Start: 2024-03-31 07:31:02 GMT Package: pbhoney Source: pbsuite Version: 15.8.24+dfsg-7 Installed-Size: 3809 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3:any, python3-pbsuite-utils (= 15.8.24+dfsg-7), python3-pbbanana (= 15.8.24+dfsg-7), python3-pysam, python3-networkx, python3-h5py, python3-numpy, python3-intervaltree-bio, blasr, samtools Recommends: pbdagcon Description: genomic structural variation discovery Homepage: http://sourceforge.net/projects/pb-jelly Description-md5: 10f81042bd82750e013162caaa443ce8 Section: science Priority: optional Filename: pool/main/p/pbsuite/pbhoney_15.8.24+dfsg-7_all.deb Size: 1056464 MD5sum: 08c672cce1e27c3d471f69cf5ddc4c99 SHA256: d9bb1beb81aa0d6aa4d4e43011ab3ad2079e7cf49e9834c27a6eaa12b8f4f74f 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 --scriptsdir /etc/piuparts/scripts-no-usr-share-doc --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 pbhoney=15.8.24+dfsg-7 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.4.1~202403190841~1.4-4-g85045c69 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --scriptsdir /etc/piuparts/scripts-no-usr-share-doc --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 pbhoney=15.8.24+dfsg-7 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmp69b_vyvj 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp69b_vyvj 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m0.6s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m0.6s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj/proc'] 0m0.6s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj/proc'] 0m0.6s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj/dev/pts'] 0m0.6s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj/dev/pts'] 0m0.6s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj/dev/ptmx'] 0m0.6s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj/dev/ptmx'] 0m0.6s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/5', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj/dev/console'] 0m0.6s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/5', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj/dev/console'] 0m0.6s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj/dev/shm'] 0m0.6s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj/dev/shm'] 0m0.6s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m0.6s DEBUG: Created policy-rc.d and chmodded it. 0m0.6s DEBUG: Created resolv.conf. 0m0.6s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp69b_vyvj/tmp/scripts/ 0m0.6s DEBUG: Copying scriptsdir /etc/piuparts/scripts-no-usr-share-doc to /srv/piuparts.debian.org/tmp/tmp69b_vyvj/tmp/scripts/ 0m0.6s INFO: Running scripts post_chroot_unpack 0m0.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'apt-get', 'update'] 0m4.9s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [198 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9916 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7200 kB] Fetched 17.3 MB in 3s (5319 kB/s) Reading package lists... 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'apt-get', 'update'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'apt-get', '-yf', 'dist-upgrade'] 0m6.4s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: libgnutls30t64 1 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 1435 kB of archives. After this operation, 30.7 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 libgnutls30t64 amd64 3.8.4-2 [1435 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1435 kB in 0s (18.2 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 ... 5219 files and directories currently installed.) Preparing to unpack .../libgnutls30t64_3.8.4-2_amd64.deb ... Unpacking libgnutls30t64:amd64 (3.8.4-2) over (3.8.3-1.1+b1) ... Setting up libgnutls30t64:amd64 (3.8.4-2) ... Processing triggers for libc-bin (2.37-15.1) ... 0m6.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'apt-get', '-yf', 'dist-upgrade'] 0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m6.7s DUMP: 4061a8546edecf36ebcf28aad5f1fc2d - 0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m6.7s INFO: Running scripts post_setup 0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/post_setup_disable_usr_share_doc'] 0m6.7s DUMP: dpkg-query: no packages found matching systemd dpkg-query: no packages found matching systemd-sysv dpkg-query: no packages found matching sysv-rc 0m6.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/post_setup_disable_usr_share_doc'] 0m6.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/post_setup_dummy_users'] 0m8.0s 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 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/post_setup_dummy_users'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/post_setup_forbid_home'] 0m8.0s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m8.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/post_setup_forbid_home'] 0m8.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/post_setup_force-unsafe-io'] 0m8.1s 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' 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/post_setup_force-unsafe-io'] 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/post_setup_minimize'] 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/post_setup_minimize'] 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/post_setup_squeeze-backports'] 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/post_setup_squeeze-backports'] 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/post_setup_zz_backports'] 0m8.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/post_setup_zz_backports'] 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'apt-get', 'clean'] 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'apt-get', 'clean'] 0m8.2s DEBUG: Recording chroot state 0m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m8.6s DUMP: install ok installed apt apt 2.7.14 install ok installed base-files base-files 13 install ok installed base-passwd base-passwd 3.6.3 install ok installed bash bash 5.2.21-2 install ok installed bsdutils bsdutils 1:2.39.3-11 install ok installed coreutils coreutils 9.4-3.1 install ok installed dash dash 0.5.12-6 install ok installed debconf debconf 1.5.86 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.17 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.6 install ok installed e2fsprogs e2fsprogs 1.47.0-2.4 install ok installed findutils findutils 4.9.0-5 install ok installed gcc-14-base:amd64 gcc-14-base 14-20240315-1 install ok installed gpgv gpgv 2.2.40-3 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.23+nmu2 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed libacl1:amd64 