Start: 2024-09-22 15:17:12 GMT Package: pbsuite Version: 15.8.24+dfsg-7 Installed-Size: 12 Maintainer: Debian Med Packaging Team Architecture: all Depends: pbjelly, pbhoney Description: software for Pacific Biosciences sequencing data Homepage: http://sourceforge.net/projects/pb-jelly Description-md5: ff8ccb949cd3eb854a02e196473aab76 Section: metapackages Priority: optional Filename: pool/main/p/pbsuite/pbsuite_15.8.24+dfsg-7_all.deb Size: 5416 MD5sum: 80704159612e111baa609ec8833fa8e3 SHA256: f980757bb7167f22f2f7ac2b51b9f3a1dccfeac55c59b3f80bd1aa78a9e9aea1 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-log-alternatives --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz -d sid --no-upgrade-test --apt pbsuite=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 1.4.4~202408201642~1.4.3-11-g36a88c35 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts-log-alternatives --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz -d sid --no-upgrade-test --apt pbsuite=15.8.24+dfsg-7 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-32-amd64 #1 SMP Debian 5.10.223-1 (2024-08-10) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpikpj6suy 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpikpj6suy 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpikpj6suy/proc'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpikpj6suy/proc'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpikpj6suy/dev/pts'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpikpj6suy/dev/pts'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpikpj6suy/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpikpj6suy/dev/ptmx'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpikpj6suy/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpikpj6suy/dev/ptmx'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpikpj6suy/dev/console'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpikpj6suy/dev/console'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpikpj6suy/dev/shm'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpikpj6suy/dev/shm'] 0m0.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m0.4s DEBUG: Created policy-rc.d and chmodded it. 0m0.4s DEBUG: Created resolv.conf. 0m0.4s DEBUG: Copying scriptsdir /etc/piuparts/scripts-log-alternatives to /srv/piuparts.debian.org/tmp/tmpikpj6suy/tmp/scripts/ 0m0.4s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpikpj6suy/tmp/scripts/ 0m0.4s INFO: Running scripts post_chroot_unpack 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'apt-get', 'update'] 0m3.4s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [202 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9957 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7309 kB] Fetched 17.5 MB in 2s (7744 kB/s) Reading package lists... 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'apt-get', 'update'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'apt-get', '-yf', 'dist-upgrade'] 0m4.0s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'apt-get', '-yf', 'dist-upgrade'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.6s DUMP: f6ddda661f5b24416c726af0f00366ef - 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.6s INFO: Running scripts post_setup 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/post_setup_dummy_users'] 0m5.1s 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 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/post_setup_dummy_users'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/post_setup_forbid_home'] 0m5.1s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/post_setup_forbid_home'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.1s 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' 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/post_setup_minimize'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/post_setup_minimize'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/post_setup_zz_backports'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/post_setup_zz_backports'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'apt-get', 'clean'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'apt-get', 'clean'] 0m5.2s DEBUG: Recording chroot state 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.6s DUMP: install ok installed apt apt 2.9.8 install ok installed base-files base-files 13.5 install ok installed base-passwd base-passwd 3.6.4 install ok installed bash bash 5.2.32-1+b1 install ok installed bsdutils bsdutils 1:2.40.2-8 install ok installed coreutils coreutils 9.4-3.1 install ok installed dash dash 0.5.12-9 install ok installed debconf debconf 1.5.87 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.20 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.1-1 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-5 install ok installed gpgv gpgv 2.2.43-8+b1 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 1.67 install ok installed libacl1:amd64 libacl1 2.3.2-2 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.8 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:4.0.1-1 install ok installed libaudit1:amd64 libaudit1 1:4.0.1-1 install ok installed libblkid1:amd64 libblkid1 2.40.2-8 install ok installed libbsd0:amd64 libbsd0 0.12.2-1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.40-2 install ok installed libc6:amd64 libc6 2.40-2 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-2 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libcom-err2:amd64 libcom-err2 1.47.1-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-7 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.272 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.1-1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-5 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-6 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.6-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.50-4 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3 install ok installed liblzma5:amd64 liblzma5 5.6.2-2 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.40.2-8 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b1 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1+b1 install ok installed libselinux1:amd64 libselinux1 3.7-3 install ok installed libsemanage-common libsemanage-common 3.7-2 install ok installed libsemanage2:amd64 libsemanage2 3.7-2 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-8 install ok installed libss2:amd64 libss2 1.47.1-1 install ok installed libssl3t64:amd64 libssl3t64 3.3.2-1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-5 install ok installed libsystemd0:amd64 libsystemd0 256.6-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtinfo6:amd64 libtinfo6 6.5-2 install ok installed libudev1:amd64 libudev1 256.6-1 install ok installed libunistring5:amd64 libunistring5 1.2-1 install ok installed libuuid1:amd64 libuuid1 2.40.2-8 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1 install ok installed login login 1:4.16.0-2+really2.40.2-8 install ok installed login.defs login.defs 1:4.16.0-4 install ok installed logsave logsave 1.47.1-1 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed mount mount 2.40.2-8 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.2-1 install ok installed passwd passwd 1:4.16.0-4 install ok installed perl-base perl-base 5.38.2-5 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.10-2 