Start: 2023-11-04 03:23:01 GMT [testing] Package: libgenomicsdb-java Source: genomicsdb Version: 1.4.4-3 Installed-Size: 465 Maintainer: Debian Med Packaging Team Architecture: all Depends: libcommons-io-java (>= 2.11.0), libgetopt-java, libguava-java, libhtsjdk-java (>= 3.0.2), libjson-simple-java, liblog4j2-java (>= 2.19.0), libprotobuf-java, libprotobuf-java-format-java (>= 1.3), libgenomicsdb-jni (>= 1.4.4-3), libgenomicsdb-jni (<< 1.4.4-3.1~) 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_1.4.4-3_all.deb Size: 391580 MD5sum: 38b84f68713f9d8fe5a659932dc55536 SHA256: be907eca323a8da7878b0e9b12b4947d8c5eaaee65f7d4f200719ad7503e1c0e [sid] Package: libgenomicsdb-java Source: genomicsdb Version: 1.5.0-2 Installed-Size: 461 Maintainer: Debian Med Packaging Team Architecture: all Depends: libcommons-io-java (>= 2.11.0), libgetopt-java, libgoogle-gson-java, libguava-java, libhtsjdk-java (>= 3.0.2), libjson-simple-java, liblog4j2-java (>= 2.19.0), libprotobuf-java, libgenomicsdb-jni (>= 1.5.0-2), libgenomicsdb-jni (<< 1.5.0-2.1~) 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_1.5.0-2_all.deb Size: 389108 MD5sum: 84842d672729c698b178fc6ead6d7e9d SHA256: 2b06acc20c1eb7a3417c6fbda617472be53d12e840ad283319285662f65f4dbe Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt libgenomicsdb-java=1.5.0-2 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 1.2 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt libgenomicsdb-java=1.5.0-2 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-26-amd64 #1 SMP Debian 5.10.197-1 (2023-09-29) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpk8ek2be6 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpk8ek2be6 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m1.4s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m1.4s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6/proc'] 0m1.4s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6/proc'] 0m1.4s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6/dev/pts'] 0m1.4s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6/dev/pts'] 0m1.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6/dev/ptmx'] 0m1.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6/dev/ptmx'] 0m1.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6/dev/console'] 0m1.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6/dev/console'] 0m1.4s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6/dev/shm'] 0m1.4s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6/dev/shm'] 0m1.4s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m1.5s DEBUG: Created policy-rc.d and chmodded it. 0m1.5s DEBUG: Created resolv.conf. 0m1.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpk8ek2be6/tmp/scripts/ 0m1.5s INFO: Running scripts post_chroot_unpack 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'apt-get', 'update'] 0m2.4s DUMP: Hit:1 http://deb.debian.org/debian bookworm InRelease Reading package lists... 0m2.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'apt-get', 'update'] 0m2.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'apt-get', '-yf', 'dist-upgrade'] 0m2.7s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'apt-get', '-yf', 'dist-upgrade'] 0m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.0s DUMP: 58258f9b3702140f6ddb34dae593c101 - 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.0s INFO: Running scripts post_setup 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/post_setup_dummy_users'] 0m4.0s 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 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/post_setup_dummy_users'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/post_setup_forbid_home'] 0m4.0s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/post_setup_forbid_home'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.1s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' dpkg-divert: warning: diverting file '/bin/sync' from an Essential package with rename is dangerous, use --no-rename '/bin/sync' -> 'true' 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/post_setup_minimize'] 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/post_setup_minimize'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/post_setup_zz_backports'] 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/post_setup_zz_backports'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.1s DUMP: install ok installed apt apt 2.7.6 install ok installed base-files base-files 13 install ok installed base-passwd base-passwd 3.6.2 install ok installed bash bash 5.2.15-2+b6 install ok installed bsdutils bsdutils 1:2.39.2-4 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.12-6 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.14 install ok installed diffutils diffutils 1:3.8-4 install ok installed dpkg dpkg 1.22.0 install ok installed e2fsprogs e2fsprogs 1.47.0-2+b1 install ok installed findutils findutils 4.9.0-5 install ok installed gcc-13-base:amd64 gcc-13-base 13.2.0-5 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.11-3 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu1 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.7.6 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.1.1-1 install ok installed libaudit1:amd64 libaudit1 1:3.1.1-1 install ok installed libblkid1:amd64 libblkid1 2.39.2-4 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.37-12 install ok installed libc6:amd64 libc6 2.37-12 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3 install ok installed libcap2:amd64 libcap2 1:2.66-4 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-2 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.271 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2+b1 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libgcc-s1:amd64 libgcc-s1 13.2.0-5 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.2-3 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2 install ok installed libgnutls30:amd64 libgnutls30 3.8.1-4+b1 install ok installed libgpg-error0:amd64 libgpg-error0 1.47-2 install ok installed libhogweed6:amd64 libhogweed6 3.9.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.4-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.4-0.1 install ok installed libmd0:amd64 libmd0 1.1.0-1 install ok installed libmount1:amd64 libmount1 2.39.2-4 install ok installed libnettle8:amd64 libnettle8 3.9.1-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.0-5 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-9.1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-9.1 install ok installed libpam-runtime libpam-runtime 1.5.2-9.1 install ok installed libpam0g:amd64 libpam0g 1.5.2-9.1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+b3 install ok installed libselinux1:amd64 libselinux1 3.5-1 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1 install ok installed libsepol2:amd64 libsepol2 3.5-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.39.2-4 install ok installed libss2:amd64 libss2 1.47.0-2+b1 install ok installed libstdc++6:amd64 libstdc++6 13.2.0-5 install ok installed libsystemd0:amd64 libsystemd0 254.5-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3 install ok installed libtinfo6:amd64 libtinfo6 6.4+20231016-1 install ok installed libudev1:amd64 libudev1 254.5-1 install ok installed libunistring5:amd64 libunistring5 1.1-2 install ok installed libuuid1:amd64 libuuid1 2.39.2-4 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-2 install ok installed login login 1:4.13+dfsg1-3 install ok installed logsave logsave 1.47.0-2+b1 install ok installed mawk mawk 1.3.4.20230808-1 install ok installed mount mount 2.39.2-4 install ok installed ncurses-base ncurses-base 6.4+20231016-1 install ok installed ncurses-bin ncurses-bin 6.4+20231016-1 install ok installed passwd passwd 1:4.13+dfsg1-3 install ok installed perl-base perl-base 5.36.0-9 install ok installed sed sed 4.9-1 install ok installed sysvinit-utils sysvinit-utils 3.08-3 install ok installed tar tar 1.34+dfsg-1.2 install ok installed tzdata tzdata 2023c-10 install ok installed usr-is-merged usr-is-merged 37 install ok installed util-linux util-linux 2.39.2-4 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-3 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.1s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m4.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6'] 0m4.