Start: 2024-04-13 03:05:06 GMT [sid] Package: sra-toolkit Source: sra-sdk (3.0.3+dfsg-6) Version: 3.0.3+dfsg-6+b1 Installed-Size: 17345 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libbz2-1.0, libc6 (>= 2.34), libgcc-s1 (>= 3.0), libhdf5-103-1t64, libmagic1t64 (>= 5.12), libncbi-vdb3 (>= 3.0.2+dfsg), libncbi-wvdb3 (>= 3.0.2+dfsg), libre2-10 (>= 20201101+dfsg), libssl3t64 (>= 3.0.0), libstdc++6 (>= 13.1), libxml2 (>= 2.7.4), zlib1g (>= 1:1.2.2) Recommends: med-config 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_3.0.3+dfsg-6+b1_amd64.deb Size: 6796144 MD5sum: d032f232dda53d9aef82eca1463ba1a3 SHA256: c2c7f9e58d6a3d90910ac47fb5b3c31e1e1593065c22e36e89fdcd7b4db36564 [experimental] Package: sra-toolkit Source: sra-sdk Version: 3.0.9+dfsg-2 Installed-Size: 16522 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.0), libhdf5-103-1t64, libmagic1t64 (>= 5.12), libncbi-vdb3 (>= 3.0.9+dfsg), libncbi-wvdb3 (>= 3.0.9+dfsg), libstdc++6 (>= 13.1), libxml2 (>= 2.7.4), zlib1g (>= 1:1.2.2) Recommends: med-config 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_3.0.9+dfsg-2_amd64.deb Size: 6177916 MD5sum: a5cbd4838549df9c335c9d1d859d77f1 SHA256: 987f0b367a5bd22e3e929b6cd63c31d7765bb76bccb2934071c43040f0d5462d 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/sid-merged-usr_amd64.tar.gz -d sid -d experimental -B /srv/piuparts.debian.org/slave/refchroot/sid2experimental/reference-chroot-metadata.dat --apt sra-toolkit=3.0.9+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 --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz -d sid -d experimental -B /srv/piuparts.debian.org/slave/refchroot/sid2experimental/reference-chroot-metadata.dat --apt sra-toolkit=3.0.9+dfsg-2 0m0.0s INFO: Running on: Linux piu-slave-ubc-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/tmpvbih0ac4 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpvbih0ac4 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4/proc'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4/proc'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4/dev/pts'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4/dev/pts'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4/dev/ptmx'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4/dev/ptmx'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4/dev/console'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4/dev/console'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4/dev/shm'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4/dev/shm'] 0m0.4s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid 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/tmpvbih0ac4/tmp/scripts/ 0m0.5s INFO: Running scripts post_chroot_unpack 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'apt-get', 'update'] 0m4.8s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [198 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9901 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7191 kB] Fetched 17.3 MB in 3s (5363 kB/s) Reading package lists... 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'apt-get', 'update'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'apt-get', '-yf', 'dist-upgrade'] 0m8.0s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: apt libapt-pkg6.0t64 libc-bin libc6 4 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 5721 kB of archives. After this operation, 37.9 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 libc6 amd64 2.37-17 [2753 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0t64 amd64 2.9.0 [986 kB] Get:3 http://deb.debian.org/debian sid/main amd64 apt amd64 2.9.0 [1379 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libc-bin amd64 2.37-17 [603 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 5721 kB in 0s (51.1 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 ... 5200 files and directories currently installed.) Preparing to unpack .../libc6_2.37-17_amd64.deb ... Unpacking libc6:amd64 (2.37-17) over (2.37-16) ... Setting up libc6:amd64 (2.37-17) ... (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 ... 5200 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0t64_2.9.0_amd64.deb ... Unpacking libapt-pkg6.0t64:amd64 (2.9.0) over (2.7.14) ... Setting up libapt-pkg6.0t64:amd64 (2.9.0) ... (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 ... 5200 files and directories currently installed.) Preparing to unpack .../archives/apt_2.9.0_amd64.deb ... Unpacking apt (2.9.0) over (2.7.14) ... Setting up apt (2.9.0) ... (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 ... 5200 files and directories currently installed.) Preparing to unpack .../libc-bin_2.37-17_amd64.deb ... Unpacking libc-bin (2.37-17) over (2.37-16) ... Setting up libc-bin (2.37-17) ... 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'apt-get', '-yf', 'dist-upgrade'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m9.4s DUMP: db8b93866b36bf380e87593bad0874b1 - 0m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m9.4s INFO: Running scripts post_setup 0m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/post_setup_dummy_users'] 0m10.6s 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 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/post_setup_dummy_users'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/post_setup_forbid_home'] 0m10.6s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/post_setup_forbid_home'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/post_setup_force-unsafe-io'] 0m10.6s 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' 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/post_setup_force-unsafe-io'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/post_setup_minimize'] 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/post_setup_minimize'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/post_setup_squeeze-backports'] 0m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/post_setup_squeeze-backports'] 0m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/post_setup_zz_backports'] 0m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/post_setup_zz_backports'] 0m10.