Start: 2025-03-07 15:43:53 GMT
[testing]
Package: igblast
Source: ncbi-igblast (1.19.0-1)
Version: 1.19.0-1+b1
Installed-Size: 226928
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Architecture: amd64
Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.0), libstdc++6 (>= 11)
Description: Immunoglobulin and T cell receptor variable domain sequence analysis
Homepage: https://ncbi.github.io/igblast/
Description-md5: 2962314d8994f10816be6f57d21f8ffc
Section: science
Priority: optional
Filename: pool/main/n/ncbi-igblast/igblast_1.19.0-1+b1_amd64.deb
Size: 38239560
MD5sum: 3d0a8526b1ae4438539a817e773cfa70
SHA256: 5c4557e8b6be5f30dbb2adaddc70f91559fc77cfed2686284c0c6ebe39524c37
[sid]
Package: igblast
Source: ncbi-igblast
Version: 1.20.0-2
Installed-Size: 69530
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Architecture: amd64
Depends: libbz2-1.0, libc6 (>= 2.38), libgcc-s1 (>= 3.0), libgomp1 (>= 6), libncbi-vdb3 (>= 3.0.9+dfsg), libstdc++6 (>= 14), libzstd1 (>= 1.5.5), zlib1g (>= 1:1.2.11.dfsg)
Recommends: ncbi-blast+
Description: Immunoglobulin and T cell receptor variable domain sequence analysis
Homepage: https://ncbi.github.io/igblast/
Description-md5: 2962314d8994f10816be6f57d21f8ffc
Section: science
Priority: optional
Filename: pool/main/n/ncbi-igblast/igblast_1.20.0-2_amd64.deb
Size: 18843528
MD5sum: 1e2ed825eecc01062da8cd1a08cb4b49
SHA256: 127c1aa5bc0939ae6af5ecf29368b02882fb33489285b08c86b50f8698be93c1
Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/bin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt igblast=1.20.0-2
0m0.0s INFO: ------------------------------------------------------------------------------
0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile.
0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ
0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong.
0m0.0s INFO: ------------------------------------------------------------------------------
0m0.0s INFO: piuparts version 1.5.2~202503032318~1.5.1-8-g1db83cba starting up.
0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/bin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt igblast=1.20.0-2
0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-34-amd64 #1 SMP Debian 5.10.234-1 (2025-02-24) x86_64
0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmp2syewsvc
0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp2syewsvc
0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz']
0m0.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz']
0m0.2s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp2syewsvc/proc']
0m0.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp2syewsvc/proc']
0m0.2s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp2syewsvc/dev/pts']
0m0.2s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp2syewsvc/dev/pts']
0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp2syewsvc/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp2syewsvc/dev/ptmx']
0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp2syewsvc/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp2syewsvc/dev/ptmx']
0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmp2syewsvc/dev/console']
0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmp2syewsvc/dev/console']
0m0.2s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp2syewsvc/dev/shm']
0m0.2s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp2syewsvc/dev/shm']
0m0.2s DEBUG: sources.list:
deb http://deb.debian.org/debian/ trixie main
0m0.2s DEBUG: Created policy-rc.d and chmodded it.
0m0.2s DEBUG: Created resolv.conf.
0m0.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp2syewsvc/tmp/scripts/
0m0.2s INFO: Running scripts post_chroot_unpack
0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated']
0m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated']
0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'apt-get', 'update']
0m1.5s DUMP:
Get:1 http://deb.debian.org/debian trixie InRelease [175 kB]
Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9513 kB]
Get:3 http://deb.debian.org/debian trixie/main Translation-en [6378 kB]
Fetched 16.1 MB in 1s (18.9 MB/s)
Reading package lists...
0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'apt-get', 'update']
0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'apt-get', '-yf', 'dist-upgrade']
0m2.4s DUMP:
Reading package lists...
Building dependency tree...
Calculating upgrade...
The following packages will be upgraded:
apt libapt-pkg7.0
2 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
Need to get 2545 kB of archives.
After this operation, 2048 B of additional disk space will be used.
Get:1 http://deb.debian.org/debian trixie/main amd64 libapt-pkg7.0 amd64 2.9.31 [1105 kB]
Get:2 http://deb.debian.org/debian trixie/main amd64 apt amd64 2.9.31 [1441 kB]
Fetched 2545 kB in 0s (29.6 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 ... 4909 files and directories currently installed.)
Preparing to unpack .../libapt-pkg7.0_2.9.31_amd64.deb ...
Unpacking libapt-pkg7.0:amd64 (2.9.31) over (2.9.30) ...
Setting up libapt-pkg7.0:amd64 (2.9.31) ...
(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 ... 4909 files and directories currently installed.)
