Start: 2023-02-04 15:26:59 GMT [testing] Package: density-fitness Version: 1.0.8-2 Installed-Size: 5548 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), libcifpp5 (>= 5.0.5), libclipper2 (>= 2.1.20201109), libgcc-s1 (>= 3.0), libpdb-redo3 (>= 3.0.4), libstdc++6 (>= 11), libzeep5.1 (>= 5.1.7), zlib1g (>= 1:1.2.2) Description: Calculates per-residue electron density scores Homepage: https://github.com/PDB-REDO/density-fitness Description-md5: a0d73a3885bbe1e21b3bb9575d5b6f5c Section: science Priority: optional Filename: pool/main/d/density-fitness/density-fitness_1.0.8-2_amd64.deb Size: 458612 MD5sum: b2302d9ee26848541485da943f3ba3f5 SHA256: a4ae5a8afbcc7a09a6507db13b61a59e8c86ce774064e7f1d5699109c25b3c9b [sid] Package: density-fitness Version: 1.0.8-4 Installed-Size: 5548 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), libcifpp5 (>= 5.0.7.1), libclipper2 (>= 2.1.20201109), libgcc-s1 (>= 3.0), libpdb-redo3 (>= 3.0.5), libstdc++6 (>= 11), libzeep5.1 (>= 5.1.8), zlib1g (>= 1:1.2.2) Description: Calculates per-residue electron density scores Homepage: https://github.com/PDB-REDO/density-fitness Description-md5: a0d73a3885bbe1e21b3bb9575d5b6f5c Section: science Priority: optional Filename: pool/main/d/density-fitness/density-fitness_1.0.8-4_amd64.deb Size: 458732 MD5sum: 3dcb9137409b46c3f032f8b4b02fd41a SHA256: 7c615c5b1f94e2ced468e1edb1c8c5c61c475fd5153a4e9b1c03fb68f717b3ef 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 density-fitness=1.0.8-4 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 1.1.5 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 density-fitness=1.0.8-4 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpkcg3d4bm 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpkcg3d4bm 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz'] 0m2.4s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm_amd64.tar.gz'] 0m2.4s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm/proc'] 0m2.5s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm/proc'] 0m2.5s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm/dev/pts'] 0m2.5s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm/dev/pts'] 0m2.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm/dev/ptmx'] 0m2.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm/dev/ptmx'] 0m2.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm/dev/console'] 0m2.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm/dev/console'] 0m2.5s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm/dev/shm'] 0m2.5s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm/dev/shm'] 0m2.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m2.5s DEBUG: Created policy-rc.d and chmodded it. 0m2.5s DEBUG: Created resolv.conf. 0m2.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpkcg3d4bm/tmp/scripts/ 0m2.5s INFO: Running scripts post_chroot_unpack 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'apt-get', 'update'] 0m5.5s DUMP: Get:1 http://deb.debian.org/debian bookworm InRelease [171 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 Packages [8964 kB] Get:3 http://deb.debian.org/debian bookworm/main Translation-en [6046 kB] Fetched 15.2 MB in 2s (6899 kB/s) Reading package lists... 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'apt-get', 'update'] 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'apt-get', '-yf', 'dist-upgrade'] 0m7.0s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: libaudit1 libcap-ng0 libseccomp2 libselinux1 libsemanage2 libsystemd0 libudev1 7 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 710 kB of archives. After this operation, 0 B of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 libcap-ng0 amd64 0.8.3-1+b3 [17.1 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 libaudit1 amd64 1:3.0.7-1.1+b3 [46.4 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libseccomp2 amd64 2.5.4-1+b3 [46.6 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 libselinux1 amd64 3.4-1+b5 [74.0 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 libsystemd0 amd64 252.5-2 [329 kB] Get:6 http://deb.debian.org/debian bookworm/main amd64 libudev1 amd64 252.5-2 [107 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 libsemanage2 amd64 3.4-1+b5 [89.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 710 kB in 0s (8677 kB/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 ... 8043 files and directories currently installed.) Preparing to unpack .../libcap-ng0_0.8.3-1+b3_amd64.deb ... Unpacking libcap-ng0:amd64 (0.8.3-1+b3) over (0.8.3-1+b2) ... Setting up libcap-ng0:amd64 (0.8.3-1+b3) ... (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 ... 8043 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a3.0.7-1.1+b3_amd64.deb ... Unpacking libaudit1:amd64 (1:3.0.7-1.1+b3) over (1:3.0.7-1.1+b2) ... Setting up libaudit1:amd64 (1:3.0.7-1.1+b3) ... (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 ... 8043 files and directories currently installed.) Preparing to unpack .../libseccomp2_2.5.4-1+b3_amd64.deb ... Unpacking libseccomp2:amd64 (2.5.4-1+b3) over (2.5.4-1+b2) ... Setting up libseccomp2:amd64 (2.5.4-1+b3) ... (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 ... 8043 files and directories currently installed.) Preparing to unpack .../libselinux1_3.4-1+b5_amd64.deb ... Unpacking libselinux1:amd64 (3.4-1+b5) over (3.4-1+b4) ... Setting up libselinux1:amd64 (3.4-1+b5) ... (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 ... 8043 files and directories currently installed.) Preparing to unpack .../libsystemd0_252.5-2_amd64.deb ... Unpacking libsystemd0:amd64 (252.5-2) over (252.4-2) ... Setting up libsystemd0:amd64 (252.5-2) ... (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 ... 8043 files and directories currently installed.) Preparing to unpack .../libudev1_252.5-2_amd64.deb ... Unpacking libudev1:amd64 (252.5-2) over (252.4-2) ... Setting up libudev1:amd64 (252.5-2) ... (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 ... 8043 files and directories currently installed.) Preparing to unpack .../libsemanage2_3.4-1+b5_amd64.deb ... Unpacking libsemanage2:amd64 (3.4-1+b5) over (3.4-1+b4) ... Setting up libsemanage2:amd64 (3.4-1+b5) ... Processing triggers for libc-bin (2.36-8) ... 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'apt-get', '-yf', 'dist-upgrade'] 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m7.4s DUMP: 88fdc50a4fbdf634cd37ea4f23525a03 - 0m7.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m7.4s INFO: Running scripts post_setup 0m7.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/post_setup_dummy_users'] 0m8.3s 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 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/post_setup_dummy_users'] 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/post_setup_forbid_home'] 0m8.3s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/post_setup_forbid_home'] 0m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/post_setup_force-unsafe-io'] 0m8.4s 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' 0m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/post_setup_force-unsafe-io'] 0m8.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/post_setup_minimize'] 0m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/post_setup_minimize'] 0m8.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/post_setup_squeeze-backports'] 0m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/post_setup_squeeze-backports'] 0m8.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/post_setup_zz_backports'] 0m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/post_setup_zz_backports'] 0m8.