Start: 2024-03-02 04:40:43 GMT [testing] Package: python3-cctbx Source: cctbx (2022.9+ds2+~3.11.2+ds1-6) Version: 2022.9+ds2+~3.11.2+ds1-6+b1 Installed-Size: 276324 Maintainer: Debian Science Maintainers Architecture: amd64 Depends: ca-certificates, libcctbx-dev (= 2022.9+ds2+~3.11.2+ds1-6+b1), libcctbx0 (= 2022.9+ds2+~3.11.2+ds1-6+b1), python3-pycbf (>= 0.9.7+dfsg1-2~), python3 (<< 3.12), python3 (>= 3.11~), python3-matplotlib, python3-mrcfile, python3-numpy (>= 1:1.22.0), python3-numpy-abi9, 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-numpy1.74.0 (>= 1.74.0), libboost-numpy1.74.0-py311, libboost-python1.74.0 (>= 1.74.0), libboost-python1.74.0-py311, libboost-thread1.74.0 (>= 1.74.0), libc6 (>= 2.34), libcbf1 (>= 0.9.7+dfsg1-2~), libccp4c0 (>= 8.0.0), libgcc-s1 (>= 4.0), libgl1, libglu1-mesa | libglu1, libhdf5-103-1, libmmdb2-0 (>= 2.0.22), libssm2 (>= 1.4.0), libstdc++6 (>= 11) 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_2022.9+ds2+~3.11.2+ds1-6+b1_amd64.deb Size: 35865584 MD5sum: f27282ff2dc5a37c62e04b72d285cfca SHA256: 6e3c75961b5a43fe52ebe6bc79ca1a73844a0beb042358155c75b3fd198188ee [sid] Package: python3-cctbx Source: cctbx Version: 2023.12+ds2+~3.17.0+ds1-4 Installed-Size: 501959 Maintainer: Debian Science Maintainers Architecture: amd64 Depends: ca-certificates, libcctbx-dev (= 2023.12+ds2+~3.17.0+ds1-4), libcctbx0 (= 2023.12+ds2+~3.17.0+ds1-4), python3-pycbf (>= 0.9.7+dfsg1-2~), python3 (<< 3.13), python3 (>= 3.11~), python3-h5py (>= 3), python3-matplotlib, python3-mrcfile, python3-numpy (>= 1:1.22.0), python3-numpy-abi9, python3-nxmx, python3-orderedset, 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-py311, libboost-numpy1.83.0-py312, libboost-python1.83.0 (>= 1.83.0), libboost-python1.83.0-py311, libboost-python1.83.0-py312, libboost-thread1.83.0 (>= 1.83.0), libc6 (>= 2.34), libcbf1t64 (>= 0.9.7+dfsg1-2~), libccp4c0 (>= 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 (>= 13.1) 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_2023.12+ds2+~3.17.0+ds1-4_amd64.deb Size: 50134860 MD5sum: 21abbf20e7beff55eaa010e9ec4923ae SHA256: c7f518562c87755b767b6de113da1cefbeb159cc5a0af722debc75e8e4674850 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt 'python3-cctbx=2023.12+ds2+~3.17.0+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 1.3.1~202401311821~1.3-2-g28295102 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt 'python3-cctbx=2023.12+ds2+~3.17.0+ds1-4' 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmprx0kbrwv 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmprx0kbrwv 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m0.5s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv/proc'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv/proc'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv/dev/pts'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv/dev/pts'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv/dev/ptmx'] 0m0.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv/dev/ptmx'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv/dev/console'] 0m0.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/1', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv/dev/console'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv/dev/shm'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv/dev/shm'] 0m0.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m0.5s DEBUG: Created policy-rc.d and chmodded it. 0m0.5s DEBUG: Created resolv.conf. 0m0.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmprx0kbrwv/tmp/scripts/ 0m0.5s INFO: Running scripts post_chroot_unpack 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'apt-get', 'update'] 0m1.6s DUMP: Hit:1 http://deb.debian.org/debian bookworm InRelease Reading package lists... 0m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'apt-get', 'update'] 0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'apt-get', '-yf', 'dist-upgrade'] 0m2.2s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'apt-get', '-yf', 'dist-upgrade'] 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.6s DUMP: 0942a352c5bc637c4fdbc12bf31cd5ba - 0m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.6s INFO: Running scripts post_setup 0m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/post_setup_dummy_users'] 0m3.5s 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 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/post_setup_dummy_users'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/post_setup_forbid_home'] 0m3.5s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/post_setup_forbid_home'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.6s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' dpkg-divert: warning: diverting file '/bin/sync' from an Essential package with rename is dangerous, use --no-rename '/bin/sync' -> 'true' 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/post_setup_minimize'] 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/post_setup_minimize'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/post_setup_zz_backports'] 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/post_setup_zz_backports'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.6s DUMP: install ok installed adduser adduser 3.134 install ok installed apt apt 2.6.1 install ok installed base-files base-files 12.4+deb12u5 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b2 install ok installed bsdutils bsdutils 1:2.38.1-5+b1 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.12-2 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.3+deb12u1 install ok installed debianutils debianutils 5.7-0.5~deb12u1 install ok installed diffutils diffutils 1:3.8-4 install ok installed dpkg dpkg 1.21.22 install ok installed e2fsprogs e2fsprogs 1.47.0-2 install ok installed findutils findutils 4.9.0-4 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-14 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.8-5 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu1 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.6.1 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.0.9-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.9-1 install ok installed libblkid1:amd64 libblkid1 2.38.1-5+b1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-9+deb12u4 install ok installed libc6:amd64 libc6 2.36-9+deb12u4 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3 install ok installed libcap2:amd64 libcap2 1:2.66-4 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.33-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.270 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-14 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-3 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.9-2+deb12u2 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.1-0.2 install ok installed libmd0:amd64 libmd0 1.0.4-2 install ok installed libmount1:amd64 libmount1 2.38.1-5+b1 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-6+deb12u1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-6+deb12u1 install ok installed libpam-runtime libpam-runtime 1.5.2-6+deb12u1 install ok installed libpam0g:amd64 libpam0g 1.5.2-6+deb12u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-1 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+b3 install ok installed libselinux1:amd64 libselinux1 3.4-1+b6 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b5 install ok installed libsepol2:amd64 libsepol2 3.4-2.1 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-5+b1 install ok installed libss2:amd64 libss2 1.47.0-2 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-14 install ok installed libsystemd0:amd64 libsystemd0 252.22-1~deb12u1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.4-4 install ok installed libudev1:amd64 libudev1 252.22-1~deb12u1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+b1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.4+dfsg2-5 install ok installed login login 1:4.13+dfsg1-1+b1 install ok installed logsave logsave 1.47.0-2 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mount mount 2.38.1-5+b1 install ok installed ncurses-base ncurses-base 6.4-4 install ok installed ncurses-bin ncurses-bin 6.4-4 install ok installed passwd passwd 1:4.13+dfsg1-1+b1 install ok installed perl-base perl-base 5.36.0-7+deb12u1 install ok installed sed sed 4.9-1 install ok installed sysvinit-utils sysvinit-utils 3.06-4 install ok installed tar tar 1.34+dfsg-1.2+deb12u1 install ok installed tzdata tzdata 2024a-0+deb12u1 install ok installed usr-is-merged usr-is-merged 37~deb12u1 install ok installed util-linux util-linux 2.38.1-5+b1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+b1 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.6s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m3.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv'] 0m4.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv'] 0m4.1s INFO: Running scripts is_testable 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/is_testable_uninstallable'] 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/is_testable_uninstallable'] 0m4.1s INFO: Running scripts pre_test 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_test_exceptions'] 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_test_exceptions'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_test_root_password'] 0m4.2s DUMP: New password: Retype new password: passwd: password updated successfully 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_test_root_password'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'apt-cache', 'show', '--no-all-versions', 'python3-cctbx'] 0m4.4s DUMP: Package: python3-cctbx Source: cctbx (2022.9+ds2+~3.11.2+ds1-6) Version: 2022.9+ds2+~3.11.2+ds1-6+b1 Installed-Size: 276324 Maintainer: Debian Science Maintainers Architecture: amd64 Depends: ca-certificates, libcctbx-dev (= 2022.9+ds2+~3.11.2+ds1-6+b1), libcctbx0 (= 2022.9+ds2+~3.11.2+ds1-6+b1), python3-pycbf (>= 0.9.7+dfsg1-2~), python3 (<< 3.12), python3 (>= 3.11~), python3-matplotlib, python3-mrcfile, python3-numpy (>= 1:1.22.0), python3-numpy-abi9, 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-numpy1.74.0 (>= 1.74.0), libboost-numpy1.74.0-py311, libboost-python1.74.0 (>= 1.74.0), libboost-python1.74.0-py311, libboost-thread1.74.0 (>= 1.74.0), libc6 (>= 2.34), libcbf1 (>= 0.9.7+dfsg1-2~), libccp4c0 (>= 8.0.0), libgcc-s1 (>= 4.0), libgl1, libglu1-mesa | libglu1, libhdf5-103-1, libmmdb2-0 (>= 2.0.22), libssm2 (>= 1.4.0), libstdc++6 (>= 11) 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_2022.9+ds2+~3.11.2+ds1-6+b1_amd64.deb Size: 35865584 MD5sum: f27282ff2dc5a37c62e04b72d285cfca SHA256: 6e3c75961b5a43fe52ebe6bc79ca1a73844a0beb042358155c75b3fd198188ee 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'apt-cache', 'show', '--no-all-versions', 'python3-cctbx'] 0m4.4s INFO: apt-cache knows about the following packages: python3-cctbx 0m4.4s INFO: Running scripts pre_install 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_install_database-server'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_install_database-server'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_install_exceptions'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_install_exceptions'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_install_extras'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_install_extras'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'apt-cache', 'policy'] 0m4.5s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.5,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'apt-cache', 'policy'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'apt-cache', 'policy', 'python3-cctbx'] 0m4.6s DUMP: python3-cctbx: Installed: (none) Candidate: 2022.9+ds2+~3.11.2+ds1-6+b1 Version table: 2022.9+ds2+~3.11.2+ds1-6+b1 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'apt-cache', 'policy', 'python3-cctbx'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'apt-get', '-y', 'install', 'python3-cctbx'] 1m45.7s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: adwaita-icon-theme at-spi2-common binutils binutils-common binutils-x86-64-linux-gnu blt ca-certificates cpp cpp-12 dbus dbus-bin dbus-daemon dbus-session-bus-common dbus-system-bus-common dbus-user-session dconf-gsettings-backend dconf-service dmsetup fontconfig fontconfig-config fonts-dejavu-core fonts-font-awesome fonts-lato fonts-lyx g++ g++-12 gcc gcc-12 gtk-update-icon-cache hicolor-icon-theme libaec0 libann-cctbx-dev libann-cctbx0 libantlr3c-3.4-0 libapparmor1 libargon2-1 libasan8 libatk-bridge2.0-0 libatk1.0-0 libatomic1 libatspi2.0-0 libavahi-client3 libavahi-common-data libavahi-common3 libbinutils libblas3 libboost-dev libboost-numpy1.74.0 libboost-python-dev libboost-python1.74-dev libboost-python1.74.0 libboost-thread1.74.0 libboost1.74-dev libbrotli1 libbsd0 libc-dev-bin libc6-dev libcairo-gobject2 libcairo2 libcbf1 libcc1-0 libccp4-data libccp4-dev libccp4c0 libccp4f0 libcctbx-dev libcctbx0 libcolord2 libcrypt-dev libcryptsetup12 libctf-nobfd0 libctf0 libcups2 libcurl3-gnutls libcurl4 libdatrie1 libdbus-1-3 libdconf1 libdeflate0 libdevmapper1.02.1 libdouble-conversion3 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libegl-mesa0 libegl1 libelf1 libepoxy0 libevdev2 libexpat1 libexpat1-dev libfdisk1 libfontconfig1 libfreetype6 libfribidi0 libgbm1 libgcc-12-dev libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgfortran5 libgl1 libgl1-mesa-dri libgl1-mesa-glx libglapi-mesa libglew2.2 libglib2.0-0 libglu1-mesa libglvnd0 libglx-mesa0 libglx0 libgomp1 libgprofng0 libgraphite2-3 libgssapi-krb5-2 libgtk-3-0 libgtk-3-common libgudev-1.0-0 libharfbuzz0b libhdf5-103-1 libhdf5-hl-100 libice6 libicu72 libimagequant0 libinput-bin libinput10 libip4tc2 libisl23 libitm1 libjansson4 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libjson-c5 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap-2.5-0 liblerc4 libllvm15 liblsan0 libmd4c0 libmmdb2-0 libmpc3 libmpfr6 libmtdev1 libncursesw6 libnetcdf19 libnghttp2-14 libnotify4 libnsl-dev libnsl2 libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread 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 libpng16-16 libproc2-0 libpsl5 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.11 libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib libqhull-r8.0 libqt5core5a libqt5dbus5 libqt5designer5 libqt5gui5 libqt5help5 libqt5network5 libqt5opengl5 libqt5printsupport5 libqt5sql5 libqt5test5 libqt5widgets5 libqt5xml5 libquadmath0 libraqm0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libsm6 libsqlite3-0 libssh2-1 libssl3 libssm2 libstdc++-12-dev libsystemd-shared libsz2 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc-dev libtirpc3 libtk8.6 libtsan2 libubsan1 libwacom-common libwacom9 libwayland-client0 libwayland-cursor0 libwayland-egl1 libwayland-server0 libwebp7 libwebpdemux2 libwebpmux3 libwxbase3.2-1 libwxgtk-gl3.2-1 libwxgtk3.2-1 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 libxsimd-dev libxslt1.1 libxss1 libxtst6 libxxf86vm1 libz3-4 linux-libc-dev media-types openssl procps pymol-data python-matplotlib-data python3 python3-all python3-all-dev python3-appdirs python3-attr python3-beniget python3-brotli python3-certifi python3-chardet python3-charset-normalizer python3-contourpy python3-cycler python3-dateutil