Start: 2023-07-25 21:30:39 GMT [testing] Package: libpromod3-modelling3.2 Source: promod3 (3.2.1+ds-6) Version: 3.2.1+ds-6+b1 Installed-Size: 921 Maintainer: Debichem Team Architecture: amd64 Depends: libboost-filesystem1.74.0 (>= 1.74.0), libc6 (>= 2.32), libgcc-s1 (>= 4.0), libost-base2.3 (>= 2.3.1), libost-conop2.3 (>= 2.3.1), libost-geom2.3 (>= 2.3.1), libost-io2.3 (>= 2.3.1), libost-mol-mm2.3 (>= 2.3.1), libost-mol2.3 (>= 2.3.1), libost-seq2.3 (>= 2.3.1), libpromod3-core3.2 (>= 3.2.1+ds), libpromod3-loop3.2 (>= 3.2.1+ds), libpromod3-scoring3.2 (>= 3.2.1+ds), libpromod3-sidechain3.2 (>= 3.2.1+ds), libstdc++6 (>= 11) Description: protein homology modelling engine Homepage: https://openstructure.org/promod3/ Description-md5: ed662fcd37699c83b00770498305af3a Tag: role::shared-lib Section: libs Priority: optional Filename: pool/main/p/promod3/libpromod3-modelling3.2_3.2.1+ds-6+b1_amd64.deb Size: 296376 MD5sum: 702fb8507e408f1643bbafb796309c1d SHA256: 3bed9ffaed69202ae8f4e2c7b675d2f6ba7d9ef95eccf7769a0eb2e6902df032 [sid] Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt libpromod3-modelling3.2=None 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 1.1.8~202306121314~1.1.7-9-g57dfbde6 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt libpromod3-modelling3.2=None 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-23-amd64 #1 SMP Debian 5.10.179-2 (2023-07-14) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpd2rkyya2 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpd2rkyya2 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz'] 0m2.3s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz'] 0m2.3s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2/proc'] 0m2.3s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2/proc'] 0m2.3s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2/dev/pts'] 0m2.3s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2/dev/pts'] 0m2.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2/dev/ptmx'] 0m2.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2/dev/ptmx'] 0m2.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2/dev/console'] 0m2.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2/dev/console'] 0m2.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2/dev/shm'] 0m2.3s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2/dev/shm'] 0m2.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m2.3s DEBUG: Created policy-rc.d and chmodded it. 0m2.3s DEBUG: Created resolv.conf. 0m2.3s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpd2rkyya2/tmp/scripts/ 0m2.3s INFO: Running scripts post_chroot_unpack 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'apt-get', 'update'] 0m5.6s DUMP: Get:1 http://deb.debian.org/debian bookworm InRelease [151 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 Packages [8906 kB] Get:3 http://deb.debian.org/debian bookworm/main Translation-en [6078 kB] Fetched 15.1 MB in 2s (6220 kB/s) Reading package lists... 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'apt-get', 'update'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'apt-get', '-yf', 'dist-upgrade'] 0m7.7s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: base-files libc-bin libc6 libsystemd0 libudev1 5 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 3867 kB of archives. After this operation, 7168 B of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 base-files amd64 12.4+deb12u1 [70.7 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 libc6 amd64 2.36-9+deb12u1 [2753 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libc-bin amd64 2.36-9+deb12u1 [606 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 libsystemd0 amd64 252.12-1~deb12u1 [330 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 libudev1 amd64 252.12-1~deb12u1 [107 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 3867 kB in 0s (54.4 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 ... 6098 files and directories currently installed.) Preparing to unpack .../base-files_12.4+deb12u1_amd64.deb ... Unpacking base-files (12.4+deb12u1) over (12.4) ... Setting up base-files (12.4+deb12u1) ... Installing new version of config file /etc/debian_version ... (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 ... 6098 files and directories currently installed.) Preparing to unpack .../libc6_2.36-9+deb12u1_amd64.deb ... Unpacking libc6:amd64 (2.36-9+deb12u1) over (2.36-9) ... Setting up libc6:amd64 (2.36-9+deb12u1) ... (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 ... 6098 files and directories currently installed.) Preparing to unpack .../libc-bin_2.36-9+deb12u1_amd64.deb ... Unpacking libc-bin (2.36-9+deb12u1) over (2.36-9) ... Setting up libc-bin (2.36-9+deb12u1) ... (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 ... 6098 files and directories currently installed.) Preparing to unpack .../libsystemd0_252.12-1~deb12u1_amd64.deb ... Unpacking libsystemd0:amd64 (252.12-1~deb12u1) over (252.6-1) ... Setting up libsystemd0:amd64 (252.12-1~deb12u1) ... (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 ... 6098 files and directories currently installed.) Preparing to unpack .../libudev1_252.12-1~deb12u1_amd64.deb ... Unpacking libudev1:amd64 (252.12-1~deb12u1) over (252.6-1) ... Setting up libudev1:amd64 (252.12-1~deb12u1) ... Processing triggers for libc-bin (2.36-9+deb12u1) ... 0m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'apt-get', '-yf', 'dist-upgrade'] 0m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m8.2s DUMP: 06167fd988d2fa1ed9015ed386bb0220 - 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m8.2s INFO: Running scripts post_setup 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/post_setup_dummy_users'] 0m9.0s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/post_setup_dummy_users'] 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/post_setup_forbid_home'] 0m9.1s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/post_setup_forbid_home'] 0m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/post_setup_force-unsafe-io'] 0m9.1s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' dpkg-divert: warning: diverting file '/bin/sync' from an Essential package with rename is dangerous, use --no-rename '/bin/sync' -> 'true' 0m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/post_setup_force-unsafe-io'] 0m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/post_setup_minimize'] 0m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/post_setup_minimize'] 0m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/post_setup_squeeze-backports'] 0m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/post_setup_squeeze-backports'] 0m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/post_setup_zz_backports'] 0m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/post_setup_zz_backports'] 