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m8.4s DUMP: install ok installed apt apt 2.5.5 install ok installed base-files base-files 12.3 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2 install ok installed bsdutils bsdutils 1:2.38.1-4 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 2021.1.1 install ok installed debianutils debianutils 5.7-0.4 install ok installed diffutils diffutils 1:3.8-3 install ok installed dpkg dpkg 1.21.19 install ok installed e2fsprogs e2fsprogs 1.46.6~rc1-1.1 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 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 2.5.5 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.0.7-1.1 install ok installed libaudit1:amd64 libaudit1 1:3.0.7-1.1+b3 install ok installed libblkid1:amd64 libblkid1 2.38.1-4 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-8 install ok installed libc6:amd64 libc6 2.36-8 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3 install ok installed libcap2:amd64 libcap2 1:2.66-3 install ok installed libcom-err2:amd64 libcom-err2 1.46.6~rc1-1.1 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 0.266 install ok installed libext2fs2:amd64 libext2fs2 1.46.6~rc1-1.1 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libfile-find-rule-perl libfile-find-rule-perl 0.34-3 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 libgdbm-compat4:amd64 libgdbm-compat4 1.23-3 install ok installed libgdbm6:amd64 libgdbm6 1.23-3 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.8-4 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 5.4.1-0.0 install ok installed libmd0:amd64 libmd0 1.0.4-2 install ok installed libmount1:amd64 libmount1 2.38.1-4 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libnumber-compare-perl libnumber-compare-perl 0.03-3 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 libperl5.36:amd64 libperl5.36 5.36.0-7 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+b3 install ok installed libselinux1:amd64 libselinux1 3.4-1+b5 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 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-4 install ok installed libss2:amd64 libss2 1.46.6~rc1-1.1 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-14 install ok installed libsystemd0:amd64 libsystemd0 252.5-2 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtext-glob-perl libtext-glob-perl 0.11-3 install ok installed libtinfo6:amd64 libtinfo6 6.4-2 install ok installed libudev1:amd64 libudev1 252.5-2 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-4 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.2+dfsg2-3 install ok installed login login 1:4.13+dfsg1-1 install ok installed logsave logsave 1.46.6~rc1-1.1 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mount mount 2.38.1-4 install ok installed ncurses-base ncurses-base 6.4-2 install ok installed ncurses-bin ncurses-bin 6.4-2 install ok installed passwd passwd 1:4.13+dfsg1-1 install ok installed perl perl 5.36.0-7 install ok installed perl-base perl-base 5.36.0-7 install ok installed perl-modules-5.36 perl-modules-5.36 5.36.0-7 install ok installed sed sed 4.9-1 install ok installed sysvinit-utils sysvinit-utils 3.06-2 install ok installed tar tar 1.34+dfsg-1 install ok installed tzdata tzdata 2022g-2 install ok installed usr-is-merged usr-is-merged 35 install ok installed usrmerge usrmerge 35 install ok installed util-linux util-linux 2.38.1-4 install ok installed util-linux-extra util-linux-extra 2.38.1-4 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m8.4s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m8.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm'] 0m8.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm'] 0m8.9s INFO: Running scripts is_testable 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/is_testable_uninstallable'] 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/is_testable_uninstallable'] 0m8.9s INFO: Running scripts pre_test 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_test_exceptions'] 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_test_exceptions'] 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_test_root_password'] 0m8.9s DUMP: New password: Retype new password: passwd: password updated successfully 0m8.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_test_root_password'] 0m8.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'apt-cache', 'show', '--no-all-versions', 'density-fitness'] 0m9.2s DUMP: Package: density-fitness Version: 1.0.8-2 Installed-Size: 5548 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), libcifpp5 (>= 5.0.5), libclipper2 (>= 2.1.20201109), libgcc-s1 (>= 3.0), libpdb-redo3 (>= 3.0.4), libstdc++6 (>= 11), libzeep5.1 (>= 5.1.7), zlib1g (>= 1:1.2.2) Description-en: Calculates per-residue electron density scores The program density-fitness calculates electron density metrics, for main- (includes C? atom) and side-chain atoms of individual residues. . For this calculation, the program uses the structure model in either PDB or mmCIF format and the electron density from the 2mFo-DFc and mFo-DFc maps. If these maps are not readily available, the MTZ file and model can be used to calculate maps clipper. Density-fitness support both X-ray and electron diffraction data. . This program is essentially a reimplementation of edstats, a program available from the CCP4 suite. However, the output now contains only the RSR, SRSR and RSCC fields as in edstats with the addition of EDIAm and OPIA and no longer requires pre-calculated map coefficients. Description-md5: a0d73a3885bbe1e21b3bb9575d5b6f5c Homepage: https://github.com/PDB-REDO/density-fitness Section: science Priority: optional Filename: pool/main/d/density-fitness/density-fitness_1.0.8-2_amd64.deb Size: 458612 MD5sum: b2302d9ee26848541485da943f3ba3f5 SHA256: a4ae5a8afbcc7a09a6507db13b61a59e8c86ce774064e7f1d5699109c25b3c9b 0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'apt-cache', 'show', '--no-all-versions', 'density-fitness'] 0m9.2s INFO: apt-cache knows about the following packages: density-fitness 0m9.2s INFO: Running scripts pre_install 0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_install_database-server'] 0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_install_database-server'] 0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_install_exceptions'] 0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_install_exceptions'] 0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_install_extras'] 0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_install_extras'] 0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_install_foreign_architecture'] 0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_install_foreign_architecture'] 0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m9.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m9.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'apt-cache', 'policy'] 0m9.3s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release o=Debian,a=testing,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'apt-cache', 'policy'] 0m9.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'apt-cache', 'policy', 'density-fitness'] 0m9.3s DUMP: density-fitness: Installed: (none) Candidate: 1.0.8-2 Version table: 1.0.8-2 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m9.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'apt-cache', 'policy', 'density-fitness'] 0m9.