python3-decorator python3-dev python3-distutils python3-fonttools python3-fs python3-gast python3-idna python3-kiwisolver python3-lib2to3 python3-lxml python3-lz4 python3-matplotlib python3-minimal python3-mpmath python3-mrcfile python3-numpy python3-opengl python3-packaging python3-pil python3-pil.imagetk python3-pint python3-pkg-resources python3-ply python3-procrunner python3-pycbf python3-pymol python3-pyparsing python3-pyqt5 python3-pyqt5.qtopengl python3-pyqt5.sip python3-pythran python3-requests python3-scipy python3-six python3-sympy python3-tk python3-tqdm python3-tz python3-ufolib2 python3-urllib3 python3-wxgtk4.0 python3.11 python3.11-dev python3.11-minimal 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: binutils-doc blt-demo cpp-doc gcc-12-locales cpp-12-doc g++-multilib g++-12-multilib gcc-12-doc gcc-multilib make manpages-dev autoconf automake libtool flex bison gdb gcc-doc gcc-12-multilib libboost-doc libboost1.74-doc gccxml libboost-atomic1.74-dev libboost-chrono1.74-dev libboost-container1.74-dev libboost-context1.74-dev libboost-contract1.74-dev libboost-coroutine1.74-dev libboost-date-time1.74-dev libboost-exception1.74-dev libboost-fiber1.74-dev libboost-filesystem1.74-dev libboost-graph1.74-dev libboost-graph-parallel1.74-dev libboost-iostreams1.74-dev libboost-locale1.74-dev libboost-log1.74-dev libboost-math1.74-dev libboost-mpi1.74-dev libboost-mpi-python1.74-dev libboost-numpy1.74-dev libboost-program-options1.74-dev libboost-random1.74-dev libboost-regex1.74-dev libboost-serialization1.74-dev libboost-stacktrace1.74-dev libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev glibc-doc colord cups-common glew-utils low-memory-monitor krb5-doc krb5-user gvfs libjs-jquery-ui-docs liblcms2-utils notification-daemon pciutils qgnomeplatform-qt5 qt5-image-formats-plugins lm-sensors libstdc++-12-doc tcl8.6 tk8.6 libwacom-bin libxsimd-doc python3-doc python3-venv python-attr-doc python-cycler-doc python-lxml-doc cm-super-minimal dvipng ffmpeg fonts-staypuft ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common python3-cairocffi python3-gi python3-gi-cairo python3-gobject python3-sip python3-tornado texlive-extra-utils texlive-latex-extra python-mpmath-doc python3-gmpy2 gfortran python3-pytest libgle3 python-pil-doc python3-setuptools python-ply-doc 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 python3.11-venv python3.11-doc binfmt-support readline-doc systemd-container systemd-homed systemd-userdbd systemd-boot systemd-resolved libfido2-1 libqrencode4 libtss2-esys-3.0.2-0 libtss2-mu0 libtss2-rc0 polkitd | policykit-1 Recommended packages: librsvg2-common at-spi2-core manpages manpages-dev libc-devtools 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 psmisc python3-bs4 python3-html5lib libglut-dev python3-olefile isympy-common systemd-timesyncd | time-daemon libnss-systemd The following NEW packages will be installed: adwaita-icon-theme at-spi2-common binutils binutils-common binutils-x86-64-linux-gnu blt ca-certificates cpp cpp-12 dbus dbus-bin dbus-daemon dbus-session-bus-common dbus-system-bus-common dbus-user-session dconf-gsettings-backend dconf-service dmsetup fontconfig fontconfig-config fonts-dejavu-core fonts-font-awesome fonts-lato fonts-lyx g++ g++-12 gcc gcc-12 gtk-update-icon-cache hicolor-icon-theme libaec0 libann-cctbx-dev libann-cctbx0 libantlr3c-3.4-0 libapparmor1 libargon2-1 libasan8 libatk-bridge2.0-0 libatk1.0-0 libatomic1 libatspi2.0-0 libavahi-client3 libavahi-common-data libavahi-common3 libbinutils libblas3 libboost-dev libboost-numpy1.74.0 libboost-python-dev libboost-python1.74-dev libboost-python1.74.0 libboost-thread1.74.0 libboost1.74-dev libbrotli1 libbsd0 libc-dev-bin libc6-dev libcairo-gobject2 libcairo2 libcbf1 libcc1-0 libccp4-data libccp4-dev libccp4c0 libccp4f0 libcctbx-dev libcctbx0 libcolord2 libcrypt-dev libcryptsetup12 libctf-nobfd0 libctf0 libcups2 libcurl3-gnutls libcurl4 libdatrie1 libdbus-1-3 libdconf1 libdeflate0 libdevmapper1.02.1 libdouble-conversion3 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libegl-mesa0 libegl1 libelf1 libepoxy0 libevdev2 libexpat1 libexpat1-dev libfdisk1 libfontconfig1 libfreetype6 libfribidi0 libgbm1 libgcc-12-dev libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgfortran5 libgl1 libgl1-mesa-dri libgl1-mesa-glx libglapi-mesa libglew2.2 libglib2.0-0 libglu1-mesa libglvnd0 libglx-mesa0 libglx0 libgomp1 libgprofng0 libgraphite2-3 libgssapi-krb5-2 libgtk-3-0 libgtk-3-common libgudev-1.0-0 libharfbuzz0b libhdf5-103-1 libhdf5-hl-100 libice6 libicu72 libimagequant0 libinput-bin libinput10 libip4tc2 libisl23 libitm1 libjansson4 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libjson-c5 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap-2.5-0 liblerc4 libllvm15 liblsan0 libmd4c0 libmmdb2-0 libmpc3 libmpfr6 libmtdev1 libncursesw6 libnetcdf19 libnghttp2-14 libnotify4 libnsl-dev libnsl2 libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread 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 libpng16-16 libproc2-0 libpsl5 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.11 libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib libqhull-r8.0 libqt5core5a libqt5dbus5 libqt5designer5 libqt5gui5 libqt5help5 libqt5network5 libqt5opengl5 libqt5printsupport5 libqt5sql5 libqt5test5 libqt5widgets5 libqt5xml5 libquadmath0 libraqm0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libsm6 libsqlite3-0 libssh2-1 libssl3 libssm2 libstdc++-12-dev libsystemd-shared libsz2 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc-dev libtirpc3 libtk8.6 libtsan2 libubsan1 libwacom-common libwacom9 libwayland-client0 libwayland-cursor0 libwayland-egl1 libwayland-server0 libwebp7 libwebpdemux2 libwebpmux3 libwxbase3.2-1 libwxgtk-gl3.2-1 libwxgtk3.2-1 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 libxsimd-dev libxslt1.1 libxss1 libxtst6 libxxf86vm1 libz3-4 linux-libc-dev media-types openssl procps pymol-data python-matplotlib-data python3 python3-all python3-all-dev python3-appdirs python3-attr python3-beniget python3-brotli python3-cctbx python3-certifi python3-chardet python3-charset-normalizer python3-contourpy python3-cycler python3-dateutil python3-decorator python3-dev python3-distutils python3-fonttools python3-fs python3-gast python3-idna python3-kiwisolver python3-lib2to3 python3-lxml python3-lz4 python3-matplotlib python3-minimal python3-mpmath python3-mrcfile python3-numpy python3-opengl python3-packaging python3-pil python3-pil.imagetk python3-pint python3-pkg-resources python3-ply python3-procrunner python3-pycbf python3-pymol python3-pyparsing python3-pyqt5 python3-pyqt5.qtopengl python3-pyqt5.sip python3-pythran python3-requests python3-scipy python3-six python3-sympy python3-tk python3-tqdm python3-tz python3-ufolib2 python3-urllib3 python3-wxgtk4.0 python3.11 python3.11-dev python3.11-minimal 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, 357 newly installed, 0 to remove and 0 not upgraded. Need to get 329 MB of archives. After this operation, 1669 MB of additional disk space will be used. 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bookworm/main amd64 libsystemd-shared amd64 252.22-1~deb12u1 [1691 kB] Get:12 http://deb.debian.org/debian bookworm/main amd64 systemd amd64 252.22-1~deb12u1 [3032 kB] Get:13 http://deb.debian.org/debian bookworm/main amd64 systemd-sysv amd64 252.22-1~deb12u1 [41.9 kB] Get:14 http://deb.debian.org/debian bookworm/main amd64 libdbus-1-3 amd64 1.14.10-1~deb12u1 [201 kB] Get:15 http://deb.debian.org/debian bookworm/main amd64 dbus-bin amd64 1.14.10-1~deb12u1 [105 kB] Get:16 http://deb.debian.org/debian bookworm/main amd64 dbus-session-bus-common all 1.14.10-1~deb12u1 [78.2 kB] Get:17 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get:18 http://deb.debian.org/debian bookworm/main amd64 dbus-daemon amd64 1.14.10-1~deb12u1 [184 kB] Get:19 http://deb.debian.org/debian bookworm/main amd64 dbus-system-bus-common all 1.14.10-1~deb12u1 [79.3 kB] Get:20 http://deb.debian.org/debian bookworm/main amd64 dbus amd64 1.14.10-1~deb12u1 [97.4 kB] Get:21 http://deb.debian.org/debian bookworm/main amd64 fonts-lato all 2.0-2.1 [2696 kB] Get:22 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get:23 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get:24 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get:25 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get:26 http://deb.debian.org/debian bookworm/main amd64 libncursesw6 amd64 6.4-4 [134 kB] Get:27 http://deb.debian.org/debian bookworm/main amd64 libkrb5support0 amd64 1.20.1-2+deb12u1 [32.4 kB] Get:28 http://deb.debian.org/debian bookworm/main amd64 libk5crypto3 amd64 1.20.1-2+deb12u1 [78.9 kB] Get:29 http://deb.debian.org/debian bookworm/main amd64 libkeyutils1 amd64 1.6.3-2 [8808 B] Get:30 http://deb.debian.org/debian bookworm/main amd64 libkrb5-3 amd64 1.20.1-2+deb12u1 [332 kB] Get:31 http://deb.debian.org/debian bookworm/main amd64 libgssapi-krb5-2 amd64 1.20.1-2+deb12u1 [134 kB] Get:32 http://deb.debian.org/debian bookworm/main amd64 libtirpc-common all 1.3.3+ds-1 [14.0 kB] Get:33 http://deb.debian.org/debian bookworm/main amd64 libtirpc3 amd64 1.3.3+ds-1 [85.2 kB] Get:34 http://deb.debian.org/debian bookworm/main amd64 libnsl2 amd64 1.3.0-2 [39.5 kB] Get:35 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get:36 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get:37 http://deb.debian.org/debian bookworm/main amd64 libsqlite3-0 amd64 3.40.1-2 [837 kB] Get:38 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get:39 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get:40 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get:41 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get:42 http://deb.debian.org/debian bookworm/main amd64 libproc2-0 amd64 2:4.0.2-3 [62.8 kB] Get:43 http://deb.debian.org/debian bookworm/main amd64 procps amd64 2:4.0.2-3 [709 kB] Get:44 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.11-1~deb12u2 [1419 kB] Get:45 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB] Get:46 http://deb.debian.org/debian bookworm/main amd64 libpam-systemd amd64 252.22-1~deb12u1 [225 kB] Get:47 http://deb.debian.org/debian bookworm/main amd64 hicolor-icon-theme all 0.17-2 [11.4 kB] Get:48 http://deb.debian.org/debian bookworm/main amd64 libgdk-pixbuf2.0-common all 2.42.10+dfsg-1 [306 kB] Get:49 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2 [1398 kB] Get:50 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get:51 http://deb.debian.org/debian bookworm/main amd64 libxml2 amd64 2.9.14+dfsg-1.3~deb12u1 [687 kB] Get:52 http://deb.debian.org/debian bookworm/main amd64 shared-mime-info amd64 2.2-1 [729 kB] Get:53 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB] Get:54 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB] Get:55 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get:56 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB] Get:57 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB] Get:58 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.2+deb12u1 [286 kB] Get:59 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-6+deb12u1 [316 kB] Get:60 http://deb.debian.org/debian bookworm/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.10+dfsg-1+b1 [139 kB] Get:61 http://deb.debian.org/debian bookworm/main amd64 gtk-update-icon-cache amd64 3.24.38-2~deb12u1 [44.0 kB] Get:62 http://deb.debian.org/debian bookworm/main amd64 adwaita-icon-theme all 43-1 [5124 kB] Get:63 http://deb.debian.org/debian bookworm/main amd64 at-spi2-common all 2.46.0-5 [162 kB] Get:64 http://deb.debian.org/debian bookworm/main amd64 binutils-common amd64 2.40-2 [2487 kB] Get:65 http://deb.debian.org/debian bookworm/main amd64 libbinutils amd64 2.40-2 [572 kB] Get:66 http://deb.debian.org/debian bookworm/main amd64 libctf-nobfd0 amd64 2.40-2 [153 kB] Get:67 http://deb.debian.org/debian bookworm/main amd64 libctf0 amd64 2.40-2 [89.8 kB] Get:68 http://deb.debian.org/debian bookworm/main amd64 libgprofng0 amd64 2.40-2 [812 kB] Get:69 http://deb.debian.org/debian bookworm/main amd64 libjansson4 amd64 2.14-2 [40.8 kB] Get:70 http://deb.debian.org/debian bookworm/main amd64 binutils-x86-64-linux-gnu amd64 2.40-2 [2246 kB] Get:71 http://deb.debian.org/debian bookworm/main amd64 binutils amd64 2.40-2 [65.0 kB] Get:72 http://deb.debian.org/debian bookworm/main amd64 libtcl8.6 amd64 8.6.13+dfsg-2 [1035 kB] Get:73 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get:74 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-5 [399 kB] Get:75 http://deb.debian.org/debian bookworm/main amd64 fonts-dejavu-core all 2.37-6 [1068 kB] Get:76 http://deb.debian.org/debian bookworm/main amd64 fontconfig-config amd64 2.14.1-4 [315 kB] Get:77 http://deb.debian.org/debian bookworm/main amd64 libfontconfig1 amd64 2.14.1-4 [386 kB] Get:78 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get:79 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get:80 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:81 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get:82 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2+deb12u2 [292 kB] Get:83 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2+deb12u2 [760 kB] Get:84 http://deb.debian.org/debian bookworm/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get:85 http://deb.debian.org/debian bookworm/main amd64 libxft2 amd64 2.3.6-1 [61.8 kB] Get:86 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get:87 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB] Get:88 http://deb.debian.org/debian bookworm/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get:89 http://deb.debian.org/debian bookworm/main amd64 libtk8.6 amd64 8.6.13-2 [781 kB] Get:90 http://deb.debian.org/debian bookworm/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-4.1 [593 kB] Get:91 http://deb.debian.org/debian bookworm/main amd64 blt amd64 2.5.3+dfsg-4.1 [14.9 kB] Get:92 http://deb.debian.org/debian bookworm/main amd64 libisl23 amd64 0.25-1.1 [683 kB] Get:93 http://deb.debian.org/debian bookworm/main amd64 libmpfr6 amd64 4.2.0-1 [701 kB] Get:94 http://deb.debian.org/debian bookworm/main amd64 libmpc3 amd64 1.3.1-1 [51.5 kB] Get:95 http://deb.debian.org/debian bookworm/main amd64 cpp-12 amd64 12.2.0-14 [9764 kB] Get:96 http://deb.debian.org/debian bookworm/main amd64 cpp amd64 4:12.2.0-3 [6836 B] Get:97 http://deb.debian.org/debian bookworm/main amd64 dbus-user-session amd64 1.14.10-1~deb12u1 [78.1 kB] Get:98 http://deb.debian.org/debian bookworm/main amd64 libdconf1 amd64 0.40.0-4 [40.9 kB] Get:99 http://deb.debian.org/debian bookworm/main amd64 dconf-service amd64 0.40.0-4 [31.6 kB] Get:100 http://deb.debian.org/debian bookworm/main amd64 dconf-gsettings-backend amd64 0.40.0-4 [27.8 kB] Get:101 http://deb.debian.org/debian bookworm/main amd64 fontconfig amd64 2.14.1-4 [449 kB] Get:102 http://deb.debian.org/debian bookworm/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get:103 http://deb.debian.org/debian bookworm/main amd64 fonts-lyx all 2.3.7-1 [186 kB] Get:104 http://deb.debian.org/debian bookworm/main amd64 libcc1-0 amd64 12.2.0-14 [41.7 kB] Get:105 http://deb.debian.org/debian bookworm/main amd64 libgomp1 amd64 12.2.0-14 [116 kB] Get:106 http://deb.debian.org/debian bookworm/main amd64 libitm1 amd64 12.2.0-14 [26.1 kB] Get:107 