Preparing to unpack .../archives/apt_2.9.31_amd64.deb ...
Unpacking apt (2.9.31) over (2.9.30) ...
Setting up apt (2.9.31) ...
Processing triggers for libc-bin (2.40-7) ...
0m2.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'apt-get', '-yf', 'dist-upgrade']
0m2.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'sh', '-c', 'apt-cache dumpavail | md5sum']
0m2.9s DUMP:
e8efb52abab8cae86d169d54cc775a24 -
0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'sh', '-c', 'apt-cache dumpavail | md5sum']
0m2.9s INFO: Running scripts post_setup
0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/post_setup_dummy_users']
0m3.3s 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
0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/post_setup_dummy_users']
0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/post_setup_forbid_home']
0m3.3s DUMP:
Disabling /home
Adding 'local diversion of /home to /home.distrib'
0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/post_setup_forbid_home']
0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/post_setup_force-unsafe-io']
0m3.3s 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'
0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/post_setup_force-unsafe-io']
0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/post_setup_minimize']
0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/post_setup_minimize']
0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/post_setup_squeeze-backports']
0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/post_setup_squeeze-backports']
0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/post_setup_zz_backports']
0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/post_setup_zz_backports']
0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n']
0m3.3s DUMP:
install ok installed apt apt 2.9.31
install ok installed base-files base-files 13.6
install ok installed base-passwd base-passwd 3.6.6
install ok installed bash bash 5.2.37-1.1
install ok installed bsdutils bsdutils 1:2.40.4-5
install ok installed coreutils coreutils 9.5-1+b1
install ok installed dash dash 0.5.12-12
install ok installed debconf debconf 1.5.89
install ok installed debian-archive-keyring debian-archive-keyring 2023.4
install ok installed debianutils debianutils 5.21
install ok installed diffutils diffutils 1:3.10-2
install ok installed dpkg dpkg 1.22.15
install ok installed findutils findutils 4.10.0-3
install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-17
install ok installed grep grep 3.11-4
install ok installed gzip gzip 1.13-1
install ok installed hostname hostname 3.25
install ok installed init-system-helpers init-system-helpers 1.68
install ok installed libacl1:amd64 libacl1 2.3.2-2+b1
install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 2.9.31
install ok installed libattr1:amd64 libattr1 1:2.5.2-3
install ok installed libaudit-common libaudit-common 1:4.0.2-2
install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2+b2
install ok installed libblkid1:amd64 libblkid1 2.40.4-5
install ok installed libbsd0:amd64 libbsd0 0.12.2-2
install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6
install ok installed libc-bin libc-bin 2.40-7
install ok installed libc6:amd64 libc6 2.40-7
install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1
install ok installed libcap2:amd64 libcap2 1:2.66-5+b1
install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1
install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9
install ok installed libdebconfclient0:amd64 libdebconfclient0 0.277
install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-17
install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3
install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1
install ok installed liblz4-1:amd64 liblz4-1 1.10.0-3
install ok installed liblzma5:amd64 liblzma5 5.6.4-1
install ok installed libmd0:amd64 libmd0 1.1.0-2+b1
install ok installed libmount1:amd64 libmount1 2.40.4-5
install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1
install ok installed libpam-modules:amd64 libpam-modules 1.7.0-3
install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-3
install ok installed libpam-runtime libpam-runtime 1.7.0-3
install ok installed libpam0g:amd64 libpam0g 1.7.0-3
install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.45-1
install ok installed libseccomp2:amd64 libseccomp2 2.5.5-2+b1
install ok installed libselinux1:amd64 libselinux1 3.8-4
install ok installed libsemanage-common libsemanage-common 3.8-1
install ok installed libsemanage2:amd64 libsemanage2 3.8-1+b1
install ok installed libsepol2:amd64 libsepol2 3.8-1
install ok installed libsmartcols1:amd64 libsmartcols1 2.40.4-5
install ok installed libssl3t64:amd64 libssl3t64 3.4.1-1
install ok installed libstdc++6:amd64 libstdc++6 14.2.0-17
install ok installed libsystemd0:amd64 libsystemd0 257.3-1
install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-1
install ok installed libudev1:amd64 libudev1 257.3-1
install ok installed libuuid1:amd64 libuuid1 2.40.4-5
install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2
install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-2
install ok installed login login 1:4.16.0-2+really2.40.4-5
install ok installed login.defs login.defs 1:4.17.3-1
install ok installed mawk mawk 1.3.4.20250131-1
install ok installed mount mount 2.40.4-5
