Start: 2024-08-23 05:24:19 GMT [bookworm] Package: ruby-crb-blast Version: 0.6.9-4 Installed-Size: 52 Maintainer: Debian Ruby Extras Maintainers Architecture: all Depends: ncbi-blast+, ruby | ruby-interpreter, ruby-bio, ruby-fixwhich, ruby-threach, ruby-trollop Description: Run conditional reciprocal best blast Homepage: https://github.com/cboursnell/crb-blast Description-md5: b8694674f553b0ae33fd1ec67da3861a Ruby-Versions: all Section: ruby Priority: optional Filename: pool/main/r/ruby-crb-blast/ruby-crb-blast_0.6.9-4_all.deb Size: 12024 MD5sum: 2104a581b8545f129c2e35c6dc51c56e SHA256: 1d92b86b07f6832624e7a9e7ce343f78b979605e896f7ed7e64386c4a247c801 [bookworm-next] Package: ruby-crb-blast Version: 0.6.9-4 Installed-Size: 52 Maintainer: Debian Ruby Extras Maintainers Architecture: all Depends: ncbi-blast+, ruby | ruby-interpreter, ruby-bio, ruby-fixwhich, ruby-threach, ruby-trollop Description: Run conditional reciprocal best blast Homepage: https://github.com/cboursnell/crb-blast Description-md5: b8694674f553b0ae33fd1ec67da3861a Ruby-Versions: all Section: ruby Priority: optional Filename: pool/main/r/ruby-crb-blast/ruby-crb-blast_0.6.9-4_all.deb Size: 12024 MD5sum: 2104a581b8545f129c2e35c6dc51c56e SHA256: 1d92b86b07f6832624e7a9e7ce343f78b979605e896f7ed7e64386c4a247c801 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --warn-on-usr-move fail --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz -d bookworm -d bookworm-next -B /srv/piuparts.debian.org/slave/refchroot/bookworm2next/reference-chroot-metadata.dat --apt ruby-crb-blast=0.6.9-4 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.4.4~202408201642~1.4.3-11-g36a88c35 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --warn-on-usr-move fail --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz -d bookworm -d bookworm-next -B /srv/piuparts.debian.org/slave/refchroot/bookworm2next/reference-chroot-metadata.dat --apt ruby-crb-blast=0.6.9-4 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-32-amd64 #1 SMP Debian 5.10.223-1 (2024-08-10) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpj2q2w9w4 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpj2q2w9w4 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4/proc'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4/proc'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4/dev/pts'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4/dev/pts'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4/dev/ptmx'] 0m0.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4/dev/ptmx'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4/dev/console'] 0m0.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4/dev/console'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4/dev/shm'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4/dev/shm'] 0m0.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m0.5s DEBUG: Created policy-rc.d and chmodded it. 0m0.5s DEBUG: Created resolv.conf. 0m0.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpj2q2w9w4/tmp/scripts/ 0m0.5s INFO: Running scripts post_chroot_unpack 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'apt-get', 'update'] 0m1.6s DUMP: Hit:1 http://deb.debian.org/debian bookworm InRelease Reading package lists... 0m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'apt-get', 'update'] 0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'apt-get', '-yf', 'dist-upgrade'] 0m2.0s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'apt-get', '-yf', 'dist-upgrade'] 0m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.3s DUMP: 913e17be84ed63a3110ce3137c1d003a - 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.3s INFO: Running scripts post_setup 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/post_setup_dummy_users'] 0m3.0s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/post_setup_dummy_users'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/post_setup_forbid_home'] 0m3.0s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/post_setup_forbid_home'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.1s 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' 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/post_setup_minimize'] 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/post_setup_minimize'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/post_setup_zz_backports'] 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/post_setup_zz_backports'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.1s 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+deb12u6 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+deb12u1 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+deb12u1 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+deb12u7 install ok installed libc6:amd64 libc6 2.36-9+deb12u7 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+deb12u3 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+deb12u1 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+deb12u1 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 252.26-1~deb12u2 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.4-4 install ok installed libudev1:amd64 libudev1 252.26-1~deb12u2 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+deb12u1 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+deb12u1 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 2024a-0+deb12u1 install ok installed usr-is-merged usr-is-merged 37~deb12u1 install ok installed util-linux util-linux 2.38.1-5+deb12u1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+deb12u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.1s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/bookworm2next/reference-chroot-metadata.dat 0m3.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4'] 0m3.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4'] 0m3.4s INFO: Running scripts is_testable 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/is_testable_uninstallable'] 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/is_testable_uninstallable'] 0m3.4s INFO: Running scripts pre_test 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_test_exceptions'] 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_test_exceptions'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_test_root_password'] 0m3.4s DUMP: New password: Retype new password: passwd: password updated successfully 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_test_root_password'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'apt-cache', 'show', '--no-all-versions', 'ruby-crb-blast'] 0m3.7s DUMP: Package: ruby-crb-blast Version: 0.6.9-4 Installed-Size: 52 Maintainer: Debian Ruby Extras Maintainers Architecture: all Depends: ncbi-blast+, ruby | ruby-interpreter, ruby-bio, ruby-fixwhich, ruby-threach, ruby-trollop Description-en: Run conditional reciprocal best blast CRB-BLAST is a novel method for finding orthologs between one set of sequences and another. This is particularly useful in genome and transcriptome annotation. . CRB-BLAST initially performs a standard reciprocal best BLAST. It does this by performing BLAST alignments of query->target and target->query. Reciprocal best BLAST hits are those where the best match for any given query sequence in the query->target alignment is also the best hit of the match in the reverse (target->query) alignment. . Reciprocal best BLAST is a very conservative way to assign orthologs. The main innovation in CRB-BLAST is to learn an appropriate e-value cutoff to apply to each pairwise alignment by taking into account the overall relatedness of the two datasets being compared. This is done by fitting a function to the distribution of alignment e-values