http://deb.debian.org/debian bookworm/main amd64 libatomic1 amd64 12.2.0-14 [9328 B] Get:108 http://deb.debian.org/debian bookworm/main amd64 libasan8 amd64 12.2.0-14 [2195 kB] Get:109 http://deb.debian.org/debian bookworm/main amd64 liblsan0 amd64 12.2.0-14 [969 kB] Get:110 http://deb.debian.org/debian bookworm/main amd64 libtsan2 amd64 12.2.0-14 [2196 kB] Get:111 http://deb.debian.org/debian bookworm/main amd64 libubsan1 amd64 12.2.0-14 [883 kB] Get:112 http://deb.debian.org/debian bookworm/main amd64 libquadmath0 amd64 12.2.0-14 [144 kB] Get:113 http://deb.debian.org/debian bookworm/main amd64 libgcc-12-dev amd64 12.2.0-14 [2437 kB] Get:114 http://deb.debian.org/debian bookworm/main amd64 gcc-12 amd64 12.2.0-14 [19.3 MB] Get:115 http://deb.debian.org/debian bookworm/main amd64 gcc amd64 4:12.2.0-3 [5216 B] Get:116 http://deb.debian.org/debian bookworm/main amd64 libc-dev-bin amd64 2.36-9+deb12u4 [45.4 kB] Get:117 http://deb.debian.org/debian bookworm/main amd64 linux-libc-dev amd64 6.1.76-1 [1930 kB] Get:118 http://deb.debian.org/debian bookworm/main amd64 libcrypt-dev amd64 1:4.4.33-2 [118 kB] Get:119 http://deb.debian.org/debian bookworm/main amd64 libtirpc-dev amd64 1.3.3+ds-1 [191 kB] Get:120 http://deb.debian.org/debian bookworm/main amd64 libnsl-dev amd64 1.3.0-2 [66.4 kB] Get:121 http://deb.debian.org/debian bookworm/main amd64 rpcsvc-proto amd64 1.4.3-1 [63.3 kB] Get:122 http://deb.debian.org/debian bookworm/main amd64 libc6-dev amd64 2.36-9+deb12u4 [1897 kB] Get:123 http://deb.debian.org/debian bookworm/main amd64 libstdc++-12-dev amd64 12.2.0-14 [2046 kB] Get:124 http://deb.debian.org/debian bookworm/main amd64 g++-12 amd64 12.2.0-14 [10.7 MB] Get:125 http://deb.debian.org/debian bookworm/main amd64 g++ amd64 4:12.2.0-3 [1356 B] Get:126 http://deb.debian.org/debian bookworm/main amd64 libaec0 amd64 1.0.6-1+b1 [21.1 kB] Get:127 http://deb.debian.org/debian bookworm/main amd64 libann-cctbx0 amd64 1.1.2+doc-9+b1 [32.4 kB] Get:128 http://deb.debian.org/debian bookworm/main amd64 libann-cctbx-dev amd64 1.1.2+doc-9+b1 [44.6 kB] Get:129 http://deb.debian.org/debian bookworm/main amd64 libantlr3c-3.4-0 amd64 3.4+dfsg-4 [49.5 kB] Get:130 http://deb.debian.org/debian bookworm/main amd64 libatk1.0-0 amd64 2.46.0-5 [49.6 kB] Get:131 http://deb.debian.org/debian bookworm/main amd64 libxi6 amd64 2:1.8-1+b1 [84.2 kB] Get:132 http://deb.debian.org/debian bookworm/main amd64 libatspi2.0-0 amd64 2.46.0-5 [75.4 kB] Get:133 http://deb.debian.org/debian bookworm/main amd64 libatk-bridge2.0-0 amd64 2.46.0-5 [64.6 kB] Get:134 http://deb.debian.org/debian bookworm/main amd64 libavahi-common-data amd64 0.8-10 [107 kB] Get:135 http://deb.debian.org/debian bookworm/main amd64 libavahi-common3 amd64 0.8-10 [41.6 kB] Get:136 http://deb.debian.org/debian bookworm/main amd64 libavahi-client3 amd64 0.8-10 [45.5 kB] Get:137 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB] Get:138 http://deb.debian.org/debian bookworm/main amd64 libboost1.74-dev amd64 1.74.0+ds1-21 [9508 kB] Get:139 http://deb.debian.org/debian bookworm/main amd64 libboost-dev amd64 1.74.0.3 [4548 B] Get:140 http://deb.debian.org/debian bookworm/main amd64 libboost-python1.74.0 amd64 1.74.0+ds1-21 [289 kB] Get:141 http://deb.debian.org/debian bookworm/main amd64 libboost-numpy1.74.0 amd64 1.74.0+ds1-21 [229 kB] Get:142 http://deb.debian.org/debian bookworm/main amd64 libpython3.11 amd64 3.11.2-6 [1988 kB] Get:143 http://deb.debian.org/debian bookworm/main amd64 libexpat1-dev amd64 2.5.0-1 [150 kB] Get:144 http://deb.debian.org/debian bookworm/main amd64 zlib1g-dev amd64 1:1.2.13.dfsg-1 [916 kB] Get:145 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-dev amd64 3.11.2-6 [4738 kB] Get:146 http://deb.debian.org/debian bookworm/main amd64 libpython3-dev amd64 3.11.2-1+b1 [9572 B] Get:147 http://deb.debian.org/debian bookworm/main amd64 python3.11-dev amd64 3.11.2-6 [615 kB] Get:148 http://deb.debian.org/debian bookworm/main amd64 python3-lib2to3 all 3.11.2-3 [76.3 kB] Get:149 http://deb.debian.org/debian bookworm/main amd64 python3-distutils all 3.11.2-3 [131 kB] Get:150 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:151 http://deb.debian.org/debian bookworm/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get:152 http://deb.debian.org/debian bookworm/main amd64 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get:153 http://deb.debian.org/debian bookworm/main amd64 python3-dev amd64 3.11.2-1+b1 [26.2 kB] Get:154 http://deb.debian.org/debian bookworm/main amd64 libboost-python1.74-dev amd64 1.74.0+ds1-21 [310 kB] Get:155 http://deb.debian.org/debian bookworm/main amd64 libboost-python-dev amd64 1.74.0.3 [4632 B] Get:156 http://deb.debian.org/debian bookworm/main amd64 libboost-thread1.74.0 amd64 1.74.0+ds1-21 [257 kB] Get:157 http://deb.debian.org/debian bookworm/main amd64 libpixman-1-0 amd64 0.42.2-1 [546 kB] Get:158 http://deb.debian.org/debian bookworm/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get:159 http://deb.debian.org/debian bookworm/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get:160 http://deb.debian.org/debian bookworm/main amd64 libcairo2 amd64 1.16.0-7 [575 kB] Get:161 http://deb.debian.org/debian bookworm/main amd64 libcairo-gobject2 amd64 1.16.0-7 [112 kB] Get:162 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get:163 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get:164 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get:165 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1+deb12u1 [72.4 kB] Get:166 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get:167 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:168 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get:169 http://deb.debian.org/debian bookworm/main amd64 libcurl4 amd64 7.88.1-10+deb12u5 [390 kB] Get:170 http://deb.debian.org/debian bookworm/main amd64 libsz2 amd64 1.0.6-1+b1 [7804 B] Get:171 http://deb.debian.org/debian bookworm/main amd64 libhdf5-103-1 amd64 1.10.8+repack1-1 [1237 kB] Get:172 http://deb.debian.org/debian bookworm/main amd64 libcbf1 amd64 0.9.7+dfsg1-2+b2 [353 kB] Get:173 http://deb.debian.org/debian bookworm/main amd64 libccp4-data all 8.0.0-2 [62.3 kB] Get:174 http://deb.debian.org/debian bookworm/main amd64 libccp4c0 amd64 8.0.0-2 [88.5 kB] Get:175 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get:176 http://deb.debian.org/debian bookworm/main amd64 libmmdb2-0 amd64 2.0.22-1 [338 kB] Get:177 http://deb.debian.org/debian bookworm/main amd64 libccp4f0 amd64 8.0.0-2 [210 kB] Get:178 http://deb.debian.org/debian bookworm/main amd64 libccp4-dev amd64 8.0.0-2 [42.8 kB] Get:179 http://deb.debian.org/debian bookworm/main amd64 libcctbx0 amd64 2022.9+ds2+~3.11.2+ds1-6+b1 [2369 kB] Get:180 http://deb.debian.org/debian bookworm/main amd64 libcctbx-dev amd64 2022.9+ds2+~3.11.2+ds1-6+b1 [1148 kB] Get:181 http://deb.debian.org/debian bookworm/main amd64 liblcms2-2 amd64 2.14-2 [154 kB] Get:182 http://deb.debian.org/debian bookworm/main amd64 libcolord2 amd64 1.4.6-2.2 [137 kB] Get:183 http://deb.debian.org/debian bookworm/main amd64 libcups2 amd64 2.4.2-3+deb12u5 [245 kB] Get:184 http://deb.debian.org/debian bookworm/main amd64 libcurl3-gnutls amd64 7.88.1-10+deb12u5 [385 kB] Get:185 http://deb.debian.org/debian bookworm/main amd64 libdatrie1 amd64 0.2.13-2+b1 [43.3 kB] Get:186 http://deb.debian.org/debian bookworm/main amd64 libdouble-conversion3 amd64 3.2.1-1 [41.5 kB] Get:187 http://deb.debian.org/debian bookworm/main amd64 libdrm-common all 2.4.114-1 [7112 B] Get:188 http://deb.debian.org/debian bookworm/main amd64 libdrm2 amd64 2.4.114-1+b1 [37.5 kB] Get:189 http://deb.debian.org/debian bookworm/main amd64 libdrm-amdgpu1 amd64 2.4.114-1+b1 [20.9 kB] Get:190 http://deb.debian.org/debian bookworm/main amd64 libpciaccess0 amd64 0.17-2 [51.4 kB] Get:191 http://deb.debian.org/debian bookworm/main amd64 libdrm-intel1 amd64 2.4.114-1+b1 [64.0 kB] Get:192 http://deb.debian.org/debian bookworm/main amd64 libdrm-nouveau2 amd64 2.4.114-1+b1 [19.1 kB] Get:193 http://deb.debian.org/debian bookworm/main amd64 libdrm-radeon1 amd64 2.4.114-1+b1 [21.8 kB] Get:194 http://deb.debian.org/debian bookworm/main amd64 libedit2 amd64 3.1-20221030-2 [93.0 kB] Get:195 http://deb.debian.org/debian bookworm/main amd64 libwayland-server0 amd64 1.21.0-1 [35.9 kB] Get:196 http://deb.debian.org/debian bookworm/main amd64 libgbm1 amd64 22.3.6-1+deb12u1 [38.0 kB] Get:197 http://deb.debian.org/debian bookworm/main amd64 libglapi-mesa amd64 22.3.6-1+deb12u1 [35.7 kB] Get:198 http://deb.debian.org/debian bookworm/main amd64 libwayland-client0 amd64 1.21.0-1 [28.3 kB] Get:199 http://deb.debian.org/debian bookworm/main amd64 libx11-xcb1 amd64 2:1.8.4-2+deb12u2 [192 kB] Get:200 http://deb.debian.org/debian bookworm/main amd64 libxcb-dri2-0 amd64 1.15-1 [107 kB] Get:201 http://deb.debian.org/debian bookworm/main amd64 libxcb-dri3-0 amd64 1.15-1 [107 kB] Get:202 http://deb.debian.org/debian bookworm/main amd64 libxcb-present0 amd64 1.15-1 [105 kB] Get:203 http://deb.debian.org/debian bookworm/main amd64 libxcb-randr0 amd64 1.15-1 [117 kB] Get:204 http://deb.debian.org/debian bookworm/main amd64 libxcb-sync1 amd64 1.15-1 [109 kB] Get:205 http://deb.debian.org/debian bookworm/main amd64 libxcb-xfixes0 amd64 1.15-1 [109 kB] Get:206 http://deb.debian.org/debian bookworm/main amd64 libxshmfence1 amd64 1.3-1 [8820 B] Get:207 http://deb.debian.org/debian bookworm/main amd64 libegl-mesa0 amd64 22.3.6-1+deb12u1 [114 kB] Get:208 http://deb.debian.org/debian bookworm/main amd64 libelf1 amd64 0.188-2.1 [174 kB] Get:209 http://deb.debian.org/debian bookworm/main amd64 libepoxy0 amd64 1.5.10-1 [189 kB] Get:210 http://deb.debian.org/debian bookworm/main amd64 libevdev2 amd64 1.13.0+dfsg-1 [34.0 kB] Get:211 http://deb.debian.org/debian bookworm/main amd64 libfribidi0 amd64 1.0.8-2.1 [65.0 kB] Get:212 http://deb.debian.org/debian bookworm/main amd64 libglvnd0 amd64 1.6.0-1 [51.8 kB] Get:213 http://deb.debian.org/debian bookworm/main amd64 libxcb-glx0 amd64 1.15-1 [122 kB] Get:214 http://deb.debian.org/debian bookworm/main amd64 libxfixes3 amd64 1:6.0.0-2 [22.7 kB] Get:215 http://deb.debian.org/debian bookworm/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get:216 http://deb.debian.org/debian bookworm/main amd64 libz3-4 amd64 4.8.12-3.1 [7216 kB] Get:217 http://deb.debian.org/debian bookworm/main amd64 libllvm15 amd64 1:15.0.6-4+b1 [23.1 MB] Get:218 http://deb.debian.org/debian bookworm/main amd64 libsensors-config all 1:3.6.0-7.1 [14.3 kB] Get:219 http://deb.debian.org/debian bookworm/main amd64 libsensors5 amd64 1:3.6.0-7.1 [34.2 kB] Get:220 http://deb.debian.org/debian bookworm/main amd64 libgl1-mesa-dri amd64 22.3.6-1+deb12u1 [7239 kB] Get:221 http://deb.debian.org/debian bookworm/main amd64 libglx-mesa0 amd64 22.3.6-1+deb12u1 [147 kB] Get:222 http://deb.debian.org/debian bookworm/main amd64 libglx0 amd64 1.6.0-1 [34.4 kB] Get:223 http://deb.debian.org/debian bookworm/main amd64 libgl1 amd64 1.6.0-1 [88.4 kB] Get:224 http://deb.debian.org/debian bookworm/main amd64 libgl1-mesa-glx amd64 22.3.6-1+deb12u1 [14.5 kB] Get:225 http://deb.debian.org/debian bookworm/main amd64 libglew2.2 amd64 2.2.0-4+b1 [175 kB] Get:226 http://deb.debian.org/debian bookworm/main amd64 libopengl0 amd64 1.6.0-1 [30.6 kB] Get:227 http://deb.debian.org/debian bookworm/main amd64 libglu1-mesa amd64 9.0.2-1.1 [178 kB] Get:228 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get:229 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB] Get:230 http://deb.debian.org/debian bookworm/main amd64 libthai-data all 0.1.29-1 [176 kB] Get:231 http://deb.debian.org/debian bookworm/main amd64 libthai0 amd64 0.1.29-1 [57.5 kB] Get:232 http://deb.debian.org/debian bookworm/main amd64 libpango-1.0-0 amd64 1.50.12+ds-1 [212 kB] Get:233 http://deb.debian.org/debian bookworm/main amd64 libpangoft2-1.0-0 amd64 1.50.12+ds-1 [47.4 kB] Get:234 http://deb.debian.org/debian bookworm/main amd64 libpangocairo-1.0-0 amd64 1.50.12+ds-1 [34.2 kB] Get:235 http://deb.debian.org/debian bookworm/main amd64 libwayland-cursor0 amd64 1.21.0-1 [14.4 kB] Get:236 http://deb.debian.org/debian bookworm/main amd64 libwayland-egl1 amd64 1.21.0-1 [8640 B] Get:237 http://deb.debian.org/debian bookworm/main amd64 libxcomposite1 amd64 1:0.4.5-1 [16.6 kB] Get:238 http://deb.debian.org/debian bookworm/main amd64 libxcursor1 amd64 1:1.2.1-1 [40.9 kB] Get:239 http://deb.debian.org/debian bookworm/main amd64 libxdamage1 amd64 1:1.1.6-1 [15.1 kB] Get:240 http://deb.debian.org/debian bookworm/main amd64 libxinerama1 amd64 2:1.1.4-3 [17.8 kB] Get:241 http://deb.debian.org/debian bookworm/main amd64 xkb-data all 2.35.1-1 [764 kB] Get:242 http://deb.debian.org/debian bookworm/main amd64 libxkbcommon0 amd64 1.5.0-1 [106 kB] Get:243 http://deb.debian.org/debian bookworm/main amd64 libxrandr2 amd64 2:1.5.2-2+b1 [39.2 kB] Get:244 http://deb.debian.org/debian bookworm/main amd64 libgtk-3-common all 3.24.38-2~deb12u1 [3895 kB] Get:245 http://deb.debian.org/debian bookworm/main amd64 libgtk-3-0 amd64 3.24.38-2~deb12u1 [2846 kB] Get:246 http://deb.debian.org/debian bookworm/main amd64 libgudev-1.0-0 amd64 237-2 [15.1 kB] Get:247 http://deb.debian.org/debian bookworm/main amd64 libhdf5-hl-100 amd64 1.10.8+repack1-1 [67.8 kB] Get:248 http://deb.debian.org/debian bookworm/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB] Get:249 http://deb.debian.org/debian bookworm/main amd64 libimagequant0 amd64 2.17.0-1 [32.5 kB] Get:250 http://deb.debian.org/debian bookworm/main amd64 libwacom-common all 2.6.0-1 [58.4 kB] Get:251 http://deb.debian.org/debian bookworm/main amd64 libwacom9 amd64 2.6.0-1 [21.5 kB] Get:252 http://deb.debian.org/debian bookworm/main amd64 libinput-bin amd64 1.22.1-1 [23.2 kB] Get:253 http://deb.debian.org/debian bookworm/main amd64 libmtdev1 amd64 1.1.6-1 [23.0 kB] Get:254 http://deb.debian.org/debian bookworm/main amd64 libinput10 amd64 1.22.1-1 [125 kB] Get:255 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get:256 http://deb.debian.org/debian bookworm/main amd64 libopenblas0-pthread amd64 0.3.21+ds-4 [6709 kB] Get:257 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get:258 http://deb.debian.org/debian bookworm/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1 [28.9 kB] Get:259 http://deb.debian.org/debian bookworm/main amd64 libmd4c0 amd64 0.4.8-1 [44.2 kB] Get:260 http://deb.debian.org/debian bookworm/main amd64 libnetcdf19 amd64 1:4.9.0-3+b1 [476 kB] Get:261 http://deb.debian.org/debian bookworm/main amd64 libnotify4 amd64 0.8.1-1 [30.1 kB] Get:262 http://deb.debian.org/debian bookworm/main amd64 libopenblas0 amd64 0.3.21+ds-4 [32.6 kB] Get:263 http://deb.debian.org/debian bookworm/main amd64 libopenblas-pthread-dev amd64 0.3.21+ds-4 [4971 kB] Get:264 http://deb.debian.org/debian bookworm/main amd64 libopenblas-dev amd64 0.3.21+ds-4 [44.9 kB] Get:265 http://deb.debian.org/debian bookworm/main amd64 libopenjp2-7 amd64 2.5.0-2 [189 kB] Get:266 http://deb.debian.org/debian bookworm/main amd64 libpcre2-16-0 amd64 10.42-1 [245 kB] Get:267 http://deb.debian.org/debian bookworm/main amd64 libpcre2-32-0 amd64 10.42-1 [234 kB] Get:268 http://deb.debian.org/debian bookworm/main amd64 libpython3-all-dev amd64 3.11.2-1+b1 [1068 B] Get:269 http://deb.debian.org/debian bookworm/main amd64 libqhull-r8.0 amd64 2020.2-5 [248 kB] Get:270 http://deb.debian.org/debian