install ok installed ncurses-base ncurses-base 6.5+20250216-1
install ok installed ncurses-bin ncurses-bin 6.5+20250216-1
install ok installed openssl-provider-legacy openssl-provider-legacy 3.4.1-1
install ok installed passwd passwd 1:4.17.3-1
install ok installed perl-base perl-base 5.40.1-2
install ok installed sed sed 4.9-2
install ok installed sqv sqv 1.2.1-6+b1
install ok installed sysvinit-utils sysvinit-utils 3.14-3
install ok installed tar tar 1.35+dfsg-3.1
install ok installed tzdata tzdata 2025a-2
install ok installed usr-is-merged usr-is-merged 39+nmu2
install ok installed util-linux util-linux 2.40.4-5
install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1
0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n']
0m3.3s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat
0m3.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp2syewsvc']
0m3.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp2syewsvc']
0m3.5s INFO: Running scripts is_testable
0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/is_testable_uninstallable']
0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/is_testable_uninstallable']
0m3.5s INFO: Running scripts pre_test
0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_test_exceptions']
0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_test_exceptions']
0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_test_root_password']
0m3.6s DUMP:
New password: Retype new password: passwd: password updated successfully
0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_test_root_password']
0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'apt-cache', 'show', '--no-all-versions', 'igblast']
0m3.7s DUMP:
Package: igblast
Source: ncbi-igblast (1.19.0-1)
Version: 1.19.0-1+b1
Installed-Size: 226928
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Architecture: amd64
Depends: libc6 (>= 2.34), libgcc-s1 (>= 3.0), libstdc++6 (>= 11)
Description-en: Immunoglobulin and T cell receptor variable domain sequence analysis
IgBLAST allows users to view the matches to the germline V, D, and J
genes, details at rearrangement junctions, the delineation of IG V
domain framework regions, and complementarity determining regions.
IgBLAST has the capability to analyse nucleotide and protein
sequences, and can process sequences in batches. Furthermore,
IgBLAST allows searches against the germline gene databases and other
sequence databases simultaneously to minimize the chance of missing
possibly the best matching germline V gene.
Description-md5: 2962314d8994f10816be6f57d21f8ffc
Homepage: https://ncbi.github.io/igblast/
Section: science
Priority: optional
Filename: pool/main/n/ncbi-igblast/igblast_1.19.0-1+b1_amd64.deb
Size: 38239560
MD5sum: 3d0a8526b1ae4438539a817e773cfa70
SHA256: 5c4557e8b6be5f30dbb2adaddc70f91559fc77cfed2686284c0c6ebe39524c37
0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'apt-cache', 'show', '--no-all-versions', 'igblast']
0m3.7s INFO: apt-cache knows about the following packages: igblast
0m3.7s INFO: Running scripts pre_install
0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_install_database-server']
0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_install_database-server']
0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_install_exceptions']
0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_install_exceptions']
0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_install_extras']
0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_install_extras']
0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_install_foreign_architecture']
0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_install_foreign_architecture']
0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_install_foreign_architecture_i386']
0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_install_foreign_architecture_i386']
0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'apt-cache', 'policy']
0m3.7s DUMP:
Package files:
100 /var/lib/dpkg/status
release a=now
500 http://deb.debian.org/debian trixie/main amd64 Packages
release o=Debian,a=testing,n=trixie,l=Debian,c=main,b=amd64
origin deb.debian.org
Pinned packages:
0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'apt-cache', 'policy']
0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'apt-cache', 'policy', 'igblast']
0m3.7s DUMP:
igblast:
Installed: (none)
Candidate: 1.19.0-1+b1
Version table:
1.19.0-1+b1 500
500 http://deb.debian.org/debian trixie/main amd64 Packages
0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'apt-cache', 'policy', 'igblast']
0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'apt-get', '-y', 'install', 'igblast']
0m6.5s DUMP:
Reading package lists...
Building dependency tree...
Reading state information...
The following NEW packages will be installed:
igblast
0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded.
Need to get 38.2 MB of archives.
After this operation, 232 MB of additional disk space will be used.
Get:1 http://deb.debian.org/debian trixie/main amd64 igblast amd64 1.19.0-1+b1 [38.2 MB]
Fetched 38.2 MB in 2s (24.4 MB/s)
Selecting previously unselected package igblast.
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Preparing to unpack .../igblast_1.19.0-1+b1_amd64.deb ...
Unpacking igblast (1.19.0-1+b1) ...
Setting up igblast (1.19.0-1+b1) ...