0m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m9.1s DUMP: install ok installed adduser adduser 3.134 install ok installed apt apt 2.6.1 install ok installed base-files base-files 12.4+deb12u1 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b2 install ok installed bsdutils bsdutils 1:2.38.1-5+b1 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.12-2 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.3 install ok installed debianutils debianutils 5.7-0.4 install ok installed diffutils diffutils 1:3.8-4 install ok installed dpkg dpkg 1.21.22 install ok installed e2fsprogs e2fsprogs 1.47.0-2 install ok installed findutils findutils 4.9.0-4 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-14 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.8-5 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu1 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.6.1 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.0.9-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.9-1 install ok installed libblkid1:amd64 libblkid1 2.38.1-5+b1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-9+deb12u1 install ok installed libc6:amd64 libc6 2.36-9+deb12u1 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3 install ok installed libcap2:amd64 libcap2 1:2.66-4 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.33-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.270 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-14 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-3 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.9-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.1-0.2 install ok installed libmd0:amd64 libmd0 1.0.4-2 install ok installed libmount1:amd64 libmount1 2.38.1-5+b1 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-6 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-6 install ok installed libpam-runtime libpam-runtime 1.5.2-6 install ok installed libpam0g:amd64 libpam0g 1.5.2-6 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-1 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+b3 install ok installed libselinux1:amd64 libselinux1 3.4-1+b6 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b5 install ok installed libsepol2:amd64 libsepol2 3.4-2.1 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-5+b1 install ok installed libss2:amd64 libss2 1.47.0-2 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-14 install ok installed libsystemd0:amd64 libsystemd0 252.12-1~deb12u1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.4-4 install ok installed libudev1:amd64 libudev1 252.12-1~deb12u1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+b1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.4+dfsg2-5 install ok installed login login 1:4.13+dfsg1-1+b1 install ok installed logsave logsave 1.47.0-2 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mount mount 2.38.1-5+b1 install ok installed ncurses-base ncurses-base 6.4-4 install ok installed ncurses-bin ncurses-bin 6.4-4 install ok installed passwd passwd 1:4.13+dfsg1-1+b1 install ok installed perl-base perl-base 5.36.0-7 install ok installed sed sed 4.9-1 install ok installed sysvinit-utils sysvinit-utils 3.06-4 install ok installed tar tar 1.34+dfsg-1.2 install ok installed tzdata tzdata 2023c-5 install ok installed usr-is-merged usr-is-merged 35 install ok installed util-linux util-linux 2.38.1-5+b1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+b1 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m9.1s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m9.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2'] 0m9.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2'] 0m9.6s INFO: Running scripts is_testable 0m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/is_testable_uninstallable'] 0m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/is_testable_uninstallable'] 0m9.6s INFO: Running scripts pre_test 0m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/pre_test_exceptions'] 0m9.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/pre_test_exceptions'] 0m9.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/pre_test_root_password'] 0m9.7s DUMP: New password: Retype new password: passwd: password updated successfully 0m9.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/pre_test_root_password'] 0m9.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'apt-cache', 'show', '--no-all-versions', 'libpromod3-modelling3.2'] 0m9.9s DUMP: Package: libpromod3-modelling3.2 Source: promod3 (3.2.1+ds-6) Version: 3.2.1+ds-6+b1 Installed-Size: 921 Maintainer: Debichem Team Architecture: amd64 Depends: libboost-filesystem1.74.0 (>= 1.74.0), libc6 (>= 2.32), libgcc-s1 (>= 4.0), libost-base2.3 (>= 2.3.1), libost-conop2.3 (>= 2.3.1), libost-geom2.3 (>= 2.3.1), libost-io2.3 (>= 2.3.1), libost-mol-mm2.3 (>= 2.3.1), libost-mol2.3 (>= 2.3.1), libost-seq2.3 (>= 2.3.1), libpromod3-core3.2 (>= 3.2.1+ds), libpromod3-loop3.2 (>= 3.2.1+ds), libpromod3-scoring3.2 (>= 3.2.1+ds), libpromod3-sidechain3.2 (>= 3.2.1+ds), libstdc++6 (>= 11) Description-en: protein homology modelling engine ProMod3 is a modelling engine based on the OpenStructure computational structural biology framework that can perform all steps required to generate a protein model by homology. Its modular design aims at implementing flexible modelling pipelines and fast prototyping of novel algorithms. . This package contains the shared library for modelling engine. Description-md5: ed662fcd37699c83b00770498305af3a Homepage: https://openstructure.org/promod3/ Tag: role::shared-lib Section: libs Priority: optional Filename: pool/main/p/promod3/libpromod3-modelling3.2_3.2.1+ds-6+b1_amd64.deb Size: 296376 MD5sum: 702fb8507e408f1643bbafb796309c1d SHA256: 3bed9ffaed69202ae8f4e2c7b675d2f6ba7d9ef95eccf7769a0eb2e6902df032 0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'apt-cache', 'show', '--no-all-versions', 'libpromod3-modelling3.2'] 0m9.9s INFO: apt-cache knows about the following packages: libpromod3-modelling3.2 0m9.9s INFO: Running scripts pre_install 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/pre_install_database-server'] 0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/pre_install_database-server'] 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/pre_install_exceptions'] 0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/pre_install_exceptions'] 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/pre_install_extras'] 0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/pre_install_extras'] 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/pre_install_foreign_architecture'] 0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/pre_install_foreign_architecture'] 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m9.