bookworm/main amd64 libqt5core5a amd64 5.15.8+dfsg-11 [1809 kB] Get:271 http://deb.debian.org/debian bookworm/main amd64 libqt5dbus5 amd64 5.15.8+dfsg-11 [211 kB] Get:272 http://deb.debian.org/debian bookworm/main amd64 libegl1 amd64 1.6.0-1 [33.7 kB] Get:273 http://deb.debian.org/debian bookworm/main amd64 libqt5network5 amd64 5.15.8+dfsg-11 [674 kB] Get:274 http://deb.debian.org/debian bookworm/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get:275 http://deb.debian.org/debian bookworm/main amd64 libxcb-icccm4 amd64 0.4.1-1.1 [27.4 kB] Get:276 http://deb.debian.org/debian bookworm/main amd64 libxcb-util1 amd64 0.4.0-1+b1 [23.2 kB] Get:277 http://deb.debian.org/debian bookworm/main amd64 libxcb-image0 amd64 0.4.0-2 [22.9 kB] Get:278 http://deb.debian.org/debian bookworm/main amd64 libxcb-keysyms1 amd64 0.4.0-1+b2 [16.4 kB] Get:279 http://deb.debian.org/debian bookworm/main amd64 libxcb-render-util0 amd64 0.3.9-1+b1 [18.3 kB] Get:280 http://deb.debian.org/debian bookworm/main amd64 libxcb-shape0 amd64 1.15-1 [106 kB] Get:281 http://deb.debian.org/debian bookworm/main amd64 libxcb-xinerama0 amd64 1.15-1 [105 kB] Get:282 http://deb.debian.org/debian bookworm/main amd64 libxcb-xinput0 amd64 1.15-1 [130 kB] Get:283 http://deb.debian.org/debian bookworm/main amd64 libxcb-xkb1 amd64 1.15-1 [129 kB] Get:284 http://deb.debian.org/debian bookworm/main amd64 libxkbcommon-x11-0 amd64 1.5.0-1 [15.6 kB] Get:285 http://deb.debian.org/debian bookworm/main amd64 libqt5gui5 amd64 5.15.8+dfsg-11 [3408 kB] Get:286 http://deb.debian.org/debian bookworm/main amd64 libqt5widgets5 amd64 5.15.8+dfsg-11 [2383 kB] Get:287 http://deb.debian.org/debian bookworm/main amd64 libqt5xml5 amd64 5.15.8+dfsg-11 [122 kB] Get:288 http://deb.debian.org/debian bookworm/main amd64 libqt5designer5 amd64 5.15.8-2 [2748 kB] Get:289 http://deb.debian.org/debian bookworm/main amd64 libqt5sql5 amd64 5.15.8+dfsg-11 [122 kB] Get:290 http://deb.debian.org/debian bookworm/main amd64 libqt5help5 amd64 5.15.8-2 [149 kB] Get:291 http://deb.debian.org/debian bookworm/main amd64 libqt5opengl5 amd64 5.15.8+dfsg-11 [148 kB] Get:292 http://deb.debian.org/debian bookworm/main amd64 libqt5printsupport5 amd64 5.15.8+dfsg-11 [202 kB] Get:293 http://deb.debian.org/debian bookworm/main amd64 libqt5test5 amd64 5.15.8+dfsg-11 [146 kB] Get:294 http://deb.debian.org/debian bookworm/main amd64 libraqm0 amd64 0.7.0-4.1 [10.6 kB] Get:295 http://deb.debian.org/debian bookworm/main amd64 libssm2 amd64 1.4.0-2 [82.2 kB] Get:296 http://deb.debian.org/debian bookworm/main amd64 libwebpdemux2 amd64 1.2.4-0.2+deb12u1 [99.4 kB] Get:297 http://deb.debian.org/debian bookworm/main amd64 libwebpmux3 amd64 1.2.4-0.2+deb12u1 [109 kB] Get:298 http://deb.debian.org/debian bookworm/main amd64 libwxbase3.2-1 amd64 3.2.2+dfsg-2 [948 kB] Get:299 http://deb.debian.org/debian bookworm/main amd64 libxtst6 amd64 2:1.2.3-1.1 [28.0 kB] Get:300 http://deb.debian.org/debian bookworm/main amd64 libwxgtk3.2-1 amd64 3.2.2+dfsg-2 [4504 kB] Get:301 http://deb.debian.org/debian bookworm/main amd64 libwxgtk-gl3.2-1 amd64 3.2.2+dfsg-2 [77.7 kB] Get:302 http://deb.debian.org/debian bookworm/main amd64 libxsimd-dev amd64 8.1.0-7 [88.8 kB] Get:303 http://deb.debian.org/debian bookworm/main amd64 libxslt1.1 amd64 1.1.35-1 [242 kB] Get:304 http://deb.debian.org/debian bookworm/main amd64 pymol-data all 2.5.0+dfsg-1 [1401 kB] Get:305 http://deb.debian.org/debian bookworm/main amd64 python-matplotlib-data all 3.6.3-1 [2744 kB] Get:306 http://deb.debian.org/debian bookworm/main amd64 python3-all amd64 3.11.2-1+b1 [1056 B] Get:307 http://deb.debian.org/debian bookworm/main amd64 python3-all-dev amd64 3.11.2-1+b1 [1072 B] Get:308 http://deb.debian.org/debian bookworm/main amd64 python3-appdirs all 1.4.4-3 [13.0 kB] Get:309 http://deb.debian.org/debian bookworm/main amd64 python3-attr all 22.2.0-1 [65.4 kB] Get:310 http://deb.debian.org/debian bookworm/main amd64 python3-gast all 0.5.2-2 [9364 B] Get:311 http://deb.debian.org/debian bookworm/main amd64 python3-beniget all 0.4.1-3 [9920 B] Get:312 http://deb.debian.org/debian bookworm/main amd64 python3-brotli amd64 1.0.9-2+b6 [281 kB] Get:313 http://deb.debian.org/debian bookworm/main amd64 python3-pycbf amd64 0.9.7+dfsg1-2+b2 [163 kB] Get:314 http://deb.debian.org/debian bookworm/main amd64 python3-six all 1.16.0-4 [17.5 kB] Get:315 http://deb.debian.org/debian bookworm/main amd64 python3-dateutil all 2.8.2-2 [78.3 kB] Get:316 http://deb.debian.org/debian bookworm/main amd64 python3-pil amd64 9.4.0-1.1+b1 [472 kB] Get:317 http://deb.debian.org/debian bookworm/main amd64 python3-tk amd64 3.11.2-3 [98.3 kB] Get:318 http://deb.debian.org/debian bookworm/main amd64 python3-pil.imagetk amd64 9.4.0-1.1+b1 [74.4 kB] Get:319 http://deb.debian.org/debian bookworm/main amd64 python3-pyparsing all 3.0.9-1 [138 kB] Get:320 http://deb.debian.org/debian bookworm/main amd64 python3-pkg-resources all 66.1.1-1 [296 kB] Get:321 http://deb.debian.org/debian bookworm/main amd64 python3-numpy amd64 1:1.24.2-1 [5209 kB] Get:322 http://deb.debian.org/debian bookworm/main amd64 python3-contourpy amd64 1.0.7-1+b1 [176 kB] Get:323 http://deb.debian.org/debian bookworm/main amd64 python3-cycler all 0.11.0-1 [8020 B] Get:324 http://deb.debian.org/debian bookworm/main amd64 python3-decorator all 5.1.1-3 [14.9 kB] Get:325 http://deb.debian.org/debian bookworm/main amd64 python3-ply all 3.11-5 [65.8 kB] Get:326 http://deb.debian.org/debian bookworm/main amd64 python3-pythran amd64 0.11.0+ds-7 [427 kB] Get:327 http://deb.debian.org/debian bookworm/main amd64 python3-scipy amd64 1.10.1-2 [15.2 MB] Get:328 http://deb.debian.org/debian bookworm/main amd64 python3-ufolib2 all 0.14.0+dfsg1-1 [34.3 kB] Get:329 http://deb.debian.org/debian bookworm/main amd64 python3-mpmath all 1.2.1-2 [418 kB] Get:330 http://deb.debian.org/debian bookworm/main amd64 python3-sympy all 1.11.1-1 [4358 kB] Get:331 http://deb.debian.org/debian bookworm/main amd64 python3-tz all 2022.7.1-4 [30.1 kB] Get:332 http://deb.debian.org/debian bookworm/main amd64 python3-fs all 2.4.16-2 [95.2 kB] Get:333 http://deb.debian.org/debian bookworm/main amd64 python3-lxml amd64 4.9.2-1+b1 [1194 kB] Get:334 http://deb.debian.org/debian bookworm/main amd64 python3-lz4 amd64 4.0.2+dfsg-1+b2 [25.0 kB] Get:335 http://deb.debian.org/debian bookworm/main amd64 unicode-data all 15.0.0-1 [7984 kB] Get:336 http://deb.debian.org/debian bookworm/main amd64 python3-fonttools amd64 4.38.0-1+b1 [1012 kB] Get:337 http://deb.debian.org/debian bookworm/main amd64 python3-kiwisolver amd64 1.4.4-1+b1 [60.1 kB] Get:338 http://deb.debian.org/debian bookworm/main amd64 python3-packaging all 23.0-1 [32.5 kB] Get:339 http://deb.debian.org/debian bookworm/main amd64 python3-matplotlib amd64 3.6.3-1+b1 [6921 kB] Get:340 http://deb.debian.org/debian bookworm/main amd64 sphinx-rtd-theme-common all 1.2.0+dfsg-1 [997 kB] Get:341 http://deb.debian.org/debian bookworm/main amd64 python3-mrcfile all 1.4.3-3 [113 kB] Get:342 http://deb.debian.org/debian bookworm/main amd64 python3-pint all 0.19.2-1 [186 kB] Get:343 http://deb.debian.org/debian bookworm/main amd64 python3-procrunner amd64 1.1.0-1+b1 [12.3 kB] Get:344 http://deb.debian.org/debian bookworm/main amd64 python3-opengl all 3.1.6+dfsg-3 [605 kB] Get:345 http://deb.debian.org/debian bookworm/main amd64 python3-pyqt5.sip amd64 12.11.1-1 [56.4 kB] Get:346 http://deb.debian.org/debian bookworm/main amd64 python3-pyqt5 amd64 5.15.9+dfsg-1 [2489 kB] Get:347 http://deb.debian.org/debian bookworm/main amd64 python3-pyqt5.qtopengl amd64 5.15.9+dfsg-1 [206 kB] Get:348 http://deb.debian.org/debian bookworm/main amd64 python3-pymol amd64 2.5.0+dfsg-1+b3 [3703 kB] Get:349 http://deb.debian.org/debian bookworm/main amd64 python3-certifi all 2022.9.24-1 [153 kB] Get:350 http://deb.debian.org/debian bookworm/main amd64 python3-charset-normalizer all 3.0.1-2 [49.3 kB] Get:351 http://deb.debian.org/debian bookworm/main amd64 python3-idna all 3.3-1 [39.4 kB] Get:352 http://deb.debian.org/debian bookworm/main amd64 python3-urllib3 all 1.26.12-1 [117 kB] Get:353 http://deb.debian.org/debian bookworm/main amd64 python3-chardet all 5.1.0+dfsg-2 [110 kB] Get:354 http://deb.debian.org/debian bookworm/main amd64 python3-requests all 2.28.1+dfsg-1 [67.9 kB] Get:355 http://deb.debian.org/debian bookworm/main amd64 python3-tqdm all 4.64.1-1 [97.7 kB] Get:356 http://deb.debian.org/debian bookworm/main amd64 python3-wxgtk4.0 amd64 4.2.0+dfsg-3 [7200 kB] Get:357 http://deb.debian.org/debian bookworm/main amd64 python3-cctbx amd64 2022.9+ds2+~3.11.2+ds1-6+b1 [35.9 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 329 MB in 2s (132 MB/s) Selecting previously unselected package libssl3:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6100 files and directories currently installed.) Preparing to unpack .../00-libssl3_3.0.11-1~deb12u2_amd64.deb ... Unpacking libssl3:amd64 (3.0.11-1~deb12u2) ... Selecting previously unselected package libargon2-1:amd64. Preparing to unpack .../01-libargon2-1_0~20171227-0.3+deb12u1_amd64.deb ... Unpacking libargon2-1:amd64 (0~20171227-0.3+deb12u1) ... Selecting previously unselected package dmsetup. 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Setting up libsystemd-shared:amd64 (252.22-1~deb12u1) ... Setting up libdevmapper1.02.1:amd64 (2:1.02.185-2) ... Setting up libcryptsetup12:amd64 (2:2.6.1-4~deb12u2) ... Setting up systemd (252.22-1~deb12u1) ... Created symlink /etc/systemd/system/getty.target.wants/getty@tty1.service → /lib/systemd/system/getty@.service. Created symlink /etc/systemd/system/multi-user.target.wants/remote-fs.target → /lib/systemd/system/remote-fs.target. Created symlink /etc/systemd/system/sysinit.target.wants/systemd-pstore.service → /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. "/home" already exists and is not a directory. Setting up dmsetup (2:1.02.185-2) ... Selecting previously unselected package systemd-sysv. (Reading database ... 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Setting up media-types (10.0.0) ... Setting up libgraphite2-3:amd64 (1.3.14-1) ... Setting up liblcms2-2:amd64 (2.14-2) ... Setting up libpixman-1-0:amd64 (0.42.2-1) ... Setting up libwayland-server0:amd64 (1.21.0-1) ... Setting up libpciaccess0:amd64 (0.17-2) ... Setting up systemd-sysv (252.22-1~deb12u1) ... Setting up libxau6:amd64 (1:1.0.9-1) ... Setting up libdouble-conversion3:amd64 (3.2.1-1) ... Setting up libkeyutils1:amd64 (1.6.3-2) ... Setting up libpsl5:amd64 (0.21.2-1) ... Setting up fonts-lato (2.0-2.1) ... Setting up libicu72:amd64 (72.1-3) ... Setting up liblerc4:amd64 (4.0.0+ds-2) ... Setting up libantlr3c-3.4-0:amd64 (3.4+dfsg-4) ... Setting up hicolor-icon-theme (0.17-2) ... Setting up libdatrie1:amd64 (0.2.13-2+b1) ... Setting up libmmdb2-0:amd64 (2.0.22-1) ... Setting up libglib2.0-0:amd64 (2.74.6-2) ... Setting up libglvnd0:amd64 (1.6.0-1) ... Setting up libtirpc-common (1.3.3+ds-1) ... Setting up fonts-lyx (2.3.7-1) ... Setting up libbrotli1:amd64 (1.0.9-2+b6) ... Setting up libsqlite3-0:amd64 (3.40.1-2) ... Setting up libgdk-pixbuf2.0-common (2.42.10+dfsg-1) ... Setting up binutils-common:amd64 (2.40-2) ... Setting up x11-common (1:7.7+23) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of restart. Setting up libsensors-config (1:3.6.0-7.1) ... Setting up libnghttp2-14:amd64 (1.52.0-1+deb12u1) ... Setting up libdeflate0:amd64 (1.14-1) ... Setting up linux-libc-dev:amd64 (6.1.76-1) ... Setting up libctf-nobfd0:amd64 (2.40-2) ... Setting up libqhull-r8.0:amd64 (2020.2-5) ... Setting up xkb-data (2.35.1-1) ... Setting up libccp4-data (8.0.0-2) ... Setting up libgomp1:amd64 (12.2.0-14) ... Setting up libjbig0:amd64 (2.1-6.1) ... Setting up libpcre2-16-0:amd64 (10.42-1) ... Setting up libaec0:amd64 (1.0.6-1+b1) ... Setting up libcolord2:amd64 (1.4.6-2.2) ... Setting up libopengl0:amd64 (1.6.0-1) ... Setting up libjansson4:amd64 (2.14-2) ... Setting up libkrb5support0:amd64 (1.20.1-2+deb12u1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Setting up libdconf1:amd64 (0.40.0-4) ... Setting up unicode-data (15.0.0-1) ... Setting up libxsimd-dev:amd64 (8.1.0-7) ... Setting up libz3-4:amd64 (4.8.12-3.1) ... Setting up libpcre2-32-0:amd64 (10.42-1) ... Setting up libblas3:amd64 (3.11.0-2) ... 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 rpcsvc-proto (1.4.3-1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-2) ... Setting up libann-cctbx0 (1.1.2+doc-9+b1) ... Setting up libx11-data (2:1.8.4-2+deb12u2) ... Setting up libepoxy0:amd64 (1.5.10-1) ... Setting up libmpfr6:amd64 (4.2.0-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libavahi-common-data:amd64 (0.8-10) ... Setting up libdbus-1-3:amd64 (1.14.10-1~deb12u1) ... Setting up libfribidi0:amd64 (1.0.8-2.1) ... Setting up libquadmath0:amd64 (12.2.0-14) ... Setting up libimagequant0:amd64 (2.17.0-1) ... Setting up libproc2-0:amd64 (2:4.0.2-3) ... Setting up pymol-data (2.5.0+dfsg-1) ... Setting up libpng16-16:amd64 (1.6.39-2) ... Setting up libmpc3:amd64 (1.3.1-1) ... Setting up libatomic1:amd64 (12.2.0-14) ... Setting up libtcl8.6:amd64 (8.6.13+dfsg-2) ... Setting up fonts-dejavu-core (2.37-6) ... Setting up libccp4c0:amd64 (8.0.0-2) ... Setting up libsensors5:amd64 (1:3.6.0-7.1) ... Setting up libncursesw6:amd64 (6.4-4) ... Setting up libk5crypto3:amd64 (1.20.1-2+deb12u1) ... Setting up libglapi-mesa:amd64 (22.3.6-1+deb12u1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg-10) ... Setting up libgfortran5:amd64 (12.2.0-14) ... Setting up libmtdev1:amd64 (1.1.6-1) ... Setting up libwebp7:amd64 (1.2.4-0.2+deb12u1) ... Setting up libubsan1:amd64 (12.2.0-14) ... Setting up libxshmfence1:amd64 (1.3-1) ... Setting up at-spi2-common (2.46.0-5) ... Setting up libcrypt-dev:amd64 (1:4.4.33-2) ... Setting up libtiff6:amd64 (4.5.0-6+deb12u1) ... Setting up dbus-session-bus-common (1.14.10-1~deb12u1) ... Setting up libasan8:amd64 (12.2.0-14) ... Setting up procps (2:4.0.2-3) ... Setting up libmd4c0:amd64 (0.4.8-1) ... Setting up libopenjp2-7:amd64 (2.5.0-2) ... Setting up libthai-data (0.1.29-1) ... Setting up libssh2-1:amd64 (1.10.0-3+b1) ... Setting up libatk1.0-0:amd64 (2.46.0-5) ... Setting up libkrb5-3:amd64 (1.20.1-2+deb12u1) ... Setting up libglu1-mesa:amd64 (9.0.2-1.1) ... Setting up libwayland-egl1:amd64 (1.21.0-1) ... Setting up libtsan2:amd64 (12.2.0-14) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libbinutils:amd64 (2.40-2) ... Setting up dbus-system-bus-common (1.14.10-1~deb12u1) ... Setting up libboost-python1.74.0 (1.74.0+ds1-21) ... Setting up libisl23:amd64 (0.25-1.1) ... Setting up libc-dev-bin (2.36-9+deb12u4) ... Setting up python-matplotlib-data (3.6.3-1) ... Setting up openssl (3.0.11-1~deb12u2) ... Setting up libwebpmux3:amd64 (1.2.4-0.2+deb12u1) ... Setting up libbsd0:amd64 (0.11.7-2) ... Setting up libdrm-common (2.4.114-1) ... Setting up libelf1:amd64 (0.188-2.1) ... Setting up libevdev2:amd64 (1.13.0+dfsg-1) ... Setting up readline-common (8.2-1.3) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3~deb12u1) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Setting up sphinx-rtd-theme-common (1.2.0+dfsg-1) ... Setting up libcc1-0:amd64 (12.2.0-14) ... Setting up dbus-bin (1.14.10-1~deb12u1) ... Setting up libgudev-1.0-0:amd64 (237-2) ... Setting up liblsan0:amd64 (12.2.0-14) ... Setting up libsz2:amd64 (1.0.6-1+b1) ... Setting up libitm1:amd64 (12.2.0-14) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libboost-thread1.74.0:amd64 (1.74.0+ds1-21) ... Setting up libboost-numpy1.74.0 (1.74.0+ds1-21) ... Setting up libann-cctbx-dev (1.1.2+doc-9+b1) ... Setting up libccp4f0:amd64 (8.0.0-2) ... Setting up libwacom-common (2.6.0-1) ... Setting up libxkbcommon0:amd64 (1.5.0-1) ... Setting up libwayland-client0:amd64 (1.21.0-1) ... Setting up libctf0:amd64 (2.40-2) ... Setting up libice6:amd64 (2:1.0.10-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up liblapack3:amd64 (3.11.0-2) ... 