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024a-4 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-8 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'dpkg-divert', '--list'] 0m5.6s 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 /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6 diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64 diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64 diversion of /libx32 to /.libx32.usr-is-merged by base-files local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /lib32 to /.lib32.usr-is-merged by base-files diversion of /libo32 to /.libo32.usr-is-merged by base-files 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'dpkg-divert', '--list'] 0m5.6s INFO: Running scripts is_testable 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/is_testable_uninstallable'] 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/is_testable_uninstallable'] 0m5.6s INFO: apt-cache does not know about any of the requested packages 0m5.6s INFO: Running scripts pre_test 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/pre_test_exceptions'] 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/pre_test_exceptions'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/pre_test_root_password'] 0m5.7s DUMP: New password: Retype new password: passwd: password updated successfully 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/pre_test_root_password'] 0m5.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpikpj6suy'] 0m6.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpikpj6suy'] 0m6.4s DEBUG: No broken symlinks as far as we can find. 0m6.4s INFO: Running scripts pre_install 0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/pre_install_database-server'] 0m6.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/pre_install_database-server'] 0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/pre_install_exceptions'] 0m6.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/pre_install_exceptions'] 0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/pre_install_extras'] 0m6.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/pre_install_extras'] 0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/pre_install_log_alternatives'] 0m6.5s DUMP: Adding 'local diversion of /usr/bin/update-alternatives to /usr/bin/update-alternatives.orig' dpkg-divert: warning: diverting file '/usr/bin/update-alternatives' from an Essential package with rename is dangerous, use --no-rename 0m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/pre_install_log_alternatives'] 0m6.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpikpj6suy'] 0m6.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpikpj6suy'] 0m7.1s DEBUG: No broken symlinks as far as we can find. 0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'apt-cache', 'policy'] 0m7.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'apt-cache', 'policy'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'apt-cache', 'policy', 'pbsuite'] 0m7.9s DUMP: pbsuite: 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 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'apt-cache', 'policy', 'pbsuite'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'apt-get', '-y', 'install', 'pbsuite=15.8.24+dfsg-7'] 0m24.4s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: blasr libaec0 libblas3 libblasr5.3.5 libbrotli1 libcurl3t64-gnutls libcurl4t64 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 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnsl2 libpbbam2.4.0 libpbcopper2.3.0 libpbseq libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1t64 libsz2 libtirpc-common libtirpc3t64 media-types netbase pbhoney pbjelly python3 python3-autocommand python3-h5py python3-h5py-serial python3-inflect python3-intervaltree python3-intervaltree-bio python3-jaraco.context python3-jaraco.functools python3-minimal python3-more-itertools python3-networkx python3-numpy python3-pbbanana python3-pbsuite-utils python3-pkg-resources python3-pysam python3-sortedcontainers python3-typeguard python3-typing-extensions python3.12 python3.12-minimal readline-common samtools Suggested packages: krb5-doc krb5-user python3-doc python3-tk python3-venv python-h5py-doc gcc gfortran python-numpy-doc python3-dev python3-pytest python3-setuptools python-sortedcontainers-doc python3.12-venv python3.12-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 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 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnsl2 libpbbam2.4.0 libpbcopper2.3.0 libpbseq libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1t64 libsz2 libtirpc-common libtirpc3t64 media-types netbase pbhoney pbjelly pbsuite python3 python3-autocommand python3-h5py python3-h5py-serial python3-inflect python3-intervaltree python3-intervaltree-bio python3-jaraco.context python3-jaraco.functools python3-minimal python3-more-itertools python3-networkx python3-numpy python3-pbbanana python3-pbsuite-utils python3-pkg-resources python3-pysam python3-sortedcontainers python3-typeguard python3-typing-extensions python3.12 python3.12-minimal readline-common samtools 0 upgraded, 75 newly installed, 0 to remove and 0 not upgraded. Need to get 44.8 MB of archives. After this operation, 217 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 libpython3.12-minimal amd64 3.12.6-1 [814 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.6.3-1 [105 kB] Get:3 http://deb.debian.org/debian sid/main amd64 python3.12-minimal amd64 3.12.6-1 [2168 kB] Get:4 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.12.6-1 [26.7 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 libncursesw6 amd64 6.5-2 [135 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get:11 http://deb.debian.org/debian sid/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3 [82.7 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libnsl2 amd64 1.3.0-3+b2 [40.3 kB] Get:16 http://deb.debian.org/debian sid/main amd64 readline-common all 8.2-5 [69.3 kB] Get:17 http://deb.debian.org/debian sid/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libsqlite3-0 amd64 3.46.1-1 [913 kB] Get:19 http://deb.debian.org/debian sid/main amd64 libpython3.12-stdlib amd64 3.12.6-1 [1963 kB] Get:20 http://deb.debian.org/debian sid/main amd64 python3.12 amd64 3.12.6-1 [669 kB] Get:21 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.12.6-1 [9692 B] Get:22 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.12.6-1 [27.8 kB] Get:23 http://deb.debian.org/debian sid/main amd64 libbrotli1 amd64 1.1.0-2+b4 [300 kB] Get:24 http://deb.debian.org/debian sid/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get:25 http://deb.debian.org/debian sid/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get:26 http://deb.debian.org/debian sid/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3 [187 kB] Get:27 http://deb.debian.org/debian sid/main amd64 libnghttp2-14 amd64 1.63.0-1 [74.8 kB] Get:28 http://deb.debian.org/debian sid/main amd64 libpsl5t64 amd64 0.21.2-1.1 [56.8 kB] Get:29 http://deb.debian.org/debian sid/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b4 [58.5 kB] Get:30 http://deb.debian.org/debian sid/main amd64 libssh2-1t64 amd64 1.11.0-7 [216 kB] Get:31 http://deb.debian.org/debian sid/main amd64 libcurl4t64 amd64 8.10.1-1 [352 kB] Get:32 http://deb.debian.org/debian sid/main