libacl1 2.3.2-1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.7.14 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:3.1.2-2.1 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-2.1 install ok installed libblkid1:amd64 libblkid1 2.39.3-11 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5.1 install ok installed libc-bin libc-bin 2.37-15.1 install ok installed libc6:amd64 libc6 2.37-15.1 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.4-2 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2.4 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-4 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.271+b3 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.0-2.4 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14-20240315-1 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.3-2 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.4-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.47-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.9.1-2.2 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1+b2 install ok installed liblzma5:amd64 liblzma5 5.6.1+really5.4.5-1 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.39.3-11 install ok installed libnettle8t64:amd64 libnettle8t64 3.9.1-2.2 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.3-4 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-6 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-6 install ok installed libpam-runtime libpam-runtime 1.5.3-6 install ok installed libpam0g:amd64 libpam0g 1.5.3-6 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b1 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1 install ok installed libselinux1:amd64 libselinux1 3.5-2+b1 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b3 install ok installed libsepol2:amd64 libsepol2 3.5-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.39.3-11 install ok installed libss2:amd64 libss2 1.47.0-2.4 install ok installed libssl3t64:amd64 libssl3t64 3.1.5-1.1 install ok installed libstdc++6:amd64 libstdc++6 14-20240315-1 install ok installed libsystemd0:amd64 libsystemd0 255.4-1+b1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtinfo6:amd64 libtinfo6 6.4+20240113-1 install ok installed libudev1:amd64 libudev1 255.4-1+b1 install ok installed libunistring5:amd64 libunistring5 1.2-1 install ok installed libuuid1:amd64 libuuid1 2.39.3-11 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-2 install ok installed login login 1:4.13+dfsg1-4 install ok installed logsave logsave 1.47.0-2.4 install ok installed mawk mawk 1.3.4.20240123-1 install ok installed mount mount 2.39.3-11 install ok installed ncurses-base ncurses-base 6.4+20240113-1 install ok installed ncurses-bin ncurses-bin 6.4+20240113-1 install ok installed passwd passwd 1:4.13+dfsg1-4 install ok installed perl-base perl-base 5.38.2-3.2 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.08-7 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024a-1 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.39.3-11 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg-3.1 0m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'dpkg-divert', '--list'] 0m8.6s DUMP: diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64 local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64 local diversion of /home to /home.distrib diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64 diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64 local diversion of /usr/bin/sync to /usr/bin/sync.distrib 0m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'dpkg-divert', '--list'] 0m8.6s INFO: Running scripts is_testable 0m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/is_testable_uninstallable'] 0m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/is_testable_uninstallable'] 0m8.6s INFO: apt-cache does not know about any of the requested packages 0m8.6s INFO: Running scripts pre_test 0m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/pre_test_exceptions'] 0m8.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/pre_test_exceptions'] 0m8.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/pre_test_root_password'] 0m8.7s DUMP: New password: Retype new password: passwd: password updated successfully 0m8.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/pre_test_root_password'] 0m8.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj'] 0m9.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj'] 0m9.4s DEBUG: No broken symlinks as far as we can find. 0m9.4s INFO: Running scripts pre_install 0m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/pre_install_database-server'] 0m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/pre_install_database-server'] 0m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/pre_install_exceptions'] 0m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/pre_install_exceptions'] 0m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/pre_install_extras'] 0m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/pre_install_extras'] 0m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/pre_install_foreign_architecture'] 0m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/pre_install_foreign_architecture'] 0m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m9.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj'] 0m9.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj'] 0m10.1s DEBUG: No broken symlinks as far as we can find. 0m10.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'apt-cache', 'policy'] 0m11.3s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m11.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'apt-cache', 'policy'] 0m11.