Start: 2024-04-05 11:02:14 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 --warn-on-usr-move fail --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz -d bookworm --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 1.4.1~202403190841~1.4-4-g85045c69 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 --warn-on-usr-move fail --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz -d bookworm --no-upgrade-test --apt pbsuite=15.8.24+dfsg-7 0m0.0s INFO: Running on: Linux piu-slave-conova-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/tmp_3qca00p 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp_3qca00p 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp_3qca00p/proc'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp_3qca00p/proc'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp_3qca00p/dev/pts'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp_3qca00p/dev/pts'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp_3qca00p/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp_3qca00p/dev/ptmx'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp_3qca00p/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp_3qca00p/dev/ptmx'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmp_3qca00p/dev/console'] 0m0.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmp_3qca00p/dev/console'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp_3qca00p/dev/shm'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp_3qca00p/dev/shm'] 0m0.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m0.5s DEBUG: Created policy-rc.d and chmodded it. 0m0.5s DEBUG: Created resolv.conf. 0m0.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts-log-alternatives to /srv/piuparts.debian.org/tmp/tmp_3qca00p/tmp/scripts/ 0m0.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp_3qca00p/tmp/scripts/ 0m0.5s INFO: Running scripts post_chroot_unpack 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'apt-get', 'update'] 0m1.7s DUMP: Hit:1 http://deb.debian.org/debian bookworm InRelease Reading package lists... 0m1.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'apt-get', 'update'] 0m1.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'apt-get', '-yf', 'dist-upgrade'] 0m2.2s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'apt-get', '-yf', 'dist-upgrade'] 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.6s DUMP: 0942a352c5bc637c4fdbc12bf31cd5ba - 0m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.6s INFO: Running scripts post_setup 0m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/post_setup_dummy_users'] 0m3.5s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/post_setup_dummy_users'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/post_setup_forbid_home'] 0m3.5s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/post_setup_forbid_home'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.5s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/post_setup_minimize'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/post_setup_minimize'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/post_setup_zz_backports'] 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/post_setup_zz_backports'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'apt-get', 'clean'] 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'apt-get', 'clean'] 0m3.6s DEBUG: Recording chroot state 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.2s DUMP: install ok installed adduser adduser 3.134 install ok installed apt apt 2.6.1 install ok installed base-files base-files 12.4+deb12u5 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b2 install ok installed bsdutils bsdutils 1:2.38.1-5+b1 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.12-2 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.3+deb12u1 install ok installed debianutils debianutils 5.7-0.5~deb12u1 install ok installed diffutils diffutils 1:3.8-4 install ok installed dpkg dpkg 1.21.22 install ok installed e2fsprogs e2fsprogs 1.47.0-2 install ok installed findutils findutils 4.9.0-4 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-14 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.8-5 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu1 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.6.1 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.0.9-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.9-1 install ok installed libblkid1:amd64 libblkid1 2.38.1-5+b1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-9+deb12u4 install ok installed libc6:amd64 libc6 2.36-9+deb12u4 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3 install ok installed libcap2:amd64 libcap2 1:2.66-4 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.33-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.270 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-14 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-3 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.9-2+deb12u2 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.1-0.2 install ok installed libmd0:amd64 libmd0 1.0.4-2 install ok installed libmount1:amd64 libmount1 2.38.1-5+b1 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-6+deb12u1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-6+deb12u1 install ok installed libpam-runtime libpam-runtime 1.5.2-6+deb12u1 install ok installed libpam0g:amd64 libpam0g 1.5.2-6+deb12u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-1 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+b3 install ok installed libselinux1:amd64 libselinux1 3.4-1+b6 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b5 install ok installed libsepol2:amd64 libsepol2 3.4-2.1 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-5+b1 install ok installed libss2:amd64 libss2 1.47.0-2 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-14 install ok installed