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'apt-get', '-y', 'install', 'density-fitness'] 0m15.0s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: adduser ibverbs-providers libatomic1 libboost-regex1.74.0 libbsd0 libccp4-data libccp4c0 libcifpp-data libcifpp5 libclipper2 libevent-core-2.1-7 libevent-pthreads-2.1-7 libfabric1 libgsl27 libgslcblas0 libhwloc-plugins libhwloc15 libibverbs1 libicu72 libmmdb2-0 libmunge2 libnewuoa0 libnl-3-200 libnl-route-3-200 libnuma1 libopenmpi3 libpciaccess0 libpdb-redo3 libpmix2 libpsm-infinipath1 libpsm2-2 librdmacm1 libucx0 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 libzeep5.1 ocl-icd-libopencl1 sfftw2 Suggested packages: liblocale-gettext-perl cron quota gsl-ref-psdoc | gsl-doc-pdf | gsl-doc-info | gsl-ref-html libhwloc-contrib-plugins pciutils opencl-icd mpi-defaults-bin sfftw-dev The following NEW packages will be installed: adduser density-fitness ibverbs-providers libatomic1 libboost-regex1.74.0 libbsd0 libccp4-data libccp4c0 libcifpp-data libcifpp5 libclipper2 libevent-core-2.1-7 libevent-pthreads-2.1-7 libfabric1 libgsl27 libgslcblas0 libhwloc-plugins libhwloc15 libibverbs1 libicu72 libmmdb2-0 libmunge2 libnewuoa0 libnl-3-200 libnl-route-3-200 libnuma1 libopenmpi3 libpciaccess0 libpdb-redo3 libpmix2 libpsm-infinipath1 libpsm2-2 librdmacm1 libucx0 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 libzeep5.1 ocl-icd-libopencl1 sfftw2 0 upgraded, 45 newly installed, 0 to remove and 0 not upgraded. Need to get 23.8 MB of archives. After this operation, 99.9 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 adduser all 3.130 [117 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libboost-regex1.74.0 amd64 1.74.0+ds1-20 [487 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 libcifpp-data all 5.0.5-6 [452 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 libcifpp5 amd64 5.0.5-6 [795 kB] Get:6 http://deb.debian.org/debian bookworm/main amd64 libccp4-data all 8.0.0-2 [62.3 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 libccp4c0 amd64 8.0.0-2 [88.5 kB] Get:8 http://deb.debian.org/debian bookworm/main amd64 libmmdb2-0 amd64 2.0.22-1 [338 kB] Get:9 http://deb.debian.org/debian bookworm/main amd64 libevent-core-2.1-7 amd64 2.1.12-stable-5+b1 [137 kB] Get:10 http://deb.debian.org/debian bookworm/main amd64 libevent-pthreads-2.1-7 amd64 2.1.12-stable-5+b1 [57.9 kB] Get:11 http://deb.debian.org/debian bookworm/main amd64 libnl-3-200 amd64 3.7.0-0.2+b1 [63.1 kB] Get:12 http://deb.debian.org/debian bookworm/main amd64 libnl-route-3-200 amd64 3.7.0-0.2+b1 [185 kB] Get:13 http://deb.debian.org/debian bookworm/main amd64 libibverbs1 amd64 44.0-2 [60.7 kB] Get:14 http://deb.debian.org/debian bookworm/main amd64 ibverbs-providers amd64 44.0-2 [335 kB] Get:15 http://deb.debian.org/debian bookworm/main amd64 libatomic1 amd64 12.2.0-14 [9328 B] Get:16 http://deb.debian.org/debian bookworm/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.2 [168 kB] Get:17 http://deb.debian.org/debian bookworm/main amd64 libnuma1 amd64 2.0.16-1 [21.0 kB] Get:18 http://deb.debian.org/debian bookworm/main amd64 libpsm2-2 amd64 11.2.185-2 [180 kB] Get:19 http://deb.debian.org/debian bookworm/main amd64 librdmacm1 amd64 44.0-2 [68.6 kB] Get:20 http://deb.debian.org/debian bookworm/main amd64 libfabric1 amd64 1.17.0-3 [627 kB] Get:21 http://deb.debian.org/debian bookworm/main amd64 libhwloc15 amd64 2.9.0-1 [154 kB] Get:22 http://deb.debian.org/debian bookworm/main amd64 libmunge2 amd64 0.5.15-2 [19.5 kB] Get:23 http://deb.debian.org/debian bookworm/main amd64 libpciaccess0 amd64 0.17-2 [51.4 kB] Get:24 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get:25 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get:26 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:27 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get:28 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.3-3 [292 kB] Get:29 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.3-3 [759 kB] Get:30 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.1+b3 [687 kB] Get:31 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get:32 http://deb.debian.org/debian bookworm/main amd64 libxnvctrl0 amd64 515.86.01-1 [13.0 kB] Get:33 http://deb.debian.org/debian bookworm/main amd64 ocl-icd-libopencl1 amd64 2.3.1-1 [43.0 kB] Get:34 http://deb.debian.org/debian bookworm/main amd64 libhwloc-plugins amd64 2.9.0-1 [17.5 kB] Get:35 http://deb.debian.org/debian bookworm/main amd64 libpmix2 amd64 4.2.2-1 [621 kB] Get:36 http://deb.debian.org/debian bookworm/main amd64 libucx0 amd64 1.13.1-1 [860 kB] Get:37 http://deb.debian.org/debian bookworm/main amd64 libopenmpi3 amd64 4.1.4-3 [2423 kB] Get:38 http://deb.debian.org/debian bookworm/main amd64 sfftw2 amd64 2.1.5-6 [247 kB] Get:39 http://deb.debian.org/debian bookworm/main amd64 libclipper2 amd64 2.1.20201109-1 [1156 kB] Get:40 http://deb.debian.org/debian bookworm/main amd64 libgslcblas0 amd64 2.7.1+dfsg-3+b1 [116 kB] Get:41 http://deb.debian.org/debian bookworm/main amd64 libgsl27 amd64 2.7.1+dfsg-3+b1 [948 kB] Get:42 http://deb.debian.org/debian bookworm/main amd64 libnewuoa0 amd64 0.1.2-1 [18.6 kB] Get:43 http://deb.debian.org/debian bookworm/main amd64 libpdb-redo3 amd64 3.0.4-3 [325 kB] Get:44 http://deb.debian.org/debian bookworm/main amd64 libzeep5.1 amd64 5.1.8-1 [593 kB] Get:45 http://deb.debian.org/debian bookworm/main amd64 density-fitness amd64 1.0.8-2 [459 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 23.8 MB in 0s (70.9 MB/s) Selecting previously unselected package adduser. (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 ... 8045 files and directories currently installed.) Preparing to unpack .../archives/adduser_3.130_all.deb ... Unpacking adduser (3.130) ... Setting up adduser (3.130) ... Selecting previously unselected package libicu72: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 ... 8105 files and directories currently installed.) Preparing to unpack .../00-libicu72_72.1-3_amd64.deb ... Unpacking libicu72:amd64 (72.1-3) ... Selecting previously unselected package libboost-regex1.74.0:amd64. Preparing to unpack .../01-libboost-regex1.74.0_1.74.0+ds1-20_amd64.deb ... Unpacking libboost-regex1.74.0:amd64 (1.74.0+ds1-20) ... Selecting previously unselected package libcifpp-data. Preparing to unpack .../02-libcifpp-data_5.0.5-6_all.deb ... Unpacking libcifpp-data (5.0.5-6) ... Selecting previously unselected package libcifpp5:amd64. Preparing to unpack .../03-libcifpp5_5.0.5-6_amd64.deb ... Unpacking libcifpp5:amd64 (5.0.5-6) ... Selecting previously unselected package libccp4-data. Preparing to unpack .../04-libccp4-data_8.0.0-2_all.deb ... Unpacking libccp4-data (8.0.0-2) ... Selecting previously unselected package libccp4c0:amd64. Preparing to unpack .../05-libccp4c0_8.0.0-2_amd64.deb ... Unpacking libccp4c0:amd64 (8.0.0-2) ... Selecting previously unselected package libmmdb2-0:amd64. Preparing to unpack .../06-libmmdb2-0_2.0.22-1_amd64.deb ... Unpacking libmmdb2-0:amd64 (2.0.22-1) ... Selecting previously unselected package libevent-core-2.1-7:amd64. Preparing to unpack .../07-libevent-core-2.1-7_2.1.12-stable-5+b1_amd64.deb ... Unpacking libevent-core-2.1-7:amd64 (2.1.12-stable-5+b1) ... Selecting previously unselected package libevent-pthreads-2.1-7:amd64. Preparing to unpack .../08-libevent-pthreads-2.1-7_2.1.12-stable-5+b1_amd64.deb ... Unpacking libevent-pthreads-2.1-7:amd64 (2.1.12-stable-5+b1) ... Selecting previously unselected package libnl-3-200:amd64. Preparing to unpack .../09-libnl-3-200_3.7.0-0.2+b1_amd64.deb ... Unpacking libnl-3-200:amd64 (3.7.0-0.2+b1) ... Selecting previously unselected package libnl-route-3-200:amd64. Preparing to unpack .../10-libnl-route-3-200_3.7.0-0.2+b1_amd64.deb ... Unpacking libnl-route-3-200:amd64 (3.7.0-0.2+b1) ... Selecting previously unselected package libibverbs1:amd64. Preparing to unpack .../11-libibverbs1_44.0-2_amd64.deb ... Unpacking libibverbs1:amd64 (44.0-2) ... Selecting previously unselected package ibverbs-providers:amd64. Preparing to unpack .../12-ibverbs-providers_44.0-2_amd64.deb ... Unpacking ibverbs-providers:amd64 (44.0-2) ... Selecting previously unselected package libatomic1:amd64. Preparing to unpack .../13-libatomic1_12.2.0-14_amd64.deb ... Unpacking libatomic1:amd64 (12.2.0-14) ... Selecting previously unselected package libpsm-infinipath1. Preparing to unpack .../14-libpsm-infinipath1_3.3+20.604758e7-6.2_amd64.deb ... Unpacking libpsm-infinipath1 (3.3+20.604758e7-6.2) ... Selecting previously unselected package libnuma1:amd64. Preparing to unpack .../15-libnuma1_2.0.16-1_amd64.deb ... Unpacking libnuma1:amd64 (2.0.16-1) ... Selecting previously unselected package libpsm2-2. Preparing to unpack .../16-libpsm2-2_11.2.185-2_amd64.deb ... Unpacking libpsm2-2 (11.2.185-2) ... Selecting previously unselected package