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'apt-cache', 'policy', 'pbhoney'] 0m11.4s DUMP: pbhoney: Installed: (none) Candidate: 15.8.24+dfsg-7 Version table: 15.8.24+dfsg-7 500 500 http://deb.debian.org/debian sid/main amd64 Packages 0m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'apt-cache', 'policy', 'pbhoney'] 0m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'apt-get', '-y', 'install', 'pbhoney=15.8.24+dfsg-7'] 0m33.7s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: blasr libaec0 libblas3 libblasr5.3.5 libbrotli1 libcurl3t64-gnutls libcurl4t64 libdb5.3t64 libdeflate0 libexpat1 libgfortran5 libgssapi-krb5-2 libhdf5-103-1t64 libhdf5-cpp-103-1t64 libhdf5-hl-100t64 libhts3t64 libhtscodecs2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 liblzf1 libncurses6 libncursesw6 libnghttp2-14 libpbbam2.4.0 libpbcopper2.3.0 libpbseq libpsl5t64 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1t64 libsz2 media-types netbase pbjelly python3 python3-h5py python3-h5py-serial python3-intervaltree python3-intervaltree-bio python3-minimal python3-networkx python3-numpy python3-pbbanana python3-pbsuite-utils python3-pkg-resources python3-pysam python3-sortedcontainers python3.11 python3.11-minimal readline-common samtools Suggested packages: krb5-doc krb5-user python3-doc python3-tk python3-venv python-h5py-doc gcc gfortran python3-dev python3-pytest python3-setuptools python-sortedcontainers-doc python3.11-venv python3.11-doc binutils binfmt-support readline-doc cwltool Recommended packages: ca-certificates krb5-locales libldap-common libgpm2 publicsuffix libsasl2-modules pbdagcon python3-gdal python3-matplotlib python3-pydot python3-pygraphviz python3-scipy python3-yaml The following NEW packages will be installed: blasr libaec0 libblas3 libblasr5.3.5 libbrotli1 libcurl3t64-gnutls libcurl4t64 libdb5.3t64 libdeflate0 libexpat1 libgfortran5 libgssapi-krb5-2 libhdf5-103-1t64 libhdf5-cpp-103-1t64 libhdf5-hl-100t64 libhts3t64 libhtscodecs2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 liblzf1 libncurses6 libncursesw6 libnghttp2-14 libpbbam2.4.0 libpbcopper2.3.0 libpbseq libpsl5t64 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1t64 libsz2 media-types netbase pbhoney pbjelly python3 python3-h5py python3-h5py-serial python3-intervaltree python3-intervaltree-bio python3-minimal python3-networkx python3-numpy python3-pbbanana python3-pbsuite-utils python3-pkg-resources python3-pysam python3-sortedcontainers python3.11 python3.11-minimal readline-common samtools 0 upgraded, 62 newly installed, 0 to remove and 0 not upgraded. Need to get 34.6 MB of archives. After this operation, 174 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 libpython3.11-minimal amd64 3.11.8-3+b2 [817 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get:3 http://deb.debian.org/debian sid/main amd64 python3.11-minimal amd64 3.11.8-3+b2 [1879 kB] Get:4 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get:5 http://deb.debian.org/debian sid/main amd64 media-types all 10.1.0 [26.9 kB] Get:6 http://deb.debian.org/debian sid/main amd64 netbase all 6.4 [12.8 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-6 [697 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libncursesw6 amd64 6.4+20240113-1 [135 kB] Get:9 http://deb.debian.org/debian sid/main amd64 readline-common all 8.2-4 [69.3 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libsqlite3-0 amd64 3.45.2-1 [895 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libpython3.11-stdlib amd64 3.11.8-3+b2 [1792 kB] Get:13 http://deb.debian.org/debian sid/main amd64 python3.11 amd64 3.11.8-3+b2 [597 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get:15 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get:16 http://deb.debian.org/debian sid/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get:17 http://deb.debian.org/debian sid/main amd64 libkrb5support0 amd64 1.20.1-6+b1 [33.3 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libk5crypto3 amd64 1.20.1-6+b1 [79.8 kB] Get:19 http://deb.debian.org/debian sid/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get:20 http://deb.debian.org/debian sid/main amd64 libkrb5-3 amd64 1.20.1-6+b1 [333 kB] Get:21 http://deb.debian.org/debian sid/main amd64 libgssapi-krb5-2 amd64 1.20.1-6+b1 [135 kB] Get:22 http://deb.debian.org/debian sid/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-6 [19.5 kB] Get:23 http://deb.debian.org/debian sid/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-6 [56.9 kB] Get:24 http://deb.debian.org/debian sid/main amd64 libldap-2.5-0 amd64 2.5.16+dfsg-2 [185 kB] Get:25 http://deb.debian.org/debian sid/main amd64 libnghttp2-14 amd64 1.60.0-1 [75.3 kB] Get:26 http://deb.debian.org/debian sid/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get:27 http://deb.debian.org/debian sid/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b3 [58.5 kB] Get:28 http://deb.debian.org/debian sid/main amd64 libssh2-1t64 amd64 1.11.0-4.1+b1 [215 kB] Get:29 http://deb.debian.org/debian sid/main amd64 libcurl4t64 amd64 8.7.1-1 [440 kB] Get:30 http://deb.debian.org/debian sid/main amd64 libaec0 amd64 1.1.3-1 [23.4 kB] Get:31 http://deb.debian.org/debian sid/main amd64 libsz2 amd64 1.1.3-1 [7740 B] Get:32 http://deb.debian.org/debian sid/main amd64 libhdf5-103-1t64 amd64 1.10.10+repack-3.3 [1241 kB] Get:33 http://deb.debian.org/debian sid/main amd64 libhdf5-cpp-103-1t64 amd64 1.10.10+repack-3.3 [131 kB] Get:34 http://deb.debian.org/debian sid/main amd64 libcurl3t64-gnutls amd64 8.7.1-1 [432 kB] Get:35 http://deb.debian.org/debian sid/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get:36 http://deb.debian.org/debian sid/main amd64 libhtscodecs2 amd64 1.6.0-1+b1 [93.0 kB] Get:37 http://deb.debian.org/debian sid/main amd64 libhts3t64 amd64 1.19+ds-1.1+b1 [448 kB] Get:38 http://deb.debian.org/debian sid/main amd64 libpbcopper2.3.0 amd64 2.3.0+dfsg-2 [740 kB] Get:39 http://deb.debian.org/debian sid/main amd64 libpbbam2.4.0 amd64 2.4.0+dfsg-1+b3 [819 kB] Get:40 http://deb.debian.org/debian sid/main amd64 libblasr5.3.5 amd64 5.3.5+dfsg-6+b3 [1113 kB] Get:41 http://deb.debian.org/debian sid/main amd64 libpbseq amd64 5.3.5+dfsg-6+b3 [5004 B] Get:42 http://deb.debian.org/debian sid/main amd64 blasr amd64 5.3.5+dfsg-6+b3 [224 kB] Get:43 http://deb.debian.org/debian sid/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get:44 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14-20240315-1 [836 kB] Get:45 http://deb.debian.org/debian sid/main amd64 libhdf5-hl-100t64 amd64 1.10.10+repack-3.3 [63.3 kB] Get:46 http://deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get:47 http://deb.debian.org/debian sid/main amd64 liblzf1 amd64 3.6-4 [10.1 kB] Get:48 http://deb.debian.org/debian sid/main amd64 libncurses6 amd64 6.4+20240113-1 [104 kB] Get:49 http://deb.debian.org/debian sid/main amd64 python3-pysam amd64 0.22.0+ds-1+b2 [4646 kB] Get:50 http://deb.debian.org/debian sid/main amd64 python3-pbsuite-utils all 15.8.24+dfsg-7 [509 kB] Get:51 http://deb.debian.org/debian sid/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get:52 http://deb.debian.org/debian sid/main amd64 python3-networkx all 2.8.8-2 [1425 kB] Get:53 http://deb.debian.org/debian sid/main amd64 pbjelly all 15.8.24+dfsg-7 [967 kB] Get:54 http://deb.debian.org/debian sid/main amd64 python3-pbbanana all 15.8.24+dfsg-7 [20.1 kB] Get:55 http://deb.debian.org/debian sid/main amd64 python3-numpy amd64 1:1.26.4+ds-6 [5472 kB] Get:56 http://deb.debian.org/debian sid/main amd64 python3-h5py-serial amd64 3.10.0-1+b2 [1400 kB] Get:57 http://deb.debian.org/debian sid/main amd64 python3-h5py all 3.10.0-1 [14.4 kB] Get:58 http://deb.debian.org/debian sid/main amd64 python3-sortedcontainers all 2.4.0-2 [31.9 kB] Get:59 http://deb.debian.org/debian sid/main amd64 python3-intervaltree all 3.0.2-1.1 [26.3 kB] Get:60 http://deb.debian.org/debian sid/main amd64 python3-intervaltree-bio all 1.0.1-4 [8640 B] Get:61 http://deb.debian.org/debian sid/main amd64 samtools amd64 1.19.2-1+b1 [645 kB] Get:62 http://deb.debian.org/debian sid/main amd64 pbhoney all 15.8.24+dfsg-7 [1056 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 34.6 MB in 5s (6929 kB/s) Selecting previously unselected package libpython3.11-minimal: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 ... 