libsystemd0:amd64 libsystemd0 252.22-1~deb12u1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.4-4 install ok installed libudev1:amd64 libudev1 252.22-1~deb12u1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+b1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.4+dfsg2-5 install ok installed login login 1:4.13+dfsg1-1+b1 install ok installed logsave logsave 1.47.0-2 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mount mount 2.38.1-5+b1 install ok installed ncurses-base ncurses-base 6.4-4 install ok installed ncurses-bin ncurses-bin 6.4-4 install ok installed passwd passwd 1:4.13+dfsg1-1+b1 install ok installed perl-base perl-base 5.36.0-7+deb12u1 install ok installed sed sed 4.9-1 install ok installed sysvinit-utils sysvinit-utils 3.06-4 install ok installed tar tar 1.34+dfsg-1.2+deb12u1 install ok installed tzdata tzdata 2024a-0+deb12u1 install ok installed usr-is-merged usr-is-merged 37~deb12u1 install ok installed util-linux util-linux 2.38.1-5+b1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+b1 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'dpkg-divert', '--list'] 0m4.2s DUMP: local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'dpkg-divert', '--list'] 0m4.2s INFO: Running scripts is_testable 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/is_testable_uninstallable'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/is_testable_uninstallable'] 0m4.2s INFO: apt-cache does not know about any of the requested packages 0m4.2s INFO: Running scripts pre_test 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/pre_test_exceptions'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/pre_test_exceptions'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/pre_test_root_password'] 0m4.3s DUMP: New password: Retype new password: passwd: password updated successfully 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/pre_test_root_password'] 0m4.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_3qca00p'] 0m4.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_3qca00p'] 0m5.6s DEBUG: No broken symlinks as far as we can find. 0m5.6s INFO: Running scripts pre_install 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/pre_install_database-server'] 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/pre_install_database-server'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/pre_install_exceptions'] 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/pre_install_exceptions'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/pre_install_extras'] 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/pre_install_extras'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/pre_install_log_alternatives'] 0m5.6s 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 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/pre_install_log_alternatives'] 0m5.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_3qca00p'] 0m6.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_3qca00p'] 0m6.9s DEBUG: No broken symlinks as far as we can find. 0m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'apt-cache', 'policy'] 0m7.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.5,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'apt-cache', 'policy'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', '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 bookworm/main amd64 Packages 0m7.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'apt-cache', 'policy', 'pbsuite'] 0m7.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', '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 libcurl3-gnutls libcurl4 libdeflate0 libexpat1 libgfortran5 libgssapi-krb5-2 libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-hl-100 libhts3 libhtscodecs2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 liblzf1 libncurses6 libncursesw6 libnghttp2-14 libnsl2 libpbbam2.1.0 libpbcopper2.0.0 libpbseq libpsl5 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libquadmath0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libssl3 libsz2 libtirpc-common libtirpc3 media-types 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 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 libcurl3-gnutls libcurl4 libdeflate0 libexpat1 libgfortran5 libgssapi-krb5-2 libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-hl-100 libhts3 libhtscodecs2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 liblzf1 libncurses6 libncursesw6 libnghttp2-14 libnsl2 libpbbam2.1.0 libpbcopper2.0.0 libpbseq libpsl5 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libquadmath0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libssl3 libsz2 libtirpc-common libtirpc3 media-types pbhoney pbjelly pbsuite 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, 66 newly installed, 0 to remove and 0 not upgraded. Need to get 32.0 MB of archives. After this operation, 129 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 libssl3 amd64 3.0.11-1~deb12u2 [2019 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get:6 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 libncursesw6 amd64 6.4-4 [134 kB] Get:8 http://deb.debian.org/debian bookworm/main amd64 libkrb5support0 amd64 1.20.1-2+deb12u1 [32.4 kB] Get:9 http://deb.debian.org/debian bookworm/main amd64 libk5crypto3 amd64 1.20.1-2+deb12u1 [78.9 kB] Get:10 http://deb.debian.org/debian bookworm/main amd64 libkeyutils1 amd64 1.6.3-2 [8808 B] Get:11 http://deb.debian.org/debian bookworm/main amd64 libkrb5-3 amd64 1.20.1-2+deb12u1 [332 kB] Get:12 http://deb.debian.org/debian bookworm/main amd64 libgssapi-krb5-2 amd64 1.20.1-2+deb12u1 [134 kB] Get:13 http://deb.debian.org/debian bookworm/main amd64 libtirpc-common all 1.3.3+ds-1 [14.0 kB] Get:14 http://deb.debian.org/debian bookworm/main amd64 libtirpc3 amd64 1.3.3+ds-1 [85.2 kB] Get:15 http://deb.debian.org/debian bookworm/main amd64 