over sequence lengths. The function provides the e-value cutoff for a sequence of given length. Description-md5: b8694674f553b0ae33fd1ec67da3861a Homepage: https://github.com/cboursnell/crb-blast Ruby-Versions: all Section: ruby Priority: optional Filename: pool/main/r/ruby-crb-blast/ruby-crb-blast_0.6.9-4_all.deb Size: 12024 MD5sum: 2104a581b8545f129c2e35c6dc51c56e SHA256: 1d92b86b07f6832624e7a9e7ce343f78b979605e896f7ed7e64386c4a247c801 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'apt-cache', 'show', '--no-all-versions', 'ruby-crb-blast'] 0m3.7s INFO: apt-cache knows about the following packages: ruby-crb-blast 0m3.7s INFO: Running scripts pre_install 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_install_database-server'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_install_database-server'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_install_exceptions'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_install_exceptions'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_install_extras'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_install_extras'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'apt-cache', 'policy'] 0m3.8s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.6,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'apt-cache', 'policy'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'apt-cache', 'policy', 'ruby-crb-blast'] 0m3.8s DUMP: ruby-crb-blast: Installed: (none) Candidate: 0.6.9-4 Version table: 0.6.9-4 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'apt-cache', 'policy', 'ruby-crb-blast'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'apt-get', '-y', 'install', 'ruby-crb-blast'] 0m13.8s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: ca-certificates libbsd0 libedit2 libexpat1 libgdbm-compat4 libgdbm6 libgomp1 libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblmdb0 libmbedcrypto7 libmbedtls14 libmbedx509-1 libncurses6 libncursesw6 libnsl2 libpcre3 libperl5.36 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libreadline8 libruby libruby3.1 libsqlite3-0 libssl3 libtirpc-common libtirpc3 libyaml-0-2 media-types ncbi-blast+ ncbi-data openssl perl perl-modules-5.36 python3 python3-minimal python3.11 python3.11-minimal rake readline-common ruby ruby-bio ruby-facade ruby-fixwhich ruby-net-telnet ruby-pathname2 ruby-rubygems ruby-sdbm ruby-threach ruby-trollop ruby-webrick ruby-xmlrpc ruby3.1 rubygems-integration Suggested packages: gdbm-l10n krb5-doc krb5-user sensible-utils perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl python3-doc python3-tk python3-venv python3.11-venv python3.11-doc binutils binfmt-support readline-doc ri ruby-dev clustalw emboss bundler Recommended packages: krb5-locales libgpm2 netbase zip blast2 hmmer mafft muscle probcons sim4 t-coffee fonts-lato libjs-jquery The following NEW packages will be installed: ca-certificates libbsd0 libedit2 libexpat1 libgdbm-compat4 libgdbm6 libgomp1 libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblmdb0 libmbedcrypto7 libmbedtls14 libmbedx509-1 libncurses6 libncursesw6 libnsl2 libpcre3 libperl5.36 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libreadline8 libruby libruby3.1 libsqlite3-0 libssl3 libtirpc-common libtirpc3 libyaml-0-2 media-types ncbi-blast+ ncbi-data openssl perl perl-modules-5.36 python3 python3-minimal python3.11 python3.11-minimal rake readline-common ruby ruby-bio ruby-crb-blast ruby-facade ruby-fixwhich ruby-net-telnet ruby-pathname2 ruby-rubygems ruby-sdbm ruby-threach ruby-trollop ruby-webrick ruby-xmlrpc ruby3.1 rubygems-integration 0 upgraded, 59 newly installed, 0 to remove and 0 not upgraded. Need to get 42.6 MB of archives. After this operation, 197 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 perl-modules-5.36 all 5.36.0-7+deb12u1 [2815 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 libgdbm6 amd64 1.23-3 [72.2 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libgdbm-compat4 amd64 1.23-3 [48.2 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 libperl5.36 amd64 5.36.0-7+deb12u1 [4218 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 perl amd64 5.36.0-7+deb12u1 [239 kB] Get:6 http://deb.debian.org/debian bookworm/main amd64 libssl3 amd64 3.0.13-1~deb12u1 [2022 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6+deb12u2 [814 kB] Get:8 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get:9 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6+deb12u2 [2067 kB] Get:10 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get:11 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get:12 http://deb.debian.org/debian bookworm/main amd64 libncursesw6 amd64 6.4-4 [134 kB] Get:13 http://deb.debian.org/debian bookworm/main amd64 libkrb5support0 amd64 1.20.1-2+deb12u1 [32.4 kB] Get:14 http://deb.debian.org/debian bookworm/main amd64 libk5crypto3 amd64 1.20.1-2+deb12u1 [78.9 kB] Get:15 http://deb.debian.org/debian bookworm/main amd64 libkeyutils1 amd64 1.6.3-2 [8808 B] Get:16 http://deb.debian.org/debian bookworm/main amd64 libkrb5-3 amd64 1.20.1-2+deb12u1 [332 kB] Get:17 http://deb.debian.org/debian bookworm/main amd64 libgssapi-krb5-2 amd64 1.20.1-2+deb12u1 [134 kB] Get:18 http://deb.debian.org/debian bookworm/main amd64 libtirpc-common all 1.3.3+ds-1 [14.0 kB] Get:19 http://deb.debian.org/debian bookworm/main amd64 libtirpc3 amd64 1.3.3+ds-1 [85.2 kB] Get:20 http://deb.debian.org/debian bookworm/main amd64 libnsl2 amd64 1.3.0-2 [39.5 kB] Get:21 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get:22 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get:23 http://deb.debian.org/debian bookworm/main amd64 libsqlite3-0 amd64 3.40.1-2 [837 kB] Get:24 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6+deb12u2 [1799 kB] Get:25 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6+deb12u2 [573 kB] Get:26 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get:27 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get:28 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.13-1~deb12u1 [1418 kB] Get:29 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB] Get:30 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get:31 http://deb.debian.org/debian bookworm/main amd64 libedit2 amd64 3.1-20221030-2 [93.0 kB] Get:32 http://deb.debian.org/debian bookworm/main amd64 libgomp1 amd64 12.2.0-14 [116 kB] Get:33 http://deb.debian.org/debian bookworm/main amd64 liblmdb0 amd64 0.9.24-1 [45.0 kB] Get:34 http://deb.debian.org/debian bookworm/main amd64 libmbedcrypto7 amd64 2.28.3-1 [277 kB] Get:35 http://deb.debian.org/debian bookworm/main amd64 libmbedx509-1 amd64 2.28.3-1 [128 kB] Get:36 http://deb.debian.org/debian bookworm/main amd64 libmbedtls14 amd64 2.28.3-1 [163 kB] Get:37 http://deb.debian.org/debian bookworm/main amd64 libncurses6 amd64 6.4-4 [103 kB] Get:38 http://deb.debian.org/debian bookworm/main amd64 libpcre3 amd64 2:8.39-15 [341 kB] Get:39 http://deb.debian.org/debian bookworm/main amd64 rubygems-integration all 1.18 [6704 B] Get:40 http://deb.debian.org/debian bookworm/main amd64 ruby3.1 amd64 3.1.2-7+deb12u1 [663 kB] Get:41 http://deb.debian.org/debian bookworm/main amd64 ruby-rubygems all 3.3.15-2 [293 kB] Get:42 http://deb.debian.org/debian bookworm/main amd64 ruby amd64 1:3.1 [5868 B] Get:43 http://deb.debian.org/debian bookworm/main amd64 rake all 13.0.6-3 [83.9 kB] Get:44 http://deb.debian.org/debian bookworm/main amd64 ruby-net-telnet all 0.2.0-1 [13.1 kB] Get:45 http://deb.debian.org/debian bookworm/main amd64 ruby-webrick all 1.8.1-1 [51.4 kB] Get:46 http://deb.debian.org/debian bookworm/main amd64 ruby-xmlrpc all 0.3.2-2 [24.4 kB] Get:47 http://deb.debian.org/debian bookworm/main amd64 ruby-sdbm amd64 1.0.0-5+b1 [15.4 kB] Get:48 http://deb.debian.org/debian bookworm/main amd64 libyaml-0-2 amd64 0.2.5-1 [53.6 kB] Get:49 http://deb.debian.org/debian bookworm/main amd64 libruby3.1 amd64 3.1.2-7+deb12u1 [5400 kB] Get:50 http://deb.debian.org/debian bookworm/main amd64 libruby amd64 1:3.1 [4972 B] Get:51 http://deb.debian.org/debian bookworm/main amd64 ncbi-data all 6.1.20170106+dfsg1-10 [3557 kB] Get:52 http://deb.debian.org/debian bookworm/main amd64 ncbi-blast+ amd64 2.12.0+ds-3+b1 [11.9 MB] Get:53 http://deb.debian.org/debian bookworm/main amd64 ruby-bio all 2.0.4-1 [655 kB] Get:54 http://deb.debian.org/debian bookworm/main amd64 ruby-facade all 1.2.1-1 [8996 B] Get:55 http://deb.debian.org/debian bookworm/main amd64 ruby-pathname2 all 1.8.2-2 [17.9 kB] Get:56 http://deb.debian.org/debian bookworm/main amd64 ruby-fixwhich all 1.0.2-2 [4284 B] Get:57 http://deb.debian.org/debian bookworm/main amd64 ruby-threach all 0.2.0-2 [5320 B] Get:58 http://deb.debian.org/debian bookworm/main amd64 ruby-trollop all 2.0-2.1 [17.0 kB] Get:59 http://deb.debian.org/debian bookworm/main amd64 ruby-crb-blast all 0.6.9-4 [12.