Start: 2024-04-22 09:57:47 GMT Package: python3-mdanalysis Source: mdanalysis (2.5.0+dfsg1-2) Version: 2.5.0+dfsg1-2+b1 Installed-Size: 19723 Maintainer: Debichem Team Architecture: amd64 Depends: python3-duecredit, python3 (<< 3.13), python3 (>= 3.11~), python3-biopython (>= 1.80), python3-fasteners, python3-griddataformats (>= 0.4.0), python3-gsd (>= 3.0.1~), python3-joblib (>= 0.12), python3-matplotlib (>= 1.5.1), python3-mmtf (>= 1.0.0), python3-networkx (>= 2.0), python3-numpy (>= 1:1.22.0), python3-numpy-abi9, python3-packaging, python3-scipy (>= 1.5.0), python3-threadpoolctl, python3-tqdm (>= 4.43.0), python3:any, libc6 (>= 2.14), libgcc-s1 (>= 3.0), libgomp1 (>= 4.9), libstdc++6 (>= 11) Recommends: python3-sklearn Suggests: python-mdanalysis-doc Description: analyse molecular dynamics files and trajectories Homepage: https://www.mdanalysis.org/ Description-md5: 9d4e18df399b20b80dcfdf83cc426a35 Section: python Priority: optional Filename: pool/main/m/mdanalysis/python3-mdanalysis_2.5.0+dfsg1-2+b1_amd64.deb Size: 2122164 MD5sum: 7441ce232cd720578d71f50f41a737b1 SHA256: e685959a5379cf99f1898b8c9cc3eef314afdf254be7072c3662cd75801132eb 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 python3-mdanalysis=2.5.0+dfsg1-2+b1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.4.1~202403190841~1.4-4-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 --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 python3-mdanalysis=2.5.0+dfsg1-2+b1 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmp1tq868yb 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp1tq868yb 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/sid-merged-usr_amd64.tar.gz'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp1tq868yb/proc'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp1tq868yb/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/tmp1tq868yb/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/tmp1tq868yb/dev/pts'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp1tq868yb/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp1tq868yb/dev/ptmx'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp1tq868yb/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp1tq868yb/dev/ptmx'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmp1tq868yb/dev/console'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmp1tq868yb/dev/console'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp1tq868yb/dev/shm'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp1tq868yb/dev/shm'] 0m0.4s 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/tmp1tq868yb/tmp/scripts/ 0m0.4s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp1tq868yb/tmp/scripts/ 0m0.5s INFO: Running scripts post_chroot_unpack 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'apt-get', 'update'] 0m2.0s DUMP: Hit:1 http://deb.debian.org/debian sid InRelease Reading package lists... 0m2.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'apt-get', 'update'] 0m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'apt-get', '-yf', 'dist-upgrade'] 0m2.7s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'apt-get', '-yf', 'dist-upgrade'] 0m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.1s DUMP: 326294950d4f9e9db2fc810016405133 - 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.1s INFO: Running scripts post_setup 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/post_setup_dummy_users'] 0m4.2s 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 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/post_setup_dummy_users'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/post_setup_forbid_home'] 0m4.3s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/post_setup_forbid_home'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.3s 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' 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/post_setup_minimize'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/post_setup_minimize'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/post_setup_zz_backports'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/post_setup_zz_backports'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'apt-get', 'clean'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'apt-get', 'clean'] 0m4.4s DEBUG: Recording chroot state 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.9s DUMP: install ok installed apt apt 2.9.1 install ok installed base-files base-files 13.1 install ok installed base-passwd base-passwd 3.6.3 install ok installed bash bash 5.2.21-2 install ok installed bsdutils bsdutils 1:2.40-6 install ok installed coreutils coreutils 9.4-3.1 install ok installed dash dash 0.5.12-6 install ok installed debconf debconf 1.5.86 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.17 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.6 install ok installed e2fsprogs e2fsprogs 1.47.0-2.4 install ok installed findutils findutils 4.9.0-5 install ok installed gcc-14-base:amd64 gcc-14-base 14-20240330-1 install ok installed gpgv gpgv 2.2.40-3 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.23+nmu2 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed libacl1:amd64 libacl1 2.3.2-1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.1 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:3.1.2-2.1 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-2.1 install ok installed libblkid1:amd64 libblkid1 2.40-6 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5.1 install ok installed libc-bin libc-bin 2.37-18 install ok installed libc6:amd64 libc6 2.37-18 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-1 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2.4 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-4 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-7 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.271+b3 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.0-2.4 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14-20240330-1 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.3-2 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.5-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.47-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.9.1-2.2 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-2 install ok installed liblzma5:amd64 liblzma5 5.6.1+really5.4.5-1 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.40-6 install ok installed libnettle8t64:amd64 libnettle8t64 3.9.1-2.2 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.3-4 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7 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 install ok installed libselinux1:amd64 libselinux1 3.5-2+b2 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b3 install ok installed libsepol2:amd64 libsepol2 3.5-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.40-6 install ok installed libss2:amd64 libss2 1.47.0-2.4 install ok installed libssl3t64:amd64 libssl3t64 3.2.1-3 install ok installed libstdc++6:amd64 libstdc++6 14-20240330-1 install ok installed libsystemd0:amd64 libsystemd0 255.4-1+b1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtinfo6:amd64 libtinfo6 6.4+20240414-1 install ok installed libudev1:amd64 libudev1 255.4-1+b1 install ok installed libunistring5:amd64 libunistring5 1.2-1 install ok installed libuuid1:amd64 libuuid1 2.40-6 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-2 install ok installed login login 1:4.13+dfsg1-4 install ok installed logsave logsave 1.47.0-2.4 install ok installed mawk mawk 1.3.4.20240123-1 install ok installed mount mount 2.40-6 install ok installed ncurses-base ncurses-base 6.4+20240414-1 install ok installed ncurses-bin ncurses-bin 6.4+20240414-1 install ok installed passwd passwd 1:4.13+dfsg1-4 install ok installed perl-base perl-base 5.38.2-3.2+b2 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.09-1 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024a-3 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40-6 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg-3.1 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'dpkg-divert', '--list'] 0m4.9s DUMP: diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64 local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64 local diversion of /home to /home.distrib diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64 diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64 local diversion of /usr/bin/sync to /usr/bin/sync.distrib 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'dpkg-divert', '--list'] 0m4.9s INFO: Running scripts is_testable 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/is_testable_uninstallable'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/is_testable_uninstallable'] 0m4.9s INFO: apt-cache does not know about any of the requested packages 0m4.9s INFO: Running scripts pre_test 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/pre_test_exceptions'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/pre_test_exceptions'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/pre_test_root_password'] 0m4.9s DUMP: New password: Retype new password: passwd: password updated successfully 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/pre_test_root_password'] 0m4.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1tq868yb'] 0m5.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1tq868yb'] 0m5.7s DEBUG: No broken symlinks as far as we can find. 0m5.7s INFO: Running scripts pre_install 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/pre_install_database-server'] 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/pre_install_database-server'] 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/pre_install_exceptions'] 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/pre_install_exceptions'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/pre_install_extras'] 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/pre_install_extras'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/pre_install_log_alternatives'] 0m5.8s 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 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/pre_install_log_alternatives'] 0m5.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1tq868yb'] 0m6.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1tq868yb'] 0m6.5s DEBUG: No broken symlinks as far as we can find. 0m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'apt-cache', 'policy'] 0m7.5s 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: 0m7.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'apt-cache', 'policy'] 0m7.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'apt-cache', 'policy', 'python3-mdanalysis'] 0m7.6s DUMP: python3-mdanalysis: Installed: (none) Candidate: 2.5.0+dfsg1-2+b1 Version table: 2.5.0+dfsg1-2+b1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 0m7.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'apt-cache', 'policy', 'python3-mdanalysis'] 0m7.