libnsl2 amd64 1.3.0-2 [39.5 kB] Get:16 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get:17 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get:18 http://deb.debian.org/debian bookworm/main amd64 libsqlite3-0 amd64 3.40.1-2 [837 kB] Get:19 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get:20 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get:21 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get:22 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get:23 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get:24 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get:25 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get:26 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get:27 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1+deb12u1 [72.4 kB] Get:28 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get:29 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:30 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get:31 http://deb.debian.org/debian bookworm/main amd64 libcurl4 amd64 7.88.1-10+deb12u5 [390 kB] Get:32 http://deb.debian.org/debian bookworm/main amd64 libaec0 amd64 1.0.6-1+b1 [21.1 kB] Get:33 http://deb.debian.org/debian bookworm/main amd64 libsz2 amd64 1.0.6-1+b1 [7804 B] Get:34 http://deb.debian.org/debian bookworm/main amd64 libhdf5-103-1 amd64 1.10.8+repack1-1 [1237 kB] Get:35 http://deb.debian.org/debian bookworm/main amd64 libhdf5-cpp-103-1 amd64 1.10.8+repack1-1 [128 kB] Get:36 http://deb.debian.org/debian bookworm/main amd64 libcurl3-gnutls amd64 7.88.1-10+deb12u5 [385 kB] Get:37 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get:38 http://deb.debian.org/debian bookworm/main amd64 libhtscodecs2 amd64 1.3.0-4 [87.5 kB] Get:39 http://deb.debian.org/debian bookworm/main amd64 libhts3 amd64 1.16+ds-3 [430 kB] Get:40 http://deb.debian.org/debian bookworm/main amd64 libpbcopper2.0.0 amd64 2.0.0+dfsg-2 [606 kB] Get:41 http://deb.debian.org/debian bookworm/main amd64 libpbbam2.1.0 amd64 2.1.0+dfsg-2 [762 kB] Get:42 http://deb.debian.org/debian bookworm/main amd64 libblasr5.3.5 amd64 5.3.5+dfsg-4+b2 [1094 kB] Get:43 http://deb.debian.org/debian bookworm/main amd64 libpbseq amd64 5.3.5+dfsg-4+b2 [5764 B] Get:44 http://deb.debian.org/debian bookworm/main amd64 blasr amd64 5.3.5+dfsg-6 [223 kB] Get:45 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB] Get:46 http://deb.debian.org/debian bookworm/main amd64 libquadmath0 amd64 12.2.0-14 [144 kB] Get:47 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get:48 http://deb.debian.org/debian bookworm/main amd64 libhdf5-hl-100 amd64 1.10.8+repack1-1 [67.8 kB] Get:49 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get:50 http://deb.debian.org/debian bookworm/main amd64 liblzf1 amd64 3.6-3 [10.2 kB] Get:51 http://deb.debian.org/debian bookworm/main amd64 libncurses6 amd64 6.4-4 [103 kB] Get:52 http://deb.debian.org/debian bookworm/main amd64 python3-pysam amd64 0.20.0+ds-3+b1 [1681 kB] Get:53 http://deb.debian.org/debian bookworm/main amd64 python3-pbsuite-utils all 15.8.24+dfsg-7 [509 kB] Get:54 http://deb.debian.org/debian bookworm/main amd64 python3-pkg-resources all 66.1.1-1 [296 kB] Get:55 http://deb.debian.org/debian bookworm/main amd64 python3-networkx all 2.8.8-1 [1425 kB] Get:56 http://deb.debian.org/debian bookworm/main amd64 pbjelly all 15.8.24+dfsg-7 [967 kB] Get:57 http://deb.debian.org/debian bookworm/main amd64 python3-pbbanana all 15.8.24+dfsg-7 [20.1 kB] Get:58 http://deb.debian.org/debian bookworm/main amd64 python3-numpy amd64 1:1.24.2-1 [5209 kB] Get:59 http://deb.debian.org/debian bookworm/main amd64 python3-h5py-serial amd64 3.7.0-8 [804 kB] Get:60 http://deb.debian.org/debian bookworm/main amd64 python3-h5py all 3.7.0-8 [10.3 kB] Get:61 http://deb.debian.org/debian bookworm/main amd64 python3-sortedcontainers all 2.4.0-2 [31.9 kB] Get:62 http://deb.debian.org/debian bookworm/main amd64 python3-intervaltree all 3.0.2-1.1 [26.3 kB] Get:63 http://deb.debian.org/debian bookworm/main amd64 python3-intervaltree-bio all 1.0.1-4 [8640 B] Get:64 http://deb.debian.org/debian bookworm/main amd64 samtools amd64 1.16.1-1 [607 kB] Get:65 http://deb.debian.org/debian bookworm/main amd64 pbhoney all 15.8.24+dfsg-7 [1056 kB] Get:66 http://deb.debian.org/debian bookworm/main amd64 pbsuite all 15.8.24+dfsg-7 [5416 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 32.0 MB in 1s (50.1 MB/s) Selecting previously unselected package libssl3: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 ... 6103 files and directories currently installed.) Preparing to unpack .../libssl3_3.0.11-1~deb12u2_amd64.deb ... Unpacking libssl3:amd64 (3.0.11-1~deb12u2) ... Selecting previously unselected package libpython3.11-minimal:amd64. Preparing to unpack .../libpython3.11-minimal_3.11.2-6_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.5.0-1_amd64.deb ... Unpacking libexpat1:amd64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_amd64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libssl3:amd64 (3.0.11-1~deb12u2) ... Setting up libpython3.11-minimal:amd64 (3.11.2-6) ... Setting up libexpat1:amd64 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... Selecting previously unselected package python3-minimal. (Reading database ... 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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 ... 6939 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.2-1+b1_amd64.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../01-libbrotli1_1.0.9-2+b6_amd64.deb ... Unpacking libbrotli1:amd64 (1.0.9-2+b6) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../02-libsasl2-modules-db_2.1.28+dfsg-10_amd64.deb ... 