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m10.7s DUMP: install ok installed apt apt 2.9.0 install ok installed base-files base-files 13 install ok installed base-passwd base-passwd 3.6.3 install ok installed bash bash 5.2.21-2 install ok installed bsdutils bsdutils 1:2.40-5 install ok installed coreutils coreutils 9.4-3.1 install ok installed dash dash 0.5.12-6 install ok installed debconf debconf 1.5.86 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.17 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.6 install ok installed e2fsprogs e2fsprogs 1.47.0-2.4 install ok installed findutils findutils 4.9.0-5 install ok installed gcc-14-base:amd64 gcc-14-base 14-20240330-1 install ok installed gpgv gpgv 2.2.40-3 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.23+nmu2 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed libacl1:amd64 libacl1 2.3.2-1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.0 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:3.1.2-2.1 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-2.1 install ok installed libblkid1:amd64 libblkid1 2.40-5 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5.1 install ok installed libc-bin libc-bin 2.37-17 install ok installed libc6:amd64 libc6 2.37-17 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.4-2 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2.4 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-4 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-6 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.271+b3 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.0-2.4 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14-20240330-1 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.3-2 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.5-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.47-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.9.1-2.2 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-2 install ok installed liblzma5:amd64 liblzma5 5.6.1+really5.4.5-1 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.40-5 install ok installed libnettle8t64:amd64 libnettle8t64 3.9.1-2.2 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.3-4 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b1 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1 install ok installed libselinux1:amd64 libselinux1 3.5-2+b2 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b3 install ok installed libsepol2:amd64 libsepol2 3.5-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.40-5 install ok installed libss2:amd64 libss2 1.47.0-2.4 install ok installed libssl3t64:amd64 libssl3t64 3.2.1-3 install ok installed libstdc++6:amd64 libstdc++6 14-20240330-1 install ok installed libsystemd0:amd64 libsystemd0 255.4-1+b1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtinfo6:amd64 libtinfo6 6.4+20240113-1 install ok installed libudev1:amd64 libudev1 255.4-1+b1 install ok installed libunistring5:amd64 libunistring5 1.2-1 install ok installed libuuid1:amd64 libuuid1 2.40-5 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-2 install ok installed login login 1:4.13+dfsg1-4 install ok installed logsave logsave 1.47.0-2.4 install ok installed mawk mawk 1.3.4.20240123-1 install ok installed mount mount 2.40-5 install ok installed ncurses-base ncurses-base 6.4+20240113-1 install ok installed ncurses-bin ncurses-bin 6.4+20240113-1 install ok installed passwd passwd 1:4.13+dfsg1-4 install ok installed perl-base perl-base 5.38.2-3.2+b2 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.08-7 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024a-2 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40-5 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg-3.1 0m10.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m10.7s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/sid2experimental/reference-chroot-metadata.dat 0m11.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4'] 0m11.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4'] 0m11.4s INFO: Running scripts is_testable 0m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/is_testable_uninstallable'] 0m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/is_testable_uninstallable'] 0m11.4s INFO: Running scripts pre_test 0m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_test_exceptions'] 0m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_test_exceptions'] 0m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_test_root_password'] 0m11.4s DUMP: New password: Retype new password: passwd: password updated successfully 0m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_test_root_password'] 0m11.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'apt-cache', 'show', '--no-all-versions', 'sra-toolkit'] 0m11.8s DUMP: Package: sra-toolkit Source: sra-sdk (3.0.3+dfsg-6) Version: 3.0.3+dfsg-6+b1 Installed-Size: 17345 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libbz2-1.0, libc6 (>= 2.34), libgcc-s1 (>= 3.0), libhdf5-103-1t64, libmagic1t64 (>= 5.12), libncbi-vdb3 (>= 3.0.2+dfsg), libncbi-wvdb3 (>= 3.0.2+dfsg), libre2-10 (>= 20201101+dfsg), libssl3t64 (>= 3.0.0), libstdc++6 (>= 13.1), libxml2 (>= 2.7.4), zlib1g (>= 1:1.2.2) Recommends: med-config 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_3.0.3+dfsg-6+b1_amd64.deb Size: 6796144 MD5sum: d032f232dda53d9aef82eca1463ba1a3 SHA256: c2c7f9e58d6a3d90910ac47fb5b3c31e1e1593065c22e36e89fdcd7b4db36564 0m11.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'apt-cache', 'show', '--no-all-versions', 'sra-toolkit'] 0m11.8s INFO: apt-cache knows about the following packages: sra-toolkit 0m11.8s INFO: Running scripts pre_install 0m11.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_install_database-server'] 0m11.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_install_database-server'] 0m11.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_install_exceptions'] 0m11.