Start: 2024-04-19 00:01:21 GMT [bullseye] Package: sra-toolkit Source: sra-sdk Version: 2.10.9+dfsg-2 Installed-Size: 10056 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.29), libfuse2 (>= 2.6), libkdf5-2 (>= 2.10.9+dfsg), libmagic1 (>= 5.12), libncbi-vdb2 (>= 2.10.9+dfsg), libncbi-wvdb2 (>= 2.10.9+dfsg), libstdc++6 (>= 5.2), libxml2 (>= 2.7.4), zlib1g (>= 1:1.2.2) Recommends: med-config (>= 2.1) Description: utilities for the NCBI Sequence Read Archive Homepage: https://github.com/ncbi/sra-tools/ Description-md5: 1a61cd8ef6f417d5f86c6c13697e7a05 Section: science Priority: optional Filename: pool/main/s/sra-sdk/sra-toolkit_2.10.9+dfsg-2_amd64.deb Size: 5177976 MD5sum: 13337ede4e24d402dbe99d24a4be45f2 SHA256: 569481465c3305b19472ffedcdaa0a8c7dc129311231ea12856ec3607b0a7b95 [bullseye-next] Package: sra-toolkit Source: sra-sdk Version: 2.10.9+dfsg-2 Installed-Size: 10056 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.29), libfuse2 (>= 2.6), libkdf5-2 (>= 2.10.9+dfsg), libmagic1 (>= 5.12), libncbi-vdb2 (>= 2.10.9+dfsg), libncbi-wvdb2 (>= 2.10.9+dfsg), libstdc++6 (>= 5.2), libxml2 (>= 2.7.4), zlib1g (>= 1:1.2.2) Recommends: med-config (>= 2.1) Description: utilities for the NCBI Sequence Read Archive Homepage: https://github.com/ncbi/sra-tools/ Description-md5: 1a61cd8ef6f417d5f86c6c13697e7a05 Section: science Priority: optional Filename: pool/main/s/sra-sdk/sra-toolkit_2.10.9+dfsg-2_amd64.deb Size: 5177976 MD5sum: 13337ede4e24d402dbe99d24a4be45f2 SHA256: 569481465c3305b19472ffedcdaa0a8c7dc129311231ea12856ec3607b0a7b95 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --warn-on-usr-move fail --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz -d bullseye -d bullseye-next -B /srv/piuparts.debian.org/slave/refchroot/bullseye2next/reference-chroot-metadata.dat --apt sra-toolkit=2.10.9+dfsg-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 1.4.1~202403190841~1.4-4-g85045c69 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --warn-on-usr-move fail --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz -d bullseye -d bullseye-next -B /srv/piuparts.debian.org/slave/refchroot/bullseye2next/reference-chroot-metadata.dat --apt sra-toolkit=2.10.9+dfsg-2 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpcxo_2y5f 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpcxo_2y5f 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f/proc'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f/proc'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f/dev/pts'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f/dev/pts'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f/dev/ptmx'] 0m0.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f/dev/ptmx'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f/dev/console'] 0m0.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f/dev/console'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f/dev/shm'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f/dev/shm'] 0m0.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ bullseye main 0m0.5s DEBUG: Created policy-rc.d and chmodded it. 0m0.5s DEBUG: Created resolv.conf. 0m0.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpcxo_2y5f/tmp/scripts/ 0m0.5s INFO: Running scripts post_chroot_unpack 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'apt-get', 'update'] 0m1.6s DUMP: Hit:1 http://deb.debian.org/debian bullseye InRelease Reading package lists... 0m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'apt-get', 'update'] 0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'apt-get', '-yf', 'dist-upgrade'] 0m2.1s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'apt-get', '-yf', 'dist-upgrade'] 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.4s DUMP: 29fcf27583012b383113cec2bf757015 - 0m2.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.4s INFO: Running scripts post_setup 0m2.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/post_setup_dummy_users'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/post_setup_dummy_users'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/post_setup_forbid_home'] 0m3.5s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/post_setup_forbid_home'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.5s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/post_setup_minimize'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/post_setup_minimize'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/post_setup_zz_backports'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/post_setup_zz_backports'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.5s DUMP: install ok installed adduser adduser 3.118+deb11u1 install ok installed apt apt 2.2.4 install ok installed base-files base-files 11.1+deb11u9 install ok installed base-passwd base-passwd 3.5.51 install ok installed bash bash 5.1-2+deb11u1 install ok installed bsdutils bsdutils 1:2.36.1-8+deb11u1 install ok installed coreutils coreutils 8.32-4+b1 install ok installed dash dash 0.5.11+git20200708+dd9ef66-5 install ok installed debconf debconf 1.5.77 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1+deb11u1 install ok installed debianutils debianutils 4.11.2 install ok installed diffutils diffutils 1:3.7-5 install ok installed dpkg dpkg 1.20.13 install ok installed e2fsprogs e2fsprogs 1.46.2-2 install ok installed findutils findutils 4.8.0-1 install ok installed gcc-10-base:amd64 gcc-10-base 10.2.1-6 install ok installed gcc-9-base:amd64 gcc-9-base 9.3.0-22 install ok installed gpgv gpgv 2.2.27-2+deb11u2 install ok installed grep grep 3.6-1+deb11u1 install ok installed gzip gzip 1.10-4+deb11u1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.60 install ok installed libacl1:amd64 libacl1 2.2.53-10 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.2.4 install ok installed libattr1:amd64 libattr1 1:2.4.48-6 install ok installed libaudit-common libaudit-common 1:3.0-2 install ok installed libaudit1:amd64 libaudit1 1:3.0-2 install ok installed libblkid1:amd64 libblkid1 2.36.1-8+deb11u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4 install ok installed libc-bin libc-bin 2.31-13+deb11u8 install ok installed libc6:amd64 libc6 2.31-13+deb11u8 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2+b1 install ok installed libcom-err2:amd64 libcom-err2 