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Preparing to unpack .../19-libpbbam2.1.0_2.1.0+dfsg-2_amd64.deb ... Unpacking libpbbam2.1.0:amd64 (2.1.0+dfsg-2) ... Selecting previously unselected package libblasr5.3.5:amd64. Preparing to unpack .../20-libblasr5.3.5_5.3.5+dfsg-4+b2_amd64.deb ... Unpacking libblasr5.3.5:amd64 (5.3.5+dfsg-4+b2) ... Selecting previously unselected package libpbseq:amd64. Preparing to unpack .../21-libpbseq_5.3.5+dfsg-4+b2_amd64.deb ... Unpacking libpbseq:amd64 (5.3.5+dfsg-4+b2) ... Selecting previously unselected package blasr. Preparing to unpack .../22-blasr_5.3.5+dfsg-6_amd64.deb ... Unpacking blasr (5.3.5+dfsg-6) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../23-libblas3_3.11.0-2_amd64.deb ... Unpacking libblas3:amd64 (3.11.0-2) ... Selecting previously unselected package libquadmath0:amd64. Preparing to unpack .../24-libquadmath0_12.2.0-14_amd64.deb ... Unpacking libquadmath0:amd64 (12.2.0-14) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../25-libgfortran5_12.2.0-14_amd64.deb ... Unpacking libgfortran5:amd64 (12.2.0-14) ... Selecting previously unselected package libhdf5-hl-100:amd64. Preparing to unpack .../26-libhdf5-hl-100_1.10.8+repack1-1_amd64.deb ... Unpacking libhdf5-hl-100:amd64 (1.10.8+repack1-1) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../27-liblapack3_3.11.0-2_amd64.deb ... Unpacking liblapack3:amd64 (3.11.0-2) ... Selecting previously unselected package liblzf1:amd64. Preparing to unpack .../28-liblzf1_3.6-3_amd64.deb ... Unpacking liblzf1:amd64 (3.6-3) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../29-libncurses6_6.4-4_amd64.deb ... Unpacking libncurses6:amd64 (6.4-4) ... Selecting previously unselected package python3-pysam. Preparing to unpack .../30-python3-pysam_0.20.0+ds-3+b1_amd64.deb ... Unpacking python3-pysam (0.20.0+ds-3+b1) ... Selecting previously unselected package python3-pbsuite-utils. Preparing to unpack .../31-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 .../32-python3-pkg-resources_66.1.1-1_all.deb ... Unpacking python3-pkg-resources (66.1.1-1) ... Selecting previously unselected package python3-networkx. Preparing to unpack .../33-python3-networkx_2.8.8-1_all.deb ... Unpacking python3-networkx (2.8.8-1) ... Selecting previously unselected package pbjelly. Preparing to unpack .../34-pbjelly_15.8.24+dfsg-7_all.deb ... Unpacking pbjelly (15.8.24+dfsg-7) ... Selecting previously unselected package python3-pbbanana. Preparing to unpack .../35-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 .../36-python3-numpy_1%3a1.24.2-1_amd64.deb ... Unpacking python3-numpy (1:1.24.2-1) ... Selecting previously unselected package python3-h5py-serial. Preparing to unpack .../37-python3-h5py-serial_3.7.0-8_amd64.deb ... Unpacking python3-h5py-serial (3.7.0-8) ... Selecting previously unselected package python3-h5py. Preparing to unpack .../38-python3-h5py_3.7.0-8_all.deb ... Unpacking python3-h5py (3.7.0-8) ... Selecting previously unselected package python3-sortedcontainers. Preparing to unpack .../39-python3-sortedcontainers_2.4.0-2_all.deb ... Unpacking python3-sortedcontainers (2.4.0-2) ... Selecting previously unselected package python3-intervaltree. Preparing to unpack .../40-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 .../41-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 .../42-samtools_1.16.1-1_amd64.deb ... Unpacking samtools (1.16.1-1) ... Selecting previously unselected package pbhoney. Preparing to unpack .../43-pbhoney_15.8.24+dfsg-7_all.deb ... Unpacking pbhoney (15.8.24+dfsg-7) ... Selecting previously unselected package pbsuite. Preparing to unpack .../44-pbsuite_15.8.24+dfsg-7_all.deb ... Unpacking pbsuite (15.8.24+dfsg-7) ... Setting up libhtscodecs2:amd64 (1.3.0-4) ... Setting up media-types (10.0.0) ... Setting up libkeyutils1:amd64 (1.6.3-2) ... Setting up libpsl5:amd64 (0.21.2-1) ... Setting up libpbcopper2.0.0:amd64 (2.0.0+dfsg-2) ... Setting up libtirpc-common (1.3.3+ds-1) ... Setting up libbrotli1:amd64 (1.0.9-2+b6) ... Setting up libsqlite3-0:amd64 (3.40.1-2) ... Setting up libnghttp2-14:amd64 (1.52.0-1+deb12u1) ... Setting up libdeflate0:amd64 (1.14-1) ... Setting up libaec0:amd64 (1.0.6-1+b1) ... Setting up libkrb5support0:amd64 (1.20.1-2+deb12u1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Setting up libblas3:amd64 (3.11.0-2) ... 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+b2) ... Setting up libncurses6:amd64 (6.4-4) ... Setting up liblzf1:amd64 (3.6-3) ... Setting up libquadmath0:amd64 (12.2.0-14) ... Setting up libncursesw6:amd64 (6.4-4) ... Setting up libk5crypto3:amd64 (1.20.1-2+deb12u1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg-10) ... Setting up libgfortran5:amd64 (12.2.0-14) ... Setting up libssh2-1:amd64 (1.10.0-3+b1) ... Setting up libkrb5-3:amd64 (1.20.1-2+deb12u1) ... Setting up readline-common (8.2-1.3) ... Setting up libsz2:amd64 (1.0.6-1+b1) ... Setting up liblapack3:amd64 (3.11.0-2) ... 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 libreadline8:amd64 (8.2-1.3) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-2+deb12u1) ... Setting up libcurl4:amd64 (7.88.1-10+deb12u5) ... Setting up libtirpc3:amd64 (1.3.3+ds-1) ... Setting up libcurl3-gnutls:amd64 (7.88.1-10+deb12u5) ... Setting up libhdf5-103-1:amd64 (1.10.8+repack1-1) ... Setting up libnsl2:amd64 (1.3.0-2) ... Setting up libhdf5-cpp-103-1:amd64 (1.10.8+repack1-1) ... Setting up libhdf5-hl-100:amd64 (1.10.8+repack1-1) ... Setting up libhts3:amd64 (1.16+ds-3) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6) ... Setting up samtools (1.16.1-1) ... Setting up libpbbam2.1.0:amd64 (2.1.0+dfsg-2) ... Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6) ... Setting up python3 (3.11.2-1+b1) ... Setting up python3-sortedcontainers (2.4.0-2) ... Setting up libblasr5.3.5:amd64 (5.3.5+dfsg-4+b2) ... Setting up libpbseq:amd64 (5.3.5+dfsg-4+b2) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-pysam (0.20.0+ds-3+b1) ... Setting up python3-intervaltree (3.0.2-1.1) ... Setting up python3-pbsuite-utils (15.8.24+dfsg-7) ... Setting up blasr (5.3.5+dfsg-6) ... Setting up python3-networkx (2.8.8-1) ... Setting up python3-numpy (1:1.24.2-1) ... Setting up python3-intervaltree-bio (1.0.1-4) ... Setting up pbjelly (15.8.24+dfsg-7) ... Setting up python3-h5py-serial (3.7.0-8) ... Setting up python3-pbbanana (15.8.24+dfsg-7) ... Setting up python3-h5py (3.7.0-8) ... Setting up pbhoney (15.8.24+dfsg-7) ... Setting up pbsuite (15.8.24+dfsg-7) ... Processing triggers for libc-bin (2.36-9+deb12u4) ... 0m24.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', '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/tmp_3qca00p', 'tmp/scripts/post_install_exceptions'] 0m24.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/post_install_exceptions'] 0m24.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', '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/tmp_3qca00p', 'tmp/scripts/post_install_log_alternatives'] 0m24.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_3qca00p'] 0m25.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_3qca00p'] 0m26.9s DEBUG: No broken symlinks as far as we can find. 0m26.9s INFO: /bin converted to /usr/bin by /usr merge 0m26.9s INFO: /lib converted to /usr/lib by /usr merge 0m26.9s INFO: /lib/init converted to /usr/lib/init by /usr merge 0m26.9s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 0m26.9s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 0m26.9s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 0m26.9s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 0m26.9s INFO: /lib/terminfo converted to /usr/lib/terminfo by /usr merge 0m26.9s INFO: /lib/terminfo/E converted to /usr/lib/terminfo/E by /usr merge 0m26.9s INFO: /lib/terminfo/a converted to /usr/lib/terminfo/a by /usr merge 0m26.9s INFO: /lib/terminfo/c converted to /usr/lib/terminfo/c by /usr merge 0m26.9s INFO: /lib/terminfo/d converted to /usr/lib/terminfo/d by /usr merge 0m26.9s INFO: /lib/terminfo/h converted to /usr/lib/terminfo/h by /usr merge 0m26.9s INFO: /lib/terminfo/l converted to /usr/lib/terminfo/l by /usr merge 0m26.9s INFO: /lib/terminfo/m converted to /usr/lib/terminfo/m by /usr merge 0m26.9s INFO: /lib/terminfo/p converted to /usr/lib/terminfo/p by /usr merge 0m26.9s INFO: /lib/terminfo/r converted to /usr/lib/terminfo/r by /usr merge 0m26.9s INFO: /lib/terminfo/s converted to /usr/lib/terminfo/s by /usr merge 0m26.9s INFO: /lib/terminfo/t converted to /usr/lib/terminfo/t by /usr merge 0m26.9s INFO: /lib/terminfo/v converted to /usr/lib/terminfo/v by /usr merge 0m26.9s INFO: /lib/terminfo/w converted to /usr/lib/terminfo/w by /usr merge 0m26.9s INFO: /lib/terminfo/x converted to /usr/lib/terminfo/x by /usr merge 0m26.9s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 0m26.9s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 0m26.9s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 0m26.9s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 0m26.9s INFO: /lib64 converted to /usr/lib64 by /usr merge 0m26.9s INFO: /sbin converted to /usr/sbin by /usr merge 0m27.6s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', '-ac', '--ignore-obsolete'] 0m29.1s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', '-ac', '--ignore-obsolete'] 0m29.1s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m29.1s DUMP: 0.15.6 0m29.1s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m29.1s INFO: Running adequate version 0.15.6 now. 0m29.1s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'pbsuite'] 0m29.2s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'pbsuite'] 0m29.2s INFO: Running scripts pre_remove 0m29.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m29.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m29.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m29.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m29.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m31.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m31.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m31.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m31.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m31.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m31.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/pre_remove_exceptions'] 0m31.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/pre_remove_exceptions'] 0m31.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m31.5s DUMP: install ok installed adduser adduser 3.134 install ok installed apt apt 2.6.1 install ok installed base-files base-files 12.4+deb12u5 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b2 install ok installed blasr blasr 5.3.5+dfsg-6 install ok installed bsdutils bsdutils 1:2.38.1-5+b1 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.12-2 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.3+deb12u1 install ok installed debianutils debianutils 5.7-0.5~deb12u1 install ok installed diffutils diffutils 1:3.8-4 install ok installed dpkg dpkg 1.21.22 install ok installed e2fsprogs e2fsprogs 1.47.0-2 install ok installed findutils findutils 4.9.0-4 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-14 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.8-5 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu1 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libaec0:amd64 libaec0 1.0.6-1+b1 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.6.1 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.0.9-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.9-1 install ok installed libblas3:amd64 libblas3 3.11.0-2 install ok installed libblasr5.3.5:amd64 libblasr5.3.5 5.3.5+dfsg-4+b2 install ok installed libblkid1:amd64 libblkid1 2.38.1-5+b1 install ok installed libbrotli1:amd64 libbrotli1 1.0.9-2+b6 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-9+deb12u4 install ok installed libc6:amd64 libc6 2.36-9+deb12u4 