Start: 2024-09-13 04:30:10 GMT Package: python3-openmm Source: openmm Version: 8.1.2+dfsg-1 Installed-Size: 79976 Maintainer: Debichem Team Architecture: amd64 Replaces: python3-simtk Provides: python3-simtk Depends: libopenmm-dev, python3 (<< 3.13), python3 (>= 3.12~), python3-numpy (>= 1:1.25.0), python3-numpy-abi9, python3:any, libc6 (>= 2.14), libgcc-s1 (>= 3.0), libopenmm8.1 (>= 8.1.2+dfsg), libstdc++6 (>= 13.1) Breaks: python3-simtk Description: Python bindings for the OpenMM molecular simulation package Homepage: https://simtk.org/projects/openmm Description-md5: 05222dad319a5457a88f80787dbc2e9a Section: python Priority: optional Filename: pool/main/o/openmm/python3-openmm_8.1.2+dfsg-1_amd64.deb Size: 6533444 MD5sum: 275516de25eb9ca53d7634d74a9dd914 SHA256: ec4962566808bee2776bc070bedc048e6b9494c96115d1bd0f0977e1b0d892b4 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --install-recommends --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/trixie-merged-usr_amd64.tar.gz -d trixie --no-upgrade-test --apt python3-openmm=8.1.2+dfsg-1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.4.4~202408201135~1.4.3-10-g39df1906 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --install-recommends --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/trixie-merged-usr_amd64.tar.gz -d trixie --no-upgrade-test --apt python3-openmm=8.1.2+dfsg-1 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-32-amd64 #1 SMP Debian 5.10.223-1 (2024-08-10) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpi9i4kxmi 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpi9i4kxmi 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi/proc'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi/proc'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi/dev/pts'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi/dev/pts'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi/dev/ptmx'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi/dev/ptmx'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi/dev/console'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi/dev/console'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi/dev/shm'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi/dev/shm'] 0m0.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main 0m0.2s DEBUG: Created policy-rc.d and chmodded it. 0m0.2s DEBUG: Created resolv.conf. 0m0.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpi9i4kxmi/tmp/scripts/ 0m0.2s INFO: Running scripts post_chroot_unpack 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'apt-get', 'update'] 0m1.7s DUMP: Get:1 http://deb.debian.org/debian trixie InRelease [169 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9257 kB] Get:3 http://deb.debian.org/debian trixie/main Translation-en [6175 kB] Fetched 15.6 MB in 1s (17.8 MB/s) Reading package lists... 0m1.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'apt-get', 'update'] 0m1.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'apt-get', '-yf', 'dist-upgrade'] 0m2.3s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: gpgv libssl3t64 openssl-provider-legacy 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 2787 kB of archives. After this operation, 5120 B of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 gpgv amd64 2.2.43-8+b1 [218 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 openssl-provider-legacy amd64 3.3.2-1 [298 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 libssl3t64 amd64 3.3.2-1 [2271 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 2787 kB in 0s (68.2 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5130 files and directories currently installed.) Preparing to unpack .../gpgv_2.2.43-8+b1_amd64.deb ... Unpacking gpgv (2.2.43-8+b1) over (2.2.43-8) ... Setting up gpgv (2.2.43-8+b1) ... (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 ... 5131 files and directories currently installed.) Preparing to unpack .../openssl-provider-legacy_3.3.2-1_amd64.deb ... Unpacking openssl-provider-legacy (3.3.2-1) over (3.3.1-7) ... Setting up openssl-provider-legacy (3.3.2-1) ... (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 ... 5131 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.3.2-1_amd64.deb ... Unpacking libssl3t64:amd64 (3.3.2-1) over (3.3.1-7) ... Setting up libssl3t64:amd64 (3.3.2-1) ... Processing triggers for libc-bin (2.40-2) ... 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'apt-get', '-yf', 'dist-upgrade'] 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.5s DUMP: 5cad7ef1f31787341deddc8a69949642 - 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.5s INFO: Running scripts post_setup 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/post_setup_dummy_users'] 0m2.9s 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 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/post_setup_dummy_users'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/post_setup_forbid_home'] 0m2.9s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/post_setup_forbid_home'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.9s 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' 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/post_setup_minimize'] 