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m9.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'apt-cache', 'policy'] 0m10.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.1,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'apt-cache', 'policy'] 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'apt-cache', 'policy', 'libpromod3-modelling3.2'] 0m10.0s DUMP: libpromod3-modelling3.2: Installed: (none) Candidate: 3.2.1+ds-6+b1 Version table: 3.2.1+ds-6+b1 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m10.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'apt-cache', 'policy', 'libpromod3-modelling3.2'] 0m10.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'apt-get', '-y', 'install', 'libpromod3-modelling3.2'] 0m15.6s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libboost-filesystem1.74.0 libboost-iostreams1.74.0 libboost-regex1.74.0 libboost-thread1.74.0 libdeflate0 libdouble-conversion3 libfftw3-single3 libglib2.0-0 libgomp1 libicu72 libjbig0 libjpeg62-turbo liblerc4 libopenmm7.7 libost-base2.3 libost-conop2.3 libost-geom2.3 libost-img-alg2.3 libost-img2.3 libost-info2.3 libost-io2.3 libost-mol-alg2.3 libost-mol-mm2.3 libost-mol2.3 libost-seq-alg2.3 libost-seq2.3 libpcre2-16-0 libpng16-16 libpromod3-core3.2 libpromod3-loop3.2 libpromod3-scoring3.2 libpromod3-sidechain3.2 libqt5core5a libqt5xml5 libsqlite3-0 libtiff6 libwebp7 libxml2 shared-mime-info Suggested packages: libfftw3-bin libfftw3-dev low-memory-monitor libthai0 Recommended packages: libglib2.0-data xdg-user-dirs qttranslations5-l10n The following NEW packages will be installed: libboost-filesystem1.74.0 libboost-iostreams1.74.0 libboost-regex1.74.0 libboost-thread1.74.0 libdeflate0 libdouble-conversion3 libfftw3-single3 libglib2.0-0 libgomp1 libicu72 libjbig0 libjpeg62-turbo liblerc4 libopenmm7.7 libost-base2.3 libost-conop2.3 libost-geom2.3 libost-img-alg2.3 libost-img2.3 libost-info2.3 libost-io2.3 libost-mol-alg2.3 libost-mol-mm2.3 libost-mol2.3 libost-seq-alg2.3 libost-seq2.3 libpcre2-16-0 libpng16-16 libpromod3-core3.2 libpromod3-loop3.2 libpromod3-modelling3.2 libpromod3-scoring3.2 libpromod3-sidechain3.2 libqt5core5a libqt5xml5 libsqlite3-0 libtiff6 libwebp7 libxml2 shared-mime-info 0 upgraded, 40 newly installed, 0 to remove and 0 not upgraded. Need to get 23.2 MB of archives. After this operation, 89.6 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 libboost-filesystem1.74.0 amd64 1.74.0+ds1-21 [258 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 libboost-iostreams1.74.0 amd64 1.74.0+ds1-21 [240 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 libboost-regex1.74.0 amd64 1.74.0+ds1-21 [487 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 libboost-thread1.74.0 amd64 1.74.0+ds1-21 [257 kB] Get:6 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 libdouble-conversion3 amd64 3.2.1-1 [41.5 kB] Get:8 http://deb.debian.org/debian bookworm/main amd64 libgomp1 amd64 12.2.0-14 [116 kB] Get:9 http://deb.debian.org/debian bookworm/main amd64 libfftw3-single3 amd64 3.3.10-1 [806 kB] Get:10 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2 [1398 kB] Get:11 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB] Get:12 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB] Get:13 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB] Get:14 http://deb.debian.org/debian bookworm/main amd64 libopenmm7.7 amd64 7.7.0+dfsg-9+b1 [856 kB] Get:15 http://deb.debian.org/debian bookworm/main amd64 libost-base2.3 amd64 2.3.1-9 [32.6 kB] Get:16 http://deb.debian.org/debian bookworm/main amd64 libost-geom2.3 amd64 2.3.1-9 [64.0 kB] Get:17 http://deb.debian.org/debian bookworm/main amd64 libost-mol2.3 amd64 2.3.1-9 [335 kB] Get:18 http://deb.debian.org/debian bookworm/main amd64 libsqlite3-0 amd64 3.40.1-2 [837 kB] Get:19 http://deb.debian.org/debian bookworm/main amd64 libost-conop2.3 amd64 2.3.1-9 [184 kB] Get:20 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.3~deb12u1 [687 kB] Get:21 http://deb.debian.org/debian bookworm/main amd64 shared-mime-info amd64 2.2-1 [729 kB] Get:22 http://deb.debian.org/debian bookworm/main amd64 libpcre2-16-0 amd64 10.42-1 [245 kB] Get:23 http://deb.debian.org/debian bookworm/main amd64 libqt5core5a amd64 5.15.8+dfsg-11 [1809 kB] Get:24 http://deb.debian.org/debian bookworm/main amd64 libqt5xml5 amd64 5.15.8+dfsg-11 [122 kB] Get:25 http://deb.debian.org/debian bookworm/main amd64 libost-info2.3 amd64 2.3.1-9 [112 kB] Get:26 http://deb.debian.org/debian bookworm/main amd64 libost-img2.3 amd64 2.3.1-9 [143 kB] Get:27 http://deb.debian.org/debian bookworm/main amd64 libost-img-alg2.3 amd64 2.3.1-9 [169 kB] Get:28 http://deb.debian.org/debian bookworm/main amd64 libost-seq2.3 amd64 2.3.1-9 [87.6 kB] Get:29 http://deb.debian.org/debian bookworm/main amd64 libost-mol-alg2.3 amd64 2.3.1-9 [327 kB] Get:30 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB] Get:31 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.2 [285 kB] Get:32 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-6 [316 kB] Get:33 http://deb.debian.org/debian bookworm/main amd64 libost-io2.3 amd64 2.3.1-9 [609 kB] Get:34 http://deb.debian.org/debian bookworm/main amd64 libost-mol-mm2.3 amd64 2.3.1-9 [268 kB] Get:35 http://deb.debian.org/debian bookworm/main amd64 libost-seq-alg2.3 amd64 2.3.1-9 [246 kB] Get:36 http://deb.debian.org/debian bookworm/main amd64 libpromod3-core3.2 amd64 3.2.1+ds-6+b1 [98.5 kB] Get:37 http://deb.debian.org/debian bookworm/main amd64 libpromod3-loop3.2 amd64 3.2.1+ds-6+b1 [283 kB] Get:38 http://deb.debian.org/debian bookworm/main amd64 libpromod3-scoring3.2 amd64 3.2.1+ds-6+b1 [175 kB] Get:39 http://deb.debian.org/debian bookworm/main amd64 libpromod3-sidechain3.2 amd64 3.2.1+ds-6+b1 [235 kB] Get:40 http://deb.debian.org/debian bookworm/main amd64 libpromod3-modelling3.2 amd64 3.2.1+ds-6+b1 [296 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 23.2 MB in 0s (82.8 MB/s) Selecting previously unselected package libboost-filesystem1.74.0: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 ... 6100 files and directories currently installed.) Preparing to unpack .../00-libboost-filesystem1.74.0_1.74.0+ds1-21_amd64.deb ... Unpacking libboost-filesystem1.74.0:amd64 (1.74.0+ds1-21) ... Selecting previously unselected package libboost-iostreams1.74.0:amd64. Preparing to unpack .../01-libboost-iostreams1.74.0_1.74.0+ds1-21_amd64.deb ... Unpacking libboost-iostreams1.74.0:amd64 (1.74.0+ds1-21) ... 