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3 install ok installed libcap2:amd64 libcap2 1:2.66-4 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.33-2 install ok installed libcurl3-gnutls:amd64 libcurl3-gnutls 7.88.1-10+deb12u5 install ok installed libcurl4:amd64 libcurl4 7.88.1-10+deb12u5 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.270 install ok installed libdeflate0:amd64 libdeflate0 1.14-1 install ok installed libexpat1:amd64 libexpat1 2.5.0-1 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-14 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-3 install ok installed libgfortran5:amd64 libgfortran5 12.2.0-14 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.9-2+deb12u2 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.20.1-2+deb12u1 install ok installed libhdf5-103-1:amd64 libhdf5-103-1 1.10.8+repack1-1 install ok installed libhdf5-cpp-103-1:amd64 libhdf5-cpp-103-1 1.10.8+repack1-1 install ok installed libhdf5-hl-100:amd64 libhdf5-hl-100 1.10.8+repack1-1 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libhts3:amd64 libhts3 1.16+ds-3 install ok installed libhtscodecs2:amd64 libhtscodecs2 1.3.0-4 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed libk5crypto3:amd64 libk5crypto3 1.20.1-2+deb12u1 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.20.1-2+deb12u1 install ok installed libkrb5support0:amd64 libkrb5support0 1.20.1-2+deb12u1 install ok installed liblapack3:amd64 liblapack3 3.11.0-2 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.13+dfsg-5 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzf1:amd64 liblzf1 3.6-3 install ok installed liblzma5:amd64 liblzma5 5.4.1-0.2 install ok installed libmd0:amd64 libmd0 1.0.4-2 install ok installed libmount1:amd64 libmount1 2.38.1-5+b1 install ok installed libncurses6:amd64 libncurses6 6.4-4 install ok installed libncursesw6:amd64 libncursesw6 6.4-4 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.52.0-1+deb12u1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-6+deb12u1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-6+deb12u1 install ok installed libpam-runtime libpam-runtime 1.5.2-6+deb12u1 install ok installed libpam0g:amd64 libpam0g 1.5.2-6+deb12u1 install ok installed libpbbam2.1.0:amd64 libpbbam2.1.0 2.1.0+dfsg-2 install ok installed libpbcopper2.0.0:amd64 libpbcopper2.0.0 2.0.0+dfsg-2 install ok installed libpbseq:amd64 libpbseq 5.3.5+dfsg-4+b2 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-1 install ok installed libpsl5:amd64 libpsl5 0.21.2-1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.11.2-1+b1 install ok installed libpython3.11-minimal:amd64 libpython3.11-minimal 3.11.2-6 install ok installed libpython3.11-stdlib:amd64 libpython3.11-stdlib 3.11.2-6 install ok installed libquadmath0:amd64 libquadmath0 12.2.0-14 install ok installed libreadline8:amd64 libreadline8 8.2-1.3 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b2 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg-10 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg-10 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+b3 install ok installed libselinux1:amd64 libselinux1 3.4-1+b6 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b5 install ok installed libsepol2:amd64 libsepol2 3.4-2.1 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-5+b1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.40.1-2 install ok installed libss2:amd64 libss2 1.47.0-2 install ok installed libssh2-1:amd64 libssh2-1 1.10.0-3+b1 install ok installed libssl3:amd64 libssl3 3.0.11-1~deb12u2 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-14 install ok installed libsystemd0:amd64 libsystemd0 252.22-1~deb12u1 install ok installed libsz2:amd64 libsz2 1.0.6-1+b1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.4-4 install ok installed libtirpc-common libtirpc-common 1.3.3+ds-1 install ok installed libtirpc3:amd64 libtirpc3 1.3.3+ds-1 install ok installed libudev1:amd64 libudev1 252.22-1~deb12u1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+b1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.4+dfsg2-5 install ok installed login login 1:4.13+dfsg1-1+b1 install ok installed logsave logsave 1.47.0-2 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed media-types media-types 10.0.0 install ok installed mount mount 2.38.1-5+b1 install ok installed ncurses-base ncurses-base 6.4-4 install ok installed ncurses-bin ncurses-bin 6.4-4 install ok installed passwd passwd 1:4.13+dfsg1-1+b1 install ok installed 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 5.36.0-7+deb12u1 install ok installed python3 python3 3.11.2-1+b1 install ok installed python3-h5py python3-h5py 3.7.0-8 install ok installed python3-h5py-serial python3-h5py-serial 3.7.0-8 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 3.11.2-1+b1 install ok installed python3-networkx python3-networkx 2.8.8-1 install ok installed python3-numpy python3-numpy 1:1.24.2-1 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 66.1.1-1 install ok installed python3-pysam python3-pysam 0.20.0+ds-3+b1 install ok installed python3-sortedcontainers python3-sortedcontainers 2.4.0-2 install ok installed python3.11 python3.11 3.11.2-6 install ok installed python3.11-minimal python3.11-minimal 3.11.2-6 install ok installed readline-common readline-common 8.2-1.3 install ok installed samtools samtools 1.16.1-1 install ok installed sed sed 4.9-1 install ok installed sysvinit-utils sysvinit-utils 3.06-4 install ok installed tar tar 1.34+dfsg-1.2+deb12u1 install ok installed tzdata tzdata 2024a-0+deb12u1 install ok installed usr-is-merged usr-is-merged 37~deb12u1 install ok installed util-linux util-linux 2.38.1-5+b1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+b1 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m31.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m31.