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'apt-get', '-y', 'install', 'python3-mdanalysis=2.5.0+dfsg1-2+b1'] 1m59.3s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: blt ca-certificates fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome fonts-lato fonts-lyx fonts-urw-base35 libblas3 libbrotli1 libbsd0 libcairo2 libdeflate0 libexpat1 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0t64 libgomp1 libgraphite2-3 libharfbuzz0b libicu72 libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libncursesw6 libopenjp2-7 libpixman-1-0 libpng16-16t64 libproc2-0 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libqhull-r8.0 libraqm0 libreadline8t64 libsharpyuv0 libsqlite3-0 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxslt1.1 libxss1 media-types netbase openssl procps python-matplotlib-data python3 python3-appdirs python3-attr python3-biopython python3-brotli python3-cairo python3-certifi python3-chardet python3-charset-normalizer python3-citeproc python3-contourpy python3-cycler python3-dateutil python3-decorator python3-duecredit python3-fasteners python3-fonttools python3-freetype python3-fs python3-griddataformats python3-gsd python3-idna python3-joblib python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib python3-minimal python3-mmtf python3-monotonic python3-mpmath python3-mrcfile python3-msgpack python3-networkx python3-numpy python3-packaging python3-pil python3-pil.imagetk python3-pkg-resources python3-pyparsing python3-reportlab python3-requests python3-rlpycairo python3-scipy python3-six python3-sympy python3-threadpoolctl python3-tk python3-tqdm python3-tz python3-ufolib2 python3-unicodedata2 python3-urllib3 python3.11 python3.11-minimal readline-common sgml-base sphinx-rtd-theme-common tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core Suggested packages: blt-demo fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre low-memory-monitor libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 python3-doc python3-venv python-attr-doc bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons python3-mysqldb python3-rdflib python3-psycopg2 raxml samtools t-coffee wise python-charset-normalizer-doc python-cycler-doc python-gsd-doc python-lxml-doc cm-super-minimal dvipng ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common python3-cairocffi python3-gi python3-gi-cairo python3-gobject python3-pyqt5 python3-sip python3-tornado texlive-extra-utils texlive-latex-extra python-mdanalysis-doc python-mpmath-doc python3-gmpy2 gcc gfortran python3-dev python3-pytest python-pil-doc python3-setuptools python-pyparsing-doc pdf-viewer python3-egenix-mxtexttools python-reportlab-doc rl-accel rl-renderpm python3-cryptography python3-openssl python3-socks python-requests-doc python-scipy-doc texlive-fonts-extra python-sympy-doc tix python3-tk-dbg python3.11-venv python3.11-doc binutils binfmt-support readline-doc sgml-base-doc debhelper Recommended packages: libglib2.0-data shared-mime-info xdg-user-dirs javascript-common libgpm2 psmisc python-biopython-doc ncbi-blast+ python3-pytest python3-simplejson python3-psutil python3-bs4 python3-cssselect python3-html5lib python3-sklearn python3-gdal python3-pydot python3-pygraphviz python3-yaml python3-olefile fonts-dejavu-extra g++ | c++-compiler isympy-common The following NEW packages will be installed: blt ca-certificates fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome fonts-lato fonts-lyx fonts-urw-base35 libblas3 libbrotli1 libbsd0 libcairo2 libdeflate0 libexpat1 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0t64 libgomp1 libgraphite2-3 libharfbuzz0b libicu72 libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libncursesw6 libopenjp2-7 libpixman-1-0 libpng16-16t64 libproc2-0 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libqhull-r8.0 libraqm0 libreadline8t64 libsharpyuv0 libsqlite3-0 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxslt1.1 libxss1 media-types netbase openssl procps python-matplotlib-data python3 python3-appdirs python3-attr python3-biopython python3-brotli python3-cairo python3-certifi python3-chardet python3-charset-normalizer python3-citeproc python3-contourpy python3-cycler python3-dateutil python3-decorator python3-duecredit python3-fasteners python3-fonttools python3-freetype python3-fs python3-griddataformats python3-gsd python3-idna python3-joblib python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib python3-mdanalysis python3-minimal python3-mmtf python3-monotonic python3-mpmath python3-mrcfile python3-msgpack python3-networkx python3-numpy python3-packaging python3-pil python3-pil.imagetk python3-pkg-resources python3-pyparsing python3-reportlab python3-requests python3-rlpycairo python3-scipy python3-six python3-sympy python3-threadpoolctl python3-tk python3-tqdm python3-tz python3-ufolib2 python3-unicodedata2 python3-urllib3 python3.11 python3.11-minimal readline-common sgml-base sphinx-rtd-theme-common tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 0 upgraded, 139 newly installed, 0 to remove and 0 not upgraded. Need to get 119 MB of archives. After this operation, 491 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 fonts-lato all 2.015-1 [2780 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.6.2-1 [103 kB] Get:4 http://deb.debian.org/debian sid/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get:5 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.11.8-1 [26.3 kB] Get:6 http://deb.debian.org/debian sid/main amd64 media-types all 10.1.0 [26.9 kB] Get:7 http://deb.debian.org/debian sid/main amd64 netbase all 6.4 [12.8 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libncursesw6 amd64 6.4+20240414-1 [135 kB] Get:9 http://deb.debian.org/debian sid/main amd64 readline-common all 8.2-4 [69.3 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libreadline8t64 amd64 8.2-4 [167 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libsqlite3-0 amd64 3.45.3-1 [896 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get:13 http://deb.debian.org/debian sid/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.11.8-1 [9332 B] Get:15 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.11.8-1 [27.4 kB] Get:16 http://deb.debian.org/debian sid/main amd64 sgml-base all 1.31 [15.4 kB] Get:17 http://deb.debian.org/debian sid/main amd64 libproc2-0 amd64 2:4.0.4-4 [64.6 kB] Get:18 http://deb.debian.org/debian sid/main amd64 procps amd64 2:4.0.4-4 [880 kB] Get:19 http://deb.debian.org/debian sid/main amd64 openssl amd64 3.2.1-3 [1360 kB] Get:20 http://deb.debian.org/debian sid/main amd64 ca-certificates all 20240203 [158 kB] Get:21 http://deb.debian.org/debian sid/main amd64 libtcl8.6 amd64 8.6.14+dfsg-1 [1034 kB] Get:22 http://deb.debian.org/debian sid/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get:23 http://deb.debian.org/debian sid/main amd64 libpng16-16t64 amd64 1.6.43-5 [278 kB] Get:24 http://deb.debian.org/debian sid/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b4 [439 kB] Get:25 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:26 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:27 http://deb.debian.org/debian sid/main amd64 libfontenc1 amd64 1:1.1.8-1 [23.0 kB] Get:28 http://deb.debian.org/debian sid/main amd64 x11-common all 1:7.7+23 [252 kB] Get:29 http://deb.debian.org/debian sid/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get:30 http://deb.debian.org/debian sid/main amd64 xfonts-utils amd64 1:7.7+6 [93.0 kB] Get:31 http://deb.debian.org/debian sid/main amd64 fonts-urw-base35 all 20200910-8 [10.8 MB] Get:32 http://deb.debian.org/debian sid/main amd64 fontconfig-config amd64 2.15.0-1.1 [317 kB] Get:33 http://deb.debian.org/debian sid/main amd64 libfontconfig1 amd64 2.15.0-1.1 [388 kB] Get:34 http://deb.debian.org/debian sid/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get:35 http://deb.debian.org/debian sid/main amd64 libbsd0 amd64 0.12.2-1 [131 kB] Get:36 http://deb.debian.org/debian sid/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:37 http://deb.debian.org/debian sid/main amd64 libxcb1 amd64 1.17.0-1 [144 kB] Get:38 http://deb.debian.org/debian sid/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get:39 http://deb.debian.org/debian sid/main amd64 libx11-6 amd64 2:1.8.7-1 [802 kB] Get:40 http://deb.debian.org/debian sid/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get:41 http://deb.debian.org/debian sid/main amd64 libxft2 amd64 2.3.6-1+b1 [54.2 kB] Get:42 http://deb.debian.org/debian sid/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get:43 http://deb.debian.org/debian sid/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get:44 http://deb.debian.org/debian sid/main amd64 libtk8.6 amd64 8.6.14-1 [784 kB] Get:45 http://deb.debian.org/debian sid/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7 [586 kB] Get:46 http://deb.debian.org/debian sid/main amd64 blt amd64 2.5.3+dfsg-7 [6024 B] Get:47 http://deb.debian.org/debian sid/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get:48 http://deb.debian.org/debian sid/main amd64 fonts-lyx all 2.4.0~RC4-1 [189 kB] Get:49 http://deb.debian.org/debian sid/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get:50 http://deb.debian.org/debian sid/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get:51 http://deb.debian.org/debian sid/main amd64 libxcb-render0 amd64 1.17.0-1 [114 kB] Get:52 http://deb.debian.org/debian sid/main amd64 libxcb-shm0 amd64 1.17.0-1 [105 kB] Get:53 http://deb.debian.org/debian sid/main amd64 libcairo2 amd64 1.18.0-3+b1 [531 kB] Get:54 http://deb.debian.org/debian sid/main amd64 libdeflate0 amd64 1.20-1 [46.0 kB] Get:55 http://deb.debian.org/debian sid/main amd64 libfribidi0 amd64 1.0.13-3+b1 [71.4 kB] Get:56 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14-20240330-1 [836 kB] Get:57 http://deb.debian.org/debian sid/main amd64 libglib2.0-0t64 amd64 2.78.4-6 [1222 kB] Get:58 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14-20240330-1 [136 kB] Get:59 http://deb.debian.org/debian sid/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get:60 http://deb.debian.org/debian sid/main amd64 libharfbuzz0b amd64 8.3.0-2+b1 [2214 kB] Get:61 http://deb.debian.org/debian sid/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get:62 http://deb.debian.org/debian sid/main amd64 libimagequant0 amd64 2.18.0-1 [35.0 kB] Get:63 http://deb.debian.org/debian sid/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get:64 http://deb.debian.org/debian sid/main amd64 libjpeg62-turbo amd64 1:2.1.5-2+b2 [167 kB] Get:65 http://deb.debian.org/debian sid/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:66 http://deb.debian.org/debian sid/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get:67 http://deb.debian.org/debian sid/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get:68 http://deb.debian.org/debian sid/main amd64 libjs-sphinxdoc all 7.2.6-6 [150 kB] Get:69 