1.46.2-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.18-4 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.8 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.260 install ok installed libext2fs2:amd64 libext2fs2 1.46.2-2 install ok installed libffi7:amd64 libffi7 3.3-6 install ok installed libgcc-s1:amd64 libgcc-s1 10.2.1-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.7-6 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg-1+deb11u1 install ok installed libgnutls30:amd64 libgnutls30 3.7.1-5+deb11u4 install ok installed libgpg-error0:amd64 libgpg-error0 1.38-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.18.3-6+deb11u4 install ok installed libhogweed6:amd64 libhogweed6 3.7.3-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.0-5 install ok installed libk5crypto3:amd64 libk5crypto3 1.18.3-6+deb11u4 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.18.3-6+deb11u4 install ok installed libkrb5support0:amd64 libkrb5support0 1.18.3-6+deb11u4 install ok installed liblz4-1:amd64 liblz4-1 1.9.3-2 install ok installed liblzma5:amd64 liblzma5 5.2.5-2.1~deb11u1 install ok installed libmount1:amd64 libmount1 2.36.1-8+deb11u1 install ok installed libnettle8:amd64 libnettle8 3.7.3-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.22-1 install ok installed libpam-modules:amd64 libpam-modules 1.4.0-9+deb11u1 install ok installed libpam-modules-bin libpam-modules-bin 1.4.0-9+deb11u1 install ok installed libpam-runtime libpam-runtime 1.4.0-9+deb11u1 install ok installed libpam0g:amd64 libpam0g 1.4.0-9+deb11u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.36-2+deb11u1 install ok installed libpcre3:amd64 libpcre3 2:8.39-13 install ok installed libseccomp2:amd64 libseccomp2 2.5.1-1+deb11u1 install ok installed libselinux1:amd64 libselinux1 3.1-3 install ok installed libsemanage-common libsemanage-common 3.1-1 install ok installed libsemanage1:amd64 libsemanage1 3.1-1+b2 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.36.1-8+deb11u1 install ok installed libss2:amd64 libss2 1.46.2-2 install ok installed libssl1.1:amd64 libssl1.1 1.1.1w-0+deb11u1 install ok installed libstdc++6:amd64 libstdc++6 10.2.1-6 install ok installed libsystemd0:amd64 libsystemd0 247.3-7+deb11u4 install ok installed libtasn1-6:amd64 libtasn1-6 4.16.0-2+deb11u1 install ok installed libtinfo6:amd64 libtinfo6 6.2+20201114-2+deb11u2 install ok installed libtirpc-common libtirpc-common 1.3.1-1+deb11u1 install ok installed libtirpc3:amd64 libtirpc3 1.3.1-1+deb11u1 install ok installed libudev1:amd64 libudev1 247.3-7+deb11u4 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed libuuid1:amd64 libuuid1 2.36.1-8+deb11u1 install ok installed libxxhash0:amd64 libxxhash0 0.8.0-2 install ok installed libzstd1:amd64 libzstd1 1.4.8+dfsg-2.1 install ok installed login login 1:4.8.1-1 install ok installed logsave logsave 1.46.2-2 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.4.20200120-2 install ok installed mount mount 2.36.1-8+deb11u1 install ok installed ncurses-base ncurses-base 6.2+20201114-2+deb11u2 install ok installed ncurses-bin ncurses-bin 6.2+20201114-2+deb11u2 install ok installed passwd passwd 1:4.8.1-1 install ok installed perl-base perl-base 5.32.1-4+deb11u3 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.96-7+deb11u1 install ok installed tar tar 1.34+dfsg-1+deb11u1 install ok installed tzdata tzdata 2024a-0+deb11u1 install ok installed util-linux util-linux 2.36.1-8+deb11u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2+deb11u2 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.5s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/bullseye2next/reference-chroot-metadata.dat 0m3.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f'] 0m4.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f'] 0m4.1s INFO: Running scripts is_testable 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/is_testable_uninstallable'] 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/is_testable_uninstallable'] 0m4.1s INFO: Running scripts pre_test 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_test_exceptions'] 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_test_exceptions'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_test_root_password'] 0m4.1s DUMP: New password: Retype new password: passwd: password updated successfully 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_test_root_password'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'apt-cache', 'show', '--no-all-versions', 'sra-toolkit'] 0m4.3s DUMP: Package: sra-toolkit Source: sra-sdk Version: 2.10.9+dfsg-2 Installed-Size: 10056 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.29), libfuse2 (>= 2.6), libkdf5-2 (>= 2.10.9+dfsg), libmagic1 (>= 5.12), libncbi-vdb2 (>= 2.10.9+dfsg), libncbi-wvdb2 (>= 2.10.9+dfsg), libstdc++6 (>= 5.2), libxml2 (>= 2.7.4), zlib1g (>= 1:1.2.2) Recommends: med-config (>= 2.1) Description-en: utilities for the NCBI Sequence Read Archive Tools for reading the SRA archive, generally by converting individual runs into some commonly used format such as fastq. . The textual dumpers "sra-dump" and "vdb-dump" are provided in this release as an aid in visual inspection. It is likely that their actual output formatting will be changed in the near future to a stricter, more formalized representation[s]. PLEASE DO NOT RELY UPON THE OUTPUT FORMAT SEEN IN THIS RELEASE. . Other tools distributed in this package are: abi-dump, abi-load align-info bam-load cache-mgr cg-load copycat fasterq-dump fastq-dump, fastq-load helicos-load illumina-dump, illumina-load kar kdbmeta latf-load pacbio-load prefetch rcexplain remote-fuser sff-dump, sff-load sra-pileup, sra-sort, sra-stat, srapath srf-load test-sra vdb-config, vdb-copy, vdb-decrypt, vdb-encrypt, vdb-get, vdb-lock, vdb-passwd, vdb-unlock, vdb-validate . The "help" information will be improved in near future releases, and the tool options will become standardized across the set. More documentation will also be provided documentation on the NCBI web site. . Tool options may change in the next release. Version 1 tool options will remain supported wherever possible in order to preserve operation of any existing scripts. Description-md5: 1a61cd8ef6f417d5f86c6c13697e7a05 Homepage: https://github.com/ncbi/sra-tools/ Section: science Priority: optional Filename: pool/main/s/sra-sdk/sra-toolkit_2.10.9+dfsg-2_amd64.deb Size: 5177976 MD5sum: 13337ede4e24d402dbe99d24a4be45f2 SHA256: 569481465c3305b19472ffedcdaa0a8c7dc129311231ea12856ec3607b0a7b95 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'apt-cache', 'show', '--no-all-versions', 'sra-toolkit'] 0m4.3s INFO: apt-cache knows about the following packages: sra-toolkit 0m4.3s INFO: Running scripts pre_install 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_install_database-server'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_install_database-server'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_install_exceptions'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_install_exceptions'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_install_extras'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_install_extras'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'apt-cache', 'policy'] 0m4.4s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.9,o=Debian,a=oldstable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'apt-cache', 'policy'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'apt-cache', 'policy', 'sra-toolkit'] 0m4.5s DUMP: sra-toolkit: Installed: (none) Candidate: 2.10.9+dfsg-2 Version table: 2.10.9+dfsg-2 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'apt-cache', 'policy', 'sra-toolkit'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'apt-get', '-y', 'install', 'sra-toolkit'] 0m8.2s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: libaec0 libfuse2 libhdf5-103-1 libicu67 libkdf5-2 libmagic-mgc libmagic1 libmbedcrypto3 libmbedtls-dev libmbedtls12 libmbedx509-0 libncbi-vdb2 libncbi-wvdb2 libsz2 libxml2 Suggested packages: fuse file libmbedtls-doc Recommended packages: med-config The following NEW packages will be installed: libaec0 libfuse2 libhdf5-103-1 libicu67 libkdf5-2 libmagic-mgc libmagic1 libmbedcrypto3 libmbedtls-dev libmbedtls12 libmbedx509-0 libncbi-vdb2 libncbi-wvdb2 libsz2 libxml2 sra-toolkit 0 upgraded, 16 newly installed, 0 to remove and 0 not upgraded. Need to get 19.7 MB of archives. After this operation, 72.2 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main amd64 libaec0 amd64 1.0.4-1 [20.3 kB] Get:2 http://deb.debian.org/debian bullseye/main amd64 libfuse2 amd64 2.9.9-5 [130 kB] Get:3 http://deb.debian.org/debian bullseye/main amd64 libsz2 amd64 1.0.4-1 [6760 B] Get:4 http://deb.debian.org/debian bullseye/main amd64 libhdf5-103-1 amd64 1.10.6+repack-4+deb11u1 [1189 kB] Get:5 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get:6 http://deb.debian.org/debian bullseye/main amd64 libmbedcrypto3 amd64 2.16.9-0.1 [219 kB] Get:7 http://deb.debian.org/debian bullseye/main amd64 libmbedx509-0 amd64 2.16.9-0.1 [109 kB] Get:8 http://deb.debian.org/debian bullseye/main amd64 libmbedtls12 amd64 2.16.9-0.1 [139 kB] Get:9 http://deb.debian.org/debian bullseye/main amd64 libmbedtls-dev amd64 2.16.9-0.1 [515 kB] Get:10 http://deb.debian.org/debian bullseye/main amd64 libkdf5-2 amd64 2.10.9+dfsg-2 [20.8 kB] Get:11 http://deb.debian.org/debian bullseye/main amd64 libmagic-mgc amd64 1:5.39-3+deb11u1 [273 kB] Get:12 http://deb.debian.org/debian bullseye/main amd64 libmagic1 amd64 1:5.39-3+deb11u1 [128 kB] Get:13 http://deb.debian.org/debian bullseye/main amd64 libxml2 amd64 2.9.10+dfsg-6.7+deb11u4 [693 kB] Get:14 http://deb.debian.org/debian bullseye/main amd64 libncbi-vdb2 amd64 2.10.9+dfsg-2 [1266 kB] Get:15 http://deb.debian.org/debian bullseye/main amd64 libncbi-wvdb2 amd64 2.10.9+dfsg-2 [1159 kB] Get:16 http://deb.debian.org/debian bullseye/main amd64 sra-toolkit amd64 2.10.9+dfsg-2 [5178 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 19.7 MB in 0s (84.2 MB/s) Selecting previously unselected package libaec0: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 ... 6674 files and directories currently installed.) Preparing to unpack .../00-libaec0_1.0.4-1_amd64.deb ... Unpacking libaec0:amd64 (1.0.4-1) ... Selecting previously unselected package libfuse2:amd64. Preparing to unpack .../01-libfuse2_2.9.9-5_amd64.deb ... Unpacking libfuse2:amd64 (2.9.9-5) ... Selecting previously unselected package libsz2:amd64. Preparing to unpack .../02-libsz2_1.0.4-1_amd64.deb ... Unpacking libsz2:amd64 (1.0.4-1) ... Selecting previously unselected package libhdf5-103-1:amd64. Preparing to unpack .../03-libhdf5-103-1_1.10.6+repack-4+deb11u1_amd64.deb ... Unpacking libhdf5-103-1:amd64 (1.10.6+repack-4+deb11u1) ... Selecting previously unselected package libicu67:amd64. Preparing to unpack .../04-libicu67_67.1-7_amd64.deb ... Unpacking libicu67:amd64 (67.1-7) ... Selecting previously unselected package libmbedcrypto3:amd64. Preparing to unpack .../05-libmbedcrypto3_2.16.9-0.1_amd64.deb ... Unpacking libmbedcrypto3:amd64 (2.16.9-0.1) ... Selecting previously unselected package libmbedx509-0:amd64. Preparing to unpack .../06-libmbedx509-0_2.16.9-0.1_amd64.deb ... Unpacking libmbedx509-0:amd64 (2.16.9-0.1) ... Selecting previously unselected package libmbedtls12:amd64. Preparing to unpack .../07-libmbedtls12_2.16.9-0.1_amd64.deb ... Unpacking libmbedtls12:amd64 (2.16.9-0.1) ... Selecting previously unselected package libmbedtls-dev:amd64. Preparing to unpack .../08-libmbedtls-dev_2.16.9-0.1_amd64.deb ... Unpacking libmbedtls-dev:amd64 (2.16.9-0.1) ... Selecting previously unselected package libkdf5-2. Preparing to unpack .../09-libkdf5-2_2.10.9+dfsg-2_amd64.deb ... Unpacking libkdf5-2 (2.10.9+dfsg-2) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../10-libmagic-mgc_1%3a5.39-3+deb11u1_amd64.deb ... Unpacking libmagic-mgc (1:5.39-3+deb11u1) ... Selecting previously unselected package libmagic1:amd64. Preparing to unpack .../11-libmagic1_1%3a5.39-3+deb11u1_amd64.deb ... Unpacking libmagic1:amd64 (1:5.39-3+deb11u1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../12-libxml2_2.9.10+dfsg-6.7+deb11u4_amd64.deb ... Unpacking libxml2:amd64 (2.9.10+dfsg-6.7+deb11u4) ... Selecting previously unselected package libncbi-vdb2. Preparing to unpack .../13-libncbi-vdb2_2.10.9+dfsg-2_amd64.deb ... Unpacking libncbi-vdb2 (2.10.9+dfsg-2) ... Selecting previously unselected package libncbi-wvdb2. Preparing to unpack .../14-libncbi-wvdb2_2.10.9+dfsg-2_amd64.deb ... Unpacking libncbi-wvdb2 (2.10.9+dfsg-2) ... Selecting previously unselected package sra-toolkit. Preparing to unpack .../15-sra-toolkit_2.10.9+dfsg-2_amd64.deb ... Unpacking sra-toolkit (2.10.9+dfsg-2) ... Setting up libicu67:amd64 (67.1-7) ... Setting up libmagic-mgc (1:5.39-3+deb11u1) ... Setting up libmagic1:amd64 (1:5.39-3+deb11u1) ... Setting up libfuse2:amd64 (2.9.9-5) ... Setting up libaec0:amd64 (1.0.4-1) ... Setting up libmbedcrypto3:amd64 (2.16.9-0.1) ... Setting up libxml2:amd64 (2.9.10+dfsg-6.7+deb11u4) ... Setting up libsz2:amd64 (1.0.4-1) ... Setting up libmbedx509-0:amd64 (2.16.9-0.1) ... Setting up libmbedtls12:amd64 (2.16.9-0.1) ... Setting up libmbedtls-dev:amd64 (2.16.9-0.1) ... Setting up libncbi-vdb2 (2.10.9+dfsg-2) ... Setting up libncbi-wvdb2 (2.10.9+dfsg-2) ... Setting up libhdf5-103-1:amd64 (1.10.6+repack-4+deb11u1) ... Setting up libkdf5-2 (2.10.9+dfsg-2) ... Setting up sra-toolkit (2.10.9+dfsg-2) ... Processing triggers for libc-bin (2.31-13+deb11u8) ... 