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 42.6 MB in 0s (171 MB/s) Selecting previously unselected package perl-modules-5.36. (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 ... 6093 files and directories currently installed.) Preparing to unpack .../0-perl-modules-5.36_5.36.0-7+deb12u1_all.deb ... Unpacking perl-modules-5.36 (5.36.0-7+deb12u1) ... Selecting previously unselected package libgdbm6:amd64. Preparing to unpack .../1-libgdbm6_1.23-3_amd64.deb ... Unpacking libgdbm6:amd64 (1.23-3) ... Selecting previously unselected package libgdbm-compat4:amd64. 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Unpacking ca-certificates (20230311) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../03-libbsd0_0.11.7-2_amd64.deb ... Unpacking libbsd0:amd64 (0.11.7-2) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../04-libedit2_3.1-20221030-2_amd64.deb ... Unpacking libedit2:amd64 (3.1-20221030-2) ... Selecting previously unselected package libgomp1:amd64. Preparing to unpack .../05-libgomp1_12.2.0-14_amd64.deb ... Unpacking libgomp1:amd64 (12.2.0-14) ... Selecting previously unselected package liblmdb0:amd64. Preparing to unpack .../06-liblmdb0_0.9.24-1_amd64.deb ... Unpacking liblmdb0:amd64 (0.9.24-1) ... Selecting previously unselected package libmbedcrypto7:amd64. Preparing to unpack .../07-libmbedcrypto7_2.28.3-1_amd64.deb ... Unpacking libmbedcrypto7:amd64 (2.28.3-1) ... Selecting previously unselected package libmbedx509-1:amd64. Preparing to unpack .../08-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 .../09-libmbedtls14_2.28.3-1_amd64.deb ... Unpacking libmbedtls14:amd64 (2.28.3-1) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../10-libncurses6_6.4-4_amd64.deb ... Unpacking libncurses6:amd64 (6.4-4) ... Selecting previously unselected package libpcre3:amd64. Preparing to unpack .../11-libpcre3_2%3a8.39-15_amd64.deb ... Unpacking libpcre3:amd64 (2:8.39-15) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../12-rubygems-integration_1.18_all.deb ... Unpacking rubygems-integration (1.18) ... Selecting previously unselected package ruby3.1. Preparing to unpack .../13-ruby3.1_3.1.2-7+deb12u1_amd64.deb ... Unpacking ruby3.1 (3.1.2-7+deb12u1) ... Selecting previously unselected package ruby-rubygems. Preparing to unpack .../14-ruby-rubygems_3.3.15-2_all.deb ... Unpacking ruby-rubygems (3.3.15-2) ... Selecting previously unselected package ruby. Preparing to unpack .../15-ruby_1%3a3.1_amd64.deb ... Unpacking ruby (1:3.1) ... Selecting previously unselected package rake. Preparing to unpack .../16-rake_13.0.6-3_all.deb ... Unpacking rake (13.0.6-3) ... Selecting previously unselected package ruby-net-telnet. Preparing to unpack .../17-ruby-net-telnet_0.2.0-1_all.deb ... Unpacking ruby-net-telnet (0.2.0-1) ... Selecting previously unselected package ruby-webrick. Preparing to unpack .../18-ruby-webrick_1.8.1-1_all.deb ... Unpacking ruby-webrick (1.8.1-1) ... Selecting previously unselected package ruby-xmlrpc. Preparing to unpack .../19-ruby-xmlrpc_0.3.2-2_all.deb ... Unpacking ruby-xmlrpc (0.3.2-2) ... Selecting previously unselected package ruby-sdbm:amd64. Preparing to unpack .../20-ruby-sdbm_1.0.0-5+b1_amd64.deb ... Unpacking ruby-sdbm:amd64 (1.0.0-5+b1) ... Selecting previously unselected package libyaml-0-2:amd64. Preparing to unpack .../21-libyaml-0-2_0.2.5-1_amd64.deb ... Unpacking libyaml-0-2:amd64 (0.2.5-1) ... Selecting previously unselected package libruby3.1:amd64. Preparing to unpack .../22-libruby3.1_3.1.2-7+deb12u1_amd64.deb ... Unpacking libruby3.1:amd64 (3.1.2-7+deb12u1) ... Selecting previously unselected package libruby:amd64. Preparing to unpack .../23-libruby_1%3a3.1_amd64.deb ... Unpacking libruby:amd64 (1:3.1) ... Selecting previously unselected package ncbi-data. Preparing to unpack .../24-ncbi-data_6.1.20170106+dfsg1-10_all.deb ... Unpacking ncbi-data (6.1.20170106+dfsg1-10) ... Selecting previously unselected package ncbi-blast+. Preparing to unpack .../25-ncbi-blast+_2.12.0+ds-3+b1_amd64.deb ... Unpacking ncbi-blast+ (2.12.0+ds-3+b1) ... Selecting previously unselected package ruby-bio. Preparing to unpack .../26-ruby-bio_2.0.4-1_all.deb ... Unpacking ruby-bio (2.0.4-1) ... Selecting previously unselected package ruby-facade. Preparing to unpack .../27-ruby-facade_1.2.1-1_all.deb ... Unpacking ruby-facade (1.2.1-1) ... Selecting previously unselected package ruby-pathname2. Preparing to unpack .../28-ruby-pathname2_1.8.2-2_all.deb ... Unpacking ruby-pathname2 (1.8.2-2) ... Selecting previously unselected package ruby-fixwhich. Preparing to unpack .../29-ruby-fixwhich_1.0.2-2_all.deb ... Unpacking ruby-fixwhich (1.0.2-2) ... Selecting previously unselected package ruby-threach. Preparing to unpack .../30-ruby-threach_0.2.0-2_all.deb ... Unpacking ruby-threach (0.2.0-2) ... Selecting previously unselected package ruby-trollop. Preparing to unpack .../31-ruby-trollop_2.0-2.1_all.deb ... Unpacking ruby-trollop (2.0-2.1) ... Selecting previously unselected package ruby-crb-blast. Preparing to unpack .../32-ruby-crb-blast_0.6.9-4_all.deb ... Unpacking ruby-crb-blast (0.6.9-4) ... Setting up media-types (10.0.0) ... Setting up liblmdb0:amd64 (0.9.24-1) ... Setting up ncbi-data (6.1.20170106+dfsg1-10) ... Setting up libkeyutils1:amd64 (1.6.3-2) ... Setting up ruby-facade (1.2.1-1) ... Setting up libyaml-0-2:amd64 (0.2.5-1) ... Setting up libtirpc-common (1.3.3+ds-1) ... Setting up libsqlite3-0:amd64 (3.40.1-2) ... Setting up libgomp1:amd64 (12.2.0-14) ... Setting up libkrb5support0:amd64 (1.20.1-2+deb12u1) ... Setting up libpcre3:amd64 (2:8.39-15) ... Setting up perl-modules-5.36 (5.36.0-7+deb12u1) ... Setting up libmbedcrypto7:amd64 (2.28.3-1) ... Setting up libncurses6:amd64 (6.4-4) ... Setting up ruby-net-telnet (0.2.0-1) ... Setting up libncursesw6:amd64 (6.4-4) ... Setting up libk5crypto3:amd64 (1.20.1-2+deb12u1) ... Setting up ruby-webrick (1.8.1-1) ... Setting up ruby-pathname2 (1.8.2-2) ... Setting up libkrb5-3:amd64 (1.20.1-2+deb12u1) ... Setting up openssl (3.0.13-1~deb12u1) ... Setting up libbsd0:amd64 (0.11.7-2) ... Setting up readline-common (8.2-1.3) ... Setting up ruby-xmlrpc (0.3.2-2) ... Setting up libgdbm6:amd64 (1.23-3) ... Setting up ruby-bio (2.0.4-1) ... Setting up libmbedx509-1:amd64 (2.28.3-1) ... Setting up libmbedtls14:amd64 (2.28.3-1) ... Setting up libedit2:amd64 (3.1-20221030-2) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libgssapi-krb5-2:amd64 (1.20.1-2+deb12u1) ... Setting up libgdbm-compat4:amd64 (1.23-3) ... Setting up libperl5.36:amd64 (5.36.0-7+deb12u1) ... Setting up libtirpc3:amd64 (1.3.3+ds-1) ... Setting up rubygems-integration (1.18) ... Setting up perl (5.36.0-7+deb12u1) ... Setting up libnsl2:amd64 (1.3.0-2) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6+deb12u2) ... Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6+deb12u2) ... Setting up python3 (3.11.2-1+b1) ... Setting up ncbi-blast+ (2.12.0+ds-3+b1) ... Setting up rake (13.0.6-3) ... Setting up libruby3.1:amd64 (3.1.2-7+deb12u1) ... Setting up libruby:amd64 (1:3.1) ... Setting up ruby-rubygems (3.3.15-2) ... Setting up ruby3.1 (3.1.2-7+deb12u1) ... Setting up ruby-sdbm:amd64 (1.0.0-5+b1) ... Setting up ruby (1:3.1) ... Setting up ruby-threach (0.2.0-2) ... Setting up ruby-fixwhich (1.0.2-2) ... Setting up ruby-trollop (2.0-2.1) ... Setting up ruby-crb-blast (0.6.9-4) ... Processing triggers for libc-bin (2.36-9+deb12u7) ... Processing triggers for ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 0m13.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'apt-get', '-y', 'install', 'ruby-crb-blast'] 0m13.8s INFO: Running scripts post_install 0m13.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/post_install_exceptions'] 0m13.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/post_install_exceptions'] 0m13.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4'] 0m14.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4'] 0m14.5s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpj2q2w9w4 to bookworm-next 0m14.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main deb http://security.debian.org bookworm-security main deb http://deb.debian.org/debian/ bookworm-updates main deb http://deb.debian.org/debian/ bookworm-proposed-updates main 0m14.5s INFO: Running scripts pre_distupgrade 0m14.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m14.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m14.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_distupgrade_exceptions'] 0m14.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_distupgrade_exceptions'] 0m14.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m14.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m14.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m14.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m14.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m14.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m14.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'apt-get', 'update'] 0m16.0s DUMP: Hit:1 http://deb.debian.org/debian bookworm InRelease Get:2 http://security.debian.org bookworm-security InRelease [48.0 kB] Get:3 http://deb.debian.org/debian bookworm-updates InRelease [55.4 kB] Get:4 http://deb.debian.org/debian bookworm-proposed-updates InRelease [59.5 kB] Get:5 http://security.debian.org bookworm-security/main amd64 Packages [176 kB] Get:6 http://security.debian.org bookworm-security/main Translation-en [106 kB] Get:7 http://deb.debian.org/debian bookworm-updates/main amd64 Packages [13.8 kB] Get:8 http://deb.debian.org/debian bookworm-updates/main Translation-en [16.0 kB] Get:9 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 Packages [111 kB] Get:10 http://deb.debian.org/debian bookworm-proposed-updates/main Translation-en [64.4 kB] Fetched 650 kB in 1s (768 kB/s) Reading package lists... 0m16.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'apt-get', 'update'] 0m16.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'apt-get', '-yf', 'dist-upgrade'] 0m18.2s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: libc-bin libc6 libgssapi-krb5-2 libk5crypto3 libkrb5-3 libkrb5support0 libssl3 libsystemd0 libudev1 openssl 10 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 7827 kB of archives. After this operation, 19.5 kB of additional disk space will be used. Get:1 http://security.debian.org bookworm-security/main amd64 libgssapi-krb5-2 amd64 1.20.1-2+deb12u2 [135 kB] Get:2 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libc6 amd64 2.36-9+deb12u8 [2754 kB] Get:3 http://security.debian.org bookworm-security/main amd64 libkrb5-3 amd64 1.20.1-2+deb12u2 [332 kB] Get:4 http://security.debian.org bookworm-security/main amd64 libkrb5support0 amd64 1.20.1-2+deb12u2 [32.6 kB] Get:5 http://security.debian.org bookworm-security/main amd64 libk5crypto3 amd64 1.20.1-2+deb12u2 [78.7 kB] Get:6 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libc-bin amd64 2.36-9+deb12u8 [608 kB] Get:7 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libsystemd0 amd64 252.29-1~deb12u1 [332 kB] Get:8 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libudev1 amd64 252.29-1~deb12u1 [108 kB] Get:9 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libssl3 amd64 3.0.14-1~deb12u1 [2024 kB] Get:10 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 openssl amd64 3.0.14-1~deb12u1 [1423 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 7827 kB in 0s (101 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 ... 13020 files and directories currently installed.) Preparing to unpack .../libc6_2.36-9+deb12u8_amd64.deb ... Unpacking libc6:amd64 (2.36-9+deb12u8) over (2.36-9+deb12u7) ... Setting up libc6:amd64 (2.36-9+deb12u8) ... (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 ... 13020 files and directories currently installed.) Preparing to unpack .../libc-bin_2.36-9+deb12u8_amd64.deb ... Unpacking libc-bin (2.36-9+deb12u8) over (2.36-9+deb12u7) ... Setting up libc-bin (2.36-9+deb12u8) ... (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 ... 13020 files and directories currently installed.) Preparing to unpack .../libsystemd0_252.29-1~deb12u1_amd64.deb ... Unpacking libsystemd0:amd64 (252.29-1~deb12u1) over (252.26-1~deb12u2) ... Setting up libsystemd0:amd64 (252.29-1~deb12u1) ... (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 ... 13020 files and directories currently installed.) Preparing to unpack .../libudev1_252.29-1~deb12u1_amd64.deb ... Unpacking libudev1:amd64 (252.29-1~deb12u1) over (252.26-1~deb12u2) ... Setting up libudev1:amd64 (252.29-1~deb12u1) ... (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 ... 13020 files and directories currently installed.) Preparing to unpack .../0-libgssapi-krb5-2_1.20.1-2+deb12u2_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.20.1-2+deb12u2) over (1.20.1-2+deb12u1) ... Preparing to unpack .../1-libkrb5-3_1.20.1-2+deb12u2_amd64.deb ... Unpacking libkrb5-3:amd64 (1.20.1-2+deb12u2) over (1.20.1-2+deb12u1) ... Preparing to unpack .../2-libkrb5support0_1.20.1-2+deb12u2_amd64.deb ... Unpacking libkrb5support0:amd64 (1.20.1-2+deb12u2) over (1.20.1-2+deb12u1) ... Preparing to unpack .../3-libk5crypto3_1.20.1-2+deb12u2_amd64.deb ... Unpacking libk5crypto3:amd64 (1.20.1-2+deb12u2) over (1.20.1-2+deb12u1) ... Preparing to unpack .../4-libssl3_3.0.14-1~deb12u1_amd64.deb ... Unpacking libssl3:amd64 (3.0.14-1~deb12u1) over (3.0.13-1~deb12u1) ... Preparing to unpack .../5-openssl_3.0.14-1~deb12u1_amd64.deb ... Unpacking openssl (3.0.14-1~deb12u1) over (3.0.13-1~deb12u1) ... Setting up libssl3:amd64 (3.0.14-1~deb12u1) ... Setting up libkrb5support0:amd64 (1.20.1-2+deb12u2) ... Setting up libk5crypto3:amd64 (1.20.1-2+deb12u2) ... Setting up libkrb5-3:amd64 (1.20.1-2+deb12u2) ... Setting up openssl (3.0.14-1~deb12u1) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-2+deb12u2) ... Processing triggers for libc-bin (2.36-9+deb12u8) ... 0m18.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'apt-get', '-yf', 'dist-upgrade'] 0m18.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m18.7s DUMP: a7383adc5fdea12f93db4552c396e73a - 0m18.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m18.