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'apt-get', 'remove', 'blasr', 'libaec0:amd64', 'libblas3:amd64', 'libblasr5.3.5:amd64', 'libbrotli1:amd64', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libgfortran5:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-103-1:amd64', 'libhdf5-cpp-103-1:amd64', 'libhdf5-hl-100:amd64', 'libhts3: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', 'libnsl2:amd64', 'libpbbam2.1.0:amd64', 'libpbcopper2.0.0:amd64', 'libpbseq:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl3:amd64', 'libsz2:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'media-types', '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', 'pbsuite'] 0m34.5s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: blasr libaec0 libblas3 libblasr5.3.5 libbrotli1 libcurl3-gnutls libcurl4 libdeflate0 libexpat1 libgfortran5 libgssapi-krb5-2 libhdf5-103-1 libhdf5-cpp-103-1 libhdf5-hl-100 libhts3 libhtscodecs2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 liblzf1 libncurses6 libncursesw6 libnghttp2-14 libnsl2 libpbbam2.1.0 libpbcopper2.0.0 libpbseq libpsl5 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libquadmath0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsqlite3-0 libssh2-1 libssl3 libsz2 libtirpc-common libtirpc3 media-types pbhoney pbjelly pbsuite 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, 66 to remove and 0 not upgraded. After this operation, 129 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 ... 9540 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) ... Removing libpbseq:amd64 (5.3.5+dfsg-4+b2) ... Removing libblasr5.3.5:amd64 (5.3.5+dfsg-4+b2) ... Removing python3-h5py (3.7.0-8) ... Removing python3-h5py-serial (3.7.0-8) ... Removing libhdf5-hl-100:amd64 (1.10.8+repack1-1) ... Removing python3-numpy (1:1.24.2-1) ... Removing liblapack3:amd64 (3.11.0-2) ... Removing libblas3:amd64 (3.11.0-2) ... Removing samtools (1.16.1-1) ... Removing python3-pbsuite-utils (15.8.24+dfsg-7) ... Removing python3-pysam (0.20.0+ds-3+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 (2.8.8-1) ... Removing python3-pkg-resources (66.1.1-1) ... Removing python3 (3.11.2-1+b1) ... Removing python3.11 (3.11.2-6) ... Removing python3-minimal (3.11.2-1+b1) ... Removing python3.11-minimal (3.11.2-6) ... Removing libexpat1:amd64 (2.5.0-1) ... Removing libgfortran5:amd64 (12.2.0-14) ... Removing libpython3-stdlib:amd64 (3.11.2-1+b1) ... Removing libpython3.11-stdlib:amd64 (3.11.2-6) ... find: '/usr/lib/python3': No such file or directory Removing libnsl2:amd64 (1.3.0-2) ... Removing libtirpc3:amd64 (1.3.3+ds-1) ... Removing libhdf5-cpp-103-1:amd64 (1.10.8+repack1-1) ... Removing liblzf1:amd64 (3.6-3) ... Removing libncurses6:amd64 (6.4-4) ... Removing libncursesw6:amd64 (6.4-4) ... Removing libpbbam2.1.0:amd64 (2.1.0+dfsg-2) ... Removing libpbcopper2.0.0:amd64 (2.0.0+dfsg-2) ... Removing libpython3.11-minimal:amd64 (3.11.2-6) ... find: '/usr/lib/python3': No such file or directory Removing libquadmath0:amd64 (12.2.0-14) ... Removing libreadline8:amd64 (8.2-1.3) ... Removing libsqlite3-0:amd64 (3.40.1-2) ... Removing libtirpc-common (1.3.3+ds-1) ... Removing media-types (10.0.0) ... Removing readline-common (8.2-1.3) ... Removing libhdf5-103-1:amd64 (1.10.8+repack1-1) ... Removing libsz2:amd64 (1.0.6-1+b1) ... Removing libaec0:amd64 (1.0.6-1+b1) ... Removing libcurl4:amd64 (7.88.1-10+deb12u5) ... Removing libhts3:amd64 (1.16+ds-3) ... Removing libcurl3-gnutls:amd64 (7.88.1-10+deb12u5) ... Removing libbrotli1:amd64 (1.0.9-2+b6) ... Removing libdeflate0:amd64 (1.14-1) ... Removing libgssapi-krb5-2:amd64 (1.20.1-2+deb12u1) ... Removing libhtscodecs2:amd64 (1.3.0-4) ... Removing libkrb5-3:amd64 (1.20.1-2+deb12u1) ... Removing libk5crypto3:amd64 (1.20.1-2+deb12u1) ... Removing libkeyutils1:amd64 (1.6.3-2) ... Removing libkrb5support0:amd64 (1.20.1-2+deb12u1) ... Removing libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Removing libnghttp2-14:amd64 (1.52.0-1+deb12u1) ... Removing libpsl5:amd64 (0.21.2-1) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Removing libsasl2-2:amd64 (2.1.28+dfsg-10) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Removing libssh2-1:amd64 (1.10.0-3+b1) ... Removing libssl3:amd64 (3.0.11-1~deb12u2) ... Processing triggers for libc-bin (2.36-9+deb12u4) ... 0m34.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'apt-get', 'remove', 'blasr', 'libaec0:amd64', 'libblas3:amd64', 'libblasr5.3.5:amd64', 'libbrotli1:amd64', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libgfortran5:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-103-1:amd64', 'libhdf5-cpp-103-1:amd64', 'libhdf5-hl-100:amd64', 'libhts3: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', 'libnsl2:amd64', 'libpbbam2.1.0:amd64', 'libpbcopper2.0.0:amd64', 'libpbseq:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl3:amd64', 'libsz2:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'media-types', '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', 'pbsuite'] 0m34.5s INFO: Running scripts post_remove 0m34.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/post_remove_exceptions'] 0m34.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/post_remove_exceptions'] 0m34.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'dpkg', '--purge', 'blasr', 'libaec0:amd64', 'libblas3:amd64', 'libblasr5.3.5:amd64', 'libbrotli1:amd64', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libgfortran5:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-103-1:amd64', 'libhdf5-cpp-103-1:amd64', 'libhdf5-hl-100:amd64', 'libhts3: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', 'libnsl2:amd64', 'libpbbam2.1.0:amd64', 'libpbcopper2.0.0:amd64', 'libpbseq:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl3:amd64', 'libsz2:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'media-types', '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'] 0m34.6s 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 libcurl3-gnutls which isn't installed dpkg: warning: ignoring request to remove libcurl4 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 ... 