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/post_setup_minimize'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/post_setup_zz_backports'] 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/post_setup_zz_backports'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'apt-get', 'clean'] 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'apt-get', 'clean'] 0m3.0s DEBUG: Recording chroot state 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.2s DUMP: install ok installed apt apt 2.9.8 install ok installed base-files base-files 13.5 install ok installed base-passwd base-passwd 3.6.4 install ok installed bash bash 5.2.32-1 install ok installed bsdutils bsdutils 1:2.40.2-7 install ok installed coreutils coreutils 9.4-3.1 install ok installed dash dash 0.5.12-9 install ok installed debconf debconf 1.5.87 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.20 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.1-1 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-3 install ok installed gpgv gpgv 2.2.43-8+b1 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.23+nmu2 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed libacl1:amd64 libacl1 2.3.2-2 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.8 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:3.1.2-4 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-4+b1 install ok installed libblkid1:amd64 libblkid1 2.40.2-7 install ok installed libbsd0:amd64 libbsd0 0.12.2-1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.40-2 install ok installed libc6:amd64 libc6 2.40-2 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-2 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libcom-err2:amd64 libcom-err2 1.47.1-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-7 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.272 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.1-1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-3 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-6 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.6-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.50-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3 install ok installed liblzma5:amd64 liblzma5 5.6.2-2 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.40.2-7 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b1 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1+b1 install ok installed libselinux1:amd64 libselinux1 3.7-3 install ok installed libsemanage-common libsemanage-common 3.7-2 install ok installed libsemanage2:amd64 libsemanage2 3.7-2 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-7 install ok installed libss2:amd64 libss2 1.47.1-1 install ok installed libssl3t64:amd64 libssl3t64 3.3.2-1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-3 install ok installed libsystemd0:amd64 libsystemd0 256.5-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtinfo6:amd64 libtinfo6 6.5-2 install ok installed libudev1:amd64 libudev1 256.5-1 install ok installed libunistring5:amd64 libunistring5 1.2-1 install ok installed libuuid1:amd64 libuuid1 2.40.2-7 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1 install ok installed login login 1:4.16.0-2+really2.40.2-7 install ok installed login.defs login.defs 1:4.16.0-4 install ok installed logsave logsave 1.47.1-1 install ok installed mawk mawk 1.3.4.20240819-3 install ok installed mount mount 2.40.2-7 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.2-1 install ok installed passwd passwd 1:4.16.0-4 install ok installed perl-base perl-base 5.38.2-5 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.10-1 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024a-4 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-7 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'dpkg-divert', '--list'] 0m3.2s 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 /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6 diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64 diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64 diversion of /libx32 to /.libx32.usr-is-merged by base-files local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /lib32 to /.lib32.usr-is-merged by base-files diversion of /libo32 to /.libo32.usr-is-merged by base-files 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'dpkg-divert', '--list'] 0m3.2s INFO: Running scripts is_testable 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/is_testable_uninstallable'] 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/is_testable_uninstallable'] 0m3.2s INFO: apt-cache does not know about any of the requested packages 0m3.2s INFO: Running scripts pre_test 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/pre_test_exceptions'] 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/pre_test_exceptions'] 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/pre_test_root_password'] 0m3.2s DUMP: New password: Retype new password: passwd: password updated successfully 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/pre_test_root_password'] 0m3.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi'] 0m3.