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'apt-cache', 'show', '--no-all-versions', 'ruby-crb-blast'] 0m19.1s DUMP: Package: ruby-crb-blast Version: 0.6.9-4 Installed-Size: 52 Maintainer: Debian Ruby Extras Maintainers Architecture: all Depends: ncbi-blast+, ruby | ruby-interpreter, ruby-bio, ruby-fixwhich, ruby-threach, ruby-trollop Description-en: Run conditional reciprocal best blast CRB-BLAST is a novel method for finding orthologs between one set of sequences and another. This is particularly useful in genome and transcriptome annotation. . CRB-BLAST initially performs a standard reciprocal best BLAST. It does this by performing BLAST alignments of query->target and target->query. Reciprocal best BLAST hits are those where the best match for any given query sequence in the query->target alignment is also the best hit of the match in the reverse (target->query) alignment. . Reciprocal best BLAST is a very conservative way to assign orthologs. The main innovation in CRB-BLAST is to learn an appropriate e-value cutoff to apply to each pairwise alignment by taking into account the overall relatedness of the two datasets being compared. This is done by fitting a function to the distribution of alignment e-values over sequence lengths. The function provides the e-value cutoff for a sequence of given length. Description-md5: b8694674f553b0ae33fd1ec67da3861a Homepage: https://github.com/cboursnell/crb-blast Ruby-Versions: all Section: ruby Priority: optional Filename: pool/main/r/ruby-crb-blast/ruby-crb-blast_0.6.9-4_all.deb Size: 12024 MD5sum: 2104a581b8545f129c2e35c6dc51c56e SHA256: 1d92b86b07f6832624e7a9e7ce343f78b979605e896f7ed7e64386c4a247c801 0m19.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'apt-cache', 'show', '--no-all-versions', 'ruby-crb-blast'] 0m19.1s INFO: apt-cache knows about the following packages: ruby-crb-blast 0m19.1s INFO: Running scripts pre_install 0m19.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_install_database-server'] 0m19.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_install_database-server'] 0m19.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_install_exceptions'] 0m19.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_install_exceptions'] 0m19.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_install_extras'] 0m19.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_install_extras'] 0m19.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_install_foreign_architecture'] 0m19.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_install_foreign_architecture'] 0m19.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m19.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m19.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'apt-cache', 'policy'] 0m19.2s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 Packages release v=12-updates,o=Debian,a=proposed-updates,n=bookworm-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian bookworm-updates/main amd64 Packages release v=12-updates,o=Debian,a=stable-updates,n=bookworm-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org bookworm-security/main amd64 Packages release v=12,o=Debian,a=stable-security,n=bookworm-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.6,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m19.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'apt-cache', 'policy'] 0m19.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'apt-cache', 'policy', 'ruby-crb-blast'] 0m19.2s DUMP: ruby-crb-blast: Installed: 0.6.9-4 Candidate: 0.6.9-4 Version table: *** 0.6.9-4 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 100 /var/lib/dpkg/status 0m19.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'apt-cache', 'policy', 'ruby-crb-blast'] 0m19.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'apt-get', '-y', 'install', 'ruby-crb-blast'] 0m19.6s DUMP: Reading package lists... Building dependency tree... Reading state information... ruby-crb-blast is already the newest version (0.6.9-4). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m19.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'apt-get', '-y', 'install', 'ruby-crb-blast'] 0m19.6s INFO: Running scripts post_install 0m19.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/post_install_exceptions'] 0m19.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/post_install_exceptions'] 0m19.6s INFO: Running scripts post_distupgrade 0m19.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m19.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m19.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/post_distupgrade_exceptions'] 0m19.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/post_distupgrade_exceptions'] 0m19.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m19.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m19.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m19.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m19.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/post_distupgrade_zz_backports'] 0m19.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/post_distupgrade_zz_backports'] 0m19.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4'] 0m20.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4'] 0m20.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4'] 0m21.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4'] 0m21.0s INFO: Running scripts pre_install 0m21.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_install_database-server'] 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_install_database-server'] 0m21.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_install_exceptions'] 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_install_exceptions'] 0m21.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_install_extras'] 0m21.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_install_extras'] 0m21.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_install_foreign_architecture'] 0m21.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_install_foreign_architecture'] 0m21.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m21.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m21.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'apt-cache', 'policy'] 0m21.1s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 Packages release v=12-updates,o=Debian,a=proposed-updates,n=bookworm-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian bookworm-updates/main amd64 Packages release v=12-updates,o=Debian,a=stable-updates,n=bookworm-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org bookworm-security/main amd64 Packages release v=12,o=Debian,a=stable-security,n=bookworm-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.6,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m21.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'apt-cache', 'policy'] 0m21.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'apt-cache', 'policy', 'ruby-crb-blast'] 0m21.2s DUMP: ruby-crb-blast: Installed: 0.6.9-4 Candidate: 0.6.9-4 Version table: *** 0.6.9-4 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 100 /var/lib/dpkg/status 0m21.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'apt-cache', 'policy', 'ruby-crb-blast'] 0m21.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'apt-get', '-y', 'install', 'ruby-crb-blast=0.6.9-4'] 0m21.5s DUMP: Reading package lists... Building dependency tree... Reading state information... ruby-crb-blast is already the newest version (0.6.9-4). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m21.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'apt-get', '-y', 'install', 'ruby-crb-blast=0.6.9-4'] 0m21.5s INFO: Running scripts post_install 0m21.