Start: 2024-11-20 22:37:02 GMT [testing] Package: python3-cctbx Source: cctbx Version: 2024.8+ds2+~3.21.1+ds1-3 Installed-Size: 285141 Maintainer: Debian Science Maintainers Architecture: amd64 Depends: ca-certificates, libcctbx-dev (= 2024.8+ds2+~3.21.1+ds1-3), libcctbx0 (= 2024.8+ds2+~3.21.1+ds1-3), python3-pycbf (>= 0.9.7+dfsg1-2~), python3 (<< 3.13), python3 (>= 3.12~), python3-h5py (>= 3), python3-hdf5plugin, python3-matplotlib, python3-mrcfile, python3-natsort, python3-numpy (>= 1:1.25.0), python3-numpy-abi9, python3-nxmx, python3-ordered-set, python3-pil, python3-pint, python3-procrunner, python3-pymol, python3-requests, python3-scipy, python3-six, python3-tqdm, python3-wxgtk4.0, python3:any, libantlr3c-3.4-0 | libantlr3c-antlrdbg-3.4-0, libboost-numpy1.83.0 (>= 1.83.0), libboost-numpy1.83.0-py312, libboost-python1.83.0 (>= 1.83.0), libboost-python1.83.0-py312, libboost-thread1.83.0 (>= 1.83.0), libboost-timer1.83.0 (>= 1.83.0), libc6 (>= 2.38), libcbf1t64 (>= 0.9.7+dfsg1-2~), libccp4c0t64 (>= 8.0.0), libgcc-s1 (>= 4.0), libgl1, libglu1-mesa | libglu1, libhdf5-103-1t64, libmmdb2-0 (>= 2.0.22), libssm2 (>= 1.4.0), libstdc++6 (>= 14) Description: Python Toolbox for crystallography Homepage: https://github.com/cctbx/cctbx_project Description-md5: 82495d7385342d38e22c572566893a2d Tag: field::physics, implemented-in::python, role::program, science::calculation, science::plotting, science::visualisation, use::analysing, use::calculating, use::viewing Section: python Priority: optional Filename: pool/main/c/cctbx/python3-cctbx_2024.8+ds2+~3.21.1+ds1-3_amd64.deb Size: 37241972 MD5sum: d0c5292afeacbbc870a6eb9b5fc47c02 SHA256: 190b013ae8fea9ae85317cc1eaa57b55061420952fadd98143fbb7eed2e31717 [sid] Package: python3-cctbx Source: cctbx Version: 2024.10+ds2+~3.22.1+ds1-4 Installed-Size: 498120 Maintainer: Debian Science Maintainers Architecture: amd64 Depends: ca-certificates, libcctbx-dev (= 2024.10+ds2+~3.22.1+ds1-4), libcctbx0 (= 2024.10+ds2+~3.22.1+ds1-4), python3-legacy-cgi, python3-pycbf (>= 0.9.7+dfsg1-2~), python3 (<< 3.14), python3 (>= 3.12~), python3-h5py (>= 3), python3-hdf5plugin, python3-matplotlib, python3-mrcfile, python3-natsort, python3-numpy (>= 1:1.25.0), python3-numpy-abi9, python3-nxmx, python3-ordered-set, python3-pil, python3-pint, python3-procrunner, python3-pymol, python3-requests, python3-scipy, python3-six, python3-tqdm, python3-wxgtk4.0, python3:any, libantlr3c-3.4-0 | libantlr3c-antlrdbg-3.4-0, libboost-numpy1.83.0 (>= 1.83.0), libboost-numpy1.83.0-py312, libboost-numpy1.83.0-py313, libboost-python1.83.0 (>= 1.83.0), libboost-python1.83.0-py312, libboost-python1.83.0-py313, libboost-thread1.83.0 (>= 1.83.0), libboost-timer1.83.0 (>= 1.83.0), libc6 (>= 2.38), libcbf1t64 (>= 0.9.7+dfsg1-2~), libccp4c0t64 (>= 8.0.0), libgcc-s1 (>= 4.0), libgl1, libglu1-mesa | libglu1, libhdf5-103-1t64, libmmdb2-0 (>= 2.0.22), libssm2 (>= 1.4.0), libstdc++6 (>= 14) Description: Python Toolbox for crystallography Homepage: https://github.com/cctbx/cctbx_project Description-md5: 82495d7385342d38e22c572566893a2d Tag: field::physics, implemented-in::python, role::program, science::calculation, science::plotting, science::visualisation, use::analysing, use::calculating, use::viewing Section: python Priority: optional Filename: pool/main/c/cctbx/python3-cctbx_2024.10+ds2+~3.22.1+ds1-4_amd64.deb Size: 47162584 MD5sum: cb06a064ac73f9dec0f35000b1257001 SHA256: 21d86719291cb74ef4ca4cd3707e28127ae1cc1a8b2236287b95b090f2ea53a4 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/trixie-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt 'python3-cctbx=2024.10+ds2+~3.22.1+ds1-4' 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 1.4.5~202409272043~1.4.4-4-gf0f1b5e8 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/trixie-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt 'python3-cctbx=2024.10+ds2+~3.22.1+ds1-4' 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-33-amd64 #1 SMP Debian 5.10.226-1 (2024-10-03) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpgxjjief5 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpgxjjief5 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/trixie-merged-usr_amd64.tar.gz'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpgxjjief5/proc'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpgxjjief5/proc'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpgxjjief5/dev/pts'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpgxjjief5/dev/pts'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpgxjjief5/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpgxjjief5/dev/ptmx'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpgxjjief5/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpgxjjief5/dev/ptmx'] 0m0.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmpgxjjief5/dev/console'] 0m0.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmpgxjjief5/dev/console'] 0m0.2s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpgxjjief5/dev/shm'] 0m0.2s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpgxjjief5/dev/shm'] 0m0.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main 0m0.3s DEBUG: Created policy-rc.d and chmodded it. 0m0.3s DEBUG: Created resolv.conf. 0m0.3s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpgxjjief5/tmp/scripts/ 0m0.3s INFO: Running scripts post_chroot_unpack 0m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'apt-get', 'update'] 0m1.8s DUMP: Get:1 http://deb.debian.org/debian trixie InRelease [172 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9362 kB] Get:3 http://deb.debian.org/debian trixie/main Translation-en [6258 kB] Fetched 15.8 MB in 1s (15.1 MB/s) Reading package lists... 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'apt-get', 'update'] 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'apt-get', '-yf', 'dist-upgrade'] 0m3.2s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... The following packages will be upgraded: bsdutils debianutils libaudit-common libaudit1 libblkid1 libgnutls30t64 libmount1 libsmartcols1 libuuid1 login mount util-linux 12 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 3710 kB of archives. After this operation, 7168 B disk space will be freed. Get:1 http://deb.debian.org/debian trixie/main amd64 bsdutils amd64 1:2.40.2-11 [105 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 debianutils amd64 5.21 [92.1 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 libuuid1 amd64 2.40.2-11 [35.9 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 libblkid1 amd64 2.40.2-11 [168 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 libmount1 amd64 2.40.2-11 [199 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 libsmartcols1 amd64 2.40.2-11 [139 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 util-linux amd64 2.40.2-11 [1213 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 mount amd64 2.40.2-11 [155 kB] Get:9 http://deb.debian.org/debian trixie/main amd64 libaudit-common all 1:4.0.2-2 [12.7 kB] Get:10 http://deb.debian.org/debian trixie/main amd64 libaudit1 amd64 1:4.0.2-2 [54.9 kB] Get:11 http://deb.debian.org/debian trixie/main amd64 login amd64 1:4.16.0-2+really2.40.2-11 [81.5 kB] Get:12 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.8-2 [1454 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 3710 kB in 0s (38.4 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 ... 5158 files and directories currently installed.) Preparing to unpack .../bsdutils_1%3a2.40.2-11_amd64.deb ... Unpacking bsdutils (1:2.40.2-11) over (1:2.40.2-9) ... Setting up bsdutils (1:2.40.2-11) ... (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 ... 5158 files and directories currently installed.) Preparing to unpack .../debianutils_5.21_amd64.deb ... Unpacking debianutils (5.21) over (5.20) ... Setting up debianutils (5.21) ... (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 ... 5158 files and directories currently installed.) Preparing to unpack .../libuuid1_2.40.2-11_amd64.deb ... Unpacking libuuid1:amd64 (2.40.2-11) over (2.40.2-9) ... Setting up libuuid1:amd64 (2.40.2-11) ... (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 ... 5158 files and directories currently installed.) Preparing to unpack .../libblkid1_2.40.2-11_amd64.deb ... Unpacking libblkid1:amd64 (2.40.2-11) over (2.40.2-9) ... Setting up libblkid1:amd64 (2.40.2-11) ... (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 ... 5158 files and directories currently installed.) Preparing to unpack .../libmount1_2.40.2-11_amd64.deb ... Unpacking libmount1:amd64 (2.40.2-11) over (2.40.2-9) ... Setting up libmount1:amd64 (2.40.2-11) ... (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 ... 5158 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.40.2-11_amd64.deb ... Unpacking libsmartcols1:amd64 (2.40.2-11) over (2.40.2-9) ... Setting up libsmartcols1:amd64 (2.40.2-11) ... (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 ... 5158 files and directories currently installed.) Preparing to unpack .../util-linux_2.40.2-11_amd64.deb ... Unpacking util-linux (2.40.2-11) over (2.40.2-9) ... Setting up util-linux (2.40.2-11) ... (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 ... 5155 files and directories currently installed.) Preparing to unpack .../mount_2.40.2-11_amd64.deb ... Unpacking mount (2.40.2-11) over (2.40.2-9) ... Preparing to unpack .../libaudit-common_1%3a4.0.2-2_all.deb ... Unpacking libaudit-common (1:4.0.2-2) over (1:4.0.1-3) ... Setting up libaudit-common (1:4.0.2-2) ... (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 ... 5155 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a4.0.2-2_amd64.deb ... Unpacking libaudit1:amd64 (1:4.0.2-2) over (1:4.0.1-3) ... Setting up libaudit1:amd64 (1:4.0.2-2) ... (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 ... 5155 files and directories currently installed.) Preparing to unpack .../login_1%3a4.16.0-2+really2.40.2-11_amd64.deb ... Unpacking login (1:4.16.0-2+really2.40.2-11) over (1:4.16.0-2+really2.40.2-9) ... Preparing to unpack .../libgnutls30t64_3.8.8-2_amd64.deb ... Unpacking libgnutls30t64:amd64 (3.8.8-2) over (3.8.6-2+b1) ... Setting up libgnutls30t64:amd64 (3.8.8-2) ... Setting up mount (2.40.2-11) ... Setting up login (1:4.16.0-2+really2.40.2-11) ... Processing triggers for libc-bin (2.40-3) ... 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'apt-get', '-yf', 'dist-upgrade'] 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.3s DUMP: e7b68c25035adf22d0ff2930698c015d - 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.3s INFO: Running scripts post_setup 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/post_setup_dummy_users'] 0m4.1s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/post_setup_dummy_users'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/post_setup_forbid_home'] 0m4.1s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/post_setup_forbid_home'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.1s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/post_setup_minimize'] 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/post_setup_minimize'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/post_setup_zz_backports'] 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/post_setup_zz_backports'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.2s DUMP: install ok installed apt apt 2.9.10 install ok installed base-files base-files 13.5 install ok installed base-passwd base-passwd 3.6.5 install ok installed bash bash 5.2.32-1+b2 install ok installed bsdutils bsdutils 1:2.40.2-11 install ok installed coreutils coreutils 9.5-1+b1 install ok installed dash dash 0.5.12-9 install ok installed debconf debconf 1.5.87 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.21 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.1-1+b1 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-8 install ok installed gpgv gpgv 2.2.45-2 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.67 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.10 install ok installed libattr1:amd64 libattr1 1:2.5.2-2 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2 install ok installed libblkid1:amd64 libblkid1 2.40.2-11 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.40-3 install ok installed libc6:amd64 libc6 2.40-3 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-3+b1 install ok installed libcap2:amd64 libcap2 1:2.66-5+b1 install ok installed libcom-err2:amd64 libcom-err2 1.47.1-1+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.273 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.1-1+b1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-8 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-6 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b2 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.8-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.50-4 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3+b1 install ok installed liblzma5:amd64 liblzma5 5.6.3-1+b1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmount1:amd64 libmount1 2.40.2-11 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1+b1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2+b1 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7+b1 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7+b1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b2 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1+b3 install ok installed libselinux1:amd64 libselinux1 3.7-3+b1 install ok installed libsemanage-common libsemanage-common 3.7-2 install ok installed libsemanage2:amd64 libsemanage2 3.7-2+b1 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-11 install ok installed libss2:amd64 libss2 1.47.1-1+b1 install ok installed libssl3t64:amd64 libssl3t64 3.3.2-2 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-8 install ok installed libsystemd0:amd64 libsystemd0 256.7-3 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b3 install ok installed libtinfo6:amd64 libtinfo6 6.5-2+b1 install ok installed libudev1:amd64 libudev1 256.7-3 install ok installed libunistring5:amd64 libunistring5 1.2-1+b1 install ok installed libuuid1:amd64 libuuid1 2.40.2-11 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b2 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1+b1 install ok installed login login 1:4.16.0-2+really2.40.2-11 install ok installed login.defs login.defs 1:4.16.0-4 install ok installed logsave logsave 1.47.1-1+b1 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed mount mount 2.40.2-11 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2+b1 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.2-2 install ok installed passwd passwd 1:4.16.0-4 install ok installed perl-base perl-base 5.40.0-7 install ok installed sed sed 4.9-2 install ok installed sysvinit-utils sysvinit-utils 3.11-1 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024b-3 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-11 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.2s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m4.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgxjjief5'] 0m4.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgxjjief5'] 0m4.4s INFO: Running scripts is_testable 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/is_testable_uninstallable'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/is_testable_uninstallable'] 0m4.4s INFO: Running scripts pre_test 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_test_exceptions'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_test_exceptions'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_test_root_password'] 0m4.4s DUMP: New password: Retype new password: passwd: password updated successfully 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_test_root_password'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'apt-cache', 'show', '--no-all-versions', 'python3-cctbx'] 0m4.5s DUMP: Package: python3-cctbx Source: cctbx Version: 2024.8+ds2+~3.21.1+ds1-3 Installed-Size: 285141 Maintainer: Debian Science Maintainers Architecture: amd64 Depends: ca-certificates, libcctbx-dev (= 2024.8+ds2+~3.21.1+ds1-3), libcctbx0 (= 2024.8+ds2+~3.21.1+ds1-3), python3-pycbf (>= 0.9.7+dfsg1-2~), python3 (<< 3.13), python3 (>= 3.12~), python3-h5py (>= 3), python3-hdf5plugin, python3-matplotlib, python3-mrcfile, python3-natsort, python3-numpy (>= 1:1.25.0), python3-numpy-abi9, python3-nxmx, python3-ordered-set, python3-pil, python3-pint, python3-procrunner, python3-pymol, python3-requests, python3-scipy, python3-six, python3-tqdm, python3-wxgtk4.0, python3:any, libantlr3c-3.4-0 | libantlr3c-antlrdbg-3.4-0, libboost-numpy1.83.0 (>= 1.83.0), libboost-numpy1.83.0-py312, libboost-python1.83.0 (>= 1.83.0), libboost-python1.83.0-py312, libboost-thread1.83.0 (>= 1.83.0), libboost-timer1.83.0 (>= 1.83.0), libc6 (>= 2.38), libcbf1t64 (>= 0.9.7+dfsg1-2~), libccp4c0t64 (>= 8.0.0), libgcc-s1 (>= 4.0), libgl1, libglu1-mesa | libglu1, libhdf5-103-1t64, libmmdb2-0 (>= 2.0.22), libssm2 (>= 1.4.0), libstdc++6 (>= 14) Description-en: Python Toolbox for crystallography Computational Crystallography Toolbox contains following modules: - annlib_adaptbx: - boost_adaptbx: wrappers for Boost functionality in CCTBX - cbflib_adaptbx: - ccp4io_adaptbx: - cctbx: Libraries for general crystallographic applications, useful for both small-molecule and macro-molecular crystallography. - cma_es: - crys3d: Modules for the display of molecules, electron density, and reciprocal space data. - dxtbx: The Diffraction Image Toolbox, a library for handling X-ray detector data of arbitrary complexity from a variety of standard formats. - fable: Fortran EMulation library for porting Fortran77 to C++. - gltbx: Python bindings for OpenGL - iotbx: Working with common crystallographic file formats. - libtbx: The build system common to all other modules. This includes a very thin wrapper around the SCons software construction tool. It also contains many useful frameworks and utilities to simplify application development, including tools for regression testing, parallelization across multiprocessor systems and managed clusters, and a flexible, modular configuration syntax called PHIL (Python Hierarchial Interface Language) used throughout the CCTBX. - mmtbx: Functionality specific to macromolecular crystallography. This includes all of the machinery required for setup of geometry restraints, bulk solvent correction and scaling, analysis of macromolecular diffraction data, calculation of weighted map coefficients, and most of the methods implemented in phenix.refine. The majority of infrastructure for the MolProbity validation server (and Phenix equivalent) is also located here. - omptbx: OpenMP interface. - rstbx: A reciprocal space toolbox to autoindex small molecule Bragg diffraction, given the reciprocal space vectors. - scitbx: General scientific calculations. his includes a family of high-level C++ array types, a fast Fourier transform library, and a C++ port of the popular L-BFGS quasi-Newton minimizer. - smtbx: Small-Molecule crystallography. - spotfinder: - tbxx: - wxtbx: wxPython controls used in the Phenix GUI and various utilities . This package provide a selected collection of python modules from the cctbx project. Description-md5: 82495d7385342d38e22c572566893a2d Homepage: https://github.com/cctbx/cctbx_project Tag: field::physics, implemented-in::python, role::program, science::calculation, science::plotting, science::visualisation, use::analysing, use::calculating, use::viewing Section: python Priority: optional Filename: pool/main/c/cctbx/python3-cctbx_2024.8+ds2+~3.21.1+ds1-3_amd64.deb Size: 37241972 MD5sum: d0c5292afeacbbc870a6eb9b5fc47c02 SHA256: 190b013ae8fea9ae85317cc1eaa57b55061420952fadd98143fbb7eed2e31717 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'apt-cache', 'show', '--no-all-versions', 'python3-cctbx'] 0m4.5s INFO: apt-cache knows about the following packages: python3-cctbx 0m4.5s INFO: Running scripts pre_install 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_install_database-server'] 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_install_database-server'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_install_exceptions'] 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_install_exceptions'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_install_extras'] 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_install_extras'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'apt-cache', 'policy'] 0m4.6s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie/main amd64 Packages release o=Debian,a=testing,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'apt-cache', 'policy'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'apt-cache', 'policy', 'python3-cctbx'] 0m4.6s DUMP: python3-cctbx: Installed: (none) Candidate: 2024.8+ds2+~3.21.1+ds1-3 Version table: 2024.8+ds2+~3.21.1+ds1-3 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'apt-cache', 'policy', 'python3-cctbx'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'apt-get', '-y', 'install', 'python3-cctbx'] 1m3.0s DUMP: Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: adduser adwaita-icon-theme at-spi2-common blt ca-certificates dbus dbus-bin dbus-daemon dbus-session-bus-common dbus-system-bus-common dbus-user-session dconf-gsettings-backend dconf-service fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome fonts-lato fonts-lyx gtk-update-icon-cache hicolor-icon-theme libaec0 libann-cctbx-dev libann-cctbx0 libantlr3c-3.4-0 libapparmor1 libasan8 libatk-bridge2.0-0t64 libatk1.0-0t64 libatomic1 libatspi2.0-0t64 libavahi-client3 libavahi-common-data libavahi-common3 libblas3 libboost-numpy1.83.0 libboost-python-dev libboost-python1.83-dev libboost-python1.83.0 libboost-thread1.83.0 libboost-timer1.83.0 libboost1.83-dev libbrotli1 libc-dev-bin libc6-dev libcairo-gobject2 libcairo2 libcbf1t64 libccp4-data libccp4-dev libccp4c0t64 libccp4f0t64 libcctbx-dev libcctbx0 libcloudproviders0 libcolord2 libcrypt-dev libcups2t64 libcurl3t64-gnutls libcurl4t64 libdatrie1 libdbus-1-3 libdconf1 libdeflate0 libdouble-conversion3 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-radeon1 libdrm2 libedit2 libegl-mesa0 libegl1 libelf1t64 libepoxy0 libevdev2 libexpat1 libexpat1-dev libfontconfig1 libfreetype6 libfribidi0 libgbm1 libgcc-14-dev libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgfortran5 libgl1 libgl1-mesa-dri libglapi-mesa libglew2.2 libglib2.0-0t64 libglu1-mesa libglvnd0 libglx-mesa0 libglx0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libgtk-3-0t64 libgtk-3-common libgudev-1.0-0 libharfbuzz0b libhdf5-103-1t64 libhdf5-hl-100t64 libhwasan0 libice6 libicu72 libimagequant0 libinput-bin libinput10 libitm1 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap-2.5-0 liblerc4 libllvm19 liblsan0 liblzf1 libmd4c0 libmmdb2-0 libmtdev1t64 libncursesw6 libnetcdf19t64 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnotify4 libnsl2 libopengl0 libopenjp2-7 libpam-systemd libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpciaccess0 libpcre2-16-0 libpcre2-32-0 libpixman-1-0 libpng16-16t64 libproc2-0 libpsl5t64 libpython3-dev libpython3-stdlib libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 libqhull-r8.0 libqt5core5t64 libqt5dbus5t64 libqt5designer5 libqt5gui5t64 libqt5help5 libqt5network5t64 libqt5opengl5t64 libqt5printsupport5t64 libqt5sql5t64 libqt5test5t64 libqt5widgets5t64 libqt5xml5t64 libquadmath0 libraqm0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libsharpyuv0 libsm6 libsqlite3-0 libssh2-1t64 libssm2 libstdc++-14-dev libsystemd-shared libsz2 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libtsan2 libubsan1 libvulkan1 libwacom-common libwacom9 libwayland-client0 libwayland-cursor0 libwayland-egl1 libwayland-server0 libwebp7 libwebpdemux2 libwebpmux3 libwxbase3.2-1t64 libwxgtk-gl3.2-1t64 libwxgtk3.2-1t64 libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-present0 libxcb-randr0 libxcb-render-util0 libxcb-render0 libxcb-shape0 libxcb-shm0 libxcb-sync1 libxcb-util1 libxcb-xfixes0 libxcb-xinerama0 libxcb-xinput0 libxcb-xkb1 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxft2 libxi6 libxinerama1 libxkbcommon-x11-0 libxkbcommon0 libxml2 libxrandr2 libxrender1 libxshmfence1 libxslt1.1 libxss1 libxtst6 libxxf86vm1 libz3-4 linux-libc-dev media-types mesa-libgallium netbase openssl procps pymol-data python-matplotlib-data python3 python3-appdirs python3-attr python3-autocommand python3-brotli python3-certifi python3-chardet python3-charset-normalizer python3-contourpy python3-cycler python3-dateutil python3-decorator python3-dev python3-flexcache python3-flexparser python3-fonttools python3-fs python3-h5py python3-h5py-serial python3-hdf5plugin python3-idna python3-inflect python3-jaraco.context python3-jaraco.functools python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib python3-minimal python3-more-itertools python3-mpmath python3-mrcfile python3-natsort python3-numpy python3-nxmx python3-opengl python3-ordered-set python3-packaging python3-pil python3-pil.imagetk python3-pint python3-pkg-resources python3-platformdirs python3-procrunner python3-pycbf python3-pymol python3-pyparsing python3-pyqt5 python3-pyqt5.qtopengl python3-pyqt5.sip python3-requests python3-scipy python3-six python3-sympy python3-tk python3-tqdm python3-typeguard python3-typing-extensions python3-tz python3-ufolib2 python3-unicodedata2 python3-urllib3 python3-wxgtk4.0 python3.12 python3.12-dev python3.12-minimal python3.12-tk python3.13-tk readline-common rpcsvc-proto shared-mime-info sphinx-rtd-theme-common systemd systemd-sysv tk8.6-blt2.5 unicode-data x11-common xkb-data zlib1g-dev Suggested packages: liblocale-gettext-perl perl cron quota adwaita-icon-theme-legacy blt-demo libboost1.83-doc gccxml libboost-atomic1.83-dev libboost-chrono1.83-dev libboost-container1.83-dev libboost-context1.83-dev libboost-contract1.83-dev libboost-coroutine1.83-dev libboost-date-time1.83-dev libboost-exception1.83-dev libboost-fiber1.83-dev libboost-filesystem1.83-dev libboost-graph-parallel1.83-dev libboost-graph1.83-dev libboost-iostreams1.83-dev libboost-json1.83-dev libboost-locale1.83-dev libboost-log1.83-dev libboost-math1.83-dev libboost-mpi-python1.83-dev libboost-mpi1.83-dev libboost-nowide1.83-dev libboost-numpy1.83-dev libboost-program-options1.83-dev