Start: 2025-04-10 12:54:10 GMT
[stable]
Package: libncbi-wvdb-dev
Source: ncbi-vdb
Version: 3.0.2+dfsg-2
Installed-Size: 5190
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Architecture: amd64
Depends: libncbi-wvdb3 (= 3.0.2+dfsg-2)
Description: virtual layer update module of ncbi-vdb library (devel)
Multi-Arch: same
Homepage: https://github.com/ncbi/ncbi-vdb
Description-md5: 86b1533d3960704980cb451336afdcfe
Tag: devel::library, role::devel-lib
Section: libdevel
Priority: optional
Filename: pool/main/n/ncbi-vdb/libncbi-wvdb-dev_3.0.2+dfsg-2_amd64.deb
Size: 1187524
MD5sum: d27c722a0b7de6d43a8f41b57d6194ce
SHA256: 2cece8f7f2441f7ce74a56c1437a770dc4b1b613b59e3f160521f84ef36bbb8b
[testing]
Package: libncbi-wvdb-dev
Source: ncbi-vdb
Version: 3.0.9+dfsg-2
Installed-Size: 6050
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Architecture: amd64
Depends: libncbi-wvdb3 (= 3.0.9+dfsg-2)
Description: virtual layer update module of ncbi-vdb library (devel)
Multi-Arch: same
Homepage: https://github.com/ncbi/ncbi-vdb
Description-md5: 86b1533d3960704980cb451336afdcfe
Tag: devel::library, role::devel-lib
Section: libdevel
Priority: optional
Filename: pool/main/n/ncbi-vdb/libncbi-wvdb-dev_3.0.9+dfsg-2_amd64.deb
Size: 1311164
MD5sum: 765f6cccbc269f07ca8ae81f36acff45
SHA256: 9120e1bc0e0980bedd34c3b71316fd151ff451b0d32be2963c2ee9717d45ec85
[sid]
Package: libncbi-wvdb-dev
Source: ncbi-vdb
Version: 3.2.1+dfsg-2
Installed-Size: 5977
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Architecture: amd64
Depends: libbz2-dev, libmbedtls-dev, libzstd-dev, zlib1g-dev, libncbi-wvdb3 (= 3.2.1+dfsg-2)
Description: virtual layer update module of ncbi-vdb library (devel)
Multi-Arch: same
Homepage: https://github.com/ncbi/ncbi-vdb
Description-md5: 86b1533d3960704980cb451336afdcfe
Tag: devel::library, role::devel-lib
Section: libdevel
Priority: optional
Filename: pool/main/n/ncbi-vdb/libncbi-wvdb-dev_3.2.1+dfsg-2_amd64.deb
Size: 1285964
MD5sum: e4ab166584518707d5022fb3b89694b9
SHA256: 0e02dc63801e9c62f065dffc8d620b54c6b9aa0460702e446da4c6cca050549d
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/bookworm-merged-usr_amd64.tar.gz -d stable -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/stable22sid/reference-chroot-metadata.dat --apt libncbi-wvdb-dev=3.2.1+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 1.5.2~202503162239~1.5.1-10-g345d5865 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/bookworm-merged-usr_amd64.tar.gz -d stable -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/stable22sid/reference-chroot-metadata.dat --apt libncbi-wvdb-dev=3.2.1+dfsg-2
0m0.0s INFO: Running on: Linux piu-slave-conova-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/tmpk4d9ryh2
0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpk4d9ryh2
0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz']
0m0.3s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz']
0m0.3s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2/proc']
0m0.3s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2/proc']
0m0.3s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2/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/tmpk4d9ryh2/dev/pts']
0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2/dev/ptmx']
0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2/dev/ptmx']
0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/7', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2/dev/console']
0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/7', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2/dev/console']
0m0.4s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2/dev/shm']
0m0.4s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2/dev/shm']
0m0.4s DEBUG: sources.list:
deb http://deb.debian.org/debian/ bookworm main
0m0.4s DEBUG: Created policy-rc.d and chmodded it.
0m0.4s DEBUG: Created resolv.conf.
0m0.4s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpk4d9ryh2/tmp/scripts/
0m0.4s INFO: Running scripts post_chroot_unpack
0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated']
0m0.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated']
0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-get', 'update']
0m1.2s DUMP:
Hit:1 http://deb.debian.org/debian bookworm InRelease
Reading package lists...
0m1.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-get', 'update']
0m1.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-get', '-yf', 'dist-upgrade']
0m1.6s DUMP:
Reading package lists...
Building dependency tree...
Calculating upgrade...
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
0m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-get', '-yf', 'dist-upgrade']
0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'sh', '-c', 'apt-cache dumpavail | md5sum']
0m2.2s DUMP:
3b6124cc38d42e60354965f1a19282fe -
0m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'sh', '-c', 'apt-cache dumpavail | md5sum']
0m2.2s INFO: Running scripts post_setup
0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_setup_dummy_users']
0m3.2s 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
0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_setup_dummy_users']
0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_setup_forbid_home']
0m3.2s DUMP:
Disabling /home
Adding 'local diversion of /home to /home.distrib'
0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_setup_forbid_home']
0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_setup_force-unsafe-io']
0m3.2s 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'
0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_setup_force-unsafe-io']
0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_setup_minimize']
0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_setup_minimize']
0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_setup_squeeze-backports']
0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_setup_squeeze-backports']
0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_setup_zz_backports']
0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_setup_zz_backports']
0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n']
0m3.3s DUMP:
install ok installed adduser adduser 3.134
install ok installed apt apt 2.6.1
install ok installed base-files base-files 12.4+deb12u10
install ok installed base-passwd base-passwd 3.6.1
install ok installed bash bash 5.2.15-2+b7
install ok installed bsdutils bsdutils 1:2.38.1-5+deb12u3
install ok installed coreutils coreutils 9.1-1
install ok installed dash dash 0.5.12-2
install ok installed debconf debconf 1.5.82
install ok installed debian-archive-keyring debian-archive-keyring 2023.3+deb12u1
install ok installed debianutils debianutils 5.7-0.5~deb12u1
install ok installed diffutils diffutils 1:3.8-4
install ok installed dpkg dpkg 1.21.22
install ok installed e2fsprogs e2fsprogs 1.47.0-2
install ok installed findutils findutils 4.9.0-4
install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-14
install ok installed gpgv gpgv 2.2.40-1.1
install ok installed grep grep 3.8-5
install ok installed gzip gzip 1.12-1
install ok installed hostname hostname 3.23+nmu1
install ok installed init-system-helpers init-system-helpers 1.65.2
install ok installed libacl1:amd64 libacl1 2.3.1-3
install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.6.1
install ok installed libattr1:amd64 libattr1 1:2.5.1-4
install ok installed libaudit-common libaudit-common 1:3.0.9-1
install ok installed libaudit1:amd64 libaudit1 1:3.0.9-1
install ok installed libblkid1:amd64 libblkid1 2.38.1-5+deb12u3
install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1
install ok installed libc-bin libc-bin 2.36-9+deb12u10
install ok installed libc6:amd64 libc6 2.36-9+deb12u10
install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3
install ok installed libcap2:amd64 libcap2 1:2.66-4
install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2
install ok installed libcrypt1:amd64 libcrypt1 1:4.4.33-2
install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-1
install ok installed libdebconfclient0:amd64 libdebconfclient0 0.270
install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2
install ok installed libffi8:amd64 libffi8 3.4.4-1
install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-14
install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-3
install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1
install ok installed libgnutls30:amd64 libgnutls30 3.7.9-2+deb12u4
install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1
install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2
install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1
install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1
install ok installed liblzma5:amd64 liblzma5 5.4.1-0.2
install ok installed libmd0:amd64 libmd0 1.0.4-2
install ok installed libmount1:amd64 libmount1 2.38.1-5+deb12u3
install ok installed libnettle8:amd64 libnettle8 3.8.1-2
install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-2
install ok installed libpam-modules:amd64 libpam-modules 1.5.2-6+deb12u1
install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-6+deb12u1
install ok installed libpam-runtime libpam-runtime 1.5.2-6+deb12u1
install ok installed libpam0g:amd64 libpam0g 1.5.2-6+deb12u1
install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-1
install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+deb12u1
install ok installed libselinux1:amd64 libselinux1 3.4-1+b6
install ok installed libsemanage-common libsemanage-common 3.4-1
install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b5
install ok installed libsepol2:amd64 libsepol2 3.4-2.1
install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-5+deb12u3
install ok installed libss2:amd64 libss2 1.47.0-2
install ok installed libstdc++6:amd64 libstdc++6 12.2.0-14
install ok installed libsystemd0:amd64 libsystemd0 252.36-1~deb12u1
install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2+deb12u1
install ok installed libtinfo6:amd64 libtinfo6 6.4-4
install ok installed libudev1:amd64 libudev1 252.36-1~deb12u1
install ok installed libunistring2:amd64 libunistring2 1.0-2
install ok installed libuuid1:amd64 libuuid1 2.38.1-5+deb12u3
install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1
install ok installed libzstd1:amd64 libzstd1 1.5.4+dfsg2-5
install ok installed login login 1:4.13+dfsg1-1+b1
install ok installed logsave logsave 1.47.0-2
install ok installed mawk mawk 1.3.4.20200120-3.1
install ok installed mount mount 2.38.1-5+deb12u3
install ok installed ncurses-base ncurses-base 6.4-4
install ok installed ncurses-bin ncurses-bin 6.4-4
install ok installed passwd passwd 1:4.13+dfsg1-1+b1
install ok installed perl-base perl-base 5.36.0-7+deb12u1
install ok installed sed sed 4.9-1
install ok installed sysvinit-utils sysvinit-utils 3.06-4
install ok installed tar tar 1.34+dfsg-1.2+deb12u1
install ok installed tzdata tzdata 2025a-0+deb12u1
install ok installed usr-is-merged usr-is-merged 37~deb12u1
install ok installed util-linux util-linux 2.38.1-5+deb12u3
install ok installed util-linux-extra util-linux-extra 2.38.1-5+deb12u3
install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1
0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', '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/stable22sid/reference-chroot-metadata.dat
0m3.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2']
0m3.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2']
0m3.7s INFO: Running scripts is_testable
0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/is_testable_uninstallable']
0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/is_testable_uninstallable']
0m3.7s INFO: Running scripts pre_test
0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_test_exceptions']
0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_test_exceptions']
0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_test_root_password']
0m3.8s DUMP:
New password: Retype new password: passwd: password updated successfully
0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_test_root_password']
0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-cache', 'show', '--no-all-versions', 'libncbi-wvdb-dev']
0m4.0s DUMP:
Package: libncbi-wvdb-dev
Source: ncbi-vdb
Version: 3.0.2+dfsg-2
Installed-Size: 5190
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Architecture: amd64
Depends: libncbi-wvdb3 (= 3.0.2+dfsg-2)
Description-en: virtual layer update module of ncbi-vdb library (devel)
The (US) National Center for Biotechnology Information (NCBI)'s
Virtual/Vertical Database (VDB) is a highly compressed column-oriented
data warehousing technology developed initially to address the needs
of the Sequence Read Archive (SRA). It is unique in that it builds
databases from smaller parts that can function independently as
_documents_, supports effective and efficient compression, supports
encryption while remaining encrypted on disk, transparent distribution
and remote access.