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Unpacking libpromod3-loop3.2 (3.2.1+ds-6+b1) ... Selecting previously unselected package libpromod3-scoring3.2. Preparing to unpack .../37-libpromod3-scoring3.2_3.2.1+ds-6+b1_amd64.deb ... Unpacking libpromod3-scoring3.2 (3.2.1+ds-6+b1) ... Selecting previously unselected package libpromod3-sidechain3.2. Preparing to unpack .../38-libpromod3-sidechain3.2_3.2.1+ds-6+b1_amd64.deb ... Unpacking libpromod3-sidechain3.2 (3.2.1+ds-6+b1) ... Selecting previously unselected package libpromod3-modelling3.2. Preparing to unpack .../39-libpromod3-modelling3.2_3.2.1+ds-6+b1_amd64.deb ... Unpacking libpromod3-modelling3.2 (3.2.1+ds-6+b1) ... Setting up libdouble-conversion3:amd64 (3.2.1-1) ... Setting up libicu72:amd64 (72.1-3) ... Setting up liblerc4:amd64 (4.0.0+ds-2) ... Setting up libopenmm7.7 (7.7.0+dfsg-9+b1) ... Setting up libglib2.0-0:amd64 (2.74.6-2) ... No schema files found: doing nothing. Setting up libboost-iostreams1.74.0:amd64 (1.74.0+ds1-21) ... Setting up libsqlite3-0:amd64 (3.40.1-2) ... Setting up libdeflate0:amd64 (1.14-1) ... Setting up libboost-filesystem1.74.0:amd64 (1.74.0+ds1-21) ... Setting up libgomp1:amd64 (12.2.0-14) ... Setting up libjbig0:amd64 (2.1-6.1) ... Setting up libpcre2-16-0:amd64 (10.42-1) ... Setting up libost-base2.3 (2.3.1-9) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-2) ... Setting up libost-geom2.3 (2.3.1-9) ... Setting up libboost-regex1.74.0:amd64 (1.74.0+ds1-21) ... Setting up libpng16-16:amd64 (1.6.39-2) ... Setting up libwebp7:amd64 (1.2.4-0.2) ... Setting up libtiff6:amd64 (4.5.0-6) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3~deb12u1) ... Setting up libboost-thread1.74.0:amd64 (1.74.0+ds1-21) ... Setting up libost-mol2.3 (2.3.1-9) ... Setting up libfftw3-single3:amd64 (3.3.10-1) ... Setting up libpromod3-core3.2 (3.2.1+ds-6+b1) ... Setting up libost-conop2.3 (2.3.1-9) ... Setting up shared-mime-info (2.2-1) ... Setting up libqt5core5a:amd64 (5.15.8+dfsg-11) ... Setting up libqt5xml5:amd64 (5.15.8+dfsg-11) ... Setting up libost-info2.3 (2.3.1-9) ... Setting up libost-seq2.3 (2.3.1-9) ... Setting up libost-img2.3 (2.3.1-9) ... Setting up libost-seq-alg2.3 (2.3.1-9) ... Setting up libost-img-alg2.3 (2.3.1-9) ... Setting up libost-mol-alg2.3 (2.3.1-9) ... Setting up libost-io2.3 (2.3.1-9) ... Setting up libost-mol-mm2.3 (2.3.1-9) ... Setting up libpromod3-loop3.2 (3.2.1+ds-6+b1) ... Setting up libpromod3-sidechain3.2 (3.2.1+ds-6+b1) ... Setting up libpromod3-scoring3.2 (3.2.1+ds-6+b1) ... Setting up libpromod3-modelling3.2 (3.2.1+ds-6+b1) ... Processing triggers for libc-bin (2.36-9+deb12u1) ... 0m15.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'apt-get', '-y', 'install', 'libpromod3-modelling3.2'] 0m15.6s INFO: Running scripts post_install 0m15.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/post_install_exceptions'] 0m15.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/post_install_exceptions'] 0m15.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2'] 0m16.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2'] 0m16.1s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpd2rkyya2 to sid 0m16.1s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m16.1s INFO: Running scripts pre_distupgrade 0m16.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m16.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m16.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/pre_distupgrade_exceptions'] 0m16.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/pre_distupgrade_exceptions'] 0m16.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m16.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m16.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m16.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m16.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m16.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m16.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'apt-get', 'update'] 0m20.7s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [209 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9589 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7017 kB] Fetched 16.8 MB in 3s (4824 kB/s) Reading package lists... 0m20.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'apt-get', 'update'] 0m20.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'apt-get', '-yf', 'dist-upgrade'] 0m29.1s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: gcc-13-base The following packages will be upgraded: adduser apt base-files bash bsdutils dash debianutils findutils gcc-12-base grep libapt-pkg6.0 libaudit-common libaudit1 libblkid1 libboost-filesystem1.74.0 libboost-iostreams1.74.0 libboost-regex1.74.0 libboost-thread1.74.0 libc-bin libc6 libcrypt1 libdouble-conversion3 libgcc-s1 libgcrypt20 libglib2.0-0 libgomp1 libidn2-0 libmd0 libmount1 libp11-kit0 libpcre2-16-0 libpcre2-8-0 libpng16-16 libqt5core5a libqt5xml5 libselinux1 libsemanage-common libsemanage2 libsepol2 libsmartcols1 libsqlite3-0 libstdc++6 libsystemd0 libtasn1-6 libtiff6 libtinfo6 libudev1 libuuid1 libxml2 libzstd1 mawk mount ncurses-base ncurses-bin sysvinit-utils tzdata util-linux util-linux-extra 58 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 22.9 MB of archives. After this operation, 154 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 base-files amd64 13 [70.6 kB] Get:2 http://deb.debian.org/debian sid/main amd64 debianutils amd64 5.8-1 [103 kB] Get:3 http://deb.debian.org/debian sid/main amd64 bash amd64 5.2.15-2+b3 [1489 kB] Get:4 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.38.1-6 [94.5 kB] Get:5 http://deb.debian.org/debian sid/main amd64 dash amd64 0.5.12-6 [92.1 kB] Get:6 http://deb.debian.org/debian sid/main amd64 findutils amd64 4.9.0-5 [636 kB] Get:7 http://deb.debian.org/debian sid/main amd64 grep amd64 3.11-2 [431 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libc6 amd64 2.37-6 [2750 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libc-bin amd64 2.37-6 [600 kB] Get:10 http://deb.debian.org/debian sid/main amd64 gcc-13-base amd64 13.1.0-9 [38.9 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 13.1.0-9 [57.8 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libtinfo6 amd64 6.4+20230625-2 [339 kB] Get:13 http://deb.debian.org/debian sid/main amd64 ncurses-bin amd64 6.4+20230625-2 [426 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libaudit-common all 1:3.1.1-1 [10.8 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libaudit1 amd64 1:3.1.1-1 [47.3 kB] Get:16 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.38.1-6 [106 kB] Get:17 http://deb.debian.org/debian sid/main amd64 util-linux-extra amd64 2.38.1-6 [110 kB] Get:18 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.38.1-6 [1176 kB] Get:19 http://deb.debian.org/debian sid/main amd64 libzstd1 amd64 1.5.5+dfsg2-1 [293 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libgcrypt20 amd64 1.10.2-2 [704 kB] Get:21 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 13.1.0-9 [694 kB] Get:22 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 254~rc3-3 [354 kB] Get:23 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 254~rc3-3 [117 kB] Get:24 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0 amd64 2.7.2 [925 kB] Get:25 http://deb.debian.org/debian sid/main amd64 adduser all 3.137 [140 kB] Get:26 http://deb.debian.org/debian sid/main amd64 apt amd64 2.7.2 [1347 kB] Get:27 http://deb.debian.org/debian sid/main amd64 ncurses-base all 6.4+20230625-2 [265 kB] Get:28 http://deb.debian.org/debian sid/main amd64 sysvinit-utils amd64 3.07-1 [31.3 kB] Get:29 http://deb.debian.org/debian sid/main amd64 mount amd64 2.38.1-6 [134 kB] Get:30 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.38.1-6 [147 kB] Get:31 http://deb.debian.org/debian sid/main amd64 libcrypt1 amd64 1:4.4.36-1 [89.7 kB] Get:32 http://deb.debian.org/debian sid/main amd64 libidn2-0 amd64 2.3.4-1 [143 kB] Get:33 http://deb.debian.org/debian sid/main amd64 libmd0 amd64 1.1.0-1 [35.5 kB] Get:34 http://deb.debian.org/debian sid/main amd64 libpcre2-8-0 amd64 10.42-2 [261 kB] Get:35 http://deb.debian.org/debian sid/main amd64 libselinux1 amd64 3.5-1 [73.9 kB] Get:36 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.38.1-6 [165 kB] Get:37 http://deb.debian.org/debian sid/main amd64 libp11-kit0 amd64 0.25.0-3 [413 kB] Get:38 http://deb.debian.org/debian sid/main amd64 libsemanage-common all 3.5-1 [9908 B] Get:39 http://deb.debian.org/debian sid/main amd64 libsepol2 amd64 3.5-1 [276 kB] Get:40 http://deb.debian.org/debian sid/main amd64 libsemanage2 amd64 3.5-1 [89.7 kB] Get:41 http://deb.debian.org/debian sid/main amd64 libtasn1-6 amd64 4.19.0-3 [48.3 kB] Get:42 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.38.1-6 [28.5 kB] Get:43 http://deb.debian.org/debian sid/main amd64 mawk amd64 1.3.4.20230525-1 [120 kB] Get:44 http://deb.debian.org/debian sid/main amd64 tzdata all 2023c-7 [254 kB] Get:45 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 13.1.0-9 [131 kB] Get:46 http://deb.debian.org/debian sid/main amd64 gcc-12-base amd64 12.3.0-6 [39.8 kB] Get:47 http://deb.debian.org/debian sid/main amd64 libboost-filesystem1.74.0 amd64 1.74.0+ds1-22 [260 kB] Get:48 http://deb.debian.org/debian sid/main amd64 libboost-iostreams1.74.0 amd64 1.74.0+ds1-22 [241 kB] Get:49 http://deb.debian.org/debian sid/main amd64 libboost-regex1.74.0 amd64 1.74.0+ds1-22 [486 kB] Get:50 http://deb.debian.org/debian sid/main amd64 libboost-thread1.74.0 amd64 1.74.0+ds1-22 [258 kB] Get:51 http://deb.debian.org/debian sid/main amd64 libdouble-conversion3 amd64 3.3.0-1 [40.1 kB] Get:52 http://deb.debian.org/debian sid/main amd64 libglib2.0-0 amd64 2.76.4-4 [1433 kB] Get:53 http://deb.debian.org/debian sid/main amd64 libpcre2-16-0 amd64 10.42-2 [245 kB] Get:54 http://deb.debian.org/debian sid/main amd64 libpng16-16 amd64 1.6.40-1 [275 kB] Get:55 http://deb.debian.org/debian sid/main amd64 libqt5xml5 amd64 5.15.10+dfsg-2 [122 kB] Get:56 http://deb.debian.org/debian sid/main amd64 libqt5core5a amd64 5.15.10+dfsg-2 [1811 kB] Get:57 http://deb.debian.org/debian sid/main amd64 libsqlite3-0 amd64 3.42.0-1 [859 kB] Get:58 http://deb.debian.org/debian sid/main amd64 libtiff6 amd64 4.5.1-1 [321 kB] Get:59 http://deb.debian.org/debian sid/main amd64 libxml2 amd64 2.9.14+dfsg-1.3 [686 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 22.9 MB in 0s (106 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 ... 6496 files and directories currently installed.) Preparing to unpack .../base-files_13_amd64.deb ... Unpacking base-files (13) over (12.4+deb12u1) ... Setting up base-files (13) ... Installing new version of config file /etc/debian_version ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... (Reading database ... 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No schema files found: doing nothing. Setting up libboost-iostreams1.74.0:amd64 (1.74.0+ds1-22) ... Setting up libsqlite3-0:amd64 (3.42.0-1) ... Setting up libboost-filesystem1.74.0:amd64 (1.74.0+ds1-22) ... Setting up libgomp1:amd64 (13.1.0-9) ... Setting up libpcre2-16-0:amd64 (10.42-2) ... Setting up gcc-12-base:amd64 (12.3.0-6) ... Setting up tzdata (2023c-7) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Jul 25 21:31:08 UTC 2023. Universal Time is now: Tue Jul 25 21:31:08 UTC 2023. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libboost-regex1.74.0:amd64 (1.74.0+ds1-22) ... Setting up libpng16-16:amd64 (1.6.40-1) ... Setting up libqt5core5a:amd64 (5.15.10+dfsg-2) ... Setting up mount (2.38.1-6) ... Setting up libtiff6:amd64 (4.5.1-1) ... Setting up mawk (1.3.4.20230525-1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3) ... Setting up libboost-thread1.74.0:amd64 (1.74.0+ds1-22) ... Setting up libqt5xml5:amd64 (5.15.10+dfsg-2) ... Processing triggers for libc-bin (2.37-6) ... Processing triggers for debianutils (5.8-1) ... 0m29.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'apt-get', '-yf', 'dist-upgrade'] 0m29.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m30.7s DUMP: 9a4b33dce9e8f1c4471466a71c834bfa - 0m30.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m30.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'apt-cache', 'show', '--no-all-versions', 'libpromod3-modelling3.2'] 0m30.9s DUMP: Package: libpromod3-modelling3.2 Status: install ok installed Priority: optional Section: libs Installed-Size: 921 Maintainer: Debichem Team Architecture: amd64 Source: promod3 (3.2.1+ds-6) Version: 3.2.1+ds-6+b1 Depends: libboost-filesystem1.74.0 (>= 1.74.0), libc6 (>= 2.32), libgcc-s1 (>= 4.0), libost-base2.3 (>= 2.3.1), libost-conop2.3 (>= 2.3.1), libost-geom2.3 (>= 2.3.1), libost-io2.3 (>= 2.3.1), libost-mol-mm2.3 (>= 2.3.1), libost-mol2.3 (>= 2.3.1), libost-seq2.3 (>= 2.3.1), libpromod3-core3.2 (>= 3.2.1+ds), libpromod3-loop3.2 (>= 3.2.1+ds), libpromod3-scoring3.2 (>= 3.2.1+ds), libpromod3-sidechain3.2 (>= 3.2.1+ds), libstdc++6 (>= 11) Description: protein homology modelling engine ProMod3 is a modelling engine based on the OpenStructure computational structural biology framework that can perform all steps required to generate a protein model by homology. Its modular design aims at implementing flexible modelling pipelines and fast prototyping of novel algorithms. . This package contains the shared library for modelling engine. Description-md5: ed662fcd37699c83b00770498305af3a Homepage: https://openstructure.org/promod3/ 0m30.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'apt-cache', 'show', '--no-all-versions', 'libpromod3-modelling3.2'] 0m30.9s INFO: apt-cache does not know about any of the requested packages 0m30.9s INFO: Running scripts post_distupgrade 0m30.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m30.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m30.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/post_distupgrade_exceptions'] 0m30.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/post_distupgrade_exceptions'] 0m30.