amd64 libaec0 amd64 1.1.3-1 [23.4 kB] Get:33 http://deb.debian.org/debian sid/main amd64 libsz2 amd64 1.1.3-1 [7740 B] Get:34 http://deb.debian.org/debian sid/main amd64 libhdf5-103-1t64 amd64 1.10.10+repack-4 [1253 kB] Get:35 http://deb.debian.org/debian sid/main amd64 libhdf5-cpp-103-1t64 amd64 1.10.10+repack-4 [130 kB] Get:36 http://deb.debian.org/debian sid/main amd64 libnghttp3-9 amd64 1.4.0-1 [63.1 kB] Get:37 http://deb.debian.org/debian sid/main amd64 libngtcp2-16 amd64 1.6.0-1 [122 kB] Get:38 http://deb.debian.org/debian sid/main amd64 libngtcp2-crypto-gnutls8 amd64 1.6.0-1 [19.6 kB] Get:39 http://deb.debian.org/debian sid/main amd64 libcurl3t64-gnutls amd64 8.10.1-1 [359 kB] Get:40 http://deb.debian.org/debian sid/main amd64 libdeflate0 amd64 1.21-1 [47.3 kB] Get:41 http://deb.debian.org/debian sid/main amd64 libhtscodecs2 amd64 1.6.1-1 [95.6 kB] Get:42 http://deb.debian.org/debian sid/main amd64 libhts3t64 amd64 1.20+ds-1 [452 kB] Get:43 http://deb.debian.org/debian sid/main amd64 libpbcopper2.3.0 amd64 2.3.0+dfsg-2 [740 kB] Get:44 http://deb.debian.org/debian sid/main amd64 libpbbam2.4.0 amd64 2.4.0+dfsg-1+b3 [819 kB] Get:45 http://deb.debian.org/debian sid/main amd64 libblasr5.3.5 amd64 5.3.5+dfsg-6+b3 [1113 kB] Get:46 http://deb.debian.org/debian sid/main amd64 libpbseq amd64 5.3.5+dfsg-6+b3 [5004 B] Get:47 http://deb.debian.org/debian sid/main amd64 blasr amd64 5.3.5+dfsg-6+b3 [224 kB] Get:48 http://deb.debian.org/debian sid/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get:49 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14.2.0-5 [837 kB] Get:50 http://deb.debian.org/debian sid/main amd64 libhdf5-hl-100t64 amd64 1.10.10+repack-4 [63.9 kB] Get:51 http://deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get:52 http://deb.debian.org/debian sid/main amd64 liblzf1 amd64 3.6-4+b1 [10.4 kB] Get:53 http://deb.debian.org/debian sid/main amd64 libncurses6 amd64 6.5-2 [104 kB] Get:54 http://deb.debian.org/debian sid/main amd64 python3-pysam amd64 0.22.1+ds-2+b1 [3474 kB] Get:55 http://deb.debian.org/debian sid/main amd64 python3-pbsuite-utils all 15.8.24+dfsg-7 [509 kB] Get:56 http://deb.debian.org/debian sid/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get:57 http://deb.debian.org/debian sid/main amd64 python3-more-itertools all 10.4.0-1 [63.7 kB] Get:58 http://deb.debian.org/debian sid/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get:59 http://deb.debian.org/debian sid/main amd64 python3-typeguard all 4.3.0-1 [36.5 kB] Get:60 http://deb.debian.org/debian sid/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get:61 http://deb.debian.org/debian sid/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get:62 http://deb.debian.org/debian sid/main amd64 python3-jaraco.functools all 4.0.2-1 [11.7 kB] Get:63 http://deb.debian.org/debian sid/main amd64 python3-pkg-resources all 74.1.2-2 [213 kB] Get:64 http://deb.debian.org/debian sid/main amd64 python3-networkx all 3.2.1-4 [14.2 MB] Get:65 http://deb.debian.org/debian sid/main amd64 pbjelly all 15.8.24+dfsg-7 [967 kB] Get:66 http://deb.debian.org/debian sid/main amd64 python3-pbbanana all 15.8.24+dfsg-7 [20.1 kB] Get:67 http://deb.debian.org/debian sid/main amd64 python3-numpy amd64 1:1.26.4+ds-11 [4236 kB] Get:68 http://deb.debian.org/debian sid/main amd64 python3-h5py-serial amd64 3.11.0-5 [975 kB] Get:69 http://deb.debian.org/debian sid/main amd64 python3-h5py all 3.11.0-5 [14.7 kB] Get:70 http://deb.debian.org/debian sid/main amd64 python3-sortedcontainers all 2.4.0-2 [31.9 kB] Get:71 http://deb.debian.org/debian sid/main amd64 python3-intervaltree all 3.0.2-1.1 [26.3 kB] Get:72 http://deb.debian.org/debian sid/main amd64 python3-intervaltree-bio all 1.0.1-4 [8640 B] Get:73 http://deb.debian.org/debian sid/main amd64 samtools amd64 1.20-3 [653 kB] Get:74 http://deb.debian.org/debian sid/main amd64 pbhoney all 15.8.24+dfsg-7 [1056 kB] Get:75 http://deb.debian.org/debian sid/main amd64 pbsuite all 15.8.24+dfsg-7 [5416 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 44.8 MB in 1s (85.9 MB/s) Selecting previously unselected package libpython3.12-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 ... 5145 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.6-1_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.6-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.3-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.3-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.6-1_amd64.deb ... Unpacking python3.12-minimal (3.12.6-1) ... Setting up libpython3.12-minimal:amd64 (3.12.6-1) ... Setting up libexpat1:amd64 (2.6.3-1) ... Setting up python3.12-minimal (3.12.6-1) ... 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 ... 5465 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_amd64.deb ... 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(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 ... 6022 files and directories currently installed.) Preparing to unpack .../00-python3_3.12.6-1_amd64.deb ... Unpacking python3 (3.12.6-1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../01-libbrotli1_1.1.0-2+b4_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b4) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../02-libsasl2-modules-db_2.1.28+dfsg1-8_amd64.deb ... 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Selecting previously unselected package libssh2-1t64:amd64. Preparing to unpack .../08-libssh2-1t64_1.11.0-7_amd64.deb ... Unpacking libssh2-1t64:amd64 (1.11.0-7) ... Selecting previously unselected package libcurl4t64:amd64. Preparing to unpack .../09-libcurl4t64_8.10.1-1_amd64.deb ... Unpacking libcurl4t64:amd64 (8.10.1-1) ... Selecting previously unselected package libaec0:amd64. Preparing to unpack .../10-libaec0_1.1.3-1_amd64.deb ... Unpacking libaec0:amd64 (1.1.3-1) ... Selecting previously unselected package libsz2:amd64. Preparing to unpack .../11-libsz2_1.1.3-1_amd64.deb ... Unpacking libsz2:amd64 (1.1.3-1) ... Selecting previously unselected package libhdf5-103-1t64:amd64. Preparing to unpack .../12-libhdf5-103-1t64_1.10.10+repack-4_amd64.deb ... Unpacking libhdf5-103-1t64:amd64 (1.10.10+repack-4) ... Selecting previously unselected package libhdf5-cpp-103-1t64:amd64. Preparing to unpack .../13-libhdf5-cpp-103-1t64_1.10.10+repack-4_amd64.deb ... Unpacking libhdf5-cpp-103-1t64:amd64 (1.10.10+repack-4) ... Selecting previously unselected package libnghttp3-9:amd64. Preparing to unpack .../14-libnghttp3-9_1.4.0-1_amd64.deb ... Unpacking libnghttp3-9:amd64 (1.4.0-1) ... Selecting previously unselected package libngtcp2-16:amd64. Preparing to unpack .../15-libngtcp2-16_1.6.0-1_amd64.deb ... Unpacking libngtcp2-16:amd64 (1.6.0-1) ... Selecting previously unselected package libngtcp2-crypto-gnutls8:amd64. Preparing to unpack .../16-libngtcp2-crypto-gnutls8_1.6.0-1_amd64.deb ... Unpacking libngtcp2-crypto-gnutls8:amd64 (1.6.0-1) ... Selecting previously unselected package libcurl3t64-gnutls:amd64. Preparing to unpack .../17-libcurl3t64-gnutls_8.10.1-1_amd64.deb ... Unpacking libcurl3t64-gnutls:amd64 (8.10.1-1) ... Selecting previously unselected package libdeflate0:amd64. Preparing to unpack .../18-libdeflate0_1.21-1_amd64.deb ... Unpacking libdeflate0:amd64 (1.21-1) ... Selecting previously unselected package libhtscodecs2:amd64. Preparing to unpack .../19-libhtscodecs2_1.6.1-1_amd64.deb ... Unpacking