.
This package contains development files for updating VDB data.
Description-md5: 86b1533d3960704980cb451336afdcfe
Multi-Arch: same
Homepage: https://github.com/ncbi/ncbi-vdb
Tag: devel::library, role::devel-lib
Section: libdevel
Priority: optional
Filename: pool/main/n/ncbi-vdb/libncbi-wvdb-dev_3.0.2+dfsg-2_amd64.deb
Size: 1187524
MD5sum: d27c722a0b7de6d43a8f41b57d6194ce
SHA256: 2cece8f7f2441f7ce74a56c1437a770dc4b1b613b59e3f160521f84ef36bbb8b
0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-cache', 'show', '--no-all-versions', 'libncbi-wvdb-dev']
0m4.0s INFO: apt-cache knows about the following packages: libncbi-wvdb-dev
0m4.0s INFO: Running scripts pre_install
0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_install_database-server']
0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_install_database-server']
0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_install_exceptions']
0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_install_exceptions']
0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_install_extras']
0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_install_extras']
0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_install_foreign_architecture']
0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_install_foreign_architecture']
0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_install_foreign_architecture_i386']
0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_install_foreign_architecture_i386']
0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-cache', 'policy']
0m4.0s DUMP:
Package files:
100 /var/lib/dpkg/status
release a=now
500 http://deb.debian.org/debian bookworm/main amd64 Packages
release v=12.10,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64
origin deb.debian.org
Pinned packages:
0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-cache', 'policy']
0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-cache', 'policy', 'libncbi-wvdb-dev']
0m4.1s DUMP:
libncbi-wvdb-dev:
Installed: (none)
Candidate: 3.0.2+dfsg-2
Version table:
3.0.2+dfsg-2 500
500 http://deb.debian.org/debian bookworm/main amd64 Packages
0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-cache', 'policy', 'libncbi-wvdb-dev']
0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-get', '-y', 'install', 'libncbi-wvdb-dev']
0m5.4s DUMP:
Reading package lists...
Building dependency tree...
The following additional packages will be installed:
libmbedcrypto7 libmbedtls14 libmbedx509-1 libncbi-wvdb3 ncbi-vdb-data
The following NEW packages will be installed:
libmbedcrypto7 libmbedtls14 libmbedx509-1 libncbi-wvdb-dev libncbi-wvdb3
ncbi-vdb-data
0 upgraded, 6 newly installed, 0 to remove and 0 not upgraded.
Need to get 2907 kB of archives.
After this operation, 10.1 MB of additional disk space will be used.
Get:1 http://deb.debian.org/debian bookworm/main amd64 libmbedcrypto7 amd64 2.28.3-1 [277 kB]
Get:2 http://deb.debian.org/debian bookworm/main amd64 libmbedx509-1 amd64 2.28.3-1 [128 kB]
Get:3 http://deb.debian.org/debian bookworm/main amd64 libmbedtls14 amd64 2.28.3-1 [163 kB]
Get:4 http://deb.debian.org/debian bookworm/main amd64 ncbi-vdb-data all 3.0.2+dfsg-2 [73.3 kB]
Get:5 http://deb.debian.org/debian bookworm/main amd64 libncbi-wvdb3 amd64 3.0.2+dfsg-2 [1078 kB]
Get:6 http://deb.debian.org/debian bookworm/main amd64 libncbi-wvdb-dev amd64 3.0.2+dfsg-2 [1188 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 2907 kB in 0s (39.7 MB/s)
Selecting previously unselected package libmbedcrypto7:amd64.
(Reading database ...
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(Reading database ... 10%
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(Reading database ... 20%
(Reading database ... 25%
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(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 6093 files and directories currently installed.)
Preparing to unpack .../0-libmbedcrypto7_2.28.3-1_amd64.deb ...
Unpacking libmbedcrypto7:amd64 (2.28.3-1) ...
Selecting previously unselected package libmbedx509-1:amd64.
Preparing to unpack .../1-libmbedx509-1_2.28.3-1_amd64.deb ...
Unpacking libmbedx509-1:amd64 (2.28.3-1) ...
Selecting previously unselected package libmbedtls14:amd64.
Preparing to unpack .../2-libmbedtls14_2.28.3-1_amd64.deb ...
Unpacking libmbedtls14:amd64 (2.28.3-1) ...
Selecting previously unselected package ncbi-vdb-data.
Preparing to unpack .../3-ncbi-vdb-data_3.0.2+dfsg-2_all.deb ...
Unpacking ncbi-vdb-data (3.0.2+dfsg-2) ...
Selecting previously unselected package libncbi-wvdb3:amd64.
Preparing to unpack .../4-libncbi-wvdb3_3.0.2+dfsg-2_amd64.deb ...
Unpacking libncbi-wvdb3:amd64 (3.0.2+dfsg-2) ...
Selecting previously unselected package libncbi-wvdb-dev:amd64.
Preparing to unpack .../5-libncbi-wvdb-dev_3.0.2+dfsg-2_amd64.deb ...
Unpacking libncbi-wvdb-dev:amd64 (3.0.2+dfsg-2) ...
Setting up libmbedcrypto7:amd64 (2.28.3-1) ...
Setting up ncbi-vdb-data (3.0.2+dfsg-2) ...
Setting up libmbedx509-1:amd64 (2.28.3-1) ...
Setting up libmbedtls14:amd64 (2.28.3-1) ...
Setting up libncbi-wvdb3:amd64 (3.0.2+dfsg-2) ...
Setting up libncbi-wvdb-dev:amd64 (3.0.2+dfsg-2) ...
Processing triggers for libc-bin (2.36-9+deb12u10) ...
0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-get', '-y', 'install', 'libncbi-wvdb-dev']
0m5.4s INFO: Running scripts post_install
0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_install_exceptions']
0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_install_exceptions']
0m5.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2']
0m5.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2']
0m5.7s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpk4d9ryh2 to testing
0m5.8s DEBUG: sources.list:
deb http://deb.debian.org/debian/ trixie main
0m5.8s INFO: Running scripts pre_distupgrade
0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_distupgrade_allow_unauthenticated']
0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_distupgrade_allow_unauthenticated']
0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_distupgrade_exceptions']
0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_distupgrade_exceptions']
0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386']
0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386']
0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_distupgrade_zz_database-server']
0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_distupgrade_zz_database-server']
0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_distupgrade_zz_upgrade_early']
0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_distupgrade_zz_upgrade_early']
0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-get', 'update']
0m8.4s DUMP:
Get:1 http://deb.debian.org/debian trixie InRelease [175 kB]
Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9652 kB]
Get:3 http://deb.debian.org/debian trixie/main Translation-en [6475 kB]
Fetched 16.3 MB in 2s (8741 kB/s)
Reading package lists...
