8:amd64', 'libfido2-1:amd64', 'libfmt10:amd64', 'libfuse3-4:amd64', 'libgenomicsdb-jni', 'libgenomicsdb1', 'libgetopt-java', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgoogle-gson-java', 'libgssapi-krb5-2:amd64', 'libguava-java', 'libhamcrest-java', 'libhsa-runtime64-1:amd64', 'libhsakmt1:amd64', 'libhtsjdk-java', 'libhttpclient-java', 'libhttpcore-java', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibmad5:amd64', 'libibumad3:amd64', 'libibverbs1:amd64', 'libidn2-0:amd64', 'libjaxen-java', 'libjpeg62-turbo:amd64', 'libjson-java', 'libjson-simple-java', 'libjsr305-java', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblcms2-2:amd64', 'libldap2:amd64', 'liblightcouch-java', 'libllvm17t64:amd64', 'liblog4j2-java', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libmongodb-java', 'libmunge2:amd64', 'libmuparserx4.0.12:amd64', 'libncbi-ngs3:amd64', 'libncbi-vdb3:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngs-java:amd64', 'libngs-jni:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libnuma1:amd64', 'libopenmpi40:amd64', 'libp11-kit0:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libpmix2t64:amd64', 'libprotobuf-java', 'libprotobuf32t64:amd64', 'libpsl5t64:amd64', 'libpsm2-2', 'librdmacm1t64:amd64', 'librhino-java', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libslf4j-java', 'libsnappy-java', 'libsnappy-jni', 'libsnappy1v5:amd64', 'libssh2-1t64:amd64', 'libtasn1-6:amd64', 'libucx0:amd64', 'libunistring5:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxerces2-java', 'libxext6:amd64', 'libxml-commons-external-java', 'libxml-commons-resolver1.1-java', 'libxml2-16:amd64', 'libxnvctrl0:amd64', 'libxom-java', 'libz3-4:amd64', 'libze1:amd64', 'mpi-default-bin', 'ncbi-vdb-data', 'ocl-icd-libopencl1:amd64', 'openjdk-21-jre-headless:amd64', 'openmpi-bin', 'openmpi-common', 'openssh-client', 'openssl'] 0m24.0s DUMP: (Reading database ... 4977 files and directories currently installed.) Purging configuration files for adduser (3.153) ... Purging configuration files for ca-certificates (20250419) ... Removing dangling symlinks from /etc/ssl/certs... done. Purging configuration files for ca-certificates-java (20240118) ... dpkg: warning: ignoring request to remove default-jre-headless which isn't installed Purging configuration files for ibverbs-providers:amd64 (56.1-1+b1) ... Purging configuration files for java-common (0.76) ... dpkg: warning: ignoring request to remove junit4 which isn't installed dpkg: warning: ignoring request to remove libamd-comgr2 which isn't installed dpkg: warning: ignoring request to remove libamdhip64-5 which isn't installed dpkg: warning: ignoring request to remove libapache-pom-java which isn't installed dpkg: warning: ignoring request to remove libatinject-jsr330-api-java which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libcbor0.10 which isn't installed dpkg: warning: ignoring request to remove libcom-err2 which isn't installed dpkg: warning: ignoring request to remove libcommons-beanutils-java which isn't installed dpkg: warning: ignoring request to remove libcommons-codec-java which isn't installed dpkg: warning: ignoring request to remove libcommons-collections3-java which isn't installed dpkg: warning: ignoring request to remove libcommons-collections4-java which isn't installed dpkg: warning: ignoring request to remove libcommons-compress-java which isn't installed dpkg: warning: ignoring request to remove libcommons-io-java which isn't installed dpkg: warning: ignoring request to remove libcommons-jexl2-java which isn't installed dpkg: warning: ignoring request to remove libcommons-lang3-java which isn't installed dpkg: warning: ignoring request to remove libcommons-logging-java which isn't installed dpkg: warning: ignoring request to remove libcommons-parent-java which isn't installed dpkg: warning: ignoring request to remove libcurl4t64 which isn't installed dpkg: warning: ignoring request to remove libdrm-amdgpu1 which isn't installed dpkg: warning: ignoring request to remove libdrm-common which isn't installed dpkg: warning: ignoring request to remove libdrm2 which isn't installed dpkg: warning: ignoring request to remove libedit2 which isn't installed dpkg: warning: ignoring request to remove libelf1t64 which isn't