librdmacm1:amd64. Preparing to unpack .../17-librdmacm1_44.0-2_amd64.deb ... Unpacking librdmacm1:amd64 (44.0-2) ... Selecting previously unselected package libfabric1:amd64. Preparing to unpack .../18-libfabric1_1.17.0-3_amd64.deb ... Unpacking libfabric1:amd64 (1.17.0-3) ... Selecting previously unselected package libhwloc15:amd64. Preparing to unpack .../19-libhwloc15_2.9.0-1_amd64.deb ... Unpacking libhwloc15:amd64 (2.9.0-1) ... Selecting previously unselected package libmunge2. Preparing to unpack .../20-libmunge2_0.5.15-2_amd64.deb ... Unpacking libmunge2 (0.5.15-2) ... Selecting previously unselected package libpciaccess0:amd64. Preparing to unpack .../21-libpciaccess0_0.17-2_amd64.deb ... Unpacking libpciaccess0:amd64 (0.17-2) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../22-libxau6_1%3a1.0.9-1_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.9-1) ... Selecting previously unselected package libbsd0:amd64. Preparing to unpack .../23-libbsd0_0.11.7-2_amd64.deb ... Unpacking libbsd0:amd64 (0.11.7-2) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../24-libxdmcp6_1%3a1.1.2-3_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.2-3) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../25-libxcb1_1.15-1_amd64.deb ... Unpacking libxcb1:amd64 (1.15-1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../26-libx11-data_2%3a1.8.3-3_all.deb ... Unpacking libx11-data (2:1.8.3-3) ... Selecting previously unselected package libx11-6:amd64. Preparing to unpack .../27-libx11-6_2%3a1.8.3-3_amd64.deb ... Unpacking libx11-6:amd64 (2:1.8.3-3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../28-libxml2_2.9.14+dfsg-1.1+b3_amd64.deb ... Unpacking libxml2:amd64 (2.9.14+dfsg-1.1+b3) ... Selecting previously unselected package libxext6:amd64. Preparing to unpack .../29-libxext6_2%3a1.3.4-1+b1_amd64.deb ... Unpacking libxext6:amd64 (2:1.3.4-1+b1) ... Selecting previously unselected package libxnvctrl0:amd64. Preparing to unpack .../30-libxnvctrl0_515.86.01-1_amd64.deb ... Unpacking libxnvctrl0:amd64 (515.86.01-1) ... Selecting previously unselected package ocl-icd-libopencl1:amd64. Preparing to unpack .../31-ocl-icd-libopencl1_2.3.1-1_amd64.deb ... Unpacking ocl-icd-libopencl1:amd64 (2.3.1-1) ... Selecting previously unselected package libhwloc-plugins:amd64. Preparing to unpack .../32-libhwloc-plugins_2.9.0-1_amd64.deb ... Unpacking libhwloc-plugins:amd64 (2.9.0-1) ... Selecting previously unselected package libpmix2:amd64. Preparing to unpack .../33-libpmix2_4.2.2-1_amd64.deb ... Unpacking libpmix2:amd64 (4.2.2-1) ... Selecting previously unselected package libucx0:amd64. Preparing to unpack .../34-libucx0_1.13.1-1_amd64.deb ... Unpacking libucx0:amd64 (1.13.1-1) ... Selecting previously unselected package libopenmpi3:amd64. Preparing to unpack .../35-libopenmpi3_4.1.4-3_amd64.deb ... Unpacking libopenmpi3:amd64 (4.1.4-3) ... Selecting previously unselected package sfftw2. Preparing to unpack .../36-sfftw2_2.1.5-6_amd64.deb ... Unpacking sfftw2 (2.1.5-6) ... Selecting previously unselected package libclipper2:amd64. Preparing to unpack .../37-libclipper2_2.1.20201109-1_amd64.deb ... Unpacking libclipper2:amd64 (2.1.20201109-1) ... Selecting previously unselected package libgslcblas0:amd64. Preparing to unpack .../38-libgslcblas0_2.7.1+dfsg-3+b1_amd64.deb ... Unpacking libgslcblas0:amd64 (2.7.1+dfsg-3+b1) ... Selecting previously unselected package libgsl27:amd64. Preparing to unpack .../39-libgsl27_2.7.1+dfsg-3+b1_amd64.deb ... Unpacking libgsl27:amd64 (2.7.1+dfsg-3+b1) ... Selecting previously unselected package libnewuoa0. Preparing to unpack .../40-libnewuoa0_0.1.2-1_amd64.deb ... Unpacking libnewuoa0 (0.1.2-1) ... Selecting previously unselected package libpdb-redo3. Preparing to unpack .../41-libpdb-redo3_3.0.4-3_amd64.deb ... Unpacking libpdb-redo3 (3.0.4-3) ... Selecting previously unselected package libzeep5.1. Preparing to unpack .../42-libzeep5.1_5.1.8-1_amd64.deb ... Unpacking libzeep5.1 (5.1.8-1) ... Selecting previously unselected package density-fitness. Preparing to unpack .../43-density-fitness_1.0.8-2_amd64.deb ... Unpacking density-fitness (1.0.8-2) ... Setting up libpciaccess0:amd64 (0.17-2) ... Setting up libxau6:amd64 (1:1.0.9-1) ... Setting up libicu72:amd64 (72.1-3) ... Setting up libgslcblas0:amd64 (2.7.1+dfsg-3+b1) ... Setting up libmmdb2-0:amd64 (2.0.22-1) ... Setting up libgsl27:amd64 (2.7.1+dfsg-3+b1) ... Setting up libccp4-data (8.0.0-2) ... Setting up libnewuoa0 (0.1.2-1) ... Setting up libmunge2 (0.5.15-2) ... Setting up libx11-data (2:1.8.3-3) ... Setting up libboost-regex1.74.0:amd64 (1.74.0+ds1-20) ... Setting up libhwloc15:amd64 (2.9.0-1) ... Setting up libevent-core-2.1-7:amd64 (2.1.12-stable-5+b1) ... Setting up libatomic1:amd64 (12.2.0-14) ... Setting up libccp4c0:amd64 (8.0.0-2) ... Setting up libcifpp-data (5.0.5-6) ... Setting up libnuma1:amd64 (2.0.16-1) ... Setting up ocl-icd-libopencl1:amd64 (2.3.1-1) ... Setting up libnl-3-200:amd64 (3.7.0-0.2+b1) ... Setting up libpsm2-2 (11.2.185-2) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6.2) ... update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode Setting up libzeep5.1 (5.1.8-1) ... Setting up libbsd0:amd64 (0.11.7-2) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.1+b3) ... Setting up libevent-pthreads-2.1-7:amd64 (2.1.12-stable-5+b1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libxcb1:amd64 (1.15-1) ... Setting up libnl-route-3-200:amd64 (3.7.0-0.2+b1) ... Setting up libcifpp5:amd64 (5.0.5-6) ... Setting up libx11-6:amd64 (2:1.8.3-3) ... Setting up libibverbs1:amd64 (44.0-2) ... Setting up ibverbs-providers:amd64 (44.0-2) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libxnvctrl0:amd64 (515.86.01-1) ... Setting up librdmacm1:amd64 (44.0-2) ... Setting up libucx0:amd64 (1.13.1-1) ... Setting up libhwloc-plugins:amd64 (2.9.0-1) ... Setting up libfabric1:amd64 (1.17.0-3) ... Setting up libpmix2:amd64 (4.2.2-1) ... Setting up libopenmpi3:amd64 (4.1.4-3) ... Setting up sfftw2 (2.1.5-6) ... Setting up libclipper2:amd64 (2.1.20201109-1) ... Setting up libpdb-redo3 (3.0.4-3) ... Setting up density-fitness (1.0.8-2) ... Processing triggers for libc-bin (2.36-8) ... 0m15.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'apt-get', '-y', 'install', 'density-fitness'] 0m15.0s INFO: Running scripts post_install 0m15.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/post_install_exceptions'] 0m15.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/post_install_exceptions'] 0m15.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm'] 0m15.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm'] 0m15.6s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpkcg3d4bm to sid 0m15.6s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m15.6s INFO: Running scripts pre_distupgrade 0m15.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m15.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m15.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_distupgrade_exceptions'] 0m15.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_distupgrade_exceptions'] 0m15.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m15.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m15.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m15.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m15.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m15.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m15.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'apt-get', 'update'] 0m19.7s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [167 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9426 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [6974 kB] Fetched 16.6 MB in 3s (4948 kB/s) Reading package lists... 0m19.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'apt-get', 'update'] 0m19.