http://deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get:70 http://deb.debian.org/debian sid/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b1 [29.1 kB] Get:71 http://deb.debian.org/debian sid/main amd64 liblcms2-2 amd64 2.14-2+b1 [154 kB] Get:72 http://deb.debian.org/debian sid/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get:73 http://deb.debian.org/debian sid/main amd64 libopenjp2-7 amd64 2.5.0-2+b3 [190 kB] Get:74 http://deb.debian.org/debian sid/main amd64 libqhull-r8.0 amd64 2020.2-6+b1 [245 kB] Get:75 http://deb.debian.org/debian sid/main amd64 libraqm0 amd64 0.10.1-1+b1 [14.2 kB] Get:76 http://deb.debian.org/debian sid/main amd64 libsharpyuv0 amd64 1.3.2-0.4+b1 [108 kB] Get:77 http://deb.debian.org/debian sid/main amd64 libwebp7 amd64 1.3.2-0.4+b1 [308 kB] Get:78 http://deb.debian.org/debian sid/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB] Get:79 http://deb.debian.org/debian sid/main amd64 libwebpdemux2 amd64 1.3.2-0.4+b1 [107 kB] Get:80 http://deb.debian.org/debian sid/main amd64 libwebpmux3 amd64 1.3.2-0.4+b1 [120 kB] Get:81 http://deb.debian.org/debian sid/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b2 [692 kB] Get:82 http://deb.debian.org/debian sid/main amd64 libxslt1.1 amd64 1.1.35-1 [242 kB] Get:83 http://deb.debian.org/debian sid/main amd64 python-matplotlib-data all 3.6.3-1.1 [2743 kB] Get:84 http://deb.debian.org/debian sid/main amd64 python3-appdirs all 1.4.4-4 [12.5 kB] Get:85 http://deb.debian.org/debian sid/main amd64 python3-attr all 23.2.0-2 [65.5 kB] Get:86 http://deb.debian.org/debian sid/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get:87 http://deb.debian.org/debian sid/main amd64 python3-numpy amd64 1:1.26.4+ds-6 [5472 kB] Get:88 http://deb.debian.org/debian sid/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get:89 http://deb.debian.org/debian sid/main amd64 python3-tk amd64 3.12.3-1 [109 kB] Get:90 http://deb.debian.org/debian sid/main amd64 python3-pil.imagetk amd64 10.3.0-2 [79.5 kB] Get:91 http://deb.debian.org/debian sid/main amd64 python3-pil amd64 10.3.0-2 [564 kB] Get:92 http://deb.debian.org/debian sid/main amd64 python3-cairo amd64 1.26.0-1 [142 kB] Get:93 http://deb.debian.org/debian sid/main amd64 python3-freetype all 2.4.0-1 [80.3 kB] Get:94 http://deb.debian.org/debian sid/main amd64 python3-rlpycairo all 0.3.0-3 [9904 B] Get:95 http://deb.debian.org/debian sid/main amd64 python3-reportlab all 4.2.0-1 [1149 kB] Get:96 http://deb.debian.org/debian sid/main amd64 xml-core all 0.19 [20.1 kB] Get:97 http://deb.debian.org/debian sid/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get:98 http://deb.debian.org/debian sid/main amd64 python3-biopython amd64 1.83+dfsg1-2 [1634 kB] Get:99 http://deb.debian.org/debian sid/main amd64 python3-brotli amd64 1.1.0-2+b3 [312 kB] Get:100 http://deb.debian.org/debian sid/main amd64 python3-certifi all 2023.11.17-1 [155 kB] Get:101 http://deb.debian.org/debian sid/main amd64 python3-charset-normalizer all 3.3.2-1 [51.6 kB] Get:102 http://deb.debian.org/debian sid/main amd64 python3-lxml amd64 5.2.1-1 [1995 kB] Get:103 http://deb.debian.org/debian sid/main amd64 python3-citeproc all 0.6.0-3 [96.7 kB] Get:104 http://deb.debian.org/debian sid/main amd64 python3-contourpy amd64 1.0.7-3 [285 kB] Get:105 http://deb.debian.org/debian sid/main amd64 python3-cycler all 0.12.1-1 [9496 B] Get:106 http://deb.debian.org/debian sid/main amd64 python3-six all 1.16.0-6 [16.3 kB] Get:107 http://deb.debian.org/debian sid/main amd64 python3-dateutil all 2.9.0-2 [79.4 kB] Get:108 http://deb.debian.org/debian sid/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get:109 http://deb.debian.org/debian sid/main amd64 python3-idna all 3.6-2 [37.0 kB] Get:110 http://deb.debian.org/debian sid/main amd64 python3-urllib3 all 1.26.18-2 [116 kB] Get:111 http://deb.debian.org/debian sid/main amd64 python3-requests all 2.31.0+dfsg-1 [68.6 kB] Get:112 http://deb.debian.org/debian sid/main amd64 python3-duecredit all 0.9.1-1.1 [66.7 kB] Get:113 http://deb.debian.org/debian sid/main amd64 python3-monotonic all 1.6-2 [5728 B] Get:114 http://deb.debian.org/debian sid/main amd64 python3-fasteners all 0.18-2 [14.0 kB] Get:115 http://deb.debian.org/debian sid/main amd64 python3-scipy amd64 1.11.4-6 [19.5 MB] Get:116 http://deb.debian.org/debian sid/main amd64 python3-ufolib2 all 0.16.0+dfsg1-1 [32.9 kB] Get:117 http://deb.debian.org/debian sid/main amd64 python3-mpmath all 1.3.0-1 [419 kB] Get:118 http://deb.debian.org/debian sid/main amd64 python3-sympy all 1.12-7 [3869 kB] Get:119 http://deb.debian.org/debian sid/main amd64 python3-tz all 2024.1-2 [30.9 kB] Get:120 http://deb.debian.org/debian sid/main amd64 python3-fs all 2.4.16-4 [95.4 kB] Get:121 http://deb.debian.org/debian sid/main amd64 python3-lz4 amd64 4.0.2+dfsg-1+b3 [25.5 kB] Get:122 http://deb.debian.org/debian sid/main amd64 python3-unicodedata2 amd64 15.1.0+ds-1+b1 [299 kB] Get:123 http://deb.debian.org/debian sid/main amd64 unicode-data all 15.1.0-1 [8547 kB] Get:124 http://deb.debian.org/debian sid/main amd64 python3-fonttools amd64 4.46.0-1 [1623 kB] Get:125 http://deb.debian.org/debian sid/main amd64 sphinx-rtd-theme-common all 2.0.0+dfsg-1 [1021 kB] Get:126 http://deb.debian.org/debian sid/main amd64 python3-mrcfile all 1.4.3-3 [113 kB] Get:127 http://deb.debian.org/debian sid/main amd64 python3-griddataformats all 1.0.2-1 [2048 kB] Get:128 http://deb.debian.org/debian sid/main amd64 python3-gsd amd64 3.0.1-3+b1 [197 kB] Get:129 http://deb.debian.org/debian sid/main amd64 python3-joblib all 1.3.2-2 [218 kB] Get:130 http://deb.debian.org/debian sid/main amd64 python3-kiwisolver amd64 1.4.5-1 [80.7 kB] Get:131 http://deb.debian.org/debian sid/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get:132 http://deb.debian.org/debian sid/main amd64 python3-packaging all 24.0-1 [45.5 kB] Get:133 http://deb.debian.org/debian sid/main amd64 python3-matplotlib amd64 3.6.3-1.1 [8168 kB] Get:134 http://deb.debian.org/debian sid/main amd64 python3-msgpack amd64 1.0.3-3+b1 [96.5 kB] Get:135 http://deb.debian.org/debian sid/main amd64 python3-mmtf all 1.1.3-1 [17.0 kB] Get:136 http://deb.debian.org/debian sid/main amd64 python3-networkx all 2.8.8-2 [1425 kB] Get:137 http://deb.debian.org/debian sid/main amd64 python3-threadpoolctl all 3.1.0-1 [21.2 kB] Get:138 http://deb.debian.org/debian sid/main amd64 python3-tqdm all 4.66.2-2 [90.5 kB] Get:139 http://deb.debian.org/debian sid/main amd64 python3-mdanalysis amd64 2.5.0+dfsg1-2+b1 [2122 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 119 MB in 4s (28.8 MB/s) Selecting previously unselected package fonts-lato. 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../6-libsqlite3-0_3.45.3-1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.45.3-1) ... Selecting previously unselected package libpython3.11-stdlib:amd64. Preparing to unpack .../7-libpython3.11-stdlib_3.11.9-1_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.9-1) ... Selecting previously unselected package python3.11. 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Selecting previously unselected package python3-lxml:amd64. Preparing to unpack .../087-python3-lxml_5.2.1-1_amd64.deb ... Unpacking python3-lxml:amd64 (5.2.1-1) ... Selecting previously unselected package python3-citeproc. Preparing to unpack .../088-python3-citeproc_0.6.0-3_all.deb ... Unpacking python3-citeproc (0.6.0-3) ... Selecting previously unselected package python3-contourpy. Preparing to unpack .../089-python3-contourpy_1.0.7-3_amd64.deb ... Unpacking python3-contourpy (1.0.7-3) ... Selecting previously unselected package python3-cycler. Preparing to unpack .../090-python3-cycler_0.12.1-1_all.deb ... Unpacking python3-cycler (0.12.1-1) ... Selecting previously unselected package python3-six. Preparing to unpack .../091-python3-six_1.16.0-6_all.deb ... Unpacking python3-six (1.16.0-6) ... Selecting previously unselected package python3-dateutil. Preparing to unpack .../092-python3-dateutil_2.9.0-2_all.deb ... Unpacking python3-dateutil (2.9.0-2) ... Selecting previously unselected package python3-decorator. Preparing to unpack .../093-python3-decorator_5.1.1-5_all.deb ... Unpacking python3-decorator (5.1.1-5) ... Selecting previously unselected package python3-idna. Preparing to unpack .../094-python3-idna_3.6-2_all.deb ... Unpacking python3-idna (3.6-2) ... Selecting previously unselected package python3-urllib3. Preparing to unpack .../095-python3-urllib3_1.26.18-2_all.deb ... Unpacking python3-urllib3 (1.26.18-2) ... Selecting previously unselected package python3-requests. Preparing to unpack .../096-python3-requests_2.31.0+dfsg-1_all.deb ... Unpacking python3-requests (2.31.0+dfsg-1) ... Selecting previously unselected package python3-duecredit. Preparing to unpack .../097-python3-duecredit_0.9.1-1.1_all.deb ... Unpacking python3-duecredit (0.9.1-1.1) ... Selecting previously unselected package python3-monotonic. Preparing to unpack .../098-python3-monotonic_1.6-2_all.deb ... Unpacking python3-monotonic (1.6-2) ... Selecting previously unselected package python3-fasteners. Preparing to unpack .../099-python3-fasteners_0.18-2_all.deb ... Unpacking python3-fasteners (0.18-2) ... Selecting previously unselected package python3-scipy. Preparing to unpack .../100-python3-scipy_1.11.4-6_amd64.deb ... Unpacking python3-scipy (1.11.4-6) ... Selecting previously unselected package python3-ufolib2. Preparing to unpack .../101-python3-ufolib2_0.16.0+dfsg1-1_all.deb ... Unpacking python3-ufolib2 (0.16.0+dfsg1-1) ... Selecting previously unselected package python3-mpmath. Preparing to unpack .../102-python3-mpmath_1.3.0-1_all.deb ... Unpacking python3-mpmath (1.3.0-1) ... Selecting previously unselected package python3-sympy. Preparing to unpack .../103-python3-sympy_1.12-7_all.deb ... Unpacking python3-sympy (1.12-7) ... Selecting previously unselected package python3-tz. Preparing to unpack .../104-python3-tz_2024.1-2_all.deb ... Unpacking python3-tz (2024.1-2) ... Selecting previously unselected package python3-fs. Preparing to unpack .../105-python3-fs_2.4.16-4_all.deb ... Unpacking python3-fs (2.4.16-4) ... Selecting previously unselected package python3-lz4. Preparing to unpack .../106-python3-lz4_4.0.2+dfsg-1+b3_amd64.deb ... Unpacking python3-lz4 (4.0.2+dfsg-1+b3) ... Selecting previously unselected package python3-unicodedata2. Preparing to unpack .../107-python3-unicodedata2_15.1.0+ds-1+b1_amd64.deb ... Unpacking python3-unicodedata2 (15.1.0+ds-1+b1) ... Selecting previously unselected package unicode-data. Preparing to unpack .../108-unicode-data_15.1.0-1_all.deb ... Unpacking unicode-data (15.1.0-1) ... Selecting previously unselected package python3-fonttools. Preparing to unpack .../109-python3-fonttools_4.46.0-1_amd64.deb ... Unpacking python3-fonttools (4.46.0-1) ... Selecting previously unselected package sphinx-rtd-theme-common. Preparing to unpack .../110-sphinx-rtd-theme-common_2.0.0+dfsg-1_all.deb ... Unpacking sphinx-rtd-theme-common (2.0.0+dfsg-1) ... Selecting previously unselected package python3-mrcfile. Preparing to unpack .../111-python3-mrcfile_1.4.3-3_all.deb ... Unpacking python3-mrcfile (1.4.3-3) ... Selecting previously unselected package python3-griddataformats. Preparing to unpack .../112-python3-griddataformats_1.0.2-1_all.deb ... Unpacking python3-griddataformats (1.0.2-1) ... Selecting previously unselected package python3-gsd. Preparing to unpack .../113-python3-gsd_3.0.1-3+b1_amd64.deb ... Unpacking python3-gsd (3.0.1-3+b1) ... Selecting previously unselected package python3-joblib. Preparing to unpack .../114-python3-joblib_1.3.2-2_all.deb ... Unpacking python3-joblib (1.3.2-2) ... Selecting previously unselected package python3-kiwisolver. Preparing to unpack .../115-python3-kiwisolver_1.4.5-1_amd64.deb ... Unpacking python3-kiwisolver (1.4.5-1) ... Selecting previously unselected package python3-pyparsing. Preparing to unpack .../116-python3-pyparsing_3.1.2-1_all.deb ... Unpacking python3-pyparsing (3.1.2-1) ... Selecting previously unselected package python3-packaging. Preparing to unpack .../117-python3-packaging_24.0-1_all.deb ... Unpacking python3-packaging (24.0-1) ... Selecting previously unselected package python3-matplotlib. Preparing to unpack .../118-python3-matplotlib_3.6.3-1.1_amd64.deb ... Unpacking python3-matplotlib (3.6.3-1.1) ... Selecting previously unselected package python3-msgpack. Preparing to unpack .../119-python3-msgpack_1.0.3-3+b1_amd64.deb ... Unpacking python3-msgpack (1.0.3-3+b1) ... Selecting previously unselected package python3-mmtf. Preparing to unpack .../120-python3-mmtf_1.1.3-1_all.deb ... Unpacking python3-mmtf (1.1.3-1) ... Selecting previously unselected package python3-networkx. Preparing to unpack .../121-python3-networkx_2.8.8-2_all.deb ... Unpacking python3-networkx (2.8.8-2) ... Selecting previously unselected package python3-threadpoolctl. Preparing to unpack .../122-python3-threadpoolctl_3.1.0-1_all.deb ... Unpacking python3-threadpoolctl (3.1.0-1) ... Selecting previously unselected package python3-tqdm. Preparing to unpack .../123-python3-tqdm_4.66.2-2_all.deb ... Unpacking python3-tqdm (4.66.2-2) ... Selecting previously unselected package python3-mdanalysis. Preparing to unpack .../124-python3-mdanalysis_2.5.0+dfsg1-2+b1_amd64.deb ... Unpacking python3-mdanalysis (2.5.0+dfsg1-2+b1) ... Setting up media-types (10.1.0) ... Setting up libgraphite2-3:amd64 (1.3.14-2) ... Setting up liblcms2-2:amd64 (2.14-2+b1) ... Setting up libpixman-1-0:amd64 (0.42.2-1+b1) ... Setting up libsharpyuv0:amd64 (1.3.2-0.4+b1) ... Setting up libxau6:amd64 (1:1.0.9-1) ... Setting up fonts-lato (2.015-1) ... Setting up libicu72:amd64 (72.1-4+b1) ... Setting up liblerc4:amd64 (4.0.0+ds-4+b1) ... Setting up fonts-lyx (2.4.0~RC4-1) ... Setting up libbrotli1:amd64 (1.1.0-2+b3) ... Setting up libsqlite3-0:amd64 (3.45.3-1) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of restart. Setting up libdeflate0:amd64 (1.20-1) ... Setting up libqhull-r8.0:amd64 (2020.2-6+b1) ... Setting up libgomp1:amd64 (14-20240330-1) ... Setting up libjbig0:amd64 (2.1-6.1+b1) ... Setting up unicode-data (15.1.0-1) ... Setting up libfontenc1:amd64 (1:1.1.8-1) ... Setting up libglib2.0-0t64:amd64 (2.78.4-6) ... No schema files found: doing nothing. 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 libjpeg62-turbo:amd64 (1:2.1.5-2+b2) ... Setting up libx11-data (2:1.8.7-1) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:amd64 (1.0.13-3+b1) ... Setting up libimagequant0:amd64 (2.18.0-1) ... Setting up libproc2-0:amd64 (2:4.0.4-4) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.43-5) ... Setting up libtcl8.6:amd64 (8.6.14+dfsg-1) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libncursesw6:amd64 (6.4+20240414-1) ... Setting up libgfortran5:amd64 (14-20240330-1) ... Setting up libwebp7:amd64 (1.3.2-0.4+b1) ... Setting up libtiff6:amd64 (4.5.1+git230720-4) ... Setting up procps (2:4.0.4-4) ... Setting up libopenjp2-7:amd64 (2.5.0-2+b3) ... Setting up netbase (6.4) ... Setting up sgml-base (1.31) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up python-matplotlib-data (3.6.3-1.1) ... Setting up openssl (3.2.1-3) ... Setting up libwebpmux3:amd64 (1.3.2-0.4+b1) ... Setting up libbsd0:amd64 (0.12.2-1) ... Setting up readline-common (8.2-4) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b2) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Setting up sphinx-rtd-theme-common (2.0.0+dfsg-1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... 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 libxcb1:amd64 (1.17.0-1) ... Setting up libxcb-render0:amd64 (1.17.0-1) ... Setting up fontconfig-config (2.15.0-1.1) ... Setting up libwebpdemux2:amd64 (1.3.2-0.4+b1) ... Setting up libxcb-shm0:amd64 (1.17.0-1) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libfreetype6:amd64 (2.13.2+dfsg-1+b4) ... Setting up libjs-sphinxdoc (7.2.6-6) ... Setting up libreadline8t64:amd64 (8.2-4) ... Setting up xml-core (0.19) ... Setting up libxslt1.1:amd64 (1.1.35-1) ... Setting up libx11-6:amd64 (2:1.8.7-1) ... Setting up libharfbuzz0b:amd64 (8.3.0-2+b1) ... Setting up libfontconfig1:amd64 (2.15.0-1.1) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1+b1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1) ... Setting up libpython3.11-stdlib:amd64 (3.11.9-1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up xfonts-utils (1:7.7+6) ... Setting up libcairo2:amd64 (1.18.0-3+b1) ... Setting up libraqm0:amd64 (0.10.1-1+b1) ... Setting up libxss1:amd64 (1:1.2.3-1) ... Setting up libpython3-stdlib:amd64 (3.11.8-1) ... Setting up python3.11 (3.11.9-1) ... Setting up libxft2:amd64 (2.3.6-1+b1) ... Setting up libtk8.6:amd64 (8.6.14-1) ... Setting up python3 (3.11.8-1) ... Setting up fonts-urw-base35 (20200910-8) ... Setting up python3-freetype (2.4.0-1) ... Setting up python3-tz (2024.1-2) ... Setting up python3-monotonic (1.6-2) ... Setting up python3-six (1.16.0-6) ... Setting up python3-pil:amd64 (10.3.0-2) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-packaging (24.0-1) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up python3-certifi (2023.11.17-1) ... Setting up python3-brotli (1.1.0-2+b3) ... Setting up python3-cycler (0.12.1-1) ... Setting up python3-kiwisolver (1.4.5-1) ... Setting up python3-idna (3.6-2) ... Setting up python3-fasteners (0.18-2) ... Setting up python3-urllib3 (1.26.18-2) ... Setting up python3-lxml:amd64 (5.2.1-1) ... Setting up python3-dateutil (2.9.0-2) ... Setting up python3-msgpack (1.0.3-3+b1) ... Setting up python3-mpmath (1.3.0-1) ... Setting up python3-appdirs (1.4.4-4) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-sympy (1.12-7) ... Setting up python3-attr (23.2.0-2) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ... Setting up python3-cairo (1.26.0-1) ... Setting up python3-joblib (1.3.2-2) ... Setting up python3-lz4 (4.0.2+dfsg-1+b3) ... Setting up python3-citeproc (0.6.0-3) ... Setting up python3-charset-normalizer (3.3.2-1) ... Setting up python3-unicodedata2 (15.1.0+ds-1+b1) ... Setting up blt (2.5.3+dfsg-7) ... Setting up python3-tqdm (4.66.2-2) ... Setting up python3-threadpoolctl (3.1.0-1) ... Setting up python3-tk:amd64 (3.12.3-1) ... Setting up python3-networkx (2.8.8-2) ... Setting up python3-fs (2.4.16-4) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-pil.imagetk:amd64 (10.3.0-2) ... Setting up python3-rlpycairo (0.3.0-3) ... Setting up python3-requests (2.31.0+dfsg-1) ... Setting up python3-numpy (1:1.26.4+ds-6) ... Setting up python3-reportlab (4.2.0-1) ... Setting up python3-contourpy (1.0.7-3) ... Setting up python3-mrcfile (1.4.3-3) ... Setting up python3-scipy (1.11.4-6) ... Setting up python3-duecredit (0.9.1-1.1) ... Setting up python3-gsd (3.0.1-3+b1) ... Setting up python3-mmtf (1.1.3-1) ... Setting up python3-griddataformats (1.0.2-1) ... Setting up python3-fonttools (4.46.0-1) ... Setting up python3-ufolib2 (0.16.0+dfsg1-1) ... Setting up python3-matplotlib (3.6.3-1.1) ... Processing triggers for libc-bin (2.37-18) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.83+dfsg1-2) ... Setting up python3-mdanalysis (2.5.0+dfsg1-2+b1) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 1m59.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'apt-get', '-y', 'install', 'python3-mdanalysis=2.5.0+dfsg1-2+b1'] 1m59.3s INFO: Running scripts post_install 1m59.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/post_install_exceptions'] 1m59.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/post_install_exceptions'] 1m59.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/post_install_log_alternatives'] 1m59.3s DUMP: Removing 'local diversion of /usr/bin/update-alternatives to /usr/bin/update-alternatives.orig' LOG-ALTERNATIVES: dpkg=python3: piuparts=python3-mdanalysis=2.5.0+dfsg1-2+b1: /usr/bin/update-alternatives --auto /usr/bin/python3 LOG-ALTERNATIVES: dpkg=libblas3: piuparts=python3-mdanalysis=2.5.0+dfsg1-2+b1: /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=procps: piuparts=python3-mdanalysis=2.5.0+dfsg1-2+b1: /usr/bin/update-alternatives --remove w /usr/bin/w.procps LOG-ALTERNATIVES: dpkg=liblapack3: piuparts=python3-mdanalysis=2.5.0+dfsg1-2+b1: /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 1m59.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/post_install_log_alternatives'] 1m59.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1tq868yb'] 2m0.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1tq868yb'] 2m2.3s ERROR: WARN: Broken symlinks: /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSerifCondensed.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSerifCondensed.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSerifCondensed-Italic.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSerifCondensed-Italic.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSerifCondensed-BoldItalic.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSerifCondensed-BoldItalic.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSerifCondensed-Bold.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSerifCondensed-Bold.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSerif-Italic.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSerif-Italic.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSerif-BoldItalic.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSerif-BoldItalic.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSansCondensed.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSansCondensed.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSansCondensed-Oblique.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSansCondensed-Oblique.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSansCondensed-BoldOblique.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSansCondensed-BoldOblique.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSansCondensed-Bold.