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/post_install_exceptions'] 0m21.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/post_install_exceptions'] 0m21.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4'] 0m22.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4'] 0m22.6s DEBUG: No file moved between /{bin|sbin|lib*} and /usr/{bin|sbin|lib*}. 0m22.6s INFO: /bin converted to /usr/bin by /usr merge 0m22.6s INFO: /lib converted to /usr/lib by /usr merge 0m22.6s INFO: /lib/init converted to /usr/lib/init by /usr merge 0m22.6s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 0m22.6s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 0m22.6s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 0m22.6s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 0m22.6s INFO: /lib/terminfo converted to /usr/lib/terminfo by /usr merge 0m22.6s INFO: /lib/terminfo/E converted to /usr/lib/terminfo/E by /usr merge 0m22.6s INFO: /lib/terminfo/a converted to /usr/lib/terminfo/a by /usr merge 0m22.6s INFO: /lib/terminfo/c converted to /usr/lib/terminfo/c by /usr merge 0m22.6s INFO: /lib/terminfo/d converted to /usr/lib/terminfo/d by /usr merge 0m22.6s INFO: /lib/terminfo/h converted to /usr/lib/terminfo/h by /usr merge 0m22.6s INFO: /lib/terminfo/l converted to /usr/lib/terminfo/l by /usr merge 0m22.6s INFO: /lib/terminfo/m converted to /usr/lib/terminfo/m by /usr merge 0m22.6s INFO: /lib/terminfo/p converted to /usr/lib/terminfo/p by /usr merge 0m22.6s INFO: /lib/terminfo/r converted to /usr/lib/terminfo/r by /usr merge 0m22.6s INFO: /lib/terminfo/s converted to /usr/lib/terminfo/s by /usr merge 0m22.6s INFO: /lib/terminfo/t converted to /usr/lib/terminfo/t by /usr merge 0m22.6s INFO: /lib/terminfo/v converted to /usr/lib/terminfo/v by /usr merge 0m22.6s INFO: /lib/terminfo/w converted to /usr/lib/terminfo/w by /usr merge 0m22.6s INFO: /lib/terminfo/x converted to /usr/lib/terminfo/x by /usr merge 0m22.6s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 0m22.6s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 0m22.6s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 0m22.6s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 0m22.6s INFO: /lib64 converted to /usr/lib64 by /usr merge 0m22.6s INFO: /sbin converted to /usr/sbin by /usr merge 0m23.4s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', '-ac', '--ignore-obsolete'] 0m24.8s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', '-ac', '--ignore-obsolete'] 0m24.8s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m24.9s DUMP: 0.15.6 0m24.9s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m24.9s INFO: Running adequate version 0.15.6 now. 0m24.9s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'ruby-crb-blast'] 0m25.0s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'ruby-crb-blast'] 0m25.0s INFO: Running scripts pre_remove 0m25.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m25.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m25.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m25.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m25.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m26.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m26.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m26.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m26.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m26.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m26.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_remove_exceptions'] 0m26.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/pre_remove_exceptions'] 0m26.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m26.8s 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+deb12u6 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+deb12u1 install ok installed ca-certificates ca-certificates 20230311 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+deb12u1 install ok installed libbsd0:amd64 libbsd0 0.11.7-2 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+deb12u8 install ok installed libc6:amd64 libc6 2.36-9+deb12u8 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 libedit2:amd64 libedit2 3.1-20221030-2 install ok installed libexpat1:amd64 libexpat1 2.5.0-1 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 libgdbm-compat4:amd64 libgdbm-compat4 1.23-3 install ok installed libgdbm6:amd64 libgdbm6 1.23-3 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.9-2+deb12u3 install ok installed libgomp1:amd64 libgomp1 12.2.0-14 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.20.1-2+deb12u2 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 libk5crypto3:amd64 libk5crypto3 1.20.1-2+deb12u2 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.20.1-2+deb12u2 install ok installed libkrb5support0:amd64 libkrb5support0 1.20.1-2+deb12u2 install ok installed liblmdb0:amd64 liblmdb0 0.9.24-1 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 libmbedcrypto7:amd64 libmbedcrypto7 2.28.3-1 install ok installed libmbedtls14:amd64 libmbedtls14 2.28.3-1 install ok installed libmbedx509-1:amd64 libmbedx509-1 2.28.3-1 install ok installed libmd0:amd64 libmd0 1.0.4-2 install ok installed libmount1:amd64 libmount1 2.38.1-5+deb12u1 install ok installed libncurses6:amd64 libncurses6 6.4-4 install ok installed libncursesw6:amd64 libncursesw6 6.4-4 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 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 libpcre3:amd64 libpcre3 2:8.39-15 install ok installed libperl5.36:amd64 libperl5.36 5.36.0-7+deb12u1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.11.2-1+b1 install ok installed libpython3.11-minimal:amd64 libpython3.11-minimal 3.11.2-6+deb12u2 install ok installed libpython3.11-stdlib:amd64 libpython3.11-stdlib 3.11.2-6+deb12u2 install ok installed libreadline8:amd64 libreadline8 8.2-1.3 install ok installed libruby:amd64 libruby 1:3.1 install ok installed libruby3.1:amd64 libruby3.1 3.1.2-7+deb12u1 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+deb12u1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.40.1-2 install ok installed libss2:amd64 libss2 1.47.0-2 install ok installed libssl3:amd64 libssl3 3.0.14-1~deb12u1 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-14 install ok installed libsystemd0:amd64 libsystemd0 252.29-1~deb12u1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.4-4 install ok installed libtirpc-common libtirpc-common 1.3.3+ds-1 install ok installed libtirpc3:amd64 libtirpc3 1.3.3+ds-1 install ok installed libudev1:amd64 libudev1 252.29-1~deb12u1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+deb12u1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libyaml-0-2:amd64 libyaml-0-2 0.2.5-1 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 media-types media-types 10.0.0 install ok installed mount mount 2.38.1-5+deb12u1 install ok installed ncbi-blast+ ncbi-blast+ 2.12.0+ds-3+b1 install ok installed ncbi-data ncbi-data 6.1.20170106+dfsg1-10 install ok installed ncurses-base ncurses-base 6.4-4 install ok installed ncurses-bin ncurses-bin 6.4-4 install ok installed openssl openssl 3.0.14-1~deb12u1 install ok installed passwd passwd 1:4.13+dfsg1-1+b1 install ok installed perl perl 5.36.0-7+deb12u1 install ok installed perl-base perl-base 5.36.0-7+deb12u1 install ok installed perl-modules-5.36 perl-modules-5.36 5.36.0-7+deb12u1 install ok installed python3 python3 3.11.2-1+b1 install ok installed python3-minimal python3-minimal 3.11.2-1+b1 install ok installed python3.11 python3.11 3.11.2-6+deb12u2 install ok installed python3.11-minimal python3.11-minimal 3.11.2-6+deb12u2 install ok installed rake rake 13.0.6-3 install ok