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi'] 0m3.7s DEBUG: No broken symlinks as far as we can find. 0m3.7s INFO: Running scripts pre_install 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/pre_install_database-server'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/pre_install_database-server'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/pre_install_exceptions'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/pre_install_exceptions'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/pre_install_extras'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/pre_install_extras'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi'] 0m3.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi'] 0m4.1s DEBUG: No broken symlinks as far as we can find. 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'apt-cache', 'policy'] 0m4.4s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie/main amd64 Packages release o=Debian,a=testing,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'apt-cache', 'policy'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'apt-cache', 'policy', 'python3-openmm'] 0m4.5s DUMP: python3-openmm: Installed: (none) Candidate: 8.1.2+dfsg-1 Version table: 8.1.2+dfsg-1 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'apt-cache', 'policy', 'python3-openmm'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'apt-get', '-y', 'install', 'python3-openmm=8.1.2+dfsg-1'] 0m11.6s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: ca-certificates krb5-locales libblas3 libexpat1 libgfortran5 libgpm2 libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libncursesw6 libnsl2 libopenmm-dev libopenmm8.1 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libreadline8t64 libsqlite3-0 libtirpc-common libtirpc3t64 media-types netbase openssl python3 python3-minimal python3-numpy python3-pkg-resources python3.12 python3.12-minimal readline-common Suggested packages: gpm krb5-doc krb5-user python3-doc python3-tk python3-venv gcc gfortran python-numpy-doc python3-dev python3-pytest python3-setuptools python3.12-venv python3.12-doc binutils binfmt-support readline-doc The following NEW packages will be installed: ca-certificates krb5-locales libblas3 libexpat1 libgfortran5 libgpm2 libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libncursesw6 libnsl2 libopenmm-dev libopenmm8.1 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libreadline8t64 libsqlite3-0 libtirpc-common libtirpc3t64 media-types netbase openssl python3 python3-minimal python3-numpy python3-openmm python3-pkg-resources python3.12 python3.12-minimal readline-common 0 upgraded, 34 newly installed, 0 to remove and 0 not upgraded. Need to get 25.3 MB of archives. After this operation, 159 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 libpython3.12-minimal amd64 3.12.6-1 [814 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.3-1 [105 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 python3.12-minimal amd64 3.12.6-1 [2168 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.12.5-1 [26.7 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 libncursesw6 amd64 6.5-2 [135 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get:9 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get:10 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get:11 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get:12 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get:13 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get:14 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3 [82.7 kB] Get:15 http://deb.debian.org/debian trixie/main amd64 libnsl2 amd64 1.3.0-3+b2 [40.3 kB] Get:16 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-5 [69.3 kB] Get:17 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get:18 http://deb.debian.org/debian trixie/main amd64 libsqlite3-0 amd64 3.46.0-1 [902 kB] Get:19 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.6-1 [1963 kB] Get:20 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.6-1 [669 kB] Get:21 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.12.5-1 [9588 B] Get:22 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.12.5-1 [27.6 kB] Get:23 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.3.2-1 [1381 kB] Get:24 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get:25 http://deb.debian.org/debian trixie/main amd64 krb5-locales all 1.21.3-3 [101 kB] Get:26 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get:27 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-3 [837 kB] Get:28 http://deb.debian.org/debian trixie/main amd64 libgpm2 amd64 1.20.7-11 [14.0 kB] Get:29 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get:30 http://deb.debian.org/debian trixie/main amd64 libopenmm8.1 amd64 8.1.2+dfsg-1 [1058 kB] Get:31 http://deb.debian.org/debian trixie/main amd64 libopenmm-dev amd64 8.1.2+dfsg-1 [345 kB] Get:32 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 70.3.0-2 [264 kB] Get:33 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:1.26.4+ds-11 [4236 kB] Get:34 http://deb.debian.org/debian trixie/main amd64 python3-openmm amd64 8.1.2+dfsg-1 [6533 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 25.3 MB in 1s (19.1 MB/s) Selecting