installed dpkg: warning: ignoring request to remove liberror-prone-java which isn't installed dpkg: warning: ignoring request to remove libevent-core-2.1-7t64 which isn't installed dpkg: warning: ignoring request to remove libevent-pthreads-2.1-7t64 which isn't installed dpkg: warning: ignoring request to remove libezmorph-java which isn't installed dpkg: warning: ignoring request to remove libfabric1 which isn't installed dpkg: warning: ignoring request to remove libffi8 which isn't installed dpkg: warning: ignoring request to remove libfido2-1 which isn't installed dpkg: warning: ignoring request to remove libfmt10 which isn't installed dpkg: warning: ignoring request to remove libfuse3-4 which isn't installed dpkg: warning: ignoring request to remove libgenomicsdb-jni which isn't installed dpkg: warning: ignoring request to remove libgenomicsdb1 which isn't installed dpkg: warning: ignoring request to remove libgetopt-java which isn't installed dpkg: warning: ignoring request to remove libgnutls30t64 which isn't installed dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgoogle-gson-java which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.21.3-5) ... dpkg: warning: ignoring request to remove libguava-java which isn't installed dpkg: warning: ignoring request to remove libhamcrest-java which isn't installed dpkg: warning: ignoring request to remove libhsa-runtime64-1 which isn't installed dpkg: warning: ignoring request to remove libhsakmt1 which isn't installed dpkg: warning: ignoring request to remove libhtsjdk-java which isn't installed dpkg: warning: ignoring request to remove libhttpclient-java which isn't installed dpkg: warning: ignoring request to remove libhttpcore-java which isn't installed dpkg: warning: ignoring request to remove libhwloc-plugins which isn't installed dpkg: warning: ignoring request to remove libhwloc15 which isn't installed dpkg: warning: ignoring request to remove libibmad5 which isn't installed dpkg: warning: ignoring request to remove libibumad3 which isn't installed dpkg: warning: ignoring request to remove libibverbs1 which isn't installed dpkg: warning: ignoring request to remove libidn2-0 which isn't installed dpkg: warning: ignoring request to remove libjaxen-java which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed dpkg: warning: ignoring request to remove libjson-java which isn't installed dpkg: warning: ignoring request to remove libjson-simple-java which isn't installed dpkg: warning: ignoring request to remove libjsr305-java which isn't installed dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove liblcms2-2 which isn't installed dpkg: warning: ignoring request to remove libldap2 which isn't installed dpkg: warning: ignoring request to remove liblightcouch-java which isn't installed dpkg: warning: ignoring request to remove libllvm17t64 which isn't installed dpkg: warning: ignoring request to remove liblog4j2-java which isn't installed dpkg: warning: ignoring request to remove libmbedcrypto16 which isn't installed dpkg: warning: ignoring request to remove libmbedtls21 which isn't installed dpkg: warning: ignoring request to remove libmbedx509-7 which isn't installed dpkg: warning: ignoring request to remove libmongodb-java which isn't installed dpkg: warning: ignoring request to remove libmunge2 which isn't installed dpkg: warning: ignoring request to remove libmuparserx4.0.12 which isn't installed dpkg: warning: ignoring request to remove libncbi-ngs3 which isn't installed dpkg: warning: ignoring request to remove libncbi-vdb3 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libnghttp3-9 which isn't installed dpkg: warning: ignoring request to remove libngs-java which isn't installed dpkg: warning: ignoring request to remove libngs-jni which isn't installed Purging configuration files for libnl-3-200:amd64 (3.11.0-2) ... dpkg: warning: ignoring request to remove libnl-route-3-200 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 libnuma1 which isn't installed dpkg: warning: ignoring request to remove libopenmpi40 which isn't installed dpkg: warning: ignoring request to remove libp11-kit0 which isn't installed dpkg: warning: ignoring request to remove libpciaccess0 which isn't installed dpkg: warning: ignoring request to remove libpcsclite1 