0m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-get', 'update']
0m8.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-get', '-yf', 'dist-upgrade']
0m21.0s DUMP:
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
The following packages were automatically installed and are no longer required:
libmbedcrypto7 libmbedtls14 libmbedx509-1
Use 'sudo apt autoremove' to remove them.
The following packages will be REMOVED:
libdb5.3 libext2fs2 libhogweed6 libnettle8
The following NEW packages will be installed:
gcc-14-base libapt-pkg7.0 libbsd0 libdb5.3t64 libext2fs2t64 libhogweed6t64
liblastlog2-2 libmbedcrypto16 libmbedtls21 libmbedx509-7 libnettle8t64
libsqlite3-0 libssl3t64 libunistring5 login.defs openssl-provider-legacy sqv
The following packages will be upgraded:
adduser apt base-files base-passwd bash bsdutils coreutils dash debconf
debian-archive-keyring debianutils diffutils dpkg e2fsprogs findutils
gcc-12-base gpgv grep gzip hostname init-system-helpers libacl1 libattr1
libaudit-common libaudit1 libblkid1 libbz2-1.0 libc-bin libc6 libcap-ng0
libcap2 libcom-err2 libcrypt1 libdebconfclient0 libffi8 libgcc-s1
libgcrypt20 libgmp10 libgpg-error0 libidn2-0 liblz4-1 liblzma5 libmd0
libmount1 libncbi-wvdb-dev libncbi-wvdb3 libp11-kit0 libpam-modules
libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libseccomp2
libselinux1 libsemanage-common libsemanage2 libsepol2 libsmartcols1 libss2
libstdc++6 libsystemd0 libtasn1-6 libtinfo6 libudev1 libuuid1 libxxhash0
libzstd1 login logsave mawk mount ncbi-vdb-data ncurses-base ncurses-bin
passwd perl-base sed sysvinit-utils tar tzdata usr-is-merged util-linux
util-linux-extra zlib1g
84 upgraded, 17 newly installed, 4 to remove and 0 not upgraded.
Need to get 39.4 MB of archives.
After this operation, 24.5 MB of additional disk space will be used.
Get:1 http://deb.debian.org/debian trixie/main amd64 base-files amd64 13.7 [73.0 kB]
Get:2 http://deb.debian.org/debian trixie/main amd64 libc6 amd64 2.41-6 [2843 kB]
Get:3 http://deb.debian.org/debian trixie/main amd64 libc-bin amd64 2.41-6 [635 kB]
Get:4 http://deb.debian.org/debian trixie/main amd64 gcc-14-base amd64 14.2.0-19 [49.4 kB]
Get:5 http://deb.debian.org/debian trixie/main amd64 libgcc-s1 amd64 14.2.0-19 [72.8 kB]
Get:6 http://deb.debian.org/debian trixie/main amd64 debianutils amd64 5.21 [92.1 kB]
Get:7 http://deb.debian.org/debian trixie/main amd64 bash amd64 5.2.37-1.1+b2 [1500 kB]
Get:8 http://deb.debian.org/debian trixie/main amd64 libcap2 amd64 1:2.75-4 [27.9 kB]
Get:9 http://deb.debian.org/debian trixie/main amd64 libsystemd0 amd64 257.5-2 [453 kB]
Get:10 http://deb.debian.org/debian trixie/main amd64 bsdutils amd64 1:2.41-3 [110 kB]
Get:11 http://deb.debian.org/debian trixie/main amd64 libgmp10 amd64 2:6.3.0+dfsg-3 [560 kB]
Get:12 http://deb.debian.org/debian trixie/main amd64 libzstd1 amd64 1.5.7+dfsg-1 [304 kB]
Get:13 http://deb.debian.org/debian trixie/main amd64 libssl3t64 amd64 3.4.1-1 [2304 kB]
Get:14 http://deb.debian.org/debian trixie/main amd64 openssl-provider-legacy amd64 3.4.1-1 [302 kB]
Get:15 http://deb.debian.org/debian trixie/main amd64 zlib1g amd64 1:1.3.dfsg+really1.3.1-1+b1 [88.9 kB]
Get:16 http://deb.debian.org/debian trixie/main amd64 coreutils amd64 9.5-1+b1 [2922 kB]
Get:17 http://deb.debian.org/debian trixie/main amd64 dash amd64 0.5.12-12 [98.5 kB]
Get:18 http://deb.debian.org/debian trixie/main amd64 diffutils amd64 1:3.10-3 [385 kB]
Get:19 http://deb.debian.org/debian trixie/main amd64 tar amd64 1.35+dfsg-3.1 [815 kB]
Get:20 http://deb.debian.org/debian trixie/main amd64 dpkg amd64 1.22.18 [1545 kB]
Get:21 http://deb.debian.org/debian trixie/main amd64 findutils amd64 4.10.0-3 [700 kB]
Get:22 http://deb.debian.org/debian trixie/main amd64 grep amd64 3.11-4 [431 kB]
Get:23 http://deb.debian.org/debian trixie/main amd64 gzip amd64 1.13-1 [138 kB]
Get:24 http://deb.debian.org/debian trixie/main amd64 hostname amd64 3.25 [11.0 kB]
Get:25 http://deb.debian.org/debian trixie/main amd64 login.defs all 1:4.17.4-1 [186 kB]
Get:26 http://deb.debian.org/debian trixie/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-9 [704 kB]
Get:27 http://deb.debian.org/debian trixie/main amd64 libaudit-common all 1:4.0.2-2 [12.7 kB]
Get:28 http://deb.debian.org/debian trixie/main amd64 libcap-ng0 amd64 0.8.5-4+b1 [17.6 kB]
Get:29 http://deb.debian.org/debian trixie/main amd64 libaudit1 amd64 1:4.0.2-2+b2 [55.1 kB]
Get:30 http://deb.debian.org/debian trixie/main amd64 libcrypt1 amd64 1:4.4.38-1 [90.1 kB]
Get:31 http://deb.debian.org/debian trixie/main amd64 perl-base amd64 5.40.1-2 [1665 kB]
Get:32 http://deb.debian.org/debian trixie/main amd64 debconf all 1.5.91 [121 kB]
Get:33 http://deb.debian.org/debian trixie/main amd64 libpam0g amd64 1.7.0-3 [69.7 kB]
Get:34 http://deb.debian.org/debian trixie/main amd64 libpcre2-8-0 amd64 10.45-1 [298 kB]
Get:35 http://deb.debian.org/debian trixie/main amd64 libselinux1 amd64 3.8.1-1 [84.7 kB]
Get:36 http://deb.debian.org/debian trixie/main amd64 libpam-modules-bin amd64 1.7.0-3 [48.9 kB]
Get:37 http://deb.debian.org/debian trixie/main amd64 libpam-modules amd64 1.7.0-3 [177 kB]
Get:38 http://deb.debian.org/debian trixie/main amd64 libpam-runtime all 1.7.0-3 [248 kB]
Get:39 http://deb.debian.org/debian trixie/main amd64 login amd64 1:4.16.0-2+really2.41-3 [112 kB]
Get:40 http://deb.debian.org/debian trixie/main amd64 libtinfo6 amd64 6.5+20250216-2 [348 kB]
Get:41 http://deb.debian.org/debian trixie/main amd64 ncurses-bin amd64 6.5+20250216-2 [438 kB]
Get:42 http://deb.debian.org/debian trixie/main amd64 sed amd64 4.9-2 [329 kB]
Get:43 http://deb.debian.org/debian trixie/main amd64 libblkid1 amd64 2.41-3 [171 kB]
Get:44 http://deb.debian.org/debian trixie/main amd64 libsqlite3-0 amd64 3.46.1-2 [913 kB]
Get:45 http://deb.debian.org/debian trixie/main amd64 liblastlog2-2 amd64 2.41-3 [28.3 kB]
Get:46 http://deb.debian.org/debian trixie/main amd64 libmount1 amd64 2.41-3 [208 kB]
Get:47 http://deb.debian.org/debian trixie/main amd64 libsmartcols1 amd64 2.41-3 [142 kB]
Get:48 http://deb.debian.org/debian trixie/main amd64 libuuid1 amd64 2.41-3 [37.5 kB]
Get:49 http://deb.debian.org/debian trixie/main amd64 util-linux amd64 2.41-3 [1231 kB]
Get:50 http://deb.debian.org/debian trixie/main amd64 util-linux-extra amd64 2.41-3 [300 kB]
Get:51 http://deb.debian.org/debian trixie/main amd64 libnettle8t64 amd64 3.10.1-1 [305 kB]
Get:52 http://deb.debian.org/debian trixie/main amd64 libhogweed6t64 amd64 3.10.1-1 [335 kB]
Get:53 http://deb.debian.org/debian trixie/main amd64 sqv amd64 1.3.0-1 [661 kB]
Get:54 http://deb.debian.org/debian trixie/main amd64 libstdc++6 amd64 14.2.0-19 [714 kB]
Get:55 http://deb.debian.org/debian trixie/main amd64 libbz2-1.0 amd64 1.0.8-6 [37.9 kB]
Get:56 http://deb.debian.org/debian trixie/main amd64 libxxhash0 amd64 0.8.3-2 [27.1 kB]
Get:57 http://deb.debian.org/debian trixie/main amd64 liblz4-1 amd64 1.10.0-4 [63.9 kB]
Get:58 http://deb.debian.org/debian trixie/main amd64 liblzma5 amd64 5.8.1-1 [309 kB]
Get:59 http://deb.debian.org/debian trixie/main amd64 libudev1 amd64 257.5-2 [151 kB]
Get:60 http://deb.debian.org/debian trixie/main amd64 libapt-pkg7.0 amd64 3.0.0 [1112 kB]