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'apt-get', '-y', 'install', 'sra-toolkit'] 0m8.2s INFO: Running scripts post_install 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/post_install_exceptions'] 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/post_install_exceptions'] 0m8.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f'] 0m8.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f'] 0m8.8s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpcxo_2y5f to bullseye-next 0m8.8s DEBUG: sources.list: deb http://deb.debian.org/debian/ bullseye main deb http://security.debian.org bullseye-security main deb http://deb.debian.org/debian/ bullseye-updates main deb http://deb.debian.org/debian/ bullseye-proposed-updates main 0m8.8s INFO: Running scripts pre_distupgrade 0m8.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_distupgrade_exceptions'] 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_distupgrade_exceptions'] 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'apt-get', 'update'] 0m10.5s DUMP: Hit:1 http://deb.debian.org/debian bullseye InRelease Get:2 http://deb.debian.org/debian bullseye-updates InRelease [44.1 kB] Get:3 http://security.debian.org bullseye-security InRelease [48.4 kB] Get:4 http://deb.debian.org/debian bullseye-proposed-updates InRelease [54.0 kB] Get:5 http://deb.debian.org/debian bullseye-updates/main amd64 Packages [18.8 kB] Get:6 http://deb.debian.org/debian bullseye-updates/main Translation-en [10.9 kB] Get:7 http://security.debian.org bullseye-security/main amd64 Packages [271 kB] Get:8 http://security.debian.org bullseye-security/main Translation-en [175 kB] Get:9 http://deb.debian.org/debian bullseye-proposed-updates/main amd64 Packages [42.8 kB] Get:10 http://deb.debian.org/debian bullseye-proposed-updates/main Translation-en [26.3 kB] Fetched 691 kB in 1s (973 kB/s) Reading package lists... 0m10.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'apt-get', 'update'] 0m10.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'apt-get', '-yf', 'dist-upgrade'] 0m12.3s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: bsdutils libblkid1 libgnutls30 libmount1 libsmartcols1 libuuid1 mount util-linux 8 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 3464 kB of archives. After this operation, 0 B of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye-proposed-updates/main amd64 libgnutls30 amd64 3.7.1-5+deb11u5 [1340 kB] Get:2 http://security.debian.org bullseye-security/main amd64 bsdutils amd64 1:2.36.1-8+deb11u2 [149 kB] Get:3 http://security.debian.org bullseye-security/main amd64 util-linux amd64 2.36.1-8+deb11u2 [1142 kB] Get:4 http://security.debian.org bullseye-security/main amd64 mount amd64 2.36.1-8+deb11u2 [186 kB] Get:5 http://security.debian.org bullseye-security/main amd64 libblkid1 amd64 2.36.1-8+deb11u2 [194 kB] Get:6 http://security.debian.org bullseye-security/main amd64 libmount1 amd64 2.36.1-8+deb11u2 [212 kB] Get:7 http://security.debian.org bullseye-security/main amd64 libsmartcols1 amd64 2.36.1-8+deb11u2 [158 kB] Get:8 http://security.debian.org bullseye-security/main amd64 libuuid1 amd64 2.36.1-8+deb11u2 [83.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 3464 kB in 0s (48.5 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 7000 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.36.1-8+deb11u2_amd64.deb ... Unpacking bsdutils (1:2.36.1-8+deb11u2) over (1:2.36.1-8+deb11u1) ... Setting up bsdutils (1:2.36.1-8+deb11u2) ... (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 ... 7000 files and directories currently installed.) Preparing to unpack .../util-linux_2.36.1-8+deb11u2_amd64.deb ... Unpacking util-linux (2.36.1-8+deb11u2) over (2.36.1-8+deb11u1) ... Setting up util-linux (2.36.1-8+deb11u2) ... (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 ... 7000 files and directories currently installed.) Preparing to unpack .../mount_2.36.1-8+deb11u2_amd64.deb ... Unpacking mount (2.36.1-8+deb11u2) over (2.36.1-8+deb11u1) ... Preparing to unpack .../libblkid1_2.36.1-8+deb11u2_amd64.deb ... Unpacking libblkid1:amd64 (2.36.1-8+deb11u2) over (2.36.1-8+deb11u1) ... Setting up libblkid1:amd64 (2.36.1-8+deb11u2) ... (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 ... 7000 files and directories currently installed.) Preparing to unpack .../libgnutls30_3.7.1-5+deb11u5_amd64.deb ... Unpacking libgnutls30:amd64 (3.7.1-5+deb11u5) over (3.7.1-5+deb11u4) ... Setting up libgnutls30:amd64 (3.7.1-5+deb11u5) ... (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 ... 7000 files and directories currently installed.) Preparing to unpack .../libmount1_2.36.1-8+deb11u2_amd64.deb ... Unpacking libmount1:amd64 (2.36.1-8+deb11u2) over (2.36.1-8+deb11u1) ... Setting up libmount1:amd64 (2.36.1-8+deb11u2) ... (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 ... 7000 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.36.1-8+deb11u2_amd64.deb ... Unpacking libsmartcols1:amd64 (2.36.1-8+deb11u2) over (2.36.1-8+deb11u1) ... Setting up libsmartcols1:amd64 (2.36.1-8+deb11u2) ... (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 ... 7000 files and directories currently installed.) Preparing to unpack .../libuuid1_2.36.1-8+deb11u2_amd64.deb ... Unpacking libuuid1:amd64 (2.36.1-8+deb11u2) over (2.36.1-8+deb11u1) ... Setting up libuuid1:amd64 (2.36.1-8+deb11u2) ... Setting up mount (2.36.1-8+deb11u2) ... Processing triggers for libc-bin (2.31-13+deb11u8) ... 