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6'] 0m4.5s INFO: Running scripts is_testable 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/is_testable_uninstallable'] 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/is_testable_uninstallable'] 0m4.6s INFO: Running scripts pre_test 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_test_exceptions'] 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_test_exceptions'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_test_root_password'] 0m4.6s DUMP: New password: Retype new password: passwd: password updated successfully 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_test_root_password'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'apt-cache', 'show', '--no-all-versions', 'libgenomicsdb-java'] 0m4.8s DUMP: Package: libgenomicsdb-java Source: genomicsdb Version: 1.4.4-3 Installed-Size: 465 Maintainer: Debian Med Packaging Team Architecture: all Depends: libcommons-io-java (>= 2.11.0), libgetopt-java, libguava-java, libhtsjdk-java (>= 3.0.2), libjson-simple-java, liblog4j2-java (>= 2.19.0), libprotobuf-java, libprotobuf-java-format-java (>= 1.3), libgenomicsdb-jni (>= 1.4.4-3), libgenomicsdb-jni (<< 1.4.4-3.1~) 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_1.4.4-3_all.deb Size: 391580 MD5sum: 38b84f68713f9d8fe5a659932dc55536 SHA256: be907eca323a8da7878b0e9b12b4947d8c5eaaee65f7d4f200719ad7503e1c0e 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'apt-cache', 'show', '--no-all-versions', 'libgenomicsdb-java'] 0m4.8s INFO: apt-cache knows about the following packages: libgenomicsdb-java 0m4.8s INFO: Running scripts pre_install 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_install_database-server'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_install_database-server'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_install_exceptions'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_install_exceptions'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_install_extras'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_install_extras'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'apt-cache', 'policy'] 0m4.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.2,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'apt-cache', 'policy'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'apt-cache', 'policy', 'libgenomicsdb-java'] 0m4.9s DUMP: libgenomicsdb-java: Installed: (none) Candidate: 1.4.4-3 Version table: 1.4.4-3 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'apt-cache', 'policy', 'libgenomicsdb-java'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'apt-get', '-y', 'install', 'libgenomicsdb-java'] 0m12.0s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: adduser gcc-12-base ibverbs-providers libapache-pom-java libatinject-jsr330-api-java libatomic1 libbrotli1 libbsd0 libcbor0.8 libcommons-codec-java libcommons-compress-java libcommons-io-java libcommons-jexl2-java libcommons-logging-java libcommons-parent-java libcurl4 libedit2 liberror-prone-java libevent-core-2.1-7 libevent-pthreads-2.1-7 libfabric1 libfido2-1 libfmt9 libgenomicsdb-jni libgenomicsdb0 libgetopt-java libgomp1 libgoogle-gson-java libgssapi-krb5-2 libguava-java libhtsjdk-java libhttpclient-java libhttpcore-java libhwloc-plugins libhwloc15 libibverbs1 libicu72 libjson-simple-java libjsr305-java libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.5-0 liblightcouch-java liblog4j2-java libmbedcrypto7 libmbedtls14 libmbedx509-1 libmjson-java libmongodb-java libmunge2 libmuparserx4.0.11 libncbi-ngs3 libncbi-vdb3 libnghttp2-14 libngs-java libngs-jni libnl-3-200 libnl-route-3-200 libnuma1 libopenmpi3 libpciaccess0 libpmix2 libprotobuf-java libprotobuf-java-format-java libprotobuf32 libpsl5 libpsm-infinipath1 libpsm2-2 librdmacm1 librhino-java librtmp1 libsasl2-2 libsasl2-modules-db libslf4j-java libsnappy-java libsnappy-jni libsnappy1v5 libssh2-1 libssl3 libucx0 libunistring2 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 ncbi-vdb-data ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client Suggested packages: liblocale-gettext-perl perl cron quota libatinject-jsr330-api-java-doc libasm-java libxz-java libcommons-io-java-doc libavalon-framework-java libcommons-logging-java-doc libexcalibur-logkit-java liblog4j1.2-java libgoogle-gson-java-doc krb5-doc krb5-user picard-tools python3 libhwloc-contrib-plugins libjson-simple-doc libjsr305-java-doc 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 libjackson2-core-java libjackson2-dataformat-smile rhino opencl-icd gfortran | fortran-compiler keychain libpam-ssh monkeysphere ssh-askpass Recommended packages: ca-certificates krb5-locales libldap-common publicsuffix libsasl2-modules xauth The following NEW packages will be installed: adduser gcc-12-base ibverbs-providers libapache-pom-java libatinject-jsr330-api-java libatomic1 libbrotli1 libbsd0 libcbor0.8 libcommons-codec-java libcommons-compress-java libcommons-io-java libcommons-jexl2-java libcommons-logging-java libcommons-parent-java libcurl4 libedit2 liberror-prone-java libevent-core-2.1-7 libevent-pthreads-2.1-7 libfabric1 libfido2-1 libfmt9 libgenomicsdb-java libgenomicsdb-jni libgenomicsdb0 libgetopt-java libgomp1 libgoogle-gson-java libgssapi-krb5-2 libguava-java libhtsjdk-java libhttpclient-java libhttpcore-java libhwloc-plugins libhwloc15 libibverbs1 libicu72 libjson-simple-java libjsr305-java libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.5-0 liblightcouch-java liblog4j2-java libmbedcrypto7 libmbedtls14 libmbedx509-1 libmjson-java libmongodb-java libmunge2 libmuparserx4.0.11 libncbi-ngs3 libncbi-vdb3 libnghttp2-14 libngs-java libngs-jni libnl-3-200 libnl-route-3-200 libnuma1 libopenmpi3 libpciaccess0 libpmix2 libprotobuf-java libprotobuf-java-format-java libprotobuf32 libpsl5 libpsm-infinipath1 libpsm2-2 librdmacm1 librhino-java librtmp1 libsasl2-2 libsasl2-modules-db libslf4j-java libsnappy-java libsnappy-jni libsnappy1v5 libssh2-1 libssl3 libucx0 libunistring2 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 ncbi-vdb-data ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client 0 upgraded, 97 newly installed, 0 to remove and 0 not upgraded. Need to get 44.7 MB of archives. After this operation, 126 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 adduser all 3.134 [183 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libedit2 amd64 3.1-20221030-2 [93.0 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 libcbor0.8 amd64 0.8.0-2+b1 [27.4 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 libssl3 amd64 3.0.11-1~deb12u1 [2018 kB] Get:6 http://deb.debian.org/debian bookworm/main amd64 libfido2-1 amd64 1.12.0-2+b1 [77.2 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 libkrb5support0 amd64 1.20.1-2+deb12u1 [32.4 kB] Get:8 http://deb.debian.org/debian bookworm/main amd64 libk5crypto3 amd64 1.20.1-2+deb12u1 [78.9 kB] Get:9 http://deb.debian.org/debian bookworm/main amd64 libkeyutils1 amd64 1.6.3-2 [8808 B] Get:10 http://deb.debian.org/debian bookworm/main amd64 libkrb5-3 amd64 1.20.1-2+deb12u1 [332 kB] Get:11 http://deb.debian.org/debian bookworm/main amd64 libgssapi-krb5-2 amd64 1.20.1-2+deb12u1 [134 kB] Get:12 http://deb.debian.org/debian bookworm/main amd64 openssh-client amd64 1:9.2p1-2+deb12u1 [989 kB] Get:13 http://deb.debian.org/debian bookworm/main amd64 gcc-12-base amd64 12.2.0-14 [37.5 kB] Get:14 http://deb.debian.org/debian bookworm/main amd64 libnl-3-200 amd64 3.7.0-0.2+b1 [63.1 kB] Get:15 http://deb.debian.org/debian bookworm/main amd64 libnl-route-3-200 amd64 3.7.0-0.2+b1 [185 kB] Get:16 http://deb.debian.org/debian bookworm/main amd64 libibverbs1 amd64 44.0-2 [60.7 kB] Get:17 http://deb.debian.org/debian bookworm/main amd64 ibverbs-providers amd64 44.0-2 [335 kB] Get:18 http://deb.debian.org/debian bookworm/main amd64 libapache-pom-java all 29-2 [5276 B] Get:19 http://deb.debian.org/debian bookworm/main amd64 libatinject-jsr330-api-java all 1.0+ds1-5 [5312 B] Get:20 http://deb.debian.org/debian bookworm/main amd64 libatomic1 amd64 12.2.0-14 [9328 B] Get:21 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get:22 http://deb.debian.org/debian bookworm/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get:23 http://deb.debian.org/debian bookworm/main amd64 libcommons-codec-java all 1.15-1 [292 kB] Get:24 http://deb.debian.org/debian bookworm/main amd64 libcommons-compress-java all 1.22-1 [615 kB] Get:25 http://deb.debian.org/debian bookworm/main amd64 libcommons-io-java all 2.11.0-2 [319 kB] Get:26 http://deb.debian.org/debian bookworm/main amd64 libcommons-logging-java all 1.2-3 [62.4 kB] Get:27 http://deb.debian.org/debian bookworm/main amd64 libcommons-jexl2-java all 2.1.1-6 [256 kB] Get:28 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get:29 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get:30 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get:31 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1 [72.3 kB] Get:32 http://deb.debian.org/debian bookworm/main amd64 libunistring2 amd64 1.0-2 [437 kB] Get:33 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get:34 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:35 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get:36 http://deb.debian.org/debian bookworm/main amd64 libcurl4 amd64 7.88.1-10+deb12u3 [390 kB] Get:37 http://deb.debian.org/debian bookworm/main amd64 libjsr305-java all 0.1~+svn49-11 [26.9 kB] Get:38 http://deb.debian.org/debian bookworm/main amd64 libguava-java all 31.1-1 [2613 kB] Get:39 http://deb.debian.org/debian bookworm/main amd64 liberror-prone-java all 2.18.0-1 [22.5 kB] Get:40 http://deb.debian.org/debian bookworm/main amd64 libevent-core-2.1-7 amd64 2.1.12-stable-8 [131 kB] Get:41 http://deb.debian.org/debian bookworm/main amd64 libevent-pthreads-2.1-7 amd64 2.1.12-stable-8 [53.6 kB] Get:42 http://deb.debian.org/debian bookworm/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.2 [168 kB] Get:43 http://deb.debian.org/debian bookworm/main amd64 libnuma1 amd64 2.0.16-1 [21.0 kB] Get:44 http://deb.debian.org/debian bookworm/main amd64 libpsm2-2 amd64 11.2.185-2 [180 kB] Get:45 http://deb.debian.org/debian bookworm/main amd64 librdmacm1 amd64 44.0-2 [68.6 kB] Get:46 http://deb.debian.org/debian bookworm/main amd64 libfabric1 amd64 1.17.0-3 [627 kB] Get:47 http://deb.debian.org/debian bookworm/main amd64 libfmt9 amd64 9.1.0+ds1-2 [113 kB] Get:48 http://deb.debian.org/debian