Get:61 http://deb.debian.org/debian trixie/main amd64 libdebconfclient0 amd64 0.277 [10.4 kB]
Get:62 http://deb.debian.org/debian trixie/main amd64 base-passwd amd64 3.6.7 [53.7 kB]
Get:63 http://deb.debian.org/debian trixie/main amd64 libmd0 amd64 1.1.0-2+b1 [36.3 kB]
Get:64 http://deb.debian.org/debian trixie/main amd64 libbsd0 amd64 0.12.2-2 [131 kB]
Get:65 http://deb.debian.org/debian trixie/main amd64 libacl1 amd64 2.3.2-2+b1 [32.9 kB]
Get:66 http://deb.debian.org/debian trixie/main amd64 libattr1 amd64 1:2.5.2-3 [22.9 kB]
Get:67 http://deb.debian.org/debian trixie/main amd64 libsemanage-common all 3.8.1-1 [7812 B]
Get:68 http://deb.debian.org/debian trixie/main amd64 libsepol2 amd64 3.8.1-1 [296 kB]
Get:69 http://deb.debian.org/debian trixie/main amd64 libsemanage2 amd64 3.8.1-1 [95.3 kB]
Get:70 http://deb.debian.org/debian trixie/main amd64 passwd amd64 1:4.17.4-1 [1226 kB]
Get:71 http://deb.debian.org/debian trixie/main amd64 adduser all 3.149 [187 kB]
Get:72 http://deb.debian.org/debian trixie/main amd64 debian-archive-keyring all 2023.4 [161 kB]
Get:73 http://deb.debian.org/debian trixie/main amd64 libseccomp2 amd64 2.6.0-2 [51.7 kB]
Get:74 http://deb.debian.org/debian trixie/main amd64 apt amd64 3.0.0 [1450 kB]
Get:75 http://deb.debian.org/debian trixie/main amd64 init-system-helpers all 1.68 [38.7 kB]
Get:76 http://deb.debian.org/debian trixie/main amd64 ncurses-base all 6.5+20250216-2 [273 kB]
Get:77 http://deb.debian.org/debian trixie/main amd64 sysvinit-utils amd64 3.14-4 [34.1 kB]
Get:78 http://deb.debian.org/debian trixie/main amd64 logsave amd64 1.47.2-1+b1 [24.2 kB]
Get:79 http://deb.debian.org/debian trixie/main amd64 libext2fs2t64 amd64 1.47.2-1+b1 [212 kB]
Get:80 http://deb.debian.org/debian trixie/main amd64 e2fsprogs amd64 1.47.2-1+b1 [590 kB]
Get:81 http://deb.debian.org/debian trixie/main amd64 mount amd64 2.41-3 [162 kB]
Get:82 http://deb.debian.org/debian trixie/main amd64 libgpg-error0 amd64 1.51-4 [82.1 kB]
Get:83 http://deb.debian.org/debian trixie/main amd64 libgcrypt20 amd64 1.11.0-7 [843 kB]
Get:84 http://deb.debian.org/debian trixie/main amd64 gpgv amd64 2.2.46-6 [221 kB]
Get:85 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.7-1 [23.9 kB]
Get:86 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.3-2 [477 kB]
Get:87 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.8-2 [109 kB]
Get:88 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-3 [425 kB]
Get:89 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.20.0-2 [49.9 kB]
Get:90 http://deb.debian.org/debian trixie/main amd64 usr-is-merged all 39+nmu2 [5936 B]
Get:91 http://deb.debian.org/debian trixie/main amd64 mawk amd64 1.3.4.20250131-1 [141 kB]
Get:92 http://deb.debian.org/debian trixie/main amd64 tzdata all 2025b-1 [259 kB]
Get:93 http://deb.debian.org/debian trixie/main amd64 gcc-12-base amd64 12.4.0-5 [43.9 kB]
Get:94 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.2-1+b1 [24.3 kB]
Get:95 http://deb.debian.org/debian trixie/main amd64 libmbedcrypto16 amd64 3.6.3-1 [357 kB]
Get:96 http://deb.debian.org/debian trixie/main amd64 libmbedx509-7 amd64 3.6.3-1 [149 kB]
Get:97 http://deb.debian.org/debian trixie/main amd64 libmbedtls21 amd64 3.6.3-1 [236 kB]
Get:98 http://deb.debian.org/debian trixie/main amd64 ncbi-vdb-data all 3.0.9+dfsg-2 [74.0 kB]
Get:99 http://deb.debian.org/debian trixie/main amd64 libncbi-wvdb-dev amd64 3.0.9+dfsg-2 [1311 kB]
Get:100 http://deb.debian.org/debian trixie/main amd64 libncbi-wvdb3 amd64 3.0.9+dfsg-2 [1191 kB]
Get:101 http://deb.debian.org/debian trixie/main amd64 libss2 amd64 1.47.2-1+b1 [29.0 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 39.4 MB in 0s (154 MB/s)
(Reading database ...
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Preparing to unpack .../usr-is-merged_39+nmu2_all.deb ...
Unpacking usr-is-merged (39+nmu2) over (37~deb12u1) ...
Setting up usr-is-merged (39+nmu2) ...
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Preparing to unpack .../00-mawk_1.3.4.20250131-1_amd64.deb ...
Unpacking mawk (1.3.4.20250131-1) over (1.3.4.20200120-3.1) ...
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Unpacking tzdata (2025b-1) over (2025a-0+deb12u1) ...
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Unpacking libcom-err2:amd64 (1.47.2-1+b1) over (1.47.0-2) ...
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Unpacking libmbedcrypto16:amd64 (3.6.3-1) ...
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Unpacking ncbi-vdb-data (3.0.9+dfsg-2) over (3.0.2+dfsg-2) ...
Preparing to unpack .../08-libncbi-wvdb-dev_3.0.9+dfsg-2_amd64.deb ...
Unpacking libncbi-wvdb-dev:amd64 (3.0.9+dfsg-2) over (3.0.2+dfsg-2) ...
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Unpacking libncbi-wvdb3:amd64 (3.0.9+dfsg-2) over (3.0.2+dfsg-2) ...
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Unpacking libss2:amd64 (1.47.2-1+b1) over (1.47.0-2) ...
dpkg: warning: unable to delete old directory '/lib/x86_64-linux-gnu': Directory not empty
Setting up libcom-err2:amd64 (1.47.2-1+b1) ...
Setting up gcc-12-base:amd64 (12.4.0-5) ...
Setting up tzdata (2025b-1) ...
Current default time zone: 'Etc/UTC'
Local time is now: Thu Apr 10 12:54:30 UTC 2025.
Universal Time is now: Thu Apr 10 12:54:30 UTC 2025.
Run 'dpkg-reconfigure tzdata' if you wish to change it.
Setting up libss2:amd64 (1.47.2-1+b1) ...
Setting up logsave (1.47.2-1+b1) ...
Setting up mount (2.41-3) ...
Setting up ncbi-vdb-data (3.0.9+dfsg-2) ...
Setting up mawk (1.3.4.20250131-1) ...
Setting up libmbedcrypto16:amd64 (3.6.3-1) ...
Setting up e2fsprogs (1.47.2-1+b1) ...
Installing new version of config file /etc/cron.d/e2scrub_all ...
Installing new version of config file /etc/mke2fs.conf ...
Setting up libmbedx509-7:amd64 (3.6.3-1) ...
Setting up libmbedtls21:amd64 (3.6.3-1) ...
Setting up libncbi-wvdb3:amd64 (3.0.9+dfsg-2) ...
Setting up libncbi-wvdb-dev:amd64 (3.0.9+dfsg-2) ...
Processing triggers for debianutils (5.21) ...
Processing triggers for libc-bin (2.41-6) ...
0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-get', '-yf', 'dist-upgrade']
0m21.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'sh', '-c', 'apt-cache dumpavail | md5sum']
0m22.3s DUMP:
1855a7e2635bf22bb481caf465d80851 -
0m22.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'sh', '-c', 'apt-cache dumpavail | md5sum']
0m22.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-cache', 'show', '--no-all-versions', 'libncbi-wvdb-dev']
0m22.5s DUMP:
Package: libncbi-wvdb-dev
Source: ncbi-vdb
Version: 3.0.9+dfsg-2
Installed-Size: 6050
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Architecture: amd64
Depends: libncbi-wvdb3 (= 3.0.9+dfsg-2)
Description-en: virtual layer update module of ncbi-vdb library (devel)
The (US) National Center for Biotechnology Information (NCBI)'s
Virtual/Vertical Database (VDB) is a highly compressed column-oriented
data warehousing technology developed initially to address the needs
of the Sequence Read Archive (SRA). It is unique in that it builds
databases from smaller parts that can function independently as
_documents_, supports effective and efficient compression, supports
encryption while remaining encrypted on disk, transparent distribution
and remote access.