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_install_exceptions'] 0m11.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_install_extras'] 0m11.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_install_extras'] 0m11.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_install_foreign_architecture'] 0m11.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_install_foreign_architecture'] 0m11.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m11.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m11.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'apt-cache', 'policy'] 0m11.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m11.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'apt-cache', 'policy'] 0m11.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'apt-cache', 'policy', 'sra-toolkit'] 0m12.0s DUMP: sra-toolkit: Installed: (none) Candidate: 3.0.3+dfsg-6+b1 Version table: 3.0.3+dfsg-6+b1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 0m12.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'apt-cache', 'policy', 'sra-toolkit'] 0m12.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'apt-get', '-y', 'install', 'sra-toolkit'] 0m19.2s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libaec0 libbrotli1 libcurl4t64 libgssapi-krb5-2 libhdf5-103-1t64 libicu72 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.5-0 libmagic-mgc libmagic1t64 libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 libncbi-vdb3 libncbi-wvdb3 libnghttp2-14 libpsl5t64 libre2-10 librtmp1 libsasl2-2 libsasl2-modules-db libssh2-1t64 libsz2 libxml2 ncbi-vdb-data Suggested packages: krb5-doc krb5-user file Recommended packages: ca-certificates krb5-locales libldap-common publicsuffix libsasl2-modules med-config The following NEW packages will be installed: libaec0 libbrotli1 libcurl4t64 libgssapi-krb5-2 libhdf5-103-1t64 libicu72 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.5-0 libmagic-mgc libmagic1t64 libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 libncbi-vdb3 libncbi-wvdb3 libnghttp2-14 libpsl5t64 libre2-10 librtmp1 libsasl2-2 libsasl2-modules-db libssh2-1t64 libsz2 libxml2 ncbi-vdb-data sra-toolkit 0 upgraded, 29 newly installed, 0 to remove and 0 not upgraded. Need to get 23.5 MB of archives. After this operation, 83.8 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 libaec0 amd64 1.1.3-1 [23.4 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get:6 http://deb.debian.org/debian sid/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libldap-2.5-0 amd64 2.5.16+dfsg-2 [185 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libnghttp2-14 amd64 1.61.0-1 [75.3 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get:13 http://deb.debian.org/debian sid/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b2 [215 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libcurl4t64 amd64 8.7.1-2 [440 kB] Get:16 http://deb.debian.org/debian sid/main amd64 libsz2 amd64 1.1.3-1 [7740 B] Get:17 http://deb.debian.org/debian sid/main amd64 libhdf5-103-1t64 amd64 1.10.10+repack-3.3 [1241 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get:19 http://deb.debian.org/debian sid/main amd64 libmagic-mgc amd64 1:5.45-3 [314 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libmagic1t64 amd64 1:5.45-3 [105 kB] Get:21 http://deb.debian.org/debian sid/main amd64 libmbedcrypto7t64 amd64 2.28.8-1 [284 kB] Get:22 http://deb.debian.org/debian sid/main amd64 libmbedx509-1t64 amd64 2.28.8-1 [131 kB] Get:23 http://deb.debian.org/debian sid/main amd64 libmbedtls14t64 amd64 2.28.8-1 [167 kB] Get:24 http://deb.debian.org/debian sid/main amd64 ncbi-vdb-data all 3.0.2+dfsg-2 [73.3 kB] Get:25 http://deb.debian.org/debian sid/main amd64 libncbi-vdb3 amd64 3.0.2+dfsg-2+b1 [1049 kB] Get:26 http://deb.debian.org/debian sid/main amd64 libncbi-wvdb3 amd64 3.0.2+dfsg-2+b1 [1078 kB] Get:27 http://deb.debian.org/debian sid/main amd64 libre2-10 amd64 20230301-3+b1 [188 kB] Get:28 http://deb.debian.org/debian sid/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b2 [692 kB] Get:29 http://deb.debian.org/debian sid/main amd64 sra-toolkit amd64 3.0.3+dfsg-6+b1 [6796 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 23.5 MB in 3s (7249 kB/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 ... 5204 files and directories currently installed.) Preparing to unpack .../00-libaec0_1.1.3-1_amd64.deb ... Unpacking libaec0:amd64 (1.1.3-1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../01-libbrotli1_1.1.0-2+b3_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b3) ... Selecting previously unselected package libkrb5support0:amd64. 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Unpacking libncbi-vdb3:amd64 (3.0.2+dfsg-2+b1) ... Selecting previously unselected package libncbi-wvdb3:amd64. Preparing to unpack .../25-libncbi-wvdb3_3.0.2+dfsg-2+b1_amd64.deb ... Unpacking libncbi-wvdb3:amd64 (3.0.2+dfsg-2+b1) ... Selecting previously unselected package libre2-10:amd64. Preparing to unpack .../26-libre2-10_20230301-3+b1_amd64.deb ... Unpacking libre2-10:amd64 (20230301-3+b1) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../27-libxml2_2.9.14+dfsg-1.3+b2_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.3+b2) ... Selecting previously unselected package sra-toolkit. Preparing to unpack .../28-sra-toolkit_3.0.3+dfsg-6+b1_amd64.deb ... Unpacking sra-toolkit (3.0.3+dfsg-6+b1) ... Setting up libkeyutils1:amd64 (1.6.3-3) ... Setting up libicu72:amd64 (72.1-4+b1) ... Setting up libre2-10:amd64 (20230301-3+b1) ... Setting up libmbedcrypto7t64:amd64 (2.28.8-1) ... Setting up libmagic-mgc (1:5.45-3) ... Setting up libbrotli1:amd64 (1.1.0-2+b3) ... Setting up libmagic1t64:amd64 (1:5.45-3) ... Setting up libpsl5t64:amd64 (0.21.2-1.1) ... Setting up libnghttp2-14:amd64 (1.61.0-1) ... Setting up libaec0:amd64 (1.1.3-1) ... Setting up libkrb5support0:amd64 (1.20.1-6+b1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Setting up libk5crypto3:amd64 (1.20.1-6+b1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Setting up ncbi-vdb-data (3.0.2+dfsg-2) ... Setting up libkrb5-3:amd64 (1.20.1-6+b1) ... Setting up libssh2-1t64:amd64 (1.11.0-4.1+b2) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b2) ... Setting up libsz2:amd64 (1.1.3-1) ... Setting up libmbedx509-1t64:amd64 (2.28.8-1) ... Setting up libldap-2.5-0:amd64 (2.5.16+dfsg-2) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Setting up libmbedtls14t64:amd64 (2.28.8-1) ... Setting up libcurl4t64:amd64 (8.7.1-2) ... Setting up libncbi-vdb3:amd64 (3.0.2+dfsg-2+b1) ... Setting up libncbi-wvdb3:amd64 (3.0.2+dfsg-2+b1) ... Setting up libhdf5-103-1t64:amd64 (1.10.10+repack-3.3) ... Setting up sra-toolkit (3.0.3+dfsg-6+b1) ... Processing triggers for libc-bin (2.37-17) ... 