previously unselected package libpython3.12-minimal:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5135 files and directories currently installed.) Preparing to unpack .../libpython3.12-minimal_3.12.6-1_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.6-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../libexpat1_2.6.3-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.3-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.6-1_amd64.deb ... Unpacking python3.12-minimal (3.12.6-1) ... Setting up libpython3.12-minimal:amd64 (3.12.6-1) ... Setting up libexpat1:amd64 (2.6.3-1) ... Setting up python3.12-minimal (3.12.6-1) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5455 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.5-1_amd64.deb ... Unpacking python3-minimal (3.12.5-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package libncursesw6:amd64. Preparing to unpack .../03-libncursesw6_6.5-2_amd64.deb ... Unpacking libncursesw6:amd64 (6.5-2) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../05-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../06-libkeyutils1_1.6.3-3_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-3) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../07-libkrb5-3_1.21.3-3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../08-libgssapi-krb5-2_1.21.3-3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../09-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:amd64. Preparing to unpack .../10-libtirpc3t64_1.3.4+ds-1.3_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../11-libnsl2_1.3.0-3+b2_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b2) ... Selecting previously unselected package readline-common. Preparing to unpack .../12-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../13-libreadline8t64_8.2-5_amd64.deb ... 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 (8.2-5) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../14-libsqlite3-0_3.46.0-1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.46.0-1) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.6-1_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.6-1) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.6-1_amd64.deb ... Unpacking python3.12 (3.12.6-1) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../17-libpython3-stdlib_3.12.5-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.5-1) ... Setting up python3-minimal (3.12.5-1) ... Selecting previously unselected package python3. (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 ... 6012 files and directories currently installed.) Preparing to unpack .../00-python3_3.12.5-1_amd64.deb ... Unpacking python3 (3.12.5-1) ... Selecting previously unselected package openssl. Preparing to unpack .../01-openssl_3.3.2-1_amd64.deb ... Unpacking openssl (3.3.2-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../02-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) ... 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Selecting previously unselected package libopenmm-dev. Preparing to unpack .../09-libopenmm-dev_8.1.2+dfsg-1_amd64.deb ... Unpacking libopenmm-dev (8.1.2+dfsg-1) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../10-python3-pkg-resources_70.3.0-2_all.deb ... Unpacking python3-pkg-resources (70.3.0-2) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../11-python3-numpy_1%3a1.26.4+ds-11_amd64.deb ... Unpacking python3-numpy (1:1.26.4+ds-11) ... Selecting previously unselected package python3-openmm. Preparing to unpack .../12-python3-openmm_8.1.2+dfsg-1_amd64.deb ... Unpacking python3-openmm (8.1.2+dfsg-1) ... Setting up media-types (10.1.0) ... Setting up libkeyutils1:amd64 (1.6.3-3) ... Setting up libgpm2:amd64 (1.20.7-11) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libsqlite3-0:amd64 (3.46.0-1) ... Setting up krb5-locales (1.21.3-3) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... 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 libncursesw6:amd64 (6.5-2) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libgfortran5:amd64 (14.2.0-3) ... Setting up netbase (6.4) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up openssl (3.3.2-1) ... Setting up libopenmm8.1 (8.1.2+dfsg-1) ... Setting up readline-common (8.2-5) ... 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 libopenmm-dev (8.1.2+dfsg-1) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Setting up libnsl2:amd64 (1.3.0-3+b2) ... Setting up libpython3.12-stdlib:amd64 (3.12.6-1) ... Setting up python3.12 (3.12.6-1) ... Setting up libpython3-stdlib:amd64 (3.12.5-1) ... Setting up python3 (3.12.5-1) ... Setting up python3-pkg-resources (70.3.0-2) ... Setting up python3-numpy (1:1.26.4+ds-11) ... Setting up python3-openmm (8.1.2+dfsg-1) ... /usr/lib/python3/dist-packages/openmm/__init__.py:16: SyntaxWarning: invalid escape sequence '\p' os.environ['PATH'] = '%(lib)s;%(lib)s\plugins;%(path)s' % { /usr/lib/python3/dist-packages/openmm/app/gromacsgrofile.py:62: SyntaxWarning: invalid escape sequence '\.' return match('^[-+]?[0-9]*\.?[0-9]*([eEdD][-+]?[0-9]+)?$',word) /usr/lib/python3/dist-packages/openmm/app/internal/amber_file_parser.py:65: SyntaxWarning: invalid escape sequence '\(' FORMAT_RE_PATTERN=re.compile("([0-9]+)\(?