5222 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.8-3+b2_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.8-3+b2) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.8-3+b2_amd64.deb ... Unpacking python3.11-minimal (3.11.8-3+b2) ... Setting up libpython3.11-minimal:amd64 (3.11.8-3+b2) ... Setting up libexpat1:amd64 (2.6.2-1) ... Setting up python3.11-minimal (3.11.8-3+b2) ... Selecting previously unselected package python3-minimal. (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 ... 5540 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.11.8-1_amd64.deb ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../07-libsqlite3-0_3.45.2-1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.45.2-1) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../08-libpython3.11-stdlib_3.11.8-3+b2_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.8-3+b2) ... 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Selecting previously unselected package libblasr5.3.5:amd64. Preparing to unpack .../25-libblasr5.3.5_5.3.5+dfsg-6+b3_amd64.deb ... Unpacking libblasr5.3.5:amd64 (5.3.5+dfsg-6+b3) ... Selecting previously unselected package libpbseq:amd64. Preparing to unpack .../26-libpbseq_5.3.5+dfsg-6+b3_amd64.deb ... Unpacking libpbseq:amd64 (5.3.5+dfsg-6+b3) ... Selecting previously unselected package blasr. Preparing to unpack .../27-blasr_5.3.5+dfsg-6+b3_amd64.deb ... Unpacking blasr (5.3.5+dfsg-6+b3) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../28-libblas3_3.12.0-3_amd64.deb ... Unpacking libblas3:amd64 (3.12.0-3) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../29-libgfortran5_14-20240315-1_amd64.deb ... Unpacking libgfortran5:amd64 (14-20240315-1) ... Selecting previously unselected package libhdf5-hl-100t64:amd64. Preparing to unpack .../30-libhdf5-hl-100t64_1.10.10+repack-3.3_amd64.deb ... Unpacking libhdf5-hl-100t64:amd64 (1.10.10+repack-3.3) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../31-liblapack3_3.12.0-3_amd64.deb ... Unpacking liblapack3:amd64 (3.12.0-3) ... Selecting previously unselected package liblzf1:amd64. Preparing to unpack .../32-liblzf1_3.6-4_amd64.deb ... Unpacking liblzf1:amd64 (3.6-4) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../33-libncurses6_6.4+20240113-1_amd64.deb ... Unpacking libncurses6:amd64 (6.4+20240113-1) ... Selecting previously unselected package python3-pysam. Preparing to unpack .../34-python3-pysam_0.22.0+ds-1+b2_amd64.deb ... Unpacking python3-pysam (0.22.0+ds-1+b2) ... Selecting previously unselected package python3-pbsuite-utils. Preparing to unpack .../35-python3-pbsuite-utils_15.8.24+dfsg-7_all.deb ... Unpacking python3-pbsuite-utils (15.8.24+dfsg-7) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../36-python3-pkg-resources_68.1.2-2_all.deb ... Unpacking python3-pkg-resources (68.1.2-2) ... Selecting previously unselected package python3-networkx. Preparing to unpack .../37-python3-networkx_2.8.8-2_all.deb ... Unpacking python3-networkx (2.8.8-2) ... Selecting previously unselected package pbjelly. Preparing to unpack .../38-pbjelly_15.8.24+dfsg-7_all.deb ... Unpacking pbjelly (15.8.24+dfsg-7) ... Selecting previously unselected package python3-pbbanana. Preparing to unpack .../39-python3-pbbanana_15.8.24+dfsg-7_all.deb ... Unpacking python3-pbbanana (15.8.24+dfsg-7) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../40-python3-numpy_1%3a1.26.4+ds-6_amd64.deb ... Unpacking python3-numpy (1:1.26.4+ds-6) ... Selecting previously unselected package python3-h5py-serial. Preparing to unpack .../41-python3-h5py-serial_3.10.0-1+b2_amd64.deb ... Unpacking python3-h5py-serial (3.10.0-1+b2) ... Selecting previously unselected package python3-h5py. Preparing to unpack .../42-python3-h5py_3.10.0-1_all.deb ... Unpacking python3-h5py (3.10.0-1) ... Selecting previously unselected package python3-sortedcontainers. Preparing to unpack .../43-python3-sortedcontainers_2.4.0-2_all.deb ... Unpacking python3-sortedcontainers (2.4.0-2) ... Selecting previously unselected package python3-intervaltree. Preparing to unpack .../44-python3-intervaltree_3.0.2-1.1_all.deb ... Unpacking python3-intervaltree (3.0.2-1.1) ... Selecting previously unselected package python3-intervaltree-bio. Preparing to unpack .../45-python3-intervaltree-bio_1.0.1-4_all.deb ... Unpacking python3-intervaltree-bio (1.0.1-4) ... Selecting previously unselected package samtools. Preparing to unpack .../46-samtools_1.19.2-1+b1_amd64.deb ... Unpacking samtools (1.19.2-1+b1) ... Selecting previously unselected package pbhoney. Preparing to unpack .../47-pbhoney_15.8.24+dfsg-7_all.deb ... Unpacking pbhoney (15.8.24+dfsg-7) ... Setting up libhtscodecs2:amd64 (1.6.0-1+b1) ... Setting up media-types (10.1.0) ... Setting up libkeyutils1:amd64 (1.6.3-3) ... Setting up libbrotli1:amd64 (1.1.0-2+b3) ... Setting up libsqlite3-0:amd64 (3.45.2-1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1) ... Setting up libnghttp2-14:amd64 (1.60.0-1) ... Setting up libdeflate0:amd64 (1.20-1) ... Setting up libaec0:amd64 (1.1.3-1) ... Setting up libkrb5support0:amd64 (1.20.1-6+b1) ... Setting up libblas3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b3) ... Setting up libncurses6:amd64 (6.4+20240113-1) ... Setting up liblzf1:amd64 (3.6-4) ... Setting up libncursesw6:amd64 (6.4+20240113-1) ... Setting up libk5crypto3:amd64 (1.20.1-6+b1) ... Setting up libgfortran5:amd64 (14-20240315-1) ... Setting up libdb5.3t64:amd64 (5.3.28+dfsg2-6) ... Setting up netbase (6.4) ... Setting up libkrb5-3:amd64 (1.20.1-6+b1) ... Setting up libssh2-1t64:amd64 (1.11.0-4.1+b1) ... Setting up readline-common (8.2-4) ... Setting up libsz2:amd64 (1.1.3-1) ... Setting up libpbcopper2.3.0:amd64 (2.3.0+dfsg-2) ... Setting up liblapack3:amd64 (3.12.0-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Setting up libreadline8t64:amd64 (8.2-4) ... Setting up libpython3.11-stdlib:amd64 (3.11.8-3+b2) ... Setting up libldap-2.5-0:amd64 (2.5.16+dfsg-2) ... Setting up libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3.11 (3.11.8-3+b2) ... Setting up libcurl4t64:amd64 (8.7.1-1) ... Setting up libcurl3t64-gnutls:amd64 (8.7.1-1) ... Setting up python3 (3.11.8-1) ... Setting up python3-sortedcontainers (2.4.0-2) ... Setting up libhts3t64:amd64 (1.19+ds-1.1+b1) ... Setting up libhdf5-103-1t64:amd64 (1.10.10+repack-3.3) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up libhdf5-hl-100t64:amd64 (1.10.10+repack-3.3) ... Setting up python3-pysam (0.22.0+ds-1+b2) ... Setting up python3-intervaltree (3.0.2-1.1) ... Setting up python3-pbsuite-utils (15.8.24+dfsg-7) ... Setting up libpbbam2.4.0:amd64 (2.4.0+dfsg-1+b3) ... Setting up libhdf5-cpp-103-1t64:amd64 (1.10.10+repack-3.3) ... Setting up python3-networkx (2.8.8-2) ... Setting up samtools (1.19.2-1+b1) ... Setting up libblasr5.3.5:amd64 (5.3.5+dfsg-6+b3) ... Setting up libpbseq:amd64 (5.3.5+dfsg-6+b3) ... Setting up python3-numpy (1:1.26.4+ds-6) ... Setting up python3-intervaltree-bio (1.0.1-4) ... Setting up blasr (5.3.5+dfsg-6+b3) ... Setting up python3-h5py-serial (3.10.0-1+b2) ... Setting up python3-h5py (3.10.0-1) ... Setting up pbjelly (15.8.24+dfsg-7) ... Setting up python3-pbbanana (15.8.24+dfsg-7) ... Setting up pbhoney (15.8.24+dfsg-7) ... Processing triggers for libc-bin (2.37-15.1) ... 0m33.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'apt-get', '-y', 'install', 'pbhoney=15.8.24+dfsg-7'] 0m33.7s INFO: Running scripts post_install 0m33.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/post_install_exceptions'] 0m33.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/post_install_exceptions'] 0m33.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj'] 0m34.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj'] 0m35.2s ERROR: WARN: Broken symlinks: /usr/share/doc/libhdf5-hl-100t64/RELEASE.txt.gz -> changelog.gz (libhdf5-hl-100t64:amd64) /usr/share/doc/libhdf5-cpp-103-1t64/RELEASE.txt.gz -> changelog.gz (libhdf5-cpp-103-1t64:amd64) /usr/share/doc/libhdf5-103-1t64/RELEASE.txt.gz -> changelog.gz (libhdf5-103-1t64:amd64) /usr/share/doc/python3.11/python-policy.txt.gz -> ../python3/python-policy.txt.gz (python3) /usr/share/doc/python3.11/changelog.gz -> NEWS.gz (python3.11) 0m35.3s INFO: /bin converted to /usr/bin by /usr merge 0m35.3s INFO: /lib converted to /usr/lib by /usr merge 0m35.3s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 0m35.3s INFO: /lib64 converted to /usr/lib64 by /usr merge 0m35.3s INFO: /sbin converted to /usr/sbin by /usr merge 0m35.7s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', '-ac', '--ignore-obsolete'] 0m37.0s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', '-ac', '--ignore-obsolete'] 0m37.0s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m37.0s DUMP: 0.15.6 0m37.0s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m37.0s INFO: Running adequate version 0.15.6 now. 0m37.0s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'pbhoney'] 0m37.2s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'pbhoney'] 0m37.2s INFO: Running scripts pre_remove 0m37.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m37.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m37.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m37.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m37.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m38.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m38.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m38.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m38.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m39.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m39.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/pre_remove_exceptions'] 0m39.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/pre_remove_exceptions'] 0m39.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m39.1s DUMP: install ok installed apt apt 2.7.14 install ok installed base-files base-files 13 install ok installed base-passwd base-passwd 3.6.3 install ok installed bash bash 5.2.21-2 install ok installed blasr blasr 5.3.5+dfsg-6+b3 install ok installed bsdutils bsdutils 1:2.39.3-11 install ok installed coreutils coreutils 9.4-3.1 install ok installed dash dash 0.5.12-6 install ok installed debconf debconf 1.5.86 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.17 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.6 install ok installed e2fsprogs e2fsprogs 1.47.0-2.4 install ok installed findutils findutils 4.9.0-5 install ok installed gcc-14-base:amd64 gcc-14-base 14-20240315-1 install ok installed gpgv gpgv 2.2.40-3 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.23+nmu2 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed libacl1:amd64 libacl1 2.3.2-1 install ok installed libaec0:amd64 libaec0 1.1.3-1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.7.14 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:3.1.2-2.1 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-2.1 install ok installed libblas3:amd64 libblas3 3.12.0-3 install ok installed libblasr5.3.5:amd64 libblasr5.3.5 5.3.5+dfsg-6+b3 install ok installed libblkid1:amd64 libblkid1 2.39.3-11 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b3 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5.1 install ok installed libc-bin libc-bin 2.37-15.1 install ok installed libc6:amd64 libc6 2.37-15.1 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.4-2 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2.4 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-4 install ok installed libcurl3t64-gnutls:amd64 libcurl3t64-gnutls 8.7.1-1 install ok installed libcurl4t64:amd64 libcurl4t64 8.7.1-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-6 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.271+b3 install ok installed libdeflate0:amd64 libdeflate0 1.20-1 install ok installed libexpat1:amd64 libexpat1 2.6.2-1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.0-2.4 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14-20240315-1 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.3-2 install ok installed libgfortran5:amd64 libgfortran5 14-20240315-1 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.4-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.47-3 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.20.1-6+b1 install ok installed libhdf5-103-1t64:amd64 libhdf5-103-1t64 1.10.10+repack-3.3 install ok installed libhdf5-cpp-103-1t64:amd64 libhdf5-cpp-103-1t64 1.10.10+repack-3.3 install ok installed libhdf5-hl-100t64:amd64 libhdf5-hl-100t64 1.10.10+repack-3.3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.9.1-2.2 install ok installed libhts3t64:amd64 libhts3t64 