libboost-random1.83-dev libboost-regex1.83-dev libboost-serialization1.83-dev libboost-stacktrace1.83-dev libboost-system1.83-dev libboost-test1.83-dev libboost-thread1.83-dev libboost-timer1.83-dev libboost-type-erasure1.83-dev libboost-url1.83-dev libboost-wave1.83-dev libboost1.83-tools-dev libmpfrc++-dev libntl-dev libc-devtools glibc-doc manpages-dev colord cups-common glew-utils low-memory-monitor krb5-doc krb5-user gvfs libjs-jquery-ui-docs liblcms2-utils notification-daemon libcryptsetup12 libtss2-rc0t64 pciutils qgnomeplatform-qt5 qt5-image-formats-plugins lm-sensors libstdc++-14-doc libarchive13t64 libbpf1 libdw1t64 libfido2-1 libip4tc2 libpwquality1 libqrencode4 tcl8.6 tk8.6 libwacom-bin python3-doc python3-venv python-attr-doc python-charset-normalizer-doc python-cycler-doc python-h5py-doc python-lxml-doc cm-super-minimal dvipng ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi python3-gi-cairo python3-gobject python3-sip python3-tornado texlive-extra-utils texlive-latex-extra python-mpmath-doc python3-gmpy2 python-natsort-doc gcc gfortran python-numpy-doc python3-pytest libgle3 python-pil-doc python3-setuptools python-pyparsing-doc python3-cryptography python3-openssl python3-socks python-requests-doc python-scipy-doc texlive-fonts-extra python-sympy-doc tix python3-tk-dbg wx3.2-doc python3.12-venv python3.12-doc binutils binfmt-support readline-doc systemd-container systemd-homed systemd-userdbd systemd-boot systemd-resolved systemd-repart libtss2-tcti-device0 polkitd Recommended packages: librsvg2-common at-spi2-core manpages manpages-dev libgdk-pixbuf2.0-bin libglib2.0-data xdg-user-dirs libgtk-3-bin javascript-common krb5-locales libldap-common libgpm2 publicsuffix qttranslations5-l10n libqt5svg5 qt5-gtk-platformtheme qtwayland5 libqt5sql5-sqlite | libqt5sql5-mysql | libqt5sql5-odbc | libqt5sql5-psql | libqt5sql5-tds | libqt5sql5-ibase libsasl2-modules libkmod2 mesa-vulkan-drivers | vulkan-icd psmisc linux-sysctl-defaults hdf5-filter-plugin-blosc-serial hdf5-filter-plugin-bz2-serial hdf5-filter-plugin-lz4-serial hdf5-filter-plugin-zfp-serial hdf5-plugin-lzf python3-bs4 python3-cssselect python3-html5lib libglut-dev python3-olefile g++ | c++-compiler isympy-common systemd-timesyncd | time-daemon systemd-cryptsetup libnss-systemd The following NEW packages will be installed: adduser adwaita-icon-theme at-spi2-common blt ca-certificates dbus dbus-bin dbus-daemon dbus-session-bus-common dbus-system-bus-common dbus-user-session dconf-gsettings-backend dconf-service fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome fonts-lato fonts-lyx gtk-update-icon-cache hicolor-icon-theme libaec0 libann-cctbx-dev libann-cctbx0 libantlr3c-3.4-0 libapparmor1 libasan8 libatk-bridge2.0-0t64 libatk1.0-0t64 libatomic1 libatspi2.0-0t64 libavahi-client3 libavahi-common-data libavahi-common3 libblas3 libboost-numpy1.83.0 libboost-python-dev libboost-python1.83-dev libboost-python1.83.0 libboost-thread1.83.0 libboost-timer1.83.0 libboost1.83-dev libbrotli1 libc-dev-bin libc6-dev libcairo-gobject2 libcairo2 libcbf1t64 libccp4-data libccp4-dev libccp4c0t64 libccp4f0t64 libcctbx-dev libcctbx0 libcloudproviders0 libcolord2 libcrypt-dev libcups2t64 libcurl3t64-gnutls libcurl4t64 libdatrie1 libdbus-1-3 libdconf1 libdeflate0 libdouble-conversion3 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-radeon1 libdrm2 libedit2 libegl-mesa0 libegl1 libelf1t64 libepoxy0 libevdev2 libexpat1 libexpat1-dev libfontconfig1 libfreetype6 libfribidi0 libgbm1 libgcc-14-dev libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgfortran5 libgl1 libgl1-mesa-dri libglapi-mesa libglew2.2 libglib2.0-0t64 libglu1-mesa libglvnd0 libglx-mesa0 libglx0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libgtk-3-0t64 libgtk-3-common libgudev-1.0-0 libharfbuzz0b libhdf5-103-1t64 libhdf5-hl-100t64 libhwasan0 libice6 libicu72 libimagequant0 libinput-bin libinput10 libitm1 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap-2.5-0 liblerc4 libllvm19 liblsan0 liblzf1 libmd4c0 libmmdb2-0 libmtdev1t64 libncursesw6 libnetcdf19t64 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnotify4 libnsl2 libopengl0 libopenjp2-7 libpam-systemd libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpciaccess0 libpcre2-16-0 libpcre2-32-0 libpixman-1-0 libpng16-16t64 libproc2-0 libpsl5t64 libpython3-dev libpython3-stdlib libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 libqhull-r8.0 libqt5core5t64 libqt5dbus5t64 libqt5designer5 libqt5gui5t64 libqt5help5 libqt5network5t64 libqt5opengl5t64 libqt5printsupport5t64 libqt5sql5t64 libqt5test5t64 libqt5widgets5t64 libqt5xml5t64 libquadmath0 libraqm0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libsharpyuv0 libsm6 libsqlite3-0 libssh2-1t64 libssm2 libstdc++-14-dev libsystemd-shared libsz2 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libtsan2 libubsan1 libvulkan1 libwacom-common libwacom9 libwayland-client0 libwayland-cursor0 libwayland-egl1 libwayland-server0 libwebp7 libwebpdemux2 libwebpmux3 libwxbase3.2-1t64 libwxgtk-gl3.2-1t64 libwxgtk3.2-1t64 libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-present0 libxcb-randr0 libxcb-render-util0 libxcb-render0 libxcb-shape0 libxcb-shm0 libxcb-sync1 libxcb-util1 libxcb-xfixes0 libxcb-xinerama0 libxcb-xinput0 libxcb-xkb1 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxft2 libxi6 libxinerama1 libxkbcommon-x11-0 libxkbcommon0 libxml2 libxrandr2 libxrender1 libxshmfence1 libxslt1.1 libxss1 libxtst6 libxxf86vm1 libz3-4 linux-libc-dev media-types mesa-libgallium netbase openssl procps pymol-data python-matplotlib-data python3 python3-appdirs python3-attr python3-autocommand python3-brotli python3-cctbx python3-certifi python3-chardet python3-charset-normalizer python3-contourpy python3-cycler python3-dateutil python3-decorator python3-dev python3-flexcache python3-flexparser python3-fonttools python3-fs python3-h5py python3-h5py-serial python3-hdf5plugin python3-idna python3-inflect python3-jaraco.context python3-jaraco.functools python3-kiwisolver python3-lxml python3-lz4 python3-matplotlib python3-minimal python3-more-itertools python3-mpmath python3-mrcfile python3-natsort python3-numpy python3-nxmx python3-opengl python3-ordered-set python3-packaging python3-pil python3-pil.imagetk python3-pint python3-pkg-resources python3-platformdirs python3-procrunner python3-pycbf python3-pymol python3-pyparsing python3-pyqt5 python3-pyqt5.qtopengl python3-pyqt5.sip python3-requests python3-scipy python3-six python3-sympy python3-tk python3-tqdm python3-typeguard python3-typing-extensions python3-tz python3-ufolib2 python3-unicodedata2 python3-urllib3 python3-wxgtk4.0 python3.12 python3.12-dev python3.12-minimal python3.12-tk python3.13-tk readline-common rpcsvc-proto shared-mime-info sphinx-rtd-theme-common systemd systemd-sysv tk8.6-blt2.5 unicode-data x11-common xkb-data zlib1g-dev 0 upgraded, 342 newly installed, 0 to remove and 0 not upgraded. Need to get 290 MB of archives. After this operation, 1576 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 libapparmor1 amd64 3.1.7-1+b3 [42.1 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 libsystemd-shared amd64 256.7-3 [2068 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 systemd amd64 256.7-3 [3492 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 systemd-sysv amd64 256.7-3 [58.7 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 libdbus-1-3 amd64 1.14.10-6 [203 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 dbus-bin amd64 1.14.10-6 [106 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 dbus-session-bus-common all 1.14.10-6 [79.2 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get:9 http://deb.debian.org/debian trixie/main amd64 dbus-daemon amd64 1.14.10-6 [185 kB] Get:10 http://deb.debian.org/debian trixie/main amd64 adduser all 3.137 [140 kB] Get:11 http://deb.debian.org/debian trixie/main amd64 dbus-system-bus-common all 1.14.10-6 [80.2 kB] Get:12 http://deb.debian.org/debian trixie/main amd64 dbus amd64 1.14.10-6 [98.5 kB] Get:13 http://deb.debian.org/debian trixie/main amd64 fonts-lato all 2.015-1 [2780 kB] Get:14 http://deb.debian.org/debian trixie/main amd64 libpython3.12-minimal amd64 3.12.7-3 [815 kB] Get:15 http://deb.debian.org/debian trixie/main amd64 python3.12-minimal amd64 3.12.7-3 [2162 kB] Get:16 http://deb.debian.org/debian trixie/main amd64 python3-minimal amd64 3.12.6-1 [26.7 kB] Get:17 http://deb.debian.org/debian trixie/main amd64 media-types all 10.1.0 [26.9 kB] Get:18 http://deb.debian.org/debian trixie/main amd64 netbase all 6.4 [12.8 kB] Get:19 http://deb.debian.org/debian trixie/main amd64 libncursesw6 amd64 6.5-2+b1 [136 kB] Get:20 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get:21 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get:22 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get:23 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get:24 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get:25 http://deb.debian.org/debian trixie/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get:26 http://deb.debian.org/debian trixie/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get:27 http://deb.debian.org/debian trixie/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get:28 http://deb.debian.org/debian trixie/main amd64 readline-common all 8.2-5 [69.3 kB] Get:29 http://deb.debian.org/debian trixie/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get:30 http://deb.debian.org/debian trixie/main amd64 libsqlite3-0 amd64 3.46.1-1 [913 kB] Get:31 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.7-3 [1966 kB] Get:32 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.7-3 [671 kB] Get:33 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.12.6-1 [9692 B] Get:34 http://deb.debian.org/debian trixie/main amd64 python3 amd64 3.12.6-1 [27.8 kB] Get:35 http://deb.debian.org/debian trixie/main amd64 libproc2-0 amd64 2:4.0.4-6 [64.8 kB] Get:36 http://deb.debian.org/debian trixie/main amd64 procps amd64 2:4.0.4-6 [879 kB] Get:37 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.3.2-2 [1382 kB] Get:38 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get:39 http://deb.debian.org/debian trixie/main amd64 libpam-systemd amd64 256.7-3 [280 kB] Get:40 http://deb.debian.org/debian trixie/main amd64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-1 [311 kB] Get:41 http://deb.debian.org/debian trixie/main amd64 libatomic1 amd64 14.2.0-8 [9280 B] Get:42 http://deb.debian.org/debian trixie/main amd64 libglib2.0-0t64 amd64 2.82.2-2 [1501 kB] Get:43 http://deb.debian.org/debian trixie/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get:44 http://deb.debian.org/debian trixie/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get:45 http://deb.debian.org/debian trixie/main amd64 shared-mime-info amd64 2.4-5+b1 [759 kB] Get:46 http://deb.debian.org/debian trixie/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get:47 http://deb.debian.org/debian trixie/main amd64 libpng16-16t64 amd64 1.6.44-2 [280 kB] Get:48 http://deb.debian.org/debian trixie/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get:49 http://deb.debian.org/debian trixie/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get:50 http://deb.debian.org/debian trixie/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get:51 http://deb.debian.org/debian trixie/main amd64 libsharpyuv0 amd64 1.4.0-0.1+b1 [113 kB] Get:52 http://deb.debian.org/debian trixie/main amd64 libwebp7 amd64 1.4.0-0.1+b1 [313 kB] Get:53 http://deb.debian.org/debian trixie/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get:54 http://deb.debian.org/debian trixie/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.12+dfsg-1+b1 [141 kB] Get:55 http://deb.debian.org/debian trixie/main amd64 gtk-update-icon-cache amd64 4.16.5+ds-2 [50.3 kB] Get:56 http://deb.debian.org/debian trixie/main amd64 hicolor-icon-theme all 0.18-1 [12.0 kB] Get:57 http://deb.debian.org/debian trixie/main amd64 adwaita-icon-theme all 47.0-2 [463 kB] Get:58 http://deb.debian.org/debian trixie/main amd64 at-spi2-common all 2.54.0-1 [170 kB] Get:59 http://deb.debian.org/debian trixie/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1042 kB] Get:60 http://deb.debian.org/debian trixie/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get:61 http://deb.debian.org/debian trixie/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get:62 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:63 http://deb.debian.org/debian trixie/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:64 http://deb.debian.org/debian trixie/main amd64 fontconfig-config amd64 2.15.0-1.1+b1 [318 kB] Get:65 http://deb.debian.org/debian trixie/main amd64 libfontconfig1 amd64 2.15.0-1.1+b1 [391 kB] Get:66 http://deb.debian.org/debian trixie/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get:67 http://deb.debian.org/debian trixie/main amd64 libxdmcp6 amd64 1:1.1.2-3+b2 [24.4 kB] Get:68 http://deb.debian.org/debian trixie/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get:69 http://deb.debian.org/debian trixie/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get:70 http://deb.debian.org/debian trixie/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get:71 http://deb.debian.org/debian trixie/main amd64 libxrender1 amd64 1:0.9.10-1.1+b2 [27.8 kB] Get:72 http://deb.debian.org/debian trixie/main amd64 libxft2 amd64 2.3.6-1+b2 [54.5 kB] Get:73 http://deb.debian.org/debian trixie/main amd64 libxext6 amd64 2:1.3.4-1+b2 [50.5 kB] Get:74 http://deb.debian.org/debian trixie/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get:75 http://deb.debian.org/debian trixie/main amd64 libxss1 amd64 1:1.2.3-1+b2 [17.0 kB] Get:76 http://deb.debian.org/debian trixie/main amd64 libtk8.6 amd64 8.6.15-1 [791 kB] Get:77 http://deb.debian.org/debian trixie/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7 [586 kB] Get:78 http://deb.debian.org/debian trixie/main amd64 blt amd64 2.5.3+dfsg-7 [6024 B] Get:79 http://deb.debian.org/debian trixie/main amd64 dbus-user-session amd64 1.14.10-6 [79.0 kB] Get:80 http://deb.debian.org/debian trixie/main amd64 libdconf1 amd64 0.40.0-4+b3 [41.9 kB] Get:81 http://deb.debian.org/debian trixie/main amd64 dconf-service amd64 0.40.0-4+b3 [32.6 kB] Get:82 http://deb.debian.org/debian trixie/main amd64 dconf-gsettings-backend amd64 0.40.0-4+b3 [28.8 kB] Get:83 http://deb.debian.org/debian trixie/main amd64 fontconfig amd64 2.15.0-1.1+b1 [463 kB] Get:84 http://deb.debian.org/debian trixie/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get:85 http://deb.debian.org/debian trixie/main amd64 fonts-lyx all 2.4.2.1-1 [190 kB] Get:86 http://deb.debian.org/debian trixie/main amd64 libaec0 amd64 1.1.3-1+b1 [23.8 kB] Get:87 http://deb.debian.org/debian trixie/main amd64 libann-cctbx0 amd64 1.1.2+doc-9+b1 [32.4 kB] Get:88 http://deb.debian.org/debian trixie/main amd64 libann-cctbx-dev amd64 1.1.2+doc-9+b1 [44.6 kB] Get:89 http://deb.debian.org/debian trixie/main amd64 libantlr3c-3.4-0 amd64 3.4+dfsg-4+b2 [50.6 kB] Get:90 http://deb.debian.org/debian trixie/main amd64 libasan8 amd64 14.2.0-8 [2729 kB] Get:91 http://deb.debian.org/debian trixie/main amd64 libatk1.0-0t64 amd64 2.54.0-1 [51.2 kB] Get:92 http://deb.debian.org/debian trixie/main amd64 libxi6 amd64 2:1.8.2-1 [78.9 kB] Get:93 http://deb.debian.org/debian trixie/main amd64 libatspi2.0-0t64 amd64 2.54.0-1 [76.4 kB] Get:94 http://deb.debian.org/debian trixie/main amd64 libatk-bridge2.0-0t64 amd64 2.54.0-1 [67.6 kB] Get:95 http://deb.debian.org/debian trixie/main amd64 libavahi-common-data amd64 0.8-13+b3 [112 kB] Get:96 http://deb.debian.org/debian trixie/main amd64 libavahi-common3 amd64 0.8-13+b3 [43.2 kB] Get:97 http://deb.debian.org/debian trixie/main amd64 libavahi-client3 amd64 0.8-13+b3 [47.5 kB] Get:98 http://deb.debian.org/debian trixie/main amd64 libblas3 amd64 3.12.0-3+b1 [152 kB] Get:99 http://deb.debian.org/debian trixie/main amd64 libboost-python1.83.0 amd64 1.83.0-3.2 [306 kB] Get:100 http://deb.debian.org/debian trixie/main amd64 libboost-numpy1.83.0 amd64 1.83.0-3.2 [242 kB] Get:101 http://deb.debian.org/debian trixie/main amd64 libgomp1 amd64 14.2.0-8 [137 kB] Get:102 http://deb.debian.org/debian trixie/main amd64 libitm1 amd64 14.2.0-8 [25.9 kB] Get:103 http://deb.debian.org/debian trixie/main amd64 liblsan0 amd64 14.2.0-8 [1205 kB] Get:104 http://deb.debian.org/debian trixie/main amd64 libtsan2 amd64 14.2.0-8 [2461 kB] Get:105 http://deb.debian.org/debian trixie/main amd64 libubsan1 amd64 14.2.0-8 [1075 kB] Get:106 http://deb.debian.org/debian trixie/main amd64 libhwasan0 amd64 14.2.0-8 [1489 kB] Get:107 http://deb.debian.org/debian trixie/main amd64 libquadmath0 amd64 14.2.0-8 [145 kB] Get:108 http://deb.debian.org/debian trixie/main amd64 libgcc-14-dev amd64 14.2.0-8 [2674 kB] Get:109 http://deb.debian.org/debian trixie/main amd64 libc-dev-bin amd64 2.40-3 [51.8 kB] Get:110 http://deb.debian.org/debian trixie/main amd64 linux-libc-dev all 6.11.7-1 [2454 kB] Get:111 http://deb.debian.org/debian trixie/main amd64 libcrypt-dev amd64 1:4.4.36-5 [118 kB] Get:112 http://deb.debian.org/debian trixie/main amd64 rpcsvc-proto amd64 1.4.3-1 [63.3 kB] Get:113 http://deb.debian.org/debian trixie/main amd64 libc6-dev amd64 2.40-3 [1956 kB] Get:114 http://deb.debian.org/debian trixie/main amd64 libstdc++-14-dev amd64 14.2.0-8 [2369 kB] Get:115 http://deb.debian.org/debian trixie/main amd64 libboost1.83-dev amd64 1.83.0-3.2 [10.6 MB] Get:116 http://deb.debian.org/debian trixie/main amd64 libpython3.12t64 amd64 3.12.7-3 [2153 kB] Get:117 http://deb.debian.org/debian trixie/main amd64 libexpat1-dev amd64 2.6.4-1 [158 kB] Get:118 http://deb.debian.org/debian trixie/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get:119 http://deb.debian.org/debian trixie/main amd64 libpython3.12-dev amd64 3.12.7-3 [5124 kB] Get:120 http://deb.debian.org/debian trixie/main amd64 libpython3-dev amd64 3.12.6-1 [9952 B] Get:121 http://deb.debian.org/debian trixie/main amd64 python3.12-dev amd64 3.12.7-3 [505 kB] Get:122 http://deb.debian.org/debian trixie/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:123 http://deb.debian.org/debian trixie/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get:124 http://deb.debian.org/debian trixie/main amd64 libjs-sphinxdoc all 7.4.7-4 [158 kB] Get:125 http://deb.debian.org/debian trixie/main amd64 python3-dev amd64 3.12.6-1 [26.1 kB] Get:126 http://deb.debian.org/debian trixie/main amd64 libboost-python1.83-dev amd64 1.83.0-3.2 [327 kB] Get:127 http://deb.debian.org/debian trixie/main amd64 libboost-python-dev amd64 1.83.0.2+b2 [3892 B] Get:128 http://deb.debian.org/debian trixie/main amd64 libboost-thread1.83.0 amd64 1.83.0-3.2 [269 kB] Get:129 http://deb.debian.org/debian trixie/main amd64 libboost-timer1.83.0 amd64 1.83.0-3.2 [235 kB] Get:130 http://deb.debian.org/debian trixie/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get:131 http://deb.debian.org/debian trixie/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get:132 http://deb.debian.org/debian trixie/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get:133 http://deb.debian.org/debian trixie/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get:134 http://deb.debian.org/debian trixie/main amd64 libcairo-gobject2 amd64 1.18.2-2 [130 kB] Get:135 http://deb.debian.org/debian trixie/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get:136 http://deb.debian.org/debian trixie/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get:137 http://deb.debian.org/debian trixie/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get:138 http://deb.debian.org/debian trixie/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get:139 http://deb.debian.org/debian trixie/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get:140 http://deb.debian.org/debian trixie/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get:141 http://deb.debian.org/debian trixie/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get:142 http://deb.debian.org/debian trixie/main amd64 libcurl4t64 amd64 8.11.0-1 [351 kB] Get:143 http://deb.debian.org/debian trixie/main amd64 libsz2 amd64 1.1.3-1+b1 [8080 B] Get:144 http://deb.debian.org/debian trixie/main amd64 libhdf5-103-1t64 amd64 1.10.10+repack-4 [1253 kB] Get:145 http://deb.debian.org/debian trixie/main amd64 libcbf1t64 amd64 0.9.7+dfsg1-4+b1 [364 kB] Get:146 http://deb.debian.org/debian trixie/main amd64 libccp4-data all 8.0.0-4 [62.7 kB] Get:147 http://deb.debian.org/debian trixie/main amd64 libccp4c0t64 amd64 8.0.0-4 [89.9 kB] Get:148 http://deb.debian.org/debian trixie/main amd64 libgfortran5 amd64 14.2.0-8 [836 kB] Get:149 http://deb.debian.org/debian trixie/main amd64 libmmdb2-0 amd64 2.0.22-1+b2 [342 kB] Get:150 http://deb.debian.org/debian trixie/main amd64 libccp4f0t64 amd64 8.0.0-4 [208 kB] Get:151 http://deb.debian.org/debian trixie/main amd64 libccp4-dev amd64 8.0.0-4 [42.9 kB] Get:152 http://deb.debian.org/debian trixie/main amd64 libcctbx0 amd64 2024.8+ds2+~3.21.1+ds1-3 [2352 kB] Get:153 http://deb.debian.org/debian trixie/main amd64 libcctbx-dev amd64 2024.8+ds2+~3.21.1+ds1-3 [1160 kB] Get:154 http://deb.debian.org/debian trixie/main amd64 libcloudproviders0 amd64 0.3.6-1+b1 [29.2 kB] Get:155 http://deb.debian.org/debian trixie/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get:156 http://deb.debian.org/debian trixie/main amd64 libcolord2 amd64 1.4.7-1+b2 [140 kB] Get:157 http://deb.debian.org/debian trixie/main amd64 libcups2t64 amd64 2.4.10-2 [251 kB] Get:158 http://deb.debian.org/debian trixie/main amd64 libnghttp3-9 amd64 1.4.0-1+b1 [63.6 kB] Get:159 http://deb.debian.org/debian trixie/main amd64 libngtcp2-16 amd64 1.6.0-1 [122 kB] Get:160 http://deb.debian.org/debian trixie/main amd64 libngtcp2-crypto-gnutls8 amd64 1.6.0-1 [19.6 kB] Get:161 http://deb.debian.org/debian trixie/main amd64 libcurl3t64-gnutls amd64 8.11.0-1 [359 kB] Get:162 http://deb.debian.org/debian trixie/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get:163 http://deb.debian.org/debian trixie/main amd64 libdouble-conversion3 amd64 3.3.0-1+b2 [41.8 kB] Get:164 http://deb.debian.org/debian trixie/main amd64 libdrm-common all 2.4.123-1 [8084 B] Get:165 http://deb.debian.org/debian trixie/main amd64 libdrm2 amd64 2.4.123-1 [38.7 kB] Get:166 http://deb.debian.org/debian trixie/main amd64 libdrm-amdgpu1 amd64 2.4.123-1 [22.3 kB] Get:167 http://deb.debian.org/debian trixie/main amd64 libpciaccess0 amd64 0.17-3+b2 [51.9 kB] Get:168 http://deb.debian.org/debian trixie/main amd64 libdrm-intel1 amd64 2.4.123-1 [63.7 kB] Get:169 http://deb.debian.org/debian trixie/main amd64 libdrm-radeon1 amd64 2.4.123-1 [22.3 kB] Get:170 http://deb.debian.org/debian trixie/main amd64 libedit2 amd64 3.1-20240808-1 [93.9 kB] Get:171 http://deb.debian.org/debian trixie/main amd64 libwayland-server0 amd64 1.23.0-1+b1 [34.2 kB] Get:172 http://deb.debian.org/debian trixie/main amd64 libxcb-randr0 amd64 1.17.0-2+b1 [117 kB] Get:173 http://deb.debian.org/debian trixie/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get:174 http://deb.debian.org/debian trixie/main amd64 libglapi-mesa amd64 24.2.7-1 [37.9 kB] Get:175 http://deb.debian.org/debian trixie/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get:176 http://deb.debian.org/debian trixie/main amd64 libllvm19 amd64 1:19.1.3-2 [26.0 MB] Get:177 http://deb.debian.org/debian trixie/main amd64 libsensors-config all 1:3.6.0-10 [14.6 kB] Get:178 http://deb.debian.org/debian trixie/main amd64 libsensors5 amd64 1:3.6.0-10+b1 [35.1 kB] Get:179 http://deb.debian.org/debian trixie/main amd64 libx11-xcb1 amd64 2:1.8.10-2 [241 kB] Get:180 http://deb.debian.org/debian trixie/main amd64 libxcb-dri2-0 amd64 1.17.0-2+b1 [107 kB] Get:181 http://deb.debian.org/debian trixie/main amd64 libxcb-dri3-0 amd64 1.17.0-2+b1 [107 kB] Get:182 http://deb.debian.org/debian trixie/main amd64 libxcb-present0 amd64 1.17.0-2+b1 [106 kB] Get:183 http://deb.debian.org/debian trixie/main amd64 libxcb-sync1 amd64 1.17.0-2+b1 [109 kB] Get:184 http://deb.debian.org/debian trixie/main amd64 libxcb-xfixes0 amd64 1.17.0-2+b1 [109 kB] Get:185 http://deb.debian.org/debian trixie/main amd64 libxshmfence1 amd64 1.3-1+b2 [8848 B] Get:186 http://deb.debian.org/debian trixie/main amd64 mesa-libgallium amd64 24.2.7-1 [9186 kB] Get:187 http://deb.debian.org/debian trixie/main amd64 libgbm1 amd64 24.2.7-1 [42.8 kB] Get:188 http://deb.debian.org/debian trixie/main amd64 libwayland-client0 amd64 1.23.0-1+b1 [26.6 kB] Get:189 http://deb.debian.org/debian trixie/main amd64 libegl-mesa0 amd64 24.2.7-1 [133 kB] Get:190 http://deb.debian.org/debian trixie/main amd64 libepoxy0 amd64 1.5.10-2 [193 kB] Get:191 http://deb.debian.org/debian trixie/main amd64 libevdev2 amd64 1.13.3+dfsg-1 [32.2 kB] Get:192 http://deb.debian.org/debian trixie/main amd64 libfribidi0 amd64 1.0.15-1 [71.8 kB] Get:193 http://deb.debian.org/debian trixie/main amd64 libglvnd0 amd64 1.7.0-1+b2 [52.0 kB] Get:194 http://deb.debian.org/debian trixie/main amd64 libxcb-glx0 amd64 1.17.0-2+b1 [122 kB] Get:195 http://deb.debian.org/debian trixie/main amd64 libxfixes3 amd64 1:6.0.0-2+b2 [20.3 kB] Get:196 http://deb.debian.org/debian trixie/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b3 [19.3 kB] Get:197 http://deb.debian.org/debian trixie/main amd64 libvulkan1 amd64 1.3.296.0-1 [126 kB] Get:198 http://deb.debian.org/debian trixie/main amd64 libgl1-mesa-dri amd64 24.2.7-1 [43.9 kB] Get:199 http://deb.debian.org/debian trixie/main amd64 libglx-mesa0 amd64 24.2.7-1 [154 kB] Get:200 http://deb.debian.org/debian trixie/main amd64 libglx0 amd64 1.7.0-1+b2 [34.9 kB] Get:201 http://deb.debian.org/debian trixie/main amd64 libgl1 amd64 1.7.0-1+b2 [89.5 kB] Get:202 http://deb.debian.org/debian trixie/main amd64 libglew2.2 amd64 2.2.0-4+b2 [168 kB] Get:203 http://deb.debian.org/debian trixie/main amd64 libopengl0 amd64 1.7.0-1+b2 [30.9 kB] Get:204 http://deb.debian.org/debian trixie/main amd64 libglu1-mesa amd64 9.0.2-1.1+b2 [185 kB] Get:205 http://deb.debian.org/debian trixie/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get:206 http://deb.debian.org/debian trixie/main amd64 libharfbuzz0b amd64 10.0.1-1 [477 kB] Get:207 http://deb.debian.org/debian trixie/main amd64 libthai-data all 0.1.29-2 [168 kB] Get:208 http://deb.debian.org/debian trixie/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get:209 