libhtscodecs2:amd64 (1.6.1-1) ... Selecting previously unselected package libhts3t64:amd64. Preparing to unpack .../20-libhts3t64_1.20+ds-1_amd64.deb ... Unpacking libhts3t64:amd64 (1.20+ds-1) ... Selecting previously unselected package libpbcopper2.3.0:amd64. Preparing to unpack .../21-libpbcopper2.3.0_2.3.0+dfsg-2_amd64.deb ... Unpacking libpbcopper2.3.0:amd64 (2.3.0+dfsg-2) ... Selecting previously unselected package libpbbam2.4.0:amd64. Preparing to unpack .../22-libpbbam2.4.0_2.4.0+dfsg-1+b3_amd64.deb ... Unpacking libpbbam2.4.0:amd64 (2.4.0+dfsg-1+b3) ... Selecting previously unselected package libblasr5.3.5:amd64. Preparing to unpack .../23-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 .../24-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 .../25-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 .../26-libblas3_3.12.0-3_amd64.deb ... Unpacking libblas3:amd64 (3.12.0-3) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../27-libgfortran5_14.2.0-5_amd64.deb ... Unpacking libgfortran5:amd64 (14.2.0-5) ... Selecting previously unselected package libhdf5-hl-100t64:amd64. Preparing to unpack .../28-libhdf5-hl-100t64_1.10.10+repack-4_amd64.deb ... Unpacking libhdf5-hl-100t64:amd64 (1.10.10+repack-4) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../29-liblapack3_3.12.0-3_amd64.deb ... Unpacking liblapack3:amd64 (3.12.0-3) ... Selecting previously unselected package liblzf1:amd64. Preparing to unpack .../30-liblzf1_3.6-4+b1_amd64.deb ... Unpacking liblzf1:amd64 (3.6-4+b1) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../31-libncurses6_6.5-2_amd64.deb ... Unpacking libncurses6:amd64 (6.5-2) ... Selecting previously unselected package python3-pysam. Preparing to unpack .../32-python3-pysam_0.22.1+ds-2+b1_amd64.deb ... Unpacking python3-pysam (0.22.1+ds-2+b1) ... Selecting previously unselected package python3-pbsuite-utils. Preparing to unpack .../33-python3-pbsuite-utils_15.8.24+dfsg-7_all.deb ... Unpacking python3-pbsuite-utils (15.8.24+dfsg-7) ... Selecting previously unselected package python3-autocommand. Preparing to unpack .../34-python3-autocommand_2.2.2-3_all.deb ... Unpacking python3-autocommand (2.2.2-3) ... Selecting previously unselected package python3-more-itertools. Preparing to unpack .../35-python3-more-itertools_10.4.0-1_all.deb ... Unpacking python3-more-itertools (10.4.0-1) ... Selecting previously unselected package python3-typing-extensions. Preparing to unpack .../36-python3-typing-extensions_4.12.2-2_all.deb ... Unpacking python3-typing-extensions (4.12.2-2) ... Selecting previously unselected package python3-typeguard. Preparing to unpack .../37-python3-typeguard_4.3.0-1_all.deb ... Unpacking python3-typeguard (4.3.0-1) ... Selecting previously unselected package python3-inflect. Preparing to unpack .../38-python3-inflect_7.3.1-2_all.deb ... Unpacking python3-inflect (7.3.1-2) ... Selecting previously unselected package python3-jaraco.context. Preparing to unpack .../39-python3-jaraco.context_6.0.0-1_all.deb ... Unpacking python3-jaraco.context (6.0.0-1) ... Selecting previously unselected package python3-jaraco.functools. Preparing to unpack .../40-python3-jaraco.functools_4.0.2-1_all.deb ... Unpacking python3-jaraco.functools (4.0.2-1) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../41-python3-pkg-resources_74.1.2-2_all.deb ... Unpacking python3-pkg-resources (74.1.2-2) ... Selecting previously unselected package python3-networkx. Preparing to unpack .../42-python3-networkx_3.2.1-4_all.deb ... Unpacking python3-networkx (3.2.1-4) ... Selecting previously unselected package pbjelly. Preparing to unpack .../43-pbjelly_15.8.24+dfsg-7_all.deb ... Unpacking pbjelly (15.8.24+dfsg-7) ... Selecting previously unselected package python3-pbbanana. Preparing to unpack .../44-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 .../45-python3-numpy_1%3a1.26.4+ds-11_amd64.deb ... Unpacking python3-numpy (1:1.26.4+ds-11) ... Selecting previously unselected package python3-h5py-serial. Preparing to unpack .../46-python3-h5py-serial_3.11.0-5_amd64.deb ... Unpacking python3-h5py-serial (3.11.0-5) ... Selecting previously unselected package python3-h5py. Preparing to unpack .../47-python3-h5py_3.11.0-5_all.deb ... Unpacking python3-h5py (3.11.0-5) ... Selecting previously unselected package python3-sortedcontainers. Preparing to unpack .../48-python3-sortedcontainers_2.4.0-2_all.deb ... Unpacking python3-sortedcontainers (2.4.0-2) ... Selecting previously unselected package python3-intervaltree. Preparing to unpack .../49-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 .../50-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 .../51-samtools_1.20-3_amd64.deb ... Unpacking samtools (1.20-3) ... Selecting previously unselected package pbhoney. Preparing to unpack .../52-pbhoney_15.8.24+dfsg-7_all.deb ... Unpacking pbhoney (15.8.24+dfsg-7) ... Selecting previously unselected package pbsuite. Preparing to unpack .../53-pbsuite_15.8.24+dfsg-7_all.deb ... Unpacking pbsuite (15.8.24+dfsg-7) ... Setting up libhtscodecs2:amd64 (1.6.1-1) ... Setting up media-types (10.1.0) ... Setting up libkeyutils1:amd64 (1.6.3-3) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libbrotli1:amd64 (1.1.0-2+b4) ... Setting up libsqlite3-0:amd64 (3.46.1-1) ... Setting up libpsl5t64:amd64 (0.21.2-1.1) ... Setting up libnghttp2-14:amd64 (1.63.0-1) ... Setting up libdeflate0:amd64 (1.21-1) ... Setting up libaec0:amd64 (1.1.3-1) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... 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+b4) ... Setting up libncurses6:amd64 (6.5-2) ... Setting up liblzf1:amd64 (3.6-4+b1) ... Setting up libncursesw6:amd64 (6.5-2) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Setting up libgfortran5:amd64 (14.2.0-5) ... Setting up libnghttp3-9:amd64 (1.4.0-1) ... Setting up netbase (6.4) ... Setting up libngtcp2-16:amd64 (1.6.0-1) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libssh2-1t64:amd64 (1.11.0-7) ... Setting up readline-common (8.2-5) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.6.0-1) ... 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 libldap-2.5-0:amd64 (2.5.18+dfsg-3) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up libcurl4t64:amd64 (8.10.1-1) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Setting up libcurl3t64-gnutls:amd64 (8.10.1-1) ... Setting up libnsl2:amd64 (1.3.0-3+b2) ... Setting up libhts3t64:amd64 (1.20+ds-1) ... Setting up libhdf5-103-1t64:amd64 (1.10.10+repack-4) ... Setting up libhdf5-hl-100t64:amd64 (1.10.10+repack-4) ... Setting up libpython3.12-stdlib:amd64 (3.12.6-1) ... Setting up python3.12 (3.12.6-1) ... Setting up libpbbam2.4.0:amd64 (2.4.0+dfsg-1+b3) ... Setting up libhdf5-cpp-103-1t64:amd64 (1.10.10+repack-4) ... Setting up samtools (1.20-3) ... Setting up libblasr5.3.5:amd64 (5.3.5+dfsg-6+b3) ... Setting up libpbseq:amd64 (5.3.5+dfsg-6+b3) ... Setting up libpython3-stdlib:amd64 (3.12.6-1) ... Setting up blasr (5.3.5+dfsg-6+b3) ... Setting up python3 (3.12.6-1) ... Setting up python3-sortedcontainers (2.4.0-2) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up python3-more-itertools (10.4.0-1) ... Setting up python3-pysam (0.22.1+ds-2+b1) ... Setting up python3-jaraco.functools (4.0.2-1) ... Setting up python3-intervaltree (3.0.2-1.1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-pbsuite-utils (15.8.24+dfsg-7) ... /usr/lib/python3/dist-packages/pbsuite/utils/BamStat.py:75: SyntaxWarning: invalid escape sequence '\d' for i in re.findall("\d+|\^?