1.19+ds-1.1+b1 install ok installed libhtscodecs2:amd64 libhtscodecs2 1.6.0-1+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed libk5crypto3:amd64 libk5crypto3 1.20.1-6+b1 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-3 install ok installed libkrb5-3:amd64 libkrb5-3 1.20.1-6+b1 install ok installed libkrb5support0:amd64 libkrb5support0 1.20.1-6+b1 install ok installed liblapack3:amd64 liblapack3 3.12.0-3 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.16+dfsg-2 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1+b2 install ok installed liblzf1:amd64 liblzf1 3.6-4 install ok installed liblzma5:amd64 liblzma5 5.6.1+really5.4.5-1 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.39.3-11 install ok installed libncurses6:amd64 libncurses6 6.4+20240113-1 install ok installed libncursesw6:amd64 libncursesw6 6.4+20240113-1 install ok installed libnettle8t64:amd64 libnettle8t64 3.9.1-2.2 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.60.0-1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.3-4 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-6 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-6 install ok installed libpam-runtime libpam-runtime 1.5.3-6 install ok installed libpam0g:amd64 libpam0g 1.5.3-6 install ok installed libpbbam2.4.0:amd64 libpbbam2.4.0 2.4.0+dfsg-1+b3 install ok installed libpbcopper2.3.0:amd64 libpbcopper2.3.0 2.3.0+dfsg-2 install ok installed libpbseq:amd64 libpbseq 5.3.5+dfsg-6+b3 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b1 install ok installed libpsl5t64:amd64 libpsl5t64 0.21.2-1.1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.11.8-1 install ok installed libpython3.11-minimal:amd64 libpython3.11-minimal 3.11.8-3+b2 install ok installed libpython3.11-stdlib:amd64 libpython3.11-stdlib 3.11.8-3+b2 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-4 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b3 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-6 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-6 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1 install ok installed libselinux1:amd64 libselinux1 3.5-2+b1 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b3 install ok installed libsepol2:amd64 libsepol2 3.5-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.39.3-11 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.45.2-1 install ok installed libss2:amd64 libss2 1.47.0-2.4 install ok installed libssh2-1t64:amd64 libssh2-1t64 1.11.0-4.1+b1 install ok installed libssl3t64:amd64 libssl3t64 3.1.5-1.1 install ok installed libstdc++6:amd64 libstdc++6 14-20240315-1 install ok installed libsystemd0:amd64 libsystemd0 255.4-1+b1 install ok installed libsz2:amd64 libsz2 1.1.3-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtinfo6:amd64 libtinfo6 6.4+20240113-1 install ok installed libudev1:amd64 libudev1 255.4-1+b1 install ok installed libunistring5:amd64 libunistring5 1.2-1 install ok installed libuuid1:amd64 libuuid1 2.39.3-11 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-2 install ok installed login login 1:4.13+dfsg1-4 install ok installed logsave logsave 1.47.0-2.4 install ok installed mawk mawk 1.3.4.20240123-1 install ok installed media-types media-types 10.1.0 install ok installed mount mount 2.39.3-11 install ok installed ncurses-base ncurses-base 6.4+20240113-1 install ok installed ncurses-bin ncurses-bin 6.4+20240113-1 install ok installed netbase netbase 6.4 install ok installed passwd passwd 1:4.13+dfsg1-4 install ok installed pbhoney pbhoney 15.8.24+dfsg-7 install ok installed pbjelly pbjelly 15.8.24+dfsg-7 install ok installed perl-base perl-base 5.38.2-3.2 install ok installed python3 python3 3.11.8-1 install ok installed python3-h5py python3-h5py 3.10.0-1 install ok installed python3-h5py-serial python3-h5py-serial 3.10.0-1+b2 install ok installed python3-intervaltree python3-intervaltree 3.0.2-1.1 install ok installed python3-intervaltree-bio python3-intervaltree-bio 1.0.1-4 install ok installed python3-minimal python3-minimal 3.11.8-1 install ok installed python3-networkx python3-networkx 2.8.8-2 install ok installed python3-numpy python3-numpy 1:1.26.4+ds-6 install ok installed python3-pbbanana python3-pbbanana 15.8.24+dfsg-7 install ok installed python3-pbsuite-utils python3-pbsuite-utils 15.8.24+dfsg-7 install ok installed python3-pkg-resources python3-pkg-resources 68.1.2-2 install ok installed python3-pysam python3-pysam 0.22.0+ds-1+b2 install ok installed python3-sortedcontainers python3-sortedcontainers 2.4.0-2 install ok installed python3.11 python3.11 3.11.8-3+b2 install ok installed python3.11-minimal python3.11-minimal 3.11.8-3+b2 install ok installed readline-common readline-common 8.2-4 install ok installed samtools samtools 1.19.2-1+b1 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.08-7 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024a-1 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.39.3-11 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg-3.1 0m39.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m39.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'apt-get', 'remove', 'blasr', 'libaec0:amd64', 'libblas3:amd64', 'libblasr5.3.5:amd64', 'libbrotli1:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64:amd64', 'libdb5.3t64:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libgfortran5:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-103-1t64:amd64', 'libhdf5-cpp-103-1t64:amd64', 'libhdf5-hl-100t64:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap-2.5-0:amd64', 'liblzf1:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libpbbam2.4.0:amd64', 'libpbcopper2.3.0:amd64', 'libpbseq:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libsz2:amd64', 'media-types', 'netbase', 'pbjelly', 'python3', 'python3-h5py', 'python3-h5py-serial', 'python3-intervaltree', 'python3-intervaltree-bio', 'python3-minimal', 'python3-networkx', 'python3-numpy', 'python3-pbbanana', 'python3-pbsuite-utils', 'python3-pkg-resources', 'python3-pysam', 'python3-sortedcontainers', 'python3.11', 'python3.11-minimal', 'readline-common', 'samtools', 'pbhoney'] 0m43.0s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: blasr libaec0 libblas3 libblasr5.3.5 libbrotli1 libcurl3t64-gnutls libcurl4t64 libdb5.3t64 libdeflate0 libexpat1 libgfortran5 libgssapi-krb5-2 libhdf5-103-1t64 libhdf5-cpp-103-1t64 libhdf5-hl-100t64 libhts3t64 libhtscodecs2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 liblzf1 libncurses6 libncursesw6 libnghttp2-14 libpbbam2.4.0 libpbcopper2.3.0 libpbseq libpsl5t64 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1t64 libsz2 media-types netbase pbhoney pbjelly python3 python3-h5py python3-h5py-serial python3-intervaltree python3-intervaltree-bio python3-minimal python3-networkx python3-numpy python3-pbbanana python3-pbsuite-utils python3-pkg-resources python3-pysam python3-sortedcontainers python3.11 python3.11-minimal readline-common samtools 0 upgraded, 0 newly installed, 62 to remove and 0 not upgraded. After this operation, 174 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 ... 