0m12.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'apt-get', '-yf', 'dist-upgrade'] 0m12.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m12.7s DUMP: bbf40232d9f3e1bf497d03d645104d5a - 0m12.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m12.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'apt-cache', 'show', '--no-all-versions', 'sra-toolkit'] 0m13.0s DUMP: Package: sra-toolkit Source: sra-sdk Version: 2.10.9+dfsg-2 Installed-Size: 10056 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.29), libfuse2 (>= 2.6), libkdf5-2 (>= 2.10.9+dfsg), libmagic1 (>= 5.12), libncbi-vdb2 (>= 2.10.9+dfsg), libncbi-wvdb2 (>= 2.10.9+dfsg), libstdc++6 (>= 5.2), libxml2 (>= 2.7.4), zlib1g (>= 1:1.2.2) Recommends: med-config (>= 2.1) Description-en: utilities for the NCBI Sequence Read Archive Tools for reading the SRA archive, generally by converting individual runs into some commonly used format such as fastq. . The textual dumpers "sra-dump" and "vdb-dump" are provided in this release as an aid in visual inspection. It is likely that their actual output formatting will be changed in the near future to a stricter, more formalized representation[s]. PLEASE DO NOT RELY UPON THE OUTPUT FORMAT SEEN IN THIS RELEASE. . Other tools distributed in this package are: abi-dump, abi-load align-info bam-load cache-mgr cg-load copycat fasterq-dump fastq-dump, fastq-load helicos-load illumina-dump, illumina-load kar kdbmeta latf-load pacbio-load prefetch rcexplain remote-fuser sff-dump, sff-load sra-pileup, sra-sort, sra-stat, srapath srf-load test-sra vdb-config, vdb-copy, vdb-decrypt, vdb-encrypt, vdb-get, vdb-lock, vdb-passwd, vdb-unlock, vdb-validate . The "help" information will be improved in near future releases, and the tool options will become standardized across the set. More documentation will also be provided documentation on the NCBI web site. . Tool options may change in the next release. Version 1 tool options will remain supported wherever possible in order to preserve operation of any existing scripts. Description-md5: 1a61cd8ef6f417d5f86c6c13697e7a05 Homepage: https://github.com/ncbi/sra-tools/ Section: science Priority: optional Filename: pool/main/s/sra-sdk/sra-toolkit_2.10.9+dfsg-2_amd64.deb Size: 5177976 MD5sum: 13337ede4e24d402dbe99d24a4be45f2 SHA256: 569481465c3305b19472ffedcdaa0a8c7dc129311231ea12856ec3607b0a7b95 0m13.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'apt-cache', 'show', '--no-all-versions', 'sra-toolkit'] 0m13.0s INFO: apt-cache knows about the following packages: sra-toolkit 0m13.0s INFO: Running scripts pre_install 0m13.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_install_database-server'] 0m13.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_install_database-server'] 0m13.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_install_exceptions'] 0m13.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_install_exceptions'] 0m13.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_install_extras'] 0m13.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_install_extras'] 0m13.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_install_foreign_architecture'] 0m13.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_install_foreign_architecture'] 0m13.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m13.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m13.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'apt-cache', 'policy'] 0m13.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye-proposed-updates/main amd64 Packages release v=11-updates,o=Debian,a=oldstable-proposed-updates,n=bullseye-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian bullseye-updates/main amd64 Packages release v=11-updates,o=Debian,a=oldstable-updates,n=bullseye-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org bullseye-security/main amd64 Packages release v=11,o=Debian,a=oldstable-security,n=bullseye-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.9,o=Debian,a=oldstable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m13.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'apt-cache', 'policy'] 0m13.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'apt-cache', 'policy', 'sra-toolkit'] 0m13.1s DUMP: sra-toolkit: Installed: 2.10.9+dfsg-2 Candidate: 2.10.9+dfsg-2 Version table: *** 2.10.9+dfsg-2 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 100 /var/lib/dpkg/status 0m13.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'apt-cache', 'policy', 'sra-toolkit'] 0m13.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'apt-get', '-y', 'install', 'sra-toolkit'] 0m13.6s DUMP: Reading package lists... Building dependency tree... Reading state information... sra-toolkit is already the newest version (2.10.9+dfsg-2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'apt-get', '-y', 'install', 'sra-toolkit'] 0m13.6s INFO: Running scripts post_install 0m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/post_install_exceptions'] 0m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/post_install_exceptions'] 0m13.6s INFO: Running scripts post_distupgrade 0m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/post_distupgrade_exceptions'] 0m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/post_distupgrade_exceptions'] 0m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m13.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m13.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m13.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m13.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/post_distupgrade_zz_backports'] 0m13.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/post_distupgrade_zz_backports'] 0m13.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f'] 0m14.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f'] 0m14.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f'] 0m14.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f'] 0m14.7s INFO: Running scripts pre_install 0m14.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_install_database-server'] 0m14.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_install_database-server'] 0m14.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_install_exceptions'] 0m14.