installed readline-common readline-common 8.2-1.3 install ok installed ruby ruby 1:3.1 install ok installed ruby-bio ruby-bio 2.0.4-1 install ok installed ruby-crb-blast ruby-crb-blast 0.6.9-4 install ok installed ruby-facade ruby-facade 1.2.1-1 install ok installed ruby-fixwhich ruby-fixwhich 1.0.2-2 install ok installed ruby-net-telnet ruby-net-telnet 0.2.0-1 install ok installed ruby-pathname2 ruby-pathname2 1.8.2-2 install ok installed ruby-rubygems ruby-rubygems 3.3.15-2 install ok installed ruby-sdbm:amd64 ruby-sdbm 1.0.0-5+b1 install ok installed ruby-threach ruby-threach 0.2.0-2 install ok installed ruby-trollop ruby-trollop 2.0-2.1 install ok installed ruby-webrick ruby-webrick 1.8.1-1 install ok installed ruby-xmlrpc ruby-xmlrpc 0.3.2-2 install ok installed ruby3.1 ruby3.1 3.1.2-7+deb12u1 install ok installed rubygems-integration rubygems-integration 1.18 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 2024a-0+deb12u1 install ok installed usr-is-merged usr-is-merged 37~deb12u1 install ok installed util-linux util-linux 2.38.1-5+deb12u1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+deb12u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m26.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m26.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'apt-get', 'remove', 'ca-certificates', 'libbsd0:amd64', 'libedit2:amd64', 'libexpat1:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblmdb0:amd64', 'libmbedcrypto7:amd64', 'libmbedtls14:amd64', 'libmbedx509-1:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libpcre3:amd64', 'libperl5.36:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libreadline8:amd64', 'libruby:amd64', 'libruby3.1:amd64', 'libsqlite3-0:amd64', 'libssl3:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libyaml-0-2:amd64', 'media-types', 'ncbi-blast+-', 'ncbi-data', 'openssl', 'perl', 'perl-modules-5.36', 'python3', 'python3-minimal', 'python3.11', 'python3.11-minimal', 'rake', 'readline-common', 'ruby', 'ruby-bio', 'ruby-facade', 'ruby-fixwhich', 'ruby-net-telnet', 'ruby-pathname2', 'ruby-rubygems', 'ruby-sdbm:amd64', 'ruby-threach', 'ruby-trollop', 'ruby-webrick', 'ruby-xmlrpc', 'ruby3.1', 'rubygems-integration', 'ruby-crb-blast'] 0m28.6s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: ca-certificates libbsd0 libedit2 libexpat1 libgdbm-compat4 libgdbm6 libgomp1 libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblmdb0 libmbedcrypto7 libmbedtls14 libmbedx509-1 libncurses6 libncursesw6 libnsl2 libpcre3 libperl5.36 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libreadline8 libruby libruby3.1 libsqlite3-0 libssl3 libtirpc-common libtirpc3 libyaml-0-2 media-types ncbi-blast+ ncbi-data openssl perl perl-modules-5.36 python3 python3-minimal python3.11 python3.11-minimal rake readline-common ruby ruby-bio ruby-crb-blast ruby-facade ruby-fixwhich ruby-net-telnet ruby-pathname2 ruby-rubygems ruby-sdbm ruby-threach ruby-trollop ruby-webrick ruby-xmlrpc ruby3.1 rubygems-integration 0 upgraded, 0 newly installed, 59 to remove and 0 not upgraded. After this operation, 197 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 ... 13019 files and directories currently installed.) Removing ruby-crb-blast (0.6.9-4) ... Removing ruby-trollop (2.0-2.1) ... Removing ruby-threach (0.2.0-2) ... Removing ncbi-blast+ (2.12.0+ds-3+b1) ... Removing python3 (3.11.2-1+b1) ... Removing python3.11 (3.11.2-6+deb12u2) ... Removing python3-minimal (3.11.2-1+b1) ... Removing python3.11-minimal (3.11.2-6+deb12u2) ... Removing libexpat1:amd64 (2.5.0-1) ... Removing perl (5.36.0-7+deb12u1) ... Removing libperl5.36:amd64 (5.36.0-7+deb12u1) ... Removing libgdbm-compat4:amd64 (1.23-3) ... Removing libgdbm6:amd64 (1.23-3) ... Removing libgomp1:amd64 (12.2.0-14) ... Removing libpython3-stdlib:amd64 (3.11.2-1+b1) ... Removing libpython3.11-stdlib:amd64 (3.11.2-6+deb12u2) ... find: '/usr/lib/python3': No such file or directory Removing libnsl2:amd64 (1.3.0-2) ... Removing libtirpc3:amd64 (1.3.3+ds-1) ... Removing libgssapi-krb5-2:amd64 (1.20.1-2+deb12u2) ... Removing libkrb5-3:amd64 (1.20.1-2+deb12u2) ... Removing libk5crypto3:amd64 (1.20.1-2+deb12u2) ... Removing libkeyutils1:amd64 (1.6.3-2) ... Removing libkrb5support0:amd64 (1.20.1-2+deb12u2) ... Removing liblmdb0:amd64 (0.9.24-1) ... Removing libmbedtls14:amd64 (2.28.3-1) ... Removing libmbedx509-1:amd64 (2.28.3-1) ... Removing libmbedcrypto7:amd64 (2.28.3-1) ... Removing libncursesw6:amd64 (6.4-4) ... Removing libpcre3:amd64 (2:8.39-15) ... Removing libpython3.11-minimal:amd64 (3.11.2-6+deb12u2) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8:amd64 (8.2-1.3) ... Removing libsqlite3-0:amd64 (3.40.1-2) ... Removing libtirpc-common (1.3.3+ds-1) ... Removing media-types (10.0.0) ... Removing ncbi-data (6.1.20170106+dfsg1-10) ... Removing perl-modules-5.36 (5.36.0-7+deb12u1) ... Removing readline-common (8.2-1.3) ... Removing ruby-bio (2.0.4-1) ... Removing ruby-fixwhich (1.0.2-2) ... Removing ruby-pathname2 (1.8.2-2) ... Removing ruby-facade (1.2.1-1) ... Removing ruby-sdbm:amd64 (1.0.0-5+b1) ... Removing libruby3.1:amd64 (3.1.2-7+deb12u1) ... Removing rake (13.0.6-3) ... Removing ruby (1:3.1) ... Removing ruby-rubygems (3.3.15-2) ... Removing libedit2:amd64 (3.1-20221030-2) ... Removing libbsd0:amd64 (0.11.7-2) ... Removing libncurses6:amd64 (6.4-4) ... Removing libruby:amd64 (1:3.1) ... Removing libyaml-0-2:amd64 (0.2.5-1) ... Removing ruby-net-telnet (0.2.0-1) ... Removing ruby-xmlrpc (0.3.2-2) ... Removing ruby-webrick (1.8.1-1) ... Removing ruby3.1 (3.1.2-7+deb12u1) ... Removing rubygems-integration (1.18) ... Removing ca-certificates (20230311) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing openssl (3.0.14-1~deb12u1) ... Removing libssl3:amd64 (3.0.14-1~deb12u1) ... Processing triggers for libc-bin (2.36-9+deb12u8) ... 0m28.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'apt-get', 'remove', 'ca-certificates', 'libbsd0:amd64', 'libedit2:amd64', 'libexpat1:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblmdb0:amd64', 'libmbedcrypto7:amd64', 'libmbedtls14:amd64', 'libmbedx509-1:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libpcre3:amd64', 'libperl5.36:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libreadline8:amd64', 'libruby:amd64', 'libruby3.1:amd64', 'libsqlite3-0:amd64', 'libssl3:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libyaml-0-2:amd64', 'media-types', 'ncbi-blast+-', 'ncbi-data', 'openssl', 'perl', 'perl-modules-5.36', 'python3', 'python3-minimal', 'python3.11', 'python3.11-minimal', 'rake', 'readline-common', 'ruby', 'ruby-bio', 'ruby-facade', 'ruby-fixwhich', 'ruby-net-telnet', 'ruby-pathname2', 'ruby-rubygems', 'ruby-sdbm:amd64', 'ruby-threach', 'ruby-trollop', 'ruby-webrick', 'ruby-xmlrpc', 'ruby3.1', 'rubygems-integration', 'ruby-crb-blast'] 0m28.6s INFO: Running scripts post_remove 0m28.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/post_remove_exceptions'] 0m28.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/post_remove_exceptions'] 0m28.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'dpkg', '--purge', 'ca-certificates', 'libbsd0:amd64', 'libedit2:amd64', 'libexpat1:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblmdb0:amd64', 'libmbedcrypto7:amd64', 'libmbedtls14:amd64', 'libmbedx509-1:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libpcre3:amd64', 'libperl5.36:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libreadline8:amd64', 'libruby:amd64', 'libruby3.1:amd64', 'libsqlite3-0:amd64', 'libssl3:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libyaml-0-2:amd64', 'media-types', 'ncbi-blast+', 'ncbi-data', 'openssl', 'perl', 'perl-modules-5.36', 'python3', 'python3-minimal', 'python3.11', 'python3.11-minimal', 'rake', 'readline-common', 'ruby', 'ruby-bio', 'ruby-facade', 'ruby-fixwhich', 'ruby-net-telnet', 'ruby-pathname2', 'ruby-rubygems', 'ruby-sdbm:amd64', 'ruby-threach', 'ruby-trollop', 'ruby-webrick', 'ruby-xmlrpc', 'ruby3.1', 'rubygems-integration'] 0m28.7s DUMP: (Reading database ... 