0m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'apt-get', '-y', 'install', 'igblast']
0m6.5s INFO: Running scripts post_install
0m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/post_install_exceptions']
0m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/post_install_exceptions']
0m6.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp2syewsvc']
0m6.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp2syewsvc']
0m6.7s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmp2syewsvc to sid
0m6.7s DEBUG: sources.list:
deb http://deb.debian.org/debian/ sid main
0m6.7s INFO: Running scripts pre_distupgrade
0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_distupgrade_allow_unauthenticated']
0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_distupgrade_allow_unauthenticated']
0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_distupgrade_exceptions']
0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_distupgrade_exceptions']
0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386']
0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386']
0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_distupgrade_zz_database-server']
0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_distupgrade_zz_database-server']
0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_distupgrade_zz_upgrade_early']
0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_distupgrade_zz_upgrade_early']
0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'apt-get', 'update']
0m8.7s DUMP:
Get:1 http://deb.debian.org/debian sid InRelease [205 kB]
Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.1 MB]
Get:3 http://deb.debian.org/debian sid/main Translation-en [7377 kB]
Fetched 17.7 MB in 1s (12.1 MB/s)
Reading package lists...
0m8.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'apt-get', 'update']
0m8.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'apt-get', '-yf', 'dist-upgrade']
0m11.8s DUMP:
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
The following NEW packages will be installed:
libgomp1 libmbedcrypto16 libmbedtls21 libmbedx509-7 libncbi-vdb3
ncbi-vdb-data
The following packages will be upgraded:
base-files dpkg igblast libc-bin libc6 libcap2 liblz4-1 libsystemd0
libtinfo6 libudev1 ncurses-base ncurses-bin
12 upgraded, 6 newly installed, 0 to remove and 0 not upgraded.
Need to get 27.8 MB of archives.
After this operation, 155 MB disk space will be freed.
Get:1 http://deb.debian.org/debian sid/main amd64 libc6 amd64 2.41-3 [2841 kB]
Get:2 http://deb.debian.org/debian sid/main amd64 libc-bin amd64 2.41-3 [635 kB]
Get:3 http://deb.debian.org/debian sid/main amd64 base-files amd64 13.7 [73.0 kB]
Get:4 http://deb.debian.org/debian sid/main amd64 dpkg amd64 1.22.17 [1545 kB]
Get:5 http://deb.debian.org/debian sid/main amd64 ncurses-bin amd64 6.5+20250216-2 [438 kB]
Get:6 http://deb.debian.org/debian sid/main amd64 ncurses-base all 6.5+20250216-2 [273 kB]
Get:7 http://deb.debian.org/debian sid/main amd64 libcap2 amd64 1:2.73-4 [27.3 kB]
Get:8 http://deb.debian.org/debian sid/main amd64 liblz4-1 amd64 1.10.0-4 [63.9 kB]
Get:9 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 257.4-1 [451 kB]
Get:10 http://deb.debian.org/debian sid/main amd64 libtinfo6 amd64 6.5+20250216-2 [348 kB]
Get:11 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 257.4-1 [149 kB]
Get:12 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14.2.0-17 [137 kB]
Get:13 http://deb.debian.org/debian sid/main amd64 libmbedcrypto16 amd64 3.6.2-3 [355 kB]
Get:14 http://deb.debian.org/debian sid/main amd64 libmbedx509-7 amd64 3.6.2-3 [147 kB]
Get:15 http://deb.debian.org/debian sid/main amd64 libmbedtls21 amd64 3.6.2-3 [234 kB]
Get:16 http://deb.debian.org/debian sid/main amd64 ncbi-vdb-data all 3.0.9+dfsg-2 [74.0 kB]
Get:17 http://deb.debian.org/debian sid/main amd64 libncbi-vdb3 amd64 3.0.9+dfsg-2 [1189 kB]
Get:18 http://deb.debian.org/debian sid/main amd64 igblast amd64 1.20.0-2 [18.8 MB]
Preconfiguring packages ...
Fetched 27.8 MB in 1s (21.8 MB/s)
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Preparing to unpack .../libc6_2.41-3_amd64.deb ...
Unpacking libc6:amd64 (2.41-3) over (2.40-7) ...
Setting up libc6:amd64 (2.41-3) ...
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Preparing to unpack .../dpkg_1.22.17_amd64.deb ...
Unpacking dpkg (1.22.17) over (1.22.15) ...
Setting up dpkg (1.22.17) ...
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Preparing to unpack .../ncurses-bin_6.5+20250216-2_amd64.deb ...
Unpacking ncurses-bin (6.5+20250216-2) over (6.5+20250216-1) ...
Setting up ncurses-bin (6.5+20250216-2) ...
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Preparing to unpack .../ncurses-base_6.5+20250216-2_all.deb ...
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Preparing to unpack .../libcap2_1%3a2.73-4_amd64.deb ...
Unpacking libcap2:amd64 (1:2.73-4) over (1:2.66-5+b1) ...
Setting up libcap2:amd64 (1:2.73-4) ...