9019 files and directories currently installed.) Removing pbhoney (15.8.24+dfsg-7) ... Removing python3-pbbanana (15.8.24+dfsg-7) ... Removing pbjelly (15.8.24+dfsg-7) ... Removing blasr (5.3.5+dfsg-6+b3) ... Removing libpbseq:amd64 (5.3.5+dfsg-6+b3) ... Removing libblasr5.3.5:amd64 (5.3.5+dfsg-6+b3) ... Removing python3-h5py (3.10.0-1) ... Removing python3-h5py-serial (3.10.0-1+b2) ... Removing libhdf5-hl-100t64:amd64 (1.10.10+repack-3.3) ... Removing python3-numpy (1:1.26.4+ds-6) ... Removing liblapack3:amd64 (3.12.0-3) ... Removing libblas3:amd64 (3.12.0-3) ... Removing samtools (1.19.2-1+b1) ... Removing python3-pbsuite-utils (15.8.24+dfsg-7) ... Removing python3-pysam (0.22.0+ds-1+b2) ... Removing python3-intervaltree-bio (1.0.1-4) ... Removing python3-intervaltree (3.0.2-1.1) ... Removing python3-sortedcontainers (2.4.0-2) ... Removing python3-networkx (2.8.8-2) ... Removing python3-pkg-resources (68.1.2-2) ... Removing python3 (3.11.8-1) ... Removing python3.11 (3.11.8-3+b2) ... Removing libpython3-stdlib:amd64 (3.11.8-1) ... Removing libpython3.11-stdlib:amd64 (3.11.8-3+b2) ... find: '/usr/lib/python3': No such file or directory Removing python3-minimal (3.11.8-1) ... Removing python3.11-minimal (3.11.8-3+b2) ... Removing libexpat1:amd64 (2.6.2-1) ... Removing libgfortran5:amd64 (14-20240315-1) ... Removing libhdf5-cpp-103-1t64:amd64 (1.10.10+repack-3.3) ... Removing liblzf1:amd64 (3.6-4) ... Removing libncurses6:amd64 (6.4+20240113-1) ... Removing libncursesw6:amd64 (6.4+20240113-1) ... Removing libpbbam2.4.0:amd64 (2.4.0+dfsg-1+b3) ... Removing libpbcopper2.3.0:amd64 (2.3.0+dfsg-2) ... Removing libpython3.11-minimal:amd64 (3.11.8-3+b2) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8t64:amd64 (8.2-4) ... Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Removing libsqlite3-0:amd64 (3.45.2-1) ... Removing media-types (10.1.0) ... Removing netbase (6.4) ... Removing readline-common (8.2-4) ... Removing libhdf5-103-1t64:amd64 (1.10.10+repack-3.3) ... Removing libsz2:amd64 (1.1.3-1) ... Removing libaec0:amd64 (1.1.3-1) ... Removing libcurl4t64:amd64 (8.7.1-1) ... Removing libhts3t64:amd64 (1.19+ds-1.1+b1) ... Removing libcurl3t64-gnutls:amd64 (8.7.1-1) ... Removing libbrotli1:amd64 (1.1.0-2+b3) ... Removing libldap-2.5-0:amd64 (2.5.16+dfsg-2) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-6) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-6) ... Removing libdb5.3t64:amd64 (5.3.28+dfsg2-6) ... Removing libdeflate0:amd64 (1.20-1) ... Removing libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... Removing libhtscodecs2:amd64 (1.6.0-1+b1) ... Removing libkrb5-3:amd64 (1.20.1-6+b1) ... Removing libk5crypto3:amd64 (1.20.1-6+b1) ... Removing libkeyutils1:amd64 (1.6.3-3) ... Removing libkrb5support0:amd64 (1.20.1-6+b1) ... Removing libnghttp2-14:amd64 (1.60.0-1) ... Removing libpsl5t64:amd64 (0.21.2-1.1) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b3) ... Removing libssh2-1t64:amd64 (1.11.0-4.1+b1) ... Processing triggers for libc-bin (2.37-15.1) ... 0m43.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'apt-get', 'remove', 'blasr', 'libaec0:amd64', 'libblas3:amd64', 'libblasr5.3.5:amd64', 'libbrotli1:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64:amd64', 'libdb5.3t64:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libgfortran5:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-103-1t64:amd64', 'libhdf5-cpp-103-1t64:amd64', 'libhdf5-hl-100t64:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap-2.5-0:amd64', 'liblzf1:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libpbbam2.4.0:amd64', 'libpbcopper2.3.0:amd64', 'libpbseq:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libsz2:amd64', 'media-types', 'netbase', 'pbjelly', 'python3', 'python3-h5py', 'python3-h5py-serial', 'python3-intervaltree', 'python3-intervaltree-bio', 'python3-minimal', 'python3-networkx', 'python3-numpy', 'python3-pbbanana', 'python3-pbsuite-utils', 'python3-pkg-resources', 'python3-pysam', 'python3-sortedcontainers', 'python3.11', 'python3.11-minimal', 'readline-common', 'samtools', 'pbhoney'] 0m43.0s INFO: Running scripts post_remove 0m43.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/post_remove_exceptions'] 0m43.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/post_remove_exceptions'] 0m43.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'dpkg', '--purge', 'blasr', 'libaec0:amd64', 'libblas3:amd64', 'libblasr5.3.5:amd64', 'libbrotli1:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64:amd64', 'libdb5.3t64:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libgfortran5:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-103-1t64:amd64', 'libhdf5-cpp-103-1t64:amd64', 'libhdf5-hl-100t64:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap-2.5-0:amd64', 'liblzf1:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libpbbam2.4.0:amd64', 'libpbcopper2.3.0:amd64', 'libpbseq:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libsz2:amd64', 'media-types', 'netbase', 'pbjelly', 'python3', 'python3-h5py', 'python3-h5py-serial', 'python3-intervaltree', 'python3-intervaltree-bio', 'python3-minimal', 'python3-networkx', 'python3-numpy', 'python3-pbbanana', 'python3-pbsuite-utils', 'python3-pkg-resources', 'python3-pysam', 'python3-sortedcontainers', 'python3.11', 'python3.11-minimal', 'readline-common', 'samtools'] 0m43.1s DUMP: dpkg: warning: ignoring request to remove blasr which isn't installed dpkg: warning: ignoring request to remove libaec0 which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libblasr5.3.5 which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libcurl3t64-gnutls which isn't installed dpkg: warning: ignoring request to remove libcurl4t64 which isn't installed dpkg: warning: ignoring request to remove libdb5.3t64 which isn't installed dpkg: warning: ignoring request to remove libdeflate0 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed (Reading database ... 