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'apt-get', '-yf', 'dist-upgrade'] 0m22.0s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: density-fitness diffutils e2fsprogs libcifpp-data libcifpp5 libcom-err2 libext2fs2 liblzma5 libpdb-redo3 libss2 libxnvctrl0 logsave tar 13 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 4279 kB of archives. After this operation, 61.4 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 diffutils amd64 1:3.8-4 [352 kB] Get:2 http://deb.debian.org/debian sid/main amd64 tar amd64 1.34+dfsg-1.1 [836 kB] Get:3 http://deb.debian.org/debian sid/main amd64 logsave amd64 1.46.6-1 [19.3 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libext2fs2 amd64 1.46.6-1 [203 kB] Get:5 http://deb.debian.org/debian sid/main amd64 e2fsprogs amd64 1.46.6-1 [566 kB] Get:6 http://deb.debian.org/debian sid/main amd64 liblzma5 amd64 5.4.1-0.1 [205 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libcifpp-data all 5.0.7.1-1 [452 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libcifpp5 amd64 5.0.7.1-1 [802 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libpdb-redo3 amd64 3.0.5-2 [329 kB] Get:10 http://deb.debian.org/debian sid/main amd64 density-fitness amd64 1.0.8-4 [459 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libcom-err2 amd64 1.46.6-1 [19.4 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libss2 amd64 1.46.6-1 [24.2 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libxnvctrl0 amd64 520.56.06-1 [12.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 4279 kB in 0s (36.8 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 ... 8967 files and directories currently installed.) Preparing to unpack .../diffutils_1%3a3.8-4_amd64.deb ... Unpacking diffutils (1:3.8-4) over (1:3.8-3) ... Setting up diffutils (1:3.8-4) ... (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 ... 8967 files and directories currently installed.) Preparing to unpack .../tar_1.34+dfsg-1.1_amd64.deb ... Unpacking tar (1.34+dfsg-1.1) over (1.34+dfsg-1) ... Setting up tar (1.34+dfsg-1.1) ... (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 ... 8967 files and directories currently installed.) Preparing to unpack .../logsave_1.46.6-1_amd64.deb ... Unpacking logsave (1.46.6-1) over (1.46.6~rc1-1.1) ... Preparing to unpack .../libext2fs2_1.46.6-1_amd64.deb ... Unpacking libext2fs2:amd64 (1.46.6-1) over (1.46.6~rc1-1.1) ... Setting up libext2fs2:amd64 (1.46.6-1) ... (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 ... 8967 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.46.6-1_amd64.deb ... Unpacking e2fsprogs (1.46.6-1) over (1.46.6~rc1-1.1) ... Preparing to unpack .../liblzma5_5.4.1-0.1_amd64.deb ... Unpacking liblzma5:amd64 (5.4.1-0.1) over (5.4.1-0.0) ... Setting up liblzma5:amd64 (5.4.1-0.1) ... (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 ... 8967 files and directories currently installed.) Preparing to unpack .../0-libcifpp-data_5.0.7.1-1_all.deb ... Unpacking libcifpp-data (5.0.7.1-1) over (5.0.5-6) ... Preparing to unpack .../1-libcifpp5_5.0.7.1-1_amd64.deb ... Unpacking libcifpp5:amd64 (5.0.7.1-1) over (5.0.5-6) ... Preparing to unpack .../2-libpdb-redo3_3.0.5-2_amd64.deb ... Unpacking libpdb-redo3 (3.0.5-2) over (3.0.4-3) ... Preparing to unpack .../3-density-fitness_1.0.8-4_amd64.deb ... Unpacking density-fitness (1.0.8-4) over (1.0.8-2) ... Preparing to unpack .../4-libcom-err2_1.46.6-1_amd64.deb ... Unpacking libcom-err2:amd64 (1.46.6-1) over (1.46.6~rc1-1.1) ... Preparing to unpack .../5-libss2_1.46.6-1_amd64.deb ... Unpacking libss2:amd64 (1.46.6-1) over (1.46.6~rc1-1.1) ... Preparing to unpack .../6-libxnvctrl0_520.56.06-1_amd64.deb ... Unpacking libxnvctrl0:amd64 (520.56.06-1) over (515.86.01-1) ... Setting up libcom-err2:amd64 (1.46.6-1) ... Setting up libxnvctrl0:amd64 (520.56.06-1) ... Setting up libss2:amd64 (1.46.6-1) ... Setting up libcifpp-data (5.0.7.1-1) ... Installing new version of config file /etc/cron.weekly/update-libcifpp-data ... Setting up logsave (1.46.6-1) ... Setting up e2fsprogs (1.46.6-1) ... Setting up libcifpp5:amd64 (5.0.7.1-1) ... Setting up libpdb-redo3 (3.0.5-2) ... Setting up density-fitness (1.0.8-4) ... Processing triggers for libc-bin (2.36-8) ... 0m22.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'apt-get', '-yf', 'dist-upgrade'] 0m22.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m22.3s DUMP: 9fbb3f0e4fbd7da6fd1ae9af76b04365 - 0m22.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m22.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'apt-cache', 'show', '--no-all-versions', 'density-fitness'] 0m22.5s DUMP: Package: density-fitness Version: 1.0.8-4 Installed-Size: 5548 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.34), libcifpp5 (>= 5.0.7.1), libclipper2 (>= 2.1.20201109), libgcc-s1 (>= 3.0), libpdb-redo3 (>= 3.0.5), libstdc++6 (>= 11), libzeep5.1 (>= 5.1.8), zlib1g (>= 1:1.2.2) Description-en: Calculates per-residue electron density scores The program density-fitness calculates electron density metrics, for main- (includes C? atom) and side-chain atoms of individual residues. . For this calculation, the program uses the structure model in either PDB or mmCIF format and the electron density from the 2mFo-DFc and mFo-DFc maps. If these maps are not readily available, the MTZ file and model can be used to calculate maps clipper. Density-fitness support both X-ray and electron diffraction data. . This program is essentially a reimplementation of edstats, a program available from the CCP4 suite. However, the output now contains only the RSR, SRSR and RSCC fields as in edstats with the addition of EDIAm and OPIA and no longer requires pre-calculated map coefficients. Description-md5: a0d73a3885bbe1e21b3bb9575d5b6f5c Homepage: https://github.com/PDB-REDO/density-fitness Section: science Priority: optional Filename: pool/main/d/density-fitness/density-fitness_1.0.8-4_amd64.deb Size: 458732 MD5sum: 3dcb9137409b46c3f032f8b4b02fd41a SHA256: 7c615c5b1f94e2ced468e1edb1c8c5c61c475fd5153a4e9b1c03fb68f717b3ef 0m22.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'apt-cache', 'show', '--no-all-versions', 'density-fitness'] 0m22.5s INFO: apt-cache knows about the following packages: density-fitness 0m22.5s INFO: Running scripts pre_install 0m22.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_install_database-server'] 0m22.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_install_database-server'] 0m22.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_install_exceptions'] 0m22.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_install_exceptions'] 0m22.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_install_extras'] 0m22.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_install_extras'] 0m22.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_install_foreign_architecture'] 0m22.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_install_foreign_architecture'] 0m22.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m22.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m22.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'apt-cache', 'policy'] 0m22.7s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m22.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'apt-cache', 'policy'] 0m22.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'apt-cache', 'policy', 'density-fitness'] 0m22.7s DUMP: density-fitness: Installed: 1.0.8-4 Candidate: 1.0.8-4 Version table: *** 1.0.8-4 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m22.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'apt-cache', 'policy', 'density-fitness'] 0m22.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'apt-get', '-y', 'install', 'density-fitness'] 0m23.2s DUMP: Reading package lists... Building dependency tree... Reading state information... density-fitness is already the newest version (1.0.8-4). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m23.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'apt-get', '-y', 'install', 'density-fitness'] 0m23.2s INFO: Running scripts post_install 0m23.