bookworm/main amd64 libgetopt-java all 1.0.14+dfsg-6 [25.7 kB] Get:49 http://deb.debian.org/debian bookworm/main amd64 libmjson-java all 1.4.0-3 [60.4 kB] Get:50 http://deb.debian.org/debian bookworm/main amd64 libmbedcrypto7 amd64 2.28.3-1 [277 kB] Get:51 http://deb.debian.org/debian bookworm/main amd64 libmbedx509-1 amd64 2.28.3-1 [128 kB] Get:52 http://deb.debian.org/debian 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libhtsjdk-java all 3.0.4+dfsg-2 [1813 kB] Get:63 http://deb.debian.org/debian bookworm/main amd64 libjson-simple-java all 2.3.0-1 [63.8 kB] Get:64 http://deb.debian.org/debian bookworm/main amd64 libgoogle-gson-java all 2.10-1 [261 kB] Get:65 http://deb.debian.org/debian bookworm/main amd64 libhttpcore-java all 4.4.16-1 [636 kB] Get:66 http://deb.debian.org/debian bookworm/main amd64 libhttpclient-java all 4.5.14-1 [1247 kB] Get:67 http://deb.debian.org/debian bookworm/main amd64 liblightcouch-java all 0.2.0-1 [75.0 kB] Get:68 http://deb.debian.org/debian bookworm/main amd64 libmongodb-java all 3.6.3-2 [1901 kB] Get:69 http://deb.debian.org/debian bookworm/main amd64 libslf4j-java all 1.7.32-1 [144 kB] Get:70 http://deb.debian.org/debian bookworm/main amd64 liblog4j2-java all 2.19.0-2 [2310 kB] Get:71 http://deb.debian.org/debian bookworm/main amd64 libprotobuf-java all 3.21.12-3 [1257 kB] Get:72 http://deb.debian.org/debian bookworm/main amd64 libprotobuf-java-format-java all 1.3-1.1 [90.3 kB] Get:73 http://deb.debian.org/debian bookworm/main amd64 libgomp1 amd64 12.2.0-14 [116 kB] Get:74 http://deb.debian.org/debian bookworm/main amd64 libmuparserx4.0.11 amd64 4.0.11-2 [192 kB] Get:75 http://deb.debian.org/debian bookworm/main amd64 libprotobuf32 amd64 3.21.12-3 [932 kB] Get:76 http://deb.debian.org/debian bookworm/main amd64 libhwloc15 amd64 2.9.0-1 [154 kB] Get:77 http://deb.debian.org/debian bookworm/main amd64 libmunge2 amd64 0.5.15-2 [19.5 kB] Get:78 http://deb.debian.org/debian bookworm/main amd64 libpciaccess0 amd64 0.17-2 [51.4 kB] Get:79 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get:80 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:81 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get:82 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2+deb12u1 [292 kB] Get:83 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2+deb12u1 [759 kB] Get:84 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get:85 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.3~deb12u1 [687 kB] Get:86 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get:87 http://deb.debian.org/debian bookworm/main amd64 libxnvctrl0 amd64 525.85.05-3~deb12u1 [13.5 kB] Get:88 http://deb.debian.org/debian bookworm/main amd64 ocl-icd-libopencl1 amd64 2.3.1-1 [43.0 kB] Get:89 http://deb.debian.org/debian bookworm/main amd64 libhwloc-plugins amd64 2.9.0-1 [17.5 kB] Get:90 http://deb.debian.org/debian bookworm/main amd64 libpmix2 amd64 4.2.2-1+b1 [622 kB] Get:91 http://deb.debian.org/debian bookworm/main amd64 libucx0 amd64 1.13.1-1 [860 kB] Get:92 http://deb.debian.org/debian bookworm/main amd64 libopenmpi3 amd64 4.1.4-3+b1 [2422 kB] Get:93 http://deb.debian.org/debian bookworm/main amd64 openmpi-common all 4.1.4-3 [167 kB] Get:94 http://deb.debian.org/debian bookworm/main amd64 openmpi-bin amd64 4.1.4-3+b1 [226 kB] Get:95 http://deb.debian.org/debian bookworm/main amd64 libgenomicsdb0 amd64 1.4.4-3 [1527 kB] Get:96 http://deb.debian.org/debian bookworm/main amd64 libgenomicsdb-jni amd64 1.4.4-3 [126 kB] Get:97 http://deb.debian.org/debian bookworm/main amd64 libgenomicsdb-java all 1.4.4-3 [392 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 44.7 MB in 0s (148 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 ... 5198 files and directories currently installed.) Preparing to unpack .../archives/adduser_3.134_all.deb ... Unpacking adduser (3.134) ... Setting up adduser (3.134) ... Selecting previously unselected package libbsd0:amd64. (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 ... 5275 files and directories currently installed.) Preparing to unpack .../00-libbsd0_0.11.7-2_amd64.deb ... Unpacking libbsd0:amd64 (0.11.7-2) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../01-libedit2_3.1-20221030-2_amd64.deb ... Unpacking libedit2:amd64 (3.1-20221030-2) ... Selecting previously unselected package libcbor0.8:amd64. Preparing to unpack .../02-libcbor0.8_0.8.0-2+b1_amd64.deb ... 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Setting up ocl-icd-libopencl1:amd64 (2.3.1-1) ... Setting up libnl-3-200:amd64 (3.7.0-0.2+b1) ... Setting up libpsm2-2 (11.2.185-2) ... Setting up openmpi-common (4.1.4-3) ... Setting up ncbi-vdb-data (3.0.2+dfsg-2) ... Setting up libssh2-1:amd64 (1.10.0-3+b1) ... Setting up libkrb5-3:amd64 (1.20.1-2+deb12u1) ... Setting up libprotobuf-java-format-java (1.3-1.1) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6.2) ... update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode Setting up libhttpcore-java (4.4.16-1) ... Setting up libfido2-1:amd64 (1.12.0-2+b1) ... Setting up libbsd0:amd64 (0.11.7-2) ... Setting up libsnappy-jni (1.1.8.3-1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3~deb12u1) ... Setting up libprotobuf-java (3.21.12-3) ... Setting up libevent-pthreads-2.1-7:amd64 (2.1.12-stable-8) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libpsl5:amd64 (0.21.2-1) ... Setting up libxcb1:amd64 (1.15-1) ... Setting up libmbedx509-1:amd64 (2.28.3-1) ... Setting up libmbedtls14:amd64 (2.28.3-1) ... Setting up libedit2:amd64 (3.1-20221030-2) ... Setting up libcommons-parent-java (56-1) ... Setting up libncbi-vdb3:amd64 (3.0.2+dfsg-2) ... Setting up libcommons-logging-java (1.2-3) ... Setting up libgomp1:amd64 (12.2.0-14) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Setting up libnl-route-3-200:amd64 (3.7.0-0.2+b1) ... Setting up libcommons-jexl2-java (2.1.1-6) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-2+deb12u1) ... Setting up libcurl4:amd64 (7.88.1-10+deb12u3) ... Setting up libx11-6:amd64 (2:1.8.4-2+deb12u1) ... Setting up libsnappy-java (1.1.8.3-1) ... Setting up libcommons-codec-java (1.15-1) ... Setting up libncbi-ngs3:amd64 (3.0.3+dfsg-6~deb12u1) ... Setting up libibverbs1:amd64 (44.0-2) ... Setting up libngs-jni:amd64 (3.0.3+dfsg-6~deb12u1) ... Setting up libcommons-compress-java (1.22-1) ... Setting up ibverbs-providers:amd64 (44.0-2) ... Setting up libcommons-io-java (2.11.0-2) ... Setting up openssh-client (1:9.2p1-2+deb12u1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libxnvctrl0:amd64 (525.85.05-3~deb12u1) ... Setting up libhttpclient-java (4.5.14-1) ... Setting up liblightcouch-java (0.2.0-1) ... Setting up libngs-java:amd64 (3.0.3+dfsg-6~deb12u1) ... Setting up libhtsjdk-java (3.0.4+dfsg-2) ... Setting up librdmacm1:amd64 (44.0-2) ... Setting up libucx0:amd64 (1.13.1-1) ... Setting up liblog4j2-java (2.19.0-2) ... Setting up libhwloc-plugins:amd64 (2.9.0-1) ... Setting up libfabric1:amd64 (1.17.0-3) ... Setting up libpmix2:amd64 (4.2.2-1+b1) ... Setting up libopenmpi3:amd64 (4.1.4-3+b1) ... Setting up openmpi-bin (4.1.4-3+b1) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libgenomicsdb0 (1.4.4-3) ... Setting up libgenomicsdb-jni (1.4.4-3) ... Setting up liberror-prone-java (2.18.0-1) ... Setting up libguava-java (31.1-1) ... Setting up libgenomicsdb-java (1.4.4-3) ... Processing triggers for libc-bin (2.37-12) ... 0m12.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'apt-get', '-y', 'install', 'libgenomicsdb-java'] 0m12.0s INFO: Running scripts post_install 0m12.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/post_install_exceptions'] 0m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/post_install_exceptions'] 0m12.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6'] 0m12.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6'] 0m12.5s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpk8ek2be6 to sid 0m12.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m12.5s INFO: Running scripts pre_distupgrade 0m12.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m12.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m12.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_distupgrade_exceptions'] 0m12.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_distupgrade_exceptions'] 0m12.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m12.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m12.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m12.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m12.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m12.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m12.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'apt-get', 'update'] 0m15.4s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [198 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9576 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7059 kB] Fetched 16.8 MB in 2s (7873 kB/s) Reading package lists... 0m15.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'apt-get', 'update'] 0m15.