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Preparing to unpack .../liblz4-1_1.10.0-4_amd64.deb ...
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Preparing to unpack .../libsystemd0_257.4-1_amd64.deb ...
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Setting up libsystemd0:amd64 (257.4-1) ...
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Preparing to unpack .../libtinfo6_6.5+20250216-2_amd64.deb ...
Unpacking libtinfo6:amd64 (6.5+20250216-2) over (6.5+20250216-1) ...
Setting up libtinfo6:amd64 (6.5+20250216-2) ...
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Preparing to unpack .../libudev1_257.4-1_amd64.deb ...
Unpacking libudev1:amd64 (257.4-1) over (257.3-1) ...
Setting up libudev1:amd64 (257.4-1) ...
Selecting previously unselected package libgomp1:amd64.
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Preparing to unpack .../0-libgomp1_14.2.0-17_amd64.deb ...
Unpacking libgomp1:amd64 (14.2.0-17) ...
Selecting previously unselected package libmbedcrypto16:amd64.
Preparing to unpack .../1-libmbedcrypto16_3.6.2-3_amd64.deb ...
Unpacking libmbedcrypto16:amd64 (3.6.2-3) ...
Selecting previously unselected package libmbedx509-7:amd64.
Preparing to unpack .../2-libmbedx509-7_3.6.2-3_amd64.deb ...
Unpacking libmbedx509-7:amd64 (3.6.2-3) ...
Selecting previously unselected package libmbedtls21:amd64.
Preparing to unpack .../3-libmbedtls21_3.6.2-3_amd64.deb ...
Unpacking libmbedtls21:amd64 (3.6.2-3) ...
Selecting previously unselected package ncbi-vdb-data.
Preparing to unpack .../4-ncbi-vdb-data_3.0.9+dfsg-2_all.deb ...
Unpacking ncbi-vdb-data (3.0.9+dfsg-2) ...
Selecting previously unselected package libncbi-vdb3:amd64.
Preparing to unpack .../5-libncbi-vdb3_3.0.9+dfsg-2_amd64.deb ...
Unpacking libncbi-vdb3:amd64 (3.0.9+dfsg-2) ...
Preparing to unpack .../6-igblast_1.20.0-2_amd64.deb ...
Unpacking igblast (1.20.0-2) over (1.19.0-1+b1) ...
Setting up libgomp1:amd64 (14.2.0-17) ...
Setting up ncbi-vdb-data (3.0.9+dfsg-2) ...
Setting up libmbedcrypto16:amd64 (3.6.2-3) ...
Setting up libmbedx509-7:amd64 (3.6.2-3) ...
Setting up libmbedtls21:amd64 (3.6.2-3) ...
Setting up libncbi-vdb3:amd64 (3.0.9+dfsg-2) ...
Setting up igblast (1.20.0-2) ...
Processing triggers for libc-bin (2.41-3) ...
0m11.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'apt-get', '-yf', 'dist-upgrade']
0m11.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'sh', '-c', 'apt-cache dumpavail | md5sum']
0m12.0s DUMP:
f414d94d72896f43b597061d2e69e0d2 -
0m12.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'sh', '-c', 'apt-cache dumpavail | md5sum']
0m12.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'apt-cache', 'show', '--no-all-versions', 'igblast']
0m12.1s DUMP:
Package: igblast
Source: ncbi-igblast
Version: 1.20.0-2
Installed-Size: 69530
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Architecture: amd64
Depends: libbz2-1.0, libc6 (>= 2.38), libgcc-s1 (>= 3.0), libgomp1 (>= 6), libncbi-vdb3 (>= 3.0.9+dfsg), libstdc++6 (>= 14), libzstd1 (>= 1.5.5), zlib1g (>= 1:1.2.11.dfsg)
Recommends: ncbi-blast+
Description-en: Immunoglobulin and T cell receptor variable domain sequence analysis
IgBLAST allows users to view the matches to the germline V, D, and J
genes, details at rearrangement junctions, the delineation of IG V
domain framework regions, and complementarity determining regions.
IgBLAST has the capability to analyse nucleotide and protein
sequences, and can process sequences in batches. Furthermore,
IgBLAST allows searches against the germline gene databases and other
sequence databases simultaneously to minimize the chance of missing
possibly the best matching germline V gene.