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/post_install_exceptions'] 0m23.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/post_install_exceptions'] 0m23.3s INFO: Running scripts post_distupgrade 0m23.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m23.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m23.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/post_distupgrade_exceptions'] 0m23.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/post_distupgrade_exceptions'] 0m23.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m23.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m23.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m23.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m23.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/post_distupgrade_zz_backports'] 0m23.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/post_distupgrade_zz_backports'] 0m23.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm'] 0m23.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm'] 0m23.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm'] 0m24.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm'] 0m24.0s INFO: Running scripts pre_install 0m24.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_install_database-server'] 0m24.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_install_database-server'] 0m24.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_install_exceptions'] 0m24.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_install_exceptions'] 0m24.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_install_extras'] 0m24.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_install_extras'] 0m24.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_install_foreign_architecture'] 0m24.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_install_foreign_architecture'] 0m24.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m24.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m24.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'apt-cache', 'policy'] 0m24.2s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m24.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'apt-cache', 'policy'] 0m24.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'apt-cache', 'policy', 'density-fitness'] 0m24.2s DUMP: density-fitness: Installed: 1.0.8-4 Candidate: 1.0.8-4 Version table: *** 1.0.8-4 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m24.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'apt-cache', 'policy', 'density-fitness'] 0m24.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'apt-get', '-y', 'install', 'density-fitness=1.0.8-4'] 0m24.7s DUMP: Reading package lists... Building dependency tree... Reading state information... density-fitness is already the newest version (1.0.8-4). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m24.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'apt-get', '-y', 'install', 'density-fitness=1.0.8-4'] 0m24.7s INFO: Running scripts post_install 0m24.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/post_install_exceptions'] 0m24.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/post_install_exceptions'] 0m24.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm'] 0m25.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm'] 0m26.0s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', '-ac', '--ignore-obsolete'] 0m27.4s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', '-ac', '--ignore-obsolete'] 0m27.4s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m27.4s DUMP: 0.15.6 0m27.4s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m27.4s INFO: Running adequate version 0.15.6 now. 0m27.4s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'density-fitness'] 0m27.5s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'density-fitness'] 0m27.5s INFO: Running scripts pre_remove 0m27.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m27.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m27.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m27.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m27.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m30.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m30.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m30.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m30.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m30.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m30.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_remove_exceptions'] 0m30.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/pre_remove_exceptions'] 0m30.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m30.5s DUMP: install ok installed adduser adduser 3.130 install ok installed apt apt 2.5.5 install ok installed base-files base-files 12.3 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2 install ok installed bsdutils bsdutils 1:2.38.1-4 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 2021.1.1 install ok installed debianutils debianutils 5.7-0.4 install ok installed density-fitness density-fitness 1.0.8-4 install ok installed diffutils diffutils 1:3.8-4 install ok installed dpkg dpkg 1.21.19 install ok installed e2fsprogs e2fsprogs 1.46.6-1 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 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 ibverbs-providers:amd64 ibverbs-providers 44.0-2 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 2.5.5 install ok installed libatomic1:amd64 libatomic1 12.2.0-14 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.0.7-1.1 install ok installed libaudit1:amd64 libaudit1 1:3.0.7-1.1+b3 install ok installed libblkid1:amd64 libblkid1 2.38.1-4 install ok installed libboost-regex1.74.0:amd64 libboost-regex1.74.0 1.74.0+ds1-20 install ok installed libbsd0:amd64 libbsd0 0.11.7-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-8 install ok installed libc6:amd64 libc6 2.36-8 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3 install ok installed libcap2:amd64 libcap2 1:2.66-3 install ok installed libccp4-data libccp4-data 8.0.0-2 install ok installed libccp4c0:amd64 libccp4c0 8.0.0-2 install ok installed libcifpp-data libcifpp-data 5.0.7.1-1 install ok installed libcifpp5:amd64 libcifpp5 5.0.7.1-1 install ok installed libclipper2:amd64 libclipper2 2.1.20201109-1 install ok installed libcom-err2:amd64 libcom-err2 1.46.6-1 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 0.266 install ok installed libevent-core-2.1-7:amd64 libevent-core-2.1-7 2.1.12-stable-5+b1 install ok installed libevent-pthreads-2.1-7:amd64 libevent-pthreads-2.1-7 2.1.12-stable-5+b1 install ok installed libext2fs2:amd64 libext2fs2 1.46.6-1 install ok installed libfabric1:amd64 libfabric1 1.17.0-3 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libfile-find-rule-perl libfile-find-rule-perl 0.34-3 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 libgdbm-compat4:amd64 libgdbm-compat4 1.23-3 install ok installed libgdbm6:amd64 libgdbm6 1.23-3 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.8-4 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libgsl27:amd64 libgsl27 2.7.1+dfsg-3+b1 install ok installed libgslcblas0:amd64 libgslcblas0 2.7.1+dfsg-3+b1 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libhwloc-plugins:amd64 libhwloc-plugins 2.9.0-1 install ok installed libhwloc15:amd64 libhwloc15 2.9.0-1 install ok installed libibverbs1:amd64 libibverbs1 44.0-2 install ok installed libicu72:amd64 libicu72 72.1-3 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 5.4.1-0.1 install ok installed libmd0:amd64 libmd0 1.0.4-2 install ok installed libmmdb2-0:amd64 libmmdb2-0 2.0.22-1 install ok installed libmount1:amd64 libmount1 2.38.1-4 install ok installed libmunge2 libmunge2 0.5.15-2 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libnewuoa0 libnewuoa0 0.1.2-1 install ok installed libnl-3-200:amd64 libnl-3-200 3.7.0-0.2+b1 install ok installed libnl-route-3-200:amd64 libnl-route-3-200 3.7.0-0.2+b1 