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'apt-get', '-yf', 'dist-upgrade'] 0m21.9s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: gcc-12-base libcbor0.8 libprotobuf-java-format-java libunistring2 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: libcbor0.10 The following packages will be upgraded: adduser bsdutils diffutils dpkg gcc-12-base gcc-13-base ibverbs-providers libatomic1 libblkid1 libbsd0 libcommons-compress-java libcommons-logging-java libcurl4 libedit2 libfido2-1 libgcc-s1 libgenomicsdb-java libgenomicsdb-jni libgenomicsdb0 libgomp1 libgoogle-gson-java libgssapi-krb5-2 libguava-java libhtsjdk-java libhwloc-plugins libhwloc15 libibverbs1 libicu72 libk5crypto3 libkrb5-3 libkrb5support0 libmbedcrypto7 libmbedtls14 libmbedx509-1 libmount1 libmunge2 libncbi-ngs3 libnghttp2-14 libngs-java libngs-jni libopenmpi3 libpmix2 libprotobuf-java libprotobuf32 libpsl5 librdmacm1 libsasl2-2 libsasl2-modules-db libseccomp2 libsmartcols1 libsnappy-java libsnappy-jni libsnappy1v5 libssh2-1 libssl3 libstdc++6 libucx0 libuuid1 libx11-6 libx11-data libxml2 libxnvctrl0 mount ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client usr-is-merged util-linux 69 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 36.9 MB of archives. After this operation, 1473 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.39.2-5 [96.8 kB] Get:2 http://deb.debian.org/debian sid/main amd64 diffutils amd64 1:3.10-1 [375 kB] Get:3 http://deb.debian.org/debian sid/main amd64 dpkg amd64 1.22.1 [1561 kB] Get:4 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.39.2-5 [1225 kB] Get:5 http://deb.debian.org/debian sid/main amd64 mount amd64 2.39.2-5 [143 kB] Get:6 http://deb.debian.org/debian sid/main amd64 adduser all 3.137 [140 kB] Get:7 http://deb.debian.org/debian sid/main amd64 gcc-13-base amd64 13.2.0-6 [40.5 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 13.2.0-6 [694 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 13.2.0-6 [57.8 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.39.2-5 [159 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.39.2-5 [190 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libseccomp2 amd64 2.5.4-2 [46.8 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.39.2-5 [116 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.39.2-5 [29.5 kB] Get:15 http://deb.debian.org/debian sid/main amd64 usr-is-merged all 38 [5504 B] Get:16 http://deb.debian.org/debian sid/main amd64 libbsd0 amd64 0.11.7-4 [115 kB] Get:17 http://deb.debian.org/debian sid/main amd64 libedit2 amd64 3.1-20230828-1 [93.1 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libcbor0.10 amd64 0.10.2-1.1 [27.8 kB] Get:19 http://deb.debian.org/debian sid/main amd64 libssl3 amd64 3.0.12-1 [2018 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libfido2-1 amd64 1.13.0-1+b1 [77.6 kB] Get:21 http://deb.debian.org/debian sid/main amd64 libgssapi-krb5-2 amd64 1.20.1-5 [135 kB] Get:22 http://deb.debian.org/debian sid/main amd64 libkrb5-3 amd64 1.20.1-5 [332 kB] Get:23 http://deb.debian.org/debian sid/main amd64 libk5crypto3 amd64 1.20.1-5 [79.6 kB] Get:24 http://deb.debian.org/debian sid/main amd64 libkrb5support0 amd64 1.20.1-5 [32.9 kB] Get:25 http://deb.debian.org/debian sid/main amd64 openssh-client amd64 1:9.4p1-1 [986 kB] Get:26 http://deb.debian.org/debian sid/main amd64 libatomic1 amd64 13.2.0-6 [9288 B] Get:27 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 13.2.0-6 [131 kB] Get:28 http://deb.debian.org/debian sid/main amd64 gcc-12-base amd64 12.3.0-11 [40.7 kB] Get:29 http://deb.debian.org/debian sid/main amd64 libibverbs1 amd64 48.0-1 [61.2 kB] Get:30 http://deb.debian.org/debian sid/main amd64 ibverbs-providers amd64 48.0-1 [340 kB] Get:31 http://deb.debian.org/debian sid/main amd64 libcommons-compress-java all 1.24.0-1 [630 kB] Get:32 http://deb.debian.org/debian sid/main amd64 libcommons-logging-java all 1.2-4 [60.2 kB] Get:33 http://deb.debian.org/debian sid/main amd64 libnghttp2-14 amd64 1.57.0-1 [73.6 kB] Get:34 http://deb.debian.org/debian sid/main amd64 libpsl5 amd64 0.21.2-1+b1 [59.1 kB] Get:35 http://deb.debian.org/debian sid/main amd64 libssh2-1 amd64 1.11.0-2 [214 kB] Get:36 http://deb.debian.org/debian sid/main amd64 libcurl4 amd64 8.4.0-2 [413 kB] Get:37 http://deb.debian.org/debian sid/main amd64 libgoogle-gson-java all 2.10.1-1 [262 kB] Get:38 http://deb.debian.org/debian sid/main amd64 libguava-java all 32.0.1-1 [2708 kB] Get:39 http://deb.debian.org/debian sid/main amd64 libngs-java amd64 3.0.3+dfsg-6 [110 kB] Get:40 http://deb.debian.org/debian sid/main amd64 libngs-jni amd64 3.0.3+dfsg-6 [23.4 kB] Get:41 http://deb.debian.org/debian sid/main amd64 libncbi-ngs3 amd64 3.0.3+dfsg-6 [154 kB] Get:42 http://deb.debian.org/debian sid/main amd64 libsnappy1v5 amd64 1.1.10-1 [27.3 kB] Get:43 http://deb.debian.org/debian sid/main amd64 libsnappy-jni amd64 1.1.10.5-1 [6360 B] Get:44 http://deb.debian.org/debian sid/main amd64 libsnappy-java all 1.1.10.5-1 [87.4 kB] Get:45 http://deb.debian.org/debian sid/main amd64 libhtsjdk-java all 3.0.5+dfsg-1 [1814 kB] Get:46 http://deb.debian.org/debian sid/main amd64 libprotobuf-java all 3.21.12-7 [1259 kB] Get:47 http://deb.debian.org/debian sid/main amd64 libprotobuf32 amd64 3.21.12-7 [963 kB] Get:48 http://deb.debian.org/debian sid/main amd64 librdmacm1 amd64 48.0-1 [69.5 kB] Get:49 http://deb.debian.org/debian sid/main amd64 libucx0 amd64 1.15.0-1 [940 kB] Get:50 http://deb.debian.org/debian sid/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get:51 http://deb.debian.org/debian sid/main amd64 libx11-6 amd64 2:1.8.7-1 [802 kB] Get:52 http://deb.debian.org/debian sid/main amd64 libicu72 amd64 72.1-4 [9396 kB] Get:53 http://deb.debian.org/debian sid/main amd64 libxml2 amd64 2.9.14+dfsg-1.3 [686 kB] Get:54 http://deb.debian.org/debian sid/main amd64 libxnvctrl0 amd64 525.125.06-1 [13.5 kB] Get:55 http://deb.debian.org/debian sid/main amd64 ocl-icd-libopencl1 amd64 2.3.2-1 [39.7 kB] Get:56 http://deb.debian.org/debian sid/main amd64 libhwloc15 amd64 2.9.3-1 [155 kB] Get:57 http://deb.debian.org/debian sid/main amd64 libhwloc-plugins amd64 2.9.3-1 [17.6 kB] Get:58 http://deb.debian.org/debian sid/main amd64 libmunge2 amd64 0.5.15-3 [19.7 kB] Get:59 http://deb.debian.org/debian sid/main amd64 libpmix2 amd64 5.0.1-2 [643 kB] Get:60 http://deb.debian.org/debian sid/main amd64 libopenmpi3 amd64 4.1.6-1 [2427 kB] Get:61 http://deb.debian.org/debian sid/main amd64 openmpi-common all 4.1.6-1 [168 kB] Get:62 http://deb.debian.org/debian sid/main amd64 openmpi-bin amd64 4.1.6-1 [225 kB] Get:63 http://deb.debian.org/debian sid/main amd64 libgenomicsdb-java all 1.5.0-2 [389 kB] Get:64 http://deb.debian.org/debian sid/main amd64 libgenomicsdb-jni amd64 1.5.0-2 [115 kB] Get:65 http://deb.debian.org/debian sid/main amd64 libgenomicsdb0 amd64 1.5.0-2 [1577 kB] Get:66 http://deb.debian.org/debian sid/main amd64 libmbedcrypto7 amd64 2.28.5-1 [279 kB] Get:67 http://deb.debian.org/debian sid/main amd64 libmbedx509-1 amd64 2.28.5-1 [129 kB] Get:68 http://deb.debian.org/debian sid/main amd64 libmbedtls14 amd64 2.28.5-1 [165 kB] Get:69 http://deb.debian.org/debian sid/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-3 [19.3 kB] Get:70 http://deb.debian.org/debian sid/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-3 [56.6 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 36.9 MB in 0s (107 MB/s) (Reading database ... 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Processing triggers for libc-bin (2.37-12) ... 0m21.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'apt-get', '-yf', 'dist-upgrade'] 0m21.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m22.5s DUMP: c48ab4f11d80435924fce20b7e57a03a - 0m22.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m22.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'apt-cache', 'show', '--no-all-versions', 'libgenomicsdb-java'] 0m22.7s DUMP: Package: libgenomicsdb-java Source: genomicsdb Version: 1.5.0-2 Installed-Size: 461 Maintainer: Debian Med Packaging Team Architecture: all Depends: libcommons-io-java (>= 2.11.0), libgetopt-java, libgoogle-gson-java, libguava-java, libhtsjdk-java (>= 3.0.2), libjson-simple-java, liblog4j2-java (>= 2.19.0), libprotobuf-java, libgenomicsdb-jni (>= 1.5.0-2), libgenomicsdb-jni (<< 1.5.0-2.1~) 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_1.5.0-2_all.deb Size: 389108 MD5sum: 84842d672729c698b178fc6ead6d7e9d SHA256: 2b06acc20c1eb7a3417c6fbda617472be53d12e840ad283319285662f65f4dbe 0m22.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'apt-cache', 'show', '--no-all-versions', 'libgenomicsdb-java'] 0m22.7s INFO: apt-cache knows about the following packages: libgenomicsdb-java 0m22.7s INFO: Running scripts pre_install 0m22.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_install_database-server'] 0m22.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_install_database-server'] 0m22.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_install_exceptions'] 0m22.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_install_exceptions'] 0m22.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_install_extras'] 0m22.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_install_extras'] 0m22.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_install_foreign_architecture'] 0m22.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_install_foreign_architecture'] 0m22.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m22.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m22.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'apt-cache', 'policy'] 0m22.8s 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: 0m22.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'apt-cache', 'policy'] 0m22.