Description-md5: 2962314d8994f10816be6f57d21f8ffc
Homepage: https://ncbi.github.io/igblast/
Section: science
Priority: optional
Filename: pool/main/n/ncbi-igblast/igblast_1.20.0-2_amd64.deb
Size: 18843528
MD5sum: 1e2ed825eecc01062da8cd1a08cb4b49
SHA256: 127c1aa5bc0939ae6af5ecf29368b02882fb33489285b08c86b50f8698be93c1
0m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'apt-cache', 'show', '--no-all-versions', 'igblast']
0m12.1s INFO: apt-cache knows about the following packages: igblast
0m12.1s INFO: Running scripts pre_install
0m12.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_install_database-server']
0m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_install_database-server']
0m12.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_install_exceptions']
0m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_install_exceptions']
0m12.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_install_extras']
0m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_install_extras']
0m12.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_install_foreign_architecture']
0m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_install_foreign_architecture']
0m12.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_install_foreign_architecture_i386']
0m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_install_foreign_architecture_i386']
0m12.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'apt-cache', 'policy']
0m12.1s 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:
0m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'apt-cache', 'policy']
0m12.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'apt-cache', 'policy', 'igblast']
0m12.1s DUMP:
igblast:
Installed: 1.20.0-2
Candidate: 1.20.0-2
Version table:
*** 1.20.0-2 500
500 http://deb.debian.org/debian sid/main amd64 Packages
100 /var/lib/dpkg/status
0m12.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'apt-cache', 'policy', 'igblast']
0m12.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'apt-get', '-y', 'install', 'igblast']
0m12.4s DUMP:
Reading package lists...
Building dependency tree...
Reading state information...
igblast is already the newest version (1.20.0-2).
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
0m12.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'apt-get', '-y', 'install', 'igblast']
0m12.4s INFO: Running scripts post_install
0m12.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/post_install_exceptions']
0m12.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/post_install_exceptions']
0m12.4s INFO: Running scripts post_distupgrade
0m12.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/post_distupgrade_base_cleanup']
0m12.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/post_distupgrade_base_cleanup']
0m12.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/post_distupgrade_exceptions']
0m12.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/post_distupgrade_exceptions']
0m12.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/post_distupgrade_force-unsafe-io']
0m12.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/post_distupgrade_force-unsafe-io']
0m12.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/post_distupgrade_squeeze-backports']
0m12.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/post_distupgrade_squeeze-backports']
0m12.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/post_distupgrade_zz_backports']
0m12.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/post_distupgrade_zz_backports']
0m12.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp2syewsvc']
0m12.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp2syewsvc']
0m12.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp2syewsvc']
0m12.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp2syewsvc']
0m12.8s INFO: Running scripts pre_install
0m12.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_install_database-server']
0m12.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_install_database-server']
0m12.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_install_exceptions']
0m12.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_install_exceptions']
0m12.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_install_extras']
0m12.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_install_extras']
0m12.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_install_foreign_architecture']
0m12.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_install_foreign_architecture']
0m12.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_install_foreign_architecture_i386']
0m12.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_install_foreign_architecture_i386']
0m12.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'apt-cache', 'policy']
0m12.9s 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:
0m12.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'apt-cache', 'policy']
0m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'apt-cache', 'policy', 'igblast']
0m12.9s DUMP:
igblast:
Installed: 1.20.0-2
Candidate: 1.20.0-2
Version table:
*** 1.20.0-2 500
500 http://deb.debian.org/debian sid/main amd64 Packages
100 /var/lib/dpkg/status
0m12.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'apt-cache', 'policy', 'igblast']
0m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'apt-get', '-y', 'install', 'igblast=1.20.0-2']
0m13.1s DUMP:
Reading package lists...
Building dependency tree...
Reading state information...
igblast is already the newest version (1.20.0-2).
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
0m13.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'apt-get', '-y', 'install', 'igblast=1.20.0-2']
0m13.1s INFO: Running scripts post_install
0m13.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/post_install_exceptions']
0m13.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/post_install_exceptions']
0m13.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp2syewsvc']
0m13.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp2syewsvc']
0m13.5s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', '-ac', '--ignore-obsolete']
0m14.0s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', '-ac', '--ignore-obsolete']
0m14.0s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate']
0m14.0s DUMP:
0.15.6
0m14.0s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate']
0m14.0s INFO: Running adequate version 0.15.6 now.