http://deb.debian.org/debian trixie/main amd64 libpango-1.0-0 amd64 1.54.0+ds-3 [223 kB] Get:210 http://deb.debian.org/debian trixie/main amd64 libpangoft2-1.0-0 amd64 1.54.0+ds-3 [54.2 kB] Get:211 http://deb.debian.org/debian trixie/main amd64 libpangocairo-1.0-0 amd64 1.54.0+ds-3 [35.2 kB] Get:212 http://deb.debian.org/debian trixie/main amd64 libwayland-cursor0 amd64 1.23.0-1+b1 [11.7 kB] Get:213 http://deb.debian.org/debian trixie/main amd64 libwayland-egl1 amd64 1.23.0-1+b1 [5664 B] Get:214 http://deb.debian.org/debian trixie/main amd64 libxcomposite1 amd64 1:0.4.6-1 [16.3 kB] Get:215 http://deb.debian.org/debian trixie/main amd64 libxcursor1 amd64 1:1.2.2-1+b1 [37.6 kB] Get:216 http://deb.debian.org/debian trixie/main amd64 libxdamage1 amd64 1:1.1.6-1+b2 [15.5 kB] Get:217 http://deb.debian.org/debian trixie/main amd64 libxinerama1 amd64 2:1.1.4-3+b2 [16.0 kB] Get:218 http://deb.debian.org/debian trixie/main amd64 xkb-data all 2.42-1 [790 kB] Get:219 http://deb.debian.org/debian trixie/main amd64 libxkbcommon0 amd64 1.6.0-1+b2 [111 kB] Get:220 http://deb.debian.org/debian trixie/main amd64 libxrandr2 amd64 2:1.5.4-1+b1 [36.3 kB] Get:221 http://deb.debian.org/debian trixie/main amd64 libgtk-3-common all 3.24.43-4 [4657 kB] Get:222 http://deb.debian.org/debian trixie/main amd64 libgtk-3-0t64 amd64 3.24.43-4 [2754 kB] Get:223 http://deb.debian.org/debian trixie/main amd64 libgudev-1.0-0 amd64 238-5+b1 [14.8 kB] Get:224 http://deb.debian.org/debian trixie/main amd64 libhdf5-hl-100t64 amd64 1.10.10+repack-4 [63.9 kB] Get:225 http://deb.debian.org/debian trixie/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get:226 http://deb.debian.org/debian trixie/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB] Get:227 http://deb.debian.org/debian trixie/main amd64 libwacom-common all 2.13.0-1 [98.0 kB] Get:228 http://deb.debian.org/debian trixie/main amd64 libwacom9 amd64 2.13.0-1 [24.0 kB] Get:229 http://deb.debian.org/debian trixie/main amd64 libinput-bin amd64 1.26.2-1 [25.3 kB] Get:230 http://deb.debian.org/debian trixie/main amd64 libmtdev1t64 amd64 1.1.6-1.2+b1 [22.5 kB] Get:231 http://deb.debian.org/debian trixie/main amd64 libinput10 amd64 1.26.2-1 [131 kB] Get:232 http://deb.debian.org/debian trixie/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get:233 http://deb.debian.org/debian trixie/main amd64 liblapack3 amd64 3.12.0-3+b1 [2450 kB] Get:234 http://deb.debian.org/debian trixie/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b2 [29.4 kB] Get:235 http://deb.debian.org/debian trixie/main amd64 liblzf1 amd64 3.6-4+b2 [10.1 kB] Get:236 http://deb.debian.org/debian trixie/main amd64 libmd4c0 amd64 0.5.2-2+b1 [49.0 kB] Get:237 http://deb.debian.org/debian trixie/main amd64 libnetcdf19t64 amd64 1:4.9.2-7 [477 kB] Get:238 http://deb.debian.org/debian trixie/main amd64 libnotify4 amd64 0.8.3-1+b2 [25.9 kB] Get:239 http://deb.debian.org/debian trixie/main amd64 libopenjp2-7 amd64 2.5.0-2+b4 [199 kB] Get:240 http://deb.debian.org/debian trixie/main amd64 libpcre2-16-0 amd64 10.42-4+b2 [249 kB] Get:241 http://deb.debian.org/debian trixie/main amd64 libpcre2-32-0 amd64 10.42-4+b2 [237 kB] Get:242 http://deb.debian.org/debian trixie/main amd64 libqhull-r8.0 amd64 2020.2-6+b2 [248 kB] Get:243 http://deb.debian.org/debian trixie/main amd64 libqt5core5t64 amd64 5.15.15+dfsg-2 [1866 kB] Get:244 http://deb.debian.org/debian trixie/main amd64 libqt5dbus5t64 amd64 5.15.15+dfsg-2 [217 kB] Get:245 http://deb.debian.org/debian trixie/main amd64 libegl1 amd64 1.7.0-1+b2 [34.6 kB] Get:246 http://deb.debian.org/debian trixie/main amd64 libqt5network5t64 amd64 5.15.15+dfsg-2 [682 kB] Get:247 http://deb.debian.org/debian trixie/main amd64 libsm6 amd64 2:1.2.4-1 [35.2 kB] Get:248 http://deb.debian.org/debian trixie/main amd64 libxcb-icccm4 amd64 0.4.2-1 [27.5 kB] Get:249 http://deb.debian.org/debian trixie/main amd64 libxcb-util1 amd64 0.4.0-1+b2 [22.5 kB] Get:250 http://deb.debian.org/debian trixie/main amd64 libxcb-image0 amd64 0.4.0-2+b2 [22.2 kB] Get:251 http://deb.debian.org/debian trixie/main amd64 libxcb-keysyms1 amd64 0.4.0-1+b3 [15.7 kB] Get:252 http://deb.debian.org/debian trixie/main amd64 libxcb-render-util0 amd64 0.3.9-1+b2 [17.4 kB] Get:253 http://deb.debian.org/debian trixie/main amd64 libxcb-shape0 amd64 1.17.0-2+b1 [106 kB] Get:254 http://deb.debian.org/debian trixie/main amd64 libxcb-xinerama0 amd64 1.17.0-2+b1 [105 kB] Get:255 http://deb.debian.org/debian trixie/main amd64 libxcb-xinput0 amd64 1.17.0-2+b1 [130 kB] Get:256 http://deb.debian.org/debian trixie/main amd64 libxcb-xkb1 amd64 1.17.0-2+b1 [130 kB] Get:257 http://deb.debian.org/debian trixie/main amd64 libxkbcommon-x11-0 amd64 1.6.0-1+b2 [16.3 kB] Get:258 http://deb.debian.org/debian trixie/main amd64 libqt5gui5t64 amd64 5.15.15+dfsg-2 [3498 kB] Get:259 http://deb.debian.org/debian trixie/main amd64 libqt5widgets5t64 amd64 5.15.15+dfsg-2 [2400 kB] Get:260 http://deb.debian.org/debian trixie/main amd64 libqt5xml5t64 amd64 5.15.15+dfsg-2 [126 kB] Get:261 http://deb.debian.org/debian trixie/main amd64 libqt5designer5 amd64 5.15.15-2 [2759 kB] Get:262 http://deb.debian.org/debian trixie/main amd64 libqt5sql5t64 amd64 5.15.15+dfsg-2 [125 kB] Get:263 http://deb.debian.org/debian trixie/main amd64 libqt5help5 amd64 5.15.15-2 [151 kB] Get:264 http://deb.debian.org/debian trixie/main amd64 libqt5opengl5t64 amd64 5.15.15+dfsg-2 [150 kB] Get:265 http://deb.debian.org/debian trixie/main amd64 libqt5printsupport5t64 amd64 5.15.15+dfsg-2 [206 kB] Get:266 http://deb.debian.org/debian trixie/main amd64 libqt5test5t64 amd64 5.15.15+dfsg-2 [151 kB] Get:267 http://deb.debian.org/debian trixie/main amd64 libraqm0 amd64 0.10.1-1+b2 [14.1 kB] Get:268 http://deb.debian.org/debian trixie/main amd64 libssm2 amd64 1.4.0-2+b3 [84.3 kB] Get:269 http://deb.debian.org/debian trixie/main amd64 libwebpdemux2 amd64 1.4.0-0.1+b1 [111 kB] Get:270 http://deb.debian.org/debian trixie/main amd64 libwebpmux3 amd64 1.4.0-0.1+b1 [123 kB] Get:271 http://deb.debian.org/debian trixie/main amd64 libwxbase3.2-1t64 amd64 3.2.6+dfsg-2 [1041 kB] Get:272 http://deb.debian.org/debian trixie/main amd64 libxtst6 amd64 2:1.2.3-1.1+b2 [25.9 kB] Get:273 http://deb.debian.org/debian trixie/main amd64 libwxgtk3.2-1t64 amd64 3.2.6+dfsg-2 [4695 kB] Get:274 http://deb.debian.org/debian trixie/main amd64 libwxgtk-gl3.2-1t64 amd64 3.2.6+dfsg-2 [84.1 kB] Get:275 http://deb.debian.org/debian trixie/main amd64 libxslt1.1 amd64 1.1.35-1.1+b1 [233 kB] Get:276 http://deb.debian.org/debian trixie/main amd64 pymol-data all 3.0.0+dfsg-1 [1433 kB] Get:277 http://deb.debian.org/debian trixie/main amd64 python-matplotlib-data all 3.8.3-3 [2731 kB] Get:278 http://deb.debian.org/debian trixie/main amd64 python3-appdirs all 1.4.4-4 [12.5 kB] Get:279 http://deb.debian.org/debian trixie/main amd64 python3-attr all 23.2.0-2 [65.5 kB] Get:280 http://deb.debian.org/debian trixie/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get:281 http://deb.debian.org/debian trixie/main amd64 python3-brotli amd64 1.1.0-2+b6 [321 kB] Get:282 http://deb.debian.org/debian trixie/main amd64 python3-pycbf amd64 0.9.7+dfsg1-4+b1 [165 kB] Get:283 http://deb.debian.org/debian trixie/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get:284 http://deb.debian.org/debian trixie/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get:285 http://deb.debian.org/debian trixie/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get:286 http://deb.debian.org/debian trixie/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get:287 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get:288 http://deb.debian.org/debian trixie/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get:289 http://deb.debian.org/debian trixie/main amd64 python3-pkg-resources all 74.1.2-2 [213 kB] Get:290 http://deb.debian.org/debian trixie/main amd64 python3-numpy amd64 1:1.26.4+ds-12 [4738 kB] Get:291 http://deb.debian.org/debian trixie/main amd64 python3-h5py-serial amd64 3.11.0-5 [975 kB] Get:292 http://deb.debian.org/debian trixie/main amd64 python3-h5py all 3.11.0-5 [14.7 kB] Get:293 http://deb.debian.org/debian trixie/main amd64 python3-hdf5plugin all 4.0.1-3 [22.9 kB] Get:294 http://deb.debian.org/debian trixie/main amd64 python3-dateutil all 2.9.0-3 [79.3 kB] Get:295 http://deb.debian.org/debian trixie/main amd64 python3-pil amd64 10.4.0-1+b1 [522 kB] Get:296 http://deb.debian.org/debian trixie/main amd64 python3.12-tk amd64 3.12.7-3 [112 kB] Get:297 http://deb.debian.org/debian trixie/main amd64 python3.13-tk amd64 3.13.0-2 [103 kB] Get:298 http://deb.debian.org/debian trixie/main amd64 python3-tk amd64 3.12.7-1 [9444 B] Get:299 http://deb.debian.org/debian trixie/main amd64 python3-pil.imagetk amd64 10.4.0-1+b1 [79.8 kB] Get:300 http://deb.debian.org/debian trixie/main amd64 python3-pyparsing all 3.1.2-1 [146 kB] Get:301 http://deb.debian.org/debian trixie/main amd64 python3-contourpy amd64 1.3.0-2+b1 [264 kB] Get:302 http://deb.debian.org/debian trixie/main amd64 python3-cycler all 0.12.1-1 [9496 B] Get:303 http://deb.debian.org/debian trixie/main amd64 python3-tz all 2024.1-2 [30.9 kB] Get:304 http://deb.debian.org/debian trixie/main amd64 python3-six all 1.16.0-7 [16.4 kB] Get:305 http://deb.debian.org/debian trixie/main amd64 python3-fs all 2.4.16-4 [95.4 kB] Get:306 http://deb.debian.org/debian trixie/main amd64 python3-lxml amd64 5.3.0-1+b1 [1676 kB] Get:307 http://deb.debian.org/debian trixie/main amd64 python3-lz4 amd64 4.0.2+dfsg-1+b5 [25.6 kB] Get:308 http://deb.debian.org/debian trixie/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get:309 http://deb.debian.org/debian trixie/main amd64 python3-scipy amd64 1.13.1-6 [20.2 MB] Get:310 http://deb.debian.org/debian trixie/main amd64 python3-mpmath all 1.3.0-1 [419 kB] Get:311 http://deb.debian.org/debian trixie/main amd64 python3-sympy all 1.13.3-1 [4147 kB] Get:312 http://deb.debian.org/debian trixie/main amd64 python3-ufolib2 all 0.16.1+dfsg1-1 [32.9 kB] Get:313 http://deb.debian.org/debian trixie/main amd64 python3-unicodedata2 amd64 15.1.0+ds-1+b3 [299 kB] Get:314 http://deb.debian.org/debian trixie/main amd64 unicode-data all 15.1.0-1 [8547 kB] Get:315 http://deb.debian.org/debian trixie/main amd64 python3-fonttools amd64 4.54.1-4+b1 [1631 kB] Get:316 http://deb.debian.org/debian trixie/main amd64 python3-kiwisolver amd64 1.4.7-2+b1 [77.0 kB] Get:317 http://deb.debian.org/debian trixie/main amd64 python3-packaging all 24.1-1 [45.8 kB] Get:318 http://deb.debian.org/debian trixie/main amd64 python3-matplotlib amd64 3.8.3-3+b1 [5654 kB] Get:319 http://deb.debian.org/debian trixie/main amd64 sphinx-rtd-theme-common all 3.0.2+dfsg-1 [1023 kB] Get:320 http://deb.debian.org/debian trixie/main amd64 python3-mrcfile all 1.5.3-3 [119 kB] Get:321 http://deb.debian.org/debian trixie/main amd64 python3-natsort all 8.0.2-2 [39.0 kB] Get:322 http://deb.debian.org/debian trixie/main amd64 python3-flexcache all 0.3-2 [13.5 kB] Get:323 http://deb.debian.org/debian trixie/main amd64 python3-flexparser all 0.4-1 [42.9 kB] Get:324 http://deb.debian.org/debian trixie/main amd64 python3-platformdirs all 4.3.6-1 [16.6 kB] Get:325 http://deb.debian.org/debian trixie/main amd64 python3-pint all 0.24.4-1 [225 kB] Get:326 http://deb.debian.org/debian trixie/main amd64 python3-nxmx all 0.0.3-3 [15.4 kB] Get:327 http://deb.debian.org/debian trixie/main amd64 python3-ordered-set all 4.1.0-1 [9628 B] Get:328 http://deb.debian.org/debian trixie/main amd64 python3-procrunner all 2.3.3-2 [13.9 kB] Get:329 http://deb.debian.org/debian trixie/main amd64 python3-opengl all 3.1.7+dfsg-1 [604 kB] Get:330 http://deb.debian.org/debian trixie/main amd64 python3-pyqt5.sip amd64 12.15.0-1+b1 [66.2 kB] Get:331 http://deb.debian.org/debian trixie/main amd64 python3-pyqt5 amd64 5.15.11+dfsg-1+b1 [2521 kB] Get:332 http://deb.debian.org/debian trixie/main amd64 python3-pyqt5.qtopengl amd64 5.15.11+dfsg-1+b1 [208 kB] Get:333 http://deb.debian.org/debian trixie/main amd64 python3-pymol amd64 3.0.0+dfsg-1+b1 [7208 kB] Get:334 http://deb.debian.org/debian trixie/main amd64 python3-certifi all 2024.8.30+dfsg-1 [9576 B] Get:335 http://deb.debian.org/debian trixie/main amd64 python3-charset-normalizer amd64 3.4.0-1+b1 [140 kB] Get:336 http://deb.debian.org/debian trixie/main amd64 python3-idna all 3.8-2 [41.6 kB] Get:337 http://deb.debian.org/debian trixie/main amd64 python3-urllib3 all 2.0.7-2 [111 kB] Get:338 http://deb.debian.org/debian trixie/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get:339 http://deb.debian.org/debian trixie/main amd64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get:340 http://deb.debian.org/debian trixie/main amd64 python3-tqdm all 4.67.0-1 [90.2 kB] Get:341 http://deb.debian.org/debian trixie/main amd64 python3-wxgtk4.0 amd64 4.2.2+dfsg-1+b1 [9449 kB] Get:342 http://deb.debian.org/debian trixie/main amd64 python3-cctbx amd64 2024.8+ds2+~3.21.1+ds1-3 [37.2 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 290 MB in 4s (80.8 MB/s) Selecting previously unselected package libapparmor1: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 ... 5158 files and directories currently installed.) Preparing to unpack .../libapparmor1_3.1.7-1+b3_amd64.deb ... Unpacking libapparmor1:amd64 (3.1.7-1+b3) ... Selecting previously unselected package libsystemd-shared:amd64. Preparing to unpack .../libsystemd-shared_256.7-3_amd64.deb ... Unpacking libsystemd-shared:amd64 (256.7-3) ... Selecting previously unselected package systemd. Preparing to unpack .../systemd_256.7-3_amd64.deb ... Unpacking systemd (256.7-3) ... Setting up libapparmor1:amd64 (3.1.7-1+b3) ... Setting up libsystemd-shared:amd64 (256.7-3) ... Setting up systemd (256.7-3) ... Created symlink '/etc/systemd/system/getty.target.wants/getty@tty1.service' → '/usr/lib/systemd/system/getty@.service'. Created symlink '/etc/systemd/system/multi-user.target.wants/remote-fs.target' → '/usr/lib/systemd/system/remote-fs.target'. Created symlink '/etc/systemd/system/sysinit.target.wants/systemd-pstore.service' → '/usr/lib/systemd/system/systemd-pstore.service'. Initializing machine ID from random generator. Creating group 'systemd-journal' with GID 999. Creating group 'systemd-network' with GID 998. Creating user 'systemd-network' (systemd Network Management) with UID 998 and GID 998. [ESC][0;1;39m/usr/lib/tmpfiles.d/legacy.conf:13: Duplicate line for path "/run/lock", ignoring.[ESC][0m [ESC][0;1;31m"/home" already exists and is not a directory.[ESC][0m Selecting previously unselected package systemd-sysv. (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 ... 6109 files and directories currently installed.) Preparing to unpack .../0-systemd-sysv_256.7-3_amd64.deb ... Unpacking systemd-sysv (256.7-3) ... Selecting previously unselected package libdbus-1-3:amd64. Preparing to unpack .../1-libdbus-1-3_1.14.10-6_amd64.deb ... Unpacking libdbus-1-3:amd64 (1.14.10-6) ... Selecting previously unselected package dbus-bin. Preparing to unpack .../2-dbus-bin_1.14.10-6_amd64.deb ... Unpacking dbus-bin (1.14.10-6) ... Selecting previously unselected package dbus-session-bus-common. Preparing to unpack .../3-dbus-session-bus-common_1.14.10-6_all.deb ... Unpacking dbus-session-bus-common (1.14.10-6) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../4-libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package dbus-daemon. Preparing to unpack .../5-dbus-daemon_1.14.10-6_amd64.deb ... Unpacking dbus-daemon (1.14.10-6) ... Selecting previously unselected package adduser. Preparing to unpack .../6-adduser_3.137_all.deb ... Unpacking adduser (3.137) ... Setting up adduser (3.137) ... Selecting previously unselected package dbus-system-bus-common. (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 ... 6252 files and directories currently installed.) Preparing to unpack .../dbus-system-bus-common_1.14.10-6_all.deb ... Unpacking dbus-system-bus-common (1.14.10-6) ... Selecting previously unselected package dbus. Preparing to unpack .../dbus_1.14.10-6_amd64.deb ... Unpacking dbus (1.14.10-6) ... Selecting previously unselected package fonts-lato. Preparing to unpack .../fonts-lato_2.015-1_all.deb ... Unpacking fonts-lato (2.015-1) ... Selecting previously unselected package libpython3.12-minimal:amd64. Preparing to unpack .../libpython3.12-minimal_3.12.7-3_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.7-3) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../python3.12-minimal_3.12.7-3_amd64.deb ... Unpacking python3.12-minimal (3.12.7-3) ... Setting up libpython3.12-minimal:amd64 (3.12.7-3) ... Setting up libexpat1:amd64 (2.6.4-1) ... Setting up python3.12-minimal (3.12.7-3) ... Selecting previously unselected package python3-minimal. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6618 files and directories currently installed.) Preparing to unpack .../00-python3-minimal_3.12.6-1_amd64.deb ... Unpacking python3-minimal (3.12.6-1) ... Selecting previously unselected package media-types. Preparing to unpack .../01-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) ... Selecting previously unselected package netbase. Preparing to unpack .../02-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Selecting previously unselected package libncursesw6:amd64. Preparing to unpack .../03-libncursesw6_6.5-2+b1_amd64.deb ... Unpacking libncursesw6:amd64 (6.5-2+b1) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../04-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../05-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../06-libkeyutils1_1.6.3-4_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-4) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../07-libkrb5-3_1.21.3-3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-3) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../08-libgssapi-krb5-2_1.21.3-3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) ... Selecting previously unselected package libtirpc-common. Preparing to unpack .../09-libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) ... Selecting previously unselected package libtirpc3t64:amd64. Preparing to unpack .../10-libtirpc3t64_1.3.4+ds-1.3+b1_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Selecting previously unselected package libnsl2:amd64. Preparing to unpack .../11-libnsl2_1.3.0-3+b3_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b3) ... Selecting previously unselected package readline-common. Preparing to unpack .../12-readline-common_8.2-5_all.deb ... Unpacking readline-common (8.2-5) ... Selecting previously unselected package libreadline8t64:amd64. Preparing to unpack .../13-libreadline8t64_8.2-5_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-5) ... Selecting previously unselected package libsqlite3-0:amd64. Preparing to unpack .../14-libsqlite3-0_3.46.1-1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.46.1-1) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../15-libpython3.12-stdlib_3.12.7-3_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.7-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../16-python3.12_3.12.7-3_amd64.deb ... Unpacking python3.12 (3.12.7-3) ... Selecting previously unselected package libpython3-stdlib:amd64. Preparing to unpack .../17-libpython3-stdlib_3.12.6-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.6-1) ... Setting up python3-minimal (3.12.6-1) ... Selecting previously unselected package python3. (Reading database ... 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Setting up libboost-python1.83.0 (1.83.0-3.2) ... Setting up liblcms2-2:amd64 (2.16-2) ... Setting up libpixman-1-0:amd64 (0.44.0-3) ... Setting up libsharpyuv0:amd64 (1.4.0-0.1+b1) ... Setting up libwayland-server0:amd64 (1.23.0-1+b1) ... Setting up libpciaccess0:amd64 (0.17-3+b2) ... Setting up systemd-sysv (256.7-3) ... Setting up libxau6:amd64 (1:1.0.11-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3+b2) ... Setting up libdouble-conversion3:amd64 (3.3.0-1+b2) ... Setting up libkeyutils1:amd64 (1.6.3-4) ... Setting up libxcb1:amd64 (1.17.0-2+b1) ... Setting up fonts-lato (2.015-1) ... Setting up libicu72:amd64 (72.1-5+b1) ... Setting up libxcb-xfixes0:amd64 (1.17.0-2+b1) ... Setting up liblerc4:amd64 (4.0.0+ds-5) ... Setting up libantlr3c-3.4-0:amd64 (3.4+dfsg-4+b2) ... Setting up hicolor-icon-theme (0.18-1) ... Setting up libxcb-xinput0:amd64 (1.17.0-2+b1) ... Setting up libdatrie1:amd64 (0.2.13-3+b1) ... Setting up libmmdb2-0:amd64 (2.0.22-1+b2) ... Setting up libboost-timer1.83.0:amd64 (1.83.0-3.2) ... Setting up libxcb-render0:amd64 (1.17.0-2+b1) ... Setting up libglvnd0:amd64 (1.7.0-1+b2) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up fonts-lyx (2.4.2.1-1) ... Setting up libxcb-glx0:amd64 (1.17.0-2+b1) ... Setting up libbrotli1:amd64 (1.1.0-2+b6) ... Setting up libedit2:amd64 (3.1-20240808-1) ... Setting up libsqlite3-0:amd64 (3.46.1-1) ... Setting up libgdk-pixbuf2.0-common (2.42.12+dfsg-1) ... Setting up libxcb-keysyms1:amd64 (0.4.0-1+b3) ... Setting up libxcb-shape0:amd64 (1.17.0-2+b1) ... Setting up x11-common (1:7.7+23.1) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libsensors-config (1:3.6.0-10) ... Setting up libpsl5t64:amd64 (0.21.2-1.1+b1) ... Setting up libnghttp2-14:amd64 (1.64.0-1) ... Setting up libdeflate0:amd64 (1.22-1) ... Setting up linux-libc-dev (6.11.7-1) ... Setting up libboost-thread1.83.0:amd64 (1.83.0-3.2) ... Setting up libqhull-r8.0:amd64 (2020.2-6+b2) ... Setting up libxcb-render-util0:amd64 (0.3.9-1+b2) ... Setting up xkb-data (2.42-1) ... Setting up libxcb-shm0:amd64 (1.17.0-2+b1) ... Setting up libxcb-icccm4:amd64 (0.4.2-1) ... Setting up libccp4-data (8.0.0-4) ... Setting up libgomp1:amd64 (14.2.0-8) ... Setting up libjbig0:amd64 (2.1-6.1+b2) ... Setting up libpcre2-16-0:amd64 (10.42-4+b2) ... Setting up libaec0:amd64 (1.1.3-1+b1) ... Setting up libopengl0:amd64 (1.7.0-1+b2) ... Setting up libelf1t64:amd64 (0.192-4) ... Setting up libxcb-util1:amd64 (0.4.0-1+b2) ... Setting up libxcb-xkb1:amd64 (1.17.0-2+b1) ... Setting up libxcb-image0:amd64 (0.4.0-2+b2) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Setting up libxcb-present0:amd64 (1.17.0-2+b1) ... Setting up unicode-data (15.1.0-1) ... Setting up libboost-numpy1.83.0 (1.83.0-3.2) ... Setting up libz3-4:amd64 (4.13.3-1) ... Setting up libpcre2-32-0:amd64 (10.42-4+b2) ... Setting up libblas3:amd64 (3.12.0-3+b1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libxcb-xinerama0:amd64 (1.17.0-2+b1) ... Setting up rpcsvc-proto (1.4.3-1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Setting up libann-cctbx0 (1.1.2+doc-9+b1) ... Setting up libx11-data (2:1.8.10-2) ... Setting up libepoxy0:amd64 (1.5.10-2) ... Setting up libxcb-sync1:amd64 (1.17.0-2+b1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up libavahi-common-data:amd64 (0.8-13+b3) ... Setting up libdbus-1-3:amd64 (1.14.10-6) ... Setting up liblzf1:amd64 (3.6-4+b2) ... Setting up libfribidi0:amd64 (1.0.15-1) ... Setting up libquadmath0:amd64 (14.2.0-8) ... Setting up libimagequant0:amd64 (2.18.0-1+b2) ... Setting up libproc2-0:amd64 (2:4.0.4-6) ... Setting up pymol-data (3.0.0+dfsg-1) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16t64:amd64 (1.6.44-2) ... Setting up libatomic1:amd64 (14.2.0-8) ... Setting up libtcl8.6:amd64 (8.6.15+dfsg-2) ... Setting up fonts-dejavu-core (2.37-8) ... Setting up libsensors5:amd64 (1:3.6.0-10+b1) ... Setting up libncursesw6:amd64 (6.5-2+b1) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up libglapi-mesa:amd64 (24.2.7-1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Setting up libgfortran5:amd64 (14.2.0-8) ... Setting up libvulkan1:amd64 (1.3.296.0-1) ... Setting up libnghttp3-9:amd64 (1.4.0-1+b1) ... Setting up libwebp7:amd64 (1.4.0-0.1+b1) ... Setting up libubsan1:amd64 (14.2.0-8) ... Setting up libxcb-dri2-0:amd64 (1.17.0-2+b1) ... Setting up libmtdev1t64:amd64 (1.1.6-1.2+b1) ... Setting up libxshmfence1:amd64 (1.3-1+b2) ... Setting up libhwasan0:amd64 (14.2.0-8) ... Setting up at-spi2-common (2.54.0-1) ... Setting up libccp4c0t64:amd64 (8.0.0-4) ... Setting up libcrypt-dev:amd64 (1:4.4.36-5) ... Setting up libtiff6:amd64 (4.5.1+git230720-5) ... Setting up libxcb-randr0:amd64 (1.17.0-2+b1) ... Setting up dbus-session-bus-common (1.14.10-6) ... Setting up libasan8:amd64 (14.2.0-8) ... Setting up procps (2:4.0.4-6) ... Setting up libmd4c0:amd64 (0.5.2-2+b1) ... Setting up libopenjp2-7:amd64 (2.5.0-2+b4) ... Setting up libx11-6:amd64 (2:1.8.10-2) ... Setting up libthai-data (0.1.29-2) ... Setting up netbase (6.4) ... Setting up libngtcp2-16:amd64 (1.6.0-1) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up libglu1-mesa:amd64 (9.0.2-1.1+b2) ... Setting up libwayland-egl1:amd64 (1.23.0-1+b1) ... Setting up libssh2-1t64:amd64 (1.11.1-1) ... Setting up libtsan2:amd64 (14.2.0-8) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up dbus-system-bus-common (1.14.10-6) ... Setting up libc-dev-bin (2.40-3) ... Setting up python-matplotlib-data (3.8.3-3) ... Setting up openssl (3.3.2-2) ... Setting up libwebpmux3:amd64 (1.4.0-0.1+b1) ... Setting up libdrm-common (2.4.123-1) ... Setting up libxcomposite1:amd64 (1:0.4.6-1) ... Setting up libevdev2:amd64 (1.13.3+dfsg-1) ... Setting up readline-common (8.2-5) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Setting up sphinx-rtd-theme-common (3.0.2+dfsg-1) ... Setting up dbus-bin (1.14.10-6) ... Setting up liblsan0:amd64 (14.2.0-8) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.6.0-1) ... Setting up libsz2:amd64 (1.1.3-1+b1) ... Setting up libitm1:amd64 (14.2.0-8) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libann-cctbx-dev (1.1.2+doc-9+b1) ... Setting up libwacom-common (2.13.0-1) ... Setting up libxkbcommon0:amd64 (1.6.0-1+b2) ... Setting up libwayland-client0:amd64 (1.23.0-1+b1) ... Setting up libxcb-dri3-0:amd64 (1.17.0-2+b1) ... Setting up libllvm19:amd64 (1:19.1.3-2) ... Setting up libx11-xcb1:amd64 (2:1.8.10-2) ... Setting up libice6:amd64 (2:1.1.1-1) ... Setting up liblapack3:amd64 (3.12.0-3+b1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxdamage1:amd64 (1:1.1.6-1+b2) ... Setting up libssm2:amd64 (1.4.0-2+b3) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b2) ... Setting up fontconfig-config (2.15.0-1.1+b1) ... Setting up libwebpdemux2:amd64 (1.4.0-0.1+b1) ... Setting up libavahi-common3:amd64 (0.8-13+b3) ... Setting up libxext6:amd64 (2:1.3.4-1+b2) ... Setting up dbus-daemon (1.14.10-6) ... Setting up libccp4f0t64:amd64 (8.0.0-4) ... Setting up libldap-2.5-0:amd64 (2.5.18+dfsg-3+b1) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b3) ... Setting up libthai0:amd64 (0.1.29-2+b1) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libglib2.0-0t64:amd64 (2.82.2-2) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libxfixes3:amd64 (1:6.0.0-2+b2) ... Setting up dbus (1.14.10-6) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up shared-mime-info (2.4-5+b1) ... Setting up libxinerama1:amd64 (2:1.1.4-3+b2) ... Setting up libxkbcommon-x11-0:amd64 (1.6.0-1+b2) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libxrandr2:amd64 (2:1.5.4-1+b1) ... Setting up libjs-sphinxdoc (7.4.7-4) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up libdrm2:amd64 (2.4.123-1) ... Setting up libwayland-cursor0:amd64 (1.23.0-1+b1) ... Setting up libxslt1.1:amd64 (1.1.35-1.1+b1) ... Setting up libpam-systemd:amd64 (256.7-3) ... Setting up libc6-dev:amd64 (2.40-3) ... Setting up libharfbuzz0b:amd64 (10.0.1-1) ... Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-1+b1) ... Setting up libxss1:amd64 (1:1.2.3-1+b2) ... Setting up libfontconfig1:amd64 (2.15.0-1.1+b1) ... Setting up libgcc-14-dev:amd64 (14.2.0-8) ... Setting up libstdc++-14-dev:amd64 (14.2.0-8) ... Setting up libsm6:amd64 (2:1.2.4-1) ... Setting up libavahi-client3:amd64 (0.8-13+b3) ... Setting up libgudev-1.0-0:amd64 (238-5+b1) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1+b2) ... Setting up libdrm-amdgpu1:amd64 (2.4.123-1) ... Setting up gtk-update-icon-cache (4.16.5+ds-2) ... Setting up fontconfig (2.15.0-1.1+b1) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.6-1+b2) ... Setting up libboost1.83-dev:amd64 (1.83.0-3.2) ... Setting up libatk1.0-0t64:amd64 (2.54.0-1) ... Setting up libxi6:amd64 (2:1.8.2-1) ... Setting up libcurl4t64:amd64 (8.11.0-1) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up libccp4-dev:amd64 (8.0.0-4) ... Setting up libwacom9:amd64 (2.13.0-1) ... Setting up libdrm-radeon1:amd64 (2.4.123-1) ... Setting up libxtst6:amd64 (2:1.2.3-1.1+b2) ... Setting up libtk8.6:amd64 (8.6.15-1) ... Setting up libxcursor1:amd64 (1:1.2.2-1+b1) ... Setting up libpango-1.0-0:amd64 (1.54.0+ds-3) ... Setting up libdrm-intel1:amd64 (2.4.123-1) ... Setting up python3.12-tk (3.12.7-3) ... Setting up libcurl3t64-gnutls:amd64 (8.11.0-1) ... Setting up libcloudproviders0:amd64 (0.3.6-1+b1) ... Setting up libcairo2:amd64 (1.18.2-2) ... Setting up python3.13-tk (3.13.0-2) ... Setting up libcolord2:amd64 (1.4.7-1+b2) ... Setting up libinput-bin (1.26.2-1) ... Setting up libdconf1:amd64 (0.40.0-4+b3) ... Setting up dbus-user-session (1.14.10-6) ... Setting up libqt5core5t64:amd64 (5.15.15+dfsg-2) ... Setting up libexpat1-dev:amd64 (2.6.4-1) ... Setting up adwaita-icon-theme (47.0-2) ... update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode Setting up libnotify4:amd64 (0.8.3-1+b2) ... Setting up libatspi2.0-0t64:amd64 (2.54.0-1) ... Setting up libraqm0:amd64 (0.10.1-1+b2) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libnsl2:amd64 (1.3.0-3+b3) ... Setting up libqt5sql5t64:amd64 (5.15.15+dfsg-2) ... Setting up libcairo-gobject2:amd64 (1.18.2-2) ... Setting up libwxbase3.2-1t64:amd64 (3.2.6+dfsg-2) ... Setting up libpangoft2-1.0-0:amd64 (1.54.0+ds-3) ... Setting up libhdf5-103-1t64:amd64 (1.10.10+repack-4) ... Setting up libcups2t64:amd64 (2.4.10-2) ... Setting up libpangocairo-1.0-0:amd64 (1.54.0+ds-3) ... Setting up libatk-bridge2.0-0t64:amd64 (2.54.0-1) ... Setting up libinput10:amd64 (1.26.2-1) ... Setting up libhdf5-hl-100t64:amd64 (1.10.10+repack-4) ... Setting up mesa-libgallium:amd64 (24.2.7-1) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ... Setting up libnetcdf19t64:amd64 (1:4.9.2-7) ... Setting up libqt5dbus5t64:amd64 (5.15.15+dfsg-2) ... Setting up libcbf1t64:amd64 (0.9.7+dfsg1-4+b1) ... Setting up libpython3.12-stdlib:amd64 (3.12.7-3) ... Setting up libgbm1:amd64 (24.2.7-1) ... Setting up blt (2.5.3+dfsg-7) ... Setting up python3.12 (3.12.7-3) ... Setting up libgl1-mesa-dri:amd64 (24.2.7-1) ... Setting up libqt5network5t64:amd64 (5.15.15+dfsg-2) ... Setting up libqt5xml5t64:amd64 (5.15.15+dfsg-2) ... Setting up dconf-service (0.40.0-4+b3) ... Setting up libqt5test5t64:amd64 (5.15.15+dfsg-2) ... Setting up libpython3.12t64:amd64 (3.12.7-3) ... Setting up libegl-mesa0:amd64 (24.2.7-1) ... Setting up libegl1:amd64 (1.7.0-1+b2) ... Setting up libpython3-stdlib:amd64 (3.12.6-1) ... Setting up libcctbx0 (2024.8+ds2+~3.21.1+ds1-3) ... Setting up libglx-mesa0:amd64 (24.2.7-1) ... Setting up libglx0:amd64 (1.7.0-1+b2) ... Setting up dconf-gsettings-backend:amd64 (0.40.0-4+b3) ... Setting up python3 (3.12.6-1) ... Setting up libpython3.12-dev:amd64 (3.12.7-3) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-platformdirs (4.3.6-1) ... Setting up python3-tz (2024.1-2) ... Setting up python3-natsort (8.0.2-2) ... Setting up python3-six (1.16.0-7) ... Setting up python3-pil:amd64 (10.4.0-1+b1) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-packaging (24.1-1) ... Setting up libgl1:amd64 (1.7.0-1+b2) ... Setting up python3-pyparsing (3.1.2-1) ... Setting up python3-certifi (2024.8.30+dfsg-1) ... Setting up python3-brotli (1.1.0-2+b6) ... Setting up python3-cycler (0.12.1-1) ... Setting up python3-pycbf (0.9.7+dfsg1-4+b1) ... Setting up python3-kiwisolver (1.4.7-2+b1) ... Setting up python3-idna (3.8-2) ... Setting up python3.12-dev (3.12.7-3) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up libglew2.2:amd64 (2.2.0-4+b2) ... Setting up python3-urllib3 (2.0.7-2) ... Setting up python3-pyqt5.sip (12.15.0-1+b1) ... Setting up python3-lxml:amd64 (5.3.0-1+b1) ... Setting up python3-dateutil (2.9.0-3) ... Setting up python3-flexcache (0.3-2) ... Setting up python3-mpmath (1.3.0-1) ... Setting up python3-appdirs (1.4.4-4) ... Setting up python3-procrunner (2.3.3-2) ... Setting up libgtk-3-common (3.24.43-4) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up python3-sympy (1.13.3-1) ... Setting up python3-attr (23.2.0-2) ... Setting up libpython3-dev:amd64 (3.12.6-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up python3-lz4 (4.0.2+dfsg-1+b5) ... Setting up python3-charset-normalizer (3.4.0-1+b1) ... Setting up python3-unicodedata2 (15.1.0+ds-1+b3) ... Setting up python3-tqdm (4.67.0-1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up python3-ordered-set (4.1.0-1) ... Setting up python3-tk:amd64 (3.12.7-1) ... Setting up python3-opengl (3.1.7+dfsg-1) ... /usr/lib/python3/dist-packages/OpenGL/GL/AMD/vertex_shader_tessellator.py:1: SyntaxWarning: invalid escape sequence '\ ' '''OpenGL extension AMD.vertex_shader_tessellator Setting up python3-inflect (7.3.1-2) ... Setting up libqt5gui5t64:amd64 (5.15.15+dfsg-2) ... Setting up python3-flexparser (0.4-1) ... Setting up python3-pil.imagetk:amd64 (10.4.0-1+b1) ... Setting up python3-dev (3.12.6-1) ... Setting up libgtk-3-0t64:amd64 (3.24.43-4) ... Setting up libboost-python1.83-dev (1.83.0-3.2) ... Setting up libwxgtk3.2-1t64:amd64 (3.2.6+dfsg-2) ... Setting up python3-pkg-resources (74.1.2-2) ... Setting up libwxgtk-gl3.2-1t64:amd64 (3.2.6+dfsg-2) ... Setting up libqt5widgets5t64:amd64 (5.15.15+dfsg-2) ... Setting up python3-wxgtk4.0 (4.2.2+dfsg-1+b1) ... Setting up libqt5help5:amd64 (5.15.15-2) ... Setting up libboost-python-dev (1.83.0.2+b2) ... Setting up python3-fs (2.4.16-4) ... Setting up python3-pint (0.24.4-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-requests (2.32.3+dfsg-1) ... Setting up python3-numpy (1:1.26.4+ds-12) ... Setting up python3-contourpy (1.3.0-2+b1) ... Setting up libqt5opengl5t64:amd64 (5.15.15+dfsg-2) ... Setting up libcctbx-dev (2024.8+ds2+~3.21.1+ds1-3) ... Setting up libqt5printsupport5t64:amd64 (5.15.15+dfsg-2) ... Setting up python3-mrcfile (1.5.3-3) ... Setting up python3-scipy (1.13.1-6) ... Setting up libqt5designer5:amd64 (5.15.15-2) ... Setting up python3-h5py-serial (3.11.0-5) ... Setting up python3-h5py (3.11.0-5) ... Setting up python3-hdf5plugin (4.0.1-3) ... Setting up python3-nxmx (0.0.3-3) ... Setting up python3-pyqt5 (5.15.11+dfsg-1+b1) ... Setting up python3-pyqt5.qtopengl (5.15.11+dfsg-1+b1) ... Setting up python3-pymol (3.0.0+dfsg-1+b1) ... Setting up python3-fonttools (4.54.1-4+b1) ... Setting up python3-ufolib2 (0.16.1+dfsg1-1) ... Setting up python3-matplotlib (3.8.3-3+b1) ... Setting up python3-cctbx (2024.8+ds2+~3.21.1+ds1-3) ... /usr/lib/python3/dist-packages/iotbx/pdb/utils.py:8: SyntaxWarning: invalid escape sequence '\{' """ Iterator to generate strings of length n_chars, using upper-case, /usr/lib/python3/dist-packages/iotbx/pdb/utils.py:46: SyntaxWarning: invalid escape sequence '\/' special_characters = """[]_,.;:"&<>()\/\{}'`~!@#$%*|+-""" /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:777: SyntaxWarning: invalid escape sequence '\o' width=pairwise_differences_db, label='$\omega_{hkl}$' /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:792: SyntaxWarning: invalid escape sequence '\o' axes[0].set_ylabel('Distribution of $\omega_{hbk}$') /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:793: SyntaxWarning: invalid escape sequence '\o' axes[0].set_xlabel('Normalized PD ($\omega_{hbk}$)') /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:812: SyntaxWarning: invalid escape sequence '\o' axes[1].set_xlabel('Sorted Normalized PD ($\omega_{hbk}$)') /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:831: SyntaxWarning: invalid escape sequence '\s' axes[2].set_ylabel('Standard Deviation of $I_{hbk}/\sigma_{hbk}$') /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:860: SyntaxWarning: invalid escape sequence '\m' axes_sadd.set_ylabel('$s_{\mathrm{fac}}^2 \\times s_{\mathrm{add}}^2$') Processing triggers for libc-bin (2.40-3) ... Processing triggers for systemd (256.7-3) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 1m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'apt-get', '-y', 'install', 'python3-cctbx'] 1m3.0s INFO: Running scripts post_install 1m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/post_install_exceptions'] 1m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/post_install_exceptions'] 1m3.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgxjjief5'] 1m5.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgxjjief5'] 1m5.0s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpgxjjief5 to sid 1m5.0s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 1m5.0s INFO: Running scripts pre_distupgrade 1m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 1m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 1m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_distupgrade_exceptions'] 1m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_distupgrade_exceptions'] 1m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 1m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 1m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_distupgrade_zz_database-server'] 1m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_distupgrade_zz_database-server'] 1m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 1m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 1m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'apt-get', 'update'] 1m7.3s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [202 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [10.0 MB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7335 kB] Fetched 17.6 MB in 2s (9831 kB/s) Reading package lists... 1m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'apt-get', 'update'] 1m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'apt-get', '-yf', 'dist-upgrade'] 1m29.0s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following NEW packages will be installed: python3-legacy-cgi The following packages will be upgraded: apt libapt-pkg6.0t64 libblas3 libboost-numpy1.83.0 libboost-python1.83-dev libboost-python1.83.0 libboost-thread1.83.0 libboost-timer1.83.0 libboost1.83-dev libcctbx-dev libcctbx0 libglib2.0-0t64 liblapack3 libpam-systemd libpcre2-16-0 libpcre2-32-0 libpcre2-8-0 libpython3-dev libpython3-stdlib libsystemd-shared libsystemd0 libudev1 libxdmcp6 libxkbcommon-x11-0 libxkbcommon0 linux-libc-dev login.defs passwd python3 python3-attr python3-cctbx python3-dev python3-fonttools python3-h5py python3-h5py-serial python3-minimal python3-packaging python3-pkg-resources systemd systemd-sysv 40 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. Need to get 84.3 MB of archives. After this operation, 225 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 libpam-systemd amd64 257~rc2-3 [291 kB] Get:2 http://deb.debian.org/debian sid/main amd64 systemd amd64 257~rc2-3 [3603 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libsystemd-shared amd64 257~rc2-3 [2133 kB] Get:4 http://deb.debian.org/debian sid/main amd64 systemd-sysv amd64 257~rc2-3 [59.3 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 257~rc2-3 [447 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 257~rc2-3 [147 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0t64 amd64 2.9.13 [1104 kB] Get:8 http://deb.debian.org/debian sid/main amd64 apt amd64 2.9.13 [1392 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libpython3-dev amd64 3.12.7-1 [9976 B] Get:10 http://deb.debian.org/debian sid/main amd64 python3-dev amd64 3.12.7-1 [26.1 kB] Get:11 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.12.7-1 [26.8 kB] Get:12 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.12.7-1 [27.8 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.12.7-1 [9712 B] Get:14 http://deb.debian.org/debian sid/main amd64 login.defs all 1:4.16.0-5 [185 kB] Get:15 http://deb.debian.org/debian sid/main amd64 passwd amd64 1:4.16.0-5 [1232 kB] Get:16 http://deb.debian.org/debian sid/main amd64 libpcre2-8-0 amd64 10.44-4 [275 kB] Get:17 http://deb.debian.org/debian sid/main amd64 libblas3 amd64 3.12.0-4 [152 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libboost-python1.83-dev amd64 1.83.0-3.2+b1 [328 kB] Get:19 http://deb.debian.org/debian sid/main amd64 libboost1.83-dev amd64 1.83.0-3.2+b1 [10.6 MB] Get:20 http://deb.debian.org/debian sid/main amd64 libboost-python1.83.0 amd64 1.83.0-3.2+b1 [320 kB] Get:21 http://deb.debian.org/debian sid/main amd64 libboost-numpy1.83.0 amd64 1.83.0-3.2+b1 [242 kB] Get:22 http://deb.debian.org/debian sid/main amd64 libboost-thread1.83.0 amd64 1.83.0-3.2+b1 [269 kB] Get:23 http://deb.debian.org/debian sid/main amd64 libboost-timer1.83.0 amd64 1.83.0-3.2+b1 [235 kB] Get:24 http://deb.debian.org/debian sid/main amd64 python3-cctbx amd64 2024.10+ds2+~3.22.1+ds1-4 [47.2 MB] Get:25 http://deb.debian.org/debian sid/main amd64 libcctbx-dev amd64 2024.10+ds2+~3.22.1+ds1-4 [1161 kB] Get:26 http://deb.debian.org/debian sid/main amd64 libcctbx0 amd64 2024.10+ds2+~3.22.1+ds1-4 [2345 kB] Get:27 http://deb.debian.org/debian sid/main amd64 python3-legacy-cgi all 2.6.1-2 [16.1 kB] Get:28 http://deb.debian.org/debian sid/main amd64 python3-h5py all 3.11.0-8 [14.9 kB] Get:29 http://deb.debian.org/debian sid/main amd64 python3-h5py-serial amd64 3.11.0-8+b1 [1460 kB] Get:30 http://deb.debian.org/debian sid/main amd64 libglib2.0-0t64 amd64 2.82.2-3 [1501 kB] Get:31 http://deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.12.0-4 [2450 kB] Get:32 http://deb.debian.org/debian sid/main amd64 libpcre2-16-0 amd64 10.44-4 [261 kB] Get:33 http://deb.debian.org/debian sid/main amd64 libpcre2-32-0 amd64 10.44-4 [248 kB] Get:34 http://deb.debian.org/debian sid/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get:35 http://deb.debian.org/debian sid/main amd64 libxkbcommon-x11-0 amd64 1.7.0-1 [16.1 kB] Get:36 http://deb.debian.org/debian sid/main amd64 libxkbcommon0 amd64 1.7.0-1 [113 kB] Get:37 http://deb.debian.org/debian sid/main amd64 linux-libc-dev all 6.11.9-1 [2459 kB] Get:38 http://deb.debian.org/debian sid/main amd64 python3-attr all 24.2.0-1 [68.4 kB] Get:39 http://deb.debian.org/debian sid/main amd64 python3-pkg-resources all 75.2.0-1 [213 kB] Get:40 http://deb.debian.org/debian sid/main amd64 python3-fonttools amd64 4.55.0-1 [1634 kB] Get:41 http://deb.debian.org/debian sid/main amd64 python3-packaging all 24.2-1 [55.3 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 84.3 MB in 2s (37.6 MB/s) (Reading database ... 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Unpacking libcctbx-dev (2024.10+ds2+~3.22.1+ds1-4) over (2024.8+ds2+~3.21.1+ds1-3) ... Preparing to unpack .../09-libcctbx0_2024.10+ds2+~3.22.1+ds1-4_amd64.deb ... Unpacking libcctbx0 (2024.10+ds2+~3.22.1+ds1-4) over (2024.8+ds2+~3.21.1+ds1-3) ... Selecting previously unselected package python3-legacy-cgi. Preparing to unpack .../10-python3-legacy-cgi_2.6.1-2_all.deb ... Unpacking python3-legacy-cgi (2.6.1-2) ... Preparing to unpack .../11-python3-h5py_3.11.0-8_all.deb ... Unpacking python3-h5py (3.11.0-8) over (3.11.0-5) ... Preparing to unpack .../12-python3-h5py-serial_3.11.0-8+b1_amd64.deb ... Unpacking python3-h5py-serial (3.11.0-8+b1) over (3.11.0-5) ... Preparing to unpack .../13-libglib2.0-0t64_2.82.2-3_amd64.deb ... Unpacking libglib2.0-0t64:amd64 (2.82.2-3) over (2.82.2-2) ... Preparing to unpack .../14-liblapack3_3.12.0-4_amd64.deb ... Unpacking liblapack3:amd64 (3.12.0-4) over (3.12.0-3+b1) ... Preparing to unpack .../15-libpcre2-16-0_10.44-4_amd64.deb ... 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Preparing to unpack .../23-python3-fonttools_4.55.0-1_amd64.deb ... Unpacking python3-fonttools (4.55.0-1) over (4.54.1-4+b1) ... Preparing to unpack .../24-python3-packaging_24.2-1_all.deb ... Unpacking python3-packaging (24.2-1) over (24.1-1) ... Setting up libboost-python1.83.0 (1.83.0-3.2+b1) ... Setting up systemd-sysv (257~rc2-3) ... Setting up libxdmcp6:amd64 (1:1.1.5-1) ... Setting up libboost1.83-dev:amd64 (1.83.0-3.2+b1) ... Setting up libpython3-dev:amd64 (3.12.7-1) ... Setting up libboost-timer1.83.0:amd64 (1.83.0-3.2+b1) ... Setting up linux-libc-dev (6.11.9-1) ... Setting up libboost-thread1.83.0:amd64 (1.83.0-3.2+b1) ... Setting up libpcre2-16-0:amd64 (10.44-4) ... Setting up libboost-numpy1.83.0 (1.83.0-3.2+b1) ... Setting up libpcre2-32-0:amd64 (10.44-4) ... Setting up libglib2.0-0t64:amd64 (2.82.2-3) ... Setting up libblas3:amd64 (3.12.0-4) ... Setting up libpam-systemd:amd64 (257~rc2-3) ... Setting up libpython3-stdlib:amd64 (3.12.7-1) ... Setting up libxkbcommon0:amd64 (1.7.0-1) ... Setting up libcctbx0 (2024.10+ds2+~3.22.1+ds1-4) ... Setting up liblapack3:amd64 (3.12.0-4) ... Setting up python3 (3.12.7-1) ... Setting up python3-packaging (24.2-1) ... Setting up python3-dev (3.12.7-1) ... Setting up libboost-python1.83-dev (1.83.0-3.2+b1) ... Setting up libxkbcommon-x11-0:amd64 (1.7.0-1) ... Setting up python3-legacy-cgi (2.6.1-2) ... Setting up libcctbx-dev (2024.10+ds2+~3.22.1+ds1-4) ... Setting up python3-pkg-resources (75.2.0-1) ... Setting up python3-attr (24.2.0-1) ... Setting up python3-h5py-serial (3.11.0-8+b1) ... Setting up python3-fonttools (4.55.0-1) ... Setting up python3-h5py (3.11.0-8) ... Setting up python3-cctbx (2024.10+ds2+~3.22.1+ds1-4) ... /usr/lib/python3/dist-packages/iotbx/pdb/utils.py:8: SyntaxWarning: invalid escape sequence '\{' """ Iterator to generate strings of length n_chars, using upper-case, /usr/lib/python3/dist-packages/iotbx/pdb/utils.py:46: SyntaxWarning: invalid escape sequence '\/' special_characters = """[]_,.;:"&<>()\/\{}'`~!@#$%*|+-""" /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:724: SyntaxWarning: invalid escape sequence '\o' width=pairwise_differences_db, label='$\omega_{hkl}$' /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:739: SyntaxWarning: invalid escape sequence '\o' axes[0].set_ylabel('Distribution of $\omega_{hbk}$') /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:740: SyntaxWarning: invalid escape sequence '\o' axes[0].set_xlabel('Normalized PD ($\omega_{hbk}$)') /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:759: SyntaxWarning: invalid escape sequence '\o' axes[1].set_xlabel('Sorted Normalized PD ($\omega_{hbk}$)') /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:778: SyntaxWarning: invalid escape sequence '\s' axes[2].set_ylabel('Standard Deviation of $I_{hbk}/\sigma_{hbk}$') /usr/lib/python3/dist-packages/xfel/merging/application/errors/error_modifier_mm24.py:807: SyntaxWarning: invalid escape sequence '\m' axes_sadd.set_ylabel('$s_{\mathrm{fac}}^2 \\times s_{\mathrm{add}}^2$') Processing triggers for dbus (1.14.10-6) ... Processing triggers for shared-mime-info (2.4-5+b1) ... Processing triggers for libc-bin (2.40-3) ... 1m29.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'apt-get', '-yf', 'dist-upgrade'] 1m29.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m29.6s DUMP: a6bb0ab3d08215369a0c45aae52cccdf - 1m29.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m29.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'apt-cache', 'show', '--no-all-versions', 'python3-cctbx'] 1m29.7s DUMP: Package: python3-cctbx Source: cctbx Version: 2024.10+ds2+~3.22.1+ds1-4 Installed-Size: 498120 Maintainer: Debian Science Maintainers Architecture: amd64 Depends: ca-certificates, libcctbx-dev (= 2024.10+ds2+~3.22.1+ds1-4), libcctbx0 (= 2024.10+ds2+~3.22.1+ds1-4), python3-legacy-cgi, python3-pycbf (>= 0.9.7+dfsg1-2~), python3 (<< 3.14), python3 (>= 3.12~), python3-h5py (>= 3), python3-hdf5plugin, python3-matplotlib, python3-mrcfile, python3-natsort, python3-numpy (>= 1:1.25.0), python3-numpy-abi9, python3-nxmx, python3-ordered-set, python3-pil, python3-pint, python3-procrunner, python3-pymol, python3-requests, python3-scipy, python3-six, python3-tqdm, python3-wxgtk4.0, python3:any, libantlr3c-3.4-0 | libantlr3c-antlrdbg-3.4-0, libboost-numpy1.83.0 (>= 1.83.0), libboost-numpy1.83.0-py312, libboost-numpy1.83.0-py313, libboost-python1.83.0 (>= 1.83.0), libboost-python1.83.0-py312, libboost-python1.83.0-py313, libboost-thread1.83.0 (>= 1.83.0), libboost-timer1.83.0 (>= 1.83.0), libc6 (>= 2.38), libcbf1t64 (>= 0.9.7+dfsg1-2~), libccp4c0t64 (>= 8.0.0), libgcc-s1 (>= 4.0), libgl1, libglu1-mesa | libglu1, libhdf5-103-1t64, libmmdb2-0 (>= 2.0.22), libssm2 (>= 1.4.0), libstdc++6 (>= 14) Description-en: Python Toolbox for crystallography Computational Crystallography Toolbox contains following modules: - annlib_adaptbx: - boost_adaptbx: wrappers for Boost functionality in CCTBX - cbflib_adaptbx: - ccp4io_adaptbx: - cctbx: Libraries for general crystallographic applications, useful for both small-molecule and macro-molecular crystallography. - cma_es: - crys3d: Modules for the display of molecules, electron density, and reciprocal space data. - dxtbx: The Diffraction Image Toolbox, a library for handling X-ray detector data of arbitrary complexity from a variety of standard formats. - fable: Fortran EMulation library for porting Fortran77 to C++. - gltbx: Python bindings for OpenGL - iotbx: Working with common crystallographic file formats. - libtbx: The build system common to all other modules. This includes a very thin wrapper around the SCons software construction tool. It also contains many useful frameworks and utilities to simplify application development, including tools for regression testing, parallelization across multiprocessor systems and managed clusters, and a flexible, modular configuration syntax called PHIL (Python Hierarchial Interface Language) used throughout the CCTBX. - mmtbx: Functionality specific to macromolecular crystallography. This includes all of the machinery required for setup of geometry restraints, bulk solvent correction and scaling, analysis of macromolecular diffraction data, calculation of weighted map coefficients, and most of the methods implemented in phenix.refine. The majority of infrastructure for the MolProbity validation server (and Phenix equivalent) is also located here. - omptbx: OpenMP interface. - rstbx: A reciprocal space toolbox to autoindex small molecule Bragg diffraction, given the reciprocal space vectors. - scitbx: General scientific calculations. his includes a family of high-level C++ array types, a fast Fourier transform library, and a C++ port of the popular L-BFGS quasi-Newton minimizer. - smtbx: Small-Molecule crystallography. - spotfinder: - tbxx: - wxtbx: wxPython controls used in the Phenix GUI and various utilities . This package provide a selected collection of python modules from the cctbx project. Description-md5: 82495d7385342d38e22c572566893a2d Homepage: https://github.com/cctbx/cctbx_project Tag: field::physics, implemented-in::python, role::program, science::calculation, science::plotting, science::visualisation, use::analysing, use::calculating, use::viewing Section: python Priority: optional Filename: pool/main/c/cctbx/python3-cctbx_2024.10+ds2+~3.22.1+ds1-4_amd64.deb Size: 47162584 MD5sum: cb06a064ac73f9dec0f35000b1257001 SHA256: 21d86719291cb74ef4ca4cd3707e28127ae1cc1a8b2236287b95b090f2ea53a4 1m29.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'apt-cache', 'show', '--no-all-versions', 'python3-cctbx'] 1m29.7s INFO: apt-cache knows about the following packages: python3-cctbx 1m29.7s INFO: Running scripts pre_install 1m29.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_install_database-server'] 1m29.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_install_database-server'] 1m29.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_install_exceptions'] 1m29.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_install_exceptions'] 1m29.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_install_extras'] 1m29.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_install_extras'] 1m29.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_install_foreign_architecture'] 1m29.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_install_foreign_architecture'] 1m29.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m29.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m29.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'apt-cache', 'policy'] 1m29.8s 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: 1m29.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'apt-cache', 'policy'] 1m29.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'apt-cache', 'policy', 'python3-cctbx'] 1m29.8s DUMP: python3-cctbx: Installed: 2024.10+ds2+~3.22.1+ds1-4 Candidate: 2024.10+ds2+~3.22.1+ds1-4 Version table: *** 2024.10+ds2+~3.22.1+ds1-4 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 1m29.