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'apt-cache', 'policy', 'libgenomicsdb-java'] 0m22.8s DUMP: libgenomicsdb-java: Installed: 1.5.0-2 Candidate: 1.5.0-2 Version table: *** 1.5.0-2 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m22.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'apt-cache', 'policy', 'libgenomicsdb-java'] 0m22.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'apt-get', '-y', 'install', 'libgenomicsdb-java'] 0m23.3s DUMP: Reading package lists... Building dependency tree... Reading state information... libgenomicsdb-java is already the newest version (1.5.0-2). The following packages were automatically installed and are no longer required: gcc-12-base libcbor0.8 libprotobuf-java-format-java libunistring2 Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m23.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'apt-get', '-y', 'install', 'libgenomicsdb-java'] 0m23.3s INFO: Running scripts post_install 0m23.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/post_install_exceptions'] 0m23.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/post_install_exceptions'] 0m23.3s INFO: Running scripts post_distupgrade 0m23.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m23.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m23.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/post_distupgrade_exceptions'] 0m23.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/post_distupgrade_exceptions'] 0m23.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m23.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m23.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m23.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m23.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/post_distupgrade_zz_backports'] 0m23.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/post_distupgrade_zz_backports'] 0m23.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6'] 0m23.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6'] 0m23.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6'] 0m24.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6'] 0m24.3s INFO: Running scripts pre_install 0m24.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_install_database-server'] 0m24.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_install_database-server'] 0m24.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_install_exceptions'] 0m24.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_install_exceptions'] 0m24.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_install_extras'] 0m24.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_install_extras'] 0m24.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_install_foreign_architecture'] 0m24.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_install_foreign_architecture'] 0m24.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m24.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m24.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'apt-cache', 'policy'] 0m24.4s 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: 0m24.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'apt-cache', 'policy'] 0m24.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'apt-cache', 'policy', 'libgenomicsdb-java'] 0m24.4s DUMP: libgenomicsdb-java: Installed: 1.5.0-2 Candidate: 1.5.0-2 Version table: *** 1.5.0-2 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m24.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'apt-cache', 'policy', 'libgenomicsdb-java'] 0m24.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'apt-get', '-y', 'install', 'libgenomicsdb-java=1.5.0-2'] 0m24.8s DUMP: Reading package lists... Building dependency tree... Reading state information... libgenomicsdb-java is already the newest version (1.5.0-2). The following packages were automatically installed and are no longer required: gcc-12-base libcbor0.8 libprotobuf-java-format-java libunistring2 Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m24.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'apt-get', '-y', 'install', 'libgenomicsdb-java=1.5.0-2'] 0m24.8s INFO: Running scripts post_install 0m24.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/post_install_exceptions'] 0m24.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/post_install_exceptions'] 0m24.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6'] 0m25.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6'] 0m25.2s INFO: /bin converted to /usr/bin by /usr merge 0m25.2s INFO: /lib converted to /usr/lib by /usr merge 0m25.2s INFO: /lib/init converted to /usr/lib/init by /usr merge 0m25.2s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 0m25.2s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 0m25.2s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 0m25.2s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 0m25.2s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 0m25.2s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 0m25.2s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 0m25.2s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 0m25.2s INFO: /lib64 converted to /usr/lib64 by /usr merge 0m25.2s INFO: /sbin converted to /usr/sbin by /usr merge 0m25.6s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', '-ac', '--ignore-obsolete'] 0m26.4s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', '-ac', '--ignore-obsolete'] 0m26.4s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m26.4s DUMP: 0.15.6 0m26.4s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m26.4s INFO: Running adequate version 0.15.6 now. 0m26.4s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'libgenomicsdb-java'] 0m26.5s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'libgenomicsdb-java'] 0m26.5s INFO: Running scripts pre_remove 0m26.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m26.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m26.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m26.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m26.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m28.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m28.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m28.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m28.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m28.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m28.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_remove_exceptions'] 0m28.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/pre_remove_exceptions'] 0m28.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m28.6s DUMP: install ok installed adduser adduser 3.137 install ok installed apt apt 2.7.6 install ok installed base-files base-files 13 install ok installed base-passwd base-passwd 3.6.2 install ok installed bash bash 5.2.15-2+b6 install ok installed bsdutils bsdutils 1:2.39.2-5 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.12-6 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.14 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.1 install ok installed e2fsprogs e2fsprogs 1.47.0-2+b1 install ok installed findutils findutils 4.9.0-5 install ok installed gcc-12-base:amd64 gcc-12-base 12.3.0-11 install ok installed gcc-13-base:amd64 gcc-13-base 13.2.0-6 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.11-3 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu1 install ok installed ibverbs-providers:amd64 ibverbs-providers 48.0-1 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libapache-pom-java libapache-pom-java 29-2 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.7.6 install ok installed libatinject-jsr330-api-java libatinject-jsr330-api-java 1.0+ds1-5 install ok installed libatomic1:amd64 libatomic1 13.2.0-6 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.1.1-1 install ok installed libaudit1:amd64 libaudit1 1:3.1.1-1 install ok installed libblkid1:amd64 libblkid1 2.39.2-5 install ok installed libbrotli1:amd64 libbrotli1 1.0.9-2+b6 install ok installed libbsd0:amd64 libbsd0 0.11.7-4 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.37-12 install ok installed libc6:amd64 libc6 2.37-12 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3 install ok installed libcap2:amd64 libcap2 1:2.66-4 install ok installed libcbor0.10:amd64 libcbor0.10 0.10.2-1.1 install ok installed libcbor0.8:amd64 libcbor0.8 0.8.0-2+b1 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2+b1 install ok installed libcommons-codec-java libcommons-codec-java 1.15-1 install ok installed libcommons-compress-java libcommons-compress-java 1.24.0-1 install ok installed libcommons-io-java libcommons-io-java 2.11.0-2 install ok installed libcommons-jexl2-java libcommons-jexl2-java 2.1.1-6 install ok installed libcommons-logging-java libcommons-logging-java 1.2-4 install ok installed libcommons-parent-java libcommons-parent-java 56-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-2 install ok installed libcurl4:amd64 libcurl4 8.4.0-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-2 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.271 install ok installed libedit2:amd64 libedit2 3.1-20230828-1 install ok installed liberror-prone-java liberror-prone-java 2.18.0-1 install ok installed libevent-core-2.1-7:amd64 libevent-core-2.1-7 2.1.12-stable-8 install ok installed libevent-pthreads-2.1-7:amd64 libevent-pthreads-2.1-7 2.1.12-stable-8 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2+b1 install