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 cpp-12 (12.2.0-14) ... Setting up libxcb1:amd64 (1.15-1) ... Setting up libopenblas0-pthread:amd64 (0.3.21+ds-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so.0 to provide /usr/lib/x86_64-linux-gnu/libopenblas.so.0 (libopenblas.so.0-x86_64-linux-gnu) in auto mode Setting up libxcb-xfixes0:amd64 (1.15-1) ... Setting up libssm2:amd64 (1.4.0-2) ... Setting up libxcb-xinput0:amd64 (1.15-1) ... Setting up libccp4-dev:amd64 (8.0.0-2) ... Setting up libxcb-render0:amd64 (1.15-1) ... Setting up libwacom9:amd64 (2.6.0-1) ... Setting up fontconfig-config (2.14.1-4) ... Setting up libxcb-glx0:amd64 (1.15-1) ... Setting up libwebpdemux2:amd64 (1.2.4-0.2+deb12u1) ... Setting up libedit2:amd64 (3.1-20221030-2) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up libxcb-keysyms1:amd64 (0.4.0-1+b2) ... Setting up libxcb-shape0:amd64 (1.15-1) ... Setting up libavahi-common3:amd64 (0.8-10) ... Setting up libxcb-render-util0:amd64 (0.3.9-1+b1) ... Setting up libxcb-shm0:amd64 (1.15-1) ... Setting up libxcb-icccm4:amd64 (0.4.1-1.1) ... Setting up dbus-daemon (1.14.10-1~deb12u1) ... Setting up libwxbase3.2-1:amd64 (3.2.2+dfsg-2) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Setting up libxcb-util1:amd64 (0.4.0-1+b1) ... Setting up libinput-bin (1.22.1-1) ... Setting up libxcb-xkb1:amd64 (1.15-1) ... Setting up libxcb-image0:amd64 (0.4.0-2) ... Setting up libxcb-present0:amd64 (1.15-1) ... Setting up libthai0:amd64 (0.1.29-1) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libgprofng0:amd64 (2.40-2) ... Setting up libxcb-xinerama0:amd64 (1.15-1) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libfreetype6:amd64 (2.12.1+dfsg-5) ... Setting up libxcb-sync1:amd64 (1.15-1) ... Setting up dbus (1.14.10-1~deb12u1) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libgcc-12-dev:amd64 (12.2.0-14) ... Setting up shared-mime-info (2.2-1) ... Setting up libxkbcommon-x11-0:amd64 (1.5.0-1) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-2+deb12u1) ... Setting up libqt5core5a:amd64 (5.15.8+dfsg-11) ... Setting up libjs-sphinxdoc (5.3.0-4) ... Setting up libxcb-dri2-0:amd64 (1.15-1) ... Setting up libdrm2:amd64 (2.4.114-1+b1) ... Setting up libopenblas0:amd64 (0.3.21+ds-4) ... Setting up libqt5dbus5:amd64 (5.15.8+dfsg-11) ... Setting up libwayland-cursor0:amd64 (1.21.0-1) ... Setting up libxcb-randr0:amd64 (1.15-1) ... Setting up cpp (4:12.2.0-3) ... Setting up libllvm15:amd64 (1:15.0.6-4+b1) ... Setting up libxslt1.1:amd64 (1.1.35-1) ... Setting up libpam-systemd:amd64 (252.22-1~deb12u1) ... Setting up libcurl4:amd64 (7.88.1-10+deb12u5) ... Setting up libx11-6:amd64 (2:1.8.4-2+deb12u2) ... Setting up libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-1+b1) ... Setting up libfontconfig1:amd64 (2.14.1-4) ... Setting up libqt5test5:amd64 (5.15.8+dfsg-11) ... Setting up libxcomposite1:amd64 (1:0.4.5-1) ... Setting up libsm6:amd64 (2:1.2.3-1) ... Setting up libavahi-client3:amd64 (0.8-10) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1) ... Setting up binutils-x86-64-linux-gnu (2.40-2) ... Setting up libdrm-amdgpu1:amd64 (2.4.114-1+b1) ... Setting up libopenblas-pthread-dev:amd64 (0.3.21+ds-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblas.so to provide /usr/lib/x86_64-linux-gnu/libopenblas.so (libopenblas.so-x86_64-linux-gnu) in auto mode Setting up libtirpc3:amd64 (1.3.3+ds-1) ... Setting up libxcb-dri3-0:amd64 (1.15-1) ... Setting up libinput10:amd64 (1.22.1-1) ... Setting up gtk-update-icon-cache (3.24.38-2~deb12u1) ... Setting up libx11-xcb1:amd64 (2:1.8.4-2+deb12u2) ... Setting up fontconfig (2.14.1-4) ... Regenerating fonts cache... done. Setting up libdrm-nouveau2:amd64 (2.4.114-1+b1) ... Setting up libxdamage1:amd64 (1:1.1.6-1) ... Setting up libxrender1:amd64 (1:0.9.10-1.1) ... Setting up libgbm1:amd64 (22.3.6-1+deb12u1) ... Setting up libdrm-radeon1:amd64 (2.4.114-1+b1) ... Setting up libpango-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libdrm-intel1:amd64 (2.4.114-1+b1) ... Setting up libgl1-mesa-dri:amd64 (22.3.6-1+deb12u1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libcurl3-gnutls:amd64 (7.88.1-10+deb12u5) ... Setting up binutils (2.40-2) ... Setting up libcairo2:amd64 (1.16.0-7) ... Setting up libqt5network5:amd64 (5.15.8+dfsg-11) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up libqt5sql5:amd64 (5.15.8+dfsg-11) ... Setting up dbus-user-session (1.14.10-1~deb12u1) ... Setting up libopenblas-dev:amd64 (0.3.21+ds-4) ... Setting up libqt5xml5:amd64 (5.15.8+dfsg-11) ... Setting up libegl-mesa0:amd64 (22.3.6-1+deb12u1) ... Setting up libtirpc-dev:amd64 (1.3.3+ds-1) ... Setting up adwaita-icon-theme (43-1) ... 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 gcc-12 (12.2.0-14) ... Setting up libxfixes3:amd64 (1:6.0.0-2) ... Setting up libnotify4:amd64 (0.8.1-1) ... Setting up libraqm0:amd64 (0.7.0-4.1) ... Setting up libxinerama1:amd64 (2:1.1.4-3) ... Setting up libxrandr2:amd64 (2:1.5.2-2+b1) ... Setting up libcups2:amd64 (2.4.2-3+deb12u5) ... Setting up libhdf5-103-1:amd64 (1.10.8+repack1-1) ... Setting up libnsl2:amd64 (1.3.0-2) ... Setting up libegl1:amd64 (1.6.0-1) ... Setting up libcairo-gobject2:amd64 (1.16.0-7) ... Setting up libxss1:amd64 (1:1.2.3-1) ... Setting up libpangoft2-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libpangocairo-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libhdf5-hl-100:amd64 (1.10.8+repack1-1) ... Setting up libxft2:amd64 (2.3.6-1) ... Setting up libglx-mesa0:amd64 (22.3.6-1+deb12u1) ... Setting up libxi6:amd64 (2:1.8-1+b1) ... Setting up libglx0:amd64 (1.6.0-1) ... Setting up libxtst6:amd64 (2:1.2.3-1.1) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6) ... Setting up libtk8.6:amd64 (8.6.13-2) ... Setting up libxcursor1:amd64 (1:1.2.1-1) ... Setting up dconf-service (0.40.0-4) ... Setting up libatspi2.0-0:amd64 (2.46.0-5) ... Setting up gcc (4:12.2.0-3) ... Setting up libcbf1:amd64 (0.9.7+dfsg1-2+b2) ... Setting up libatk-bridge2.0-0:amd64 (2.46.0-5) ... Setting up libgl1:amd64 (1.6.0-1) ... Setting up libglew2.2:amd64 (2.2.0-4+b1) ... Setting up libnetcdf19:amd64 (1:4.9.0-3+b1) ... Setting up libgl1-mesa-glx:amd64 (22.3.6-1+deb12u1) ... Setting up libnsl-dev:amd64 (1.3.0-2) ... Setting up libc6-dev:amd64 (2.36-9+deb12u4) ... Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up libcctbx0 (2022.9+ds2+~3.11.2+ds1-6+b1) ... Setting up python3.11 (3.11.2-6) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-4.1) ... Setting up libpython3.11:amd64 (3.11.2-6) ... Setting up dconf-gsettings-backend:amd64 (0.40.0-4) ... Setting up libstdc++-12-dev:amd64 (12.2.0-14) ... Setting up blt (2.5.3+dfsg-4.1) ... Setting up libqt5gui5:amd64 (5.15.8+dfsg-11) ... Setting up libqt5widgets5:amd64 (5.15.8+dfsg-11) ... Setting up python3 (3.11.2-1+b1) ... Setting up python3-opengl (3.1.6+dfsg-3) ... Setting up libqt5help5:amd64 (5.15.8-2) ... Setting up python3-tz (2022.7.1-4) ... Setting up python3-six (1.16.0-4) ... Setting up libqt5printsupport5:amd64 (5.15.8+dfsg-11) ... Setting up python3-decorator (5.1.1-3) ... Setting up python3-packaging (23.0-1) ... Setting up libexpat1-dev:amd64 (2.5.0-1) ... Setting up python3-pyparsing (3.0.9-1) ... Setting up python3-certifi (2022.9.24-1) ... Setting up python3-brotli (1.0.9-2+b6) ... Setting up python3-cycler (0.11.0-1) ... Setting up python3-pycbf (0.9.7+dfsg1-2+b2) ... Setting up python3-kiwisolver (1.4.4-1+b1) ... Setting up python3-idna (3.3-1) ... Setting up python3-urllib3 (1.26.12-1) ... Setting up zlib1g-dev:amd64 (1:1.2.13.dfsg-1) ... Setting up python3-pyqt5.sip (12.11.1-1) ... Setting up libqt5opengl5:amd64 (5.15.8+dfsg-11) ... Setting up python3-lxml:amd64 (4.9.2-1+b1) ... Setting up python3-dateutil (2.8.2-2) ... Setting up python3-mpmath (1.2.1-2) ... Setting up python3-lib2to3 (3.11.2-3) ... Setting up python3-appdirs (1.4.4-3) ... Setting up python3-procrunner (1.1.0-1+b1) ... Setting up libgtk-3-common (3.24.38-2~deb12u1) ... Setting up g++-12 (12.2.0-14) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-distutils (3.11.2-3) ... Setting up python3-sympy (1.11.1-1) ... Setting up python3-attr (22.2.0-1) ... Setting up libboost1.74-dev:amd64 (1.74.0+ds1-21) ... Setting up libqt5designer5:amd64 (5.15.8-2) ... Setting up python3-lz4 (4.0.2+dfsg-1+b2) ... Setting up python3-charset-normalizer (3.0.1-2) ... Setting up libgtk-3-0:amd64 (3.24.38-2~deb12u1) ... Setting up python3-ply (3.11-5) ... Setting up python3-tqdm (4.64.1-1) ... Setting up python3-gast (0.5.2-2) ... Setting up python3-all (3.11.2-1+b1) ... Setting up python3-tk:amd64 (3.11.2-3) ... Setting up python3-fs (2.4.16-2) ... Setting up python3-beniget (0.4.1-3) ... Setting up python3-pint (0.19.2-1) ... Setting up python3-chardet (5.1.0+dfsg-2) ... Setting up libpython3.11-dev:amd64 (3.11.2-6) ... Setting up python3-requests (2.28.1+dfsg-1) ... Setting up python3-numpy (1:1.24.2-1) ... Setting up g++ (4:12.2.0-3) ... update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode Setting up python3-contourpy (1.0.7-1+b1) ... Setting up libboost-dev:amd64 (1.74.0.3) ... Setting up python3-pyqt5 (5.15.9+dfsg-1) ... Setting up python3-mrcfile (1.4.3-3) ... Setting up libwxgtk3.2-1:amd64 (3.2.2+dfsg-2) ... Setting up python3-pyqt5.qtopengl (5.15.9+dfsg-1) ... Setting up libpython3-dev:amd64 (3.11.2-1+b1) ... Setting up libwxgtk-gl3.2-1:amd64 (3.2.2+dfsg-2) ... Setting up python3.11-dev (3.11.2-6) ... Setting up libpython3-all-dev:amd64 (3.11.2-1+b1) ... Setting up python3-dev (3.11.2-1+b1) ... Setting up python3-pymol (2.5.0+dfsg-1+b3) ... Setting up python3-all-dev (3.11.2-1+b1) ... Setting up libboost-python1.74-dev (1.74.0+ds1-21) ... Setting up libboost-python-dev (1.74.0.3) ... Setting up python3-pythran (0.11.0+ds-7) ... Setting up libcctbx-dev (2022.9+ds2+~3.11.2+ds1-6+b1) ... Setting up python3-scipy (1.10.1-2) ... Setting up python3-fonttools (4.38.0-1+b1) ... Setting up python3-pil:amd64 (9.4.0-1.1+b1) ... Setting up python3-pil.imagetk:amd64 (9.4.0-1.1+b1) ... Setting up python3-ufolib2 (0.14.0+dfsg1-1) ... Setting up python3-matplotlib (3.6.3-1+b1) ... Setting up python3-wxgtk4.0 (4.2.0+dfsg-3) ... Setting up python3-cctbx (2022.9+ds2+~3.11.2+ds1-6+b1) ... Processing triggers for libc-bin (2.36-9+deb12u4) ... Processing triggers for systemd (252.22-1~deb12u1) ... Processing triggers for ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 1m45.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'apt-get', '-y', 'install', 'python3-cctbx'] 1m45.7s INFO: Running scripts post_install 1m45.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/post_install_exceptions'] 1m45.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/post_install_exceptions'] 1m45.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv'] 1m49.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv'] 1m49.0s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmprx0kbrwv to sid 1m49.0s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 1m49.0s INFO: Running scripts pre_distupgrade 1m49.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 1m49.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 1m49.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_distupgrade_exceptions'] 1m49.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_distupgrade_exceptions'] 1m49.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 1m49.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 1m49.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_distupgrade_zz_database-server'] 1m49.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_distupgrade_zz_database-server'] 1m49.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 1m49.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 1m49.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'apt-get', 'update'] 1m53.2s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [198 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9928 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7220 kB] Fetched 17.3 MB in 3s (6015 kB/s) Reading package lists... 1m53.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'apt-get', 'update'] 1m53.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'apt-get', '-yf', 'dist-upgrade'] 4m29.4s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libboost-dev libboost-numpy1.74.0 libboost-python1.74.0 libboost-thread1.74.0 libgl1-mesa-glx libllvm15 libnsl-dev libopenblas-dev libopenblas-pthread-dev libopenblas0 libpython3-all-dev libpython3.12-dev libpython3.12t64 libtirpc-dev libxsimd-dev python3-all-dev python3-beniget python3-gast python3-ply python3-pythran python3.12-dev xtl-dev Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libapt-pkg6.0 libboost-python1.74-dev libboost1.74-dev libcbf1 libcom-err2 libdb5.3 libelf1 libext2fs2 libglib2.0-0 libgnutls30 libhdf5-103-1 libpython3.11 libreadline8 libss2 libssl3 libtirpc3 The following NEW packages will be installed: cpp-13 cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu fonts-dejavu-mono g++-13 g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu gcc-13 gcc-13-base gcc-13-x86-64-linux-gnu gcc-14-base gcc-x86-64-linux-gnu libapt-pkg6.0t64 libboost-numpy1.83.0 libboost-python1.83-dev libboost-python1.83.0 libboost-thread1.83.0 libboost1.83-dev libcbf1t64 libcloudproviders0 libcom-err2t64 libdb5.3t64 libelf1t64 libext2fs2t64 libgcc-13-dev libglib2.0-0t64 libgnutls30t64 libhdf5-103-1t64 libhwasan0 libllvm17 liblzf1 libpython3.11t64 libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 libreadline8t64 libsframe1 libsharpyuv0 libss2t64 libssl3t64 libstdc++-13-dev libtirpc3t64 libunistring5 libuuid1t64 libvulkan1 netbase python3-h5py python3-h5py-serial python3-nxmx python3-orderedset python3-setuptools python3.12 python3.12-dev python3.12-minimal systemd-dev xtl-dev The following packages will be upgraded: adduser adwaita-icon-theme apt at-spi2-common base-files base-passwd bash binutils binutils-common binutils-x86-64-linux-gnu blt bsdutils ca-certificates coreutils cpp cpp-12 dash dbus dbus-bin dbus-daemon dbus-session-bus-common dbus-system-bus-common dbus-user-session dconf-gsettings-backend dconf-service debconf debian-archive-keyring debianutils diffutils dmsetup dpkg e2fsprogs findutils fontconfig fontconfig-config fonts-dejavu-core fonts-lato fonts-lyx g++ g++-12 gcc gcc-12 gcc-12-base gpgv grep gtk-update-icon-cache hostname init-system-helpers libacl1 libaec0 libapparmor1 libargon2-1 libasan8 libatk-bridge2.0-0 libatk1.0-0 libatomic1 libatspi2.0-0 libattr1 libaudit-common libaudit1 libavahi-client3 libavahi-common-data libavahi-common3 libbinutils libblas3 libblkid1 libboost-dev libboost-numpy1.74.0 libboost-python-dev libboost-python1.74.0 libboost-thread1.74.0 libbrotli1 libbsd0 libbz2-1.0 libc-bin libc-dev-bin libc6 libc6-dev