5229 files and directories currently installed.) Purging configuration files for libgssapi-krb5-2:amd64 (1.20.1-6+b1) ... dpkg: warning: ignoring request to remove libhdf5-103-1t64 which isn't installed dpkg: warning: ignoring request to remove libhdf5-cpp-103-1t64 which isn't installed dpkg: warning: ignoring request to remove libhdf5-hl-100t64 which isn't installed dpkg: warning: ignoring request to remove libhts3t64 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 liblapack3 which isn't installed dpkg: warning: ignoring request to remove libldap-2.5-0 which isn't installed dpkg: warning: ignoring request to remove liblzf1 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 libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libpbbam2.4.0 which isn't installed dpkg: warning: ignoring request to remove libpbcopper2.3.0 which isn't installed dpkg: warning: ignoring request to remove libpbseq which isn't installed dpkg: warning: ignoring request to remove libpsl5t64 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.11-minimal:amd64 (3.11.8-3+b2) ... dpkg: warning: ignoring request to remove libpython3.11-stdlib which isn't installed Purging configuration files for libreadline8t64:amd64 (8.2-4) ... 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 libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libssh2-1t64 which isn't installed dpkg: warning: ignoring request to remove libsz2 which isn't installed Purging configuration files for media-types (10.1.0) ... Purging configuration files for netbase (6.4) ... dpkg: warning: ignoring request to remove pbjelly which isn't installed Purging configuration files for python3 (3.11.8-1) ... dpkg: warning: ignoring request to remove python3-h5py which isn't installed dpkg: warning: ignoring request to remove python3-h5py-serial which isn't installed dpkg: warning: ignoring request to remove python3-intervaltree which isn't installed dpkg: warning: ignoring request to remove python3-intervaltree-bio which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-networkx which isn't installed dpkg: warning: ignoring request to remove python3-numpy which isn't installed dpkg: warning: ignoring request to remove python3-pbbanana which isn't installed dpkg: warning: ignoring request to remove python3-pbsuite-utils which isn't installed dpkg: warning: ignoring request to remove python3-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python3-pysam which isn't installed dpkg: warning: ignoring request to remove python3-sortedcontainers which isn't installed dpkg: warning: ignoring request to remove python3.11 which isn't installed Purging configuration files for python3.11-minimal (3.11.8-3+b2) ... Purging configuration files for readline-common (8.2-4) ... dpkg: warning: ignoring request to remove samtools which isn't installed 0m43.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'dpkg', '--purge', 'blasr', 'libaec0:amd64', 'libblas3:amd64', 'libblasr5.3.5:amd64', 'libbrotli1:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64:amd64', 'libdb5.3t64:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libgfortran5:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-103-1t64:amd64', 'libhdf5-cpp-103-1t64:amd64', 'libhdf5-hl-100t64:amd64', 'libhts3t64:amd64', 'libhtscodecs2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap-2.5-0:amd64', 'liblzf1:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libpbbam2.4.0:amd64', 'libpbcopper2.3.0:amd64', 'libpbseq:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libsz2:amd64', 'media-types', 'netbase', 'pbjelly', 'python3', 'python3-h5py', 'python3-h5py-serial', 'python3-intervaltree', 'python3-intervaltree-bio', 'python3-minimal', 'python3-networkx', 'python3-numpy', 'python3-pbbanana', 'python3-pbsuite-utils', 'python3-pkg-resources', 'python3-pysam', 'python3-sortedcontainers', 'python3.11', 'python3.11-minimal', 'readline-common', 'samtools'] 0m43.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'dpkg', '--purge', 'pbhoney'] 0m43.1s DUMP: dpkg: warning: ignoring request to remove pbhoney which isn't installed 0m43.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'dpkg', '--purge', 'pbhoney'] 0m43.1s INFO: Running scripts post_purge 0m43.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/post_purge_exceptions'] 0m43.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/post_purge_exceptions'] 0m43.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'dpkg', '--purge', '--pending'] 0m43.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'dpkg', '--purge', '--pending'] 0m43.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'dpkg', '--remove', '--pending'] 0m43.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'dpkg', '--remove', '--pending'] 0m43.1s INFO: Running scripts post_test 0m43.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/post_test_exceptions'] 0m43.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'tmp/scripts/post_test_exceptions'] 0m43.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj'] 0m43.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj'] 0m43.9s DEBUG: No broken symlinks as far as we can find. 0m43.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'dpkg-divert', '--list'] 0m43.9s DUMP: diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64 local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64 local diversion of /home to /home.distrib diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64 diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64 local diversion of /usr/bin/sync to /usr/bin/sync.distrib 0m43.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'dpkg-divert', '--list'] 0m43.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'apt-get', 'clean'] 0m43.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj', 'apt-get', 'clean'] 0m43.9s DEBUG: Recording chroot state 0m44.4s INFO: PASS: Installation and purging test. 0m44.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj/dev/shm'] 0m44.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj/dev/shm'] 0m44.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj/dev/console'] 0m44.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj/dev/console'] 0m44.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj/dev/ptmx'] 0m44.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj/dev/ptmx'] 0m44.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj/dev/pts'] 0m44.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj/dev/pts'] 0m44.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj/proc'] 0m44.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj/proc'] 0m44.9s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj'] 0m45.0s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp69b_vyvj'] 0m45.0s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp69b_vyvj 0m45.0s INFO: PASS: All tests. 0m45.0s INFO: piuparts run ends. ret=0 End: 2024-03-31 07:31:48 GMT