ok installed libfabric1:amd64 libfabric1 1.17.0-3 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libfido2-1:amd64 libfido2-1 1.13.0-1+b1 install ok installed libfmt9:amd64 libfmt9 9.1.0+ds1-2 install ok installed libgcc-s1:amd64 libgcc-s1 13.2.0-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.2-3 install ok installed libgenomicsdb-java libgenomicsdb-java 1.5.0-2 install ok installed libgenomicsdb-jni libgenomicsdb-jni 1.5.0-2 install ok installed libgenomicsdb0 libgenomicsdb0 1.5.0-2 install ok installed libgetopt-java libgetopt-java 1.0.14+dfsg-6 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2 install ok installed libgnutls30:amd64 libgnutls30 3.8.1-4+b1 install ok installed libgomp1:amd64 libgomp1 13.2.0-6 install ok installed libgoogle-gson-java libgoogle-gson-java 2.10.1-1 install ok installed libgpg-error0:amd64 libgpg-error0 1.47-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.20.1-5 install ok installed libguava-java libguava-java 32.0.1-1 install ok installed libhogweed6:amd64 libhogweed6 3.9.1-2 install ok installed libhtsjdk-java libhtsjdk-java 3.0.5+dfsg-1 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 2.9.3-1 install ok installed libhwloc15:amd64 libhwloc15 2.9.3-1 install ok installed libibverbs1:amd64 libibverbs1 48.0-1 install ok installed libicu72:amd64 libicu72 72.1-4 install ok installed libidn2-0:amd64 libidn2-0 2.3.4-1+b1 install ok installed libjson-simple-java libjson-simple-java 2.3.0-1 install ok installed libjsr305-java libjsr305-java 0.1~+svn49-11 install ok installed libk5crypto3:amd64 libk5crypto3 1.20.1-5 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.20.1-5 install ok installed libkrb5support0:amd64 libkrb5support0 1.20.1-5 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.13+dfsg-5 install ok installed liblightcouch-java liblightcouch-java 0.2.0-1 install ok installed liblog4j2-java liblog4j2-java 2.19.0-2 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.4-0.1 install ok installed libmbedcrypto7:amd64 libmbedcrypto7 2.28.5-1 install ok installed libmbedtls14:amd64 libmbedtls14 2.28.5-1 install ok installed libmbedx509-1:amd64 libmbedx509-1 2.28.5-1 install ok installed libmd0:amd64 libmd0 1.1.0-1 install ok installed libmjson-java libmjson-java 1.4.0-3 install ok installed libmongodb-java libmongodb-java 3.6.3-2 install ok installed libmount1:amd64 libmount1 2.39.2-5 install ok installed libmunge2:amd64 libmunge2 0.5.15-3 install ok installed libmuparserx4.0.11:amd64 libmuparserx4.0.11 4.0.11-2 install ok installed libncbi-ngs3:amd64 libncbi-ngs3 3.0.3+dfsg-6 install ok installed libncbi-vdb3:amd64 libncbi-vdb3 3.0.2+dfsg-2 install ok installed libnettle8:amd64 libnettle8 3.9.1-2 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.57.0-1 install ok installed libngs-java:amd64 libngs-java 3.0.3+dfsg-6 install ok installed libngs-jni:amd64 libngs-jni 3.0.3+dfsg-6 install ok installed libnl-3-200:amd64 libnl-3-200 3.7.0-0.2+b1 install ok installed libnl-route-3-200:amd64 libnl-route-3-200 3.7.0-0.2+b1 install ok installed libnuma1:amd64 libnuma1 2.0.16-1 install ok installed libopenmpi3:amd64 libopenmpi3 4.1.6-1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.0-5 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-9.1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-9.1 install ok installed libpam-runtime libpam-runtime 1.5.2-9.1 install ok installed libpam0g:amd64 libpam0g 1.5.2-9.1 install ok installed libpciaccess0:amd64 libpciaccess0 0.17-2 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4 install ok installed libpmix2:amd64 libpmix2 5.0.1-2 install ok installed libprotobuf-java libprotobuf-java 3.21.12-7 install ok installed libprotobuf-java-format-java libprotobuf-java-format-java 1.3-1.1 install ok installed libprotobuf32:amd64 libprotobuf32 3.21.12-7 install ok installed libpsl5:amd64 libpsl5 0.21.2-1+b1 install ok installed libpsm-infinipath1 libpsm-infinipath1 3.3+20.604758e7-6.2 install ok installed libpsm2-2 libpsm2-2 11.2.185-2 install ok installed librdmacm1:amd64 librdmacm1 48.0-1 install ok installed librhino-java librhino-java 1.7.14-2.1 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b2 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-3 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-3 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-2 install ok installed libselinux1:amd64 libselinux1 3.5-1 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1 install ok installed libsepol2:amd64 libsepol2 3.5-1 install ok installed libslf4j-java libslf4j-java 1.7.32-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.39.2-5 install ok installed libsnappy-java libsnappy-java 1.1.10.5-1 install ok installed libsnappy-jni libsnappy-jni 1.1.10.5-1 install ok installed libsnappy1v5:amd64 libsnappy1v5 1.1.10-1 install ok installed libss2:amd64 libss2 1.47.0-2+b1 install ok installed libssh2-1:amd64 libssh2-1 1.11.0-2 install ok installed libssl3:amd64 libssl3 3.0.12-1 install ok installed libstdc++6:amd64 libstdc++6 13.2.0-6 install ok installed libsystemd0:amd64 libsystemd0 254.5-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3 install ok installed libtinfo6:amd64 libtinfo6 6.4+20231016-1 install ok installed libucx0:amd64 libucx0 1.15.0-1 install ok installed libudev1:amd64 libudev1 254.5-1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libunistring5:amd64 libunistring5 1.1-2 install ok installed libuuid1:amd64 libuuid1 2.39.2-5 install ok installed libx11-6:amd64 libx11-6 2:1.8.7-1 install ok installed libx11-data libx11-data 2:1.8.7-1 install ok installed libxau6:amd64 libxau6 1:1.0.9-1 install ok installed libxcb1:amd64 libxcb1 1.15-1 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b1 install ok installed libxml2:amd64 libxml2 2.9.14+dfsg-1.3 install ok installed libxnvctrl0:amd64 libxnvctrl0 525.125.06-1 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-2 install ok installed login login 1:4.13+dfsg1-3 install ok installed logsave logsave 1.47.0-2+b1 install ok installed mawk mawk 1.3.4.20230808-1 install ok installed mount mount 2.39.2-5 install ok installed ncbi-vdb-data ncbi-vdb-data 3.0.2+dfsg-2 install ok installed ncurses-base ncurses-base 6.4+20231016-1 install ok installed ncurses-bin ncurses-bin 6.4+20231016-1 install ok installed ocl-icd-libopencl1:amd64 ocl-icd-libopencl1 2.3.2-1 install ok installed openmpi-bin openmpi-bin 4.1.6-1 install ok installed openmpi-common openmpi-common 4.1.6-1 install ok installed openssh-client openssh-client 1:9.4p1-1 install ok installed passwd passwd 1:4.13+dfsg1-3 install ok installed perl-base perl-base 5.36.0-9 install ok installed sed sed 4.9-1 install ok installed sysvinit-utils sysvinit-utils 3.08-3 install ok installed tar tar 1.34+dfsg-1.2 install ok installed tzdata tzdata 2023c-10 install ok installed usr-is-merged usr-is-merged 38 install ok installed util-linux util-linux 2.39.2-5 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-3 0m28.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m28.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'apt-get', 'remove', 'adduser', 'gcc-12-base:amd64', 'ibverbs-providers:amd64', 'libapache-pom-java', 'libatinject-jsr330-api-java', 'libatomic1:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcbor0.10:amd64', 'libcbor0.8:amd64', 'libcommons-codec-java', 'libcommons-compress-java', 'libcommons-io-java', 'libcommons-jexl2-java', 'libcommons-logging-java', 'libcommons-parent-java', 'libcurl4:amd64', 'libedit2:amd64', 'liberror-prone-java', 'libevent-core-2.1-7:amd64', 'libevent-pthreads-2.1-7:amd64', 'libfabric1:amd64', 'libfido2-1:amd64', 'libfmt9:amd64', 'libgenomicsdb-jni', 'libgenomicsdb0', 'libgetopt-java', 'libgomp1:amd64', 'libgoogle-gson-java', 'libgssapi-krb5-2:amd64', 'libguava-java', 'libhtsjdk-java', 'libhttpclient-java', 'libhttpcore-java', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibverbs1:amd64', 'libicu72:amd64', 'libjson-simple-java', 'libjsr305-java', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libldap-2.5-0:amd64', 'liblightcouch-java', 'liblog4j2-java', 'libmbedcrypto7:amd64', 'libmbedtls14:amd64', 'libmbedx509-1:amd64', 'libmjson-java', 'libmongodb-java', 'libmunge2:amd64', 'libmuparserx4.0.11:amd64', 'libncbi-ngs3:amd64', 'libncbi-vdb3:amd64', 'libnghttp2-14:amd64', 'libngs-java:amd64', 'libngs-jni:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnuma1:amd64', 'libopenmpi3:amd64', 'libpciaccess0:amd64', 'libpmix2:amd64', 'libprotobuf-java', 'libprotobuf-java-format-java', 'libprotobuf32:amd64', 'libpsl5:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'librdmacm1:amd64', 'librhino-java', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libslf4j-java', 'libsnappy-java', 'libsnappy-jni', 'libsnappy1v5:amd64', 'libssh2-1:amd64', 'libssl3:amd64', 'libucx0:amd64', 'libunistring2:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxml2:amd64', 'libxnvctrl0:amd64', 'ncbi-vdb-data', 'ocl-icd-libopencl1:amd64', 'openmpi-bin', 'openmpi-common', 'openssh-client', 'libgenomicsdb-java'] 0m29.6s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: adduser gcc-12-base ibverbs-providers libapache-pom-java libatinject-jsr330-api-java libatomic1 libbrotli1 libbsd0 libcbor0.10 libcbor0.8 libcommons-codec-java libcommons-compress-java libcommons-io-java libcommons-jexl2-java libcommons-logging-java libcommons-parent-java libcurl4 libedit2 liberror-prone-java libevent-core-2.1-7 libevent-pthreads-2.1-7 libfabric1 libfido2-1 libfmt9 libgenomicsdb-java libgenomicsdb-jni libgenomicsdb0 libgetopt-java libgomp1 libgoogle-gson-java libgssapi-krb5-2 libguava-java libhtsjdk-java libhttpclient-java libhttpcore-java libhwloc-plugins libhwloc15 libibverbs1 libicu72 libjson-simple-java libjsr305-java libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.5-0 liblightcouch-java liblog4j2-java libmbedcrypto7 libmbedtls14 libmbedx509-1 libmjson-java libmongodb-java libmunge2 libmuparserx4.0.11 libncbi-ngs3 libncbi-vdb3 libnghttp2-14 libngs-java libngs-jni libnl-3-200 libnl-route-3-200 libnuma1 libopenmpi3 libpciaccess0 libpmix2 libprotobuf-java libprotobuf-java-format-java libprotobuf32 libpsl5 libpsm-infinipath1 libpsm2-2 librdmacm1 librhino-java librtmp1 libsasl2-2 libsasl2-modules-db libslf4j-java libsnappy-java libsnappy-jni libsnappy1v5 libssh2-1 libssl3 libucx0 libunistring2 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 ncbi-vdb-data ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client 0 upgraded, 0 newly installed, 98 to remove and 0 not upgraded. After this operation, 127 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 ... 