Start: 2023-08-30 21:23:42 GMT Package: bio-eagle Source: bio-eagle (2.4.1-3) Version: 2.4.1-3+b1 Installed-Size: 619 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libboost-iostreams1.74.0 (>= 1.74.0), libboost-program-options1.74.0 (>= 1.74.0), libc6 (>= 2.29), libgcc-s1 (>= 3.0), libgomp1 (>= 6), libhts3 (>= 1.10), libopenblas0, libstdc++6 (>= 5.2) Recommends: med-config (>= 2.1) Suggests: bio-eagle-examples Description: Haplotype phasing within a genotyped cohort or using a phased reference panel Homepage: https://data.broadinstitute.org/alkesgroup/Eagle/ Description-md5: ea6e8307bcd12f756aab2c02e5d41b0e Tag: field::biology, field::biology:bioinformatics, implemented-in::c++, interface::commandline, role::program, use::analysing Section: science Priority: optional Filename: pool/main/b/bio-eagle/bio-eagle_2.4.1-3+b1_amd64.deb Size: 224080 MD5sum: 344ae770ea5281c881a1010052c1af4b SHA256: 3a3432961525c3962316ef2fb4b45697a9537f1a6b0988ad3efaa31067baaf04 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 --merged-usr -i /usr/lib32/ -i /usr/libx32/ --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz -d sid --no-upgrade-test --apt bio-eagle=2.4.1-3+b1 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 1.1.8~202306121314~1.1.7-9-g57dfbde6 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 --merged-usr -i /usr/lib32/ -i /usr/libx32/ --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz -d sid --no-upgrade-test --apt bio-eagle=2.4.1-3+b1 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-25-amd64 #1 SMP Debian 5.10.191-1 (2023-08-16) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpkeh0ea2k 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpkeh0ea2k 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m1.9s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m1.9s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k/proc'] 0m1.9s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k/proc'] 0m1.9s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k/dev/pts'] 0m1.9s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k/dev/pts'] 0m1.9s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k/dev/ptmx'] 0m1.9s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k/dev/ptmx'] 0m1.9s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k/dev/console'] 0m1.9s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k/dev/console'] 0m1.9s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k/dev/shm'] 0m1.9s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k/dev/shm'] 0m2.0s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m2.0s DEBUG: Created policy-rc.d and chmodded it. 0m2.0s DEBUG: Created resolv.conf. 0m2.0s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpkeh0ea2k/tmp/scripts/ 0m2.0s INFO: Running scripts post_chroot_unpack 0m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'apt-get', 'update'] 0m6.5s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [210 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9564 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7008 kB] Fetched 16.8 MB in 3s (5185 kB/s) Reading package lists... 0m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'apt-get', 'update'] 0m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'apt-get', '-yf', 'dist-upgrade'] 0m8.5s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: debianutils dpkg libpcre2-8-0 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 1934 kB of archives. After this operation, 9216 B disk space will be freed. Get:1 http://deb.debian.org/debian sid/main amd64 debianutils amd64 5.11 [103 kB] Get:2 http://deb.debian.org/debian sid/main amd64 dpkg amd64 1.22.0 [1569 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libpcre2-8-0 amd64 10.42-4 [261 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1934 kB in 0s (26.1 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5199 files and directories currently installed.) Preparing to unpack .../debianutils_5.11_amd64.deb ... Unpacking debianutils (5.11) over (5.10) ... Setting up debianutils (5.11) ... (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 ... 5199 files and directories currently installed.) Preparing to unpack .../archives/dpkg_1.22.0_amd64.deb ... Unpacking dpkg (1.22.0) over (1.21.22) ... Setting up dpkg (1.22.0) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5196 files and directories currently installed.) Preparing to unpack .../libpcre2-8-0_10.42-4_amd64.deb ... Unpacking libpcre2-8-0:amd64 (10.42-4) over (10.42-3) ... Setting up libpcre2-8-0:amd64 (10.42-4) ... Processing triggers for libc-bin (2.37-7) ... 0m8.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'apt-get', '-yf', 'dist-upgrade'] 0m8.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m8.8s DUMP: 1f79207761a6e868a9b43d17ef9f7e37 - 0m8.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m8.8s INFO: Running scripts post_setup 0m8.