([a-zA-Z]+)([0-9]+)\.?([0-9]*)\)?") /usr/lib/python3/dist-packages/openmm/app/internal/pdbstructure.py:1071: SyntaxWarning: invalid escape sequence '\.' if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file): /usr/lib/python3/dist-packages/openmm/app/internal/pdbstructure.py:1082: SyntaxWarning: invalid escape sequence '\.' if not re.match("pdb.%2s.\.ent\.gz" % subdir , pdb_file): /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:358: SyntaxWarning: invalid escape sequence '\S' "(?:_(.+?)[.](\S+))" "|" # _category.attribute /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:360: SyntaxWarning: invalid escape sequence '\s' "(?:['](.*?)(?:[']\s|[']$))" "|" # single quoted strings /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:361: SyntaxWarning: invalid escape sequence '\s' "(?:[\"](.*?)(?:[\"]\s|[\"]$))" "|" # double quoted strings /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:363: SyntaxWarning: invalid escape sequence '\s' "(?:\s*#.*$)" "|" # comments (dumped) /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:365: SyntaxWarning: invalid escape sequence '\S' "(\S+)" # unquoted words /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:416: SyntaxWarning: invalid escape sequence '\S' """ Tokenizer method for the mmCIF syntax file - /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:444: SyntaxWarning: invalid escape sequence '\S' "(?:_(.+?)[.](\S+))" "|" # _category.attribute /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:446: SyntaxWarning: invalid escape sequence '\s' "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:448: SyntaxWarning: invalid escape sequence '\s' "(?:\s*#.*$)" "|" # comments (dumped) /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxParser.py:450: SyntaxWarning: invalid escape sequence '\S' "(\S+)" # unquoted words /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:347: SyntaxWarning: invalid escape sequence '\S' "(?:_(.+?)[.](\S+))" "|" # _category.attribute /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:349: SyntaxWarning: invalid escape sequence '\s' "(?:['](.*?)(?:[']\s|[']$))" "|" # single quoted strings /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:350: SyntaxWarning: invalid escape sequence '\s' "(?:[\"](.*?)(?:[\"]\s|[\"]$))" "|" # double quoted strings /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:352: SyntaxWarning: invalid escape sequence '\s' "(?:\s*#.*$)" "|" # comments (dumped) /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:354: SyntaxWarning: invalid escape sequence '\S' "(\S+)" # unquoted words /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:419: SyntaxWarning: invalid escape sequence '\S' "(?:_(.+?)[.](\S+))" "|" # _category.attribute /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:421: SyntaxWarning: invalid escape sequence '\s' "(?:['\"](.*?)(?:['\"]\s|['\"]$))" "|" # quoted strings /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:423: SyntaxWarning: invalid escape sequence '\s' "(?:\s*#.*$)" "|" # comments (dumped) /usr/lib/python3/dist-packages/openmm/app/internal/pdbx/reader/PdbxReader.py:425: SyntaxWarning: invalid escape sequence '\S' "(\S+)" # unquoted words /usr/lib/python3/dist-packages/openmm/app/metadynamics.py:247: SyntaxWarning: invalid escape sequence '\.' pattern = re.compile('bias_(.*)_(.*)\.npy') /usr/lib/python3/dist-packages/openmm/openmm.py:1556: SyntaxWarning: invalid escape sequence '\S' match = re.search("<([^?]\S*)", inputString) Processing triggers for libc-bin (2.40-2) ... 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. 0m11.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'apt-get', '-y', 'install', 'python3-openmm=8.1.2+dfsg-1'] 0m11.6s INFO: Running scripts post_install 0m11.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/post_install_exceptions'] 0m11.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/post_install_exceptions'] 0m11.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi'] 0m11.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi'] 0m12.4s DEBUG: No broken symlinks as far as we can find. 0m12.6s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', '-ac', '--ignore-obsolete'] 0m13.3s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', '-ac', '--ignore-obsolete'] 0m13.3s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m13.3s DUMP: 0.15.6 0m13.3s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m13.3s INFO: Running adequate version 0.15.6 now. 0m13.3s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'python3-openmm'] 0m13.3s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'python3-openmm'] 0m13.3s INFO: Running scripts pre_remove 0m13.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m13.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m13.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m13.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m13.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m13.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m13.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m13.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m13.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m13.