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_install_exceptions'] 0m14.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_install_extras'] 0m14.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_install_extras'] 0m14.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_install_foreign_architecture'] 0m14.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_install_foreign_architecture'] 0m14.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m14.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m14.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'apt-cache', 'policy'] 0m14.8s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye-proposed-updates/main amd64 Packages release v=11-updates,o=Debian,a=oldstable-proposed-updates,n=bullseye-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian bullseye-updates/main amd64 Packages release v=11-updates,o=Debian,a=oldstable-updates,n=bullseye-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org bullseye-security/main amd64 Packages release v=11,o=Debian,a=oldstable-security,n=bullseye-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.9,o=Debian,a=oldstable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m14.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'apt-cache', 'policy'] 0m14.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'apt-cache', 'policy', 'sra-toolkit'] 0m14.9s DUMP: sra-toolkit: Installed: 2.10.9+dfsg-2 Candidate: 2.10.9+dfsg-2 Version table: *** 2.10.9+dfsg-2 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 100 /var/lib/dpkg/status 0m14.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'apt-cache', 'policy', 'sra-toolkit'] 0m14.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'apt-get', '-y', 'install', 'sra-toolkit=2.10.9+dfsg-2'] 0m15.3s DUMP: Reading package lists... Building dependency tree... Reading state information... sra-toolkit is already the newest version (2.10.9+dfsg-2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m15.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'apt-get', '-y', 'install', 'sra-toolkit=2.10.9+dfsg-2'] 0m15.3s INFO: Running scripts post_install 0m15.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/post_install_exceptions'] 0m15.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/post_install_exceptions'] 0m15.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f'] 0m15.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f'] 0m16.0s DEBUG: No file moved between /{bin|sbin|lib*} and /usr/{bin|sbin|lib*}. 0m16.0s INFO: /bin converted to /usr/bin by /usr merge 0m16.0s INFO: /lib converted to /usr/lib by /usr merge 0m16.0s INFO: /lib/init converted to /usr/lib/init by /usr merge 0m16.0s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 0m16.0s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 0m16.0s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 0m16.0s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 0m16.0s INFO: /lib/terminfo converted to /usr/lib/terminfo by /usr merge 0m16.0s INFO: /lib/terminfo/E converted to /usr/lib/terminfo/E by /usr merge 0m16.0s INFO: /lib/terminfo/a converted to /usr/lib/terminfo/a by /usr merge 0m16.0s INFO: /lib/terminfo/c converted to /usr/lib/terminfo/c by /usr merge 0m16.0s INFO: /lib/terminfo/d converted to /usr/lib/terminfo/d by /usr merge 0m16.0s INFO: /lib/terminfo/h converted to /usr/lib/terminfo/h by /usr merge 0m16.0s INFO: /lib/terminfo/l converted to /usr/lib/terminfo/l by /usr merge 0m16.0s INFO: /lib/terminfo/m converted to /usr/lib/terminfo/m by /usr merge 0m16.0s INFO: /lib/terminfo/p converted to /usr/lib/terminfo/p by /usr merge 0m16.0s INFO: /lib/terminfo/r converted to /usr/lib/terminfo/r by /usr merge 0m16.0s INFO: /lib/terminfo/s converted to /usr/lib/terminfo/s by /usr merge 0m16.0s INFO: /lib/terminfo/t converted to /usr/lib/terminfo/t by /usr merge 0m16.0s INFO: /lib/terminfo/v converted to /usr/lib/terminfo/v by /usr merge 0m16.0s INFO: /lib/terminfo/w converted to /usr/lib/terminfo/w by /usr merge 0m16.0s INFO: /lib/terminfo/x converted to /usr/lib/terminfo/x by /usr merge 0m16.0s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 0m16.0s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 0m16.0s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 0m16.0s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 0m16.0s INFO: /lib64 converted to /usr/lib64 by /usr merge 0m16.0s INFO: /sbin converted to /usr/sbin by /usr merge 0m16.7s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', '-ac', '--ignore-obsolete'] 0m17.9s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', '-ac', '--ignore-obsolete'] 0m17.9s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m17.9s DUMP: 0.15.6 0m17.9s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m17.9s INFO: Running adequate version 0.15.6 now. 0m17.9s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'sra-toolkit'] 0m18.6s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'sra-toolkit'] 0m18.6s INFO: Running scripts pre_remove 0m18.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m18.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m18.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m18.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m18.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m20.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m20.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m20.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m20.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m20.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m20.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_remove_exceptions'] 0m20.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/pre_remove_exceptions'] 0m20.