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/post_setup_dummy_users'] 0m10.0s 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 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/post_setup_dummy_users'] 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/post_setup_forbid_home'] 0m10.0s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/post_setup_forbid_home'] 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/post_setup_force-unsafe-io'] 0m10.0s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' dpkg-divert: warning: diverting file '/bin/sync' from an Essential package with rename is dangerous, use --no-rename '/bin/sync' -> 'true' 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/post_setup_force-unsafe-io'] 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/post_setup_minimize'] 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/post_setup_minimize'] 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/post_setup_squeeze-backports'] 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/post_setup_squeeze-backports'] 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/post_setup_zz_backports'] 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/post_setup_zz_backports'] 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'apt-get', 'clean'] 0m10.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'apt-get', 'clean'] 0m10.1s DEBUG: Recording chroot state 0m10.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m10.5s DUMP: install ok installed apt apt 2.7.3 install ok installed base-files base-files 13 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b4 install ok installed bsdutils bsdutils 1:2.39.2-1 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.12-6 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.11 install ok installed diffutils diffutils 1:3.8-4 install ok installed dpkg dpkg 1.22.0 install ok installed e2fsprogs e2fsprogs 1.47.0-2 install ok installed findutils findutils 4.9.0-5 install ok installed gcc-13-base:amd64 gcc-13-base 13.2.0-2 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.11-3 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 2.7.3 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.1.1-1 install ok installed libaudit1:amd64 libaudit1 1:3.1.1-1 install ok installed libblkid1:amd64 libblkid1 2.39.2-1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.37-7 install ok installed libc6:amd64 libc6 2.37-7 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 1:4.4.36-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-2 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 13.2.0-2 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.2-2 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2 install ok installed libgnutls30:amd64 libgnutls30 3.8.1-4 install ok installed libgpg-error0:amd64 libgpg-error0 1.47-2 install ok installed libhogweed6:amd64 libhogweed6 3.9.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.4-1 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 libmd0:amd64 libmd0 1.1.0-1 install ok installed libmount1:amd64 libmount1 2.39.2-1 install ok installed libnettle8:amd64 libnettle8 3.9.1-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.0-4 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-7 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-7 install ok installed libpam-runtime libpam-runtime 1.5.2-7 install ok installed libpam0g:amd64 libpam0g 1.5.2-7 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+b3 install ok installed libselinux1:amd64 libselinux1 3.5-1 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1 install ok installed libsepol2:amd64 libsepol2 3.5-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.39.2-1 install ok installed libss2:amd64 libss2 1.47.0-2 install ok installed libstdc++6:amd64 libstdc++6 13.2.0-2 install ok installed libsystemd0:amd64 libsystemd0 254.1-3 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3 install ok installed libtinfo6:amd64 libtinfo6 6.4+20230625-2 install ok installed libudev1:amd64 libudev1 254.1-3 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.39.2-1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-1 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 1.3.4.20230808-1 install ok installed mount mount 2.39.2-1 install ok installed ncurses-base ncurses-base 6.4+20230625-2 install ok installed ncurses-bin ncurses-bin 6.4+20230625-2 install ok installed passwd passwd 1:4.13+dfsg1-1+b1 install ok installed perl-base perl-base 5.36.0-8 install ok installed sed sed 4.9-1 install ok installed sysvinit-utils sysvinit-utils 3.07-1 install ok installed tar tar 1.34+dfsg-1.2 install ok installed tzdata tzdata 2023c-10 install ok installed usr-is-merged usr-is-merged 37 install ok installed util-linux util-linux 2.39.2-1 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-3 0m10.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m10.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'dpkg-divert', '--list'] 0m10.6s DUMP: local diversion of /bin/sync to /bin/sync.distrib local diversion of /home to /home.distrib 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'dpkg-divert', '--list'] 0m10.6s INFO: Running scripts is_testable 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/is_testable_uninstallable'] 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/is_testable_uninstallable'] 0m10.6s INFO: apt-cache does not know about any of the requested packages 0m10.6s INFO: Running scripts pre_test 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/pre_test_exceptions'] 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/pre_test_exceptions'] 0m10.