0m19.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'apt-get', '-y', 'install', 'sra-toolkit'] 0m19.2s INFO: Running scripts post_install 0m19.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/post_install_exceptions'] 0m19.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/post_install_exceptions'] 0m19.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4'] 0m19.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4'] 0m19.5s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpvbih0ac4 to experimental 0m19.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main deb http://deb.debian.org/debian/ experimental main 0m19.5s INFO: Running scripts pre_distupgrade 0m19.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m19.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m19.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_distupgrade_exceptions'] 0m19.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_distupgrade_exceptions'] 0m19.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m19.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m19.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m19.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m19.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m19.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m19.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'apt-get', 'update'] 0m23.1s DUMP: Hit:1 http://deb.debian.org/debian sid InRelease Get:2 http://deb.debian.org/debian experimental InRelease [101 kB] Get:3 http://deb.debian.org/debian experimental/main amd64 Packages [729 kB] Get:4 http://deb.debian.org/debian experimental/main Translation-en [382 kB] Fetched 1213 kB in 2s (513 kB/s) Reading package lists... 0m23.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'apt-get', 'update'] 0m23.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'apt-get', '-yf', 'dist-upgrade'] 0m24.1s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m24.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'apt-get', '-yf', 'dist-upgrade'] 0m24.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m24.5s DUMP: a5ba5e0b95a038e2d9edeb1ce81a2a59 - 0m24.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m24.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'apt-cache', 'show', '--no-all-versions', 'sra-toolkit'] 0m24.7s DUMP: Package: sra-toolkit Source: sra-sdk (3.0.3+dfsg-6) Version: 3.0.3+dfsg-6+b1 Installed-Size: 17345 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libbz2-1.0, libc6 (>= 2.34), libgcc-s1 (>= 3.0), libhdf5-103-1t64, libmagic1t64 (>= 5.12), libncbi-vdb3 (>= 3.0.2+dfsg), libncbi-wvdb3 (>= 3.0.2+dfsg), libre2-10 (>= 20201101+dfsg), libssl3t64 (>= 3.0.0), libstdc++6 (>= 13.1), libxml2 (>= 2.7.4), zlib1g (>= 1:1.2.2) Recommends: med-config 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_3.0.3+dfsg-6+b1_amd64.deb Size: 6796144 MD5sum: d032f232dda53d9aef82eca1463ba1a3 SHA256: c2c7f9e58d6a3d90910ac47fb5b3c31e1e1593065c22e36e89fdcd7b4db36564 0m24.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'apt-cache', 'show', '--no-all-versions', 'sra-toolkit'] 0m24.7s INFO: apt-cache knows about the following packages: sra-toolkit 0m24.7s INFO: Running scripts pre_install 0m24.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_install_database-server'] 0m24.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_install_database-server'] 0m24.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_install_exceptions'] 0m24.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_install_exceptions'] 0m24.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_install_extras'] 0m24.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_install_extras'] 0m24.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_install_foreign_architecture'] 0m24.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_install_foreign_architecture'] 0m24.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m24.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m24.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'apt-cache', 'policy'] 0m24.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 1 http://deb.debian.org/debian experimental/main amd64 Packages release o=Debian,a=experimental,n=rc-buggy,l=Debian,c=main,b=amd64 origin deb.debian.org 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: 0m24.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'apt-cache', 'policy'] 0m24.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'apt-cache', 'policy', 'sra-toolkit'] 0m24.9s DUMP: sra-toolkit: Installed: 3.0.3+dfsg-6+b1 Candidate: 3.0.3+dfsg-6+b1 Version table: 3.0.9+dfsg-2 1 1 http://deb.debian.org/debian experimental/main amd64 Packages *** 3.0.3+dfsg-6+b1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m24.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'apt-cache', 'policy', 'sra-toolkit'] 0m24.