.
This package contains development files for updating VDB data.
Description-md5: 86b1533d3960704980cb451336afdcfe
Multi-Arch: same
Homepage: https://github.com/ncbi/ncbi-vdb
Tag: devel::library, role::devel-lib
Section: libdevel
Priority: optional
Filename: pool/main/n/ncbi-vdb/libncbi-wvdb-dev_3.0.9+dfsg-2_amd64.deb
Size: 1311164
MD5sum: 765f6cccbc269f07ca8ae81f36acff45
SHA256: 9120e1bc0e0980bedd34c3b71316fd151ff451b0d32be2963c2ee9717d45ec85
0m22.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-cache', 'show', '--no-all-versions', 'libncbi-wvdb-dev']
0m22.5s INFO: apt-cache knows about the following packages: libncbi-wvdb-dev
0m22.5s INFO: Running scripts pre_install
0m22.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_install_database-server']
0m22.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_install_database-server']
0m22.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_install_exceptions']
0m22.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_install_exceptions']
0m22.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_install_extras']
0m22.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_install_extras']
0m22.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_install_foreign_architecture']
0m22.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_install_foreign_architecture']
0m22.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_install_foreign_architecture_i386']
0m22.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_install_foreign_architecture_i386']
0m22.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-cache', 'policy']
0m22.6s 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:
0m22.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-cache', 'policy']
0m22.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-cache', 'policy', 'libncbi-wvdb-dev']
0m22.7s DUMP:
libncbi-wvdb-dev:
Installed: 3.0.9+dfsg-2
Candidate: 3.0.9+dfsg-2
Version table:
*** 3.0.9+dfsg-2 500
500 http://deb.debian.org/debian trixie/main amd64 Packages
100 /var/lib/dpkg/status
0m22.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-cache', 'policy', 'libncbi-wvdb-dev']
0m22.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-get', '-y', 'install', 'libncbi-wvdb-dev']
0m23.4s DUMP:
Reading package lists...
Building dependency tree...
Reading state information...
libncbi-wvdb-dev is already the newest version (3.0.9+dfsg-2).
The following packages were automatically installed and are no longer required:
libmbedcrypto7 libmbedtls14 libmbedx509-1
Use 'sudo apt autoremove' to remove them.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
0m23.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-get', '-y', 'install', 'libncbi-wvdb-dev']
0m23.4s INFO: Running scripts post_install
0m23.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_install_exceptions']
0m23.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_install_exceptions']
0m23.4s INFO: Running scripts post_distupgrade
0m23.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_distupgrade_base_cleanup']
0m23.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_distupgrade_base_cleanup']
0m23.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_distupgrade_exceptions']
0m23.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_distupgrade_exceptions']
0m23.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_distupgrade_force-unsafe-io']
0m23.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_distupgrade_force-unsafe-io']
0m23.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_distupgrade_squeeze-backports']
0m23.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_distupgrade_squeeze-backports']
0m23.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_distupgrade_zz_backports']
0m23.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_distupgrade_zz_backports']
0m23.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2']
0m23.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2']
0m23.8s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpk4d9ryh2 to sid
0m23.8s DEBUG: sources.list:
deb http://deb.debian.org/debian/ sid main
0m23.8s INFO: Running scripts pre_distupgrade
0m23.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_distupgrade_allow_unauthenticated']
0m23.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_distupgrade_allow_unauthenticated']
0m23.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_distupgrade_exceptions']
0m23.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_distupgrade_exceptions']
0m23.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386']
0m23.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386']
0m23.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_distupgrade_zz_database-server']
0m23.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_distupgrade_zz_database-server']
0m23.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_distupgrade_zz_upgrade_early']
0m23.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_distupgrade_zz_upgrade_early']
0m23.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-get', 'update']
0m26.6s DUMP:
Get:1 http://deb.debian.org/debian sid InRelease [205 kB]
Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.2 MB]
Get:3 http://deb.debian.org/debian sid/main Translation-en [7416 kB]
Fetched 17.8 MB in 2s (9521 kB/s)
Reading package lists...
0m26.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-get', 'update']
0m26.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-get', '-yf', 'dist-upgrade']
0m31.5s DUMP:
Reading package lists...
Building dependency tree...
Reading state information...
Calculating upgrade...
The following packages were automatically installed and are no longer required:
libmbedcrypto7 libmbedtls14 libmbedx509-1
Use 'sudo apt autoremove' to remove them.
The following NEW packages will be installed:
libbz2-dev libc-dev-bin libc6-dev libcrypt-dev libmbedtls-dev libzstd-dev
linux-libc-dev rpcsvc-proto zlib1g-dev
The following packages will be upgraded:
adduser bash bsdutils coreutils debian-archive-keyring libblkid1 libcap2
libdebconfclient0 liblastlog2-2 libmount1 libncbi-wvdb-dev libncbi-wvdb3
libsmartcols1 libsqlite3-0 libssl3t64 libuuid1 login mount ncbi-vdb-data
openssl-provider-legacy util-linux util-linux-extra
22 upgraded, 9 newly installed, 0 to remove and 0 not upgraded.
Need to get 20.5 MB of archives.
After this operation, 32.5 MB of additional disk space will be used.
Get:1 http://deb.debian.org/debian sid/main amd64 bash amd64 5.2.37-2 [1500 kB]
Get:2 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.41-4 [110 kB]
Get:3 http://deb.debian.org/debian sid/main amd64 coreutils amd64 9.7-1 [3012 kB]
Get:4 http://deb.debian.org/debian sid/main amd64 util-linux-extra amd64 2.41-4 [300 kB]
Get:5 http://deb.debian.org/debian sid/main amd64 liblastlog2-2 amd64 2.41-4 [28.4 kB]
Get:6 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.41-4 [37.6 kB]
Get:7 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.41-4 [171 kB]
Get:8 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.41-4 [209 kB]
Get:9 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.41-4 [143 kB]
Get:10 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.41-4 [1234 kB]
Get:11 http://deb.debian.org/debian sid/main amd64 mount amd64 2.41-4 [162 kB]
Get:12 http://deb.debian.org/debian sid/main amd64 libsqlite3-0 amd64 3.46.1-3 [913 kB]
Get:13 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.16.0-2+really2.41-4 [112 kB]
Get:14 http://deb.debian.org/debian sid/main amd64 adduser all 3.150 [187 kB]
Get:15 http://deb.debian.org/debian sid/main amd64 debian-archive-keyring all 2025.1 [179 kB]
Get:16 http://deb.debian.org/debian sid/main amd64 libcap2 amd64 1:2.75-5 [28.0 kB]
Get:17 http://deb.debian.org/debian sid/main amd64 libdebconfclient0 amd64 0.278 [10.5 kB]
Get:18 http://deb.debian.org/debian sid/main amd64 openssl-provider-legacy amd64 3.5.0-1 [307 kB]
Get:19 http://deb.debian.org/debian sid/main amd64 libssl3t64 amd64 3.5.0-1 [2432 kB]
Get:20 http://deb.debian.org/debian sid/main amd64 libc-dev-bin amd64 2.41-6 [57.0 kB]
Get:21 http://deb.debian.org/debian sid/main amd64 linux-libc-dev all 6.12.21-1 [2542 kB]
Get:22 http://deb.debian.org/debian sid/main amd64 libcrypt-dev amd64 1:4.4.38-1 [119 kB]
Get:23 http://deb.debian.org/debian sid/main amd64 rpcsvc-proto amd64 1.4.3-1 [63.3 kB]
Get:24 http://deb.debian.org/debian sid/main amd64 libc6-dev amd64 2.41-6 [1988 kB]
Get:25 http://deb.debian.org/debian sid/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB]
Get:26 http://deb.debian.org/debian sid/main amd64 libmbedtls-dev amd64 3.6.3-1 [827 kB]
Get:27 http://deb.debian.org/debian sid/main amd64 libzstd-dev amd64 1.5.7+dfsg-1 [371 kB]
Get:28 http://deb.debian.org/debian sid/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB]
Get:29 http://deb.debian.org/debian sid/main amd64 ncbi-vdb-data all 3.2.1+dfsg-2 [88.5 kB]
Get:30 http://deb.debian.org/debian sid/main amd64 libncbi-wvdb-dev amd64 3.2.1+dfsg-2 [1286 kB]
Get:31 http://deb.debian.org/debian sid/main amd64 libncbi-wvdb3 amd64 3.2.1+dfsg-2 [1167 kB]
Fetched 20.5 MB in 0s (134 MB/s)
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Unpacking bash (5.2.37-2) over (5.2.37-1.1+b2) ...