[ATCGN]+", md): /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:49: SyntaxWarning: invalid escape sequence '\s' splRE = re.compile("\s+") /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:60: SyntaxWarning: invalid escape sequence '\s' splRE = re.compile("\s+") /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:87: SyntaxWarning: invalid escape sequence '\s' self[key] = list(map(int, re.split("\s+", self[key].getvalue().strip()))) /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:475: SyntaxWarning: invalid escape sequence '\d' subreadGrab = re.compile(".*/(\d+)_(\d+)$") /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:499: SyntaxWarning: invalid escape sequence '\s' data = re.split("\s+",line) /usr/lib/python3/dist-packages/pbsuite/utils/FileHandlers.py:609: SyntaxWarning: invalid escape sequence '\s' data = re.split("\s+",line) /usr/lib/python3/dist-packages/pbsuite/utils/VCFIO.py:110: SyntaxWarning: invalid escape sequence '\s' METARE = re.compile(('##\s*(?P\w+)\s*=\s*\<\s*ID\s*=\s*(?P\w+)\s*' /usr/lib/python3/dist-packages/pbsuite/utils/VCFIO.py:111: SyntaxWarning: invalid escape sequence '\s' ',\s*(Number\s*=\s*(?P[0-9.])\s*,' /usr/lib/python3/dist-packages/pbsuite/utils/VCFIO.py:112: SyntaxWarning: invalid escape sequence '\s' '\s*Type\s*=\s*(?P\w+)\s*,)?' /usr/lib/python3/dist-packages/pbsuite/utils/VCFIO.py:113: SyntaxWarning: invalid escape sequence '\s' '\s*Description\s*=\s*"(?P.*)"\s*\>\s*'),\ /usr/lib/python3/dist-packages/pbsuite/utils/jellyoutputrename.py:22: SyntaxWarning: invalid escape sequence '\d' regex = re.compile("ref\d{7}") Setting up python3-typeguard (4.3.0-1) ... Setting up python3-inflect (7.3.1-2) ... Setting up python3-intervaltree-bio (1.0.1-4) ... Setting up python3-pkg-resources (74.1.2-2) ... Setting up python3-networkx (3.2.1-4) ... Setting up python3-numpy (1:1.26.4+ds-11) ... Setting up pbjelly (15.8.24+dfsg-7) ... /usr/lib/python3/dist-packages/pbsuite/jelly/Extraction.py:59: SyntaxWarning: invalid escape sequence '\d' getSub = re.compile("(.*)##(\d+)#(\d+)##$") /usr/lib/python3/dist-packages/pbsuite/jelly/Extraction.py:326: SyntaxWarning: invalid escape sequence '\s' splRE = re.compile("\s+") /usr/lib/python3/dist-packages/pbsuite/jelly/Setup.py:16: SyntaxWarning: invalid escape sequence '\|' refParser = re.compile("(.*)\|(ref\d{7})/?(\d+)?$") /usr/lib/python3/dist-packages/pbsuite/jelly/Stages.py:82: SyntaxWarning: invalid escape sequence '\d' nprocRe = re.compile("--nproc (\d+)") /usr/lib/python3/dist-packages/pbsuite/jelly/m4pie.py:17: SyntaxWarning: invalid escape sequence '\d' """ /usr/lib/python3/dist-packages/pbsuite/jelly/m4pie.py:108: SyntaxWarning: invalid escape sequence '\d' datGrab = re.compile("^(?P\d+)(?P[pe])(?P\d+)__(?P.*)$") Setting up python3-h5py-serial (3.11.0-5) ... Setting up python3-pbbanana (15.8.24+dfsg-7) ... /usr/lib/python3/dist-packages/pbsuite/banana/MakeOverlapTable.py:10: SyntaxWarning: invalid escape sequence '\d' subreadGrab = re.compile(".*/(\d+)_(\d+)$") /usr/lib/python3/dist-packages/pbsuite/banana/MakeOverlapTable.py:26: SyntaxWarning: invalid escape sequence '\s' data = re.split("\s+",line) /usr/lib/python3/dist-packages/pbsuite/banana/MakeReciprocal.py:12: SyntaxWarning: invalid escape sequence '\d' subreadGrab = re.compile(".*/(\d+)_(\d+)$") /usr/lib/python3/dist-packages/pbsuite/banana/MakeReciprocal.py:36: SyntaxWarning: invalid escape sequence '\s' data = re.split("\s+",line) /usr/lib/python3/dist-packages/pbsuite/banana/OLCAssembly.py:277: SyntaxWarning: invalid escape sequence '\:' _exe("grep iid alignments.overlaps_realigned | cut -f2 -d\: > internal.ids") /usr/lib/python3/dist-packages/pbsuite/banana/OLCAssembly.py:304: SyntaxWarning: invalid escape sequence '\d' getContigName = re.compile("(\d+)_contig") /usr/lib/python3/dist-packages/pbsuite/banana/chunkyBlasr.py:123: SyntaxWarning: invalid escape sequence '\ ' "awk -F\ '{{if ($1 < 500) print $2}}' | " Setting up python3-h5py (3.11.0-5) ... Setting up pbhoney (15.8.24+dfsg-7) ... /usr/lib/python3/dist-packages/pbsuite/honey/Force.py:523: SyntaxWarning: invalid escape sequence '\?' forceRe = re.compile("(?PTrue|False|\?)\[(?P.*)\|(?P.*)\]") /usr/lib/python3/dist-packages/pbsuite/honey/bampie.py:85: SyntaxWarning: invalid escape sequence '\d' """ /usr/lib/python3/dist-packages/pbsuite/honey/bampie.py:166: SyntaxWarning: invalid escape sequence '\d' datGrab = re.compile("^(?P\d+)(?P[pe])(?P[01])(?P.*):(?P\d+)__(?P.*)$") /usr/lib/python3/dist-packages/pbsuite/honey/realign.py:199: SyntaxWarning: invalid escape sequence '\d' for i in re.findall("\d+|\^?[ATCGN]+", md): Setting up pbsuite (15.8.24+dfsg-7) ... Processing triggers for libc-bin (2.40-2) ... 0m24.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'apt-get', '-y', 'install', 'pbsuite=15.8.24+dfsg-7'] 0m24.4s INFO: Running scripts post_install 0m24.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/post_install_exceptions'] 0m24.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/post_install_exceptions'] 0m24.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/post_install_log_alternatives'] 0m24.4s DUMP: Removing 'local diversion of /usr/bin/update-alternatives to /usr/bin/update-alternatives.orig' LOG-ALTERNATIVES: dpkg=python3: piuparts=pbsuite=15.8.24+dfsg-7: /usr/bin/update-alternatives --auto /usr/bin/python3 LOG-ALTERNATIVES: dpkg=libblas3: piuparts=pbsuite=15.8.24+dfsg-7: /usr/bin/update-alternatives --install /usr/lib/x86_64-linux-gnu/libblas.so.3 libblas.so.3-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 10 LOG-ALTERNATIVES: dpkg=liblapack3: piuparts=pbsuite=15.8.24+dfsg-7: /usr/bin/update-alternatives --install /usr/lib/x86_64-linux-gnu/liblapack.so.3 liblapack.so.3-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 10 0m24.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/post_install_log_alternatives'] 0m24.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpikpj6suy'] 0m25.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpikpj6suy'] 0m26.4s ERROR: WARN: Broken symlinks: /usr/share/doc/python3-networkx/html/_static/sphinx_highlight.js -> ../../../../javascript/sphinxdoc/1.0/sphinx_highlight.js (python3-networkx) /usr/share/doc/python3-networkx/html/_static/searchtools.js -> ../../../../javascript/sphinxdoc/1.0/searchtools.js (python3-networkx) /usr/share/doc/python3-networkx/html/_static/language_data.js -> ../../../../javascript/sphinxdoc/1.0/language_data.js (python3-networkx) /usr/share/doc/python3-networkx/html/_static/doctools.js -> ../../../../javascript/sphinxdoc/1.0/doctools.js (python3-networkx) 0m27.1s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', '-ac', '--ignore-obsolete'] 0m28.4s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', '-ac', '--ignore-obsolete'] 0m28.4s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m28.4s DUMP: 0.15.6 0m28.4s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m28.4s INFO: Running adequate version 0.15.6 now. 0m28.4s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'pbsuite'] 0m28.5s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'pbsuite'] 0m28.5s INFO: Running scripts pre_remove 0m28.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m28.