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'apt-get', '-y', '-t', 'experimental', 'install', 'sra-toolkit'] 0m30.2s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 libre2-10 Use 'sudo apt autoremove' to remove them. The following additional packages will be installed: libmbedcrypto16 libmbedtls21 libmbedx509-7 libncbi-vdb3 libncbi-wvdb3 ncbi-vdb-data The following NEW packages will be installed: libmbedcrypto16 libmbedtls21 libmbedx509-7 The following packages will be upgraded: libncbi-vdb3 libncbi-wvdb3 ncbi-vdb-data sra-toolkit 4 upgraded, 3 newly installed, 0 to remove and 7 not upgraded. Need to get 9328 kB of archives. After this operation, 1444 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian experimental/main amd64 libmbedcrypto16 amd64 3.6.0-2 [349 kB] Get:2 http://deb.debian.org/debian experimental/main amd64 libmbedx509-7 amd64 3.6.0-2 [144 kB] Get:3 http://deb.debian.org/debian experimental/main amd64 libmbedtls21 amd64 3.6.0-2 [231 kB] Get:4 http://deb.debian.org/debian experimental/main amd64 ncbi-vdb-data all 3.0.9+dfsg-1 [74.0 kB] Get:5 http://deb.debian.org/debian experimental/main amd64 libncbi-vdb3 amd64 3.0.9+dfsg-1 [1176 kB] Get:6 http://deb.debian.org/debian experimental/main amd64 libncbi-wvdb3 amd64 3.0.9+dfsg-1 [1177 kB] Get:7 http://deb.debian.org/debian experimental/main amd64 sra-toolkit amd64 3.0.9+dfsg-2 [6178 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 9328 kB in 3s (3120 kB/s) Selecting previously unselected package libmbedcrypto16: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 ... 5590 files and directories currently installed.) Preparing to unpack .../0-libmbedcrypto16_3.6.0-2_amd64.deb ... Unpacking libmbedcrypto16:amd64 (3.6.0-2) ... Selecting previously unselected package libmbedx509-7:amd64. Preparing to unpack .../1-libmbedx509-7_3.6.0-2_amd64.deb ... Unpacking libmbedx509-7:amd64 (3.6.0-2) ... Selecting previously unselected package libmbedtls21:amd64. Preparing to unpack .../2-libmbedtls21_3.6.0-2_amd64.deb ... Unpacking libmbedtls21:amd64 (3.6.0-2) ... Preparing to unpack .../3-ncbi-vdb-data_3.0.9+dfsg-1_all.deb ... Unpacking ncbi-vdb-data (3.0.9+dfsg-1) over (3.0.2+dfsg-2) ... Preparing to unpack .../4-libncbi-vdb3_3.0.9+dfsg-1_amd64.deb ... Unpacking libncbi-vdb3:amd64 (3.0.9+dfsg-1) over (3.0.2+dfsg-2+b1) ... Preparing to unpack .../5-libncbi-wvdb3_3.0.9+dfsg-1_amd64.deb ... Unpacking libncbi-wvdb3:amd64 (3.0.9+dfsg-1) over (3.0.2+dfsg-2+b1) ... Preparing to unpack .../6-sra-toolkit_3.0.9+dfsg-2_amd64.deb ... Unpacking sra-toolkit (3.0.9+dfsg-2) over (3.0.3+dfsg-6+b1) ... Setting up ncbi-vdb-data (3.0.9+dfsg-1) ... Setting up libmbedcrypto16:amd64 (3.6.0-2) ... Setting up libmbedx509-7:amd64 (3.6.0-2) ... Setting up libmbedtls21:amd64 (3.6.0-2) ... Setting up libncbi-vdb3:amd64 (3.0.9+dfsg-1) ... Setting up libncbi-wvdb3:amd64 (3.0.9+dfsg-1) ... Setting up sra-toolkit (3.0.9+dfsg-2) ... Installing new version of config file /etc/ncbi/default.kfg ... Processing triggers for libc-bin (2.37-17) ... 0m30.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'apt-get', '-y', '-t', 'experimental', 'install', 'sra-toolkit'] 0m30.2s INFO: Running scripts post_install 0m30.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/post_install_exceptions'] 0m30.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/post_install_exceptions'] 0m30.2s INFO: Running scripts post_distupgrade 0m30.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m30.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m30.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/post_distupgrade_exceptions'] 0m30.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/post_distupgrade_exceptions'] 0m30.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m30.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m30.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m30.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m30.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/post_distupgrade_zz_backports'] 0m30.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/post_distupgrade_zz_backports'] 0m30.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4'] 0m30.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4'] 0m30.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4'] 0m30.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4'] 0m30.9s INFO: Running scripts pre_install 0m30.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_install_database-server'] 0m30.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_install_database-server'] 0m30.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_install_exceptions'] 0m30.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_install_exceptions'] 0m30.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_install_extras'] 0m31.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_install_extras'] 0m31.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_install_foreign_architecture'] 0m31.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_install_foreign_architecture'] 0m31.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m31.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m31.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'apt-cache', 'policy'] 0m31.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 1 http://deb.debian.org/debian experimental/main amd64 Packages release o=Debian,a=experimental,n=rc-buggy,l=Debian,c=main,b=amd64 origin deb.debian.org 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: 0m31.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'apt-cache', 'policy'] 0m31.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'apt-cache', 'policy', 'sra-toolkit'] 0m31.1s DUMP: sra-toolkit: Installed: 3.0.9+dfsg-2 Candidate: 3.0.9+dfsg-2 Version table: *** 3.0.9+dfsg-2 100 1 http://deb.debian.org/debian experimental/main amd64 Packages 100 /var/lib/dpkg/status 3.0.3+dfsg-6+b1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 0m31.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'apt-cache', 'policy', 'sra-toolkit'] 0m31.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'apt-get', '-y', '-t', 'experimental', 'install', 'sra-toolkit=3.0.9+dfsg-2'] 0m31.9s DUMP: Reading package lists... Building dependency tree... Reading state information... sra-toolkit is already the newest version (3.0.9+dfsg-2). The following packages were automatically installed and are no longer required: libmbedcrypto7t64 libmbedtls14t64 libmbedx509-1t64 libre2-10 Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 7 not upgraded. 