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m13.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/pre_remove_exceptions'] 0m13.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/pre_remove_exceptions'] 0m13.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m13.9s DUMP: install ok installed apt apt 2.9.8 install ok installed base-files base-files 13.5 install ok installed base-passwd base-passwd 3.6.4 install ok installed bash bash 5.2.32-1 install ok installed bsdutils bsdutils 1:2.40.2-7 install ok installed ca-certificates ca-certificates 20240203 install ok installed coreutils coreutils 9.4-3.1 install ok installed dash dash 0.5.12-9 install ok installed debconf debconf 1.5.87 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.20 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.1-1 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-3 install ok installed gpgv gpgv 2.2.43-8+b1 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.23+nmu2 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed krb5-locales krb5-locales 1.21.3-3 install ok installed libacl1:amd64 libacl1 2.3.2-2 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.8 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:3.1.2-4 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-4+b1 install ok installed libblas3:amd64 libblas3 3.12.0-3 install ok installed libblkid1:amd64 libblkid1 2.40.2-7 install ok installed libbsd0:amd64 libbsd0 0.12.2-1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.40-2 install ok installed libc6:amd64 libc6 2.40-2 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-2 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libcom-err2:amd64 libcom-err2 1.47.1-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-7 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.272 install ok installed libexpat1:amd64 libexpat1 2.6.3-1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.1-1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-3 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-6 install ok installed libgfortran5:amd64 libgfortran5 14.2.0-3 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.6-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.50-3 install ok installed libgpm2:amd64 libgpm2 1.20.7-11 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.21.3-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed libk5crypto3:amd64 libk5crypto3 1.21.3-3 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-3 install ok installed libkrb5-3:amd64 libkrb5-3 1.21.3-3 install ok installed libkrb5support0:amd64 libkrb5support0 1.21.3-3 install ok installed liblapack3:amd64 liblapack3 3.12.0-3 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3 install ok installed liblzma5:amd64 liblzma5 5.6.2-2 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.40.2-7 install ok installed libncursesw6:amd64 libncursesw6 6.5-2 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-3+b2 install ok installed libopenmm-dev libopenmm-dev 8.1.2+dfsg-1 install ok installed libopenmm8.1 libopenmm8.1 8.1.2+dfsg-1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.12.5-1 install ok installed libpython3.12-minimal:amd64 libpython3.12-minimal 3.12.6-1 install ok installed libpython3.12-stdlib:amd64 libpython3.12-stdlib 3.12.6-1 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-5 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1+b1 install ok installed libselinux1:amd64 libselinux1 3.7-3 install ok installed libsemanage-common libsemanage-common 3.7-2 install ok installed libsemanage2:amd64 libsemanage2 3.7-2 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-7 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.0-1 install ok installed libss2:amd64 libss2 1.47.1-1 install ok installed libssl3t64:amd64 libssl3t64 3.3.2-1 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-3 install ok installed libsystemd0:amd64 libsystemd0 256.5-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtinfo6:amd64 libtinfo6 6.5-2 install ok installed libtirpc-common libtirpc-common 1.3.4+ds-1.3 install ok installed libtirpc3t64:amd64 libtirpc3t64 1.3.4+ds-1.3 install ok installed libudev1:amd64 libudev1 256.5-1 install ok installed libunistring5:amd64 libunistring5 1.2-1 install ok installed libuuid1:amd64 libuuid1 2.40.2-7 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1 install ok installed login login 1:4.16.0-2+really2.40.2-7 install ok installed login.defs login.defs 1:4.16.0-4 install ok installed logsave logsave 1.47.1-1 install ok installed mawk mawk 1.3.4.20240819-3 install ok installed media-types media-types 10.1.0 install ok installed mount mount 2.40.2-7 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2 install ok installed netbase netbase 6.4 install ok installed openssl openssl 3.3.2-1 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.2-1 install ok installed passwd passwd 1:4.16.0-4 install ok installed perl-base perl-base 5.38.2-5 install ok installed python3 python3 3.12.5-1 install ok installed python3-minimal python3-minimal 3.12.5-1 install ok installed python3-numpy python3-numpy 1:1.26.4+ds-11 install ok installed python3-openmm python3-openmm 8.1.2+dfsg-1 install ok installed python3-pkg-resources python3-pkg-resources 70.3.0-2 install ok installed python3.12 python3.12 3.12.6-1 install ok installed python3.12-minimal python3.12-minimal 3.12.6-1 install ok installed readline-common readline-common 8.2-5 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.10-1 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024a-4 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-7 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1 0m13.