which isn't installed dpkg: warning: ignoring request to remove libpmix2t64 which isn't installed dpkg: warning: ignoring request to remove libprotobuf-java which isn't installed dpkg: warning: ignoring request to remove libprotobuf32t64 which isn't installed dpkg: warning: ignoring request to remove libpsl5t64 which isn't installed dpkg: warning: ignoring request to remove libpsm2-2 which isn't installed dpkg: warning: ignoring request to remove librdmacm1t64 which isn't installed dpkg: warning: ignoring request to remove librhino-java 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 libslf4j-java which isn't installed dpkg: warning: ignoring request to remove libsnappy-java which isn't installed dpkg: warning: ignoring request to remove libsnappy-jni which isn't installed dpkg: warning: ignoring request to remove libsnappy1v5 which isn't installed dpkg: warning: ignoring request to remove libssh2-1t64 which isn't installed dpkg: warning: ignoring request to remove libtasn1-6 which isn't installed dpkg: warning: ignoring request to remove libucx0 which isn't installed dpkg: warning: ignoring request to remove libunistring5 which isn't installed dpkg: warning: ignoring request to remove libx11-6 which isn't installed dpkg: warning: ignoring request to remove libx11-data which isn't installed dpkg: warning: ignoring request to remove libxau6 which isn't installed dpkg: warning: ignoring request to remove libxcb1 which isn't installed dpkg: warning: ignoring request to remove libxdmcp6 which isn't installed dpkg: warning: ignoring request to remove libxerces2-java which isn't installed dpkg: warning: ignoring request to remove libxext6 which isn't installed dpkg: warning: ignoring request to remove libxml-commons-external-java which isn't installed Purging configuration files for libxml-commons-resolver1.1-java (1.2-11) ... dpkg: warning: ignoring request to remove libxml2-16 which isn't installed dpkg: warning: ignoring request to remove libxnvctrl0 which isn't installed dpkg: warning: ignoring request to remove libxom-java which isn't installed dpkg: warning: ignoring request to remove libz3-4 which isn't installed dpkg: warning: ignoring request to remove libze1 which isn't installed dpkg: warning: ignoring request to remove mpi-default-bin which isn't installed Purging configuration files for ncbi-vdb-data (3.2.1+dfsg-2) ... dpkg: warning: ignoring request to remove ocl-icd-libopencl1 which isn't installed Purging configuration files for openjdk-21-jre-headless:amd64 (21.0.9~8ea-1) ... Purging configuration files for openmpi-bin (5.0.8-10+b1) ... dpkg: warning: ignoring request to remove openmpi-common which isn't installed Purging configuration files for openssh-client (1:10.0p1-8) ... Purging configuration files for openssl (3.5.4-1) ... 0m24.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'dpkg', '--purge', 'adduser', 'ca-certificates', 'ca-certificates-java', 'default-jre-headless', 'ibverbs-providers:amd64', 'java-common', 'junit4', 'libamd-comgr2:amd64', 'libamdhip64-5:amd64', 'libapache-pom-java', 'libatinject-jsr330-api-java', 'libbrotli1:amd64', 'libcbor0.10:amd64', 'libcom-err2:amd64', 'libcommons-beanutils-java', 'libcommons-codec-java', 'libcommons-collections3-java', 'libcommons-collections4-java', 'libcommons-compress-java', 'libcommons-io-java', 'libcommons-jexl2-java', 'libcommons-lang3-java', 'libcommons-logging-java', 'libcommons-parent-java', 'libcurl4t64:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1t64:amd64', 'liberror-prone-java', 'libevent-core-2.1-7t64:amd64', 'libevent-pthreads-2.1-7t64:amd64', 'libezmorph-java', 'libfabric1:amd64', 'libffi8:amd64', 'libfido2-1:amd64', 'libfmt10:amd64', 'libfuse3-4:amd64', 'libgenomicsdb-jni', 'libgenomicsdb1', 'libgetopt-java', 'libgnutls30t64:amd64', 'libgomp1:amd64', 'libgoogle-gson-java', 'libgssapi-krb5-2:amd64', 'libguava-java', 'libhamcrest-java', 'libhsa-runtime64-1:amd64', 'libhsakmt1:amd64', 'libhtsjdk-java', 'libhttpclient-java', 'libhttpcore-java', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibmad5:amd64', 'libibumad3:amd64', 'libibverbs1:amd64', 'libidn2-0:amd64', 'libjaxen-java', 'libjpeg62-turbo:amd64', 'libjson-java', 'libjson-simple-java', 'libjsr305-java', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblcms2-2:amd64', 