0m31.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'apt-get', '-y', '-t', 'experimental', 'install', 'sra-toolkit=3.0.9+dfsg-2'] 0m31.9s INFO: Running scripts post_install 0m31.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/post_install_exceptions'] 0m31.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/post_install_exceptions'] 0m31.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4'] 0m32.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4'] /srv/piuparts.debian.org/sbin/piuparts:1639: DeprecationWarning: The 'warn' function is deprecated, use 'warning' instead logging.warn("History of available packages does not match - reference chroot may be outdated") 0m32.3s WARNING: History of available packages does not match - reference chroot may be outdated 0m32.3s DEBUG: reference: 580fba10d16e7630917600c8536792c2 db5c96be2cd297fc37b47a4d3b094498 0m32.3s DEBUG: current : db8b93866b36bf380e87593bad0874b1 a5ba5e0b95a038e2d9edeb1ce81a2a59 0m32.3s INFO: /bin converted to /usr/bin by /usr merge 0m32.3s INFO: /lib converted to /usr/lib by /usr merge 0m32.3s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 0m32.3s INFO: /lib64 converted to /usr/lib64 by /usr merge 0m32.3s INFO: /sbin converted to /usr/sbin by /usr merge 0m32.6s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', '-ac', '--ignore-obsolete'] 0m33.6s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', '-ac', '--ignore-obsolete'] 0m33.6s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m33.6s DUMP: 0.15.6 0m33.6s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m33.6s INFO: Running adequate version 0.15.6 now. 0m33.6s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'sra-toolkit'] 0m34.9s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'sra-toolkit'] 0m34.9s INFO: Running scripts pre_remove 0m34.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m34.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m34.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m34.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m34.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m36.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m36.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m36.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m36.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m36.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m36.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_remove_exceptions'] 0m36.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/pre_remove_exceptions'] 0m36.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m36.5s DUMP: install ok installed apt apt 2.9.0 install ok installed base-files base-files 13 install ok installed base-passwd base-passwd 3.6.3 install ok installed bash bash 5.2.21-2 install ok installed bsdutils bsdutils 1:2.40-5 install ok installed coreutils coreutils 9.4-3.1 install ok installed dash dash 0.5.12-6 install ok installed debconf debconf 1.5.86 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.17 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.6 install ok installed e2fsprogs e2fsprogs 1.47.0-2.4 install ok installed findutils findutils 4.9.0-5 install ok installed gcc-14-base:amd64 gcc-14-base 14-20240330-1 install ok installed gpgv gpgv 2.2.40-3 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.23+nmu2 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed libacl1:amd64 libacl1 2.3.2-1 install ok installed libaec0:amd64 libaec0 1.1.3-1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.0 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:3.1.2-2.1 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-2.1 install ok installed libblkid1:amd64 libblkid1 2.40-5 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b3 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5.1 install ok installed libc-bin libc-bin 2.37-17 install ok installed libc6:amd64 libc6 2.37-17 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.4-2 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2.4 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-4 install ok installed libcurl4t64:amd64 libcurl4t64 8.7.1-2 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-6 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.271+b3 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.0-2.4 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14-20240330-1 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.3-2 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.5-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.47-3 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.20.1-6+b1 install ok installed libhdf5-103-1t64:amd64 libhdf5-103-1t64 1.10.10+repack-3.3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.9.1-2.2 install ok installed libicu72:amd64 libicu72 72.1-4+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed libk5crypto3:amd64 libk5crypto3 1.20.1-6+b1 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-3 install ok installed libkrb5-3:amd64 libkrb5-3 1.20.1-6+b1 install ok installed libkrb5support0:amd64 libkrb5support0 1.20.1-6+b1 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.16+dfsg-2 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-2 install ok installed liblzma5:amd64 liblzma5 5.6.1+really5.4.5-1 install ok installed libmagic-mgc libmagic-mgc 1:5.45-3 install ok installed libmagic1t64:amd64 libmagic1t64 1:5.45-3 install ok installed libmbedcrypto16:amd64 libmbedcrypto16 3.6.0-2 install ok installed libmbedcrypto7t64:amd64 libmbedcrypto7t64 2.28.8-1 install ok installed libmbedtls14t64:amd64 libmbedtls14t64 2.28.8-1 install ok installed libmbedtls21:amd64 libmbedtls21 3.6.0-2 install ok installed libmbedx509-1t64:amd64 libmbedx509-1t64 2.28.8-1 install ok installed libmbedx509-7:amd64 libmbedx509-7 3.6.0-2 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.40-5 install ok installed libncbi-vdb3:amd64 libncbi-vdb3 3.0.9+dfsg-1 install ok installed libncbi-wvdb3:amd64 