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSansCondensed-Bold.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSans-Oblique.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSans-Oblique.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSans-ExtraLight.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSans-ExtraLight.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuSans-BoldOblique.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuSans-BoldOblique.ttf (python3-reportlab) /usr/lib/python3/dist-packages/reportlab/fonts/DejaVuMathTeXGyre.ttf -> ../../../../../share/fonts/truetype/dejavu/DejaVuMathTeXGyre.ttf (python3-reportlab) /usr/share/doc/python3-mrcfile/html/_static/_sphinx_javascript_frameworks_compat.js -> ../../../../javascript/sphinxdoc/1.0/_sphinx_javascript_frameworks_compat.js (python3-mrcfile) 2m2.3s INFO: /bin converted to /usr/bin by /usr merge 2m2.3s INFO: /lib converted to /usr/lib by /usr merge 2m2.3s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 2m2.3s INFO: /lib64 converted to /usr/lib64 by /usr merge 2m2.3s INFO: /sbin converted to /usr/sbin by /usr merge 2m3.3s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', '-ac', '--ignore-obsolete'] 2m6.0s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', '-ac', '--ignore-obsolete'] 2m6.0s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 2m6.0s DUMP: 0.15.6 2m6.0s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 2m6.0s INFO: Running adequate version 0.15.6 now. 2m6.0s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'python3-mdanalysis'] 2m6.2s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'python3-mdanalysis'] 2m6.2s INFO: Running scripts pre_remove 2m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 2m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 2m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 2m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 2m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 2m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 2m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 2m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 2m9.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 2m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 2m9.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/pre_remove_exceptions'] 2m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/pre_remove_exceptions'] 2m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 2m9.4s DUMP: install ok installed apt apt 2.9.1 install ok installed base-files base-files 13.1 install ok installed base-passwd base-passwd 3.6.3 install ok installed bash bash 5.2.21-2 install ok installed blt blt 2.5.3+dfsg-7 install ok installed bsdutils bsdutils 1:2.40-6 install ok installed ca-certificates ca-certificates 20240203 install ok installed coreutils coreutils 9.4-3.1 install ok installed dash dash 0.5.12-6 install ok installed debconf debconf 1.5.86 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.17 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.6 install ok installed e2fsprogs e2fsprogs 1.47.0-2.4 install ok installed findutils findutils 4.9.0-5 install ok installed fontconfig-config fontconfig-config 2.15.0-1.1 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-8 install ok installed fonts-dejavu-mono fonts-dejavu-mono 2.37-8 install ok installed fonts-font-awesome fonts-font-awesome 5.0.10+really4.7.0~dfsg-4.1 install ok installed fonts-lato fonts-lato 2.015-1 install ok installed fonts-lyx fonts-lyx 2.4.0~RC4-1 install ok installed fonts-urw-base35 fonts-urw-base35 20200910-8 install ok installed gcc-14-base:amd64 gcc-14-base 14-20240330-1 install ok installed gpgv gpgv 2.2.40-3 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.23+nmu2 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed libacl1:amd64 libacl1 2.3.2-1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.1 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:3.1.2-2.1 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-2.1 install ok installed libblas3:amd64 libblas3 3.12.0-3 install ok installed libblkid1:amd64 libblkid1 2.40-6 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b3 install ok installed libbsd0:amd64 libbsd0 0.12.2-1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5.1 install ok installed libc-bin libc-bin 2.37-18 install ok installed libc6:amd64 libc6 2.37-18 install ok installed libcairo2:amd64 libcairo2 1.18.0-3+b1 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-1 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2.4 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-4 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-7 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.271+b3 install ok installed libdeflate0:amd64 libdeflate0 1.20-1 install ok installed libexpat1:amd64 libexpat1 2.6.2-1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.0-2.4 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libfontconfig1:amd64 libfontconfig1 2.15.0-1.1 install ok installed libfontenc1:amd64 libfontenc1 1:1.1.8-1 install ok installed libfreetype6:amd64 libfreetype6 2.13.2+dfsg-1+b4 install ok installed libfribidi0:amd64 libfribidi0 1.0.13-3+b1 install ok installed libgcc-s1:amd64 libgcc-s1 14-20240330-1 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.3-2 install ok installed libgfortran5:amd64 libgfortran5 14-20240330-1 install ok installed libglib2.0-0t64:amd64 libglib2.0-0t64 2.78.4-6 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.5-2 install ok installed libgomp1:amd64 libgomp1 14-20240330-1 install ok installed libgpg-error0:amd64 libgpg-error0 1.47-3 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-2 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 8.3.0-2+b1 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.9.1-2.2 install ok installed libicu72:amd64 libicu72 72.1-4+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed libimagequant0:amd64 libimagequant0 2.18.0-1 install ok installed libjbig0:amd64 libjbig0 2.1-6.1+b1 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-2+b2 install ok installed libjs-jquery libjs-jquery 3.6.1+dfsg+~3.5.14-1 install ok installed libjs-jquery-ui libjs-jquery-ui 1.13.2+dfsg-1 install ok installed libjs-sphinxdoc libjs-sphinxdoc 7.2.6-6 install ok installed libjs-underscore libjs-underscore 1.13.4~dfsg+~1.11.4-3 install ok installed liblapack3:amd64 liblapack3 3.12.0-3 install ok installed liblbfgsb0:amd64 liblbfgsb0 3.0+dfsg.4-1+b1 install ok installed liblcms2-2:amd64 liblcms2-2 2.14-2+b1 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-4+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-2 install ok installed liblzma5:amd64 liblzma5 5.6.1+really5.4.5-1 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.40-6 install ok installed libncursesw6:amd64 libncursesw6 6.4+20240414-1 install ok installed libnettle8t64:amd64 libnettle8t64 3.9.1-2.2 install ok installed libopenjp2-7:amd64 libopenjp2-7 2.5.0-2+b3 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.3-4 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 libpixman-1-0:amd64 libpixman-1-0 0.42.2-1+b1 install ok installed libpng16-16t64:amd64 libpng16-16t64 1.6.43-5 install ok installed libproc2-0:amd64 libproc2-0 2:4.0.4-4 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.11.8-1 install ok installed libpython3.11-minimal:amd64 libpython3.11-minimal 3.11.9-1 install ok installed libpython3.11-stdlib:amd64 libpython3.11-stdlib 3.11.9-1 install ok installed libqhull-r8.0:amd64 libqhull-r8.0 2020.2-6+b1 install ok installed libraqm0:amd64 libraqm0 0.10.1-1+b1 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-4 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1 install ok installed libselinux1:amd64 libselinux1 3.5-2+b2 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b3 install ok installed libsepol2:amd64 libsepol2 3.5-2 install ok installed libsharpyuv0:amd64 libsharpyuv0 1.3.2-0.4+b1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40-6 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.45.3-1 install ok installed libss2:amd64 libss2 1.47.0-2.4 install ok installed libssl3t64:amd64 libssl3t64 3.2.1-3 install ok installed libstdc++6:amd64 libstdc++6 14-20240330-1 install ok installed libsystemd0:amd64 libsystemd0 255.4-1+b1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.14+dfsg-1 install ok installed libtiff6:amd64 libtiff6 4.5.1+git230720-4 install ok installed libtinfo6:amd64 libtinfo6 6.4+20240414-1 install ok installed libtk8.6:amd64 libtk8.6 8.6.14-1 install ok installed libudev1:amd64 libudev1 255.4-1+b1 install ok installed libunistring5:amd64 libunistring5 1.2-1 install ok installed libuuid1:amd64 libuuid1 2.40-6 install ok installed libwebp7:amd64 libwebp7 1.3.2-0.4+b1 install ok installed libwebpdemux2:amd64 libwebpdemux2 1.3.2-0.4+b1 install ok installed libwebpmux3:amd64 libwebpmux3 1.3.2-0.4+b1 install ok installed libx11-6:amd64 libx11-6 2:1.8.7-1 install ok installed libx11-data libx11-data 2:1.8.7-1 install ok installed libxau6:amd64 libxau6 1:1.0.9-1 install ok installed libxcb-render0:amd64 libxcb-render0 1.17.0-1 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.17.0-1 install ok installed libxcb1:amd64 libxcb1 1.17.0-1 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b1 install ok installed libxft2:amd64 libxft2 2.3.6-1+b1 install ok installed libxml2:amd64 libxml2 2.9.14+dfsg-1.3+b2 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1.1 install ok installed libxslt1.1:amd64 libxslt1.1 1.1.35-1 install ok installed libxss1:amd64 libxss1 1:1.2.3-1 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-2 install ok installed login login 1:4.13+dfsg1-4 install ok installed logsave logsave 1.47.0-2.4 install ok installed mawk mawk 1.3.4.20240123-1 install ok installed media-types media-types 10.1.0 install ok installed mount mount 2.40-6 install ok installed ncurses-base ncurses-base 6.4+20240414-1 install ok installed ncurses-bin ncurses-bin 6.4+20240414-1 install ok installed netbase netbase 6.4 install ok installed openssl openssl 3.2.1-3 install ok installed passwd passwd 1:4.13+dfsg1-4 install ok installed perl-base perl-base 5.38.2-3.2+b2 install ok installed procps procps 2:4.0.4-4 install ok installed python-matplotlib-data python-matplotlib-data 3.6.3-1.1 install ok installed python3 python3 3.11.8-1 install ok installed python3-appdirs python3-appdirs 1.4.4-4 install ok installed python3-attr python3-attr 23.2.0-2 install ok installed python3-biopython python3-biopython 1.83+dfsg1-2 install ok installed python3-brotli python3-brotli 1.1.0-2+b3 install ok installed python3-cairo python3-cairo 1.26.0-1 install ok installed python3-certifi python3-certifi 2023.11.17-1 install ok installed python3-chardet python3-chardet 5.2.0+dfsg-1 install ok installed python3-charset-normalizer python3-charset-normalizer 3.3.2-1 install ok installed python3-citeproc python3-citeproc 