libcairo-gobject2 libcairo2 libcap-ng0 libcap2 libcc1-0 libcctbx-dev libcctbx0 libcolord2 libcrypt-dev libcrypt1 libcryptsetup12 libctf-nobfd0 libctf0 libcups2 libcurl3-gnutls libcurl4 libdatrie1 libdbus-1-3 libdconf1 libdebconfclient0 libdeflate0 libdevmapper1.02.1 libdouble-conversion3 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libegl-mesa0 libegl1 libepoxy0 libevdev2 libexpat1 libexpat1-dev libfdisk1 libffi8 libfontconfig1 libfreetype6 libfribidi0 libgbm1 libgcc-12-dev libgcc-s1 libgcrypt20 libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgfortran5 libgl1 libgl1-mesa-dri libgl1-mesa-glx libglapi-mesa libglvnd0 libglx-mesa0 libglx0 libgmp10 libgomp1 libgpg-error0 libgprofng0 libgraphite2-3 libgssapi-krb5-2 libgtk-3-0 libgtk-3-common libgudev-1.0-0 libharfbuzz0b libhdf5-hl-100 libhogweed6 libicu72 libidn2-0 libimagequant0 libinput-bin libinput10 libip4tc2 libisl23 libitm1 libjansson4 libjbig0 libjpeg62-turbo libjs-sphinxdoc libjson-c5 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap-2.5-0 liblerc4 libllvm15 liblsan0 liblz4-1 liblzma5 libmd0 libmd4c0 libmmdb2-0 libmount1 libmpc3 libmpfr6 libmtdev1 libncursesw6 libnetcdf19 libnettle8 libnghttp2-14 libnotify4 libnsl-dev libnsl2 libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread libopengl0 libopenjp2-7 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam-systemd libpam0g libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpciaccess0 libpcre2-16-0 libpcre2-32-0 libpcre2-8-0 libpixman-1-0 libpng16-16 libproc2-0 libpsl5 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib libqhull-r8.0 libqt5core5a libqt5dbus5 libqt5designer5 libqt5gui5 libqt5help5 libqt5network5 libqt5opengl5 libqt5printsupport5 libqt5sql5 libqt5test5 libqt5widgets5 libqt5xml5 libquadmath0 libraqm0 libsasl2-2 libsasl2-modules-db libseccomp2 libselinux1 libsemanage-common libsemanage2 libsensors-config libsensors5 libsepol2 libsmartcols1 libsqlite3-0 libssh2-1 libssm2 libstdc++-12-dev libstdc++6 libsystemd-shared libsystemd0 libsz2 libtasn1-6 libtcl8.6 libthai-data libthai0 libtiff6 libtinfo6 libtirpc-common libtirpc-dev libtk8.6 libtsan2 libubsan1 libudev1 libuuid1 libwacom-common libwacom9 libwayland-client0 libwayland-cursor0 libwayland-egl1 libwayland-server0 libwebp7 libwebpdemux2 libwebpmux3 libwxbase3.2-1 libwxgtk-gl3.2-1 libwxgtk3.2-1 libx11-6 libx11-data libx11-xcb1 libxcb-icccm4 libxcb-image0 libxft2 libxi6 libxkbcommon-x11-0 libxkbcommon0 libxml2 libxsimd-dev libxxhash0 libz3-4 libzstd1 linux-libc-dev login logsave mawk media-types mount ncurses-base ncurses-bin openssl passwd perl-base procps python3 python3-all python3-all-dev python3-appdirs python3-attr python3-brotli python3-cctbx python3-certifi python3-chardet python3-charset-normalizer python3-contourpy python3-dateutil python3-decorator python3-dev python3-distutils python3-fonttools python3-fs python3-idna python3-kiwisolver python3-lib2to3 python3-lxml python3-lz4 python3-matplotlib python3-minimal python3-numpy python3-opengl python3-packaging python3-pil python3-pil.imagetk python3-pkg-resources python3-ply python3-procrunner python3-pycbf python3-pymol python3-pyparsing python3-pyqt5 python3-pyqt5.qtopengl python3-pyqt5.sip python3-pythran python3-requests python3-scipy python3-sympy python3-tk python3-tqdm python3-tz python3-ufolib2 python3-urllib3 python3-wxgtk4.0 python3.11 python3.11-dev python3.11-minimal readline-common sed shared-mime-info sphinx-rtd-theme-common systemd systemd-sysv sysvinit-utils tar tk8.6-blt2.5 tzdata unicode-data usr-is-merged util-linux util-linux-extra xkb-data zlib1g zlib1g-dev 367 upgraded, 57 newly installed, 16 to remove and 0 not upgraded. Need to get 471 MB of archives. After this operation, 780 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 base-files amd64 13 [70.6 kB] Get:2 http://deb.debian.org/debian sid/main amd64 debianutils amd64 5.17 [89.0 kB] Get:3 http://deb.debian.org/debian sid/main amd64 bash amd64 5.2.21-2 [1492 kB] Get:4 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.39.3-7 [96.9 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libnsl-dev amd64 1.3.0-3 [66.9 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libcrypt-dev amd64 1:4.4.36-4 [119 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libc6-dev amd64 2.37-15.1 [1905 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libc-dev-bin amd64 2.37-15.1 [47.1 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libtirpc-common all 1.3.4+ds-1.1 [10.8 kB] Get:10 http://deb.debian.org/debian sid/main amd64 libtirpc-dev amd64 1.3.4+ds-1.1 [189 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libzstd1 amd64 1.5.5+dfsg2-2 [295 kB] Get:12 http://deb.debian.org/debian sid/main amd64 gcc-14-base amd64 14-20240221-2.1 [42.8 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 14-20240221-2.1 [72.2 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 14-20240221-2.1 [713 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libbz2-1.0 amd64 1.0.8-5+b2 [38.2 kB] Get:16 http://deb.debian.org/debian sid/main amd64 libgpg-error0 amd64 1.47-3 [77.8 kB] Get:17 http://deb.debian.org/debian sid/main amd64 libgcrypt20 amd64 1.10.3-2 [708 kB] Get:18 http://deb.debian.org/debian sid/main amd64 liblz4-1 amd64 1.9.4-1+b2 [61.6 kB] Get:19 http://deb.debian.org/debian sid/main amd64 liblzma5 amd64 5.6.0-0.2 [250 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libacl1 amd64 2.3.2-1 [32.4 kB] Get:21 http://deb.debian.org/debian sid/main amd64 libapparmor1 amd64 3.0.12-1+b2 [41.5 kB] Get:22 http://deb.debian.org/debian sid/main amd64 libaudit-common all 1:3.1.2-2.1 [11.4 kB] Get:23 http://deb.debian.org/debian sid/main amd64 libcap-ng0 amd64 0.8.4-2 [16.9 kB] Get:24 http://deb.debian.org/debian sid/main amd64 libaudit1 amd64 1:3.1.2-2.1 [48.5 kB] Get:25 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.39.3-7 [159 kB] Get:26 http://deb.debian.org/debian sid/main amd64 libcap2 amd64 1:2.66-5 [27.4 kB] Get:27 http://deb.debian.org/debian sid/main amd64 libcrypt1 amd64 1:4.4.36-4 [89.8 kB] Get:28 http://deb.debian.org/debian sid/main amd64 openssl amd64 3.1.5-1.1 [1241 kB] Get:29 http://deb.debian.org/debian sid/main amd64 zlib1g-dev amd64 1:1.3.dfsg-3.1 [918 kB] Get:30 http://deb.debian.org/debian sid/main amd64 zlib1g amd64 1:1.3.dfsg-3.1 [87.6 kB] Get:31 http://deb.debian.org/debian sid/main amd64 libssh2-1 amd64 1.11.0-4 [215 kB] Get:32 http://deb.debian.org/debian sid/main amd64 dbus-session-bus-common all 1.14.10-4 [79.0 kB] Get:33 http://deb.debian.org/debian sid/main amd64 perl-base amd64 5.38.2-3 [1643 kB] Get:34 http://deb.debian.org/debian sid/main amd64 debconf all 1.5.86 [119 kB] Get:35 http://deb.debian.org/debian sid/main amd64 libpam0g amd64 1.5.3-6 [67.7 kB] Get:36 http://deb.debian.org/debian sid/main amd64 libpcre2-8-0 amd64 10.42-4+b1 [262 kB] Get:37 http://deb.debian.org/debian sid/main amd64 libselinux1 amd64 3.5-2 [74.8 kB] Get:38 http://deb.debian.org/debian sid/main amd64 libsystemd-shared amd64 255.4-1 [1936 kB] Get:39 http://deb.debian.org/debian sid/main amd64 systemd amd64 255.4-1 [3528 kB] Get:40 http://deb.debian.org/debian sid/main amd64 systemd-dev all 255.4-1 [59.7 kB] Get:41 http://deb.debian.org/debian sid/main amd64 libpam-systemd amd64 255.4-1 [260 kB] Get:42 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 255.4-1 [364 kB] Get:43 http://deb.debian.org/debian sid/main amd64 libpam-modules-bin amd64 1.5.3-6 [54.2 kB] Get:44 http://deb.debian.org/debian sid/main amd64 libpam-modules amd64 1.5.3-6 [260 kB] Get:45 http://deb.debian.org/debian sid/main amd64 libpam-runtime all 1.5.3-6 [140 kB] Get:46 http://deb.debian.org/debian sid/main amd64 systemd-sysv amd64 255.4-1 [50.4 kB] Get:47 http://deb.debian.org/debian sid/main amd64 dbus-user-session amd64 1.14.10-4 [78.9 kB] Get:48 http://deb.debian.org/debian sid/main amd64 libexpat1-dev amd64 2.6.0-1 [154 kB] Get:49 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.6.0-1 [101 kB] Get:50 http://deb.debian.org/debian sid/main amd64 dbus-system-bus-common all 1.14.10-4 [80.1 kB] Get:51 http://deb.debian.org/debian sid/main amd64 dbus-bin amd64 1.14.10-4 [106 kB] Get:52 http://deb.debian.org/debian sid/main amd64 dbus amd64 1.14.10-4 [98.3 kB] Get:53 http://deb.debian.org/debian sid/main amd64 dbus-daemon amd64 1.14.10-4 [184 kB] Get:54 http://deb.debian.org/debian sid/main amd64 libsemanage-common all 3.5-1 [9908 B] Get:55 http://deb.debian.org/debian sid/main amd64 libsepol2 amd64 3.5-2 [277 kB] Get:56 http://deb.debian.org/debian sid/main amd64 libsemanage2 amd64 3.5-1+b2 [90.3 kB] Get:57 http://deb.debian.org/debian sid/main amd64 passwd amd64 1:4.13+dfsg1-4 [973 kB] Get:58 http://deb.debian.org/debian sid/main amd64 adduser all 3.137 [140 kB] Get:59 http://deb.debian.org/debian sid/main amd64 usr-is-merged all 39 [5572 B] Get:60 http://deb.debian.org/debian sid/main amd64 libdbus-1-3 amd64 1.14.10-4 [203 kB] Get:61 http://deb.debian.org/debian sid/main amd64 libqt5dbus5 amd64 5.15.10+dfsg-7 [213 kB] Get:62 http://deb.debian.org/debian sid/main amd64 libqt5xml5 amd64 5.15.10+dfsg-7 [123 kB] Get:63 http://deb.debian.org/debian sid/main amd64 xkb-data all 2.41-2 [795 kB] Get:64 http://deb.debian.org/debian sid/main amd64 libx11-data all 2:1.8.7-1 [328 kB] Get:65 http://deb.debian.org/debian sid/main amd64 libx11-xcb1 amd64 2:1.8.7-1 [232 kB] Get:66 http://deb.debian.org/debian sid/main amd64 libx11-6 amd64 2:1.8.7-1 [802 kB] Get:67 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get:68 http://deb.debian.org/debian sid/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get:69 http://deb.debian.org/debian sid/main amd64 fontconfig-config amd64 2.15.0-1 [317 kB] Get:70 http://deb.debian.org/debian sid/main amd64 libbrotli1 amd64 1.1.0-2+b3 [305 kB] Get:71 http://deb.debian.org/debian sid/main amd64 libpng16-16 amd64 1.6.43-1 [277 kB] Get:72 http://deb.debian.org/debian sid/main amd64 libfreetype6 amd64 2.13.2+dfsg-1+b1 [439 kB] Get:73 http://deb.debian.org/debian sid/main amd64 libfontconfig1 amd64 2.15.0-1 [388 kB] Get:74 http://deb.debian.org/debian sid/main amd64 fontconfig amd64 2.15.0-1 [462 kB] Get:75 http://deb.debian.org/debian sid/main amd64 libdrm-common all 2.4.120-2 [7688 B] Get:76 http://deb.debian.org/debian sid/main amd64 libdrm2 amd64 2.4.120-2 [38.1 kB] Get:77 http://deb.debian.org/debian sid/main amd64 libopengl0 amd64 1.7.0-1 [30.8 kB] Get:78 http://deb.debian.org/debian sid/main amd64 libgl1 amd64 1.7.0-1 [89.7 kB] Get:79 http://deb.debian.org/debian sid/main amd64 libffi8 amd64 3.4.6-1 [23.6 kB] Get:80 http://deb.debian.org/debian sid/main amd64 libwayland-server0 amd64 1.22.0-2.1+b1 [33.0 kB] Get:81 http://deb.debian.org/debian sid/main amd64 libegl-mesa0 amd64 24.0.2-1 [119 kB] Get:82 http://deb.debian.org/debian sid/main amd64 libgbm1 amd64 24.0.2-1 [40.6 kB] Get:83 http://deb.debian.org/debian sid/main amd64 libwayland-client0 amd64 1.22.0-2.1+b1 [25.7 kB] Get:84 http://deb.debian.org/debian sid/main amd64 libvulkan1 amd64 1.3.275.0-1 [124 kB] Get:85 http://deb.debian.org/debian sid/main amd64 libdrm-amdgpu1 amd64 2.4.120-2 [21.4 kB] Get:86 http://deb.debian.org/debian sid/main amd64 libelf1t64 amd64 0.190-1.1 [176 kB] Get:87 http://deb.debian.org/debian sid/main amd64 libmd0 amd64 1.1.0-2 [35.8 kB] Get:88 http://deb.debian.org/debian sid/main amd64 libbsd0 amd64 0.12.1-1 [129 kB] Get:89 http://deb.debian.org/debian sid/main amd64 libncursesw6 amd64 6.4+20240113-1 [135 kB] Get:90 http://deb.debian.org/debian sid/main amd64 libtinfo6 amd64 6.4+20240113-1 [342 kB] Get:91 http://deb.debian.org/debian sid/main amd64 libedit2 amd64 3.1-20230828-1 [93.1 kB] Get:92 http://deb.debian.org/debian sid/main amd64 libicu72 amd64 72.1-4+b1 [9395 kB] Get:93 http://deb.debian.org/debian sid/main amd64 libxml2 amd64 2.9.14+dfsg-1.3+b2 [692 kB] Get:94 http://deb.debian.org/debian sid/main amd64 libz3-4 amd64 4.8.12-3.1+b2 [7346 kB] Get:95 http://deb.debian.org/debian sid/main amd64 libllvm17 amd64 1:17.0.6-5 [23.7 MB] Get:96 http://deb.debian.org/debian sid/main amd64 libpciaccess0 amd64 0.17-3 [51.6 kB] Get:97 http://deb.debian.org/debian sid/main amd64 libdrm-intel1 amd64 2.4.120-2 [62.7 kB] Get:98 http://deb.debian.org/debian sid/main amd64 libdrm-nouveau2 amd64 2.4.120-2 [19.3 kB] Get:99 http://deb.debian.org/debian sid/main amd64 libdrm-radeon1 amd64 2.4.120-2 [22.2 kB] Get:100 http://deb.debian.org/debian sid/main amd64 libsensors-config all 1:3.6.0-9 [14.6 kB] Get:101 http://deb.debian.org/debian sid/main amd64 libsensors5 amd64 1:3.6.0-9 [34.6 kB] Get:102 http://deb.debian.org/debian sid/main amd64 libgl1-mesa-dri amd64 24.0.2-1 [8278 kB] Get:103 http://deb.debian.org/debian sid/main amd64 libglx-mesa0 amd64 24.0.2-1 [151 kB] Get:104 http://deb.debian.org/debian sid/main amd64 libglapi-mesa amd64 24.0.2-1 [36.1 kB] Get:105 http://deb.debian.org/debian sid/main amd64 libglx0 amd64 1.7.0-1 [34.7 kB] Get:106 http://deb.debian.org/debian sid/main amd64 libegl1 amd64 1.7.0-1 [34.0 kB] Get:107 http://deb.debian.org/debian sid/main amd64 libglvnd0 amd64 1.7.0-1 [51.3 kB] Get:108 http://deb.debian.org/debian sid/main amd64 shared-mime-info amd64 2.4-1 [751 kB] Get:109 http://deb.debian.org/debian sid/main amd64 libgssapi-krb5-2 amd64 1.20.1-5+b1 [135 kB] Get:110 http://deb.debian.org/debian sid/main amd64 libkrb5-3 amd64 1.20.1-5+b1 [333 kB] Get:111 http://deb.debian.org/debian sid/main amd64 libk5crypto3 amd64 1.20.1-5+b1 [80.0 kB] Get:112 http://deb.debian.org/debian sid/main amd64 libkrb5support0 amd64 1.20.1-5+b1 [33.2 kB] Get:113 http://deb.debian.org/debian sid/main amd64 libcom-err2t64 amd64 1.47.0-2.3 [20.2 kB] Get:114 http://deb.debian.org/debian sid/main amd64 libext2fs2t64 amd64 1.47.0-2.3 [206 kB] Get:115 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.39.3-7 [29.9 kB] Get:116 http://deb.debian.org/debian sid/main amd64 libuuid1t64 amd64 2.39.3-6.1 [30.0 kB] Get:117 http://deb.debian.org/debian sid/main amd64 logsave amd64 1.47.0-2.3 [19.9 kB] Get:118 http://deb.debian.org/debian sid/main amd64 libss2t64 amd64 1.47.0-2.3 [24.9 kB] Get:119 http://deb.debian.org/debian sid/main amd64 e2fsprogs amd64 1.47.0-2.3 [571 kB] Get:120 http://deb.debian.org/debian sid/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get:121 http://deb.debian.org/debian sid/main amd64 libunistring5 amd64 1.1-2 [421 kB] Get:122 http://deb.debian.org/debian sid/main amd64 libidn2-0 amd64 2.3.7-2 [128 kB] Get:123 http://deb.debian.org/debian sid/main amd64 libnettle8 amd64 3.9.1-2+b1 [296 kB] Get:124 http://deb.debian.org/debian sid/main amd64 libp11-kit0 amd64 0.25.3-4 [418 kB] Get:125 http://deb.debian.org/debian sid/main amd64 libnghttp2-14 amd64 1.59.0-1 [74.3 kB] Get:126 http://deb.debian.org/debian sid/main amd64 libpsl5 amd64 0.21.2-1+b1 [59.1 kB] Get:127 http://deb.debian.org/debian sid/main amd64 libcurl3-gnutls amd64 8.6.0-3 [421 kB] Get:128 http://deb.debian.org/debian sid/main amd64 libavahi-client3 amd64 0.8-13+b1 [47.1 kB] Get:129 http://deb.debian.org/debian sid/main amd64 libavahi-common3 amd64 0.8-13+b1 [43.3 kB] Get:130 http://deb.debian.org/debian sid/main amd64 libavahi-common-data amd64 0.8-13+b1 [111 kB] Get:131 http://deb.debian.org/debian sid/main amd64 libcups2 amd64 2.4.7-1+b1 [247 kB] Get:132 http://deb.debian.org/debian sid/main amd64 libdebconfclient0 amd64 0.271+b1 [10.2 kB] Get:133 http://deb.debian.org/debian