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m31.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m31.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m31.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m31.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/post_distupgrade_zz_backports'] 0m31.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/post_distupgrade_zz_backports'] 0m31.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2'] 0m31.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2'] 0m31.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2'] 0m32.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2'] 0m32.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2'] 0m32.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2'] 0m32.9s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', '-ac', '--ignore-obsolete'] 0m34.1s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', '-ac', '--ignore-obsolete'] 0m34.1s INFO: Running scripts pre_remove 0m34.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m34.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m34.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m34.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m34.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m35.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m35.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m35.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m35.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m35.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m35.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/pre_remove_exceptions'] 0m35.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/pre_remove_exceptions'] 0m35.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m35.5s DUMP: install ok installed adduser adduser 3.137 install ok installed apt apt 2.7.2 install ok installed base-files base-files 13 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b3 install ok installed bsdutils bsdutils 1:2.38.1-6 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.12-6 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.3 install ok installed debianutils debianutils 5.8-1 install ok installed diffutils diffutils 1:3.8-4 install ok installed dpkg dpkg 1.21.22 install ok installed e2fsprogs e2fsprogs 1.47.0-2 install ok installed findutils findutils 4.9.0-5 install ok installed gcc-12-base:amd64 gcc-12-base 12.3.0-6 install ok installed gcc-13-base:amd64 gcc-13-base 13.1.0-9 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.11-2 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu1 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.7.2 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.1.1-1 install ok installed libaudit1:amd64 libaudit1 1:3.1.1-1 install ok installed libblkid1:amd64 libblkid1 2.38.1-6 install ok installed libboost-filesystem1.74.0:amd64 libboost-filesystem1.74.0 1.74.0+ds1-22 install ok installed libboost-iostreams1.74.0:amd64 libboost-iostreams1.74.0 1.74.0+ds1-22 install ok installed libboost-regex1.74.0:amd64 libboost-regex1.74.0 1.74.0+ds1-22 install ok installed libboost-thread1.74.0:amd64 libboost-thread1.74.0 1.74.0+ds1-22 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.37-6 install ok installed libc6:amd64 libc6 2.37-6 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3 install ok installed libcap2:amd64 libcap2 1:2.66-4 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.270 install ok installed libdeflate0:amd64 libdeflate0 1.14-1 install ok installed libdouble-conversion3:amd64 libdouble-conversion3 3.3.0-1 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libfftw3-single3:amd64 libfftw3-single3 3.3.10-1 install ok installed libgcc-s1:amd64 libgcc-s1 13.1.0-9 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.2-2 install ok installed libglib2.0-0:amd64 libglib2.0-0 2.76.4-4 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.9-2 install ok installed libgomp1:amd64 libgomp1 13.1.0-9 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libicu72:amd64 libicu72 72.1-3 install ok installed libidn2-0:amd64 libidn2-0 2.3.4-1 install ok installed libjbig0:amd64 libjbig0 2.1-6.1 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-2 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-2 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.1-0.2 install ok installed libmd0:amd64 libmd0 1.1.0-1 install ok installed libmount1:amd64 libmount1 2.38.1-6 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libopenmm7.7 libopenmm7.7 7.7.0+dfsg-9+b1 install ok installed libost-base2.3 libost-base2.3 2.3.1-9 install ok installed libost-conop2.3 libost-conop2.3 2.3.1-9 install ok installed libost-geom2.3 libost-geom2.3 2.3.1-9 install ok installed libost-img-alg2.3 libost-img-alg2.3 2.3.1-9 install ok installed libost-img2.3 libost-img2.3 2.3.1-9 install ok installed libost-info2.3 libost-info2.3 2.3.1-9 install ok installed libost-io2.3 libost-io2.3 2.3.1-9 install ok installed libost-mol-alg2.3 libost-mol-alg2.3 2.3.1-9 install ok installed libost-mol-mm2.3 libost-mol-mm2.3 2.3.1-9 install ok installed libost-mol2.3 libost-mol2.3 2.3.1-9 install ok installed libost-seq-alg2.3 libost-seq-alg2.3 2.3.1-9 install ok installed libost-seq2.3 libost-seq2.3 2.3.1-9 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.0-3 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-6 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-6 install ok installed libpam-runtime libpam-runtime 1.5.2-6 install ok installed libpam0g:amd64 libpam0g 1.5.2-6 install ok installed libpcre2-16-0:amd64 libpcre2-16-0 10.42-2 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-2 install ok installed libpng16-16:amd64 libpng16-16 1.6.40-1 install ok installed libpromod3-core3.2 libpromod3-core3.2 3.2.1+ds-6+b1 install ok installed libpromod3-loop3.2 libpromod3-loop3.2 3.2.1+ds-6+b1 install ok installed libpromod3-modelling3.2 libpromod3-modelling3.2 3.2.1+ds-6+b1 install ok installed libpromod3-scoring3.2 libpromod3-scoring3.2 3.2.1+ds-6+b1 install ok installed libpromod3-sidechain3.2 libpromod3-sidechain3.2 3.2.1+ds-6+b1 install ok installed libqt5core5a:amd64 libqt5core5a 5.15.10+dfsg-2 install ok installed libqt5xml5:amd64 libqt5xml5 5.15.10+dfsg-2 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+b3 install ok installed libselinux1:amd64 libselinux1 3.5-1 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1 install ok installed libsepol2:amd64 libsepol2 3.5-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-6 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.42.0-1 install ok installed libss2:amd64 libss2 1.47.0-2 install ok installed libstdc++6:amd64 libstdc++6 13.1.0-9 install ok installed libsystemd0:amd64 libsystemd0 254~rc3-3 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3 