Setting up bash (5.2.37-2) ...
update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode
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Leaving 'diversion of /sbin/ctrlaltdel to /sbin/ctrlaltdel.usr-is-merged by util-linux-extra'
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Leaving 'diversion of /sbin/mkfs.minix to /sbin/mkfs.minix.usr-is-merged by util-linux-extra'
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Preparing to unpack .../libmount1_2.41-4_amd64.deb ...
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Setting up libmount1:amd64 (2.41-4) ...
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Setting up libsmartcols1:amd64 (2.41-4) ...
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Preparing to unpack .../util-linux_2.41-4_amd64.deb ...
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Preparing to unpack .../mount_2.41-4_amd64.deb ...
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Preparing to unpack .../libsqlite3-0_3.46.1-3_amd64.deb ...
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Setting up libsqlite3-0:amd64 (3.46.1-3) ...
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Preparing to unpack .../login_1%3a4.16.0-2+really2.41-4_amd64.deb ...
Unpacking login (1:4.16.0-2+really2.41-4) over (1:4.16.0-2+really2.41-3) ...
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Setting up adduser (3.150) ...
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Preparing to unpack .../debian-archive-keyring_2025.1_all.deb ...
Unpacking debian-archive-keyring (2025.1) over (2023.4) ...
Setting up debian-archive-keyring (2025.1) ...
Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-buster-stable.asc ...
Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-buster-security-automatic.asc ...
Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-buster-automatic.asc ...
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Preparing to unpack .../libcap2_1%3a2.75-5_amd64.deb ...
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Setting up libcap2:amd64 (1:2.75-5) ...
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Preparing to unpack .../libdebconfclient0_0.278_amd64.deb ...
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Setting up libdebconfclient0:amd64 (0.278) ...
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Preparing to unpack .../openssl-provider-legacy_3.5.0-1_amd64.deb ...
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Setting up openssl-provider-legacy (3.5.0-1) ...
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Preparing to unpack .../libssl3t64_3.5.0-1_amd64.deb ...
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Setting up libssl3t64:amd64 (3.5.0-1) ...
Selecting previously unselected package libc-dev-bin.
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Selecting previously unselected package linux-libc-dev.
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Unpacking libcrypt-dev:amd64 (1:4.4.38-1) ...
Selecting previously unselected package rpcsvc-proto.
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Unpacking rpcsvc-proto (1.4.3-1) ...
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Unpacking libc6-dev:amd64 (2.41-6) ...
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Unpacking libbz2-dev:amd64 (1.0.8-6) ...
Selecting previously unselected package libmbedtls-dev:amd64.
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Unpacking libmbedtls-dev:amd64 (3.6.3-1) ...
Selecting previously unselected package libzstd-dev:amd64.
Preparing to unpack .../07-libzstd-dev_1.5.7+dfsg-1_amd64.deb ...
Unpacking libzstd-dev:amd64 (1.5.7+dfsg-1) ...
Selecting previously unselected package zlib1g-dev:amd64.
Preparing to unpack .../08-zlib1g-dev_1%3a1.3.dfsg+really1.3.1-1+b1_amd64.deb ...
Unpacking zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ...
Preparing to unpack .../09-ncbi-vdb-data_3.2.1+dfsg-2_all.deb ...
Unpacking ncbi-vdb-data (3.2.1+dfsg-2) over (3.0.9+dfsg-2) ...
Preparing to unpack .../10-libncbi-wvdb-dev_3.2.1+dfsg-2_amd64.deb ...
Unpacking libncbi-wvdb-dev:amd64 (3.2.1+dfsg-2) over (3.0.9+dfsg-2) ...
Preparing to unpack .../11-libncbi-wvdb3_3.2.1+dfsg-2_amd64.deb ...
Unpacking libncbi-wvdb3:amd64 (3.2.1+dfsg-2) over (3.0.9+dfsg-2) ...
Setting up libzstd-dev:amd64 (1.5.7+dfsg-1) ...
Setting up linux-libc-dev (6.12.21-1) ...
Setting up libmbedtls-dev:amd64 (3.6.3-1) ...
Setting up rpcsvc-proto (1.4.3-1) ...
Setting up mount (2.41-4) ...
Setting up libcrypt-dev:amd64 (1:4.4.38-1) ...
Setting up ncbi-vdb-data (3.2.1+dfsg-2) ...
Setting up libc-dev-bin (2.41-6) ...
Setting up util-linux-extra (2.41-4) ...
Setting up login (1:4.16.0-2+really2.41-4) ...
Setting up libncbi-wvdb3:amd64 (3.2.1+dfsg-2) ...
Setting up libc6-dev:amd64 (2.41-6) ...
Setting up libbz2-dev:amd64 (1.0.8-6) ...
Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ...
Setting up libncbi-wvdb-dev:amd64 (3.2.1+dfsg-2) ...
Processing triggers for debianutils (5.21) ...
Processing triggers for libc-bin (2.41-6) ...
0m31.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-get', '-yf', 'dist-upgrade']
0m31.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'sh', '-c', 'apt-cache dumpavail | md5sum']
0m32.1s DUMP:
f39af8f11fd12bb7d28feb2935e986d9 -
0m32.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'sh', '-c', 'apt-cache dumpavail | md5sum']
0m32.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-cache', 'show', '--no-all-versions', 'libncbi-wvdb-dev']
0m32.5s DUMP:
Package: libncbi-wvdb-dev
Source: ncbi-vdb
Version: 3.2.1+dfsg-2
Installed-Size: 5977
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Architecture: amd64
Depends: libbz2-dev, libmbedtls-dev, libzstd-dev, zlib1g-dev, libncbi-wvdb3 (= 3.2.1+dfsg-2)
Description-en: virtual layer update module of ncbi-vdb library (devel)
The (US) National Center for Biotechnology Information (NCBI)'s
Virtual/Vertical Database (VDB) is a highly compressed column-oriented
data warehousing technology developed initially to address the needs
of the Sequence Read Archive (SRA). It is unique in that it builds
databases from smaller parts that can function independently as
_documents_, supports effective and efficient compression, supports
encryption while remaining encrypted on disk, transparent distribution
and remote access.
.
This package contains development files for updating VDB data.
Description-md5: 86b1533d3960704980cb451336afdcfe
Multi-Arch: same
Homepage: https://github.com/ncbi/ncbi-vdb
Tag: devel::library, role::devel-lib
Section: libdevel
Priority: optional
Filename: pool/main/n/ncbi-vdb/libncbi-wvdb-dev_3.2.1+dfsg-2_amd64.deb
Size: 1285964
MD5sum: e4ab166584518707d5022fb3b89694b9
SHA256: 0e02dc63801e9c62f065dffc8d620b54c6b9aa0460702e446da4c6cca050549d
0m32.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-cache', 'show', '--no-all-versions', 'libncbi-wvdb-dev']
0m32.5s INFO: apt-cache knows about the following packages: libncbi-wvdb-dev
0m32.5s INFO: Running scripts pre_install
0m32.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_install_database-server']
0m32.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_install_database-server']
0m32.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_install_exceptions']
0m32.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_install_exceptions']
0m32.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_install_extras']
0m32.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_install_extras']
0m32.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_install_foreign_architecture']
0m32.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_install_foreign_architecture']
0m32.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_install_foreign_architecture_i386']
0m32.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_install_foreign_architecture_i386']
0m32.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-cache', 'policy']
0m32.6s DUMP:
Package files:
100 /var/lib/dpkg/status
release a=now
500 http://deb.debian.org/debian sid/main amd64 Packages
release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64
origin deb.debian.org
Pinned packages:
0m32.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-cache', 'policy']
0m32.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-cache', 'policy', 'libncbi-wvdb-dev']
0m32.6s DUMP:
libncbi-wvdb-dev:
Installed: 3.2.1+dfsg-2
Candidate: 3.2.1+dfsg-2
Version table:
*** 3.2.1+dfsg-2 500
500 http://deb.debian.org/debian sid/main amd64 Packages
100 /var/lib/dpkg/status
0m32.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-cache', 'policy', 'libncbi-wvdb-dev']
0m32.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-get', '-y', 'install', 'libncbi-wvdb-dev']
0m33.3s DUMP:
Reading package lists...
Building dependency tree...
Reading state information...
libncbi-wvdb-dev is already the newest version (3.2.1+dfsg-2).