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m20.4s DUMP: install ok installed adduser adduser 3.118+deb11u1 install ok installed apt apt 2.2.4 install ok installed base-files base-files 11.1+deb11u9 install ok installed base-passwd base-passwd 3.5.51 install ok installed bash bash 5.1-2+deb11u1 install ok installed bsdutils bsdutils 1:2.36.1-8+deb11u2 install ok installed coreutils coreutils 8.32-4+b1 install ok installed dash dash 0.5.11+git20200708+dd9ef66-5 install ok installed debconf debconf 1.5.77 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1+deb11u1 install ok installed debianutils debianutils 4.11.2 install ok installed diffutils diffutils 1:3.7-5 install ok installed dpkg dpkg 1.20.13 install ok installed e2fsprogs e2fsprogs 1.46.2-2 install ok installed findutils findutils 4.8.0-1 install ok installed gcc-10-base:amd64 gcc-10-base 10.2.1-6 install ok installed gcc-9-base:amd64 gcc-9-base 9.3.0-22 install ok installed gpgv gpgv 2.2.27-2+deb11u2 install ok installed grep grep 3.6-1+deb11u1 install ok installed gzip gzip 1.10-4+deb11u1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.60 install ok installed libacl1:amd64 libacl1 2.2.53-10 install ok installed libaec0:amd64 libaec0 1.0.4-1 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.2.4 install ok installed libattr1:amd64 libattr1 1:2.4.48-6 install ok installed libaudit-common libaudit-common 1:3.0-2 install ok installed libaudit1:amd64 libaudit1 1:3.0-2 install ok installed libblkid1:amd64 libblkid1 2.36.1-8+deb11u2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4 install ok installed libc-bin libc-bin 2.31-13+deb11u8 install ok installed libc6:amd64 libc6 2.31-13+deb11u8 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2+b1 install ok installed libcom-err2:amd64 libcom-err2 1.46.2-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.18-4 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.8 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.260 install ok installed libext2fs2:amd64 libext2fs2 1.46.2-2 install ok installed libffi7:amd64 libffi7 3.3-6 install ok installed libfuse2:amd64 libfuse2 2.9.9-5 install ok installed libgcc-s1:amd64 libgcc-s1 10.2.1-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.7-6 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg-1+deb11u1 install ok installed libgnutls30:amd64 libgnutls30 3.7.1-5+deb11u5 install ok installed libgpg-error0:amd64 libgpg-error0 1.38-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.18.3-6+deb11u4 install ok installed libhdf5-103-1:amd64 libhdf5-103-1 1.10.6+repack-4+deb11u1 install ok installed libhogweed6:amd64 libhogweed6 3.7.3-1 install ok installed libicu67:amd64 libicu67 67.1-7 install ok installed libidn2-0:amd64 libidn2-0 2.3.0-5 install ok installed libk5crypto3:amd64 libk5crypto3 1.18.3-6+deb11u4 install ok installed libkdf5-2 libkdf5-2 2.10.9+dfsg-2 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.18.3-6+deb11u4 install ok installed libkrb5support0:amd64 libkrb5support0 1.18.3-6+deb11u4 install ok installed liblz4-1:amd64 liblz4-1 1.9.3-2 install ok installed liblzma5:amd64 liblzma5 5.2.5-2.1~deb11u1 install ok installed libmagic-mgc libmagic-mgc 1:5.39-3+deb11u1 install ok installed libmagic1:amd64 libmagic1 1:5.39-3+deb11u1 install ok installed libmbedcrypto3:amd64 libmbedcrypto3 2.16.9-0.1 install ok installed libmbedtls-dev:amd64 libmbedtls-dev 2.16.9-0.1 install ok installed libmbedtls12:amd64 libmbedtls12 2.16.9-0.1 install ok installed libmbedx509-0:amd64 libmbedx509-0 2.16.9-0.1 install ok installed libmount1:amd64 libmount1 2.36.1-8+deb11u2 install ok installed libncbi-vdb2 libncbi-vdb2 2.10.9+dfsg-2 install ok installed libncbi-wvdb2 libncbi-wvdb2 2.10.9+dfsg-2 install ok installed libnettle8:amd64 libnettle8 3.7.3-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.22-1 install ok installed libpam-modules:amd64 libpam-modules 1.4.0-9+deb11u1 install ok installed libpam-modules-bin libpam-modules-bin 1.4.0-9+deb11u1 install ok installed libpam-runtime libpam-runtime 1.4.0-9+deb11u1 install ok installed libpam0g:amd64 libpam0g 1.4.0-9+deb11u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.36-2+deb11u1 install ok installed libpcre3:amd64 libpcre3 2:8.39-13 install ok installed libseccomp2:amd64 libseccomp2 2.5.1-1+deb11u1 install ok installed libselinux1:amd64 libselinux1 3.1-3 install ok installed libsemanage-common libsemanage-common 3.1-1 install ok installed libsemanage1:amd64 libsemanage1 3.1-1+b2 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.36.1-8+deb11u2 install ok installed libss2:amd64 libss2 1.46.2-2 install ok installed libssl1.1:amd64 libssl1.1 1.1.1w-0+deb11u1 install ok installed libstdc++6:amd64 libstdc++6 10.2.1-6 install ok installed libsystemd0:amd64 libsystemd0 247.3-7+deb11u4 install ok installed libsz2:amd64 libsz2 1.0.4-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.16.0-2+deb11u1 install ok installed libtinfo6:amd64 libtinfo6 6.2+20201114-2+deb11u2 install ok installed libtirpc-common libtirpc-common 1.3.1-1+deb11u1 install ok installed libtirpc3:amd64 libtirpc3 1.3.1-1+deb11u1 install ok installed libudev1:amd64 libudev1 247.3-7+deb11u4 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed libuuid1:amd64 libuuid1 2.36.1-8+deb11u2 install ok installed libxml2:amd64 libxml2 2.9.10+dfsg-6.7+deb11u4 install ok installed libxxhash0:amd64 libxxhash0 0.8.0-2 install ok installed libzstd1:amd64 libzstd1 1.4.8+dfsg-2.1 install ok installed login login 1:4.8.1-1 install ok installed logsave logsave 1.46.2-2 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.4.20200120-2 install ok installed mount mount 2.36.1-8+deb11u2 install ok installed ncurses-base ncurses-base 6.2+20201114-2+deb11u2 install ok installed ncurses-bin ncurses-bin 6.2+20201114-2+deb11u2 install ok installed passwd passwd 1:4.8.1-1 install ok installed perl-base perl-base 5.32.1-4+deb11u3 install ok installed sed sed 4.7-1 install ok installed sra-toolkit sra-toolkit 2.10.9+dfsg-2 install ok installed sysvinit-utils sysvinit-utils 2.96-7+deb11u1 install ok installed tar tar 1.34+dfsg-1+deb11u1 install ok installed tzdata tzdata 2024a-0+deb11u1 install ok installed util-linux util-linux 2.36.1-8+deb11u2 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2+deb11u2 0m20.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m20.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'apt-get', 'remove', 'libaec0:amd64', 'libfuse2:amd64', 'libhdf5-103-1:amd64', 'libicu67:amd64', 'libkdf5-2', 'libmagic-mgc', 'libmagic1:amd64', 'libmbedcrypto3:amd64', 'libmbedtls-dev:amd64', 'libmbedtls12:amd64', 'libmbedx509-0:amd64', 'libncbi-vdb2', 'libncbi-wvdb2', 'libsz2:amd64', 'libxml2:amd64', 'sra-toolkit'] 0m21.2s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: libaec0 libfuse2 libhdf5-103-1 libicu67 libkdf5-2 libmagic-mgc libmagic1 libmbedcrypto3 libmbedtls-dev libmbedtls12 libmbedx509-0 libncbi-vdb2 libncbi-wvdb2 libsz2 libxml2 sra-toolkit 0 upgraded, 0 newly installed, 16 to remove and 0 not upgraded. After this operation, 72.2 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 ... 