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/pre_test_root_password'] 0m10.6s DUMP: New password: Retype new password: passwd: password updated successfully 0m10.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/pre_test_root_password'] 0m10.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k'] 0m10.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k'] 0m11.3s DEBUG: No broken symlinks as far as we can find. 0m11.3s INFO: Running scripts pre_install 0m11.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/pre_install_database-server'] 0m11.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/pre_install_database-server'] 0m11.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/pre_install_exceptions'] 0m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/pre_install_exceptions'] 0m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/pre_install_extras'] 0m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/pre_install_extras'] 0m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/pre_install_foreign_architecture'] 0m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/pre_install_foreign_architecture'] 0m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m11.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k'] 0m11.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k'] 0m12.1s DEBUG: No broken symlinks as far as we can find. 0m12.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'apt-cache', 'policy'] 0m13.2s 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: 0m13.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'apt-cache', 'policy'] 0m13.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'apt-cache', 'policy', 'bio-eagle'] 0m13.2s DUMP: bio-eagle: Installed: (none) Candidate: 2.4.1-3+b1 Version table: 2.4.1-3+b1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 0m13.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'apt-cache', 'policy', 'bio-eagle'] 0m13.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'apt-get', '-y', 'install', 'bio-eagle=2.4.1-3+b1'] 0m16.5s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libboost-iostreams1.74.0 libboost-program-options1.74.0 libbrotli1 libcurl3-gnutls libdeflate0 libgfortran5 libgomp1 libgssapi-krb5-2 libhts3 libhtscodecs2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.5-0 libnghttp2-14 libopenblas0 libopenblas0-pthread libpsl5 librtmp1 libsasl2-2 libsasl2-modules-db libssh2-1 libssl3 Suggested packages: bio-eagle-examples krb5-doc krb5-user Recommended packages: med-config ca-certificates krb5-locales libldap-common publicsuffix libsasl2-modules The following NEW packages will be installed: bio-eagle libboost-iostreams1.74.0 libboost-program-options1.74.0 libbrotli1 libcurl3-gnutls libdeflate0 libgfortran5 libgomp1 libgssapi-krb5-2 libhts3 libhtscodecs2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.5-0 libnghttp2-14 libopenblas0 libopenblas0-pthread libpsl5 librtmp1 libsasl2-2 libsasl2-modules-db libssh2-1 libssl3 0 upgraded, 25 newly installed, 0 to remove and 0 not upgraded. Need to get 12.9 MB of archives. After this operation, 65.8 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 libboost-iostreams1.74.0 amd64 1.74.0+ds1-22 [241 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libboost-program-options1.74.0 amd64 1.74.0+ds1-22 [332 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 13.2.0-2 [131 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libkrb5support0 amd64 1.20.1-3 [32.3 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libk5crypto3 amd64 1.20.1-3 [79.1 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libkeyutils1 amd64 1.6.3-2 [8808 B] Get:8 http://deb.debian.org/debian sid/main amd64 libssl3 amd64 3.0.10-1 [2014 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libkrb5-3 amd64 1.20.1-3 [333 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libgssapi-krb5-2 amd64 1.20.1-3 [134 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-3 [19.3 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-3 [56.6 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libnghttp2-14 amd64 1.55.1-1 [72.8 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get:16 http://deb.debian.org/debian sid/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:17 http://deb.debian.org/debian sid/main amd64 libssh2-1 amd64 1.11.0-2 [214 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libcurl3-gnutls amd64 8.2.1-2 [383 kB] Get:19 http://deb.debian.org/debian sid/main amd64 libdeflate0 amd64 1.18-1 [40.9 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libhtscodecs2 amd64 1.5.1-1 [91.5 kB] Get:21 http://deb.debian.org/debian sid/main amd64 libhts3 amd64 1.17+ds-1 [439 kB] Get:22 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 13.2.0-2 [804 kB] Get:23 http://deb.debian.org/debian sid/main amd64 libopenblas0-pthread amd64 0.3.23+ds-3 [6684 kB] Get:24 http://deb.debian.org/debian sid/main amd64 libopenblas0 amd64 0.3.23+ds-3 [34.2 kB] Get:25 http://deb.debian.org/debian sid/main amd64 bio-eagle amd64 2.4.1-3+b1 [224 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 12.9 MB in 0s (60.8 MB/s) Selecting previously unselected package libboost-iostreams1.74.0:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5198 files and directories currently installed.) Preparing to unpack .../00-libboost-iostreams1.74.0_1.74.0+ds1-22_amd64.deb ... Unpacking libboost-iostreams1.74.0:amd64 (1.74.0+ds1-22) ... Selecting previously unselected package libboost-program-options1.74.0:amd64. Preparing to unpack .../01-libboost-program-options1.74.0_1.74.0+ds1-22_amd64.deb ... Unpacking libboost-program-options1.74.0:amd64 (1.74.0+ds1-22) ... Selecting previously unselected package libgomp1:amd64. Preparing to unpack .../02-libgomp1_13.2.0-2_amd64.deb ... Unpacking libgomp1:amd64 (13.2.0-2) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../03-libbrotli1_1.0.9-2+b6_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2+b6) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../04-libkrb5support0_1.20.1-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.20.1-3) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../05-libk5crypto3_1.20.1-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.20.1-3) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../06-libkeyutils1_1.6.3-2_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-2) ... Selecting previously unselected package libssl3:amd64. Preparing to unpack .../07-libssl3_3.0.10-1_amd64.deb ... Unpacking libssl3:amd64 (3.0.10-1) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../08-libkrb5-3_1.20.1-3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.20.1-3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../09-libgssapi-krb5-2_1.20.1-3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.20.1-3) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../10-libsasl2-modules-db_2.1.28+dfsg1-3_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.28+dfsg1-3) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../11-libsasl2-2_2.1.28+dfsg1-3_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.28+dfsg1-3) ... Selecting previously unselected package libldap-2.5-0:amd64. Preparing to unpack .../12-libldap-2.5-0_2.5.13+dfsg-5_amd64.deb ... Unpacking libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../13-libnghttp2-14_1.55.1-1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.55.1-1) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../14-libpsl5_0.21.2-1_amd64.deb ... Unpacking libpsl5:amd64 (0.21.2-1) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../15-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../16-libssh2-1_1.11.0-2_amd64.deb ... Unpacking libssh2-1:amd64 (1.11.0-2) ... Selecting previously unselected package libcurl3-gnutls:amd64. Preparing to unpack .../17-libcurl3-gnutls_8.2.1-2_amd64.deb ... Unpacking libcurl3-gnutls:amd64 (8.2.1-2) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../18-libdeflate0_1.18-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.18-1) ... Selecting previously unselected package libhtscodecs2:amd64. Preparing to unpack .../19-libhtscodecs2_1.5.1-1_amd64.deb ... Unpacking libhtscodecs2:amd64 (1.5.1-1) ... Selecting previously unselected package libhts3:amd64. Preparing to unpack .../20-libhts3_1.17+ds-1_amd64.deb ... Unpacking libhts3:amd64 (1.17+ds-1) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../21-libgfortran5_13.2.0-2_amd64.deb ... Unpacking libgfortran5:amd64 (13.2.0-2) ... Selecting previously unselected package libopenblas0-pthread:amd64. Preparing to unpack .../22-libopenblas0-pthread_0.3.23+ds-3_amd64.deb ... Unpacking libopenblas0-pthread:amd64 (0.3.23+ds-3) ... Selecting previously unselected package libopenblas0:amd64. Preparing to unpack .../23-libopenblas0_0.3.23+ds-3_amd64.deb ... Unpacking libopenblas0:amd64 (0.3.23+ds-3) ... Selecting previously unselected package bio-eagle. Preparing to unpack .../24-bio-eagle_2.4.1-3+b1_amd64.deb ... Unpacking bio-eagle (2.4.1-3+b1) ... Setting up libhtscodecs2:amd64 (1.5.1-1) ... Setting up libkeyutils1:amd64 (1.6.3-2) ... Setting up libpsl5:amd64 (0.21.2-1) ... Setting up libboost-iostreams1.74.0:amd64 (1.74.0+ds1-22) ... Setting up libboost-program-options1.74.0:amd64 (1.74.0+ds1-22) ... Setting up libbrotli1:amd64 (1.0.9-2+b6) ... Setting up libssl3:amd64 (3.0.10-1) ... Setting up libnghttp2-14:amd64 (1.55.1-1) ... Setting up libdeflate0:amd64 (1.18-1) ... Setting up libgomp1:amd64 (13.2.0-2) ... Setting up libkrb5support0:amd64 (1.20.1-3) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-3) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libk5crypto3:amd64 (1.20.1-3) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-3) ... Setting up libgfortran5:amd64 (13.2.0-2) ... Setting up libssh2-1:amd64 (1.11.0-2) ... Setting up libkrb5-3:amd64 (1.20.1-3) ... Setting up libopenblas0-pthread:amd64 (0.3.23+ds-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so.0 to provide /usr/lib/x86_64-linux-gnu/libopenblas.so.0 (libopenblas.so.0-x86_64-linux-gnu) in auto mode Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-3) ... Setting up libopenblas0:amd64 (0.3.23+ds-3) ... Setting up libcurl3-gnutls:amd64 (8.2.1-2) ... Setting up libhts3:amd64 (1.17+ds-1) ... Setting up bio-eagle (2.4.1-3+b1) ... Processing triggers for libc-bin (2.37-7) ... 