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m28.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m28.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m28.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m29.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m29.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m29.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m29.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m29.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m29.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/pre_remove_exceptions'] 0m30.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/pre_remove_exceptions'] 0m30.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m30.0s DUMP: install ok installed apt apt 2.9.8 install ok installed base-files base-files 13.5 install ok installed base-passwd base-passwd 3.6.4 install ok installed bash bash 5.2.32-1+b1 install ok installed blasr blasr 5.3.5+dfsg-6+b3 install ok installed bsdutils bsdutils 1:2.40.2-8 install ok installed coreutils coreutils 9.4-3.1 install ok installed dash dash 0.5.12-9 install ok installed debconf debconf 1.5.87 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.20 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.1-1 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-5 install ok installed gpgv gpgv 2.2.43-8+b1 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 1.67 install ok installed libacl1:amd64 libacl1 2.3.2-2 install ok installed libaec0:amd64 libaec0 1.1.3-1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.8 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:4.0.1-1 install ok installed libaudit1:amd64 libaudit1 1:4.0.1-1 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 2.40.2-8 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b4 install ok installed libbsd0:amd64 libbsd0 0.12.2-1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.40-2 install ok installed libc6:amd64 libc6 2.40-2 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-2 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libcom-err2:amd64 libcom-err2 1.47.1-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libcurl3t64-gnutls:amd64 libcurl3t64-gnutls 8.10.1-1 install ok installed libcurl4t64:amd64 libcurl4t64 8.10.1-1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-7 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.272 install ok installed libdeflate0:amd64 libdeflate0 1.21-1 install ok installed libexpat1:amd64 libexpat1 2.6.3-1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.1-1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-5 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-6 install ok installed libgfortran5:amd64 libgfortran5 14.2.0-5 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.6-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.50-4 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.21.3-3 install ok installed libhdf5-103-1t64:amd64 libhdf5-103-1t64 1.10.10+repack-4 install ok installed libhdf5-cpp-103-1t64:amd64 libhdf5-cpp-103-1t64 1.10.10+repack-4 install ok installed libhdf5-hl-100t64:amd64 libhdf5-hl-100t64 1.10.10+repack-4 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1 install ok installed libhts3t64:amd64 libhts3t64 1.20+ds-1 install ok installed libhtscodecs2:amd64 libhtscodecs2 1.6.1-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed libk5crypto3:amd64 libk5crypto3 1.21.3-3 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-3 install ok installed libkrb5-3:amd64 libkrb5-3 1.21.3-3 install ok installed libkrb5support0:amd64 libkrb5support0 1.21.3-3 install ok installed liblapack3:amd64 liblapack3 3.12.0-3 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.18+dfsg-3 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3 install ok installed liblzf1:amd64 liblzf1 3.6-4+b1 install ok installed liblzma5:amd64 liblzma5 5.6.2-2 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.40.2-8 install ok installed libncurses6:amd64 libncurses6 6.5-2 install ok installed libncursesw6:amd64 libncursesw6 6.5-2 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.63.0-1 install ok installed libnghttp3-9:amd64 libnghttp3-9 1.4.0-1 install ok installed libngtcp2-16:amd64 libngtcp2-16 1.6.0-1 install ok installed libngtcp2-crypto-gnutls8:amd64 libngtcp2-crypto-gnutls8 1.6.0-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-3+b2 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7 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 3.12.6-1 install ok installed libpython3.12-minimal:amd64 libpython3.12-minimal 3.12.6-1 install ok installed libpython3.12-stdlib:amd64 libpython3.12-stdlib 3.12.6-1 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-5 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b4 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-8 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-8 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1+b1 install ok installed libselinux1:amd64 libselinux1 3.7-3 install ok installed libsemanage-common libsemanage-common 3.7-2 install ok installed libsemanage2:amd64 libsemanage2 3.7-2 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-8 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-1 install ok installed libss2:amd64 libss2 1.47.1-1 install ok installed libssh2-1t64:amd64 libssh2-1t64 1.11.0-7 install ok installed libssl3t64:amd64 libssl3t64 3.3.2-1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-5 install ok installed libsystemd0:amd64 libsystemd0 256.6-1 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 6.5-2 install ok installed libtirpc-common libtirpc-common 1.3.4+ds-1.3 install ok installed libtirpc3t64:amd64 libtirpc3t64 1.3.4+ds-1.3 install ok installed libudev1:amd64 libudev1 256.6-1 install ok installed libunistring5:amd64 libunistring5 1.2-1 install ok installed libuuid1:amd64 libuuid1 2.40.2-8 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1 install ok installed login login 1:4.16.0-2+really2.40.2-8 install ok installed login.defs login.defs 1:4.16.0-4 install ok installed logsave logsave 1.47.1-1 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed media-types media-types 10.1.0 install ok installed mount mount 2.40.2-8 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2 install ok installed netbase netbase 6.4 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.2-1 install ok installed passwd passwd 1:4.16.0-4 install ok installed pbhoney pbhoney 15.8.24+dfsg-7 install ok installed pbjelly pbjelly 15.8.24+dfsg-7 install ok installed pbsuite pbsuite 15.8.24+dfsg-7 install ok installed perl-base perl-base 5.38.2-5 install ok installed python3 python3 3.12.6-1 install ok installed python3-autocommand python3-autocommand 2.2.2-3 install ok installed python3-h5py python3-h5py 3.11.0-5 install ok installed python3-h5py-serial python3-h5py-serial 3.11.0-5 install ok installed python3-inflect python3-inflect 7.3.1-2 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-jaraco.context python3-jaraco.context 6.0.0-1 install ok installed python3-jaraco.functools python3-jaraco.functools 4.0.2-1 install ok installed python3-minimal python3-minimal 3.12.6-1 install ok installed python3-more-itertools python3-more-itertools 10.4.0-1 install ok installed python3-networkx python3-networkx 3.2.1-4 install ok installed python3-numpy python3-numpy 1:1.26.4+ds-11 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 74.1.2-2 install ok installed python3-pysam python3-pysam 0.22.1+ds-2+b1 install ok installed python3-sortedcontainers python3-sortedcontainers 2.4.0-2 install ok installed python3-typeguard python3-typeguard 4.3.0-1 install ok installed python3-typing-extensions python3-typing-extensions 4.12.2-2 install ok installed python3.12 python3.12 3.12.6-1 install ok installed python3.12-minimal python3.12-minimal 3.12.6-1 install ok installed readline-common readline-common 8.2-5 install ok installed samtools samtools 1.20-3 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.10-2 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024a-4 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-8 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1 0m30.