7342 files and directories currently installed.) Removing libgenomicsdb-java (1.5.0-2) ... Removing libgenomicsdb-jni (1.5.0-2) ... Removing libgenomicsdb0 (1.5.0-2) ... Removing openmpi-bin (4.1.6-1) ... Removing libopenmpi3:amd64 (4.1.6-1) ... Removing libucx0:amd64 (1.15.0-1) ... Removing libfabric1:amd64 (1.17.0-3) ... Removing librdmacm1:amd64 (48.0-1) ... Removing openssh-client (1:9.4p1-1) ... Removing gcc-12-base:amd64 (12.3.0-11) ... Removing ibverbs-providers:amd64 (48.0-1) ... Removing libhtsjdk-java (3.0.5+dfsg-1) ... 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-logging-java (1.2-4) ... Removing libcommons-compress-java (1.24.0-1) ... Removing libprotobuf-java (3.21.12-7) ... Removing libatomic1:amd64 (13.2.0-6) ... Removing libcurl4:amd64 (8.4.0-2) ... Removing libbrotli1:amd64 (1.0.9-2+b6) ... Removing libpmix2:amd64 (5.0.1-2) ... Removing libhwloc-plugins:amd64 (2.9.3-1) ... Removing libxnvctrl0:amd64 (525.125.06-1) ... Removing libxext6:amd64 (2:1.3.4-1+b1) ... Removing libx11-6:amd64 (2:1.8.7-1) ... Removing libxcb1:amd64 (1.15-1) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libedit2:amd64 (3.1-20230828-1) ... Removing libbsd0:amd64 (0.11.7-4) ... Removing libfido2-1:amd64 (1.13.0-1+b1) ... Removing libcbor0.10:amd64 (0.10.2-1.1) ... Removing libcbor0.8:amd64 (0.8.0-2+b1) ... Removing libcommons-codec-java (1.15-1) ... Removing libcommons-io-java (2.11.0-2) ... Removing libevent-pthreads-2.1-7:amd64 (2.1.12-stable-8) ... Removing libevent-core-2.1-7:amd64 (2.1.12-stable-8) ... Removing libfmt9:amd64 (9.1.0+ds1-2) ... Removing libgetopt-java (1.0.14+dfsg-6) ... Removing libgomp1:amd64 (13.2.0-6) ... Removing libgoogle-gson-java (2.10.1-1) ... Removing libgssapi-krb5-2:amd64 (1.20.1-5) ... Removing libhttpcore-java (4.4.16-1) ... Removing libhwloc15:amd64 (2.9.3-1) ... Removing libxml2:amd64 (2.9.14+dfsg-1.3) ... Removing libicu72:amd64 (72.1-4) ... Removing libjson-simple-java (2.3.0-1) ... Removing libkrb5-3:amd64 (1.20.1-5) ... Removing libk5crypto3:amd64 (1.20.1-5) ... Removing libkeyutils1:amd64 (1.6.3-2) ... Removing libkrb5support0:amd64 (1.20.1-5) ... Removing libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Removing libngs-java:amd64 (3.0.3+dfsg-6) ... Removing libngs-jni:amd64 (3.0.3+dfsg-6) ... Removing libncbi-ngs3:amd64 (3.0.3+dfsg-6) ... Removing libncbi-vdb3:amd64 (3.0.2+dfsg-2) ... Removing libmbedtls14:amd64 (2.28.5-1) ... Removing libmbedx509-1:amd64 (2.28.5-1) ... Removing libmbedcrypto7:amd64 (2.28.5-1) ... Removing libmjson-java (1.4.0-3) ... Removing libmongodb-java (3.6.3-2) ... Removing libmunge2:amd64 (0.5.15-3) ... Removing libmuparserx4.0.11:amd64 (4.0.11-2) ... Removing libnghttp2-14:amd64 (1.57.0-1) ... Removing libpsm2-2 (11.2.185-2) ... Removing libnuma1:amd64 (2.0.16-1) ... Removing libpciaccess0:amd64 (0.17-2) ... Removing libprotobuf-java-format-java (1.3-1.1) ... Removing libprotobuf32:amd64 (3.21.12-7) ... Removing libpsl5:amd64 (0.21.2-1+b1) ... Removing libpsm-infinipath1 (3.3+20.604758e7-6.2) ... update-alternatives: warning: alternative /usr/lib/libpsm1/libpsm_infinipath.so.1.16 (part of link group libpsm_infinipath.so.1) doesn't exist; removing from list of alternatives update-alternatives: warning: /etc/alternatives/libpsm_infinipath.so.1 is dangling; it will be updated with best choice Removing librhino-java (1.7.14-2.1) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-3) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-3) ... Removing libslf4j-java (1.7.32-1) ... Removing libsnappy-java (1.1.10.5-1) ... Removing libsnappy-jni (1.1.10.5-1) ... Removing libsnappy1v5:amd64 (1.1.10-1) ... Removing libssh2-1:amd64 (1.11.0-2) ... Removing libssl3:amd64 (3.0.12-1) ... Removing libunistring2:amd64 (1.0-2) ... Removing libx11-data (2:1.8.7-1) ... Removing libxau6:amd64 (1:1.0.9-1) ... Removing ncbi-vdb-data (3.0.2+dfsg-2) ... Removing ocl-icd-libopencl1:amd64 (2.3.2-1) ... Removing openmpi-common (4.1.6-1) ... Removing libibverbs1:amd64 (48.0-1) ... Removing adduser (3.137) ... Removing libcommons-parent-java (56-1) ... Removing libapache-pom-java (29-2) ... Removing libnl-route-3-200:amd64 (3.7.0-0.2+b1) ... Removing libnl-3-200:amd64 (3.7.0-0.2+b1) ... Removing liberror-prone-java (2.18.0-1) ... Removing libguava-java (32.0.1-1) ... Removing libatinject-jsr330-api-java (1.0+ds1-5) ... Removing libjsr305-java (0.1~+svn49-11) ... Processing triggers for libc-bin (2.37-12) ... 0m29.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'apt-get', 'remove', 'adduser', 'gcc-12-base:amd64', 'ibverbs-providers:amd64', 'libapache-pom-java', 'libatinject-jsr330-api-java', 'libatomic1:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcbor0.10:amd64', 'libcbor0.8:amd64', 'libcommons-codec-java', 'libcommons-compress-java', 'libcommons-io-java', 'libcommons-jexl2-java', 'libcommons-logging-java', 'libcommons-parent-java', 'libcurl4:amd64', 'libedit2:amd64', 'liberror-prone-java', 'libevent-core-2.1-7:amd64', 'libevent-pthreads-2.1-7:amd64', 'libfabric1:amd64', 'libfido2-1:amd64', 'libfmt9:amd64', 'libgenomicsdb-jni', 'libgenomicsdb0', 'libgetopt-java', 'libgomp1:amd64', 'libgoogle-gson-java', 'libgssapi-krb5-2:amd64', 'libguava-java', 'libhtsjdk-java', 'libhttpclient-java', 'libhttpcore-java', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibverbs1:amd64', 'libicu72:amd64', 'libjson-simple-java', 'libjsr305-java', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libldap-2.5-0:amd64', 'liblightcouch-java', 'liblog4j2-java', 'libmbedcrypto7:amd64', 'libmbedtls14:amd64', 'libmbedx509-1:amd64', 'libmjson-java', 'libmongodb-java', 'libmunge2:amd64', 'libmuparserx4.0.11:amd64', 'libncbi-ngs3:amd64', 'libncbi-vdb3:amd64', 'libnghttp2-14:amd64', 'libngs-java:amd64', 'libngs-jni:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnuma1:amd64', 'libopenmpi3:amd64', 'libpciaccess0:amd64', 'libpmix2:amd64', 'libprotobuf-java', 'libprotobuf-java-format-java', 'libprotobuf32:amd64', 'libpsl5:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'librdmacm1:amd64', 'librhino-java', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libslf4j-java', 'libsnappy-java', 'libsnappy-jni', 'libsnappy1v5:amd64', 'libssh2-1:amd64', 'libssl3:amd64', 'libucx0:amd64', 'libunistring2:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxml2:amd64', 'libxnvctrl0:amd64', 'ncbi-vdb-data', 'ocl-icd-libopencl1:amd64', 'openmpi-bin', 'openmpi-common', 'openssh-client', 'libgenomicsdb-java'] 0m29.6s INFO: Running scripts post_remove 0m29.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/post_remove_exceptions'] 0m29.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/post_remove_exceptions'] 0m29.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'dpkg', '--purge', 'adduser', 'gcc-12-base:amd64', 'ibverbs-providers:amd64', 'libapache-pom-java', 'libatinject-jsr330-api-java', 'libatomic1:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcbor0.10:amd64', 'libcbor0.8:amd64', 'libcommons-codec-java', 'libcommons-compress-java', 'libcommons-io-java', 'libcommons-jexl2-java', 'libcommons-logging-java', 'libcommons-parent-java', 'libcurl4:amd64', 'libedit2:amd64', 'liberror-prone-java', 'libevent-core-2.1-7:amd64', 'libevent-pthreads-2.1-7:amd64', 'libfabric1:amd64', 'libfido2-1:amd64', 'libfmt9:amd64', 'libgenomicsdb-jni', 'libgenomicsdb0', 'libgetopt-java', 'libgomp1:amd64', 'libgoogle-gson-java', 'libgssapi-krb5-2:amd64', 'libguava-java', 'libhtsjdk-java', 'libhttpclient-java', 'libhttpcore-java', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibverbs1:amd64', 'libicu72:amd64', 'libjson-simple-java', 'libjsr305-java', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libldap-2.5-0:amd64', 'liblightcouch-java', 'liblog4j2-java', 'libmbedcrypto7:amd64', 'libmbedtls14:amd64', 'libmbedx509-1:amd64', 'libmjson-java', 'libmongodb-java', 'libmunge2:amd64', 'libmuparserx4.0.11:amd64', 'libncbi-ngs3:amd64', 'libncbi-vdb3:amd64', 'libnghttp2-14:amd64', 'libngs-java:amd64', 'libngs-jni:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnuma1:amd64', 'libopenmpi3:amd64', 'libpciaccess0:amd64', 'libpmix2:amd64', 'libprotobuf-java', 'libprotobuf-java-format-java', 'libprotobuf32:amd64', 'libpsl5:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'librdmacm1:amd64', 'librhino-java', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libslf4j-java', 'libsnappy-java', 'libsnappy-jni', 'libsnappy1v5:amd64', 'libssh2-1:amd64', 'libssl3:amd64', 'libucx0:amd64', 'libunistring2:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxml2:amd64', 'libxnvctrl0:amd64', 'ncbi-vdb-data', 'ocl-icd-libopencl1:amd64', 'openmpi-bin', 'openmpi-common', 'openssh-client'] 0m29.7s DUMP: (Reading database ... 