0m14.0s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'igblast']
0m14.1s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'igblast']
0m14.1s INFO: Running scripts pre_remove
0m14.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_remove_40_find_missing_md5sums']
0m14.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_remove_40_find_missing_md5sums']
0m14.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles']
0m14.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles']
0m14.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_remove_40_find_unowned_lib_links']
0m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_remove_40_find_unowned_lib_links']
0m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_remove_50_find_bad_permissions']
0m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_remove_50_find_bad_permissions']
0m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_remove_50_find_missing_copyright']
0m14.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_remove_50_find_missing_copyright']
0m14.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_remove_exceptions']
0m14.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/pre_remove_exceptions']
0m14.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n']
0m14.4s DUMP:
install ok installed apt apt 2.9.31
install ok installed base-files base-files 13.7
install ok installed base-passwd base-passwd 3.6.6
install ok installed bash bash 5.2.37-1.1
install ok installed bsdutils bsdutils 1:2.40.4-5
install ok installed coreutils coreutils 9.5-1+b1
install ok installed dash dash 0.5.12-12
install ok installed debconf debconf 1.5.89
install ok installed debian-archive-keyring debian-archive-keyring 2023.4
install ok installed debianutils debianutils 5.21
install ok installed diffutils diffutils 1:3.10-2
install ok installed dpkg dpkg 1.22.17
install ok installed findutils findutils 4.10.0-3
install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-17
install ok installed grep grep 3.11-4
install ok installed gzip gzip 1.13-1
install ok installed hostname hostname 3.25
install ok installed igblast igblast 1.20.0-2
install ok installed init-system-helpers init-system-helpers 1.68
install ok installed libacl1:amd64 libacl1 2.3.2-2+b1
install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 2.9.31
install ok installed libattr1:amd64 libattr1 1:2.5.2-3
install ok installed libaudit-common libaudit-common 1:4.0.2-2
install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2+b2
install ok installed libblkid1:amd64 libblkid1 2.40.4-5
install ok installed libbsd0:amd64 libbsd0 0.12.2-2
install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6
install ok installed libc-bin libc-bin 2.41-3
install ok installed libc6:amd64 libc6 2.41-3
install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1
install ok installed libcap2:amd64 libcap2 1:2.73-4
install ok installed libcrypt1:amd64 libcrypt1 1:4.4.38-1
install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9
install ok installed libdebconfclient0:amd64 libdebconfclient0 0.277
install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-17
install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3
install ok installed libgomp1:amd64 libgomp1 14.2.0-17
install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1
install ok installed liblz4-1:amd64 liblz4-1 1.10.0-4
install ok installed liblzma5:amd64 liblzma5 5.6.4-1
install ok installed libmbedcrypto16:amd64 libmbedcrypto16 3.6.2-3
install ok installed libmbedtls21:amd64 libmbedtls21 3.6.2-3
install ok installed libmbedx509-7:amd64 libmbedx509-7 3.6.2-3
install ok installed libmd0:amd64 libmd0 1.1.0-2+b1
install ok installed libmount1:amd64 libmount1 2.40.4-5
install ok installed libncbi-vdb3:amd64 libncbi-vdb3 3.0.9+dfsg-2
install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1
install ok installed libpam-modules:amd64 libpam-modules 1.7.0-3
install ok installed libpam-modules-bin libpam-modules-bin 1.7.0-3
install ok installed libpam-runtime libpam-runtime 1.7.0-3
install ok installed libpam0g:amd64 libpam0g 1.7.0-3
install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.45-1
install ok installed libseccomp2:amd64 libseccomp2 2.5.5-2+b1
install ok installed libselinux1:amd64 libselinux1 3.8-4
install ok installed libsemanage-common libsemanage-common 3.8-1
install ok installed libsemanage2:amd64 libsemanage2 3.8-1+b1
install ok installed libsepol2:amd64 libsepol2 3.8-1
install ok installed libsmartcols1:amd64 libsmartcols1 2.40.4-5
install ok installed libssl3t64:amd64 libssl3t64 3.4.1-1
install ok installed libstdc++6:amd64 libstdc++6 14.2.0-17
install ok installed libsystemd0:amd64 libsystemd0 257.4-1
install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2
install ok installed libudev1:amd64 libudev1 257.4-1
install ok installed libuuid1:amd64 libuuid1 2.40.4-5
install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2
install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-2
install ok installed login login 1:4.16.0-2+really2.40.4-5
install ok installed login.defs login.defs 1:4.17.3-1
install ok installed mawk mawk 1.3.4.20250131-1
install ok installed mount mount 2.40.4-5
install ok installed ncbi-vdb-data ncbi-vdb-data 3.0.9+dfsg-2
install ok installed ncurses-base ncurses-base 6.5+20250216-2
install ok installed ncurses-bin ncurses-bin 6.5+20250216-2
install ok installed openssl-provider-legacy openssl-provider-legacy 3.4.1-1
install ok installed passwd passwd 1:4.17.3-1
install ok installed perl-base perl-base 5.40.1-2
install ok installed sed sed 4.9-2
install ok installed sqv sqv 1.2.1-6+b1
install ok installed sysvinit-utils sysvinit-utils 3.14-3
install ok installed tar tar 1.35+dfsg-3.1
install ok installed tzdata tzdata 2025a-2
install ok installed usr-is-merged usr-is-merged 39+nmu2
install ok installed util-linux util-linux 2.40.4-5
install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1
0m14.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n']
0m14.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'apt-get', 'remove', '--allow-remove-essential', 'libgomp1:amd64', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libncbi-vdb3:amd64', 'ncbi-vdb-data', 'igblast']
0m14.8s DUMP:
Reading package lists...