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'apt-cache', 'policy', 'python3-cctbx'] 1m29.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'apt-get', '-y', 'install', 'python3-cctbx'] 1m30.1s DUMP: Reading package lists... Building dependency tree... Reading state information... python3-cctbx is already the newest version (2024.10+ds2+~3.22.1+ds1-4). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m30.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'apt-get', '-y', 'install', 'python3-cctbx'] 1m30.1s INFO: Running scripts post_install 1m30.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/post_install_exceptions'] 1m30.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/post_install_exceptions'] 1m30.1s INFO: Running scripts post_distupgrade 1m30.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m30.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m30.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/post_distupgrade_exceptions'] 1m30.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/post_distupgrade_exceptions'] 1m30.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m30.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m30.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m30.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m30.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/post_distupgrade_zz_backports'] 1m30.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/post_distupgrade_zz_backports'] 1m30.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgxjjief5'] 1m32.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgxjjief5'] 1m32.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgxjjief5'] 1m33.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgxjjief5'] 1m33.9s INFO: Running scripts pre_install 1m33.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_install_database-server'] 1m33.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_install_database-server'] 1m33.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_install_exceptions'] 1m33.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_install_exceptions'] 1m33.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_install_extras'] 1m33.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_install_extras'] 1m33.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_install_foreign_architecture'] 1m33.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_install_foreign_architecture'] 1m33.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m33.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m33.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'apt-cache', 'policy'] 1m33.9s 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: 1m33.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'apt-cache', 'policy'] 1m33.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'apt-cache', 'policy', 'python3-cctbx'] 1m34.0s DUMP: python3-cctbx: Installed: 2024.10+ds2+~3.22.1+ds1-4 Candidate: 2024.10+ds2+~3.22.1+ds1-4 Version table: *** 2024.10+ds2+~3.22.1+ds1-4 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 1m34.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'apt-cache', 'policy', 'python3-cctbx'] 1m34.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'apt-get', '-y', 'install', 'python3-cctbx=2024.10+ds2+~3.22.1+ds1-4'] 1m34.2s DUMP: Reading package lists... Building dependency tree... Reading state information... python3-cctbx is already the newest version (2024.10+ds2+~3.22.1+ds1-4). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m34.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'apt-get', '-y', 'install', 'python3-cctbx=2024.10+ds2+~3.22.1+ds1-4'] 1m34.2s INFO: Running scripts post_install 1m34.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/post_install_exceptions'] 1m34.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/post_install_exceptions'] 1m34.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgxjjief5'] 1m36.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgxjjief5'] 1m38.0s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', '-ac', '--ignore-obsolete'] 1m42.2s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', '-ac', '--ignore-obsolete'] 1m42.2s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m42.2s DUMP: 0.15.6 1m42.2s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m42.2s INFO: Running adequate version 0.15.6 now. 1m42.2s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'python3-cctbx'] 1m44.8s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'python3-cctbx'] 1m44.8s INFO: Running scripts pre_remove 1m44.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m45.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m45.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m45.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m45.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m58.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m58.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m58.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m58.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m58.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m58.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_remove_exceptions'] 1m58.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/pre_remove_exceptions'] 1m58.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m58.7s DUMP: install ok installed adduser adduser 3.137 install ok installed adwaita-icon-theme adwaita-icon-theme 47.0-2 install ok installed apt apt 2.9.13 install ok installed at-spi2-common at-spi2-common 2.54.0-1 install ok installed base-files base-files 13.5 install ok installed base-passwd base-passwd 3.6.5 install ok installed bash bash 5.2.32-1+b2 install ok installed blt blt 2.5.3+dfsg-7 install ok installed bsdutils bsdutils 1:2.40.2-11 install ok installed ca-certificates ca-certificates 20240203 install ok installed coreutils coreutils 9.5-1+b1 install ok installed dash dash 0.5.12-9 install ok installed dbus dbus 1.14.10-6 install ok installed dbus-bin dbus-bin 1.14.10-6 install ok installed dbus-daemon dbus-daemon 1.14.10-6 install ok installed dbus-session-bus-common dbus-session-bus-common 1.14.10-6 install ok installed dbus-system-bus-common dbus-system-bus-common 1.14.10-6 install ok installed dbus-user-session dbus-user-session 1.14.10-6 install ok installed dconf-gsettings-backend:amd64 dconf-gsettings-backend 0.40.0-4+b3 install ok installed dconf-service dconf-service 0.40.0-4+b3 install ok installed debconf debconf 1.5.87 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.21 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.1-1+b1 install ok installed findutils findutils 4.10.0-3 install ok installed fontconfig fontconfig 2.15.0-1.1+b1 install ok installed fontconfig-config fontconfig-config 2.15.0-1.1+b1 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-8 install ok installed fonts-dejavu-mono fonts-dejavu-mono 2.37-8 install ok installed fonts-font-awesome fonts-font-awesome 5.0.10+really4.7.0~dfsg-4.1 install ok installed fonts-lato fonts-lato 2.015-1 install ok installed fonts-lyx fonts-lyx 2.4.2.1-1 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-8 install ok installed gpgv gpgv 2.2.45-2 install ok installed grep grep 3.11-4 install ok installed gtk-update-icon-cache gtk-update-icon-cache 4.16.5+ds-2 install ok installed gzip gzip 1.12-1.1 install ok installed hicolor-icon-theme hicolor-icon-theme 0.18-1 install ok installed hostname hostname 3.25 install ok installed init-system-helpers init-system-helpers 1.67 install ok installed libacl1:amd64 libacl1 2.3.2-2+b1 install ok installed libaec0:amd64 libaec0 1.1.3-1+b1 install ok installed libann-cctbx-dev libann-cctbx-dev 1.1.2+doc-9+b1 install ok installed libann-cctbx0 libann-cctbx0 1.1.2+doc-9+b1 install ok installed libantlr3c-3.4-0:amd64 libantlr3c-3.4-0 3.4+dfsg-4+b2 install ok installed libapparmor1:amd64 libapparmor1 3.1.7-1+b3 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.13 install ok installed libasan8:amd64 libasan8 14.2.0-8 install ok installed libatk-bridge2.0-0t64:amd64 libatk-bridge2.0-0t64 2.54.0-1 install ok installed libatk1.0-0t64:amd64 libatk1.0-0t64 2.54.0-1 install ok installed libatomic1:amd64 libatomic1 14.2.0-8 install ok installed libatspi2.0-0t64:amd64 libatspi2.0-0t64 2.54.0-1 install ok installed libattr1:amd64 libattr1 1:2.5.2-2 install ok installed libaudit-common libaudit-common 1:4.0.2-2 install ok installed libaudit1:amd64 libaudit1 1:4.0.2-2 install ok installed libavahi-client3:amd64 libavahi-client3 0.8-13+b3 install ok installed libavahi-common-data:amd64 libavahi-common-data 0.8-13+b3 install ok installed libavahi-common3:amd64 libavahi-common3 0.8-13+b3 install ok installed libblas3:amd64 libblas3 3.12.0-4 install ok installed libblkid1:amd64 libblkid1 2.40.2-11 install ok installed libboost-numpy1.83.0 libboost-numpy1.83.0 1.83.0-3.2+b1 install ok installed libboost-python-dev libboost-python-dev 1.83.0.2+b2 install ok installed libboost-python1.83-dev libboost-python1.83-dev 1.83.0-3.2+b1 install ok installed libboost-python1.83.0 libboost-python1.83.0 1.83.0-3.2+b1 install ok installed libboost-thread1.83.0:amd64 libboost-thread1.83.0 1.83.0-3.2+b1 install ok installed libboost-timer1.83.0:amd64 libboost-timer1.83.0 1.83.0-3.2+b1 install ok installed libboost1.83-dev:amd64 libboost1.83-dev 1.83.0-3.2+b1 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b6 install ok installed libbsd0:amd64 libbsd0 0.12.2-2 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.40-3 install ok installed libc-dev-bin libc-dev-bin 2.40-3 install ok installed libc6:amd64 libc6 2.40-3 install ok installed libc6-dev:amd64 libc6-dev 2.40-3 install ok installed libcairo-gobject2:amd64 libcairo-gobject2 1.18.2-2 install ok installed libcairo2:amd64 libcairo2 1.18.2-2 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-3+b1 install ok installed libcap2:amd64 libcap2 1:2.66-5+b1 install ok installed libcbf1t64:amd64 libcbf1t64 0.9.7+dfsg1-4+b1 install ok installed libccp4-data libccp4-data 8.0.0-4 install ok installed libccp4-dev:amd64 libccp4-dev 8.0.0-4 install ok installed libccp4c0t64:amd64 libccp4c0t64 8.0.0-4 install ok installed libccp4f0t64:amd64 libccp4f0t64 8.0.0-4 install ok installed libcctbx-dev libcctbx-dev 2024.10+ds2+~3.22.1+ds1-4 install ok installed libcctbx0 libcctbx0 2024.10+ds2+~3.22.1+ds1-4 install ok installed libcloudproviders0:amd64 libcloudproviders0 0.3.6-1+b1 install ok installed libcolord2:amd64 libcolord2 1.4.7-1+b2 install ok installed libcom-err2:amd64 libcom-err2 1.47.1-1+b1 install ok installed libcrypt-dev:amd64 libcrypt-dev 1:4.4.36-5 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libcups2t64:amd64 libcups2t64 2.4.10-2 install ok installed libcurl3t64-gnutls:amd64 libcurl3t64-gnutls 8.11.0-1 install ok installed libcurl4t64:amd64 libcurl4t64 8.11.0-1 install ok installed libdatrie1:amd64 libdatrie1 0.2.13-3+b1 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-9 install ok installed libdbus-1-3:amd64 libdbus-1-3 1.14.10-6 install ok installed libdconf1:amd64 libdconf1 0.40.0-4+b3 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.273 install ok installed libdeflate0:amd64 libdeflate0 1.22-1 install ok installed libdouble-conversion3:amd64 libdouble-conversion3 3.3.0-1+b2 install ok installed libdrm-amdgpu1:amd64 libdrm-amdgpu1 2.4.123-1 install ok installed libdrm-common libdrm-common 2.4.123-1 install ok installed libdrm-intel1:amd64 libdrm-intel1 2.4.123-1 install ok installed libdrm-radeon1:amd64 libdrm-radeon1 2.4.123-1 install ok installed libdrm2:amd64 libdrm2 2.4.123-1 install ok installed libedit2:amd64 libedit2 3.1-20240808-1 install ok installed libegl-mesa0:amd64 libegl-mesa0 24.2.7-1 install ok installed libegl1:amd64 libegl1 1.7.0-1+b2 install ok installed libelf1t64:amd64 libelf1t64 0.192-4 install ok installed libepoxy0:amd64 libepoxy0 1.5.10-2 install ok installed libevdev2:amd64 libevdev2 1.13.3+dfsg-1 install ok installed libexpat1:amd64 libexpat1 2.6.4-1 install ok installed libexpat1-dev:amd64 libexpat1-dev 2.6.4-1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.1-1+b1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libfontconfig1:amd64 libfontconfig1 2.15.0-1.1+b1 install ok installed libfreetype6:amd64 libfreetype6 2.13.3+dfsg-1 install ok installed libfribidi0:amd64 libfribidi0 1.0.15-1 install ok installed libgbm1:amd64 libgbm1 24.2.7-1 install ok installed libgcc-14-dev:amd64 libgcc-14-dev 14.2.0-8 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-8 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-6 install ok installed libgdk-pixbuf-2.0-0:amd64 libgdk-pixbuf-2.0-0 2.42.12+dfsg-1+b1 install ok installed libgdk-pixbuf2.0-common libgdk-pixbuf2.0-common 2.42.12+dfsg-1 install ok installed libgfortran5:amd64 libgfortran5 14.2.0-8 install ok installed libgl1:amd64 libgl1 1.7.0-1+b2 install ok installed libgl1-mesa-dri:amd64 libgl1-mesa-dri 24.2.7-1 install ok installed libglapi-mesa:amd64 libglapi-mesa 24.2.7-1 install ok installed libglew2.2:amd64 libglew2.2 2.2.0-4+b2 install ok installed libglib2.0-0t64:amd64 libglib2.0-0t64 2.82.2-3 install ok installed libglu1-mesa:amd64 libglu1-mesa 9.0.2-1.1+b2 install ok installed libglvnd0:amd64 libglvnd0 1.7.0-1+b2 install ok installed libglx-mesa0:amd64 libglx-mesa0 24.2.7-1 install ok installed libglx0:amd64 libglx0 1.7.0-1+b2 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b2 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.8-2 install ok installed libgomp1:amd64 libgomp1 14.2.0-8 install ok installed libgpg-error0:amd64 libgpg-error0 1.50-4 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-2+b1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.21.3-3 install ok installed libgtk-3-0t64:amd64 libgtk-3-0t64 3.24.43-4 install ok installed libgtk-3-common libgtk-3-common 3.24.43-4 install ok installed libgudev-1.0-0:amd64 libgudev-1.0-0 238-5+b1 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 10.0.1-1 install ok installed libhdf5-103-1t64:amd64 libhdf5-103-1t64 1.10.10+repack-4 install ok installed libhdf5-hl-100t64:amd64 libhdf5-hl-100t64 1.10.10+repack-4 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1+b1 install ok installed libhwasan0:amd64 libhwasan0 14.2.0-8 install ok installed libice6:amd64 libice6 2:1.1.1-1 install ok installed libicu72:amd64 libicu72 72.1-5+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2+b1 install ok installed libimagequant0:amd64 libimagequant0 2.18.0-1+b2 install ok installed libinput-bin libinput-bin 1.26.2-1 install ok installed libinput10:amd64 libinput10 1.26.2-1 install ok installed libitm1:amd64 libitm1 14.2.0-8 install ok installed libjbig0:amd64 libjbig0 2.1-6.1+b2 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-3+b1 install ok installed libjs-jquery libjs-jquery 3.6.1+dfsg+~3.5.14-1 install ok installed libjs-jquery-ui libjs-jquery-ui 1.13.2+dfsg-1 install ok installed libjs-sphinxdoc libjs-sphinxdoc 7.4.7-4 install ok installed libjs-underscore libjs-underscore 1.13.4~dfsg+~1.11.4-3 install ok installed libk5crypto3:amd64 libk5crypto3 1.21.3-3 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-4 install ok installed libkrb5-3:amd64 libkrb5-3 1.21.3-3 install ok installed libkrb5support0:amd64 libkrb5support0 1.21.3-3 install ok installed liblapack3:amd64 liblapack3 3.12.0-4 install ok installed liblbfgsb0:amd64 liblbfgsb0 3.0+dfsg.4-1+b2 install ok installed liblcms2-2:amd64 liblcms2-2 2.16-2 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.18+dfsg-3+b1 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-5 install ok installed libllvm19:amd64 libllvm19 1:19.1.3-2 install ok installed liblsan0:amd64 liblsan0 14.2.0-8 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3+b1 install ok installed liblzf1:amd64 liblzf1 3.6-4+b2 install ok installed liblzma5:amd64 liblzma5 5.6.3-1+b1 install ok installed libmd0:amd64 libmd0 1.1.0-2+b1 install ok installed libmd4c0:amd64 libmd4c0 0.5.2-2+b1 install ok installed libmmdb2-0:amd64 libmmdb2-0 2.0.22-1+b2 install ok installed libmount1:amd64 libmount1 2.40.2-11 install ok installed libmtdev1t64:amd64 libmtdev1t64 1.1.6-1.2+b1 install ok installed libncursesw6:amd64 libncursesw6 6.5-2+b1 install ok installed libnetcdf19t64:amd64 libnetcdf19t64 1:4.9.2-7 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1+b1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.64.0-1 install ok installed libnghttp3-9:amd64 libnghttp3-9 1.4.0-1+b1 install ok installed libngtcp2-16:amd64 libngtcp2-16 1.6.0-1 install ok installed libngtcp2-crypto-gnutls8:amd64 libngtcp2-crypto-gnutls8 1.6.0-1 install ok installed libnotify4:amd64 libnotify4 0.8.3-1+b2 install ok installed libnsl2:amd64 libnsl2 1.3.0-3+b3 install ok installed libopengl0:amd64 libopengl0 1.7.0-1+b2 install ok installed libopenjp2-7:amd64 libopenjp2-7 2.5.0-2+b4 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2+b1 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7+b1 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam-systemd:amd64 libpam-systemd 257~rc2-3 install ok installed libpam0g:amd64 libpam0g 1.5.3-7+b1 install ok installed libpango-1.0-0:amd64 libpango-1.0-0 1.54.0+ds-3 install ok installed libpangocairo-1.0-0:amd64 libpangocairo-1.0-0 1.54.0+ds-3 install ok installed libpangoft2-1.0-0:amd64 libpangoft2-1.0-0 1.54.0+ds-3 install ok installed libpciaccess0:amd64 libpciaccess0 0.17-3+b2 install ok installed libpcre2-16-0:amd64 libpcre2-16-0 10.44-4 install ok installed libpcre2-32-0:amd64 libpcre2-32-0 10.44-4 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.44-4 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.44.0-3 install ok installed libpng16-16t64:amd64 libpng16-16t64 1.6.44-2 install ok installed libproc2-0:amd64 libproc2-0 2:4.0.4-6 install ok installed libpsl5t64:amd64 libpsl5t64 0.21.2-1.1+b1 install ok installed libpython3-dev:amd64 libpython3-dev 3.12.7-1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.12.7-1 install ok installed libpython3.12-dev:amd64 libpython3.12-dev 3.12.7-3 install ok installed libpython3.12-minimal:amd64 libpython3.12-minimal 3.12.7-3 install ok installed libpython3.12-stdlib:amd64 libpython3.12-stdlib 3.12.7-3 install ok installed libpython3.12t64:amd64 libpython3.12t64 3.12.7-3 install ok installed libqhull-r8.0:amd64 libqhull-r8.0 2020.2-6+b2 install ok installed libqt5core5t64:amd64 libqt5core5t64 5.15.15+dfsg-2 install ok installed libqt5dbus5t64:amd64 libqt5dbus5t64 5.15.15+dfsg-2 install ok installed libqt5designer5:amd64 libqt5designer5 5.15.15-2 install ok installed libqt5gui5t64:amd64 libqt5gui5t64 5.15.15+dfsg-2 install ok installed libqt5help5:amd64 libqt5help5 5.15.15-2 install ok installed libqt5network5t64:amd64 libqt5network5t64 5.15.15+dfsg-2 install ok installed libqt5opengl5t64:amd64 libqt5opengl5t64 5.15.15+dfsg-2 install ok installed libqt5printsupport5t64:amd64 libqt5printsupport5t64 5.15.15+dfsg-2 install ok installed libqt5sql5t64:amd64 libqt5sql5t64 5.15.15+dfsg-2 install ok installed libqt5test5t64:amd64 libqt5test5t64 5.15.15+dfsg-2 install ok installed libqt5widgets5t64:amd64 libqt5widgets5t64 5.15.15+dfsg-2 install ok installed libqt5xml5t64:amd64 libqt5xml5t64 5.15.15+dfsg-2 install ok installed libquadmath0:amd64 libquadmath0 14.2.0-8 install ok installed libraqm0:amd64 libraqm0 0.10.1-1+b2 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-5 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b5 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-8 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-8 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1+b3 install ok installed libselinux1:amd64 libselinux1 3.7-3+b1 install ok installed libsemanage-common libsemanage-common 3.7-2 install ok installed libsemanage2:amd64 libsemanage2 3.7-2+b1 install ok installed libsensors-config libsensors-config 1:3.6.0-10 install ok installed libsensors5:amd64 libsensors5 1:3.6.0-10+b1 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsharpyuv0:amd64 libsharpyuv0 1.4.0-0.1+b1 install ok installed libsm6:amd64 libsm6 2:1.2.4-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-11 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-1 install ok installed libss2:amd64 libss2 1.47.1-1+b1 install ok installed libssh2-1t64:amd64 libssh2-1t64 1.11.1-1 install ok installed libssl3t64:amd64 libssl3t64 3.3.2-2 install ok installed libssm2:amd64 libssm2 1.4.0-2+b3 install ok installed libstdc++-14-dev:amd64 libstdc++-14-dev 14.2.0-8 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-8 install ok installed libsystemd-shared:amd64 libsystemd-shared 257~rc2-3 install ok installed libsystemd0:amd64 libsystemd0 257~rc2-3 install ok installed libsz2:amd64 libsz2 1.1.3-1+b1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b3 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.15+dfsg-2 install ok installed libthai-data libthai-data 0.1.29-2 install ok installed libthai0:amd64 libthai0 0.1.29-2+b1 install ok installed libtiff6:amd64 libtiff6 4.5.1+git230720-5 install ok installed libtinfo6:amd64 libtinfo6 6.5-2+b1 install ok installed libtirpc-common libtirpc-common 1.3.4+ds-1.3 install ok installed libtirpc3t64:amd64 libtirpc3t64 1.3.4+ds-1.3+b1 install ok installed libtk8.6:amd64 libtk8.6 8.6.15-1 install ok installed libtsan2:amd64 libtsan2 14.2.0-8 install ok installed libubsan1:amd64 libubsan1 14.2.0-8 install ok installed libudev1:amd64 libudev1 257~rc2-3 install ok installed libunistring5:amd64 libunistring5 1.2-1+b1 install ok installed libuuid1:amd64 libuuid1 2.40.2-11 install ok installed libvulkan1:amd64 libvulkan1 1.3.296.0-1 install ok installed libwacom-common libwacom-common 2.13.0-1 install ok installed libwacom9:amd64 libwacom9 2.13.0-1 install ok installed libwayland-client0:amd64 libwayland-client0 1.23.0-1+b1 install ok installed libwayland-cursor0:amd64 libwayland-cursor0 1.23.0-1+b1 install ok installed libwayland-egl1:amd64 libwayland-egl1 1.23.0-1+b1 install ok installed libwayland-server0:amd64 libwayland-server0 1.23.0-1+b1 install ok installed libwebp7:amd64 libwebp7 1.4.0-0.1+b1 install ok installed libwebpdemux2:amd64 libwebpdemux2 1.4.0-0.1+b1 install ok installed libwebpmux3:amd64 libwebpmux3 1.4.0-0.1+b1 install ok installed libwxbase3.2-1t64:amd64 libwxbase3.2-1t64 3.2.6+dfsg-2 install ok installed libwxgtk-gl3.2-1t64:amd64 libwxgtk-gl3.2-1t64 3.2.6+dfsg-2 install ok installed libwxgtk3.2-1t64:amd64 libwxgtk3.2-1t64 3.2.6+dfsg-2 install ok installed libx11-6:amd64 libx11-6 2:1.8.10-2 install ok installed libx11-data libx11-data 2:1.8.10-2 install ok installed libx11-xcb1:amd64 libx11-xcb1 2:1.8.10-2 install ok installed libxau6:amd64 libxau6 1:1.0.11-1 install ok installed libxcb-dri2-0:amd64 libxcb-dri2-0 1.17.0-2+b1 install ok installed libxcb-dri3-0:amd64 libxcb-dri3-0 1.17.0-2+b1 install ok installed libxcb-glx0:amd64 libxcb-glx0 1.17.0-2+b1 install ok installed libxcb-icccm4:amd64 libxcb-icccm4 0.4.2-1 install ok installed libxcb-image0:amd64 libxcb-image0 0.4.0-2+b2 install ok installed libxcb-keysyms1:amd64 libxcb-keysyms1 0.4.0-1+b3 install ok installed libxcb-present0:amd64 libxcb-present0 1.17.0-2+b1 install ok installed libxcb-randr0:amd64 libxcb-randr0 1.17.0-2+b1 install ok installed libxcb-render-util0:amd64 libxcb-render-util0 0.3.9-1+b2 install ok installed libxcb-render0:amd64 libxcb-render0 1.17.0-2+b1 install ok installed libxcb-shape0:amd64 libxcb-shape0 1.17.0-2+b1 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.17.0-2+b1 install ok installed libxcb-sync1:amd64 libxcb-sync1 1.17.0-2+b1 install ok installed libxcb-util1:amd64 libxcb-util1 0.4.0-1+b2 install ok installed libxcb-xfixes0:amd64 libxcb-xfixes0 1.17.0-2+b1 install ok installed libxcb-xinerama0:amd64 libxcb-xinerama0 1.17.0-2+b1 install ok installed libxcb-xinput0:amd64 libxcb-xinput0 1.17.0-2+b1 install ok installed libxcb-xkb1:amd64 libxcb-xkb1 1.17.0-2+b1 install ok installed libxcb1:amd64 libxcb1 1.17.0-2+b1 install ok installed libxcomposite1:amd64 libxcomposite1 1:0.4.6-1 install ok installed libxcursor1:amd64 libxcursor1 1:1.2.2-1+b1 install ok installed libxdamage1:amd64 libxdamage1 1:1.1.6-1+b2 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.5-1 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b2 install ok installed libxfixes3:amd64 libxfixes3 1:6.0.0-2+b2 install ok installed libxft2:amd64 libxft2 2.3.6-1+b2 install ok installed libxi6:amd64 libxi6 2:1.8.2-1 install ok installed libxinerama1:amd64 libxinerama1 2:1.1.4-3+b2 install ok installed libxkbcommon-x11-0:amd64 libxkbcommon-x11-0 1.7.0-1 install ok installed libxkbcommon0:amd64 libxkbcommon0 1.7.0-1 install ok installed libxml2:amd64 libxml2 2.12.7+dfsg+really2.9.14-0.2+b1 install ok installed libxrandr2:amd64 libxrandr2 2:1.5.4-1+b1 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1.1+b2 install ok installed libxshmfence1:amd64 libxshmfence1 1.3-1+b2 install ok installed libxslt1.1:amd64 libxslt1.1 1.1.35-1.1+b1 install ok installed libxss1:amd64 libxss1 1:1.2.3-1+b2 install ok installed libxtst6:amd64 libxtst6 2:1.2.3-1.1+b2 install ok installed libxxf86vm1:amd64 libxxf86vm1 1:1.1.4-1+b3 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b2 install ok installed libz3-4:amd64 libz3-4 4.13.3-1 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1+b1 install ok installed linux-libc-dev linux-libc-dev 6.11.9-1 install ok installed login login 1:4.16.0-2+really2.40.2-11 install ok installed login.defs login.defs 1:4.16.0-5 install ok installed logsave logsave 1.47.1-1+b1 install ok installed mawk mawk 1.3.4.20240905-1 install ok installed media-types media-types 10.1.0 install ok installed mesa-libgallium:amd64 mesa-libgallium 24.2.7-1 install ok installed mount mount 2.40.2-11 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2+b1 install ok installed netbase netbase 6.4 install ok installed openssl openssl 3.3.2-2 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.2-2 install ok installed passwd passwd 1:4.16.0-5 install ok installed perl-base perl-base 5.40.0-7 install ok installed procps procps 2:4.0.4-6 install ok installed pymol-data pymol-data 3.0.0+dfsg-1 install ok installed python-matplotlib-data python-matplotlib-data 3.8.3-3 install ok installed python3 python3 3.12.7-1 install ok installed python3-appdirs