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m13.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'apt-get', 'remove', 'ca-certificates', 'krb5-locales', 'libblas3:amd64', 'libexpat1:amd64', 'libgfortran5:amd64', 'libgpm2:amd64', 'libgssapi-krb5-2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libopenmm-dev', 'libopenmm8.1', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libreadline8t64:amd64', 'libsqlite3-0:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'media-types', 'netbase', 'openssl', 'python3', 'python3-minimal', 'python3-numpy', 'python3-pkg-resources', 'python3.12', 'python3.12-minimal', 'readline-common', 'python3-openmm'] 0m14.8s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: ca-certificates krb5-locales libblas3 libexpat1 libgfortran5 libgpm2 libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libncursesw6 libnsl2 libopenmm-dev libopenmm8.1 libpython3-stdlib libpython3.12-minimal libpython3.12-stdlib libreadline8t64 libsqlite3-0 libtirpc-common libtirpc3t64 media-types netbase openssl python3 python3-minimal python3-numpy python3-openmm python3-pkg-resources python3.12 python3.12-minimal readline-common 0 upgraded, 0 newly installed, 34 to remove and 0 not upgraded. After this operation, 159 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 ... 8088 files and directories currently installed.) Removing ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing krb5-locales (1.21.3-3) ... Removing python3-openmm (8.1.2+dfsg-1) ... Removing python3-numpy (1:1.26.4+ds-11) ... Removing liblapack3:amd64 (3.12.0-3) ... Removing libblas3:amd64 (3.12.0-3) ... Removing python3-pkg-resources (70.3.0-2) ... Removing python3 (3.12.5-1) ... Removing python3.12 (3.12.6-1) ... Removing python3-minimal (3.12.5-1) ... Removing python3.12-minimal (3.12.6-1) ... Removing libexpat1:amd64 (2.6.3-1) ... Removing libgfortran5:amd64 (14.2.0-3) ... Removing libgpm2:amd64 (1.20.7-11) ... Removing libpython3-stdlib:amd64 (3.12.5-1) ... Removing libpython3.12-stdlib:amd64 (3.12.6-1) ... find: '/usr/lib/python3': No such file or directory Removing libnsl2:amd64 (1.3.0-3+b2) ... Removing libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Removing libgssapi-krb5-2:amd64 (1.21.3-3) ... Removing libkrb5-3:amd64 (1.21.3-3) ... Removing libk5crypto3:amd64 (1.21.3-3) ... Removing libkeyutils1:amd64 (1.6.3-3) ... Removing libkrb5support0:amd64 (1.21.3-3) ... Removing libncursesw6:amd64 (6.5-2) ... Removing libopenmm-dev (8.1.2+dfsg-1) ... Removing libopenmm8.1 (8.1.2+dfsg-1) ... Removing libpython3.12-minimal:amd64 (3.12.6-1) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8t64:amd64 (8.2-5) ... Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Removing libsqlite3-0:amd64 (3.46.0-1) ... Removing libtirpc-common (1.3.4+ds-1.3) ... Removing media-types (10.1.0) ... Removing netbase (6.4) ... Removing openssl (3.3.2-1) ... Removing readline-common (8.2-5) ... Processing triggers for libc-bin (2.40-2) ... 0m14.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'apt-get', 'remove', 'ca-certificates', 'krb5-locales', 'libblas3:amd64', 'libexpat1:amd64', 'libgfortran5:amd64', 'libgpm2:amd64', 'libgssapi-krb5-2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libopenmm-dev', 'libopenmm8.1', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libreadline8t64:amd64', 'libsqlite3-0:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'media-types', 'netbase', 'openssl', 'python3', 'python3-minimal', 'python3-numpy', 'python3-pkg-resources', 'python3.12', 'python3.12-minimal', 'readline-common', 'python3-openmm'] 0m14.8s INFO: Running scripts post_remove 0m14.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/post_remove_exceptions'] 0m14.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/post_remove_exceptions'] 0m14.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'dpkg', '--purge', 'ca-certificates', 'krb5-locales', 'libblas3:amd64', 'libexpat1:amd64', 'libgfortran5:amd64', 'libgpm2:amd64', 'libgssapi-krb5-2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libopenmm-dev', 'libopenmm8.1', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libreadline8t64:amd64', 'libsqlite3-0:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'media-types', 'netbase', 'openssl', 'python3', 'python3-minimal', 'python3-numpy', 'python3-pkg-resources', 'python3.12', 'python3.12-minimal', 'readline-common'] 0m14.9s DUMP: (Reading database ... 