'libldap2:amd64', 'liblightcouch-java', 'libllvm17t64:amd64', 'liblog4j2-java', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libmongodb-java', 'libmunge2:amd64', 'libmuparserx4.0.12:amd64', 'libncbi-ngs3:amd64', 'libncbi-vdb3:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngs-java:amd64', 'libngs-jni:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libnuma1:amd64', 'libopenmpi40:amd64', 'libp11-kit0:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libpmix2t64:amd64', 'libprotobuf-java', 'libprotobuf32t64:amd64', 'libpsl5t64:amd64', 'libpsm2-2', 'librdmacm1t64:amd64', 'librhino-java', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libslf4j-java', 'libsnappy-java', 'libsnappy-jni', 'libsnappy1v5:amd64', 'libssh2-1t64:amd64', 'libtasn1-6:amd64', 'libucx0:amd64', 'libunistring5:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxerces2-java', 'libxext6:amd64', 'libxml-commons-external-java', 'libxml-commons-resolver1.1-java', 'libxml2-16:amd64', 'libxnvctrl0:amd64', 'libxom-java', 'libz3-4:amd64', 'libze1:amd64', 'mpi-default-bin', 'ncbi-vdb-data', 'ocl-icd-libopencl1:amd64', 'openjdk-21-jre-headless:amd64', 'openmpi-bin', 'openmpi-common', 'openssh-client', 'openssl'] 0m24.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'dpkg', '--purge', 'libgenomicsdb-java'] 0m24.0s DUMP: dpkg: warning: ignoring request to remove libgenomicsdb-java which isn't installed 0m24.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'dpkg', '--purge', 'libgenomicsdb-java'] 0m24.0s INFO: Running scripts post_purge 0m24.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/post_purge_exceptions'] 0m24.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/post_purge_exceptions'] 0m24.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'dpkg', '--purge', '--pending'] 0m24.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'dpkg', '--purge', '--pending'] 0m24.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'dpkg', '--remove', '--pending'] 0m24.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'dpkg', '--remove', '--pending'] 0m24.0s INFO: Running scripts post_test 0m24.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/post_test_exceptions'] 0m24.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'tmp/scripts/post_test_exceptions'] 0m24.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo'] 0m24.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo'] 0m24.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'dpkg-divert', '--list'] 0m24.2s DUMP: local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged local diversion of /home to /home.distrib diversion of /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6 diversion of /libx32 to /.libx32.usr-is-merged by base-files local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /lib32 to /.lib32.usr-is-merged by base-files diversion of /libo32 to /.libo32.usr-is-merged by base-files 0m24.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'dpkg-divert', '--list'] 0m24.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'apt-get', 'clean'] 0m24.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo', 'apt-get', 'clean'] 0m24.2s DEBUG: Recording chroot state 0m24.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo/dev/shm'] 0m24.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo/dev/shm'] 0m24.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo/dev/console'] 0m24.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo/dev/console'] 0m24.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo/dev/ptmx'] 0m24.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo/dev/ptmx'] 0m24.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo/dev/pts'] 0m24.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo/dev/pts'] 0m24.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo/proc'] 0m24.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo/proc'] 0m24.9s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo'] 0m25.0s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp5ixqmldo'] 0m25.0s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp5ixqmldo 0m25.0s INFO: PASS: Upgrading between Debian distributions. 0m25.0s INFO: PASS: All tests. 0m25.0s INFO: piuparts run ends. ret=0 End: 2025-10-02 21:37:02 GMT