install ok installed libtiff6:amd64 libtiff6 4.5.1-1 install ok installed libtinfo6:amd64 libtinfo6 6.4+20230625-2 install ok installed libudev1:amd64 libudev1 254~rc3-3 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-6 install ok installed libwebp7:amd64 libwebp7 1.2.4-0.2 install ok installed libxml2:amd64 libxml2 2.9.14+dfsg-1.3 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-1 install ok installed login login 1:4.13+dfsg1-1+b1 install ok installed logsave logsave 1.47.0-2 install ok installed mawk mawk 1.3.4.20230525-1 install ok installed mount mount 2.38.1-6 install ok installed ncurses-base ncurses-base 6.4+20230625-2 install ok installed ncurses-bin ncurses-bin 6.4+20230625-2 install ok installed passwd passwd 1:4.13+dfsg1-1+b1 install ok installed perl-base perl-base 5.36.0-7 install ok installed sed sed 4.9-1 install ok installed shared-mime-info shared-mime-info 2.2-1 install ok installed sysvinit-utils sysvinit-utils 3.07-1 install ok installed tar tar 1.34+dfsg-1.2 install ok installed tzdata tzdata 2023c-7 install ok installed usr-is-merged usr-is-merged 35 install ok installed util-linux util-linux 2.38.1-6 install ok installed util-linux-extra util-linux-extra 2.38.1-6 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m35.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m35.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'apt-get', 'remove', 'libboost-filesystem1.74.0:amd64', 'libboost-iostreams1.74.0:amd64', 'libboost-regex1.74.0:amd64', 'libboost-thread1.74.0:amd64', 'libdeflate0:amd64', 'libdouble-conversion3:amd64', 'libfftw3-single3:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libicu72:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'liblerc4:amd64', 'libopenmm7.7', 'libost-base2.3', 'libost-conop2.3', 'libost-geom2.3', 'libost-img-alg2.3', 'libost-img2.3', 'libost-info2.3', 'libost-io2.3', 'libost-mol-alg2.3', 'libost-mol-mm2.3', 'libost-mol2.3', 'libost-seq-alg2.3', 'libost-seq2.3', 'libpcre2-16-0:amd64', 'libpng16-16:amd64', 'libpromod3-core3.2', 'libpromod3-loop3.2', 'libpromod3-scoring3.2', 'libpromod3-sidechain3.2', 'libqt5core5a:amd64', 'libqt5xml5:amd64', 'libsqlite3-0:amd64', 'libtiff6:amd64', 'libwebp7:amd64', 'libxml2:amd64', 'shared-mime-info', 'libpromod3-modelling3.2'] 0m36.6s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: libboost-filesystem1.74.0 libboost-iostreams1.74.0 libboost-regex1.74.0 libboost-thread1.74.0 libdeflate0 libdouble-conversion3 libfftw3-single3 libglib2.0-0 libgomp1 libicu72 libjbig0 libjpeg62-turbo liblerc4 libopenmm7.7 libost-base2.3 libost-conop2.3 libost-geom2.3 libost-img-alg2.3 libost-img2.3 libost-info2.3 libost-io2.3 libost-mol-alg2.3 libost-mol-mm2.3 libost-mol2.3 libost-seq-alg2.3 libost-seq2.3 libpcre2-16-0 libpng16-16 libpromod3-core3.2 libpromod3-loop3.2 libpromod3-modelling3.2 libpromod3-scoring3.2 libpromod3-sidechain3.2 libqt5core5a libqt5xml5 libsqlite3-0 libtiff6 libwebp7 libxml2 shared-mime-info 0 upgraded, 0 newly installed, 40 to remove and 0 not upgraded. After this operation, 89.8 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 ... 5798 files and directories currently installed.) Removing libpromod3-modelling3.2 (3.2.1+ds-6+b1) ... Removing libpromod3-sidechain3.2 (3.2.1+ds-6+b1) ... Removing libpromod3-scoring3.2 (3.2.1+ds-6+b1) ... Removing libpromod3-loop3.2 (3.2.1+ds-6+b1) ... Removing libost-seq-alg2.3 (2.3.1-9) ... Removing libost-mol-mm2.3 (2.3.1-9) ... Removing libost-io2.3 (2.3.1-9) ... Removing libost-mol-alg2.3 (2.3.1-9) ... Removing libost-conop2.3 (2.3.1-9) ... Removing libpromod3-core3.2 (3.2.1+ds-6+b1) ... Removing libost-img-alg2.3 (2.3.1-9) ... Removing libost-img2.3 (2.3.1-9) ... Removing libboost-thread1.74.0:amd64 (1.74.0+ds1-22) ... Removing libtiff6:amd64 (4.5.1-1) ... Removing libdeflate0:amd64 (1.14-1) ... Removing libfftw3-single3:amd64 (3.3.10-1) ... Removing libgomp1:amd64 (13.1.0-9) ... Removing libjbig0:amd64 (2.1-6.1) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-2) ... Removing liblerc4:amd64 (4.0.0+ds-2) ... Removing libopenmm7.7 (7.7.0+dfsg-9+b1) ... Removing libost-seq2.3 (2.3.1-9) ... Removing libpng16-16:amd64 (1.6.40-1) ... Removing libsqlite3-0:amd64 (3.42.0-1) ... Removing libwebp7:amd64 (1.2.4-0.2) ... Removing libboost-iostreams1.74.0:amd64 (1.74.0+ds1-22) ... Removing libost-mol2.3 (2.3.1-9) ... Removing libost-info2.3 (2.3.1-9) ... Removing libboost-regex1.74.0:amd64 (1.74.0+ds1-22) ... Removing libqt5xml5:amd64 (5.15.10+dfsg-2) ... Removing libqt5core5a:amd64 (5.15.10+dfsg-2) ... Removing libdouble-conversion3:amd64 (3.3.0-1) ... Removing shared-mime-info (2.2-1) ... Removing libglib2.0-0:amd64 (2.76.4-4) ... Removing libxml2:amd64 (2.9.14+dfsg-1.3) ... Removing libicu72:amd64 (72.1-3) ... Removing libost-base2.3 (2.3.1-9) ... Removing libost-geom2.3 (2.3.1-9) ... Removing libpcre2-16-0:amd64 (10.42-2) ... Removing libboost-filesystem1.74.0:amd64 (1.74.0+ds1-22) ... Processing triggers for libc-bin (2.37-6) ... 0m36.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'apt-get', 'remove', 'libboost-filesystem1.74.0:amd64', 'libboost-iostreams1.74.0:amd64', 'libboost-regex1.74.0:amd64', 'libboost-thread1.74.0:amd64', 'libdeflate0:amd64', 'libdouble-conversion3:amd64', 'libfftw3-single3:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libicu72:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'liblerc4:amd64', 'libopenmm7.7', 'libost-base2.3', 'libost-conop2.3', 'libost-geom2.3', 'libost-img-alg2.3', 'libost-img2.3', 'libost-info2.3', 'libost-io2.3', 'libost-mol-alg2.3', 'libost-mol-mm2.3', 'libost-mol2.3', 'libost-seq-alg2.3', 'libost-seq2.3', 'libpcre2-16-0:amd64', 'libpng16-16:amd64', 'libpromod3-core3.2', 'libpromod3-loop3.2', 'libpromod3-scoring3.2', 'libpromod3-sidechain3.2', 'libqt5core5a:amd64', 'libqt5xml5:amd64', 'libsqlite3-0:amd64', 'libtiff6:amd64', 'libwebp7:amd64', 'libxml2:amd64', 'shared-mime-info', 'libpromod3-modelling3.2'] 0m36.6s INFO: Running scripts post_remove 0m36.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/post_remove_exceptions'] 0m36.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/post_remove_exceptions'] 0m36.