0.6.0-3 install ok installed python3-contourpy python3-contourpy 1.0.7-3 install ok installed python3-cycler python3-cycler 0.12.1-1 install ok installed python3-dateutil python3-dateutil 2.9.0-2 install ok installed python3-decorator python3-decorator 5.1.1-5 install ok installed python3-duecredit python3-duecredit 0.9.1-1.1 install ok installed python3-fasteners python3-fasteners 0.18-2 install ok installed python3-fonttools python3-fonttools 4.46.0-1 install ok installed python3-freetype python3-freetype 2.4.0-1 install ok installed python3-fs python3-fs 2.4.16-4 install ok installed python3-griddataformats python3-griddataformats 1.0.2-1 install ok installed python3-gsd python3-gsd 3.0.1-3+b1 install ok installed python3-idna python3-idna 3.6-2 install ok installed python3-joblib python3-joblib 1.3.2-2 install ok installed python3-kiwisolver python3-kiwisolver 1.4.5-1 install ok installed python3-lxml:amd64 python3-lxml 5.2.1-1 install ok installed python3-lz4 python3-lz4 4.0.2+dfsg-1+b3 install ok installed python3-matplotlib python3-matplotlib 3.6.3-1.1 install ok installed python3-mdanalysis python3-mdanalysis 2.5.0+dfsg1-2+b1 install ok installed python3-minimal python3-minimal 3.11.8-1 install ok installed python3-mmtf python3-mmtf 1.1.3-1 install ok installed python3-monotonic python3-monotonic 1.6-2 install ok installed python3-mpmath python3-mpmath 1.3.0-1 install ok installed python3-mrcfile python3-mrcfile 1.4.3-3 install ok installed python3-msgpack python3-msgpack 1.0.3-3+b1 install ok installed python3-networkx python3-networkx 2.8.8-2 install ok installed python3-numpy python3-numpy 1:1.26.4+ds-6 install ok installed python3-packaging python3-packaging 24.0-1 install ok installed python3-pil:amd64 python3-pil 10.3.0-2 install ok installed python3-pil.imagetk:amd64 python3-pil.imagetk 10.3.0-2 install ok installed python3-pkg-resources python3-pkg-resources 68.1.2-2 install ok installed python3-pyparsing python3-pyparsing 3.1.2-1 install ok installed python3-reportlab python3-reportlab 4.2.0-1 install ok installed python3-requests python3-requests 2.31.0+dfsg-1 install ok installed python3-rlpycairo python3-rlpycairo 0.3.0-3 install ok installed python3-scipy python3-scipy 1.11.4-6 install ok installed python3-six python3-six 1.16.0-6 install ok installed python3-sympy python3-sympy 1.12-7 install ok installed python3-threadpoolctl python3-threadpoolctl 3.1.0-1 install ok installed python3-tk:amd64 python3-tk 3.12.3-1 install ok installed python3-tqdm python3-tqdm 4.66.2-2 install ok installed python3-tz python3-tz 2024.1-2 install ok installed python3-ufolib2 python3-ufolib2 0.16.0+dfsg1-1 install ok installed python3-unicodedata2 python3-unicodedata2 15.1.0+ds-1+b1 install ok installed python3-urllib3 python3-urllib3 1.26.18-2 install ok installed python3.11 python3.11 3.11.9-1 install ok installed python3.11-minimal python3.11-minimal 3.11.9-1 install ok installed readline-common readline-common 8.2-4 install ok installed sed sed 4.9-2 install ok installed sgml-base sgml-base 1.31 install ok installed sphinx-rtd-theme-common sphinx-rtd-theme-common 2.0.0+dfsg-1 install ok installed sysvinit-utils sysvinit-utils 3.09-1 install ok installed tar tar 1.35+dfsg-3 install ok installed tk8.6-blt2.5 tk8.6-blt2.5 2.5.3+dfsg-7 install ok installed tzdata tzdata 2024a-3 install ok installed unicode-data unicode-data 15.1.0-1 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40-6 install ok installed w3c-sgml-lib w3c-sgml-lib 1.3-3 install ok installed x11-common x11-common 1:7.7+23 install ok installed xfonts-encodings xfonts-encodings 1:1.0.4-2.2 install ok installed xfonts-utils xfonts-utils 1:7.7+6 install ok installed xml-core xml-core 0.19 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg-3.1 2m9.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 2m9.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'apt-get', 'remove', 'blt', 'ca-certificates', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-font-awesome', 'fonts-lato', 'fonts-lyx', 'fonts-urw-base35', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libharfbuzz0b:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libjs-sphinxdoc', 'libjs-underscore', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libopenjp2-7:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libqhull-r8.0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libtcl8.6:amd64', 'libtiff6:amd64', 'libtk8.6:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'media-types', 'netbase', 'openssl', 'procps', 'python-matplotlib-data', 'python3', 'python3-appdirs', 'python3-attr', 'python3-biopython', 'python3-brotli', 'python3-cairo', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-citeproc', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-duecredit', 'python3-fasteners', 'python3-fonttools', 'python3-freetype', 'python3-fs', 'python3-griddataformats', 'python3-gsd', 'python3-idna', 'python3-joblib', 'python3-kiwisolver', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-minimal', 'python3-mmtf', 'python3-monotonic', 'python3-mpmath', 'python3-mrcfile', 'python3-msgpack', 'python3-networkx', 'python3-numpy', 'python3-packaging', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-pyparsing', 'python3-reportlab', 'python3-requests', 'python3-rlpycairo', 'python3-scipy', 'python3-six', 'python3-sympy', 'python3-threadpoolctl', 'python3-tk:amd64', 'python3-tqdm', 'python3-tz', 'python3-ufolib2', 'python3-unicodedata2', 'python3-urllib3', 'python3.11', 'python3.11-minimal', 'readline-common', 'sgml-base', 'sphinx-rtd-theme-common', 'tk8.6-blt2.5', 'unicode-data', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'python3-mdanalysis'] 3m3.7s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: blt ca-certificates fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome fonts-lato fonts-lyx fonts-urw-base35 libblas3 libbrotli1 libbsd0 libcairo2 libdeflate0 libexpat1 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0t64 libgomp1 libgraphite2-3 libharfbuzz0b libicu72 libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore liblapack3 liblbfgsb0 liblcms2-2 liblerc4 libncursesw6 libopenjp2-7 libpixman-1-0 libpng16-16t64 libproc2-0 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libqhull-r8.0 libraqm0 libreadline8t64 libsharpyuv0 libsqlite3-0 libtcl8.6 libtiff6 libtk8.6 libwebp7 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxml2 libxrender1 libxslt1.1 libxss1 media-types netbase openssl procps python-matplotlib-data python3 python3-appdirs python3-attr python3-biopython python3-brotli python3-cairo python3-certifi python3-chardet python3-charset-normalizer python3-citeproc python3-contourpy python3-cycler python3-dateutil python3-decorator python3-duecredit python3-fasteners python3-fonttools python3-freetype python3-fs python3-griddataformats python3-gsd python3-idna python3-joblib python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib python3-mdanalysis python3-minimal python3-mmtf python3-monotonic python3-mpmath python3-mrcfile python3-msgpack python3-networkx python3-numpy python3-packaging python3-pil python3-pil.imagetk python3-pkg-resources python3-pyparsing python3-reportlab python3-requests python3-rlpycairo python3-scipy python3-six python3-sympy python3-threadpoolctl python3-tk python3-tqdm python3-tz python3-ufolib2 python3-unicodedata2 python3-urllib3 python3.11 python3.11-minimal readline-common sgml-base sphinx-rtd-theme-common tk8.6-blt2.5 unicode-data w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 0 upgraded, 0 newly installed, 139 to remove and 0 not upgraded. After this operation, 491 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 ... 18452 files and directories currently installed.) Removing python3-mdanalysis (2.5.0+dfsg1-2+b1) ... Removing python3-biopython (1.83+dfsg1-2) ... Removing python3-reportlab (4.2.0-1) ... Removing python3-matplotlib (3.6.3-1.1) ... Removing python3-pil.imagetk:amd64 (10.3.0-2) ... Removing python3-pil:amd64 (10.3.0-2) ... Removing python3-tk:amd64 (3.12.3-1) ... Removing blt (2.5.3+dfsg-7) ... Removing python3-duecredit (0.9.1-1.1) ... Removing python3-requests (2.31.0+dfsg-1) ... Removing python3-certifi (2023.11.17-1) ... Removing ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing tk8.6-blt2.5 (2.5.3+dfsg-7) ... Removing libtk8.6:amd64 (8.6.14-1) ... Removing libxft2:amd64 (2.3.6-1+b1) ... Removing python3-rlpycairo (0.3.0-3) ... Removing python3-cairo (1.26.0-1) ... Removing libcairo2:amd64 (1.18.0-3+b1) ... Removing libfontconfig1:amd64 (2.15.0-1.1) ... Removing fontconfig-config (2.15.0-1.1) ... Removing python-matplotlib-data (3.6.3-1.1) ... Removing fonts-dejavu-core (2.37-8) ... Removing fonts-dejavu-mono (2.37-8) ... Removing python3-griddataformats (1.0.2-1) ... Removing python3-mrcfile (1.4.3-3) ... Removing sphinx-rtd-theme-common (2.0.0+dfsg-1) ... Removing fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Removing fonts-lato (2.015-1) ... Removing fonts-lyx (2.4.0~RC4-1) ... Removing fonts-urw-base35 (20200910-8) ... Removing python3-gsd (3.0.1-3+b1) ... Removing python3-mmtf (1.1.3-1) ... Removing xfonts-utils (1:7.7+6) ... Removing libraqm0:amd64 (0.10.1-1+b1) ... Removing libxss1:amd64 (1:1.2.3-1) ... Removing libxrender1:amd64 (1:0.9.10-1.1) ... Removing libxcb-shm0:amd64 (1.17.0-1) ... Removing libtiff6:amd64 (4.5.1+git230720-4) ... Removing libdeflate0:amd64 (1.20-1) ... Removing python3-tqdm (4.66.2-2) ... Removing python3-msgpack (1.0.3-3+b1) ... Removing python3-kiwisolver (1.4.5-1) ... Removing libfontenc1:amd64 (1:1.1.8-1) ... Removing libfribidi0:amd64 (1.0.13-3+b1) ... Removing libharfbuzz0b:amd64 (8.3.0-2+b1) ... Removing libglib2.0-0t64:amd64 (2.78.4-6) ... Removing libimagequant0:amd64 (2.18.0-1) ... Removing libgomp1:amd64 (14-20240330-1) ... Removing libgraphite2-3:amd64 (1.3.14-2) ... Removing python3-citeproc (0.6.0-3) ... Removing libjbig0:amd64 (2.1-6.1+b1) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-2+b2) ... Removing libjs-sphinxdoc (7.2.6-6) ... Removing libjs-jquery-ui (1.13.2+dfsg-1) ... Removing libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Removing libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Removing liblcms2-2:amd64 (2.14-2+b1) ... Removing liblerc4:amd64 (4.0.0+ds-4+b1) ... Removing python3-joblib (1.3.2-2) ... Removing procps (2:4.0.4-4) ... Removing libopenjp2-7:amd64 (2.5.0-2+b3) ... Removing libpixman-1-0:amd64 (0.42.2-1+b1) ... Removing libproc2-0:amd64 (2:4.0.4-4) ... Removing libqhull-r8.0:amd64 (2020.2-6+b1) ... Removing libwebpmux3:amd64 (1.3.2-0.4+b1) ... Removing libwebpdemux2:amd64 (1.3.2-0.4+b1) ... Removing libwebp7:amd64 (1.3.2-0.4+b1) ... Removing libsharpyuv0:amd64 (1.3.2-0.4+b1) ... Removing libtcl8.6:amd64 (8.6.14+dfsg-1) ... Removing libxcb-render0:amd64 (1.17.0-1) ... Removing libxext6:amd64 (2:1.3.4-1+b1) ... Removing openssl (3.2.1-3) ... Removing python3-chardet (5.2.0+dfsg-1) ... Removing