5146 files and directories currently installed.) Purging configuration files for ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. dpkg: warning: ignoring request to remove krb5-locales which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed dpkg: warning: ignoring request to remove libgpm2 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.21.3-3) ... dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libnsl2 which isn't installed dpkg: warning: ignoring request to remove libopenmm-dev which isn't installed dpkg: warning: ignoring request to remove libopenmm8.1 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.12-minimal:amd64 (3.12.6-1) ... dpkg: warning: ignoring request to remove libpython3.12-stdlib which isn't installed Purging configuration files for libreadline8t64:amd64 (8.2-5) ... dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed Purging configuration files for libtirpc-common (1.3.4+ds-1.3) ... Purging configuration files for libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Purging configuration files for media-types (10.1.0) ... Purging configuration files for netbase (6.4) ... Purging configuration files for openssl (3.3.2-1) ... Purging configuration files for python3 (3.12.5-1) ... dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-numpy which isn't installed dpkg: warning: ignoring request to remove python3-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python3.12 which isn't installed Purging configuration files for python3.12-minimal (3.12.6-1) ... Purging configuration files for readline-common (8.2-5) ... 0m14.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'dpkg', '--purge', 'ca-certificates', 'krb5-locales', 'libblas3:amd64', 'libexpat1:amd64', 'libgfortran5:amd64', 'libgpm2:amd64', 'libgssapi-krb5-2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libopenmm-dev', 'libopenmm8.1', 'libpython3-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libreadline8t64:amd64', 'libsqlite3-0:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'media-types', 'netbase', 'openssl', 'python3', 'python3-minimal', 'python3-numpy', 'python3-pkg-resources', 'python3.12', 'python3.12-minimal', 'readline-common'] 0m14.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'dpkg', '--purge', 'python3-openmm'] 0m14.9s DUMP: dpkg: warning: ignoring request to remove python3-openmm which isn't installed 0m14.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'dpkg', '--purge', 'python3-openmm'] 0m14.9s INFO: Running scripts post_purge 0m14.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/post_purge_exceptions'] 0m14.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/post_purge_exceptions'] 0m14.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'dpkg', '--purge', '--pending'] 0m14.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'dpkg', '--purge', '--pending'] 0m14.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'dpkg', '--remove', '--pending'] 0m14.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'dpkg', '--remove', '--pending'] 0m14.9s INFO: Running scripts post_test 0m14.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/post_test_exceptions'] 0m14.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'tmp/scripts/post_test_exceptions'] 0m14.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi'] 0m15.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi'] 0m15.3s DEBUG: No broken symlinks as far as we can find. 0m15.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'dpkg-divert', '--list'] 0m15.3s DUMP: diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64 local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64 local diversion of /home to /home.distrib diversion of /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6 diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64 diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64 diversion of /libx32 to /.libx32.usr-is-merged by base-files local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /lib32 to /.lib32.usr-is-merged by base-files diversion of /libo32 to /.libo32.usr-is-merged by base-files 0m15.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'dpkg-divert', '--list'] 0m15.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'apt-get', 'clean'] 0m15.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi', 'apt-get', 'clean'] 0m15.3s DEBUG: Recording chroot state 0m15.6s INFO: PASS: Installation and purging test. 0m15.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi/dev/shm'] 0m15.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi/dev/shm'] 0m15.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi/dev/console'] 0m15.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi/dev/console'] 0m15.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi/dev/ptmx'] 0m15.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi/dev/ptmx'] 0m15.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi/dev/pts'] 0m15.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi/dev/pts'] 0m15.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi/proc'] 0m15.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi/proc'] 0m15.8s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi'] 0m15.9s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpi9i4kxmi'] 0m15.9s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpi9i4kxmi 0m15.9s INFO: PASS: All tests. 0m15.9s INFO: piuparts run ends. ret=0 End: 2024-09-13 04:30:26 GMT