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'dpkg', '--purge', 'libboost-filesystem1.74.0:amd64', 'libboost-iostreams1.74.0:amd64', 'libboost-regex1.74.0:amd64', 'libboost-thread1.74.0:amd64', 'libdeflate0:amd64', 'libdouble-conversion3:amd64', 'libfftw3-single3:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libicu72:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'liblerc4:amd64', 'libopenmm7.7', 'libost-base2.3', 'libost-conop2.3', 'libost-geom2.3', 'libost-img-alg2.3', 'libost-img2.3', 'libost-info2.3', 'libost-io2.3', 'libost-mol-alg2.3', 'libost-mol-mm2.3', 'libost-mol2.3', 'libost-seq-alg2.3', 'libost-seq2.3', 'libpcre2-16-0:amd64', 'libpng16-16:amd64', 'libpromod3-core3.2', 'libpromod3-loop3.2', 'libpromod3-scoring3.2', 'libpromod3-sidechain3.2', 'libqt5core5a:amd64', 'libqt5xml5:amd64', 'libsqlite3-0:amd64', 'libtiff6:amd64', 'libwebp7:amd64', 'libxml2:amd64', 'shared-mime-info'] 0m36.6s DUMP: dpkg: warning: ignoring request to remove libboost-filesystem1.74.0 which isn't installed dpkg: warning: ignoring request to remove libboost-iostreams1.74.0 which isn't installed dpkg: warning: ignoring request to remove libboost-regex1.74.0 which isn't installed dpkg: warning: ignoring request to remove libboost-thread1.74.0 which isn't installed dpkg: warning: ignoring request to remove libdeflate0 which isn't installed dpkg: warning: ignoring request to remove libdouble-conversion3 which isn't installed dpkg: warning: ignoring request to remove libfftw3-single3 which isn't installed (Reading database ... 5402 files and directories currently installed.) Purging configuration files for libglib2.0-0:amd64 (2.76.4-4) ... dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libicu72 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 dpkg: warning: ignoring request to remove liblerc4 which isn't installed dpkg: warning: ignoring request to remove libopenmm7.7 which isn't installed dpkg: warning: ignoring request to remove libost-base2.3 which isn't installed dpkg: warning: ignoring request to remove libost-conop2.3 which isn't installed dpkg: warning: ignoring request to remove libost-geom2.3 which isn't installed dpkg: warning: ignoring request to remove libost-img-alg2.3 which isn't installed dpkg: warning: ignoring request to remove libost-img2.3 which isn't installed dpkg: warning: ignoring request to remove libost-info2.3 which isn't installed dpkg: warning: ignoring request to remove libost-io2.3 which isn't installed dpkg: warning: ignoring request to remove libost-mol-alg2.3 which isn't installed dpkg: warning: ignoring request to remove libost-mol-mm2.3 which isn't installed dpkg: warning: ignoring request to remove libost-mol2.3 which isn't installed dpkg: warning: ignoring request to remove libost-seq-alg2.3 which isn't installed dpkg: warning: ignoring request to remove libost-seq2.3 which isn't installed dpkg: warning: ignoring request to remove libpcre2-16-0 which isn't installed dpkg: warning: ignoring request to remove libpng16-16 which isn't installed dpkg: warning: ignoring request to remove libpromod3-core3.2 which isn't installed dpkg: warning: ignoring request to remove libpromod3-loop3.2 which isn't installed dpkg: warning: ignoring request to remove libpromod3-scoring3.2 which isn't installed dpkg: warning: ignoring request to remove libpromod3-sidechain3.2 which isn't installed Purging configuration files for libqt5core5a:amd64 (5.15.10+dfsg-2) ... dpkg: warning: ignoring request to remove libqt5xml5 which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libtiff6 which isn't installed dpkg: warning: ignoring request to remove libwebp7 which isn't installed dpkg: warning: ignoring request to remove libxml2 which isn't installed Purging configuration files for shared-mime-info (2.2-1) ... 0m36.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'dpkg', '--purge', 'libboost-filesystem1.74.0:amd64', 'libboost-iostreams1.74.0:amd64', 'libboost-regex1.74.0:amd64', 'libboost-thread1.74.0:amd64', 'libdeflate0:amd64', 'libdouble-conversion3:amd64', 'libfftw3-single3:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libicu72:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'liblerc4:amd64', 'libopenmm7.7', 'libost-base2.3', 'libost-conop2.3', 'libost-geom2.3', 'libost-img-alg2.3', 'libost-img2.3', 'libost-info2.3', 'libost-io2.3', 'libost-mol-alg2.3', 'libost-mol-mm2.3', 'libost-mol2.3', 'libost-seq-alg2.3', 'libost-seq2.3', 'libpcre2-16-0:amd64', 'libpng16-16:amd64', 'libpromod3-core3.2', 'libpromod3-loop3.2', 'libpromod3-scoring3.2', 'libpromod3-sidechain3.2', 'libqt5core5a:amd64', 'libqt5xml5:amd64', 'libsqlite3-0:amd64', 'libtiff6:amd64', 'libwebp7:amd64', 'libxml2:amd64', 'shared-mime-info'] 0m36.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'dpkg', '--purge', 'libpromod3-modelling3.2'] 0m36.6s DUMP: dpkg: warning: ignoring request to remove libpromod3-modelling3.2 which isn't installed 0m36.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'dpkg', '--purge', 'libpromod3-modelling3.2'] 0m36.6s INFO: Running scripts post_purge 0m36.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/post_purge_exceptions'] 0m36.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/post_purge_exceptions'] 0m36.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'dpkg', '--purge', '--pending'] 0m36.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'dpkg', '--purge', '--pending'] 0m36.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'dpkg', '--remove', '--pending'] 0m36.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'dpkg', '--remove', '--pending'] 0m36.7s INFO: Running scripts post_test 0m36.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/post_test_exceptions'] 0m36.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'tmp/scripts/post_test_exceptions'] 0m36.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2'] 0m37.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2'] 0m37.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'dpkg-divert', '--list'] 0m37.1s DUMP: local diversion of /bin/sync to /bin/sync.distrib local diversion of /home to /home.distrib 0m37.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'dpkg-divert', '--list'] 0m37.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'apt-get', 'clean'] 0m37.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2', 'apt-get', 'clean'] 0m37.1s DEBUG: Recording chroot state 0m38.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2/dev/shm'] 0m38.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2/dev/shm'] 0m38.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2/dev/console'] 0m38.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2/dev/console'] 0m38.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2/dev/ptmx'] 0m38.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2/dev/ptmx'] 0m38.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2/dev/pts'] 0m38.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2/dev/pts'] 0m38.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2/proc'] 0m38.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2/proc'] 0m38.4s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2'] 0m38.6s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpd2rkyya2'] 0m38.6s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpd2rkyya2 0m38.6s INFO: PASS: Upgrading between Debian distributions. 0m38.6s INFO: PASS: All tests. 0m38.6s INFO: piuparts run ends. ret=0 End: 2023-07-25 21:31:18 GMT