Building dependency tree...
Reading state information...
The following packages will be REMOVED:
igblast libgomp1 libmbedcrypto16 libmbedtls21 libmbedx509-7 libncbi-vdb3
ncbi-vdb-data
0 upgraded, 0 newly installed, 7 to remove and 0 not upgraded.
After this operation, 77.0 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 ... 5125 files and directories currently installed.)
Removing igblast (1.20.0-2) ...
Removing libgomp1:amd64 (14.2.0-17) ...
Removing libncbi-vdb3:amd64 (3.0.9+dfsg-2) ...
Removing libmbedtls21:amd64 (3.6.2-3) ...
Removing libmbedx509-7:amd64 (3.6.2-3) ...
Removing libmbedcrypto16:amd64 (3.6.2-3) ...
Removing ncbi-vdb-data (3.0.9+dfsg-2) ...
Processing triggers for libc-bin (2.41-3) ...
0m14.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'apt-get', 'remove', '--allow-remove-essential', 'libgomp1:amd64', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libncbi-vdb3:amd64', 'ncbi-vdb-data', 'igblast']
0m14.8s INFO: Running scripts post_remove
0m14.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/post_remove_exceptions']
0m14.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/post_remove_exceptions']
0m14.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'dpkg', '--purge', 'libgomp1:amd64', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libncbi-vdb3:amd64', 'ncbi-vdb-data']
0m14.8s DUMP:
dpkg: warning: ignoring request to remove libgomp1 which isn't installed
dpkg: warning: ignoring request to remove libmbedcrypto16 which isn't installed
dpkg: warning: ignoring request to remove libmbedtls21 which isn't installed
dpkg: warning: ignoring request to remove libmbedx509-7 which isn't installed
dpkg: warning: ignoring request to remove libncbi-vdb3 which isn't installed
dpkg: warning: ignoring request to remove ncbi-vdb-data which isn't installed
0m14.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'dpkg', '--purge', 'libgomp1:amd64', 'libmbedcrypto16:amd64', 'libmbedtls21:amd64', 'libmbedx509-7:amd64', 'libncbi-vdb3:amd64', 'ncbi-vdb-data']
0m14.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'dpkg', '--purge', 'igblast']
0m14.8s DUMP:
dpkg: warning: ignoring request to remove igblast which isn't installed
0m14.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'dpkg', '--purge', 'igblast']
0m14.8s INFO: Running scripts post_purge
0m14.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/post_purge_exceptions']
0m14.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/post_purge_exceptions']
0m14.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'dpkg', '--purge', '--pending']
0m14.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'dpkg', '--purge', '--pending']
0m14.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'dpkg', '--remove', '--pending']
0m14.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'dpkg', '--remove', '--pending']
0m14.8s INFO: Running scripts post_test
0m14.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/post_test_exceptions']
0m14.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'tmp/scripts/post_test_exceptions']
0m14.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp2syewsvc']
0m15.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp2syewsvc']
0m15.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'dpkg-divert', '--list']
0m15.1s DUMP:
local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged
local diversion of /home to /home.distrib
diversion of /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6
diversion of /libx32 to /.libx32.usr-is-merged by base-files
local diversion of /usr/bin/sync to /usr/bin/sync.distrib
diversion of /lib32 to /.lib32.usr-is-merged by base-files
diversion of /libo32 to /.libo32.usr-is-merged by base-files
0m15.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'dpkg-divert', '--list']
0m15.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'apt-get', 'clean']
0m15.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp2syewsvc', 'apt-get', 'clean']
0m15.1s DEBUG: Recording chroot state
0m15.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp2syewsvc/dev/shm']
0m15.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp2syewsvc/dev/shm']
0m15.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp2syewsvc/dev/console']
0m15.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp2syewsvc/dev/console']
0m15.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp2syewsvc/dev/ptmx']
0m15.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp2syewsvc/dev/ptmx']
0m15.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp2syewsvc/dev/pts']
0m15.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp2syewsvc/dev/pts']
0m15.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp2syewsvc/proc']
0m15.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp2syewsvc/proc']
0m15.7s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp2syewsvc']
0m15.8s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp2syewsvc']
0m15.8s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp2syewsvc
0m15.8s INFO: PASS: Upgrading between Debian distributions.
0m15.8s INFO: PASS: All tests.
0m15.8s INFO: piuparts run ends.
ret=0
End: 2025-03-07 15:44:09 GMT