The following packages were automatically installed and are no longer required:
libmbedcrypto7 libmbedtls14 libmbedx509-1
Use 'sudo apt autoremove' to remove them.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
0m33.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-get', '-y', 'install', 'libncbi-wvdb-dev']
0m33.3s INFO: Running scripts post_install
0m33.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_install_exceptions']
0m33.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_install_exceptions']
0m33.3s INFO: Running scripts post_distupgrade
0m33.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_distupgrade_base_cleanup']
0m33.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_distupgrade_base_cleanup']
0m33.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_distupgrade_exceptions']
0m33.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_distupgrade_exceptions']
0m33.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_distupgrade_force-unsafe-io']
0m33.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_distupgrade_force-unsafe-io']
0m33.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_distupgrade_squeeze-backports']
0m33.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_distupgrade_squeeze-backports']
0m33.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_distupgrade_zz_backports']
0m33.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_distupgrade_zz_backports']
0m33.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2']
0m34.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2']
0m34.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2']
0m34.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2']
0m34.5s INFO: Running scripts pre_install
0m34.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_install_database-server']
0m34.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_install_database-server']
0m34.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_install_exceptions']
0m34.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_install_exceptions']
0m34.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_install_extras']
0m34.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_install_extras']
0m34.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_install_foreign_architecture']
0m34.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_install_foreign_architecture']
0m34.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_install_foreign_architecture_i386']
0m34.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_install_foreign_architecture_i386']
0m34.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-cache', 'policy']
0m34.7s 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:
0m34.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-cache', 'policy']
0m34.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-cache', 'policy', 'libncbi-wvdb-dev']
0m34.7s DUMP:
libncbi-wvdb-dev:
Installed: 3.2.1+dfsg-2
Candidate: 3.2.1+dfsg-2
Version table:
*** 3.2.1+dfsg-2 500
500 http://deb.debian.org/debian sid/main amd64 Packages
100 /var/lib/dpkg/status
0m34.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-cache', 'policy', 'libncbi-wvdb-dev']
0m34.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-get', '-y', 'install', 'libncbi-wvdb-dev=3.2.1+dfsg-2']
0m35.5s DUMP:
Reading package lists...
Building dependency tree...
Reading state information...
libncbi-wvdb-dev is already the newest version (3.2.1+dfsg-2).
The following packages were automatically installed and are no longer required:
libmbedcrypto7 libmbedtls14 libmbedx509-1
Use 'sudo apt autoremove' to remove them.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
0m35.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-get', '-y', 'install', 'libncbi-wvdb-dev=3.2.1+dfsg-2']
0m35.5s INFO: Running scripts post_install
0m35.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_install_exceptions']
0m35.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_install_exceptions']
0m35.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2']
0m36.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2']
0m36.7s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', '-ac', '--ignore-obsolete']
0m37.8s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', '-ac', '--ignore-obsolete']
0m37.8s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate']
0m37.8s DUMP:
0.15.6
0m37.8s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate']
0m37.8s INFO: Running adequate version 0.15.6 now.
0m37.8s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'libncbi-wvdb-dev']
0m37.9s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'libncbi-wvdb-dev']
0m37.9s INFO: Running scripts pre_remove
0m37.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_remove_40_find_missing_md5sums']
0m38.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_remove_40_find_missing_md5sums']
0m38.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles']
0m38.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles']
0m38.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_remove_40_find_unowned_lib_links']
0m39.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_remove_40_find_unowned_lib_links']
0m39.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_remove_50_find_bad_permissions']
0m39.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_remove_50_find_bad_permissions']
0m39.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_remove_50_find_missing_copyright']
0m39.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_remove_50_find_missing_copyright']
0m39.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_remove_exceptions']
0m39.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/pre_remove_exceptions']
0m39.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n']
0m39.2s DUMP:
install ok installed adduser adduser 3.150
install ok installed apt apt 3.0.0
install ok installed base-files base-files 13.7
install ok installed base-passwd base-passwd 3.6.7
install ok installed bash bash 5.2.37-2
install ok installed bsdutils bsdutils 1:2.41-4
install ok installed coreutils coreutils 9.7-1
install ok installed dash dash 0.5.12-12
install ok installed debconf debconf 1.5.91
install ok installed debian-archive-keyring debian-archive-keyring 2025.1
install ok installed debianutils debianutils 5.21
install ok installed diffutils diffutils 1:3.10-3
install ok installed dpkg dpkg 1.22.18
install ok installed e2fsprogs e2fsprogs 1.47.2-1+b1
install ok installed findutils findutils 4.10.0-3
install ok installed gcc-12-base:amd64 gcc-12-base 12.4.0-5
install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-19
install ok installed gpgv gpgv 2.2.46-6
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-pkg6.0:amd64 libapt-pkg6.0 2.6.1
install ok installed libapt-pkg7.0:amd64 libapt-pkg7.0 3.0.0
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 2.41-4
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 libbz2-dev:amd64 libbz2-dev 1.0.8-6
install ok installed libc-bin libc-bin 2.41-6
install ok installed libc-dev-bin libc-dev-bin 2.41-6
install ok installed libc6:amd64 libc6 2.41-6
install ok installed libc6-dev:amd64 libc6-dev 2.41-6
install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-4+b1
install ok installed libcap2:amd64 libcap2 1:2.75-5
install ok installed libcom-err2:amd64 libcom-err2 1.47.2-1+b1
install ok installed libcrypt-dev:amd64 libcrypt-dev 1:4.4.38-1
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 0.278
install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.2-1+b1
install ok installed libffi8:amd64 libffi8 3.4.7-1
install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-19
install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-7
install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-3
install ok installed libgnutls30:amd64 libgnutls30 3.7.9-2+deb12u4
install ok installed libgpg-error0:amd64 libgpg-error0 1.51-4
install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10.1-1
install ok installed libidn2-0:amd64 libidn2-0 2.3.8-2
install ok installed liblastlog2-2:amd64 liblastlog2-2 2.41-4
install ok installed liblz4-1:amd64 liblz4-1 1.10.0-4
install ok installed liblzma5:amd64 liblzma5 5.8.1-1
install ok installed libmbedcrypto16:amd64 libmbedcrypto16 3.6.3-1
install ok installed libmbedcrypto7:amd64 libmbedcrypto7 2.28.3-1
install ok installed libmbedtls-dev:amd64 libmbedtls-dev 3.6.3-1
install ok installed libmbedtls14:amd64 libmbedtls14 2.28.3-1
install ok installed libmbedtls21:amd64 libmbedtls21 3.6.3-1
install ok installed libmbedx509-1:amd64 libmbedx509-1 2.28.3-1
install ok installed libmbedx509-7:amd64 libmbedx509-7 3.6.3-1
install ok installed libmd0:amd64 libmd0 1.1.0-2+b1
install ok installed libmount1:amd64 libmount1 2.41-4
install ok installed libncbi-wvdb-dev:amd64 libncbi-wvdb-dev 3.2.1+dfsg-2
install ok installed libncbi-wvdb3:amd64 libncbi-wvdb3 3.2.1+dfsg-2
install ok installed libnettle8t64:amd64 libnettle8t64 3.10.1-1
install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-3
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 2.6.0-2
install ok installed libselinux1:amd64 libselinux1 3.8.1-1
install ok installed libsemanage-common libsemanage-common 3.8.1-1
install ok installed libsemanage2:amd64 libsemanage2 3.8.1-1
install ok installed libsepol2:amd64 libsepol2 3.8.1-1
install ok installed libsmartcols1:amd64 libsmartcols1 2.41-4
install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-3
install ok installed libss2:amd64 libss2 1.47.2-1+b1
install ok installed libssl3t64:amd64 libssl3t64 3.5.0-1
install ok installed libstdc++6:amd64 libstdc++6 14.2.0-19
install ok installed libsystemd0:amd64 libsystemd0 257.5-2
install ok installed libtasn1-6:amd64 libtasn1-6 4.20.0-2
install ok installed libtinfo6:amd64 libtinfo6 6.5+20250216-2
install ok installed libudev1:amd64 libudev1 257.5-2
install ok installed libunistring2:amd64 libunistring2 1.0-2
install ok installed libunistring5:amd64 libunistring5 1.3-2
install ok installed libuuid1:amd64 libuuid1 2.41-4
install ok installed libxxhash0:amd64 libxxhash0 0.8.3-2
install ok installed libzstd-dev:amd64 libzstd-dev 1.5.7+dfsg-1
install ok installed libzstd1:amd64 libzstd1 1.5.7+dfsg-1
install ok installed linux-libc-dev linux-libc-dev 6.12.21-1
install ok installed login login 1:4.16.0-2+really2.41-4
install ok installed login.defs login.defs 1:4.17.4-1
install ok installed logsave logsave 1.47.2-1+b1
install ok installed mawk mawk 1.3.4.20250131-1
install ok installed mount mount 2.41-4
install ok installed ncbi-vdb-data ncbi-vdb-data 3.2.1+dfsg-2
install ok installed ncurses-base ncurses-base 6.5+20250216-2
install ok installed ncurses-bin ncurses-bin 6.5+20250216-2
install ok installed openssl-provider-legacy openssl-provider-legacy 3.5.0-1
install ok installed passwd passwd 1:4.17.4-1
install ok installed perl-base perl-base 5.40.1-2
install ok installed rpcsvc-proto rpcsvc-proto 1.4.3-1
install ok installed sed sed 4.9-2
install ok installed sqv sqv 1.3.0-1
install ok installed sysvinit-utils sysvinit-utils 3.14-4
install ok installed tar tar 1.35+dfsg-3.1
install ok installed tzdata tzdata 2025b-1
install ok installed usr-is-merged usr-is-merged 39+nmu2
install ok installed util-linux util-linux 2.41-4
install ok installed util-linux-extra util-linux-extra 2.41-4
install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1
install ok installed zlib1g-dev:amd64 zlib1g-dev 1:1.3.dfsg+really1.3.1-1+b1
0m39.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n']
0m39.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-get', 'remove', '--allow-remove-essential', 'libbz2-dev:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcrypt-dev:amd64', 'libmbedcrypto16:amd64', 'libmbedcrypto7:amd64', 'libmbedtls-dev:amd64', 'libmbedtls14:amd64', 'libmbedtls21:amd64', 'libmbedx509-1:amd64', 'libmbedx509-7:amd64', 'libncbi-wvdb-dev:amd64', 'libncbi-wvdb3:amd64', 'libzstd-dev:amd64', 'linux-libc-dev', 'ncbi-vdb-data', 'rpcsvc-proto', 'zlib1g-dev:amd64']
0m40.3s DUMP:
Reading package lists...