libncbi-wvdb3 3.0.9+dfsg-1 install ok installed libnettle8t64:amd64 libnettle8t64 3.9.1-2.2 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.61.0-1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.3-4 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b1 install ok installed libpsl5t64:amd64 libpsl5t64 0.21.2-1.1 install ok installed libre2-10:amd64 libre2-10 20230301-3+b1 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b4 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-6 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-6 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1 install ok installed libselinux1:amd64 libselinux1 3.5-2+b2 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b3 install ok installed libsepol2:amd64 libsepol2 3.5-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.40-5 install ok installed libss2:amd64 libss2 1.47.0-2.4 install ok installed libssh2-1t64:amd64 libssh2-1t64 1.11.0-4.1+b2 install ok installed libssl3t64:amd64 libssl3t64 3.2.1-3 install ok installed libstdc++6:amd64 libstdc++6 14-20240330-1 install ok installed libsystemd0:amd64 libsystemd0 255.4-1+b1 install ok installed libsz2:amd64 libsz2 1.1.3-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtinfo6:amd64 libtinfo6 6.4+20240113-1 install ok installed libudev1:amd64 libudev1 255.4-1+b1 install ok installed libunistring5:amd64 libunistring5 1.2-1 install ok installed libuuid1:amd64 libuuid1 2.40-5 install ok installed libxml2:amd64 libxml2 2.9.14+dfsg-1.3+b2 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-2 install ok installed login login 1:4.13+dfsg1-4 install ok installed logsave logsave 1.47.0-2.4 install ok installed mawk mawk 1.3.4.20240123-1 install ok installed mount mount 2.40-5 install ok installed ncbi-vdb-data ncbi-vdb-data 3.0.9+dfsg-1 install ok installed ncurses-base ncurses-base 6.4+20240113-1 install ok installed ncurses-bin ncurses-bin 6.4+20240113-1 install ok installed passwd passwd 1:4.13+dfsg1-4 install ok installed perl-base perl-base 5.38.2-3.2+b2 install ok installed sed sed 4.9-2 install ok installed sra-toolkit sra-toolkit 3.0.9+dfsg-2 install ok installed sysvinit-utils sysvinit-utils 3.08-7 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024a-2 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40-5 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg-3.1 0m36.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m36.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'apt-get', 'remove', 'libaec0:amd64', 'libbrotli1:amd64', 'libcurl4t64:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-103-1t64:amd64', 'libicu72:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libldap-2.5-0:amd64', 'libmagic-mgc', 'libmagic1t64:amd64', 'libmbedcrypto16:amd64', 'libmbedcrypto7t64:amd64', 'libmbedtls14t64:amd64', 'libmbedtls21:amd64', 'libmbedx509-1t64:amd64', 'libmbedx509-7:amd64', 'libncbi-vdb3:amd64', 'libncbi-wvdb3:amd64', 'libnghttp2-14:amd64', 'libpsl5t64:amd64', 'libre2-10:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libssh2-1t64:amd64', 'libsz2:amd64', 'libxml2:amd64', 'ncbi-vdb-data', 'sra-toolkit'] 0m37.8s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: libaec0 libbrotli1 libcurl4t64 libgssapi-krb5-2 libhdf5-103-1t64 libicu72 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.5-0 libmagic-mgc libmagic1t64 libmbedcrypto16 libmbedcrypto7t64 libmbedtls14t64 libmbedtls21 libmbedx509-1t64 libmbedx509-7 libncbi-vdb3 libncbi-wvdb3 libnghttp2-14 libpsl5t64 libre2-10 librtmp1 libsasl2-2 libsasl2-modules-db libssh2-1t64 libsz2 libxml2 ncbi-vdb-data sra-toolkit 0 upgraded, 0 newly installed, 32 to remove and 0 not upgraded. After this operation, 85.3 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 ... 5604 files and directories currently installed.) Removing sra-toolkit (3.0.9+dfsg-2) ... Removing libhdf5-103-1t64:amd64 (1.10.10+repack-3.3) ... Removing libsz2:amd64 (1.1.3-1) ... Removing libaec0:amd64 (1.1.3-1) ... Removing libcurl4t64:amd64 (8.7.1-2) ... Removing libbrotli1:amd64 (1.1.0-2+b3) ... Removing libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Removing libxml2:amd64 (2.9.14+dfsg-1.3+b2) ... Removing libicu72:amd64 (72.1-4+b1) ... Removing libkrb5-3:amd64 (1.20.1-6+b1) ... Removing libk5crypto3:amd64 (1.20.1-6+b1) ... Removing libkeyutils1:amd64 (1.6.3-3) ... Removing libkrb5support0:amd64 (1.20.1-6+b1) ... Removing libldap-2.5-0:amd64 (2.5.16+dfsg-2) ... Removing libmagic1t64:amd64 (1:5.45-3) ... Removing libmagic-mgc (1:5.45-3) ... Removing libncbi-wvdb3:amd64 (3.0.9+dfsg-1) ... Removing libncbi-vdb3:amd64 (3.0.9+dfsg-1) ... Removing libmbedtls14t64:amd64 (2.28.8-1) ... Removing libmbedx509-1t64:amd64 (2.28.8-1) ... Removing libmbedcrypto7t64:amd64 (2.28.8-1) ... Removing libmbedtls21:amd64 (3.6.0-2) ... Removing libmbedx509-7:amd64 (3.6.0-2) ... Removing libnghttp2-14:amd64 (1.61.0-1) ... Removing libpsl5t64:amd64 (0.21.2-1.1) ... Removing libre2-10:amd64 (20230301-3+b1) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) ... Removing libssh2-1t64:amd64 (1.11.0-4.1+b2) ... Removing ncbi-vdb-data (3.0.9+dfsg-1) ... Removing libmbedcrypto16:amd64 (3.6.0-2) ... Processing triggers for libc-bin (2.37-17) ... 0m37.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'apt-get', 'remove', 'libaec0:amd64', 'libbrotli1:amd64', 'libcurl4t64:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-103-1t64:amd64', 'libicu72:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libldap-2.5-0:amd64', 'libmagic-mgc', 'libmagic1t64:amd64', 'libmbedcrypto16:amd64', 'libmbedcrypto7t64:amd64', 'libmbedtls14t64:amd64', 'libmbedtls21:amd64', 'libmbedx509-1t64:amd64', 'libmbedx509-7:amd64', 'libncbi-vdb3:amd64', 'libncbi-wvdb3:amd64', 'libnghttp2-14:amd64', 'libpsl5t64:amd64', 'libre2-10:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libssh2-1t64:amd64', 'libsz2:amd64', 'libxml2:amd64', 'ncbi-vdb-data', 'sra-toolkit'] 0m37.8s INFO: Running scripts post_remove 0m37.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/post_remove_exceptions'] 0m37.