0m16.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'apt-get', '-y', 'install', 'bio-eagle=2.4.1-3+b1'] 0m16.5s INFO: Running scripts post_install 0m16.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/post_install_exceptions'] 0m16.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/post_install_exceptions'] 0m16.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k'] 0m16.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k'] 0m17.3s DEBUG: No broken symlinks as far as we can find. 0m17.3s INFO: /bin converted to /usr/bin by /usr merge 0m17.3s INFO: /lib converted to /usr/lib by /usr merge 0m17.3s INFO: /lib/init converted to /usr/lib/init by /usr merge 0m17.3s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 0m17.3s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 0m17.3s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 0m17.3s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 0m17.3s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 0m17.3s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 0m17.3s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 0m17.3s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 0m17.3s INFO: /lib64 converted to /usr/lib64 by /usr merge 0m17.3s INFO: /sbin converted to /usr/sbin by /usr merge 0m17.6s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', '-ac', '--ignore-obsolete'] 0m18.4s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', '-ac', '--ignore-obsolete'] 0m18.4s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m18.4s DUMP: 0.15.6 0m18.4s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m18.4s INFO: Running adequate version 0.15.6 now. 0m18.4s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'bio-eagle'] 0m18.5s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'bio-eagle'] 0m18.5s INFO: Running scripts pre_remove 0m18.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m18.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m18.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m18.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m18.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m19.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m19.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m19.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m19.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m19.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m19.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/pre_remove_exceptions'] 0m20.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/pre_remove_exceptions'] 0m20.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m20.0s DUMP: install ok installed apt apt 2.7.3 install ok installed base-files base-files 13 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b4 install ok installed bio-eagle bio-eagle 2.4.1-3+b1 install ok installed bsdutils bsdutils 1:2.39.2-1 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.12-6 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.11 install ok installed diffutils diffutils 1:3.8-4 install ok installed dpkg dpkg 1.22.0 install ok installed e2fsprogs e2fsprogs 1.47.0-2 install ok installed findutils findutils 4.9.0-5 install ok installed gcc-13-base:amd64 gcc-13-base 13.2.0-2 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.11-3 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 2.7.3 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.1.1-1 install ok installed libaudit1:amd64 libaudit1 1:3.1.1-1 install ok installed libblkid1:amd64 libblkid1 2.39.2-1 install ok installed libboost-iostreams1.74.0:amd64 libboost-iostreams1.74.0 1.74.0+ds1-22 install ok installed libboost-program-options1.74.0:amd64 libboost-program-options1.74.0 1.74.0+ds1-22 install ok installed libbrotli1:amd64 libbrotli1 1.0.9-2+b6 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.37-7 install ok installed libc6:amd64 libc6 2.37-7 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 1:4.4.36-2 install ok installed libcurl3-gnutls:amd64 libcurl3-gnutls 8.2.1-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-2 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.270 install ok installed libdeflate0:amd64 libdeflate0 1.18-1 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 13.2.0-2 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.2-2 install ok installed libgfortran5:amd64 libgfortran5 13.2.0-2 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2 install ok installed libgnutls30:amd64 libgnutls30 3.8.1-4 install ok installed libgomp1:amd64 libgomp1 13.2.0-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.47-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.20.1-3 install ok installed libhogweed6:amd64 libhogweed6 3.9.1-2 install ok installed libhts3:amd64 libhts3 1.17+ds-1 install ok installed libhtscodecs2:amd64 libhtscodecs2 1.5.1-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.4-1 install ok installed libk5crypto3:amd64 libk5crypto3 1.20.1-3 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.20.1-3 install ok installed libkrb5support0:amd64 libkrb5support0 1.20.1-3 