install ok installed libnuma1:amd64 libnuma1 2.0.16-1 install ok installed libnumber-compare-perl libnumber-compare-perl 0.03-3 install ok installed libopenmpi3:amd64 libopenmpi3 4.1.4-3 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 libpciaccess0:amd64 libpciaccess0 0.17-2 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-1 install ok installed libpdb-redo3 libpdb-redo3 3.0.5-2 install ok installed libperl5.36:amd64 libperl5.36 5.36.0-7 install ok installed libpmix2:amd64 libpmix2 4.2.2-1 install ok installed libpsm-infinipath1 libpsm-infinipath1 3.3+20.604758e7-6.2 install ok installed libpsm2-2 libpsm2-2 11.2.185-2 install ok installed librdmacm1:amd64 librdmacm1 44.0-2 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+b3 install ok installed libselinux1:amd64 libselinux1 3.4-1+b5 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 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-4 install ok installed libss2:amd64 libss2 1.46.6-1 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-14 install ok installed libsystemd0:amd64 libsystemd0 252.5-2 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtext-glob-perl libtext-glob-perl 0.11-3 install ok installed libtinfo6:amd64 libtinfo6 6.4-2 install ok installed libucx0:amd64 libucx0 1.13.1-1 install ok installed libudev1:amd64 libudev1 252.5-2 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-4 install ok installed libx11-6:amd64 libx11-6 2:1.8.3-3 install ok installed libx11-data libx11-data 2:1.8.3-3 install ok installed libxau6:amd64 libxau6 1:1.0.9-1 install ok installed libxcb1:amd64 libxcb1 1.15-1 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b1 install ok installed libxml2:amd64 libxml2 2.9.14+dfsg-1.1+b3 install ok installed libxnvctrl0:amd64 libxnvctrl0 520.56.06-1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzeep5.1 libzeep5.1 5.1.8-1 install ok installed libzstd1:amd64 libzstd1 1.5.2+dfsg2-3 install ok installed login login 1:4.13+dfsg1-1 install ok installed logsave logsave 1.46.6-1 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mount mount 2.38.1-4 install ok installed ncurses-base ncurses-base 6.4-2 install ok installed ncurses-bin ncurses-bin 6.4-2 install ok installed ocl-icd-libopencl1:amd64 ocl-icd-libopencl1 2.3.1-1 install ok installed passwd passwd 1:4.13+dfsg1-1 install ok installed perl perl 5.36.0-7 install ok installed perl-base perl-base 5.36.0-7 install ok installed perl-modules-5.36 perl-modules-5.36 5.36.0-7 install ok installed sed sed 4.9-1 install ok installed sfftw2 sfftw2 2.1.5-6 install ok installed sysvinit-utils sysvinit-utils 3.06-2 install ok installed tar tar 1.34+dfsg-1.1 install ok installed tzdata tzdata 2022g-2 install ok installed usr-is-merged usr-is-merged 35 install ok installed usrmerge usrmerge 35 install ok installed util-linux util-linux 2.38.1-4 install ok installed util-linux-extra util-linux-extra 2.38.1-4 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m30.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m30.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'apt-get', 'remove', 'adduser', 'ibverbs-providers:amd64', 'libatomic1:amd64', 'libboost-regex1.74.0:amd64', 'libbsd0:amd64', 'libccp4-data', 'libccp4c0:amd64', 'libcifpp-data', 'libcifpp5:amd64', 'libclipper2:amd64', 'libevent-core-2.1-7:amd64', 'libevent-pthreads-2.1-7:amd64', 'libfabric1:amd64', 'libgsl27:amd64', 'libgslcblas0:amd64', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibverbs1:amd64', 'libicu72:amd64', 'libmmdb2-0:amd64', 'libmunge2', 'libnewuoa0', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnuma1:amd64', 'libopenmpi3:amd64', 'libpciaccess0:amd64', 'libpdb-redo3', 'libpmix2:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'librdmacm1:amd64', 'libucx0:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxml2:amd64', 'libxnvctrl0:amd64', 'libzeep5.1', 'ocl-icd-libopencl1:amd64', 'sfftw2', 'density-fitness'] 0m31.6s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: adduser density-fitness ibverbs-providers libatomic1 libboost-regex1.74.0 libbsd0 libccp4-data libccp4c0 libcifpp-data libcifpp5 libclipper2 libevent-core-2.1-7 libevent-pthreads-2.1-7 libfabric1 libgsl27 libgslcblas0 libhwloc-plugins libhwloc15 libibverbs1 libicu72 libmmdb2-0 libmunge2 libnewuoa0 libnl-3-200 libnl-route-3-200 libnuma1 libopenmpi3 libpciaccess0 libpdb-redo3 libpmix2 libpsm-infinipath1 libpsm2-2 librdmacm1 libucx0 libx11-6 libx11-data libxau6 libxcb1 libxdmcp6 libxext6 libxml2 libxnvctrl0 libzeep5.1 ocl-icd-libopencl1 sfftw2 0 upgraded, 0 newly installed, 45 to remove and 0 not upgraded. After this operation, 100.0 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 ... 8967 files and directories currently installed.) Removing density-fitness (1.0.8-4) ... Removing libpdb-redo3 (3.0.5-2) ... Removing libclipper2:amd64 (2.1.20201109-1) ... Removing sfftw2 (2.1.5-6) ... Removing libopenmpi3:amd64 (4.1.4-3) ... Removing libucx0:amd64 (1.13.1-1) ... Removing libfabric1:amd64 (1.17.0-3) ... Removing librdmacm1:amd64 (44.0-2) ... Removing ibverbs-providers:amd64 (44.0-2) ... Removing libatomic1:amd64 (12.2.0-14) ... Removing libcifpp5:amd64 (5.0.7.1-1) ... Removing libboost-regex1.74.0:amd64 (1.74.0+ds1-20) ... Removing libpmix2:amd64 (4.2.2-1) ... Removing libhwloc-plugins:amd64 (2.9.0-1) ... Removing libxnvctrl0:amd64 (520.56.06-1) ... Removing libxext6:amd64 (2:1.3.4-1+b1) ... Removing libx11-6:amd64 (2:1.8.3-3) ... Removing libxcb1:amd64 (1.15-1) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libbsd0:amd64 (0.11.7-2) ... Removing libccp4c0:amd64 (8.0.0-2) ... Removing libccp4-data (8.0.0-2) ... Removing libcifpp-data (5.0.7.1-1) ... Removing libevent-pthreads-2.1-7:amd64 (2.1.12-stable-5+b1) ... Removing libevent-core-2.1-7:amd64 (2.1.12-stable-5+b1) ... Removing libgsl27:amd64 (2.7.1+dfsg-3+b1) ... Removing libgslcblas0:amd64 (2.7.1+dfsg-3+b1) ... Removing libhwloc15:amd64 (2.9.0-1) ... Removing libxml2:amd64 (2.9.14+dfsg-1.1+b3) ... Removing libicu72:amd64 (72.1-3) ... Removing libmmdb2-0:amd64 (2.0.22-1) ... Removing libmunge2 (0.5.15-2) ... Removing libnewuoa0 (0.1.2-1) ... Removing libpsm2-2 (11.2.185-2) ... Removing libnuma1:amd64 (2.0.16-1) ... Removing libpciaccess0:amd64 (0.17-2) ... Removing libpsm-infinipath1 (3.3+20.604758e7-6.2) ... update-alternatives: warning: alternative /usr/lib/libpsm1/libpsm_infinipath.so.1.16 (part of link group libpsm_infinipath.so.1) doesn't exist; removing from list of alternatives update-alternatives: warning: /etc/alternatives/libpsm_infinipath.so.1 is dangling; it will be updated with best choice Removing libx11-data (2:1.8.3-3) ... Removing libxau6:amd64 (1:1.0.9-1) ... Removing libzeep5.1 (5.1.8-1) ... Removing ocl-icd-libopencl1:amd64 (2.3.1-1) ... Removing libibverbs1:amd64 (44.0-2) ... Removing adduser (3.130) ... Removing libnl-route-3-200:amd64 (3.7.0-0.2+b1) ... Removing libnl-3-200:amd64 (3.7.0-0.2+b1) ... Processing triggers for libc-bin (2.36-8) ... 0m31.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'apt-get', 'remove', 'adduser', 'ibverbs-providers:amd64', 'libatomic1:amd64', 'libboost-regex1.74.0:amd64', 'libbsd0:amd64', 'libccp4-data', 'libccp4c0:amd64', 'libcifpp-data', 'libcifpp5:amd64', 'libclipper2:amd64', 'libevent-core-2.1-7:amd64', 'libevent-pthreads-2.1-7:amd64', 'libfabric1:amd64', 'libgsl27:amd64', 'libgslcblas0:amd64', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibverbs1:amd64', 'libicu72:amd64', 'libmmdb2-0:amd64', 'libmunge2', 'libnewuoa0', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnuma1:amd64', 'libopenmpi3:amd64', 'libpciaccess0:amd64', 'libpdb-redo3', 'libpmix2:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'librdmacm1:amd64', 'libucx0:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxml2:amd64', 'libxnvctrl0:amd64', 'libzeep5.1', 'ocl-icd-libopencl1:amd64', 'sfftw2', 'density-fitness'] 0m31.6s INFO: Running scripts post_remove 0m31.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/post_remove_exceptions'] 0m31.