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/post_remove_exceptions'] 0m37.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'dpkg', '--purge', 'libaec0:amd64', 'libbrotli1:amd64', 'libcurl4t64:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-103-1t64:amd64', 'libicu72:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libldap-2.5-0:amd64', 'libmagic-mgc', 'libmagic1t64:amd64', 'libmbedcrypto16:amd64', 'libmbedcrypto7t64:amd64', 'libmbedtls14t64:amd64', 'libmbedtls21:amd64', 'libmbedx509-1t64:amd64', 'libmbedx509-7:amd64', 'libncbi-vdb3:amd64', 'libncbi-wvdb3:amd64', 'libnghttp2-14:amd64', 'libpsl5t64:amd64', 'libre2-10:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libssh2-1t64:amd64', 'libsz2:amd64', 'libxml2:amd64', 'ncbi-vdb-data'] 0m37.8s DUMP: dpkg: warning: ignoring request to remove libaec0 which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libcurl4t64 which isn't installed (Reading database ... 5211 files and directories currently installed.) Purging configuration files for libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... dpkg: warning: ignoring request to remove libhdf5-103-1t64 which isn't installed dpkg: warning: ignoring request to remove libicu72 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 libmagic-mgc which isn't installed Purging configuration files for libmagic1t64:amd64 (1:5.45-3) ... dpkg: warning: ignoring request to remove libmbedcrypto16 which isn't installed dpkg: warning: ignoring request to remove libmbedcrypto7t64 which isn't installed dpkg: warning: ignoring request to remove libmbedtls14t64 which isn't installed dpkg: warning: ignoring request to remove libmbedtls21 which isn't installed dpkg: warning: ignoring request to remove libmbedx509-1t64 which isn't installed dpkg: warning: ignoring request to remove libmbedx509-7 which isn't installed dpkg: warning: ignoring request to remove libncbi-vdb3 which isn't installed dpkg: warning: ignoring request to remove libncbi-wvdb3 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libpsl5t64 which isn't installed dpkg: warning: ignoring request to remove libre2-10 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 libssh2-1t64 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 dpkg: warning: ignoring request to remove ncbi-vdb-data which isn't installed 0m37.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'dpkg', '--purge', 'libaec0:amd64', 'libbrotli1:amd64', 'libcurl4t64:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-103-1t64:amd64', 'libicu72:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libldap-2.5-0:amd64', 'libmagic-mgc', 'libmagic1t64:amd64', 'libmbedcrypto16:amd64', 'libmbedcrypto7t64:amd64', 'libmbedtls14t64:amd64', 'libmbedtls21:amd64', 'libmbedx509-1t64:amd64', 'libmbedx509-7:amd64', 'libncbi-vdb3:amd64', 'libncbi-wvdb3:amd64', 'libnghttp2-14:amd64', 'libpsl5t64:amd64', 'libre2-10:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libssh2-1t64:amd64', 'libsz2:amd64', 'libxml2:amd64', 'ncbi-vdb-data'] 0m37.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'dpkg', '--purge', 'sra-toolkit'] 0m37.8s DUMP: (Reading database ... 5209 files and directories currently installed.) Purging configuration files for sra-toolkit (3.0.9+dfsg-2) ... 0m37.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'dpkg', '--purge', 'sra-toolkit'] 0m37.8s INFO: Running scripts post_purge 0m37.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/post_purge_exceptions'] 0m37.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/post_purge_exceptions'] 0m37.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'dpkg', '--purge', '--pending'] 0m37.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'dpkg', '--purge', '--pending'] 0m37.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'dpkg', '--remove', '--pending'] 0m37.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'dpkg', '--remove', '--pending'] 0m37.9s INFO: Running scripts post_test 0m37.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/post_test_exceptions'] 0m37.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'tmp/scripts/post_test_exceptions'] 0m37.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4'] 0m38.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4'] 0m38.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'dpkg-divert', '--list'] 0m38.2s DUMP: diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64 local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64 local diversion of /home to /home.distrib diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64 diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64 local diversion of /usr/bin/sync to /usr/bin/sync.distrib 0m38.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'dpkg-divert', '--list'] 0m38.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'apt-get', 'clean'] 0m38.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4', 'apt-get', 'clean'] 0m38.2s DEBUG: Recording chroot state 0m39.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4/dev/shm'] 0m39.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4/dev/shm'] 0m39.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4/dev/console'] 0m39.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4/dev/console'] 0m39.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4/dev/ptmx'] 0m39.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4/dev/ptmx'] 0m39.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4/dev/pts'] 0m39.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4/dev/pts'] 0m39.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4/proc'] 0m39.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4/proc'] 0m39.3s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4'] 0m39.4s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpvbih0ac4'] 0m39.4s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpvbih0ac4 0m39.4s INFO: PASS: Upgrading between Debian distributions. 0m39.4s INFO: PASS: All tests. 0m39.4s INFO: piuparts run ends. ret=0 End: 2024-04-13 03:05:46 GMT