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.13+dfsg-5 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 1.1.0-1 install ok installed libmount1:amd64 libmount1 2.39.2-1 install ok installed libnettle8:amd64 libnettle8 3.9.1-2 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.55.1-1 install ok installed libopenblas0:amd64 libopenblas0 0.3.23+ds-3 install ok installed libopenblas0-pthread:amd64 libopenblas0-pthread 0.3.23+ds-3 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.0-4 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-7 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-7 install ok installed libpam-runtime libpam-runtime 1.5.2-7 install ok installed libpam0g:amd64 libpam0g 1.5.2-7 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4 install ok installed libpsl5:amd64 libpsl5 0.21.2-1 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b2 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-3 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-3 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+b3 install ok installed libselinux1:amd64 libselinux1 3.5-1 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1 install ok installed libsepol2:amd64 libsepol2 3.5-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.39.2-1 install ok installed libss2:amd64 libss2 1.47.0-2 install ok installed libssh2-1:amd64 libssh2-1 1.11.0-2 install ok installed libssl3:amd64 libssl3 3.0.10-1 install ok installed libstdc++6:amd64 libstdc++6 13.2.0-2 install ok installed libsystemd0:amd64 libsystemd0 254.1-3 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3 install ok installed libtinfo6:amd64 libtinfo6 6.4+20230625-2 install ok installed libudev1:amd64 libudev1 254.1-3 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.39.2-1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-1 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 1.3.4.20230808-1 install ok installed mount mount 2.39.2-1 install ok installed ncurses-base ncurses-base 6.4+20230625-2 install ok installed ncurses-bin ncurses-bin 6.4+20230625-2 install ok installed passwd passwd 1:4.13+dfsg1-1+b1 install ok installed perl-base perl-base 5.36.0-8 install ok installed sed sed 4.9-1 install ok installed sysvinit-utils sysvinit-utils 3.07-1 install ok installed tar tar 1.34+dfsg-1.2 install ok installed tzdata tzdata 2023c-10 install ok installed usr-is-merged usr-is-merged 37 install ok installed util-linux util-linux 2.39.2-1 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-3 0m20.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m20.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'apt-get', 'remove', 'libboost-iostreams1.74.0:amd64', 'libboost-program-options1.74.0:amd64', 'libbrotli1:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libldap-2.5-0:amd64', 'libnghttp2-14:amd64', 'libopenblas0:amd64', 'libopenblas0-pthread:amd64', 'libpsl5:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libssh2-1:amd64', 'libssl3:amd64', 'bio-eagle'] 0m21.1s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: bio-eagle libboost-iostreams1.74.0 libboost-program-options1.74.0 libbrotli1 libcurl3-gnutls libdeflate0 libgfortran5 libgomp1 libgssapi-krb5-2 libhts3 libhtscodecs2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.5-0 libnghttp2-14 libopenblas0 libopenblas0-pthread libpsl5 librtmp1 libsasl2-2 libsasl2-modules-db libssh2-1 libssl3 0 upgraded, 0 newly installed, 25 to remove and 0 not upgraded. After this operation, 65.8 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 ... 5390 files and directories currently installed.) Removing bio-eagle (2.4.1-3+b1) ... Removing libboost-iostreams1.74.0:amd64 (1.74.0+ds1-22) ... Removing libboost-program-options1.74.0:amd64 (1.74.0+ds1-22) ... Removing libhts3:amd64 (1.17+ds-1) ... Removing libcurl3-gnutls:amd64 (8.2.1-2) ... Removing libbrotli1:amd64 (1.0.9-2+b6) ... Removing libdeflate0:amd64 (1.18-1) ... Removing libopenblas0:amd64 (0.3.23+ds-3) ... Removing libopenblas0-pthread:amd64 (0.3.23+ds-3) ... Removing libgfortran5:amd64 (13.2.0-2) ... Removing libgomp1:amd64 (13.2.0-2) ... Removing libgssapi-krb5-2:amd64 (1.20.1-3) ... Removing libhtscodecs2:amd64 (1.5.1-1) ... Removing libkrb5-3:amd64 (1.20.1-3) ... Removing libk5crypto3:amd64 (1.20.1-3) ... Removing libkeyutils1:amd64 (1.6.3-2) ... Removing libkrb5support0:amd64 (1.20.1-3) ... Removing libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Removing libnghttp2-14:amd64 (1.55.1-1) ... Removing libpsl5:amd64 (0.21.2-1) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-3) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-3) ... Removing libssh2-1:amd64 (1.11.0-2) ... Removing libssl3:amd64 (3.0.10-1) ... Processing triggers for libc-bin (2.37-7) ... 0m21.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'apt-get', 'remove', 'libboost-iostreams1.74.0:amd64', 'libboost-program-options1.74.0:amd64', 'libbrotli1:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libldap-2.5-0:amd64', 'libnghttp2-14:amd64', 'libopenblas0:amd64', 'libopenblas0-pthread:amd64', 'libpsl5:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libssh2-1:amd64', 'libssl3:amd64', 'bio-eagle'] 0m21.1s INFO: Running scripts post_remove 0m21.