6106 files and directories currently installed.) Purging configuration files for ca-certificates (20230311) ... Removing dangling symlinks from /etc/ssl/certs... done. dpkg: warning: ignoring request to remove libbsd0 which isn't installed dpkg: warning: ignoring request to remove libedit2 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libgdbm-compat4 which isn't installed dpkg: warning: ignoring request to remove libgdbm6 which isn't installed dpkg: warning: ignoring request to remove libgomp1 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.20.1-2+deb12u2) ... dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove liblmdb0 which isn't installed dpkg: warning: ignoring request to remove libmbedcrypto7 which isn't installed dpkg: warning: ignoring request to remove libmbedtls14 which isn't installed dpkg: warning: ignoring request to remove libmbedx509-1 which isn't installed dpkg: warning: ignoring request to remove libncurses6 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libnsl2 which isn't installed dpkg: warning: ignoring request to remove libpcre3 which isn't installed dpkg: warning: ignoring request to remove libperl5.36 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.11-minimal:amd64 (3.11.2-6+deb12u2) ... dpkg: warning: ignoring request to remove libpython3.11-stdlib which isn't installed dpkg: warning: ignoring request to remove libreadline8 which isn't installed dpkg: warning: ignoring request to remove libruby which isn't installed dpkg: warning: ignoring request to remove libruby3.1 which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libssl3 which isn't installed Purging configuration files for libtirpc-common (1.3.3+ds-1) ... dpkg: warning: ignoring request to remove libtirpc3 which isn't installed dpkg: warning: ignoring request to remove libyaml-0-2 which isn't installed Purging configuration files for media-types (10.0.0) ... dpkg: warning: ignoring request to remove ncbi-blast+ which isn't installed Purging configuration files for ncbi-data (6.1.20170106+dfsg1-10) ... Purging configuration files for openssl (3.0.14-1~deb12u1) ... Purging configuration files for perl (5.36.0-7+deb12u1) ... dpkg: warning: ignoring request to remove perl-modules-5.36 which isn't installed Purging configuration files for python3 (3.11.2-1+b1) ... dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3.11 which isn't installed Purging configuration files for python3.11-minimal (3.11.2-6+deb12u2) ... dpkg: warning: ignoring request to remove rake which isn't installed Purging configuration files for readline-common (8.2-1.3) ... dpkg: warning: ignoring request to remove ruby which isn't installed dpkg: warning: ignoring request to remove ruby-bio which isn't installed dpkg: warning: ignoring request to remove ruby-facade which isn't installed dpkg: warning: ignoring request to remove ruby-fixwhich which isn't installed dpkg: warning: ignoring request to remove ruby-net-telnet which isn't installed dpkg: warning: ignoring request to remove ruby-pathname2 which isn't installed dpkg: warning: ignoring request to remove ruby-rubygems which isn't installed dpkg: warning: ignoring request to remove ruby-sdbm which isn't installed dpkg: warning: ignoring request to remove ruby-threach which isn't installed dpkg: warning: ignoring request to remove ruby-trollop which isn't installed dpkg: warning: ignoring request to remove ruby-webrick which isn't installed dpkg: warning: ignoring request to remove ruby-xmlrpc which isn't installed dpkg: warning: ignoring request to remove ruby3.1 which isn't installed dpkg: warning: ignoring request to remove rubygems-integration which isn't installed 0m28.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'dpkg', '--purge', 'ca-certificates', 'libbsd0:amd64', 'libedit2:amd64', 'libexpat1:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblmdb0:amd64', 'libmbedcrypto7:amd64', 'libmbedtls14:amd64', 'libmbedx509-1:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libpcre3:amd64', 'libperl5.36:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libreadline8:amd64', 'libruby:amd64', 'libruby3.1:amd64', 'libsqlite3-0:amd64', 'libssl3:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libyaml-0-2:amd64', 'media-types', 'ncbi-blast+', 'ncbi-data', 'openssl', 'perl', 'perl-modules-5.36', 'python3', 'python3-minimal', 'python3.11', 'python3.11-minimal', 'rake', 'readline-common', 'ruby', 'ruby-bio', 'ruby-facade', 'ruby-fixwhich', 'ruby-net-telnet', 'ruby-pathname2', 'ruby-rubygems', 'ruby-sdbm:amd64', 'ruby-threach', 'ruby-trollop', 'ruby-webrick', 'ruby-xmlrpc', 'ruby3.1', 'rubygems-integration'] 0m28.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'dpkg', '--purge', 'ruby-crb-blast'] 0m28.7s DUMP: dpkg: warning: ignoring request to remove ruby-crb-blast which isn't installed 0m28.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'dpkg', '--purge', 'ruby-crb-blast'] 0m28.7s INFO: Running scripts post_purge 0m28.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/post_purge_exceptions'] 0m28.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/post_purge_exceptions'] 0m28.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'dpkg', '--purge', '--pending'] 0m28.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'dpkg', '--purge', '--pending'] 0m28.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'dpkg', '--remove', '--pending'] 0m28.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'dpkg', '--remove', '--pending'] 0m28.8s INFO: Running scripts post_test 0m28.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/post_test_exceptions'] 0m28.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'tmp/scripts/post_test_exceptions'] 0m28.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4'] 0m29.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4'] 0m29.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'dpkg-divert', '--list'] 0m29.2s DUMP: local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m29.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'dpkg-divert', '--list'] 0m29.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'apt-get', 'clean'] 0m29.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4', 'apt-get', 'clean'] 0m29.2s DEBUG: Recording chroot state 0m30.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4/dev/shm'] 0m30.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4/dev/shm'] 0m30.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4/dev/console'] 0m30.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4/dev/console'] 0m30.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4/dev/ptmx'] 0m30.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4/dev/ptmx'] 0m30.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4/dev/pts'] 0m30.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4/dev/pts'] 0m30.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4/proc'] 0m30.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4/proc'] 0m30.2s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4'] 0m30.3s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpj2q2w9w4'] 0m30.3s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpj2q2w9w4 0m30.3s INFO: PASS: Upgrading between Debian distributions. 0m30.3s INFO: PASS: All tests. 0m30.3s INFO: piuparts run ends. ret=0 End: 2024-08-23 05:24:49 GMT