python3-charset-normalizer (3.3.2-1) ... Removing python3-contourpy (1.0.7-3) ... Removing python3-cycler (0.12.1-1) ... Removing python3-dateutil (2.9.0-2) ... Removing python3-fasteners (0.18-2) ... Removing python3-freetype (2.4.0-1) ... Removing python3-idna (3.6-2) ... Removing python3-monotonic (1.6-2) ... Removing python3-networkx (2.8.8-2) ... Removing python3-packaging (24.0-1) ... Removing python3-pyparsing (3.1.2-1) ... Removing python3-urllib3 (1.26.18-2) ... Removing python3-threadpoolctl (3.1.0-1) ... Removing w3c-sgml-lib (1.3-3) ... Removing xml-core (0.19) ... Removing sgml-base (1.31) ... Removing xfonts-encodings (1:1.0.4-2.2) ... Removing x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing libfreetype6:amd64 (2.13.2+dfsg-1+b4) ... Removing libbrotli1:amd64 (1.1.0-2+b3) ... Removing libx11-6:amd64 (2:1.8.7-1) ... Removing libxcb1:amd64 (1.17.0-1) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libbsd0:amd64 (0.12.2-1) ... Removing libpng16-16t64:amd64 (1.6.43-5) ... Removing libx11-data (2:1.8.7-1) ... Removing libxau6:amd64 (1:1.0.9-1) ... Removing python3-ufolib2 (0.16.0+dfsg1-1) ... Removing python3-attr (23.2.0-2) ... Removing python3-fonttools (4.46.0-1) ... Removing python3-scipy (1.11.4-6) ... Removing python3-numpy (1:1.26.4+ds-6) ... Removing liblbfgsb0:amd64 (3.0+dfsg.4-1+b1) ... Removing liblapack3:amd64 (3.12.0-3) ... Removing libblas3:amd64 (3.12.0-3) ... Removing python3-unicodedata2 (15.1.0+ds-1+b1) ... Removing python3-sympy (1.12-7) ... Removing libgfortran5:amd64 (14-20240330-1) ... Removing python3-lxml:amd64 (5.2.1-1) ... Removing libxslt1.1:amd64 (1.1.35-1) ... Removing libxml2:amd64 (2.9.14+dfsg-1.3+b2) ... Removing libicu72:amd64 (72.1-4+b1) ... Removing python3-fs (2.4.16-4) ... Removing python3-appdirs (1.4.4-4) ... Removing python3-brotli (1.1.0-2+b3) ... Removing python3-decorator (5.1.1-5) ... Removing python3-lz4 (4.0.2+dfsg-1+b3) ... Removing python3-mpmath (1.3.0-1) ... Removing python3-pkg-resources (68.1.2-2) ... Removing python3-six (1.16.0-6) ... Removing python3-tz (2024.1-2) ... Removing unicode-data (15.1.0-1) ... Removing python3 (3.11.8-1) ... Removing python3.11 (3.11.9-1) ... Removing python3-minimal (3.11.8-1) ... Removing python3.11-minimal (3.11.9-1) ... Removing libexpat1:amd64 (2.6.2-1) ... Removing libpython3-stdlib:amd64 (3.11.8-1) ... Removing libpython3.11-stdlib:amd64 (3.11.9-1) ... find: '/usr/lib/python3': No such file or directory Removing libncursesw6:amd64 (6.4+20240414-1) ... Removing libpython3.11-minimal:amd64 (3.11.9-1) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8t64:amd64 (8.2-4) ... Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Removing libsqlite3-0:amd64 (3.45.3-1) ... Removing media-types (10.1.0) ... Removing netbase (6.4) ... Removing readline-common (8.2-4) ... Processing triggers for libc-bin (2.37-18) ... 3m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'apt-get', 'remove', 'blt', 'ca-certificates', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-font-awesome', 'fonts-lato', 'fonts-lyx', 'fonts-urw-base35', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libharfbuzz0b:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libjs-sphinxdoc', 'libjs-underscore', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libopenjp2-7:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libqhull-r8.0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libtcl8.6:amd64', 'libtiff6:amd64', 'libtk8.6:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'media-types', 'netbase', 'openssl', 'procps', 'python-matplotlib-data', 'python3', 'python3-appdirs', 'python3-attr', 'python3-biopython', 'python3-brotli', 'python3-cairo', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-citeproc', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-duecredit', 'python3-fasteners', 'python3-fonttools', 'python3-freetype', 'python3-fs', 'python3-griddataformats', 'python3-gsd', 'python3-idna', 'python3-joblib', 'python3-kiwisolver', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-minimal', 'python3-mmtf', 'python3-monotonic', 'python3-mpmath', 'python3-mrcfile', 'python3-msgpack', 'python3-networkx', 'python3-numpy', 'python3-packaging', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-pyparsing', 'python3-reportlab', 'python3-requests', 'python3-rlpycairo', 'python3-scipy', 'python3-six', 'python3-sympy', 'python3-threadpoolctl', 'python3-tk:amd64', 'python3-tqdm', 'python3-tz', 'python3-ufolib2', 'python3-unicodedata2', 'python3-urllib3', 'python3.11', 'python3.11-minimal', 'readline-common', 'sgml-base', 'sphinx-rtd-theme-common', 'tk8.6-blt2.5', 'unicode-data', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'python3-mdanalysis'] 3m3.7s INFO: Running scripts post_remove 3m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/post_remove_exceptions'] 3m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/post_remove_exceptions'] 3m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'dpkg', '--purge', 'blt', 'ca-certificates', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-font-awesome', 'fonts-lato', 'fonts-lyx', 'fonts-urw-base35', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libharfbuzz0b:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libjs-sphinxdoc', 'libjs-underscore', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libopenjp2-7:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libqhull-r8.0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libtcl8.6:amd64', 'libtiff6:amd64', 'libtk8.6:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'media-types', 'netbase', 'openssl', 'procps', 'python-matplotlib-data', 'python3', 'python3-appdirs', 'python3-attr', 'python3-biopython', 'python3-brotli', 'python3-cairo', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-citeproc', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-duecredit', 'python3-fasteners', 'python3-fonttools', 'python3-freetype', 'python3-fs', 'python3-griddataformats', 'python3-gsd', 'python3-idna', 'python3-joblib', 'python3-kiwisolver', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-minimal', 'python3-mmtf', 'python3-monotonic', 'python3-mpmath', 'python3-mrcfile', 'python3-msgpack', 'python3-networkx', 'python3-numpy', 'python3-packaging', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-pyparsing', 'python3-reportlab', 'python3-requests', 'python3-rlpycairo', 'python3-scipy', 'python3-six', 'python3-sympy', 'python3-threadpoolctl', 'python3-tk:amd64', 'python3-tqdm', 'python3-tz', 'python3-ufolib2', 'python3-unicodedata2', 'python3-urllib3', 'python3.11', 'python3.11-minimal', 'readline-common', 'sgml-base', 'sphinx-rtd-theme-common', 'tk8.6-blt2.5', 'unicode-data', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core'] 3m4.4s DUMP: dpkg: warning: ignoring request to remove blt which isn't installed (Reading database ... 5269 files and directories currently installed.) Purging configuration files for ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Purging configuration files for fontconfig-config (2.15.0-1.1) ... dpkg: warning: while removing fontconfig-config, directory '/etc/fonts/conf.d' not empty so not removed Purging configuration files for fonts-dejavu-core (2.37-8) ... Purging configuration files for fonts-dejavu-mono (2.37-8) ... dpkg: warning: while removing fonts-dejavu-mono, directory '/etc/fonts' not empty so not removed Purging configuration files for fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... dpkg: warning: ignoring request to remove fonts-lato which isn't installed dpkg: warning: ignoring request to remove fonts-lyx which isn't installed Purging configuration files for fonts-urw-base35 (20200910-8) ... dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libbsd0 which isn't installed dpkg: warning: ignoring request to remove libcairo2 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 libfontconfig1 which isn't installed dpkg: warning: ignoring request to remove libfontenc1 which isn't installed dpkg: warning: ignoring request to remove libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libfribidi0 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed Purging configuration files for libglib2.0-0t64:amd64 (2.78.4-6) ... dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed dpkg: warning: ignoring request to remove libicu72 which isn't installed dpkg: warning: ignoring request to remove libimagequant0 which isn't installed dpkg: warning: ignoring request to remove libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed Purging configuration files for libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... dpkg: warning: ignoring request to remove libjs-jquery-ui which isn't installed dpkg: warning: ignoring request to remove libjs-sphinxdoc which isn't installed dpkg: warning: ignoring request to remove libjs-underscore which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove liblbfgsb0 which isn't installed dpkg: warning: ignoring request to remove liblcms2-2 which isn't installed dpkg: warning: ignoring request to remove liblerc4 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libopenjp2-7 which isn't installed dpkg: warning: ignoring request to remove libpixman-1-0 which isn't installed dpkg: warning: ignoring request to remove libpng16-16t64 which isn't installed dpkg: warning: ignoring request to remove libproc2-0 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.11-minimal:amd64 (3.11.9-1) ... dpkg: warning: ignoring request to remove libpython3.11-stdlib which isn't installed dpkg: warning: ignoring request to remove libqhull-r8.0 which isn't installed dpkg: warning: ignoring request to remove libraqm0 which isn't installed Purging configuration files for libreadline8t64:amd64 (8.2-4) ... dpkg: warning: ignoring request to remove libsharpyuv0 which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libtcl8.6 which isn't installed dpkg: warning: ignoring request to remove libtiff6 which isn't installed dpkg: warning: ignoring request to remove libtk8.6 which isn't installed dpkg: warning: ignoring request to remove libwebp7 which isn't installed dpkg: warning: ignoring request to remove libwebpdemux2 which isn't installed dpkg: warning: ignoring request to remove libwebpmux3 which isn't installed dpkg: warning: ignoring request to remove libx11-6 which isn't installed dpkg: warning: ignoring request to remove libx11-data which isn't installed dpkg: warning: ignoring request to remove libxau6 which isn't installed dpkg: warning: ignoring request to remove libxcb-render0 which isn't installed dpkg: warning: ignoring request to remove libxcb-shm0 which isn't installed dpkg: warning: ignoring request to remove libxcb1 which isn't installed dpkg: warning: ignoring request to remove libxdmcp6 which isn't installed dpkg: warning: ignoring request to remove libxext6 which isn't installed dpkg: warning: ignoring request to remove