Building dependency tree...
Reading state information...
The following packages will be REMOVED:
libbz2-dev libc-dev-bin libc6-dev libcrypt-dev libmbedcrypto16
libmbedcrypto7 libmbedtls-dev libmbedtls14 libmbedtls21 libmbedx509-1
libmbedx509-7 libncbi-wvdb-dev libncbi-wvdb3 libzstd-dev linux-libc-dev
ncbi-vdb-data rpcsvc-proto zlib1g-dev
0 upgraded, 0 newly installed, 18 to remove and 0 not upgraded.
After this operation, 44.2 MB disk space will be freed.
(Reading database ...
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 8959 files and directories currently installed.)
Removing libncbi-wvdb-dev:amd64 (3.2.1+dfsg-2) ...
Removing libbz2-dev:amd64 (1.0.8-6) ...
Removing zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ...
Removing libc6-dev:amd64 (2.41-6) ...
Removing libc-dev-bin (2.41-6) ...
Removing libcrypt-dev:amd64 (1:4.4.38-1) ...
Removing libmbedtls-dev:amd64 (3.6.3-1) ...
Removing libncbi-wvdb3:amd64 (3.2.1+dfsg-2) ...
Removing libmbedtls14:amd64 (2.28.3-1) ...
Removing libmbedx509-1:amd64 (2.28.3-1) ...
Removing libmbedcrypto7:amd64 (2.28.3-1) ...
Removing libmbedtls21:amd64 (3.6.3-1) ...
Removing libmbedx509-7:amd64 (3.6.3-1) ...
Removing libzstd-dev:amd64 (1.5.7+dfsg-1) ...
Removing linux-libc-dev (6.12.21-1) ...
Removing ncbi-vdb-data (3.2.1+dfsg-2) ...
rm: cannot remove '/usr/lib/python3/dist-packages/__pycache__/vdb.*': No such file or directory
Removing rpcsvc-proto (1.4.3-1) ...
Removing libmbedcrypto16:amd64 (3.6.3-1) ...
Processing triggers for libc-bin (2.41-6) ...
0m40.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-get', 'remove', '--allow-remove-essential', 'libbz2-dev:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcrypt-dev:amd64', 'libmbedcrypto16:amd64', 'libmbedcrypto7:amd64', 'libmbedtls-dev:amd64', 'libmbedtls14:amd64', 'libmbedtls21:amd64', 'libmbedx509-1:amd64', 'libmbedx509-7:amd64', 'libncbi-wvdb-dev:amd64', 'libncbi-wvdb3:amd64', 'libzstd-dev:amd64', 'linux-libc-dev', 'ncbi-vdb-data', 'rpcsvc-proto', 'zlib1g-dev:amd64']
0m40.3s INFO: Running scripts post_remove
0m40.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_remove_exceptions']
0m40.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_remove_exceptions']
0m40.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'dpkg', '--purge', 'libbz2-dev:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcrypt-dev:amd64', 'libmbedcrypto16:amd64', 'libmbedcrypto7:amd64', 'libmbedtls-dev:amd64', 'libmbedtls14:amd64', 'libmbedtls21:amd64', 'libmbedx509-1:amd64', 'libmbedx509-7:amd64', 'libncbi-wvdb-dev:amd64', 'libncbi-wvdb3:amd64', 'libzstd-dev:amd64', 'linux-libc-dev', 'ncbi-vdb-data', 'rpcsvc-proto', 'zlib1g-dev:amd64']
0m40.3s DUMP:
dpkg: warning: ignoring request to remove libbz2-dev which isn't installed
dpkg: warning: ignoring request to remove libc-dev-bin which isn't installed
dpkg: warning: ignoring request to remove libc6-dev which isn't installed
(Reading database ... 5386 files and directories currently installed.)
Purging configuration files for libcrypt-dev:amd64 (1:4.4.38-1) ...
dpkg: warning: ignoring request to remove libmbedcrypto16 which isn't installed
dpkg: warning: ignoring request to remove libmbedcrypto7 which isn't installed
dpkg: warning: ignoring request to remove libmbedtls-dev which isn't installed
dpkg: warning: ignoring request to remove libmbedtls14 which isn't installed
dpkg: warning: ignoring request to remove libmbedtls21 which isn't installed
dpkg: warning: ignoring request to remove libmbedx509-1 which isn't installed
dpkg: warning: ignoring request to remove libmbedx509-7 which isn't installed
dpkg: warning: ignoring request to remove libncbi-wvdb-dev which isn't installed
dpkg: warning: ignoring request to remove libncbi-wvdb3 which isn't installed
dpkg: warning: ignoring request to remove libzstd-dev which isn't installed
dpkg: warning: ignoring request to remove linux-libc-dev which isn't installed
Purging configuration files for ncbi-vdb-data (3.2.1+dfsg-2) ...
dpkg: warning: ignoring request to remove rpcsvc-proto which isn't installed
dpkg: warning: ignoring request to remove zlib1g-dev which isn't installed
0m40.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'dpkg', '--purge', 'libbz2-dev:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcrypt-dev:amd64', 'libmbedcrypto16:amd64', 'libmbedcrypto7:amd64', 'libmbedtls-dev:amd64', 'libmbedtls14:amd64', 'libmbedtls21:amd64', 'libmbedx509-1:amd64', 'libmbedx509-7:amd64', 'libncbi-wvdb-dev:amd64', 'libncbi-wvdb3:amd64', 'libzstd-dev:amd64', 'linux-libc-dev', 'ncbi-vdb-data', 'rpcsvc-proto', 'zlib1g-dev:amd64']
0m40.3s INFO: Running scripts post_purge
0m40.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_purge_exceptions']
0m40.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_purge_exceptions']
0m40.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'dpkg', '--purge', '--pending']
0m40.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'dpkg', '--purge', '--pending']
0m40.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'dpkg', '--remove', '--pending']
0m40.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'dpkg', '--remove', '--pending']
0m40.3s INFO: Running scripts post_test
0m40.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_test_exceptions']
0m40.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'tmp/scripts/post_test_exceptions']
0m40.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2']
0m40.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2']
0m40.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'dpkg-divert', '--list']
0m40.6s DUMP:
diversion of /sbin/mkfs.bfs to /sbin/mkfs.bfs.usr-is-merged by util-linux-extra
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 /sbin/mkfs.minix to /sbin/mkfs.minix.usr-is-merged by util-linux-extra
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
diversion of /sbin/mkfs.cramfs to /sbin/mkfs.cramfs.usr-is-merged by util-linux-extra
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 /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
diversion of /libx32 to /.libx32.usr-is-merged by base-files
local diversion of /usr/bin/sync to /usr/bin/sync.distrib
diversion of /sbin/ctrlaltdel to /sbin/ctrlaltdel.usr-is-merged by util-linux-extra
diversion of /sbin/fsck.minix to /sbin/fsck.minix.usr-is-merged by util-linux-extra
diversion of /lib32 to /.lib32.usr-is-merged by base-files
diversion of /libo32 to /.libo32.usr-is-merged by base-files
diversion of /sbin/fsck.cramfs to /sbin/fsck.cramfs.usr-is-merged by util-linux-extra
0m40.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'dpkg-divert', '--list']
0m40.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-get', 'clean']
0m40.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2', 'apt-get', 'clean']
0m40.7s DEBUG: Recording chroot state
0m41.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2/dev/shm']
0m41.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2/dev/shm']
0m41.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2/dev/console']
0m41.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2/dev/console']
0m41.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2/dev/ptmx']
0m41.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2/dev/ptmx']
0m41.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2/dev/pts']
0m41.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2/dev/pts']
0m41.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2/proc']
0m41.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2/proc']
0m41.9s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2']
0m42.0s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpk4d9ryh2']
0m42.0s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpk4d9ryh2
0m42.0s INFO: PASS: Upgrading between Debian distributions.
0m42.0s INFO: PASS: All tests.
0m42.0s INFO: piuparts run ends.
ret=0
End: 2025-04-10 12:54:52 GMT