python3-appdirs 1.4.4-4 install ok installed python3-attr python3-attr 24.2.0-1 install ok installed python3-autocommand python3-autocommand 2.2.2-3 install ok installed python3-brotli python3-brotli 1.1.0-2+b6 install ok installed python3-cctbx python3-cctbx 2024.10+ds2+~3.22.1+ds1-4 install ok installed python3-certifi python3-certifi 2024.8.30+dfsg-1 install ok installed python3-chardet python3-chardet 5.2.0+dfsg-1 install ok installed python3-charset-normalizer python3-charset-normalizer 3.4.0-1+b1 install ok installed python3-contourpy python3-contourpy 1.3.0-2+b1 install ok installed python3-cycler python3-cycler 0.12.1-1 install ok installed python3-dateutil python3-dateutil 2.9.0-3 install ok installed python3-decorator python3-decorator 5.1.1-5 install ok installed python3-dev python3-dev 3.12.7-1 install ok installed python3-flexcache python3-flexcache 0.3-2 install ok installed python3-flexparser python3-flexparser 0.4-1 install ok installed python3-fonttools python3-fonttools 4.55.0-1 install ok installed python3-fs python3-fs 2.4.16-4 install ok installed python3-h5py python3-h5py 3.11.0-8 install ok installed python3-h5py-serial python3-h5py-serial 3.11.0-8+b1 install ok installed python3-hdf5plugin python3-hdf5plugin 4.0.1-3 install ok installed python3-idna python3-idna 3.8-2 install ok installed python3-inflect python3-inflect 7.3.1-2 install ok installed python3-jaraco.context python3-jaraco.context 6.0.0-1 install ok installed python3-jaraco.functools python3-jaraco.functools 4.1.0-1 install ok installed python3-kiwisolver python3-kiwisolver 1.4.7-2+b1 install ok installed python3-legacy-cgi python3-legacy-cgi 2.6.1-2 install ok installed python3-lxml:amd64 python3-lxml 5.3.0-1+b1 install ok installed python3-lz4 python3-lz4 4.0.2+dfsg-1+b5 install ok installed python3-matplotlib python3-matplotlib 3.8.3-3+b1 install ok installed python3-minimal python3-minimal 3.12.7-1 install ok installed python3-more-itertools python3-more-itertools 10.5.0-1 install ok installed python3-mpmath python3-mpmath 1.3.0-1 install ok installed python3-mrcfile python3-mrcfile 1.5.3-3 install ok installed python3-natsort python3-natsort 8.0.2-2 install ok installed python3-numpy python3-numpy 1:1.26.4+ds-12 install ok installed python3-nxmx python3-nxmx 0.0.3-3 install ok installed python3-opengl python3-opengl 3.1.7+dfsg-1 install ok installed python3-ordered-set python3-ordered-set 4.1.0-1 install ok installed python3-packaging python3-packaging 24.2-1 install ok installed python3-pil:amd64 python3-pil 10.4.0-1+b1 install ok installed python3-pil.imagetk:amd64 python3-pil.imagetk 10.4.0-1+b1 install ok installed python3-pint python3-pint 0.24.4-1 install ok installed python3-pkg-resources python3-pkg-resources 75.2.0-1 install ok installed python3-platformdirs python3-platformdirs 4.3.6-1 install ok installed python3-procrunner python3-procrunner 2.3.3-2 install ok installed python3-pycbf python3-pycbf 0.9.7+dfsg1-4+b1 install ok installed python3-pymol python3-pymol 3.0.0+dfsg-1+b1 install ok installed python3-pyparsing python3-pyparsing 3.1.2-1 install ok installed python3-pyqt5 python3-pyqt5 5.15.11+dfsg-1+b1 install ok installed python3-pyqt5.qtopengl python3-pyqt5.qtopengl 5.15.11+dfsg-1+b1 install ok installed python3-pyqt5.sip python3-pyqt5.sip 12.15.0-1+b1 install ok installed python3-requests python3-requests 2.32.3+dfsg-1 install ok installed python3-scipy python3-scipy 1.13.1-6 install ok installed python3-six python3-six 1.16.0-7 install ok installed python3-sympy python3-sympy 1.13.3-1 install ok installed python3-tk:amd64 python3-tk 3.12.7-1 install ok installed python3-tqdm python3-tqdm 4.67.0-1 install ok installed python3-typeguard python3-typeguard 4.4.1-1 install ok installed python3-typing-extensions python3-typing-extensions 4.12.2-2 install ok installed python3-tz python3-tz 2024.1-2 install ok installed python3-ufolib2 python3-ufolib2 0.16.1+dfsg1-1 install ok installed python3-unicodedata2 python3-unicodedata2 15.1.0+ds-1+b3 install ok installed python3-urllib3 python3-urllib3 2.0.7-2 install ok installed python3-wxgtk4.0 python3-wxgtk4.0 4.2.2+dfsg-1+b1 install ok installed python3.12 python3.12 3.12.7-3 install ok installed python3.12-dev python3.12-dev 3.12.7-3 install ok installed python3.12-minimal python3.12-minimal 3.12.7-3 install ok installed python3.12-tk python3.12-tk 3.12.7-3 install ok installed python3.13-tk python3.13-tk 3.13.0-2 install ok installed readline-common readline-common 8.2-5 install ok installed rpcsvc-proto rpcsvc-proto 1.4.3-1 install ok installed sed sed 4.9-2 install ok installed shared-mime-info shared-mime-info 2.4-5+b1 install ok installed sphinx-rtd-theme-common sphinx-rtd-theme-common 3.0.2+dfsg-1 install ok installed systemd systemd 257~rc2-3 install ok installed systemd-sysv systemd-sysv 257~rc2-3 install ok installed sysvinit-utils sysvinit-utils 3.11-1 install ok installed tar tar 1.35+dfsg-3 install ok installed tk8.6-blt2.5 tk8.6-blt2.5 2.5.3+dfsg-7 install ok installed tzdata tzdata 2024b-3 install ok installed unicode-data unicode-data 15.1.0-1 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-11 install ok installed x11-common x11-common 1:7.7+23.1 install ok installed xkb-data xkb-data 2.42-1 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1+b1 install ok installed zlib1g-dev:amd64 zlib1g-dev 1:1.3.dfsg+really1.3.1-1+b1 1m58.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m58.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'apt-get', 'remove', 'adduser', 'adwaita-icon-theme', 'at-spi2-common', 'blt', 'ca-certificates', 'dbus', 'dbus-bin', 'dbus-daemon', 'dbus-session-bus-common', 'dbus-system-bus-common', 'dbus-user-session', 'dconf-gsettings-backend:amd64', 'dconf-service', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-font-awesome', 'fonts-lato', 'fonts-lyx', 'gtk-update-icon-cache', 'hicolor-icon-theme', 'libaec0:amd64', 'libann-cctbx-dev', 'libann-cctbx0', 'libantlr3c-3.4-0:amd64', 'libapparmor1:amd64', 'libasan8:amd64', 'libatk-bridge2.0-0t64:amd64', 'libatk1.0-0t64:amd64', 'libatomic1:amd64', 'libatspi2.0-0t64:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libblas3:amd64', 'libboost-numpy1.83.0', 'libboost-python-dev', 'libboost-python1.83-dev', 'libboost-python1.83.0', 'libboost-thread1.83.0:amd64', 'libboost-timer1.83.0:amd64', 'libboost1.83-dev:amd64', 'libbrotli1:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo-gobject2:amd64', 'libcairo2:amd64', 'libcbf1t64:amd64', 'libccp4-data', 'libccp4-dev:amd64', 'libccp4c0t64:amd64', 'libccp4f0t64:amd64', 'libcctbx-dev', 'libcctbx0', 'libcloudproviders0:amd64', 'libcolord2:amd64', 'libcrypt-dev:amd64', 'libcups2t64:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdbus-1-3:amd64', 'libdconf1:amd64', 'libdeflate0:amd64', 'libdouble-conversion3:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libedit2:amd64', 'libegl-mesa0:amd64', 'libegl1:amd64', 'libelf1t64:amd64', 'libepoxy0:amd64', 'libevdev2:amd64', 'libexpat1:amd64', 'libexpat1-dev:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgbm1:amd64', 'libgcc-14-dev:amd64', 'libgdk-pixbuf-2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgfortran5:amd64', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglapi-mesa:amd64', 'libglew2.2:amd64', 'libglib2.0-0t64:amd64', 'libglu1-mesa:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libgtk-3-0t64:amd64', 'libgtk-3-common', 'libgudev-1.0-0:amd64', 'libharfbuzz0b:amd64', 'libhdf5-103-1t64:amd64', 'libhdf5-hl-100t64:amd64', 'libhwasan0:amd64', 'libice6:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libinput-bin', 'libinput10:amd64', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libjs-sphinxdoc', 'libjs-underscore', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libllvm19:amd64', 'liblsan0:amd64', 'liblzf1:amd64', 'libmd4c0:amd64', 'libmmdb2-0:amd64', 'libmtdev1t64:amd64', 'libncursesw6:amd64', 'libnetcdf19t64:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnotify4:amd64', 'libnsl2:amd64', 'libopengl0:amd64', 'libopenjp2-7:amd64', 'libpam-systemd:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpciaccess0:amd64', 'libpcre2-16-0:amd64', 'libpcre2-32-0:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libpsl5t64:amd64', 'libpython3-dev:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-dev:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libpython3.12t64:amd64', 'libqhull-r8.0:amd64', 'libqt5core5t64:amd64', 'libqt5dbus5t64:amd64', 'libqt5designer5:amd64', 'libqt5gui5t64:amd64', 'libqt5help5:amd64', 'libqt5network5t64:amd64', 'libqt5opengl5t64:amd64', 'libqt5printsupport5t64:amd64', 'libqt5sql5t64:amd64', 'libqt5test5t64:amd64', 'libqt5widgets5t64:amd64', 'libqt5xml5t64:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libssm2:amd64', 'libstdc++-14-dev:amd64', 'libsystemd-shared:amd64', 'libsz2:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libvulkan1:amd64', 'libwacom-common', 'libwacom9:amd64', 'libwayland-client0:amd64', 'libwayland-cursor0:amd64', 'libwayland-egl1:amd64', 'libwayland-server0:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libwxbase3.2-1t64:amd64', 'libwxgtk-gl3.2-1t64:amd64', 'libwxgtk3.2-1t64:amd64', 'libx11-6:amd64', 'libx11-data', 'libx11-xcb1:amd64', 'libxau6:amd64', 'libxcb-dri2-0:amd64', 'libxcb-dri3-0:amd64', 'libxcb-glx0:amd64', 'libxcb-icccm4:amd64', 'libxcb-image0:amd64', 'libxcb-keysyms1:amd64', 'libxcb-present0:amd64', 'libxcb-randr0:amd64', 'libxcb-render-util0:amd64', 'libxcb-render0:amd64', 'libxcb-shape0:amd64', 'libxcb-shm0:amd64', 'libxcb-sync1:amd64', 'libxcb-util1:amd64', 'libxcb-xfixes0:amd64', 'libxcb-xinerama0:amd64', 'libxcb-xinput0:amd64', 'libxcb-xkb1:amd64', 'libxcb1:amd64', 'libxcomposite1:amd64', 'libxcursor1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxinerama1:amd64', 'libxkbcommon-x11-0:amd64', 'libxkbcommon0:amd64', 'libxml2:amd64', 'libxrandr2:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libz3-4:amd64', 'linux-libc-dev', 'media-types', 'mesa-libgallium:amd64', 'netbase', 'openssl', 'procps', 'pymol-data', 'python-matplotlib-data', 'python3', 'python3-appdirs', 'python3-attr', 'python3-autocommand', 'python3-brotli', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-dev', 'python3-flexcache', 'python3-flexparser', 'python3-fonttools', 'python3-fs', 'python3-h5py', 'python3-h5py-serial', 'python3-hdf5plugin', 'python3-idna', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-kiwisolver', 'python3-legacy-cgi', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-minimal', 'python3-more-itertools', 'python3-mpmath', 'python3-mrcfile', 'python3-natsort', 'python3-numpy', 'python3-nxmx', 'python3-opengl', 'python3-ordered-set', 'python3-packaging', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pint', 'python3-pkg-resources', 'python3-platformdirs', 'python3-procrunner', 'python3-pycbf', 'python3-pymol', 'python3-pyparsing', 'python3-pyqt5', 'python3-pyqt5.qtopengl', 'python3-pyqt5.sip', 'python3-requests', 'python3-scipy', 'python3-six', 'python3-sympy', 'python3-tk:amd64', 'python3-tqdm', 'python3-typeguard', 'python3-typing-extensions', 'python3-tz', 'python3-ufolib2', 'python3-unicodedata2', 'python3-urllib3', 'python3-wxgtk4.0', 'python3.12', 'python3.12-dev', 'python3.12-minimal', 'python3.12-tk', 'python3.13-tk', 'readline-common', 'rpcsvc-proto', 'shared-mime-info', 'sphinx-rtd-theme-common', 'systemd', 'systemd-sysv', 'tk8.6-blt2.5', 'unicode-data', 'x11-common', 'xkb-data', 'zlib1g-dev:amd64', 'python3-cctbx'] 2m7.0s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: adduser adwaita-icon-theme at-spi2-common blt ca-certificates dbus dbus-bin dbus-daemon dbus-session-bus-common dbus-system-bus-common dbus-user-session dconf-gsettings-backend dconf-service fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome fonts-lato fonts-lyx gtk-update-icon-cache hicolor-icon-theme libaec0 libann-cctbx-dev libann-cctbx0 libantlr3c-3.4-0 libapparmor1 libasan8 libatk-bridge2.0-0t64 libatk1.0-0t64 libatomic1 libatspi2.0-0t64 libavahi-client3 libavahi-common-data libavahi-common3 libblas3 libboost-numpy1.83.0 libboost-python-dev libboost-python1.83-dev libboost-python1.83.0 libboost-thread1.83.0 libboost-timer1.83.0 libboost1.83-dev libbrotli1 libc-dev-bin libc6-dev libcairo-gobject2 libcairo2 libcbf1t64 libccp4-data libccp4-dev libccp4c0t64 libccp4f0t64 libcctbx-dev libcctbx0 libcloudproviders0 libcolord2 libcrypt-dev libcups2t64 libcurl3t64-gnutls libcurl4t64 libdatrie1 libdbus-1-3 libdconf1 libdeflate0 libdouble-conversion3 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-radeon1 libdrm2 libedit2 libegl-mesa0 libegl1 libelf1t64 libepoxy0 libevdev2 libexpat1 libexpat1-dev libfontconfig1 libfreetype6 libfribidi0 libgbm1 libgcc-14-dev libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgfortran5 libgl1 libgl1-mesa-dri libglapi-mesa libglew2.2 libglib2.0-0t64 libglu1-mesa libglvnd0 libglx-mesa0 libglx0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libgtk-3-0t64 libgtk-3-common libgudev-1.0-0 libharfbuzz0b libhdf5-103-1t64 libhdf5-hl-100t64 libhwasan0 libice6 libicu72 libimagequant0 libinput-bin libinput10 libitm1 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap-2.5-0 liblerc4 libllvm19 liblsan0 liblzf1 libmd4c0 libmmdb2-0 libmtdev1t64 libncursesw6 libnetcdf19t64 libnghttp2-14 libnghttp3-9 libngtcp2-16 libngtcp2-crypto-gnutls8 libnotify4 libnsl2 libopengl0 libopenjp2-7 libpam-systemd libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpciaccess0 libpcre2-16-0 libpcre2-32-0 libpixman-1-0 libpng16-16t64 libproc2-0 libpsl5t64 libpython3-dev libpython3-stdlib libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 libqhull-r8.0 libqt5core5t64 libqt5dbus5t64 libqt5designer5 libqt5gui5t64 libqt5help5 libqt5network5t64 libqt5opengl5t64 libqt5printsupport5t64 libqt5sql5t64 libqt5test5t64 libqt5widgets5t64 libqt5xml5t64 libquadmath0 libraqm0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libsharpyuv0 libsm6 libsqlite3-0 libssh2-1t64 libssm2 libstdc++-14-dev libsystemd-shared libsz2 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc3t64 libtk8.6 libtsan2 libubsan1 libvulkan1 libwacom-common libwacom9 libwayland-client0 libwayland-cursor0 libwayland-egl1 libwayland-server0 libwebp7 libwebpdemux2 libwebpmux3 libwxbase3.2-1t64 libwxgtk-gl3.2-1t64 libwxgtk3.2-1t64 libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-present0 libxcb-randr0 libxcb-render-util0 libxcb-render0 libxcb-shape0 libxcb-shm0 libxcb-sync1 libxcb-util1 libxcb-xfixes0 libxcb-xinerama0 libxcb-xinput0 libxcb-xkb1 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxft2 libxi6 libxinerama1 libxkbcommon-x11-0 libxkbcommon0 libxml2 libxrandr2 libxrender1 libxshmfence1 libxslt1.1 libxss1 libxtst6 libxxf86vm1 libz3-4 linux-libc-dev media-types mesa-libgallium netbase openssl procps pymol-data python-matplotlib-data python3 python3-appdirs python3-attr python3-autocommand python3-brotli python3-cctbx python3-certifi python3-chardet python3-charset-normalizer python3-contourpy python3-cycler python3-dateutil python3-decorator python3-dev python3-flexcache python3-flexparser python3-fonttools python3-fs python3-h5py python3-h5py-serial python3-hdf5plugin python3-idna python3-inflect python3-jaraco.context python3-jaraco.functools python3-kiwisolver python3-legacy-cgi python3-lxml python3-lz4 python3-matplotlib python3-minimal python3-more-itertools python3-mpmath python3-mrcfile python3-natsort python3-numpy python3-nxmx python3-opengl python3-ordered-set python3-packaging python3-pil python3-pil.imagetk python3-pint python3-pkg-resources python3-platformdirs python3-procrunner python3-pycbf python3-pymol python3-pyparsing python3-pyqt5 python3-pyqt5.qtopengl python3-pyqt5.sip python3-requests python3-scipy python3-six python3-sympy python3-tk python3-tqdm python3-typeguard python3-typing-extensions python3-tz python3-ufolib2 python3-unicodedata2 python3-urllib3 python3-wxgtk4.0 python3.12 python3.12-dev python3.12-minimal python3.12-tk python3.13-tk readline-common rpcsvc-proto shared-mime-info sphinx-rtd-theme-common systemd systemd-sysv tk8.6-blt2.5 unicode-data x11-common xkb-data zlib1g-dev 0 upgraded, 0 newly installed, 343 to remove and 0 not upgraded. After this operation, 1800 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 ... 54279 files and directories currently installed.) Removing python3-cctbx (2024.10+ds2+~3.22.1+ds1-4) ... Removing python3-wxgtk4.0 (4.2.2+dfsg-1+b1) ... Removing libwxgtk-gl3.2-1t64:amd64 (3.2.6+dfsg-2) ... Removing libwxgtk3.2-1t64:amd64 (3.2.6+dfsg-2) ... Removing libgtk-3-0t64:amd64 (3.24.43-4) ... Removing libgtk-3-common (3.24.43-4) ... Removing dconf-gsettings-backend:amd64 (0.40.0-4+b3) ... Removing dconf-service (0.40.0-4+b3) ... Removing dbus-user-session (1.14.10-6) ... Removing libpam-systemd:amd64 (257~rc2-3) ... Removing dbus (1.14.10-6) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of stop. Removing dbus-system-bus-common (1.14.10-6) ... Removing adduser (3.137) ... Removing adwaita-icon-theme (47.0-2) ... Removing libatk-bridge2.0-0t64:amd64 (2.54.0-1) ... Removing libatk1.0-0t64:amd64 (2.54.0-1) ... Removing at-spi2-common (2.54.0-1) ... Removing python3-matplotlib (3.8.3-3+b1) ... Removing python3-pil.imagetk:amd64 (10.4.0-1+b1) ... Removing python3-pil:amd64 (10.4.0-1+b1) ... Removing python3-tk:amd64 (3.12.7-1) ... Removing blt (2.5.3+dfsg-7) ... Removing python3-requests (2.32.3+dfsg-1) ... Removing python3-certifi (2024.8.30+dfsg-1) ... Removing ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing dbus-daemon (1.14.10-6) ... Removing dbus-bin (1.14.10-6) ... Removing dbus-session-bus-common (1.14.10-6) ... Removing python3-pymol (3.0.0+dfsg-1+b1) ... Removing python3-pyqt5.qtopengl (5.15.11+dfsg-1+b1) ... Removing python3-pyqt5 (5.15.11+dfsg-1+b1) ... Removing libqt5help5:amd64 (5.15.15-2) ... Removing libqt5designer5:amd64 (5.15.15-2) ... Removing libpangocairo-1.0-0:amd64 (1.54.0+ds-3) ... Removing libpangoft2-1.0-0:amd64 (1.54.0+ds-3) ... Removing libpango-1.0-0:amd64 (1.54.0+ds-3) ... Removing tk8.6-blt2.5 (2.5.3+dfsg-7) ... Removing python3.13-tk (3.13.0-2) ... Removing libcairo-gobject2:amd64 (1.18.2-2) ... Removing libcairo2:amd64 (1.18.2-2) ... Removing python-matplotlib-data (3.8.3-3) ... Removing python3-mrcfile (1.5.3-3) ... Removing sphinx-rtd-theme-common (3.0.2+dfsg-1) ... Removing fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Removing fonts-lato (2.015-1) ... Removing fonts-lyx (2.4.2.1-1) ... Removing gtk-update-icon-cache (4.16.5+ds-2) ... Removing hicolor-icon-theme (0.18-1) ... Removing libnetcdf19t64:amd64 (1:4.9.2-7) ... Removing python3-hdf5plugin (4.0.1-3) ... Removing libcctbx-dev (2024.10+ds2+~3.22.1+ds1-4) ... Removing libann-cctbx-dev (1.1.2+doc-9+b1) ... Removing libcctbx0 (2024.10+ds2+~3.22.1+ds1-4) ... Removing libann-cctbx0 (1.1.2+doc-9+b1) ... Removing libantlr3c-3.4-0:amd64 (3.4+dfsg-4+b2) ... Removing systemd-sysv (257~rc2-3) ... Removing systemd (257~rc2-3) ... Removing libapparmor1:amd64 (3.1.7-1+b3) ... Removing libboost-python-dev (1.83.0.2+b2) ... Removing libboost-python1.83-dev (1.83.0-3.2+b1) ... Removing libboost1.83-dev:amd64 (1.83.0-3.2+b1) ... Removing libstdc++-14-dev:amd64 (14.2.0-8) ... Removing libgcc-14-dev:amd64 (14.2.0-8) ... Removing libasan8:amd64 (14.2.0-8) ... Removing libqt5xml5t64:amd64 (5.15.15+dfsg-2) ... Removing libqt5printsupport5t64:amd64 (5.15.15+dfsg-2) ... Removing libqt5test5t64:amd64 (5.15.15+dfsg-2) ... Removing libnotify4:amd64 (0.8.3-1+b2) ... Removing libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-1+b1) ... Removing libatspi2.0-0t64:amd64 (2.54.0-1) ... Removing libcups2t64:amd64 (2.4.10-2) ... Removing libavahi-client3:amd64 (0.8-13+b3) ... Removing libavahi-common3:amd64 (0.8-13+b3) ... Removing libavahi-common-data:amd64 (0.8-13+b3) ... Removing python3-nxmx (0.0.3-3) ... Removing python3-contourpy (1.3.0-2+b1) ... Removing libboost-numpy1.83.0 (1.83.0-3.2+b1) ... Removing libboost-python1.83.0 (1.83.0-3.2+b1) ... Removing libboost-thread1.83.0:amd64 (1.83.0-3.2+b1) ... Removing libboost-timer1.83.0:amd64 (1.83.0-3.2+b1) ... Removing libraqm0:amd64 (0.10.1-1+b2) ... Removing libwxbase3.2-1t64:amd64 (3.2.6+dfsg-2) ... Removing python3-dev (3.12.7-1) ... Removing python3.12-dev (3.12.7-3) ... Removing libpython3-dev:amd64 (3.12.7-1) ... Removing libpython3.12-dev:amd64 (3.12.7-3) ... Removing zlib1g-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Removing libexpat1-dev:amd64 (2.6.4-1) ... Removing libc6-dev:amd64 (2.40-3) ... Removing libc-dev-bin (2.40-3) ... Removing python3-pycbf (0.9.7+dfsg1-4+b1) ... Removing libcbf1t64:amd64 (0.9.7+dfsg1-4+b1) ... Removing libccp4-dev:amd64 (8.0.0-4) ... Removing libccp4f0t64:amd64 (8.0.0-4) ... Removing libccp4c0t64:amd64 (8.0.0-4) ... Removing libccp4-data (8.0.0-4) ... Removing libcloudproviders0:amd64 (0.3.6-1+b1) ... Removing libcolord2:amd64 (1.4.7-1+b2) ... Removing libcrypt-dev:amd64 (1:4.4.36-5) ... Removing libcurl3t64-gnutls:amd64 (8.11.0-1) ... Removing libthai0:amd64 (0.1.29-2+b1) ... Removing libdatrie1:amd64 (0.2.13-3+b1) ... Removing libdconf1:amd64 (0.40.0-4+b3) ... Removing libtiff6:amd64 (4.5.1+git230720-5) ... Removing libdeflate0:amd64 (1.22-1) ... Removing python3-opengl (3.1.7+dfsg-1) ... Removing libepoxy0:amd64 (1.5.10-2) ... Removing python3-tqdm (4.67.0-1) ... Removing python3-chardet (5.2.0+dfsg-1) ... Removing libpython3.12t64:amd64 (3.12.7-3) ... Removing libfribidi0:amd64 (1.0.15-1) ... Removing libgdk-pixbuf2.0-common (2.42.12+dfsg-1) ... Removing libglew2.2:amd64 (2.2.0-4+b2) ... Removing libglu1-mesa:amd64 (9.0.2-1.1+b2) ... Removing libopengl0:amd64 (1.7.0-1+b2) ... Removing libimagequant0:amd64 (2.18.0-1+b2) ... Removing libgomp1:amd64 (14.2.0-8) ... Removing libhwasan0:amd64 (14.2.0-8) ... Removing libitm1:amd64 (14.2.0-8) ... Removing libjbig0:amd64 (2.1-6.1+b2) ... Removing libjs-sphinxdoc (7.4.7-4) ... Removing libjs-jquery-ui (1.13.2+dfsg-1) ... Removing libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Removing libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Removing liblcms2-2:amd64 (2.16-2) ... Removing liblerc4:amd64 (4.0.0+ds-5) ... Removing liblsan0:amd64 (14.2.0-8) ... Removing libssm2:amd64 (1.4.0-2+b3) ... Removing libmmdb2-0:amd64 (2.0.22-1+b2) ... Removing procps (2:4.0.4-6) ... Removing libnghttp3-9:amd64 (1.4.0-1+b1) ... Removing libngtcp2-crypto-gnutls8:amd64 (1.6.0-1) ... Removing libngtcp2-16:amd64 (1.6.0-1) ... Removing libopenjp2-7:amd64 (2.5.0-2+b4) ... Removing libpcre2-32-0:amd64 (10.44-4) ... Removing libpixman-1-0:amd64 (0.44.0-3) ... Removing libproc2-0:amd64 (2:4.0.4-6) ... Removing libqhull-r8.0:amd64 (2020.2-6+b2) ... Removing libqt5opengl5t64:amd64 (5.15.15+dfsg-2) ... Removing libqt5sql5t64:amd64 (5.15.15+dfsg-2) ... Removing libquadmath0:amd64 (14.2.0-8) ... Removing libwebpmux3:amd64 (1.4.0-0.1+b1) ... Removing libwebpdemux2:amd64 (1.4.0-0.1+b1) ... Removing libwebp7:amd64 (1.4.0-0.1+b1) ... Removing libsharpyuv0:amd64 (1.4.0-0.1+b1) ... Removing libsystemd-shared:amd64 (257~rc2-3) ... Removing python3.12-tk (3.12.7-3) ... Removing libthai-data (0.1.29-2) ... Removing libtsan2:amd64 (14.2.0-8) ... Removing libubsan1:amd64 (14.2.0-8) ... Removing libwayland-cursor0:amd64 (1.23.0-1+b1) ... Removing libwayland-egl1:amd64 (1.23.0-1+b1) ... Removing libxtst6:amd64 (2:1.2.3-1.1+b2) ... Removing libxcomposite1:amd64 (1:0.4.6-1) ... Removing libxcursor1:amd64 (1:1.2.2-1+b1) ... Removing libxdamage1:amd64 (1:1.1.6-1+b2) ... Removing libxi6:amd64 (2:1.8.2-1) ... Removing libxinerama1:amd64 (2:1.1.4-3+b2) ... Removing libxrandr2:amd64 (2:1.5.4-1+b1) ... Removing linux-libc-dev (6.11.9-1) ... Removing openssl (3.3.2-2) ... Removing pymol-data (3.0.0+dfsg-1) ... Removing python3-charset-normalizer (3.4.0-1+b1) ... Removing python3-cycler (0.12.1-1) ... Removing python3-dateutil (2.9.0-3) ... Removing python3-pint (0.24.4-1) ... Removing python3-flexcache (0.3-2) ... Removing python3-flexparser (0.4-1) ... Removing python3-idna (3.8-2) ... Removing python3-kiwisolver (1.4.7-2+b1) ... Removing python3-legacy-cgi (2.6.1-2) ... Removing python3-natsort (8.0.2-2) ... Removing python3-ordered-set (4.1.0-1) ... Removing python3-packaging (24.2-1) ... Removing python3-platformdirs (4.3.6-1) ... Removing python3-procrunner (2.3.3-2) ... Removing python3-pyparsing (3.1.2-1) ... Removing python3-pyqt5.sip (12.15.0-1+b1) ... Removing python3-urllib3 (2.0.7-2) ... Removing rpcsvc-proto (1.4.3-1) ... Removing libtk8.6:amd64 (8.6.15-1) ... Removing libxft2:amd64 (2.3.6-1+b2) ... Removing python3-h5py (3.11.0-8) ... Removing python3-h5py-serial (3.11.0-8+b1) ... Removing libhdf5-hl-100t64:amd64 (1.10.10+repack-4) ... Removing libhdf5-103-1t64:amd64 (1.10.10+repack-4) ... Removing libsz2:amd64 (1.1.3-1+b1) ... Removing libaec0:amd64 (1.1.3-1+b1) ... Removing libqt5widgets5t64:amd64 (5.15.15+dfsg-2) ... Removing libcurl4t64:amd64 (8.11.0-1) ... Removing libldap-2.5-0:amd64 (2.5.18+dfsg-3+b1) ... Removing liblzf1:amd64 (3.6-4+b2) ... Removing libnghttp2-14:amd64 (1.64.0-1) ... Removing libpsl5t64:amd64 (0.21.2-1.1+b1) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-8) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-8) ... Removing libssh2-1t64:amd64 (1.11.1-1) ... Removing libtcl8.6:amd64 (8.6.15+dfsg-2) ... Removing libxss1:amd64 (1:1.2.3-1+b2) ... Removing libqt5gui5t64:amd64 (5.15.15+dfsg-2) ... Removing fontconfig (2.15.0-1.1+b1) ... Removing libfontconfig1:amd64 (2.15.0-1.1+b1) ... Removing fontconfig-config (2.15.0-1.1+b1) ... Removing fonts-dejavu-core (2.37-8) ... Removing fonts-dejavu-mono (2.37-8) ... Removing libinput10:amd64 (1.26.2-1) ... Removing libharfbuzz0b:amd64 (10.0.1-1) ... Removing libfreetype6:amd64 (2.13.3+dfsg-1) ... Removing libbrotli1:amd64 (1.1.0-2+b6) ... Removing libqt5network5t64:amd64 (5.15.15+dfsg-2) ... Removing libqt5dbus5t64:amd64 (5.15.15+dfsg-2) ... Removing libdbus-1-3:amd64 (1.14.10-6) ... Removing libegl1:amd64 (1.7.0-1+b2) ... Removing libegl-mesa0:amd64 (24.2.7-1) ... Removing libgl1:amd64 (1.7.0-1+b2) ... Removing libglx0:amd64 (1.7.0-1+b2) ... Removing libglx-mesa0:amd64 (24.2.7-1) ... Removing libgl1-mesa-dri:amd64 (24.2.7-1) ... Removing libgbm1:amd64 (24.2.7-1) ... Removing libinput-bin (1.26.2-1) ... Removing libglvnd0:amd64 (1.7.0-1+b2) ... Removing libgraphite2-3:amd64 (1.3.14-2+b1) ... Removing libsm6:amd64 (2:1.2.4-1) ... Removing libice6:amd64 (2:1.1.1-1) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Removing libmd4c0:amd64 (0.5.2-2+b1) ... Removing libmtdev1t64:amd64 (1.1.6-1.2+b1) ... Removing libpng16-16t64:amd64 (1.6.44-2) ... Removing libvulkan1:amd64 (1.3.296.0-1) ... Removing libwayland-client0:amd64 (1.23.0-1+b1) ... Removing libwayland-server0:amd64 (1.23.0-1+b1) ... Removing libxxf86vm1:amd64 (1:1.1.4-1+b3) ... Removing libxcb-icccm4:amd64 (0.4.2-1) ... Removing libxcb-render-util0:amd64 (0.3.9-1+b2) ... Removing libxcb-glx0:amd64 (1.17.0-2+b1) ... Removing libxcb-image0:amd64 (0.4.0-2+b2) ... Removing libxcb-keysyms1:amd64 (0.4.0-1+b3) ... Removing libxcb-randr0:amd64 (1.17.0-2+b1) ... Removing libxcb-render0:amd64 (1.17.0-2+b1) ... Removing libxcb-shape0:amd64 (1.17.0-2+b1) ... Removing libxcb-shm0:amd64 (1.17.0-2+b1) ... Removing libxcb-util1:amd64 (0.4.0-1+b2) ... Removing libxcb-xinerama0:amd64 (1.17.0-2+b1) ... Removing libxcb-xinput0:amd64 (1.17.0-2+b1) ... Removing libxkbcommon-x11-0:amd64 (1.7.0-1) ... Removing libxcb-xkb1:amd64 (1.17.0-2+b1) ... Removing libxext6:amd64 (2:1.3.4-1+b2) ... Removing libxfixes3:amd64 (1:6.0.0-2+b2) ... Removing libxkbcommon0:amd64 (1.7.0-1) ... Removing libxrender1:amd64 (1:0.9.10-1.1+b2) ... Removing x11-common (1:7.7+23.1) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing xkb-data (2.42-1) ... Removing libqt5core5t64:amd64 (5.15.15+dfsg-2) ... Removing shared-mime-info (2.4-5+b1) ... Removing libwacom9:amd64 (2.13.0-1) ... Removing libdouble-conversion3:amd64 (3.3.0-1+b2) ... Removing mesa-libgallium:amd64 (24.2.7-1) ... Removing libdrm-amdgpu1:amd64 (2.4.123-1) ... Removing libdrm-intel1:amd64 (2.4.123-1) ... Removing libdrm-radeon1:amd64 (2.4.123-1) ... Removing libllvm19:amd64 (1:19.1.3-2) ... Removing libedit2:amd64 (3.1-20240808-1) ... Removing libelf1t64:amd64 (0.192-4) ... Removing libevdev2:amd64 (1.13.3+dfsg-1) ... Removing libglapi-mesa:amd64 (24.2.7-1) ... Removing libgudev-1.0-0:amd64 (238-5+b1) ... Removing libpciaccess0:amd64 (0.17-3+b2) ... Removing libpcre2-16-0:amd64 (10.44-4) ... Removing libsensors5:amd64 (1:3.6.0-10+b1) ... Removing libsensors-config (1:3.6.0-10) ... Removing libwacom-common (2.13.0-1) ... Removing libx11-xcb1:amd64 (2:1.8.10-2) ... Removing libxcb-dri2-0:amd64 (1.17.0-2+b1) ... Removing libxcb-dri3-0:amd64 (1.17.0-2+b1) ... Removing libxcb-present0:amd64 (1.17.0-2+b1) ... Removing libxcb-sync1:amd64 (1.17.0-2+b1) ... Removing libxcb-xfixes0:amd64 (1.17.0-2+b1) ... Removing libxshmfence1:amd64 (1.3-1+b2) ... Removing libz3-4:amd64 (4.13.3-1) ... Removing libglib2.0-0t64:amd64 (2.82.2-3) ... Removing libatomic1:amd64 (14.2.0-8) ... Removing libdrm2:amd64 (2.4.123-1) ... Removing libdrm-common (2.4.123-1) ... Removing libx11-6:amd64 (2:1.8.10-2) ... Removing libx11-data (2:1.8.10-2) ... Removing libxcb1:amd64 (1.17.0-2+b1) ... Removing libxau6:amd64 (1:1.0.11-1) ... Removing libxdmcp6:amd64 (1:1.1.5-1) ... Removing python3-fonttools (4.55.0-1) ... Removing python3-scipy (1.13.1-6) ... Removing python3-numpy (1:1.26.4+ds-12) ... Removing liblbfgsb0:amd64 (3.0+dfsg.4-1+b2) ... Removing liblapack3:amd64 (3.12.0-4) ... Removing libblas3:amd64 (3.12.0-4) ... Removing python3-unicodedata2 (15.1.0+ds-1+b3) ... Removing python3-fs (2.4.16-4) ... Removing python3-pkg-resources (75.2.0-1) ... Removing python3-lz4 (4.0.2+dfsg-1+b5) ... Removing python3-sympy (1.13.3-1) ... Removing python3-inflect (7.3.1-2) ... Removing python3-typeguard (4.4.1-1) ... Removing libgfortran5:amd64 (14.2.0-8) ... Removing python3-lxml:amd64 (5.3.0-1+b1) ... Removing libxslt1.1:amd64 (1.1.35-1.1+b1) ... Removing libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Removing libicu72:amd64 (72.1-5+b1) ... Removing python3-appdirs (1.4.4-4) ... Removing python3-autocommand (2.2.2-3) ... Removing python3-brotli (1.1.0-2+b6) ... Removing python3-decorator (5.1.1-5) ... Removing python3-jaraco.context (6.0.0-1) ... Removing python3-jaraco.functools (4.1.0-1) ... Removing python3-more-itertools (10.5.0-1) ... Removing python3-mpmath (1.3.0-1) ... Removing python3-six (1.16.0-7) ... Removing python3-typing-extensions (4.12.2-2) ... Removing python3-tz (2024.1-2) ... Removing unicode-data (15.1.0-1) ... Removing python3-ufolib2 (0.16.1+dfsg1-1) ... Removing python3-attr (24.2.0-1) ... Removing python3 (3.12.7-1) ... Removing python3.12 (3.12.7-3) ... Removing python3-minimal (3.12.7-1) ... Removing python3.12-minimal (3.12.7-3) ... Removing libexpat1:amd64 (2.6.4-1) ... Removing libpython3-stdlib:amd64 (3.12.7-1) ... Removing libpython3.12-stdlib:amd64 (3.12.7-3) ... find: '/usr/lib/python3': No such file or directory Removing libnsl2:amd64 (1.3.0-3+b3) ... Removing libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Removing libgssapi-krb5-2:amd64 (1.21.3-3) ... Removing libkrb5-3:amd64 (1.21.3-3) ... Removing libk5crypto3:amd64 (1.21.3-3) ... Removing libkeyutils1:amd64 (1.6.3-4) ... Removing libkrb5support0:amd64 (1.21.3-3) ... Removing libncursesw6:amd64 (6.5-2+b1) ... Removing libpython3.12-minimal:amd64 (3.12.7-3) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8t64:amd64 (8.2-5) ... Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Removing libsqlite3-0:amd64 (3.46.1-1) ... Removing libtirpc-common (1.3.4+ds-1.3) ... Removing media-types (10.1.0) ... Removing netbase (6.4) ... Removing readline-common (8.2-5) ... Processing triggers for libc-bin (2.40-3) ... 2m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'apt-get', 'remove', 'adduser', 'adwaita-icon-theme', 'at-spi2-common', 'blt', 'ca-certificates', 'dbus', 'dbus-bin', 'dbus-daemon', 'dbus-session-bus-common', 'dbus-system-bus-common', 'dbus-user-session', 'dconf-gsettings-backend:amd64', 'dconf-service', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-font-awesome', 'fonts-lato', 'fonts-lyx', 'gtk-update-icon-cache', 'hicolor-icon-theme', 'libaec0:amd64', 'libann-cctbx-dev', 'libann-cctbx0', 'libantlr3c-3.4-0:amd64', 'libapparmor1:amd64', 'libasan8:amd64', 'libatk-bridge2.0-0t64:amd64', 'libatk1.0-0t64:amd64', 'libatomic1:amd64', 'libatspi2.0-0t64:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libblas3:amd64', 'libboost-numpy1.83.0', 'libboost-python-dev', 'libboost-python1.83-dev', 'libboost-python1.83.0', 'libboost-thread1.83.0:amd64', 'libboost-timer1.83.0:amd64', 'libboost1.83-dev:amd64', 'libbrotli1:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo-gobject2:amd64', 'libcairo2:amd64', 'libcbf1t64:amd64', 'libccp4-data', 'libccp4-dev:amd64', 'libccp4c0t64:amd64', 'libccp4f0t64:amd64', 'libcctbx-dev', 'libcctbx0', 'libcloudproviders0:amd64', 'libcolord2:amd64', 'libcrypt-dev:amd64', 'libcups2t64:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdbus-1-3:amd64', 'libdconf1:amd64', 'libdeflate0:amd64', 'libdouble-conversion3:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libedit2:amd64', 'libegl-mesa0:amd64', 'libegl1:amd64', 'libelf1t64:amd64', 'libepoxy0:amd64', 'libevdev2:amd64', 'libexpat1:amd64', 'libexpat1-dev:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgbm1:amd64', 'libgcc-14-dev:amd64', 'libgdk-pixbuf-2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgfortran5:amd64', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglapi-mesa:amd64', 'libglew2.2:amd64', 'libglib2.0-0t64:amd64', 'libglu1-mesa:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libgtk-3-0t64:amd64', 'libgtk-3-common', 'libgudev-1.0-0:amd64', 'libharfbuzz0b:amd64', 'libhdf5-103-1t64:amd64', 'libhdf5-hl-100t64:amd64', 'libhwasan0:amd64', 'libice6:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libinput-bin', 'libinput10:amd64', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libjs-sphinxdoc', 'libjs-underscore', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libllvm19:amd64', 'liblsan0:amd64', 'liblzf1:amd64', 'libmd4c0:amd64', 'libmmdb2-0:amd64', 'libmtdev1t64:amd64', 'libncursesw6:amd64', 'libnetcdf19t64:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnotify4:amd64', 'libnsl2:amd64', 'libopengl0:amd64', 'libopenjp2-7:amd64', 'libpam-systemd:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpciaccess0:amd64', 'libpcre2-16-0:amd64', 'libpcre2-32-0:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libpsl5t64:amd64', 'libpython3-dev:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-dev:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libpython3.12t64:amd64', 'libqhull-r8.0:amd64', 'libqt5core5t64:amd64', 'libqt5dbus5t64:amd64', 'libqt5designer5:amd64', 'libqt5gui5t64:amd64', 'libqt5help5:amd64', 'libqt5network5t64:amd64', 'libqt5opengl5t64:amd64', 'libqt5printsupport5t64:amd64', 'libqt5sql5t64:amd64', 'libqt5test5t64:amd64', 'libqt5widgets5t64:amd64', 'libqt5xml5t64:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libssm2:amd64', 'libstdc++-14-dev:amd64', 'libsystemd-shared:amd64', 'libsz2:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libvulkan1:amd64', 'libwacom-common', 'libwacom9:amd64', 'libwayland-client0:amd64', 'libwayland-cursor0:amd64', 'libwayland-egl1:amd64', 'libwayland-server0:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libwxbase3.2-1t64:amd64', 'libwxgtk-gl3.2-1t64:amd64', 'libwxgtk3.2-1t64:amd64', 'libx11-6:amd64', 'libx11-data', 'libx11-xcb1:amd64', 'libxau6:amd64', 'libxcb-dri2-0:amd64', 'libxcb-dri3-0:amd64', 'libxcb-glx0:amd64', 'libxcb-icccm4:amd64', 'libxcb-image0:amd64', 'libxcb-keysyms1:amd64', 'libxcb-present0:amd64', 'libxcb-randr0:amd64', 'libxcb-render-util0:amd64', 'libxcb-render0:amd64', 'libxcb-shape0:amd64', 'libxcb-shm0:amd64', 'libxcb-sync1:amd64', 'libxcb-util1:amd64', 'libxcb-xfixes0:amd64', 'libxcb-xinerama0:amd64', 'libxcb-xinput0:amd64', 'libxcb-xkb1:amd64', 'libxcb1:amd64', 'libxcomposite1:amd64', 'libxcursor1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxinerama1:amd64', 'libxkbcommon-x11-0:amd64', 'libxkbcommon0:amd64', 'libxml2:amd64', 'libxrandr2:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libz3-4:amd64', 'linux-libc-dev', 'media-types', 'mesa-libgallium:amd64', 'netbase', 'openssl', 'procps', 'pymol-data', 'python-matplotlib-data', 'python3', 'python3-appdirs', 'python3-attr', 'python3-autocommand', 'python3-brotli', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-dev', 'python3-flexcache', 'python3-flexparser', 'python3-fonttools', 'python3-fs', 'python3-h5py', 'python3-h5py-serial', 'python3-hdf5plugin', 'python3-idna', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-kiwisolver', 'python3-legacy-cgi', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-minimal', 'python3-more-itertools', 'python3-mpmath', 'python3-mrcfile', 'python3-natsort', 'python3-numpy', 'python3-nxmx', 'python3-opengl', 'python3-ordered-set', 'python3-packaging', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pint', 'python3-pkg-resources', 'python3-platformdirs', 'python3-procrunner', 'python3-pycbf', 'python3-pymol', 'python3-pyparsing', 'python3-pyqt5', 'python3-pyqt5.qtopengl', 'python3-pyqt5.sip', 'python3-requests', 'python3-scipy', 'python3-six', 'python3-sympy', 'python3-tk:amd64', 'python3-tqdm', 'python3-typeguard', 'python3-typing-extensions', 'python3-tz', 'python3-ufolib2', 'python3-unicodedata2', 'python3-urllib3', 'python3-wxgtk4.0', 'python3.12', 'python3.12-dev', 'python3.12-minimal', 'python3.12-tk', 'python3.13-tk', 'readline-common', 'rpcsvc-proto', 'shared-mime-info', 'sphinx-rtd-theme-common', 'systemd', 'systemd-sysv', 'tk8.6-blt2.5', 'unicode-data', 'x11-common', 'xkb-data', 'zlib1g-dev:amd64', 'python3-cctbx'] 2m7.0s INFO: Running scripts post_remove 2m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/post_remove_exceptions'] 2m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/post_remove_exceptions'] 2m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'dpkg', '--purge', 'adduser', 'adwaita-icon-theme', 'at-spi2-common', 'blt', 'ca-certificates', 'dbus', 'dbus-bin', 'dbus-daemon', 'dbus-session-bus-common', 'dbus-system-bus-common', 'dbus-user-session', 'dconf-gsettings-backend:amd64', 'dconf-service', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-font-awesome', 'fonts-lato', 'fonts-lyx', 'gtk-update-icon-cache', 'hicolor-icon-theme', 'libaec0:amd64', 'libann-cctbx-dev', 'libann-cctbx0', 'libantlr3c-3.4-0:amd64', 'libapparmor1:amd64', 'libasan8:amd64', 'libatk-bridge2.0-0t64:amd64', 'libatk1.0-0t64:amd64', 'libatomic1:amd64', 'libatspi2.0-0t64:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libblas3:amd64', 'libboost-numpy1.83.0', 'libboost-python-dev', 'libboost-python1.83-dev', 'libboost-python1.83.0', 'libboost-thread1.83.0:amd64', 'libboost-timer1.83.0:amd64', 'libboost1.83-dev:amd64', 'libbrotli1:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo-gobject2:amd64', 'libcairo2:amd64', 'libcbf1t64:amd64', 'libccp4-data', 'libccp4-dev:amd64', 'libccp4c0t64:amd64', 'libccp4f0t64:amd64', 'libcctbx-dev', 'libcctbx0', 'libcloudproviders0:amd64', 'libcolord2:amd64', 'libcrypt-dev:amd64', 'libcups2t64:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdbus-1-3:amd64', 'libdconf1:amd64', 'libdeflate0:amd64', 'libdouble-conversion3:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libedit2:amd64', 'libegl-mesa0:amd64', 'libegl1:amd64', 'libelf1t64:amd64', 'libepoxy0:amd64', 'libevdev2:amd64', 'libexpat1:amd64', 'libexpat1-dev:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgbm1:amd64', 'libgcc-14-dev:amd64', 'libgdk-pixbuf-2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgfortran5:amd64', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglapi-mesa:amd64', 'libglew2.2:amd64', 'libglib2.0-0t64:amd64', 'libglu1-mesa:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libgtk-3-0t64:amd64', 'libgtk-3-common', 'libgudev-1.0-0:amd64', 'libharfbuzz0b:amd64', 'libhdf5-103-1t64:amd64', 'libhdf5-hl-100t64:amd64', 'libhwasan0:amd64', 'libice6:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libinput-bin', 'libinput10:amd64', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libjs-sphinxdoc', 'libjs-underscore', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libllvm19:amd64', 'liblsan0:amd64', 'liblzf1:amd64', 'libmd4c0:amd64', 'libmmdb2-0:amd64', 'libmtdev1t64:amd64', 'libncursesw6:amd64', 'libnetcdf19t64:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnotify4:amd64', 'libnsl2:amd64', 'libopengl0:amd64', 'libopenjp2-7:amd64', 'libpam-systemd:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpciaccess0:amd64', 'libpcre2-16-0:amd64', 'libpcre2-32-0:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libpsl5t64:amd64', 'libpython3-dev:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-dev:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libpython3.12t64:amd64', 'libqhull-r8.0:amd64', 'libqt5core5t64:amd64', 'libqt5dbus5t64:amd64', 'libqt5designer5:amd64', 'libqt5gui5t64:amd64', 'libqt5help5:amd64', 'libqt5network5t64:amd64', 'libqt5opengl5t64:amd64', 'libqt5printsupport5t64:amd64', 'libqt5sql5t64:amd64', 'libqt5test5t64:amd64', 'libqt5widgets5t64:amd64', 'libqt5xml5t64:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libssm2:amd64', 'libstdc++-14-dev:amd64', 'libsystemd-shared:amd64', 'libsz2:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libvulkan1:amd64', 'libwacom-common', 'libwacom9:amd64', 'libwayland-client0:amd64', 'libwayland-cursor0:amd64', 'libwayland-egl1:amd64', 'libwayland-server0:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libwxbase3.2-1t64:amd64', 'libwxgtk-gl3.2-1t64:amd64', 'libwxgtk3.2-1t64:amd64', 'libx11-6:amd64', 'libx11-data', 'libx11-xcb1:amd64', 'libxau6:amd64', 'libxcb-dri2-0:amd64', 'libxcb-dri3-0:amd64', 'libxcb-glx0:amd64', 'libxcb-icccm4:amd64', 'libxcb-image0:amd64', 'libxcb-keysyms1:amd64', 'libxcb-present0:amd64', 'libxcb-randr0:amd64', 'libxcb-render-util0:amd64', 'libxcb-render0:amd64', 'libxcb-shape0:amd64', 'libxcb-shm0:amd64', 'libxcb-sync1:amd64', 'libxcb-util1:amd64', 'libxcb-xfixes0:amd64', 'libxcb-xinerama0:amd64', 'libxcb-xinput0:amd64', 'libxcb-xkb1:amd64', 'libxcb1:amd64', 'libxcomposite1:amd64', 'libxcursor1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxinerama1:amd64', 'libxkbcommon-x11-0:amd64', 'libxkbcommon0:amd64', 'libxml2:amd64', 'libxrandr2:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libz3-4:amd64', 'linux-libc-dev', 'media-types', 'mesa-libgallium:amd64', 'netbase', 'openssl', 'procps', 'pymol-data', 'python-matplotlib-data', 'python3', 'python3-appdirs', 'python3-attr', 'python3-autocommand', 'python3-brotli', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-dev', 'python3-flexcache', 'python3-flexparser', 'python3-fonttools', 'python3-fs', 'python3-h5py', 'python3-h5py-serial', 'python3-hdf5plugin', 'python3-idna', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-kiwisolver', 'python3-legacy-cgi', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-minimal', 'python3-more-itertools', 'python3-mpmath', 'python3-mrcfile', 'python3-natsort', 'python3-numpy', 'python3-nxmx', 'python3-opengl', 'python3-ordered-set', 'python3-packaging', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pint', 'python3-pkg-resources', 'python3-platformdirs', 'python3-procrunner', 'python3-pycbf', 'python3-pymol', 'python3-pyparsing', 'python3-pyqt5', 'python3-pyqt5.qtopengl', 'python3-pyqt5.sip', 'python3-requests', 'python3-scipy', 'python3-six', 'python3-sympy', 'python3-tk:amd64', 'python3-tqdm', 'python3-typeguard', 'python3-typing-extensions', 'python3-tz', 'python3-ufolib2', 'python3-unicodedata2', 'python3-urllib3', 'python3-wxgtk4.0', 'python3.12', 'python3.12-dev', 'python3.12-minimal', 'python3.12-tk', 'python3.13-tk', 'readline-common', 'rpcsvc-proto', 'shared-mime-info', 'sphinx-rtd-theme-common', 'systemd', 'systemd-sysv', 'tk8.6-blt2.5', 'unicode-data', 'x11-common', 'xkb-data', 'zlib1g-dev:amd64'] 2m7.4s DUMP: (Reading database ... 5235 files and directories currently installed.) Purging configuration files for adduser (3.137) ... Purging configuration files for adwaita-icon-theme (47.0-2) ... dpkg: warning: ignoring request to remove at-spi2-common which isn't installed dpkg: warning: ignoring request to remove blt which isn't installed Purging configuration files for ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Purging configuration files for dbus (1.14.10-6) ... rmdir: failed to remove '/var/run/dbus': Directory not empty rmdir: failed to remove '/var/lib/dbus': Directory not empty dpkg: warning: while removing dbus, directory '/var/lib/dbus' not empty so not removed dpkg: warning: ignoring request to remove dbus-bin which isn't installed Purging configuration files for dbus-daemon (1.14.10-6) ... dpkg: warning: ignoring request to remove dbus-session-bus-common which isn't installed dpkg: warning: ignoring request to remove dbus-system-bus-common which isn't installed Purging configuration files for dbus-user-session (1.14.10-6) ... dpkg: warning: ignoring request to remove dconf-gsettings-backend which isn't installed dpkg: warning: ignoring request to remove dconf-service which isn't installed Purging configuration files for fontconfig (2.15.0-1.1+b1) ... Purging configuration files for fontconfig-config (2.15.0-1.1+b1) ... dpkg: warning: while removing fontconfig-config, directory '/etc/fonts/conf.d' not empty so not removed Purging configuration files for fonts-dejavu-core (2.37-8) ... Purging configuration files for fonts-dejavu-mono (2.37-8) ... dpkg: warning: while removing fonts-dejavu-mono, directory '/etc/fonts' not empty so not removed Purging configuration files for fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... dpkg: warning: ignoring request to remove fonts-lato which isn't installed dpkg: warning: ignoring request to remove fonts-lyx which isn't installed dpkg: warning: ignoring request to remove gtk-update-icon-cache which isn't installed dpkg: warning: ignoring request to remove hicolor-icon-theme which isn't installed dpkg: warning: ignoring request to remove libaec0 which isn't installed dpkg: warning: ignoring request to remove libann-cctbx-dev which isn't installed dpkg: warning: ignoring request to remove libann-cctbx0 which isn't installed dpkg: warning: ignoring request to remove libantlr3c-3.4-0 which isn't installed dpkg: warning: ignoring request to remove libapparmor1 which isn't installed dpkg: warning: ignoring request to remove libasan8 which isn't installed dpkg: warning: ignoring request to remove libatk-bridge2.0-0t64 which isn't installed dpkg: warning: ignoring request to remove libatk1.0-0t64 which isn't installed dpkg: warning: ignoring request to remove libatomic1 which isn't installed dpkg: warning: ignoring request to remove libatspi2.0-0t64 which isn't installed dpkg: warning: ignoring request to remove libavahi-client3 which isn't installed dpkg: warning: ignoring request to remove libavahi-common-data which isn't installed dpkg: warning: ignoring request to remove libavahi-common3 which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libboost-numpy1.83.0 which isn't installed dpkg: warning: ignoring request to remove libboost-python-dev which isn't installed dpkg: warning: ignoring request to remove libboost-python1.83-dev which isn't installed dpkg: warning: ignoring request to remove libboost-python1.83.0 which isn't installed dpkg: warning: ignoring request to remove libboost-thread1.83.0 which isn't installed dpkg: warning: ignoring request to remove libboost-timer1.83.0 which isn't installed dpkg: warning: ignoring request to remove libboost1.83-dev which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libc-dev-bin which isn't installed dpkg: warning: ignoring request to remove libc6-dev which isn't installed dpkg: warning: ignoring request to remove libcairo-gobject2 which isn't installed dpkg: warning: ignoring request to remove libcairo2 which isn't installed dpkg: warning: ignoring request to remove libcbf1t64 which isn't installed dpkg: warning: ignoring request to remove libccp4-data which isn't installed dpkg: warning: ignoring request to remove libccp4-dev which isn't installed dpkg: warning: ignoring request to remove libccp4c0t64 which isn't installed dpkg: warning: ignoring request to remove libccp4f0t64 which isn't installed dpkg: warning: ignoring request to remove libcctbx-dev which isn't installed dpkg: warning: ignoring request to remove libcctbx0 which isn't installed dpkg: warning: ignoring request to remove libcloudproviders0 which isn't installed dpkg: warning: ignoring request to remove libcolord2 which isn't installed Purging configuration files for libcrypt-dev:amd64 (1:4.4.36-5) ... dpkg: warning: ignoring request to remove libcups2t64 which isn't installed dpkg: warning: ignoring request to remove libcurl3t64-gnutls which isn't installed dpkg: warning: ignoring request to remove libcurl4t64 which isn't installed dpkg: warning: ignoring request to remove libdatrie1 which isn't installed dpkg: warning: ignoring request to remove libdbus-1-3 which isn't installed dpkg: warning: ignoring request to remove libdconf1 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 libdrm-amdgpu1 which isn't installed dpkg: warning: ignoring request to remove libdrm-common which isn't installed dpkg: warning: ignoring request to remove libdrm-intel1 which isn't installed dpkg: warning: ignoring request to remove libdrm-radeon1 which isn't installed dpkg: warning: ignoring request to remove libdrm2 which isn't installed dpkg: warning: ignoring request to remove libedit2 which isn't installed dpkg: warning: ignoring request to remove libegl-mesa0 which isn't installed dpkg: warning: ignoring request to remove libegl1 which isn't installed dpkg: warning: ignoring request to remove libelf1t64 which isn't installed dpkg: warning: ignoring request to remove libepoxy0 which isn't installed dpkg: warning: ignoring request to remove libevdev2 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libexpat1-dev which isn't installed dpkg: warning: ignoring request to remove libfontconfig1 which isn't installed dpkg: warning: ignoring request to remove libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libfribidi0 which isn't installed dpkg: warning: ignoring request to remove libgbm1 which isn't installed dpkg: warning: ignoring request to remove libgcc-14-dev which isn't installed Purging configuration files for libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-1+b1) ... dpkg: warning: ignoring request to remove libgdk-pixbuf2.0-common which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed dpkg: warning: ignoring request to remove libgl1 which isn't installed Purging configuration files for libgl1-mesa-dri:amd64 (24.2.7-1) ... dpkg: warning: ignoring request to remove libglapi-mesa which isn't installed dpkg: warning: ignoring request to remove libglew2.2 which isn't installed Purging configuration files for libglib2.0-0t64:amd64 (2.82.2-3) ... dpkg: warning: ignoring request to remove libglu1-mesa which isn't installed dpkg: warning: ignoring request to remove libglvnd0 which isn't installed dpkg: warning: ignoring request to remove libglx-mesa0 which isn't installed dpkg: warning: ignoring request to remove libglx0 which isn't installed dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.21.3-3) ... Purging configuration files for libgtk-3-0t64:amd64 (3.24.43-4) ... Purging configuration files for libgtk-3-common (3.24.43-4) ... dpkg: warning: ignoring request to remove libgudev-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed dpkg: warning: ignoring request to remove libhdf5-103-1t64 which isn't installed dpkg: warning: ignoring request to remove libhdf5-hl-100t64 which isn't installed dpkg: warning: ignoring request to remove libhwasan0 which isn't installed dpkg: warning: ignoring request to remove libice6 which isn't installed dpkg: warning: ignoring request to remove libicu72 which isn't installed dpkg: warning: ignoring request to remove libimagequant0 which isn't installed dpkg: warning: ignoring request to remove libinput-bin which isn't installed dpkg: warning: ignoring request to remove libinput10 which isn't installed dpkg: warning: ignoring request to remove libitm1 which isn't installed dpkg: warning: ignoring request to remove libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed Purging configuration files for libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... dpkg: warning: ignoring request