libxft2 which isn't installed dpkg: warning: ignoring request to remove libxml2 which isn't installed dpkg: warning: ignoring request to remove libxrender1 which isn't installed dpkg: warning: ignoring request to remove libxslt1.1 which isn't installed dpkg: warning: ignoring request to remove libxss1 which isn't installed Purging configuration files for media-types (10.1.0) ... Purging configuration files for netbase (6.4) ... Purging configuration files for openssl (3.2.1-3) ... Purging configuration files for procps (2:4.0.4-4) ... Purging configuration files for python-matplotlib-data (3.6.3-1.1) ... Purging configuration files for python3 (3.11.8-1) ... dpkg: warning: ignoring request to remove python3-appdirs which isn't installed dpkg: warning: ignoring request to remove python3-attr which isn't installed dpkg: warning: ignoring request to remove python3-biopython which isn't installed dpkg: warning: ignoring request to remove python3-brotli which isn't installed dpkg: warning: ignoring request to remove python3-cairo which isn't installed dpkg: warning: ignoring request to remove python3-certifi which isn't installed dpkg: warning: ignoring request to remove python3-chardet which isn't installed dpkg: warning: ignoring request to remove python3-charset-normalizer which isn't installed dpkg: warning: ignoring request to remove python3-citeproc which isn't installed dpkg: warning: ignoring request to remove python3-contourpy which isn't installed dpkg: warning: ignoring request to remove python3-cycler which isn't installed dpkg: warning: ignoring request to remove python3-dateutil which isn't installed dpkg: warning: ignoring request to remove python3-decorator which isn't installed dpkg: warning: ignoring request to remove python3-duecredit which isn't installed dpkg: warning: ignoring request to remove python3-fasteners which isn't installed dpkg: warning: ignoring request to remove python3-fonttools which isn't installed dpkg: warning: ignoring request to remove python3-freetype which isn't installed dpkg: warning: ignoring request to remove python3-fs which isn't installed dpkg: warning: ignoring request to remove python3-griddataformats which isn't installed dpkg: warning: ignoring request to remove python3-gsd which isn't installed dpkg: warning: ignoring request to remove python3-idna which isn't installed dpkg: warning: ignoring request to remove python3-joblib which isn't installed dpkg: warning: ignoring request to remove python3-kiwisolver which isn't installed dpkg: warning: ignoring request to remove python3-lxml which isn't installed dpkg: warning: ignoring request to remove python3-lz4 which isn't installed dpkg: warning: ignoring request to remove python3-matplotlib which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-mmtf which isn't installed dpkg: warning: ignoring request to remove python3-monotonic which isn't installed dpkg: warning: ignoring request to remove python3-mpmath which isn't installed dpkg: warning: ignoring request to remove python3-mrcfile which isn't installed dpkg: warning: ignoring request to remove python3-msgpack 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-packaging which isn't installed dpkg: warning: ignoring request to remove python3-pil which isn't installed dpkg: warning: ignoring request to remove python3-pil.imagetk which isn't installed dpkg: warning: ignoring request to remove python3-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python3-pyparsing which isn't installed dpkg: warning: ignoring request to remove python3-reportlab which isn't installed dpkg: warning: ignoring request to remove python3-requests which isn't installed dpkg: warning: ignoring request to remove python3-rlpycairo which isn't installed dpkg: warning: ignoring request to remove python3-scipy which isn't installed dpkg: warning: ignoring request to remove python3-six which isn't installed Purging configuration files for python3-sympy (1.12-7) ... dpkg: warning: ignoring request to remove python3-threadpoolctl which isn't installed dpkg: warning: ignoring request to remove python3-tk which isn't installed dpkg: warning: ignoring request to remove python3-tqdm which isn't installed dpkg: warning: ignoring request to remove python3-tz which isn't installed dpkg: warning: ignoring request to remove python3-ufolib2 which isn't installed dpkg: warning: ignoring request to remove python3-unicodedata2 which isn't installed dpkg: warning: ignoring request to remove python3-urllib3 which isn't installed dpkg: warning: ignoring request to remove python3.11 which isn't installed Purging configuration files for python3.11-minimal (3.11.9-1) ... Purging configuration files for readline-common (8.2-4) ... Purging configuration files for sgml-base (1.31) ... dpkg: warning: ignoring request to remove sphinx-rtd-theme-common which isn't installed dpkg: warning: ignoring request to remove tk8.6-blt2.5 which isn't installed dpkg: warning: ignoring request to remove unicode-data which isn't installed Purging configuration files for w3c-sgml-lib (1.3-3) ... Purging configuration files for x11-common (1:7.7+23) ... dpkg: warning: ignoring request to remove xfonts-encodings which isn't installed Purging configuration files for xfonts-utils (1:7.7+6) ... Purging configuration files for xml-core (0.19) ... 3m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'dpkg', '--purge', 'blt', 'ca-certificates', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-font-awesome', 'fonts-lato', 'fonts-lyx', 'fonts-urw-base35', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgfortran5:amd64', 'libglib2.0-0t64:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libharfbuzz0b:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libjs-sphinxdoc', 'libjs-underscore', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libopenjp2-7:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libqhull-r8.0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'libsharpyuv0:amd64', 'libsqlite3-0:amd64', 'libtcl8.6:amd64', 'libtiff6:amd64', 'libtk8.6:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxml2:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'media-types', 'netbase', 'openssl', 'procps', 'python-matplotlib-data', 'python3', 'python3-appdirs', 'python3-attr', 'python3-biopython', 'python3-brotli', 'python3-cairo', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-citeproc', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-duecredit', 'python3-fasteners', 'python3-fonttools', 'python3-freetype', 'python3-fs', 'python3-griddataformats', 'python3-gsd', 'python3-idna', 'python3-joblib', 'python3-kiwisolver', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-minimal', 'python3-mmtf', 'python3-monotonic', 'python3-mpmath', 'python3-mrcfile', 'python3-msgpack', 'python3-networkx', 'python3-numpy', 'python3-packaging', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pkg-resources', 'python3-pyparsing', 'python3-reportlab', 'python3-requests', 'python3-rlpycairo', 'python3-scipy', 'python3-six', 'python3-sympy', 'python3-threadpoolctl', 'python3-tk:amd64', 'python3-tqdm', 'python3-tz', 'python3-ufolib2', 'python3-unicodedata2', 'python3-urllib3', 'python3.11', 'python3.11-minimal', 'readline-common', 'sgml-base', 'sphinx-rtd-theme-common', 'tk8.6-blt2.5', 'unicode-data', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core'] 3m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'dpkg', '--purge', 'python3-mdanalysis'] 3m4.5s DUMP: dpkg: warning: ignoring request to remove python3-mdanalysis which isn't installed 3m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'dpkg', '--purge', 'python3-mdanalysis'] 3m4.5s INFO: Running scripts post_purge 3m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/post_purge_exceptions'] 3m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/post_purge_exceptions'] 3m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'dpkg', '--purge', '--pending'] 3m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'dpkg', '--purge', '--pending'] 3m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'dpkg', '--remove', '--pending'] 3m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'dpkg', '--remove', '--pending'] 3m4.5s INFO: Running scripts post_test 3m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/post_test_exceptions'] 3m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'tmp/scripts/post_test_exceptions'] 3m4.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1tq868yb'] 3m4.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp1tq868yb'] 3m5.2s ERROR: WARN: Broken symlinks: /etc/fonts/conf.d/70-no-bitmaps-except-emoji.conf -> /usr/share/fontconfig/conf.avail/70-no-bitmaps-except-emoji.conf 3m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'dpkg-divert', '--list'] 3m5.2s DUMP: diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64 local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64 local diversion of /home to /home.distrib diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64 diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64 local diversion of /usr/bin/sync to /usr/bin/sync.distrib 3m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'dpkg-divert', '--list'] 3m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'apt-get', 'clean'] 3m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp1tq868yb', 'apt-get', 'clean'] 3m5.2s DEBUG: Recording chroot state 3m5.8s INFO: Warning: Package purging left files on system: /etc/fonts/ owned by: fontconfig-config, fonts-urw-base35, fonts-dejavu-core, fonts-dejavu-mono /etc/fonts/conf.d/ owned by: fontconfig-config, fonts-urw-base35, fonts-dejavu-core, fonts-dejavu-mono /etc/fonts/conf.d/70-no-bitmaps-except-emoji.conf -> /usr/share/fontconfig/conf.avail/70-no-bitmaps-except-emoji.conf not owned 3m5.8s INFO: PASS: Installation and purging test. 3m6.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp1tq868yb/dev/shm'] 3m6.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp1tq868yb/dev/shm'] 3m6.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp1tq868yb/dev/console'] 3m6.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp1tq868yb/dev/console'] 3m6.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp1tq868yb/dev/ptmx'] 3m6.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp1tq868yb/dev/ptmx'] 3m6.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp1tq868yb/dev/pts'] 3m6.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp1tq868yb/dev/pts'] 3m6.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp1tq868yb/proc'] 3m6.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp1tq868yb/proc'] 3m6.2s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp1tq868yb'] 3m6.3s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp1tq868yb'] 3m6.3s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp1tq868yb 3m6.3s INFO: PASS: All tests. 3m6.3s INFO: piuparts run ends. ret=0 End: 2024-04-22 10:00:54 GMT