5226 files and directories currently installed.) Purging configuration files for adduser (3.137) ... dpkg: warning: ignoring request to remove gcc-12-base which isn't installed Purging configuration files for ibverbs-providers:amd64 (48.0-1) ... 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 libatomic1 which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libbsd0 which isn't installed dpkg: warning: ignoring request to remove libcbor0.10 which isn't installed dpkg: warning: ignoring request to remove libcbor0.8 which isn't installed dpkg: warning: ignoring request to remove libcommons-codec-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-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 libcurl4 which isn't installed dpkg: warning: ignoring request to remove libedit2 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-2.1-7 which isn't installed dpkg: warning: ignoring request to remove libevent-pthreads-2.1-7 which isn't installed dpkg: warning: ignoring request to remove libfabric1 which isn't installed dpkg: warning: ignoring request to remove libfido2-1 which isn't installed dpkg: warning: ignoring request to remove libfmt9 which isn't installed dpkg: warning: ignoring request to remove libgenomicsdb-jni which isn't installed dpkg: warning: ignoring request to remove libgenomicsdb0 which isn't installed dpkg: warning: ignoring request to remove libgetopt-java 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 (1.20.1-5) ... dpkg: warning: ignoring request to remove libguava-java 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 libibverbs1 which isn't installed dpkg: warning: ignoring request to remove libicu72 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 libldap-2.5-0 which isn't installed dpkg: warning: ignoring request to remove liblightcouch-java which isn't installed dpkg: warning: ignoring request to remove liblog4j2-java which isn't installed dpkg: warning: ignoring request to remove libmbedcrypto7 which isn't installed dpkg: warning: ignoring request to remove libmbedtls14 which isn't installed dpkg: warning: ignoring request to remove libmbedx509-1 which isn't installed dpkg: warning: ignoring request to remove libmjson-java 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 libmuparserx4.0.11 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 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 (3.7.0-0.2+b1) ... dpkg: warning: ignoring request to remove libnl-route-3-200 which isn't installed dpkg: warning: ignoring request to remove libnuma1 which isn't installed dpkg: warning: ignoring request to remove libopenmpi3 which isn't installed dpkg: warning: ignoring request to remove libpciaccess0 which isn't installed dpkg: warning: ignoring request to remove libpmix2 which isn't installed dpkg: warning: ignoring request to remove libprotobuf-java which isn't installed dpkg: warning: ignoring request to remove libprotobuf-java-format-java which isn't installed dpkg: warning: ignoring request to remove libprotobuf32 which isn't installed dpkg: warning: ignoring request to remove libpsl5 which isn't installed Purging configuration files for libpsm-infinipath1 (3.3+20.604758e7-6.2) ... dpkg: warning: ignoring request to remove libpsm2-2 which isn't installed dpkg: warning: ignoring request to remove librdmacm1 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 libssh2-1 which isn't installed dpkg: warning: ignoring request to remove libssl3 which isn't installed dpkg: warning: ignoring request to remove libucx0 which isn't installed dpkg: warning: ignoring request to remove libunistring2 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 libxext6 which isn't installed dpkg: warning: ignoring request to remove libxml2 which isn't installed dpkg: warning: ignoring request to remove libxnvctrl0 which isn't installed dpkg: warning: ignoring request to remove ncbi-vdb-data which isn't installed dpkg: warning: ignoring request to remove ocl-icd-libopencl1 which isn't installed Purging configuration files for openmpi-bin (4.1.6-1) ... dpkg: warning: ignoring request to remove openmpi-common which isn't installed Purging configuration files for openssh-client (1:9.4p1-1) ... 0m29.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'dpkg', '--purge', 'adduser', 'gcc-12-base:amd64', 'ibverbs-providers:amd64', 'libapache-pom-java', 'libatinject-jsr330-api-java', 'libatomic1:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcbor0.10:amd64', 'libcbor0.8:amd64', 'libcommons-codec-java', 'libcommons-compress-java', 'libcommons-io-java', 'libcommons-jexl2-java', 'libcommons-logging-java', 'libcommons-parent-java', 'libcurl4:amd64', 'libedit2:amd64', 'liberror-prone-java', 'libevent-core-2.1-7:amd64', 'libevent-pthreads-2.1-7:amd64', 'libfabric1:amd64', 'libfido2-1:amd64', 'libfmt9:amd64', 'libgenomicsdb-jni', 'libgenomicsdb0', 'libgetopt-java', 'libgomp1:amd64', 'libgoogle-gson-java', 'libgssapi-krb5-2:amd64', 'libguava-java', 'libhtsjdk-java', 'libhttpclient-java', 'libhttpcore-java', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibverbs1:amd64', 'libicu72:amd64', 'libjson-simple-java', 'libjsr305-java', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libldap-2.5-0:amd64', 'liblightcouch-java', 'liblog4j2-java', 'libmbedcrypto7:amd64', 'libmbedtls14:amd64', 'libmbedx509-1:amd64', 'libmjson-java', 'libmongodb-java', 'libmunge2:amd64', 'libmuparserx4.0.11:amd64', 'libncbi-ngs3:amd64', 'libncbi-vdb3:amd64', 'libnghttp2-14:amd64', 'libngs-java:amd64', 'libngs-jni:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnuma1:amd64', 'libopenmpi3:amd64', 'libpciaccess0:amd64', 'libpmix2:amd64', 'libprotobuf-java', 'libprotobuf-java-format-java', 'libprotobuf32:amd64', 'libpsl5:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'librdmacm1:amd64', 'librhino-java', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libslf4j-java', 'libsnappy-java', 'libsnappy-jni', 'libsnappy1v5:amd64', 'libssh2-1:amd64', 'libssl3:amd64', 'libucx0:amd64', 'libunistring2:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxml2:amd64', 'libxnvctrl0:amd64', 'ncbi-vdb-data', 'ocl-icd-libopencl1:amd64', 'openmpi-bin', 'openmpi-common', 'openssh-client'] 0m29.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'dpkg', '--purge', 'libgenomicsdb-java'] 0m29.7s DUMP: dpkg: warning: ignoring request to remove libgenomicsdb-java which isn't installed 0m29.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'dpkg', '--purge', 'libgenomicsdb-java'] 0m29.7s INFO: Running scripts post_purge 0m29.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/post_purge_exceptions'] 0m29.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/post_purge_exceptions'] 0m29.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'dpkg', '--purge', '--pending'] 0m29.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'dpkg', '--purge', '--pending'] 0m29.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'dpkg', '--remove', '--pending'] 0m29.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'dpkg', '--remove', '--pending'] 0m29.7s INFO: Running scripts post_test 0m29.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/post_test_exceptions'] 0m29.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'tmp/scripts/post_test_exceptions'] 0m29.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6'] 0m30.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6'] 0m30.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'dpkg-divert', '--list'] 0m30.0s DUMP: local diversion of /bin/sync to /bin/sync.distrib local diversion of /home to /home.distrib 0m30.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'dpkg-divert', '--list'] 0m30.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'apt-get', 'clean'] 0m30.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6', 'apt-get', 'clean'] 0m30.1s DEBUG: Recording chroot state 0m30.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6/dev/shm'] 0m31.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6/dev/shm'] 0m31.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6/dev/console'] 0m31.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6/dev/console'] 0m31.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6/dev/ptmx'] 0m31.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6/dev/ptmx'] 0m31.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6/dev/pts'] 0m31.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6/dev/pts'] 0m31.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6/proc'] 0m31.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6/proc'] 0m31.1s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6'] 0m31.2s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpk8ek2be6'] 0m31.2s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpk8ek2be6 0m31.2s INFO: PASS: Upgrading between Debian distributions. 0m31.2s INFO: PASS: All tests. 0m31.2s INFO: piuparts run ends. ret=0 End: 2023-11-04 03:23:32 GMT