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m30.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'apt-get', 'remove', 'blasr', 'libaec0:amd64', 'libblas3:amd64', 'libblasr5.3.5:amd64', 'libbrotli1:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64: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', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnsl2:amd64', 'libpbbam2.4.0:amd64', 'libpbcopper2.3.0:amd64', 'libpbseq:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libsz2:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'media-types', 'netbase', 'pbhoney', 'pbjelly', 'python3', 'python3-autocommand', 'python3-h5py', 'python3-h5py-serial', 'python3-inflect', 'python3-intervaltree', 'python3-intervaltree-bio', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-minimal', 'python3-more-itertools', 'python3-networkx', 'python3-numpy', 'python3-pbbanana', 'python3-pbsuite-utils', 'python3-pkg-resources', 'python3-pysam', 'python3-sortedcontainers', 'python3-typeguard', 'python3-typing-extensions', 'python3.12', 'python3.12-minimal', 'readline-common', 'samtools', 'pbsuite'] 0m32.9s 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 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 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnsl2 libpbbam2.4.0 libpbcopper2.3.0 libpbseq libpsl5t64 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1t64 libsz2 libtirpc-common libtirpc3t64 media-types netbase pbhoney pbjelly pbsuite python3 python3-autocommand python3-h5py python3-h5py-serial python3-inflect python3-intervaltree python3-intervaltree-bio python3-jaraco.context python3-jaraco.functools python3-minimal python3-more-itertools python3-networkx python3-numpy python3-pbbanana python3-pbsuite-utils python3-pkg-resources python3-pysam python3-sortedcontainers python3-typeguard python3-typing-extensions python3.12 python3.12-minimal readline-common samtools 0 upgraded, 0 newly installed, 75 to remove and 0 not upgraded. After this operation, 217 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 ... 11153 files and directories currently installed.) Removing pbsuite (15.8.24+dfsg-7) ... 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 (3.11.0-5) ... Removing python3-h5py-serial (3.11.0-5) ... Removing libhdf5-hl-100t64:amd64 (1.10.10+repack-4) ... Removing python3-numpy (1:1.26.4+ds-11) ... Removing liblapack3:amd64 (3.12.0-3) ... Removing libblas3:amd64 (3.12.0-3) ... Removing samtools (1.20-3) ... Removing python3-pbsuite-utils (15.8.24+dfsg-7) ... Removing python3-pysam (0.22.1+ds-2+b1) ... 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 (3.2.1-4) ... Removing python3-pkg-resources (74.1.2-2) ... Removing python3-inflect (7.3.1-2) ... Removing python3-typeguard (4.3.0-1) ... Removing python3-typing-extensions (4.12.2-2) ... Removing libgfortran5:amd64 (14.2.0-5) ... Removing libhdf5-cpp-103-1t64:amd64 (1.10.10+repack-4) ... Removing liblzf1:amd64 (3.6-4+b1) ... Removing libncurses6:amd64 (6.5-2) ... Removing libpbbam2.4.0:amd64 (2.4.0+dfsg-1+b3) ... Removing libpbcopper2.3.0:amd64 (2.3.0+dfsg-2) ... Removing python3-autocommand (2.2.2-3) ... Removing python3-jaraco.context (6.0.0-1) ... Removing python3-jaraco.functools (4.0.2-1) ... Removing python3-more-itertools (10.4.0-1) ... Removing libhdf5-103-1t64:amd64 (1.10.10+repack-4) ... Removing libsz2:amd64 (1.1.3-1) ... Removing libaec0:amd64 (1.1.3-1) ... Removing libcurl4t64:amd64 (8.10.1-1) ... Removing libhts3t64:amd64 (1.20+ds-1) ... Removing libcurl3t64-gnutls:amd64 (8.10.1-1) ... Removing libbrotli1:amd64 (1.1.0-2+b4) ... Removing libdeflate0:amd64 (1.21-1) ... Removing python3 (3.12.6-1) ... Removing python3-minimal (3.12.6-1) ... Removing python3.12 (3.12.6-1) ... Removing python3.12-minimal (3.12.6-1) ... Removing libexpat1:amd64 (2.6.3-1) ... Removing libpython3-stdlib:amd64 (3.12.6-1) ... Removing libpython3.12-stdlib:amd64 (3.12.6-1) ... find: '/usr/lib/python3': No such file or directory Removing libnsl2:amd64 (1.3.0-3+b2) ... Removing libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Removing libgssapi-krb5-2:amd64 (1.21.3-3) ... Removing libhtscodecs2:amd64 (1.6.1-1) ... Removing libkrb5-3:amd64 (1.21.3-3) ... Removing libk5crypto3:amd64 (1.21.3-3) ... Removing libkeyutils1:amd64 (1.6.3-3) ... Removing libkrb5support0:amd64 (1.21.3-3) ... Removing libldap-2.5-0:amd64 (2.5.18+dfsg-3) ... Removing libncursesw6:amd64 (6.5-2) ... Removing libnghttp2-14:amd64 (1.63.0-1) ... Removing libnghttp3-9:amd64 (1.4.0-1) ... Removing libngtcp2-crypto-gnutls8:amd64 (1.6.0-1) ... Removing libngtcp2-16:amd64 (1.6.0-1) ... Removing libpsl5t64:amd64 (0.21.2-1.1) ... Removing libpython3.12-minimal:amd64 (3.12.6-1) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8t64:amd64 (8.2-5) ... 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 librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b4) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Removing libsqlite3-0:amd64 (3.46.1-1) ... Removing libssh2-1t64:amd64 (1.11.0-7) ... Removing libtirpc-common (1.3.4+ds-1.3) ... Removing media-types (10.1.0) ... Removing netbase (6.4) ... Removing readline-common (8.2-5) ... Processing triggers for libc-bin (2.40-2) ... 0m32.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'apt-get', 'remove', 'blasr', 'libaec0:amd64', 'libblas3:amd64', 'libblasr5.3.5:amd64', 'libbrotli1:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64: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', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnsl2:amd64', 'libpbbam2.4.0:amd64', 'libpbcopper2.3.0:amd64', 'libpbseq:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libsz2:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'media-types', 'netbase', 'pbhoney', 'pbjelly', 'python3', 'python3-autocommand', 'python3-h5py', 'python3-h5py-serial', 'python3-inflect', 'python3-intervaltree', 'python3-intervaltree-bio', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-minimal', 'python3-more-itertools', 'python3-networkx', 'python3-numpy', 'python3-pbbanana', 'python3-pbsuite-utils', 'python3-pkg-resources', 'python3-pysam', 'python3-sortedcontainers', 'python3-typeguard', 'python3-typing-extensions', 'python3.12', 'python3.12-minimal', 'readline-common', 'samtools', 'pbsuite'] 0m32.9s INFO: Running scripts post_remove 0m32.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/post_remove_exceptions'] 0m32.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/post_remove_exceptions'] 0m32.