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/post_remove_exceptions'] 0m31.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'dpkg', '--purge', 'adduser', 'ibverbs-providers:amd64', 'libatomic1:amd64', 'libboost-regex1.74.0:amd64', 'libbsd0:amd64', 'libccp4-data', 'libccp4c0:amd64', 'libcifpp-data', 'libcifpp5:amd64', 'libclipper2:amd64', 'libevent-core-2.1-7:amd64', 'libevent-pthreads-2.1-7:amd64', 'libfabric1:amd64', 'libgsl27:amd64', 'libgslcblas0:amd64', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibverbs1:amd64', 'libicu72:amd64', 'libmmdb2-0:amd64', 'libmunge2', 'libnewuoa0', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnuma1:amd64', 'libopenmpi3:amd64', 'libpciaccess0:amd64', 'libpdb-redo3', 'libpmix2:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'librdmacm1:amd64', 'libucx0:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxml2:amd64', 'libxnvctrl0:amd64', 'libzeep5.1', 'ocl-icd-libopencl1:amd64', 'sfftw2'] 0m31.8s DUMP: (Reading database ... 8070 files and directories currently installed.) Purging configuration files for adduser (3.130) ... Purging configuration files for ibverbs-providers:amd64 (44.0-2) ... dpkg: warning: ignoring request to remove libatomic1 which isn't installed dpkg: warning: ignoring request to remove libboost-regex1.74.0 which isn't installed dpkg: warning: ignoring request to remove libbsd0 which isn't installed dpkg: warning: ignoring request to remove libccp4-data which isn't installed dpkg: warning: ignoring request to remove libccp4c0 which isn't installed Purging configuration files for libcifpp-data (5.0.7.1-1) ... dpkg: warning: ignoring request to remove libcifpp5 which isn't installed dpkg: warning: ignoring request to remove libclipper2 which isn't installed dpkg: warning: ignoring request to remove libevent-core-2.1-7 which isn't installed dpkg: warning: ignoring request to remove libevent-pthreads-2.1-7 which isn't installed dpkg: warning: ignoring request to remove libfabric1 which isn't installed dpkg: warning: ignoring request to remove libgsl27 which isn't installed dpkg: warning: ignoring request to remove libgslcblas0 which isn't installed dpkg: warning: ignoring request to remove libhwloc-plugins which isn't installed dpkg: warning: ignoring request to remove libhwloc15 which isn't installed dpkg: warning: ignoring request to remove libibverbs1 which isn't installed dpkg: warning: ignoring request to remove libicu72 which isn't installed dpkg: warning: ignoring request to remove libmmdb2-0 which isn't installed dpkg: warning: ignoring request to remove libmunge2 which isn't installed dpkg: warning: ignoring request to remove libnewuoa0 which isn't installed Purging configuration files for libnl-3-200:amd64 (3.7.0-0.2+b1) ... dpkg: warning: ignoring request to remove libnl-route-3-200 which isn't installed dpkg: warning: ignoring request to remove libnuma1 which isn't installed dpkg: warning: ignoring request to remove libopenmpi3 which isn't installed dpkg: warning: ignoring request to remove libpciaccess0 which isn't installed dpkg: warning: ignoring request to remove libpdb-redo3 which isn't installed dpkg: warning: ignoring request to remove libpmix2 which isn't installed Purging configuration files for libpsm-infinipath1 (3.3+20.604758e7-6.2) ... dpkg: warning: ignoring request to remove libpsm2-2 which isn't installed dpkg: warning: ignoring request to remove librdmacm1 which isn't installed dpkg: warning: ignoring request to remove libucx0 which isn't installed dpkg: warning: ignoring request to remove libx11-6 which isn't installed dpkg: warning: ignoring request to remove libx11-data which isn't installed dpkg: warning: ignoring request to remove libxau6 which isn't installed dpkg: warning: ignoring request to remove libxcb1 which isn't installed dpkg: warning: ignoring request to remove libxdmcp6 which isn't installed dpkg: warning: ignoring request to remove libxext6 which isn't installed dpkg: warning: ignoring request to remove libxml2 which isn't installed dpkg: warning: ignoring request to remove libxnvctrl0 which isn't installed dpkg: warning: ignoring request to remove libzeep5.1 which isn't installed dpkg: warning: ignoring request to remove ocl-icd-libopencl1 which isn't installed dpkg: warning: ignoring request to remove sfftw2 which isn't installed 0m31.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'dpkg', '--purge', 'adduser', 'ibverbs-providers:amd64', 'libatomic1:amd64', 'libboost-regex1.74.0:amd64', 'libbsd0:amd64', 'libccp4-data', 'libccp4c0:amd64', 'libcifpp-data', 'libcifpp5:amd64', 'libclipper2:amd64', 'libevent-core-2.1-7:amd64', 'libevent-pthreads-2.1-7:amd64', 'libfabric1:amd64', 'libgsl27:amd64', 'libgslcblas0:amd64', 'libhwloc-plugins:amd64', 'libhwloc15:amd64', 'libibverbs1:amd64', 'libicu72:amd64', 'libmmdb2-0:amd64', 'libmunge2', 'libnewuoa0', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnuma1:amd64', 'libopenmpi3:amd64', 'libpciaccess0:amd64', 'libpdb-redo3', 'libpmix2:amd64', 'libpsm-infinipath1', 'libpsm2-2', 'librdmacm1:amd64', 'libucx0:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxml2:amd64', 'libxnvctrl0:amd64', 'libzeep5.1', 'ocl-icd-libopencl1:amd64', 'sfftw2'] 0m31.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'dpkg', '--purge', 'density-fitness'] 0m31.8s DUMP: dpkg: warning: ignoring request to remove density-fitness which isn't installed 0m31.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'dpkg', '--purge', 'density-fitness'] 0m31.8s INFO: Running scripts post_purge 0m31.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/post_purge_exceptions'] 0m31.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/post_purge_exceptions'] 0m31.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'dpkg', '--purge', '--pending'] 0m31.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'dpkg', '--purge', '--pending'] 0m31.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'dpkg', '--remove', '--pending'] 0m31.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'dpkg', '--remove', '--pending'] 0m31.8s INFO: Running scripts post_test 0m31.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/post_test_exceptions'] 0m31.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'tmp/scripts/post_test_exceptions'] 0m31.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm'] 0m32.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm'] 0m32.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'dpkg-divert', '--list'] 0m32.1s DUMP: local diversion of /bin/sync to /bin/sync.distrib diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m32.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'dpkg-divert', '--list'] 0m32.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'apt-get', 'clean'] 0m32.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm', 'apt-get', 'clean'] 0m32.2s DEBUG: Recording chroot state 0m32.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm/dev/shm'] 0m32.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm/dev/shm'] 0m32.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm/dev/console'] 0m32.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm/dev/console'] 0m32.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm/dev/ptmx'] 0m32.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm/dev/ptmx'] 0m32.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm/dev/pts'] 0m32.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm/dev/pts'] 0m32.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm/proc'] 0m33.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm/proc'] 0m33.0s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm'] 0m33.1s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpkcg3d4bm'] 0m33.1s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpkcg3d4bm 0m33.1s INFO: PASS: Upgrading between Debian distributions. 0m33.1s INFO: PASS: All tests. 0m33.1s INFO: piuparts run ends. ret=0 End: 2023-02-04 15:27:33 GMT