6106 files and directories currently installed.) Purging configuration files for libgssapi-krb5-2:amd64 (1.20.1-2+deb12u1) ... dpkg: warning: ignoring request to remove libhdf5-103-1 which isn't installed dpkg: warning: ignoring request to remove libhdf5-cpp-103-1 which isn't installed dpkg: warning: ignoring request to remove libhdf5-hl-100 which isn't installed dpkg: warning: ignoring request to remove libhts3 which isn't installed dpkg: warning: ignoring request to remove libhtscodecs2 which isn't installed dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove 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 libnsl2 which isn't installed dpkg: warning: ignoring request to remove libpbbam2.1.0 which isn't installed dpkg: warning: ignoring request to remove libpbcopper2.0.0 which isn't installed dpkg: warning: ignoring request to remove libpbseq which isn't installed dpkg: warning: ignoring request to remove libpsl5 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.11-minimal:amd64 (3.11.2-6) ... dpkg: warning: ignoring request to remove libpython3.11-stdlib which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed dpkg: warning: ignoring request to remove libreadline8 which isn't installed dpkg: warning: ignoring request to remove librtmp1 which isn't installed dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed dpkg: warning: ignoring request to remove libsasl2-modules-db which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libssh2-1 which isn't installed dpkg: warning: ignoring request to remove libssl3 which isn't installed dpkg: warning: ignoring request to remove libsz2 which isn't installed Purging configuration files for libtirpc-common (1.3.3+ds-1) ... dpkg: warning: ignoring request to remove libtirpc3 which isn't installed Purging configuration files for media-types (10.0.0) ... 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 (3.11.2-1+b1) ... 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 (3.11.2-6) ... Purging configuration files for readline-common (8.2-1.3) ... dpkg: warning: ignoring request to remove samtools which isn't installed 0m34.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'dpkg', '--purge', 'blasr', 'libaec0:amd64', 'libblas3:amd64', 'libblasr5.3.5:amd64', 'libbrotli1:amd64', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libgfortran5:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-103-1:amd64', 'libhdf5-cpp-103-1:amd64', 'libhdf5-hl-100:amd64', 'libhts3: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', 'libnsl2:amd64', 'libpbbam2.1.0:amd64', 'libpbcopper2.0.0:amd64', 'libpbseq:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl3:amd64', 'libsz2:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'media-types', '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'] 0m34.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'dpkg', '--purge', 'pbsuite'] 0m34.6s DUMP: dpkg: warning: ignoring request to remove pbsuite which isn't installed 0m34.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'dpkg', '--purge', 'pbsuite'] 0m34.6s INFO: Running scripts post_purge 0m34.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/post_purge_exceptions'] 0m34.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/post_purge_exceptions'] 0m34.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'dpkg', '--purge', '--pending'] 0m34.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'dpkg', '--purge', '--pending'] 0m34.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'dpkg', '--remove', '--pending'] 0m34.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'dpkg', '--remove', '--pending'] 0m34.6s INFO: Running scripts post_test 0m34.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/post_test_exceptions'] 0m34.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'tmp/scripts/post_test_exceptions'] 0m34.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_3qca00p'] 0m35.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp_3qca00p'] 0m35.9s DEBUG: No broken symlinks as far as we can find. 0m35.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'dpkg-divert', '--list'] 0m35.9s DUMP: local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m35.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'dpkg-divert', '--list'] 0m35.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'apt-get', 'clean'] 0m36.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp_3qca00p', 'apt-get', 'clean'] 0m36.0s DEBUG: Recording chroot state 0m36.7s INFO: PASS: Installation and purging test. 0m37.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp_3qca00p/dev/shm'] 0m37.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp_3qca00p/dev/shm'] 0m37.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp_3qca00p/dev/console'] 0m37.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp_3qca00p/dev/console'] 0m37.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp_3qca00p/dev/ptmx'] 0m37.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp_3qca00p/dev/ptmx'] 0m37.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp_3qca00p/dev/pts'] 0m37.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp_3qca00p/dev/pts'] 0m37.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp_3qca00p/proc'] 0m37.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp_3qca00p/proc'] 0m37.2s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp_3qca00p'] 0m37.4s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp_3qca00p'] 0m37.4s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp_3qca00p 0m37.4s INFO: PASS: All tests. 0m37.4s INFO: piuparts run ends. ret=0 End: 2024-04-05 11:02:52 GMT