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'dpkg', '--purge', 'blasr', 'libaec0:amd64', 'libblas3:amd64', 'libblasr5.3.5:amd64', 'libbrotli1:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64: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', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnsl2:amd64', 'libpbbam2.4.0:amd64', 'libpbcopper2.3.0:amd64', 'libpbseq:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libsz2:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'media-types', 'netbase', 'pbhoney', 'pbjelly', 'python3', 'python3-autocommand', 'python3-h5py', 'python3-h5py-serial', 'python3-inflect', 'python3-intervaltree', 'python3-intervaltree-bio', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-minimal', 'python3-more-itertools', 'python3-networkx', 'python3-numpy', 'python3-pbbanana', 'python3-pbsuite-utils', 'python3-pkg-resources', 'python3-pysam', 'python3-sortedcontainers', 'python3-typeguard', 'python3-typing-extensions', 'python3.12', 'python3.12-minimal', 'readline-common', 'samtools'] 0m33.0s 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 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 ... 5152 files and directories currently installed.) Purging configuration files for libgssapi-krb5-2:amd64 (1.21.3-3) ... 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 libnghttp3-9 which isn't installed dpkg: warning: ignoring request to remove libngtcp2-16 which isn't installed dpkg: warning: ignoring request to remove libngtcp2-crypto-gnutls8 which isn't installed dpkg: warning: ignoring request to remove libnsl2 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 libpython3.12-minimal:amd64 (3.12.6-1) ... dpkg: warning: ignoring request to remove libpython3.12-stdlib which isn't installed Purging configuration files for libreadline8t64:amd64 (8.2-5) ... 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 libtirpc-common (1.3.4+ds-1.3) ... Purging configuration files for libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Purging configuration files for media-types (10.1.0) ... Purging configuration files for netbase (6.4) ... dpkg: warning: ignoring request to remove pbhoney which isn't installed dpkg: warning: ignoring request to remove pbjelly which isn't installed Purging configuration files for python3 (3.12.6-1) ... dpkg: warning: ignoring request to remove python3-autocommand which isn't installed 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-inflect 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-jaraco.context which isn't installed dpkg: warning: ignoring request to remove python3-jaraco.functools which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-more-itertools 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-typeguard which isn't installed dpkg: warning: ignoring request to remove python3-typing-extensions which isn't installed dpkg: warning: ignoring request to remove python3.12 which isn't installed Purging configuration files for python3.12-minimal (3.12.6-1) ... Purging configuration files for readline-common (8.2-5) ... dpkg: warning: ignoring request to remove samtools which isn't installed 0m33.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'dpkg', '--purge', 'blasr', 'libaec0:amd64', 'libblas3:amd64', 'libblasr5.3.5:amd64', 'libbrotli1:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64: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', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnsl2:amd64', 'libpbbam2.4.0:amd64', 'libpbcopper2.3.0:amd64', 'libpbseq:amd64', 'libpsl5t64:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libsz2:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'media-types', 'netbase', 'pbhoney', 'pbjelly', 'python3', 'python3-autocommand', 'python3-h5py', 'python3-h5py-serial', 'python3-inflect', 'python3-intervaltree', 'python3-intervaltree-bio', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-minimal', 'python3-more-itertools', 'python3-networkx', 'python3-numpy', 'python3-pbbanana', 'python3-pbsuite-utils', 'python3-pkg-resources', 'python3-pysam', 'python3-sortedcontainers', 'python3-typeguard', 'python3-typing-extensions', 'python3.12', 'python3.12-minimal', 'readline-common', 'samtools'] 0m33.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'dpkg', '--purge', 'pbsuite'] 0m33.0s DUMP: dpkg: warning: ignoring request to remove pbsuite which isn't installed 0m33.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'dpkg', '--purge', 'pbsuite'] 0m33.0s INFO: Running scripts post_purge 0m33.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/post_purge_exceptions'] 0m33.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/post_purge_exceptions'] 0m33.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'dpkg', '--purge', '--pending'] 0m33.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'dpkg', '--purge', '--pending'] 0m33.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'dpkg', '--remove', '--pending'] 0m33.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'dpkg', '--remove', '--pending'] 0m33.1s INFO: Running scripts post_test 0m33.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/post_test_exceptions'] 0m33.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'tmp/scripts/post_test_exceptions'] 0m33.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpikpj6suy'] 0m33.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpikpj6suy'] 0m33.8s DEBUG: No broken symlinks as far as we can find. 0m33.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'dpkg-divert', '--list'] 0m33.8s 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 /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6 diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64 diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64 diversion of /libx32 to /.libx32.usr-is-merged by base-files local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /lib32 to /.lib32.usr-is-merged by base-files diversion of /libo32 to /.libo32.usr-is-merged by base-files 0m33.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'dpkg-divert', '--list'] 0m33.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'apt-get', 'clean'] 0m33.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpikpj6suy', 'apt-get', 'clean'] 0m33.8s DEBUG: Recording chroot state 0m34.2s INFO: PASS: Installation and purging test. 0m34.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpikpj6suy/dev/shm'] 0m34.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpikpj6suy/dev/shm'] 0m34.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpikpj6suy/dev/console'] 0m34.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpikpj6suy/dev/console'] 0m34.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpikpj6suy/dev/ptmx'] 0m34.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpikpj6suy/dev/ptmx'] 0m34.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpikpj6suy/dev/pts'] 0m34.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpikpj6suy/dev/pts'] 0m34.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpikpj6suy/proc'] 0m34.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpikpj6suy/proc'] 0m34.7s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpikpj6suy'] 0m34.8s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpikpj6suy'] 0m34.8s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpikpj6suy 0m34.8s INFO: PASS: All tests. 0m34.8s INFO: piuparts run ends. ret=0 End: 2024-09-22 15:17:47 GMT