to remove libjs-jquery-ui which isn't installed dpkg: warning: ignoring request to remove libjs-sphinxdoc which isn't installed dpkg: warning: ignoring request to remove libjs-underscore which isn't installed dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove liblbfgsb0 which isn't installed dpkg: warning: ignoring request to remove liblcms2-2 which isn't installed dpkg: warning: ignoring request to remove libldap-2.5-0 which isn't installed dpkg: warning: ignoring request to remove liblerc4 which isn't installed dpkg: warning: ignoring request to remove libllvm19 which isn't installed dpkg: warning: ignoring request to remove liblsan0 which isn't installed dpkg: warning: ignoring request to remove liblzf1 which isn't installed dpkg: warning: ignoring request to remove libmd4c0 which isn't installed dpkg: warning: ignoring request to remove libmmdb2-0 which isn't installed dpkg: warning: ignoring request to remove libmtdev1t64 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libnetcdf19t64 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libnghttp3-9 which isn't installed dpkg: warning: ignoring request to remove libngtcp2-16 which isn't installed dpkg: warning: ignoring request to remove libngtcp2-crypto-gnutls8 which isn't installed dpkg: warning: ignoring request to remove libnotify4 which isn't installed dpkg: warning: ignoring request to remove libnsl2 which isn't installed dpkg: warning: ignoring request to remove libopengl0 which isn't installed dpkg: warning: ignoring request to remove libopenjp2-7 which isn't installed dpkg: warning: ignoring request to remove libpam-systemd which isn't installed dpkg: warning: ignoring request to remove libpango-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpangocairo-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpangoft2-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpciaccess0 which isn't installed dpkg: warning: ignoring request to remove libpcre2-16-0 which isn't installed dpkg: warning: ignoring request to remove libpcre2-32-0 which isn't installed dpkg: warning: ignoring request to remove libpixman-1-0 which isn't installed dpkg: warning: ignoring request to remove libpng16-16t64 which isn't installed dpkg: warning: ignoring request to remove libproc2-0 which isn't installed dpkg: warning: ignoring request to remove libpsl5t64 which isn't installed dpkg: warning: ignoring request to remove libpython3-dev which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed dpkg: warning: ignoring request to remove libpython3.12-dev which isn't installed Purging configuration files for libpython3.12-minimal:amd64 (3.12.7-3) ... dpkg: warning: ignoring request to remove libpython3.12-stdlib which isn't installed dpkg: warning: ignoring request to remove libpython3.12t64 which isn't installed dpkg: warning: ignoring request to remove libqhull-r8.0 which isn't installed dpkg: warning: ignoring request to remove libqt5core5t64 which isn't installed dpkg: warning: ignoring request to remove libqt5dbus5t64 which isn't installed dpkg: warning: ignoring request to remove libqt5designer5 which isn't installed dpkg: warning: ignoring request to remove libqt5gui5t64 which isn't installed dpkg: warning: ignoring request to remove libqt5help5 which isn't installed dpkg: warning: ignoring request to remove libqt5network5t64 which isn't installed dpkg: warning: ignoring request to remove libqt5opengl5t64 which isn't installed dpkg: warning: ignoring request to remove libqt5printsupport5t64 which isn't installed dpkg: warning: ignoring request to remove libqt5sql5t64 which isn't installed dpkg: warning: ignoring request to remove libqt5test5t64 which isn't installed dpkg: warning: ignoring request to remove libqt5widgets5t64 which isn't installed dpkg: warning: ignoring request to remove libqt5xml5t64 which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed dpkg: warning: ignoring request to remove libraqm0 which isn't installed Purging configuration files for libreadline8t64:amd64 (8.2-5) ... dpkg: warning: ignoring request to remove librtmp1 which isn't installed dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed dpkg: warning: ignoring request to remove libsasl2-modules-db which isn't installed Purging configuration files for libsensors-config (1:3.6.0-10) ... dpkg: warning: ignoring request to remove libsensors5 which isn't installed dpkg: warning: ignoring request to remove libsharpyuv0 which isn't installed dpkg: warning: ignoring request to remove libsm6 which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libssh2-1t64 which isn't installed dpkg: warning: ignoring request to remove libssm2 which isn't installed dpkg: warning: ignoring request to remove libstdc++-14-dev which isn't installed dpkg: warning: ignoring request to remove libsystemd-shared which isn't installed dpkg: warning: ignoring request to remove libsz2 which isn't installed dpkg: warning: ignoring request to remove libtcl8.6 which isn't installed dpkg: warning: ignoring request to remove libthai-data which isn't installed dpkg: warning: ignoring request to remove libthai0 which isn't installed dpkg: warning: ignoring request to remove libtiff6 which isn't installed Purging configuration files for libtirpc-common (1.3.4+ds-1.3) ... Purging configuration files for libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... dpkg: warning: ignoring request to remove libtk8.6 which isn't installed dpkg: warning: ignoring request to remove libtsan2 which isn't installed dpkg: warning: ignoring request to remove libubsan1 which isn't installed dpkg: warning: ignoring request to remove libvulkan1 which isn't installed dpkg: warning: ignoring request to remove libwacom-common which isn't installed dpkg: warning: ignoring request to remove libwacom9 which isn't installed dpkg: warning: ignoring request to remove libwayland-client0 which isn't installed dpkg: warning: ignoring request to remove libwayland-cursor0 which isn't installed dpkg: warning: ignoring request to remove libwayland-egl1 which isn't installed dpkg: warning: ignoring request to remove libwayland-server0 which isn't installed dpkg: warning: ignoring request to remove libwebp7 which isn't installed dpkg: warning: ignoring request to remove libwebpdemux2 which isn't installed dpkg: warning: ignoring request to remove libwebpmux3 which isn't installed dpkg: warning: ignoring request to remove libwxbase3.2-1t64 which isn't installed dpkg: warning: ignoring request to remove libwxgtk-gl3.2-1t64 which isn't installed dpkg: warning: ignoring request to remove libwxgtk3.2-1t64 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 libx11-xcb1 which isn't installed dpkg: warning: ignoring request to remove libxau6 which isn't installed dpkg: warning: ignoring request to remove libxcb-dri2-0 which isn't installed dpkg: warning: ignoring request to remove libxcb-dri3-0 which isn't installed dpkg: warning: ignoring request to remove libxcb-glx0 which isn't installed dpkg: warning: ignoring request to remove libxcb-icccm4 which isn't installed dpkg: warning: ignoring request to remove libxcb-image0 which isn't installed dpkg: warning: ignoring request to remove libxcb-keysyms1 which isn't installed dpkg: warning: ignoring request to remove libxcb-present0 which isn't installed dpkg: warning: ignoring request to remove libxcb-randr0 which isn't installed dpkg: warning: ignoring request to remove libxcb-render-util0 which isn't installed dpkg: warning: ignoring request to remove libxcb-render0 which isn't installed dpkg: warning: ignoring request to remove libxcb-shape0 which isn't installed dpkg: warning: ignoring request to remove libxcb-shm0 which isn't installed dpkg: warning: ignoring request to remove libxcb-sync1 which isn't installed dpkg: warning: ignoring request to remove libxcb-util1 which isn't installed dpkg: warning: ignoring request to remove libxcb-xfixes0 which isn't installed dpkg: warning: ignoring request to remove libxcb-xinerama0 which isn't installed dpkg: warning: ignoring request to remove libxcb-xinput0 which isn't installed dpkg: warning: ignoring request to remove libxcb-xkb1 which isn't installed dpkg: warning: ignoring request to remove libxcb1 which isn't installed dpkg: warning: ignoring request to remove libxcomposite1 which isn't installed dpkg: warning: ignoring request to remove libxcursor1 which isn't installed dpkg: warning: ignoring request to remove libxdamage1 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 libxfixes3 which isn't installed dpkg: warning: ignoring request to remove libxft2 which isn't installed dpkg: warning: ignoring request to remove libxi6 which isn't installed dpkg: warning: ignoring request to remove libxinerama1 which isn't installed dpkg: warning: ignoring request to remove libxkbcommon-x11-0 which isn't installed dpkg: warning: ignoring request to remove libxkbcommon0 which isn't installed dpkg: warning: ignoring request to remove libxml2 which isn't installed dpkg: warning: ignoring request to remove libxrandr2 which isn't installed dpkg: warning: ignoring request to remove libxrender1 which isn't installed dpkg: warning: ignoring request to remove libxshmfence1 which isn't installed dpkg: warning: ignoring request to remove libxslt1.1 which isn't installed dpkg: warning: ignoring request to remove libxss1 which isn't installed dpkg: warning: ignoring request to remove libxtst6 which isn't installed dpkg: warning: ignoring request to remove libxxf86vm1 which isn't installed dpkg: warning: ignoring request to remove libz3-4 which isn't installed dpkg: warning: ignoring request to remove linux-libc-dev which isn't installed Purging configuration files for media-types (10.1.0) ... dpkg: warning: ignoring request to remove mesa-libgallium which isn't installed Purging configuration files for netbase (6.4) ... Purging configuration files for openssl (3.3.2-2) ... Purging configuration files for procps (2:4.0.4-6) ... dpkg: warning: ignoring request to remove pymol-data which isn't installed Purging configuration files for python-matplotlib-data (3.8.3-3) ... Purging configuration files for python3 (3.12.7-1) ... dpkg: warning: ignoring request to remove python3-appdirs which isn't installed dpkg: warning: ignoring request to remove python3-attr which isn't installed dpkg: warning: ignoring request to remove python3-autocommand which isn't installed dpkg: warning: ignoring request to remove python3-brotli which isn't installed dpkg: warning: ignoring request to remove python3-certifi which isn't installed dpkg: warning: ignoring request to remove python3-chardet which isn't installed dpkg: warning: ignoring request to remove python3-charset-normalizer which isn't installed dpkg: warning: ignoring request to remove python3-contourpy which isn't installed dpkg: warning: ignoring request to remove python3-cycler which isn't installed dpkg: warning: ignoring request to remove python3-dateutil which isn't installed dpkg: warning: ignoring request to remove python3-decorator which isn't installed dpkg: warning: ignoring request to remove python3-dev which isn't installed dpkg: warning: ignoring request to remove python3-flexcache which isn't installed dpkg: warning: ignoring request to remove python3-flexparser which isn't installed dpkg: warning: ignoring request to remove python3-fonttools which isn't installed dpkg: warning: ignoring request to remove python3-fs which isn't installed dpkg: warning: ignoring request to remove python3-h5py which isn't installed dpkg: warning: ignoring request to remove python3-h5py-serial which isn't installed dpkg: warning: ignoring request to remove python3-hdf5plugin which isn't installed dpkg: warning: ignoring request to remove python3-idna which isn't installed dpkg: warning: ignoring request to remove python3-inflect which isn't installed dpkg: warning: ignoring request to remove python3-jaraco.context which isn't installed dpkg: warning: ignoring request to remove python3-jaraco.functools which isn't installed dpkg: warning: ignoring request to remove python3-kiwisolver which isn't installed dpkg: warning: ignoring request to remove python3-legacy-cgi which isn't installed dpkg: warning: ignoring request to remove python3-lxml which isn't installed dpkg: warning: ignoring request to remove python3-lz4 which isn't installed dpkg: warning: ignoring request to remove python3-matplotlib which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-more-itertools which isn't installed dpkg: warning: ignoring request to remove python3-mpmath which isn't installed dpkg: warning: ignoring request to remove python3-mrcfile which isn't installed dpkg: warning: ignoring request to remove python3-natsort which isn't installed dpkg: warning: ignoring request to remove python3-numpy which isn't installed dpkg: warning: ignoring request to remove python3-nxmx which isn't installed dpkg: warning: ignoring request to remove python3-opengl which isn't installed dpkg: warning: ignoring request to remove python3-ordered-set which isn't installed dpkg: warning: ignoring request to remove python3-packaging which isn't installed dpkg: warning: ignoring request to remove python3-pil which isn't installed dpkg: warning: ignoring request to remove python3-pil.imagetk which isn't installed dpkg: warning: ignoring request to remove python3-pint which isn't installed dpkg: warning: ignoring request to remove python3-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python3-platformdirs which isn't installed dpkg: warning: ignoring request to remove python3-procrunner which isn't installed dpkg: warning: ignoring request to remove python3-pycbf which isn't installed dpkg: warning: ignoring request to remove python3-pymol which isn't installed dpkg: warning: ignoring request to remove python3-pyparsing which isn't installed dpkg: warning: ignoring request to remove python3-pyqt5 which isn't installed dpkg: warning: ignoring request to remove python3-pyqt5.qtopengl which isn't installed dpkg: warning: ignoring request to remove python3-pyqt5.sip which isn't installed dpkg: warning: ignoring request to remove python3-requests which isn't installed dpkg: warning: ignoring request to remove python3-scipy which isn't installed dpkg: warning: ignoring request to remove python3-six which isn't installed Purging configuration files for python3-sympy (1.13.3-1) ... dpkg: warning: ignoring request to remove python3-tk which isn't installed dpkg: warning: ignoring request to remove python3-tqdm which isn't installed dpkg: warning: ignoring request to remove python3-typeguard which isn't installed dpkg: warning: ignoring request to remove python3-typing-extensions which isn't installed dpkg: warning: ignoring request to remove python3-tz which isn't installed dpkg: warning: ignoring request to remove python3-ufolib2 which isn't installed dpkg: warning: ignoring request to remove python3-unicodedata2 which isn't installed dpkg: warning: ignoring request to remove python3-urllib3 which isn't installed dpkg: warning: ignoring request to remove python3-wxgtk4.0 which isn't installed dpkg: warning: ignoring request to remove python3.12 which isn't installed dpkg: warning: ignoring request to remove python3.12-dev which isn't installed Purging configuration files for python3.12-minimal (3.12.7-3) ... dpkg: warning: ignoring request to remove python3.12-tk which isn't installed dpkg: warning: ignoring request to remove python3.13-tk which isn't installed Purging configuration files for readline-common (8.2-5) ... dpkg: warning: ignoring request to remove rpcsvc-proto which isn't installed Purging configuration files for shared-mime-info (2.4-5+b1) ... dpkg: warning: ignoring request to remove sphinx-rtd-theme-common which isn't installed Purging configuration files for systemd (257~rc2-3) ... dpkg: warning: ignoring request to remove systemd-sysv which isn't installed dpkg: warning: ignoring request to remove tk8.6-blt2.5 which isn't installed dpkg: warning: ignoring request to remove unicode-data which isn't installed Purging configuration files for x11-common (1:7.7+23.1) ... dpkg: warning: ignoring request to remove xkb-data which isn't installed dpkg: warning: ignoring request to remove zlib1g-dev which isn't installed 2m7.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'dpkg', '--purge', 'adduser', 'adwaita-icon-theme', 'at-spi2-common', 'blt', 'ca-certificates', 'dbus', 'dbus-bin', 'dbus-daemon', 'dbus-session-bus-common', 'dbus-system-bus-common', 'dbus-user-session', 'dconf-gsettings-backend:amd64', 'dconf-service', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-font-awesome', 'fonts-lato', 'fonts-lyx', 'gtk-update-icon-cache', 'hicolor-icon-theme', 'libaec0:amd64', 'libann-cctbx-dev', 'libann-cctbx0', 'libantlr3c-3.4-0:amd64', 'libapparmor1:amd64', 'libasan8:amd64', 'libatk-bridge2.0-0t64:amd64', 'libatk1.0-0t64:amd64', 'libatomic1:amd64', 'libatspi2.0-0t64:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libblas3:amd64', 'libboost-numpy1.83.0', 'libboost-python-dev', 'libboost-python1.83-dev', 'libboost-python1.83.0', 'libboost-thread1.83.0:amd64', 'libboost-timer1.83.0:amd64', 'libboost1.83-dev:amd64', 'libbrotli1:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo-gobject2:amd64', 'libcairo2:amd64', 'libcbf1t64:amd64', 'libccp4-data', 'libccp4-dev:amd64', 'libccp4c0t64:amd64', 'libccp4f0t64:amd64', 'libcctbx-dev', 'libcctbx0', 'libcloudproviders0:amd64', 'libcolord2:amd64', 'libcrypt-dev:amd64', 'libcups2t64:amd64', 'libcurl3t64-gnutls:amd64', 'libcurl4t64:amd64', 'libdatrie1:amd64', 'libdbus-1-3:amd64', 'libdconf1:amd64', 'libdeflate0:amd64', 'libdouble-conversion3:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libedit2:amd64', 'libegl-mesa0:amd64', 'libegl1:amd64', 'libelf1t64:amd64', 'libepoxy0:amd64', 'libevdev2:amd64', 'libexpat1:amd64', 'libexpat1-dev:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgbm1:amd64', 'libgcc-14-dev:amd64', 'libgdk-pixbuf-2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgfortran5:amd64', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglapi-mesa:amd64', 'libglew2.2:amd64', 'libglib2.0-0t64:amd64', 'libglu1-mesa:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libgtk-3-0t64:amd64', 'libgtk-3-common', 'libgudev-1.0-0:amd64', 'libharfbuzz0b:amd64', 'libhdf5-103-1t64:amd64', 'libhdf5-hl-100t64:amd64', 'libhwasan0:amd64', 'libice6:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libinput-bin', 'libinput10:amd64', 'libitm1:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libjs-sphinxdoc', 'libjs-underscore', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libllvm19:amd64', 'liblsan0:amd64', 'liblzf1:amd64', 'libmd4c0:amd64', 'libmmdb2-0:amd64', 'libmtdev1t64:amd64', 'libncursesw6:amd64', 'libnetcdf19t64:amd64', 'libnghttp2-14:amd64', 'libnghttp3-9:amd64', 'libngtcp2-16:amd64', 'libngtcp2-crypto-gnutls8:amd64', 'libnotify4:amd64', 'libnsl2:amd64', 'libopengl0:amd64', 'libopenjp2-7:amd64', 'libpam-systemd:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpciaccess0:amd64', 'libpcre2-16-0:amd64', 'libpcre2-32-0:amd64', 'libpixman-1-0:amd64', 'libpng16-16t64:amd64', 'libproc2-0:amd64', 'libpsl5t64:amd64', 'libpython3-dev:amd64', 'libpython3-stdlib:amd64', 'libpython3.12-dev:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libpython3.12t64:amd64', 'libqhull-r8.0:amd64', 'libqt5core5t64:amd64', 'libqt5dbus5t64:amd64', 'libqt5designer5:amd64', 'libqt5gui5t64:amd64', 'libqt5help5:amd64', 'libqt5network5t64:amd64', 'libqt5opengl5t64:amd64', 'libqt5printsupport5t64:amd64', 'libqt5sql5t64:amd64', 'libqt5test5t64:amd64', 'libqt5widgets5t64:amd64', 'libqt5xml5t64:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libsqlite3-0:amd64', 'libssh2-1t64:amd64', 'libssm2:amd64', 'libstdc++-14-dev:amd64', 'libsystemd-shared:amd64', 'libsz2:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'libtk8.6:amd64', 'libtsan2:amd64', 'libubsan1:amd64', 'libvulkan1:amd64', 'libwacom-common', 'libwacom9:amd64', 'libwayland-client0:amd64', 'libwayland-cursor0:amd64', 'libwayland-egl1:amd64', 'libwayland-server0:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libwxbase3.2-1t64:amd64', 'libwxgtk-gl3.2-1t64:amd64', 'libwxgtk3.2-1t64:amd64', 'libx11-6:amd64', 'libx11-data', 'libx11-xcb1:amd64', 'libxau6:amd64', 'libxcb-dri2-0:amd64', 'libxcb-dri3-0:amd64', 'libxcb-glx0:amd64', 'libxcb-icccm4:amd64', 'libxcb-image0:amd64', 'libxcb-keysyms1:amd64', 'libxcb-present0:amd64', 'libxcb-randr0:amd64', 'libxcb-render-util0:amd64', 'libxcb-render0:amd64', 'libxcb-shape0:amd64', 'libxcb-shm0:amd64', 'libxcb-sync1:amd64', 'libxcb-util1:amd64', 'libxcb-xfixes0:amd64', 'libxcb-xinerama0:amd64', 'libxcb-xinput0:amd64', 'libxcb-xkb1:amd64', 'libxcb1:amd64', 'libxcomposite1:amd64', 'libxcursor1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxinerama1:amd64', 'libxkbcommon-x11-0:amd64', 'libxkbcommon0:amd64', 'libxml2:amd64', 'libxrandr2:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libz3-4:amd64', 'linux-libc-dev', 'media-types', 'mesa-libgallium:amd64', 'netbase', 'openssl', 'procps', 'pymol-data', 'python-matplotlib-data', 'python3', 'python3-appdirs', 'python3-attr', 'python3-autocommand', 'python3-brotli', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-dev', 'python3-flexcache', 'python3-flexparser', 'python3-fonttools', 'python3-fs', 'python3-h5py', 'python3-h5py-serial', 'python3-hdf5plugin', 'python3-idna', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-kiwisolver', 'python3-legacy-cgi', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-minimal', 'python3-more-itertools', 'python3-mpmath', 'python3-mrcfile', 'python3-natsort', 'python3-numpy', 'python3-nxmx', 'python3-opengl', 'python3-ordered-set', 'python3-packaging', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pint', 'python3-pkg-resources', 'python3-platformdirs', 'python3-procrunner', 'python3-pycbf', 'python3-pymol', 'python3-pyparsing', 'python3-pyqt5', 'python3-pyqt5.qtopengl', 'python3-pyqt5.sip', 'python3-requests', 'python3-scipy', 'python3-six', 'python3-sympy', 'python3-tk:amd64', 'python3-tqdm', 'python3-typeguard', 'python3-typing-extensions', 'python3-tz', 'python3-ufolib2', 'python3-unicodedata2', 'python3-urllib3', 'python3-wxgtk4.0', 'python3.12', 'python3.12-dev', 'python3.12-minimal', 'python3.12-tk', 'python3.13-tk', 'readline-common', 'rpcsvc-proto', 'shared-mime-info', 'sphinx-rtd-theme-common', 'systemd', 'systemd-sysv', 'tk8.6-blt2.5', 'unicode-data', 'x11-common', 'xkb-data', 'zlib1g-dev:amd64'] 2m7.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'dpkg', '--purge', 'python3-cctbx'] 2m7.4s DUMP: dpkg: warning: ignoring request to remove python3-cctbx which isn't installed 2m7.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'dpkg', '--purge', 'python3-cctbx'] 2m7.4s INFO: Running scripts post_purge 2m7.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/post_purge_exceptions'] 2m7.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/post_purge_exceptions'] 2m7.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'dpkg', '--purge', '--pending'] 2m7.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'dpkg', '--purge', '--pending'] 2m7.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'dpkg', '--remove', '--pending'] 2m7.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'dpkg', '--remove', '--pending'] 2m7.4s INFO: Running scripts post_test 2m7.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/post_test_exceptions'] 2m7.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'tmp/scripts/post_test_exceptions'] 2m7.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgxjjief5'] 2m7.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpgxjjief5'] 2m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'dpkg-divert', '--list'] 2m7.7s DUMP: diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64 local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64 local diversion of /home to /home.distrib diversion of /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6 diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64 diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64 diversion of /libx32 to /.libx32.usr-is-merged by base-files local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /lib32 to /.lib32.usr-is-merged by base-files diversion of /libo32 to /.libo32.usr-is-merged by base-files 2m7.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'dpkg-divert', '--list'] 2m7.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'apt-get', 'clean'] 2m7.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpgxjjief5', 'apt-get', 'clean'] 2m7.8s DEBUG: Recording chroot state 2m8.1s INFO: Warning: Package purging left files on system: /etc/default/locale -> ../locale.conf not owned /etc/fonts/ owned by: fontconfig-config, fonts-dejavu-core, fonts-dejavu-mono /etc/fonts/conf.d/ owned by: fontconfig-config, fonts-dejavu-core, fonts-dejavu-mono /etc/fonts/conf.d/70-no-bitmaps-except-emoji.conf -> /usr/share/fontconfig/conf.avail/70-no-bitmaps-except-emoji.conf not owned /etc/vconsole.conf -> default/keyboard not owned /root/.ssh/ not owned /var/cache/private/ not owned /var/lib/private/ not owned /var/log/private/ not owned 2m8.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpgxjjief5/dev/shm'] 2m8.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpgxjjief5/dev/shm'] 2m8.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpgxjjief5/dev/console'] 2m8.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpgxjjief5/dev/console'] 2m8.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpgxjjief5/dev/ptmx'] 2m8.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpgxjjief5/dev/ptmx'] 2m8.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpgxjjief5/dev/pts'] 2m8.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpgxjjief5/dev/pts'] 2m8.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpgxjjief5/proc'] 2m8.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpgxjjief5/proc'] 2m8.3s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpgxjjief5'] 2m8.4s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpgxjjief5'] 2m8.4s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpgxjjief5 2m8.4s INFO: PASS: Upgrading between Debian distributions. 2m8.4s INFO: PASS: All tests. 2m8.4s INFO: piuparts run ends. ret=0 End: 2024-11-20 22:39:10 GMT