7000 files and directories currently installed.) Removing sra-toolkit (2.10.9+dfsg-2) ... Removing libkdf5-2 (2.10.9+dfsg-2) ... Removing libhdf5-103-1:amd64 (1.10.6+repack-4+deb11u1) ... Removing libsz2:amd64 (1.0.4-1) ... Removing libaec0:amd64 (1.0.4-1) ... Removing libfuse2:amd64 (2.9.9-5) ... Removing libncbi-wvdb2 (2.10.9+dfsg-2) ... Removing libncbi-vdb2 (2.10.9+dfsg-2) ... Removing libxml2:amd64 (2.9.10+dfsg-6.7+deb11u4) ... Removing libicu67:amd64 (67.1-7) ... Removing libmagic1:amd64 (1:5.39-3+deb11u1) ... Removing libmagic-mgc (1:5.39-3+deb11u1) ... Removing libmbedtls-dev:amd64 (2.16.9-0.1) ... Removing libmbedtls12:amd64 (2.16.9-0.1) ... Removing libmbedx509-0:amd64 (2.16.9-0.1) ... Removing libmbedcrypto3:amd64 (2.16.9-0.1) ... Processing triggers for libc-bin (2.31-13+deb11u8) ... 0m21.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'apt-get', 'remove', 'libaec0:amd64', 'libfuse2:amd64', 'libhdf5-103-1:amd64', 'libicu67:amd64', 'libkdf5-2', 'libmagic-mgc', 'libmagic1:amd64', 'libmbedcrypto3:amd64', 'libmbedtls-dev:amd64', 'libmbedtls12:amd64', 'libmbedx509-0:amd64', 'libncbi-vdb2', 'libncbi-wvdb2', 'libsz2:amd64', 'libxml2:amd64', 'sra-toolkit'] 0m21.2s INFO: Running scripts post_remove 0m21.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/post_remove_exceptions'] 0m21.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/post_remove_exceptions'] 0m21.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'dpkg', '--purge', 'libaec0:amd64', 'libfuse2:amd64', 'libhdf5-103-1:amd64', 'libicu67:amd64', 'libkdf5-2', 'libmagic-mgc', 'libmagic1:amd64', 'libmbedcrypto3:amd64', 'libmbedtls-dev:amd64', 'libmbedtls12:amd64', 'libmbedx509-0:amd64', 'libncbi-vdb2', 'libncbi-wvdb2', 'libsz2:amd64', 'libxml2:amd64'] 0m21.2s DUMP: dpkg: warning: ignoring request to remove libaec0 which isn't installed dpkg: warning: ignoring request to remove libfuse2 which isn't installed dpkg: warning: ignoring request to remove libhdf5-103-1 which isn't installed dpkg: warning: ignoring request to remove libicu67 which isn't installed dpkg: warning: ignoring request to remove libkdf5-2 which isn't installed dpkg: warning: ignoring request to remove libmagic-mgc which isn't installed (Reading database ... 6681 files and directories currently installed.) Purging configuration files for libmagic1:amd64 (1:5.39-3+deb11u1) ... dpkg: warning: ignoring request to remove libmbedcrypto3 which isn't installed dpkg: warning: ignoring request to remove libmbedtls-dev which isn't installed dpkg: warning: ignoring request to remove libmbedtls12 which isn't installed dpkg: warning: ignoring request to remove libmbedx509-0 which isn't installed dpkg: warning: ignoring request to remove libncbi-vdb2 which isn't installed dpkg: warning: ignoring request to remove libncbi-wvdb2 which isn't installed dpkg: warning: ignoring request to remove libsz2 which isn't installed dpkg: warning: ignoring request to remove libxml2 which isn't installed 0m21.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'dpkg', '--purge', 'libaec0:amd64', 'libfuse2:amd64', 'libhdf5-103-1:amd64', 'libicu67:amd64', 'libkdf5-2', 'libmagic-mgc', 'libmagic1:amd64', 'libmbedcrypto3:amd64', 'libmbedtls-dev:amd64', 'libmbedtls12:amd64', 'libmbedx509-0:amd64', 'libncbi-vdb2', 'libncbi-wvdb2', 'libsz2:amd64', 'libxml2:amd64'] 0m21.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'dpkg', '--purge', 'sra-toolkit'] 0m21.2s DUMP: (Reading database ... 6679 files and directories currently installed.) Purging configuration files for sra-toolkit (2.10.9+dfsg-2) ... 0m21.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'dpkg', '--purge', 'sra-toolkit'] 0m21.2s INFO: Running scripts post_purge 0m21.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/post_purge_exceptions'] 0m21.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/post_purge_exceptions'] 0m21.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'dpkg', '--purge', '--pending'] 0m21.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'dpkg', '--purge', '--pending'] 0m21.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'dpkg', '--remove', '--pending'] 0m21.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'dpkg', '--remove', '--pending'] 0m21.3s INFO: Running scripts post_test 0m21.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/post_test_exceptions'] 0m21.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'tmp/scripts/post_test_exceptions'] 0m21.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f'] 0m21.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f'] 0m21.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'dpkg-divert', '--list'] 0m21.8s DUMP: local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m21.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'dpkg-divert', '--list'] 0m21.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'apt-get', 'clean'] 0m21.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f', 'apt-get', 'clean'] 0m21.8s DEBUG: Recording chroot state 0m23.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f/dev/shm'] 0m23.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f/dev/shm'] 0m23.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f/dev/console'] 0m23.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f/dev/console'] 0m23.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f/dev/ptmx'] 0m23.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f/dev/ptmx'] 0m23.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f/dev/pts'] 0m23.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f/dev/pts'] 0m23.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f/proc'] 0m23.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f/proc'] 0m23.3s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f'] 0m23.4s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpcxo_2y5f'] 0m23.4s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpcxo_2y5f 0m23.4s INFO: PASS: Upgrading between Debian distributions. 0m23.4s INFO: PASS: All tests. 0m23.4s INFO: piuparts run ends. ret=0 End: 2024-04-19 00:01:45 GMT