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/post_remove_exceptions'] 0m21.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/post_remove_exceptions'] 0m21.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'dpkg', '--purge', 'libboost-iostreams1.74.0:amd64', 'libboost-program-options1.74.0:amd64', 'libbrotli1:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libldap-2.5-0:amd64', 'libnghttp2-14:amd64', 'libopenblas0:amd64', 'libopenblas0-pthread:amd64', 'libpsl5:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libssh2-1:amd64', 'libssl3:amd64'] 0m21.1s DUMP: dpkg: warning: ignoring request to remove libboost-iostreams1.74.0 which isn't installed dpkg: warning: ignoring request to remove libboost-program-options1.74.0 which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libcurl3-gnutls which isn't installed dpkg: warning: ignoring request to remove libdeflate0 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed dpkg: warning: ignoring request to remove libgomp1 which isn't installed (Reading database ... 5198 files and directories currently installed.) Purging configuration files for libgssapi-krb5-2:amd64 (1.20.1-3) ... dpkg: warning: ignoring request to remove libhts3 which isn't installed dpkg: warning: ignoring request to remove libhtscodecs2 which isn't installed dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove libldap-2.5-0 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libopenblas0 which isn't installed dpkg: warning: ignoring request to remove libopenblas0-pthread which isn't installed dpkg: warning: ignoring request to remove libpsl5 which isn't installed dpkg: warning: ignoring request to remove librtmp1 which isn't installed dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed dpkg: warning: ignoring request to remove libsasl2-modules-db which isn't installed dpkg: warning: ignoring request to remove libssh2-1 which isn't installed dpkg: warning: ignoring request to remove libssl3 which isn't installed 0m21.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'dpkg', '--purge', 'libboost-iostreams1.74.0:amd64', 'libboost-program-options1.74.0:amd64', 'libbrotli1:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libldap-2.5-0:amd64', 'libnghttp2-14:amd64', 'libopenblas0:amd64', 'libopenblas0-pthread:amd64', 'libpsl5:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libssh2-1:amd64', 'libssl3:amd64'] 0m21.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'dpkg', '--purge', 'bio-eagle'] 0m21.1s DUMP: dpkg: warning: ignoring request to remove bio-eagle which isn't installed 0m21.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'dpkg', '--purge', 'bio-eagle'] 0m21.1s INFO: Running scripts post_purge 0m21.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/post_purge_exceptions'] 0m21.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/post_purge_exceptions'] 0m21.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'dpkg', '--purge', '--pending'] 0m21.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'dpkg', '--purge', '--pending'] 0m21.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'dpkg', '--remove', '--pending'] 0m21.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'dpkg', '--remove', '--pending'] 0m21.2s INFO: Running scripts post_test 0m21.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/post_test_exceptions'] 0m21.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'tmp/scripts/post_test_exceptions'] 0m21.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k'] 0m21.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k'] 0m22.0s DEBUG: No broken symlinks as far as we can find. 0m22.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'dpkg-divert', '--list'] 0m22.0s DUMP: local diversion of /bin/sync to /bin/sync.distrib local diversion of /home to /home.distrib 0m22.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'dpkg-divert', '--list'] 0m22.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'apt-get', 'clean'] 0m22.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k', 'apt-get', 'clean'] 0m22.0s DEBUG: Recording chroot state 0m22.5s INFO: PASS: Installation and purging test. 0m22.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k/dev/shm'] 0m22.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k/dev/shm'] 0m22.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k/dev/console'] 0m22.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k/dev/console'] 0m22.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k/dev/ptmx'] 0m22.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k/dev/ptmx'] 0m22.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k/dev/pts'] 0m22.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k/dev/pts'] 0m22.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k/proc'] 0m22.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k/proc'] 0m22.9s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k'] 0m23.0s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpkeh0ea2k'] 0m23.0s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpkeh0ea2k 0m23.0s INFO: PASS: All tests. 0m23.0s INFO: piuparts run ends. ret=0 End: 2023-08-30 21:24:05 GMT