sid/main amd64 base-passwd amd64 3.6.3 [50.8 kB] Get:134 http://deb.debian.org/debian sid/main amd64 gpgv amd64 2.2.40-1.1+b1 [649 kB] Get:135 http://deb.debian.org/debian sid/main amd64 debian-archive-keyring all 2023.4 [161 kB] Get:136 http://deb.debian.org/debian sid/main amd64 libseccomp2 amd64 2.5.5-1 [47.0 kB] Get:137 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0t64 amd64 2.7.13+b1 [984 kB] Get:138 http://deb.debian.org/debian sid/main amd64 libgmp10 amd64 2:6.3.0+dfsg-2+b1 [559 kB] Get:139 http://deb.debian.org/debian sid/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-4+b1 [19.7 kB] Get:140 http://deb.debian.org/debian sid/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-4+b1 [57.0 kB] Get:141 http://deb.debian.org/debian sid/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5+b3 [184 kB] Get:142 http://deb.debian.org/debian sid/main amd64 libgnutls30t64 amd64 3.8.3-1.1 [1425 kB] Get:143 http://deb.debian.org/debian sid/main amd64 apt amd64 2.7.13+b1 [1368 kB] Get:144 http://deb.debian.org/debian sid/main amd64 libhogweed6 amd64 3.9.1-2+b1 [328 kB] Get:145 http://deb.debian.org/debian sid/main amd64 libtasn1-6 amd64 4.19.0-3+b2 [48.9 kB] Get:146 http://deb.debian.org/debian sid/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-5 [697 kB] Get:147 http://deb.debian.org/debian sid/main amd64 libcurl4 amd64 8.6.0-3 [430 kB] Get:148 http://deb.debian.org/debian sid/main amd64 libpcre2-32-0 amd64 10.42-4+b1 [234 kB] Get:149 http://deb.debian.org/debian sid/main amd64 libwxbase3.2-1 amd64 3.2.4+dfsg-3 [1011 kB] Get:150 http://deb.debian.org/debian sid/main amd64 libcairo-gobject2 amd64 1.18.0-1+b1 [129 kB] Get:151 http://deb.debian.org/debian sid/main amd64 libpixman-1-0 amd64 0.42.2-1+b1 [556 kB] Get:152 http://deb.debian.org/debian sid/main amd64 libcairo2 amd64 1.18.0-1+b1 [531 kB] Get:153 http://deb.debian.org/debian sid/main amd64 libgdk-pixbuf2.0-common all 2.42.10+dfsg-3 [307 kB] Get:154 http://deb.debian.org/debian sid/main amd64 libjpeg62-turbo amd64 1:2.1.5-2+b2 [167 kB] Get:155 http://deb.debian.org/debian sid/main amd64 libsharpyuv0 amd64 1.3.2-0.4 [108 kB] Get:156 http://deb.debian.org/debian sid/main amd64 libwebp7 amd64 1.3.2-0.4 [308 kB] Get:157 http://deb.debian.org/debian sid/main amd64 libdeflate0 amd64 1.19-1 [41.4 kB] Get:158 http://deb.debian.org/debian sid/main amd64 libjbig0 amd64 2.1-6.1+b1 [32.0 kB] Get:159 http://deb.debian.org/debian sid/main amd64 liblerc4 amd64 4.0.0+ds-4+b1 [171 kB] Get:160 http://deb.debian.org/debian sid/main amd64 libtiff6 amd64 4.5.1+git230720-4 [322 kB] Get:161 http://deb.debian.org/debian sid/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.10+dfsg-3+b1 [138 kB] Get:162 http://deb.debian.org/debian sid/main amd64 libcloudproviders0 amd64 0.3.5-1 [28.7 kB] Get:163 http://deb.debian.org/debian sid/main amd64 libproc2-0 amd64 2:4.0.4-4 [64.6 kB] Get:164 http://deb.debian.org/debian sid/main amd64 init-system-helpers all 1.66 [39.0 kB] Get:165 http://deb.debian.org/debian sid/main amd64 procps amd64 2:4.0.4-4 [880 kB] Get:166 http://deb.debian.org/debian sid/main amd64 dconf-service amd64 0.40.0-4+b1 [32.5 kB] Get:167 http://deb.debian.org/debian sid/main amd64 dconf-gsettings-backend amd64 0.40.0-4+b1 [28.7 kB] Get:168 http://deb.debian.org/debian sid/main amd64 libdconf1 amd64 0.40.0-4+b1 [41.8 kB] Get:169 http://deb.debian.org/debian sid/main amd64 libgtk-3-common all 3.24.41-1.1 [4634 kB] Get:170 http://deb.debian.org/debian sid/main amd64 gtk-update-icon-cache amd64 3.24.41-1.1 [45.7 kB] Get:171 http://deb.debian.org/debian sid/main amd64 adwaita-icon-theme all 46~beta-4 [614 kB] Get:172 http://deb.debian.org/debian sid/main amd64 at-spi2-common all 2.51.90-1 [165 kB] Get:173 http://deb.debian.org/debian sid/main amd64 libatk1.0-0 amd64 2.50.0-1+b1 [50.1 kB] Get:174 http://deb.debian.org/debian sid/main amd64 libxi6 amd64 2:1.8.1-1 [79.0 kB] Get:175 http://deb.debian.org/debian sid/main amd64 libatspi2.0-0 amd64 2.50.0-1+b1 [74.2 kB] Get:176 http://deb.debian.org/debian sid/main amd64 libatk-bridge2.0-0 amd64 2.50.0-1+b1 [65.7 kB] Get:177 http://deb.debian.org/debian sid/main amd64 liblcms2-2 amd64 2.14-2+b1 [154 kB] Get:178 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 255.4-1 [125 kB] Get:179 http://deb.debian.org/debian sid/main amd64 libcolord2 amd64 1.4.7-1 [139 kB] Get:180 http://deb.debian.org/debian sid/main amd64 libepoxy0 amd64 1.5.10-1+b2 [191 kB] Get:181 http://deb.debian.org/debian sid/main amd64 libfribidi0 amd64 1.0.13-3+b1 [71.4 kB] Get:182 http://deb.debian.org/debian sid/main amd64 libgraphite2-3 amd64 1.3.14-2 [74.9 kB] Get:183 http://deb.debian.org/debian sid/main amd64 libharfbuzz0b amd64 8.3.0-2 [2213 kB] Get:184 http://deb.debian.org/debian sid/main amd64 libpangocairo-1.0-0 amd64 1.52.0+ds-1 [35.0 kB] Get:185 http://deb.debian.org/debian sid/main amd64 libpango-1.0-0 amd64 1.52.0+ds-1 [216 kB] Get:186 http://deb.debian.org/debian sid/main amd64 libpangoft2-1.0-0 amd64 1.52.0+ds-1 [48.0 kB] Get:187 http://deb.debian.org/debian sid/main amd64 libthai-data all 0.1.29-2 [168 kB] Get:188 http://deb.debian.org/debian sid/main amd64 libdatrie1 amd64 0.2.13-3 [37.7 kB] Get:189 http://deb.debian.org/debian sid/main amd64 libthai0 amd64 0.1.29-2 [49.1 kB] Get:190 http://deb.debian.org/debian sid/main amd64 libwayland-cursor0 amd64 1.22.0-2.1+b1 [11.3 kB] Get:191 http://deb.debian.org/debian sid/main amd64 libwayland-egl1 amd64 1.22.0-2.1+b1 [5640 B] Get:192 http://deb.debian.org/debian sid/main amd64 libxkbcommon-x11-0 amd64 1.6.0-1 [16.0 kB] Get:193 http://deb.debian.org/debian sid/main amd64 libxkbcommon0 amd64 1.6.0-1 [108 kB] Get:194 http://deb.debian.org/debian sid/main amd64 libgtk-3-0 amd64 3.24.41-1 [2726 kB] Get:195 http://deb.debian.org/debian sid/main amd64 libnotify4 amd64 0.8.3-1 [25.6 kB] Get:196 http://deb.debian.org/debian sid/main amd64 libwxgtk3.2-1 amd64 3.2.4+dfsg-3 [4558 kB] Get:197 http://deb.debian.org/debian sid/main amd64 libwxgtk-gl3.2-1 amd64 3.2.4+dfsg-3 [81.3 kB] Get:198 http://deb.debian.org/debian sid/main amd64 libwacom9 amd64 2.10.0-1 [22.4 kB] Get:199 http://deb.debian.org/debian sid/main amd64 libwacom-common all 2.10.0-1 [62.4 kB] Get:200 http://deb.debian.org/debian sid/main amd64 libevdev2 amd64 1.13.1+dfsg-1 [32.0 kB] Get:201 http://deb.debian.org/debian sid/main amd64 libgudev-1.0-0 amd64 238-3 [14.3 kB] Get:202 http://deb.debian.org/debian sid/main amd64 libglib2.0-0t64 amd64 2.78.4-2.1 [1454 kB] Get:203 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.39.3-7 [190 kB] Get:204 http://deb.debian.org/debian sid/main amd64 libinput-bin amd64 1.25.0-1 [24.6 kB] Get:205 http://deb.debian.org/debian sid/main amd64 libmtdev1 amd64 1.1.6-1+b1 [22.2 kB] Get:206 http://deb.debian.org/debian sid/main amd64 libinput10 amd64 1.25.0-1 [128 kB] Get:207 http://deb.debian.org/debian sid/main amd64 libmd4c0 amd64 0.4.8-1+b1 [45.1 kB] Get:208 http://deb.debian.org/debian sid/main amd64 libxcb-icccm4 amd64 0.4.1-1.1+b1 [26.8 kB] Get:209 http://deb.debian.org/debian sid/main amd64 libxcb-image0 amd64 0.4.0-2+b1 [22.2 kB] Get:210 http://deb.debian.org/debian sid/main amd64 libqt5gui5 amd64 5.15.10+dfsg-7 [3442 kB] Get:211 http://deb.debian.org/debian sid/main amd64 libqt5widgets5 amd64 5.15.10+dfsg-7 [2385 kB] Get:212 http://deb.debian.org/debian sid/main amd64 libqt5test5 amd64 5.15.10+dfsg-7 [148 kB] Get:213 http://deb.debian.org/debian sid/main amd64 libqt5sql5 amd64 5.15.10+dfsg-7 [123 kB] Get:214 http://deb.debian.org/debian sid/main amd64 libqt5printsupport5 amd64 5.15.10+dfsg-7 [203 kB] Get:215 http://deb.debian.org/debian sid/main amd64 libqt5opengl5 amd64 5.15.10+dfsg-7 [149 kB] Get:216 http://deb.debian.org/debian sid/main amd64 libqt5designer5 amd64 5.15.10-6 [2749 kB] Get:217 http://deb.debian.org/debian sid/main amd64 libdouble-conversion3 amd64 3.3.0-1+b1 [41.0 kB] Get:218 http://deb.debian.org/debian sid/main amd64 libpcre2-16-0 amd64 10.42-4+b1 [246 kB] Get:219 http://deb.debian.org/debian sid/main amd64 python3-pyqt5.qtopengl amd64 5.15.10+dfsg-1 [207 kB] Get:220 http://deb.debian.org/debian sid/main amd64 python3-pyqt5 amd64 5.15.10+dfsg-1 [2503 kB] Get:221 http://deb.debian.org/debian sid/main amd64 libqt5network5 amd64 5.15.10+dfsg-7 [676 kB] Get:222 http://deb.debian.org/debian sid/main amd64 libqt5core5a amd64 5.15.10+dfsg-7 [1834 kB] Get:223 http://deb.debian.org/debian sid/main amd64 libaec0 amd64 1.1.2-1 [23.4 kB] Get:224 http://deb.debian.org/debian sid/main amd64 libsz2 amd64 1.1.2-1 [7684 B] Get:225 http://deb.debian.org/debian sid/main amd64 python3-cctbx amd64 2023.12+ds2+~3.17.0+ds1-4 [50.1 MB] Get:226 http://deb.debian.org/debian sid/main amd64 libnetcdf19 amd64 1:4.9.2-3+b1 [471 kB] Get:227 http://deb.debian.org/debian sid/main amd64 libhdf5-hl-100 amd64 1.10.10+repack-3+b1 [63.3 kB] Get:228 http://deb.debian.org/debian sid/main amd64 libcbf1t64 amd64 0.9.7+dfsg1-3.1 [359 kB] Get:229 http://deb.debian.org/debian sid/main amd64 libhdf5-103-1t64 amd64 1.10.10+repack-3.1 [1242 kB] Get:230 http://deb.debian.org/debian sid/main amd64 libssl3t64 amd64 3.1.5-1.1 [2058 kB] Get:231 http://deb.debian.org/debian sid/main amd64 libkmod2 amd64 31+20240202-2 [59.6 kB] Get:232 http://deb.debian.org/debian sid/main amd64 libargon2-1 amd64 0~20190702+dfsg-4+b1 [21.1 kB] Get:233 http://deb.debian.org/debian sid/main amd64 dmsetup amd64 2:1.02.196-1 [82.4 kB] Get:234 http://deb.debian.org/debian sid/main amd64 libdevmapper1.02.1 amd64 2:1.02.196-1 [133 kB] Get:235 http://deb.debian.org/debian sid/main amd64 libjson-c5 amd64 0.17-1+b1 [44.2 kB] Get:236 http://deb.debian.org/debian sid/main amd64 libcryptsetup12 amd64 2:2.7.0-1 [246 kB] Get:237 http://deb.debian.org/debian sid/main amd64 libfdisk1 amd64 2.39.3-7 [202 kB] Get:238 http://deb.debian.org/debian sid/main amd64 mount amd64 2.39.3-7 [143 kB] Get:239 http://deb.debian.org/debian sid/main amd64 libxxhash0 amd64 0.8.2-2+b1 [26.6 kB] Get:240 http://deb.debian.org/debian sid/main amd64 tar amd64 1.35+dfsg-3 [813 kB] Get:241 http://deb.debian.org/debian sid/main amd64 dpkg amd64 1.22.5 [1510 kB] Get:242 http://deb.debian.org/debian sid/main amd64 netbase all 6.4 [12.8 kB] Get:243 http://deb.debian.org/debian sid/main amd64 python3.11 amd64 3.11.8-2 [597 kB] Get:244 http://deb.debian.org/debian sid/main amd64 python3.11-dev amd64 3.11.8-2 [509 kB] Get:245 http://deb.debian.org/debian sid/main amd64 libpython3.11t64 amd64 3.11.8-2 [1992 kB] Get:246 http://deb.debian.org/debian sid/main amd64 libpython3.11-dev amd64 3.11.8-2 [4575 kB] Get:247 http://deb.debian.org/debian sid/main amd64 libpython3.11-stdlib amd64 3.11.8-2 [1827 kB] Get:248 http://deb.debian.org/debian sid/main amd64 libpython3.11-minimal amd64 3.11.8-2 [817 kB] Get:249 http://deb.debian.org/debian sid/main amd64 python3.11-minimal amd64 3.11.8-2 [2037 kB] Get:250 http://deb.debian.org/debian sid/main amd64 python3-all-dev amd64 3.11.6-1 [1076 B] Get:251 http://deb.debian.org/debian sid/main amd64 python3-all amd64 3.11.6-1 [1060 B] Get:252 http://deb.debian.org/debian sid/main amd64 libpython3-all-dev amd64 3.11.6-1 [1072 B] Get:253 http://deb.debian.org/debian sid/main amd64 libpython3-dev amd64 3.11.6-1 [9460 B] Get:254 http://deb.debian.org/debian sid/main amd64 python3-dev amd64 3.11.6-1 [26.1 kB] Get:255 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.11.6-1 [26.2 kB] Get:256 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.11.6-1 [26.2 kB] Get:257 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.11.6-1 [9224 B] Get:258 http://deb.debian.org/debian sid/main amd64 python3-distutils all 3.11.5-1 [131 kB] Get:259 http://deb.debian.org/debian sid/main amd64 python3-lib2to3 all 3.11.5-1 [77.5 kB] Get:260 http://deb.debian.org/debian sid/main amd64 libpython3.12-minimal amd64 3.12.2-3 [807 kB] Get:261 http://deb.debian.org/debian sid/main amd64 python3.12-minimal amd64 3.12.2-3 [2187 kB] Get:262 http://deb.debian.org/debian sid/main amd64 readline-common all 8.2-3.1 [69.2 kB] Get:263 http://deb.debian.org/debian sid/main amd64 libreadline8t64 amd64 8.2-3.1 [167 kB] Get:264 http://deb.debian.org/debian sid/main amd64 media-types all 10.1.0 [26.9 kB] Get:265 http://deb.debian.org/debian sid/main amd64 tzdata all 2024a-1 [255 kB] Get:266 http://deb.debian.org/debian sid/main amd64 libsqlite3-0 amd64 3.45.1-1 [894 kB] Get:267 http://deb.debian.org/debian sid/main amd64 libpython3.12-stdlib amd64 3.12.2-3 [1929 kB] Get:268 http://deb.debian.org/debian sid/main amd64 python3.12 amd64 3.12.2-3 [653 kB] Get:269 http://deb.debian.org/debian sid/main amd64 libjs-sphinxdoc all 7.2.6-4 [150 kB] Get:270 http://deb.debian.org/debian sid/main amd64 libpython3.12t64 amd64 3.12.2-3 [2129 kB] Get:271 http://deb.debian.org/debian sid/main amd64 libpython3.12-dev amd64 3.12.2-3 [4944 kB] Get:272 http://deb.debian.org/debian sid/main amd64 python3.12-dev amd64 3.12.2-3 [506 kB] Get:273 http://deb.debian.org/debian sid/main amd64 python3-pyqt5.sip amd64 12.13.0-1+b1 [79.5 kB] Get:274 http://deb.debian.org/debian sid/main amd64 libqt5help5 amd64 5.15.10-6 [149 kB] Get:275 http://deb.debian.org/debian sid/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.1 [82.5 kB] Get:276 http://deb.debian.org/debian sid/main amd64 libnsl2 amd64 1.3.0-3 [40.0 kB] Get:277 http://deb.debian.org/debian sid/main amd64 linux-libc-dev all 6.6.15-2 [2247 kB] Get:278 http://deb.debian.org/debian sid/main amd64 libc6 amd64 2.37-15.1 [2752 kB] Get:279 http://deb.debian.org/debian sid/main amd64 libc-bin amd64 2.37-15.1 [602 kB] Get:280 http://deb.debian.org/debian sid/main amd64 coreutils amd64 9.4-3+b1 [2950 kB] Get:281 http://deb.debian.org/debian sid/main amd64 dash amd64 0.5.12-6 [92.1 kB] Get:282 http://deb.debian.org/debian sid/main amd64 diffutils amd64 1:3.10-1 [375 kB] Get:283 http://deb.debian.org/debian sid/main amd64 findutils amd64 4.9.0-5 [636 kB] Get:284 http://deb.debian.org/debian sid/main amd64 grep amd64 3.11-4 [431 kB] Get:285 http://deb.debian.org/debian sid/main amd64 hostname amd64 3.23+nmu2 [10.6 kB] Get:286 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.13+dfsg1-4 [616 kB] Get:287 http://deb.debian.org/debian sid/main amd64 ncurses-bin amd64 6.4+20240113-1 [431 kB] Get:288 http://deb.debian.org/debian sid/main amd64 sed amd64 4.9-2 [329 kB] Get:289 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.39.3-7 [117 kB] Get:290 http://deb.debian.org/debian sid/main amd64 util-linux-extra amd64 2.39.3-7 [155 kB] Get:291 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.39.3-7 [1231 kB] Get:292 http://deb.debian.org/debian sid/main amd64 ncurses-base all 6.4+20240113-1 [268 kB] Get:293 http://deb.debian.org/debian sid/main amd64 sysvinit-utils amd64 3.08-7 [32.2 kB] Get:294 http://deb.debian.org/debian sid/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Get:295 http://deb.debian.org/debian sid/main amd64 libboost-python-dev amd64 1.83.0.2+b2 [3892 B] Get:296 http://deb.debian.org/debian sid/main amd64 gcc-13-base amd64 13.2.0-16.1 [43.3 kB] Get:297 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14-20240221-2.1 [136 kB] Get:298 http://deb.debian.org/debian sid/main amd64 libitm1 amd64 14-20240221-2.1 [25.8 kB] Get:299 http://deb.debian.org/debian sid/main amd64 libatomic1 amd64 14-20240221-2.1 [9212 B] Get:300 http://deb.debian.org/debian sid/main amd64 libasan8 amd64 14-20240221-2.1 [2724 kB] Get:301 http://deb.debian.org/debian sid/main amd64 liblsan0 amd64 14-20240221-2.1 [1200 kB] Get:302 http://deb.debian.org/debian sid/main amd64 libisl23 amd64 0.26-3+b2 [652 kB] Get:303 http://deb.debian.org/debian sid/main amd64 libmpfr6 amd64 4.2.1-1+b1 [714 kB] Get:304 http://deb.debian.org/debian sid/main amd64 libmpc3 amd64 1.3.1-1+b2 [52.1 kB] Get:305 http://deb.debian.org/debian sid/main amd64 g++-12 amd64 12.3.0-15 [10.8 MB] Get:306 http://deb.debian.org/debian sid/main amd64 gcc-12 amd64 12.3.0-15 [19.5 MB] Get:307 http://deb.debian.org/debian sid/main amd64 cpp-12 amd64 12.3.0-15 [9860 kB] Get:308 http://deb.debian.org/debian sid/main amd64 libubsan1 amd64 14-20240221-2.1 [1071 kB] Get:309 http://deb.debian.org/debian sid/main amd64 libstdc++-12-dev amd64 12.3.0-15 [2069 kB] Get:310 http://deb.debian.org/debian sid/main amd64 libquadmath0 amd64 14-20240221-2.1 [147 kB] Get:311 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14-20240221-2.1 [836 kB] Get:312 http://deb.debian.org/debian sid/main amd64 libcc1-0 amd64 14-20240221-2.1 [42.0 kB] Get:313 http://deb.debian.org/debian sid/main amd64 libgcc-12-dev amd64 12.3.0-15 [2435 kB] Get:314 http://deb.debian.org/debian sid/main amd64 libtsan2 amd64 14-20240221-2.1 [2454 kB] Get:315 http://deb.debian.org/debian sid/main amd64 gcc-12-base amd64 12.3.0-15 [41.8 kB] Get:316 http://deb.debian.org/debian sid/main amd64 libgprofng0 amd64 2.42-3 [771 kB] Get:317 http://deb.debian.org/debian sid/main amd64 libctf0 amd64 2.42-3 [87.0 kB] Get:318 http://deb.debian.org/debian sid/main amd64 libctf-nobfd0 amd64 2.42-3 [152 kB] Get:319 http://deb.debian.org/debian sid/main amd64 binutils-x86-64-linux-gnu amd64 2.42-3 [2214 kB] Get:320 http://deb.debian.org/debian sid/main amd64 libbinutils amd64 2.42-3 [521 kB] Get:321 http://deb.debian.org/debian sid/main amd64 binutils amd64 2.42-3 [80.8 kB] Get:322 http://deb.debian.org/debian sid/main amd64 binutils-common amd64 2.42-3 [2538 kB] Get:323 http://deb.debian.org/debian sid/main amd64 libjansson4 amd64 2.14-2+b2 [39.9 kB] Get:324 http://deb.debian.org/debian sid/main amd64 libsframe1 amd64 2.42-3 [75.9 kB] Get:325 http://deb.debian.org/debian sid/main amd64 libhwasan0 amd64 14-20240221-2.1 [1485 kB] Get:326 http://deb.debian.org/debian sid/main amd64 libgcc-13-dev amd64 13.2.0-16.1 [2543 kB] Get:327 http://deb.debian.org/debian sid/main amd64 libstdc++-13-dev amd64 13.2.0-16.1 [2210 kB] Get:328 http://deb.debian.org/debian sid/main amd64 libboost1.83-dev amd64 1.83.0-2.1 [10.6 MB] Get:329 http://deb.debian.org/debian sid/main amd64 libboost-python1.83.0 amd64 1.83.0-2.1 [351 kB] Get:330 http://deb.debian.org/debian sid/main amd64 libboost-python1.83-dev amd64 1.83.0-2.1 [379 kB] Get:331 http://deb.debian.org/debian sid/main amd64 fonts-lato all 2.015-1 [2780 kB] Get:332 http://deb.debian.org/debian sid/main amd64 libattr1 amd64 1:2.5.2-1 [22.5 kB] Get:333 http://deb.debian.org/debian sid/main amd64 mawk amd64 1.3.4.20240123-1 [136 kB] Get:334 http://deb.debian.org/debian sid/main amd64 ca-certificates all 20240203 [158 kB] Get:335 http://deb.debian.org/debian sid/main amd64 libtcl8.6 amd64 8.6.13+dfsg-2+b1 [1033 kB] Get:336 http://deb.debian.org/debian sid/main amd64 libxft2 amd64 2.3.6-1+b1 [54.2 kB] Get:337 http://deb.debian.org/debian sid/main amd64 libtk8.6 amd64 8.6.13-2+b1 [783 kB] Get:338 http://deb.debian.org/debian sid/main amd64 blt amd64 2.5.3+dfsg-7 [6024 B] Get:339 http://deb.debian.org/debian sid/main amd64 tk8.6-blt2.5 amd64 2.5.3+dfsg-7 [586 kB] Get:340 http://deb.debian.org/debian sid/main amd64 cpp-13-x86-64-linux-gnu amd64 13.2.0-16.1 [10.3 MB] Get:341 http://deb.debian.org/debian sid/main amd64 g++ amd64 4:13.2.0-7 [1348 B] Get:342 http://deb.debian.org/debian sid/main amd64 gcc amd64 4:13.2.0-7 [5152 B] Get:343 http://deb.debian.org/debian sid/main amd64 cpp amd64 4:13.2.0-7 [1564 B] Get:344 http://deb.debian.org/debian sid/main amd64 cpp-x86-64-linux-gnu amd64 4:13.2.0-7 [4724 B] Get:345 http://deb.debian.org/debian sid/main amd64 gcc-13-x86-64-linux-gnu amd64 13.2.0-16.1 [19.8 MB] Get:346 http://deb.debian.org/debian sid/main amd64 g++-13-x86-64-linux-gnu amd64 13.2.0-16.1 [11.2 MB] Get:347 http://deb.debian.org/debian sid/main amd64 gcc-13 amd64 13.2.0-16.1 [476 kB] Get:348 http://deb.debian.org/debian sid/main amd64 g++-13 amd64 13.2.0-16.1 [14.7 kB] Get:349 http://deb.debian.org/debian sid/main amd64 gcc-x86-64-linux-gnu amd64 4:13.2.0-7 [1440 B] Get:350 http://deb.debian.org/debian sid/main amd64 g++-x86-64-linux-gnu amd64 4:13.2.0-7 [1200 B] Get:351 http://deb.debian.org/debian sid/main amd64 cpp-13 amd64 13.2.0-16.1 [1280 B] Get:352 http://deb.debian.org/debian sid/main amd64 fonts-lyx all 2.4.0~RC3-1 [189 kB] Get:353 http://deb.debian.org/debian sid/main amd64 libopenblas-pthread-dev amd64 0.3.26+ds-1 [4780 kB] Get:354 http://deb.debian.org/debian sid/main amd64 libopenblas0-pthread amd64 0.3.26+ds-1 [6807 kB] Get:355 http://deb.debian.org/debian sid/main amd64 libopenblas0 amd64 0.3.26+ds-1 [37.5 kB] Get:356 http://deb.debian.org/debian sid/main amd64 libopenblas-dev amd64 0.3.26+ds-1 [50.5 kB] Get:357 http://deb.debian.org/debian sid/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get:358 http://deb.debian.org/debian sid/main amd64 libboost-python1.74.0 amd64 1.74.0+ds1-23.1 [337 kB] Get:359 http://deb.debian.org/debian sid/main amd64 libboost-numpy1.74.0 amd64 1.74.0+ds1-23.1 [234 kB] Get:360 http://deb.debian.org/debian sid/main amd64 libboost-numpy1.83.0 amd64 1.83.0-2.1 [247 kB] Get:361 http://deb.debian.org/debian sid/main amd64 libboost-thread1.74.0 amd64 1.74.0+ds1-23.1 [256 kB] Get:362 http://deb.debian.org/debian sid/main amd64 libboost-thread1.83.0 amd64 1.83.0-2.1 [269 kB] Get:363 http://deb.debian.org/debian sid/main amd64 libcctbx-dev amd64 2023.12+ds2+~3.17.0+ds1-4 [1157 kB] Get:364 http://deb.debian.org/debian sid/main amd64 libcctbx0 amd64 2023.12+ds2+~3.17.0+ds1-4 [2375 kB] Get:365 http://deb.debian.org/debian sid/main amd64 python3-pycbf amd64 0.9.7+dfsg1-3.1 [193 kB] Get:366 http://deb.debian.org/debian sid/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get:367 http://deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get:368 http://deb.debian.org/debian sid/main amd64 python3-numpy amd64 1:1.24.2-2 [6299 kB] Get:369 http://deb.debian.org/debian sid/main amd64 liblzf1 amd64 3.6-4 [10.1 kB] Get:370 http://deb.debian.org/debian sid/main amd64 python3-h5py-serial amd64 3.10.0-1 [1399 kB] Get:371 http://deb.debian.org/debian sid/main amd64 python3-h5py all 3.10.0-1 [14.4 kB] Get:372 http://deb.debian.org/debian sid/main amd64 python3-dateutil all 2.8.2-3 [78.4 kB] Get:373 http://deb.debian.org/debian sid/main amd64 libimagequant0 amd64 2.18.0-1 [35.0 kB] Get:374 http://deb.debian.org/debian sid/main amd64 libopenjp2-7 amd64 2.5.0-2+b2 [190 kB] Get:375 http://deb.debian.org/debian sid/main amd64 libraqm0 amd64 0.10.1-1+b1 [14.2 kB] Get:376 http://deb.debian.org/debian sid/main amd64 libwebpdemux2 amd64 1.3.2-0.4 [107 kB] Get:377 http://deb.debian.org/debian sid/main amd64 libwebpmux3 amd64 1.3.2-0.4 [120 kB] Get:378 http://deb.debian.org/debian sid/main amd64 python3-pil.imagetk amd64 10.2.0-1 [77.7 kB] Get:379 http://deb.debian.org/debian sid/main amd64 python3-pil amd64 10.2.0-1 [525 kB] Get:380 http://deb.debian.org/debian sid/main amd64 python3-tk amd64 3.11.5-1 [108 kB] Get:381 http://deb.debian.org/debian sid/main amd64 python3-pyparsing all 3.1.1-1 [145 kB] Get:382 http://deb.debian.org/debian sid/main amd64 python3-contourpy amd64 1.0.7-1+b2 [287 kB] Get:383 http://deb.debian.org/debian sid/main amd64 python3-brotli amd64 1.1.0-2+b3 [312 kB] Get:384 http://deb.debian.org/debian sid/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get:385 http://deb.debian.org/debian sid/main amd64 liblbfgsb0 amd64 3.0+dfsg.4-1+b1 [29.1 kB] Get:386 http://deb.debian.org/debian sid/main amd64 python3-scipy amd64 1.11.4-6 [19.5 MB] Get:387 http://deb.debian.org/debian sid/main amd64 python3-attr all 23.2.0-2 [65.5 kB] Get:388 http://deb.debian.org/debian sid/main amd64 python3-ufolib2 all 0.16.0+dfsg1-1 [32.9 kB] Get:389 http://deb.debian.org/debian sid/main amd64 python3-sympy all 1.12-7 [3869 kB] Get:390 http://deb.debian.org/debian sid/main amd64 python3-tz all 2024.1-2 [30.9 kB] Get:391 http://deb.debian.org/debian sid/main amd64 python3-appdirs all 1.4.4-4 [12.5 kB] Get:392 http://deb.debian.org/debian sid/main amd64 python3-fs all 2.4.16-3 [95.3 kB] Get:393 http://deb.debian.org/debian sid/main amd64 python3-lxml amd64 5.1.0-1 [2092 kB] Get:394 http://deb.debian.org/debian sid/main amd64 python3-lz4 amd64 4.0.2+dfsg-1+b3 [25.5 kB] Get:395 http://deb.debian.org/debian sid/main amd64 unicode-data all 15.1.0-1 [8547 kB] Get:396 http://deb.debian.org/debian sid/main amd64 python3-fonttools amd64 4.46.0-1 [1623 kB] Get:397 http://deb.debian.org/debian sid/main amd64 python3-kiwisolver amd64 1.4.4-1+b2 [80.3 kB] Get:398 http://deb.debian.org/debian sid/main amd64 python3-packaging all 23.2-1 [44.8 kB] Get:399 http://deb.debian.org/debian sid/main amd64 libqhull-r8.0 amd64 2020.2-6+b1 [245 kB] Get:400 http://deb.debian.org/debian sid/main amd64 python3-matplotlib amd64 3.6.3-1+b2 [8166 kB] Get:401 http://deb.debian.org/debian sid/main amd64 python3-nxmx all 0.0.3-2 [15.1 kB] Get:402 http://deb.debian.org/debian sid/main amd64 python3-orderedset amd64 2.0.3+ds1-2 [91.8 kB] Get:403 http://deb.debian.org/debian sid/main amd64 python3-procrunner all 2.3.3-1 [13.8 kB] Get:404 http://deb.debian.org/debian sid/main amd64 python3-opengl all 3.1.7+dfsg-1 [604 kB] Get:405 http://deb.debian.org/debian sid/main amd64 python3-pymol amd64 2.5.0+dfsg-1+b4 [6971 kB] Get:406 http://deb.debian.org/debian sid/main amd64 python3-certifi all 2023.11.17-1 [155 kB] Get:407 http://deb.debian.org/debian sid/main amd64 python3-charset-normalizer all 3.3.2-1 [51.6 kB] Get:408 http://deb.debian.org/debian sid/main amd64 python3-idna all 3.6-2 [37.0 kB] Get:409 http://deb.debian.org/debian sid/main amd64 python3-urllib3 all 1.26.18-2 [116 kB] Get:410 http://deb.debian.org/debian sid/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get:411 http://deb.debian.org/debian sid/main amd64 python3-requests all 2.31.0+dfsg-1 [68.6 kB] Get:412 http://deb.debian.org/debian sid/main amd64 python3-tqdm all 4.64.1-2 [93.7 kB] Get:413 http://deb.debian.org/debian sid/main amd64 python3-wxgtk4.0 amd64 4.2.1+dfsg-3 [10.1 MB] Get:414 http://deb.debian.org/debian sid/main amd64 libmmdb2-0 amd64 2.0.22-1+b1 [341 kB] Get:415 http://deb.debian.org/debian sid/main amd64 libssm2 amd64 1.4.0-2+b1 [83.4 kB] Get:416 http://deb.debian.org/debian sid/main amd64 libgl1-mesa-glx amd64 23.1.3-1 [14.9 kB] Get:417 http://deb.debian.org/debian sid/main amd64 libip4tc2 amd64 1.8.10-3 [19.4 kB] Get:418 http://deb.debian.org/debian sid/main amd64 libllvm15 amd64 1:15.0.7-11 [23.2 MB] Get:419 http://deb.debian.org/debian sid/main amd64 xtl-dev all 0.7.5-3 [89.8 kB] Get:420 http://deb.debian.org/debian sid/main amd64 libxsimd-dev amd64 12.1.1-2 [124 kB] Get:421 http://deb.debian.org/debian sid/main amd64 python3-ply all 3.11-6 [63.7 kB] Get:422 http://deb.debian.org/debian sid/main amd64 python3-setuptools all 68.1.2-2 [468 kB] Get:423 http://deb.debian.org/debian sid/main amd64 python3-pythran amd64 0.15.0+ds-2 [443 kB] Get:424 http://deb.debian.org/debian sid/main amd64 sphinx-rtd-theme-common all 2.0.0+dfsg-1 [1021 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 471 MB in 3s (162 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 ... 57577 files and directories currently installed.) Preparing to unpack .../base-files_13_amd64.deb ... Unpacking base-files (13) over (12.4+deb12u5) ... Setting up base-files (13) ... Installing new version of config file /etc/debian_version ... Installing new version of config file /etc/issue ... Installing new version of config file /etc/issue.net ... (Reading database ... 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(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 ... 57579 files and directories currently installed.) Preparing to unpack .../liblzma5_5.6.0-0.2_amd64.deb ... Unpacking liblzma5:amd64 (5.6.0-0.2) over (5.4.1-0.2) ... Setting up liblzma5:amd64 (5.6.0-0.2) ... (Reading database ... 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Setting up zlib1g:amd64 (1:1.3.dfsg-3.1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 57577 files and directories currently installed.) Preparing to unpack .../libssh2-1_1.11.0-4_amd64.deb ... Unpacking libssh2-1:amd64 (1.11.0-4) over (1.10.0-3+b1) ... Preparing to unpack .../dbus-session-bus-common_1.14.10-4_all.deb ... Unpacking dbus-session-bus-common (1.14.10-4) over (1.14.10-1~deb12u1) ... Preparing to unpack .../perl-base_5.38.2-3_amd64.deb ... 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Unpacking systemd (255.4-1) over (252.22-1~deb12u1) ... dpkg: warning: unable to delete old directory '/lib/systemd/system-preset': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system-generators': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/user@0.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/user@.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/user-.slice.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/timers.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/systemd-localed.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/sysinit.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/rescue.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/rc-local.service.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/initrd.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/initrd-root-fs.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/initrd-root-device.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/graphical.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system/getty.target.wants': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/network': Directory not empty dpkg: warning: unable to delete old directory '/lib/modprobe.d': Directory not empty Selecting previously unselected package systemd-dev. Preparing to unpack .../systemd-dev_255.4-1_all.deb ... Unpacking systemd-dev (255.4-1) ... Preparing to unpack .../libpam-systemd_255.4-1_amd64.deb ... Unpacking libpam-systemd:amd64 (255.4-1) over (252.22-1~deb12u1) ... Preparing to unpack .../libsystemd0_255.4-1_amd64.deb ... Unpacking libsystemd0:amd64 (255.4-1) over (252.22-1~deb12u1) ... Setting up libsystemd0:amd64 (255.4-1) ... (Reading database ... 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Installing new version of config file /etc/systemd/logind.conf ... Installing new version of config file /etc/systemd/networkd.conf ... Installing new version of config file /etc/systemd/pstore.conf ... Installing new version of config file /etc/systemd/sleep.conf ... Installing new version of config file /etc/systemd/system.conf ... Installing new version of config file /etc/systemd/user.conf ... [ESC][0;1;31m"/home" already exists and is not a directory.[ESC][0m (Reading database ... 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(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 ... 53048 files and directories currently installed.) Removing libglib2.0-0:amd64 (2.74.6-2) ... Selecting previously unselected package libglib2.0-0t64:amd64. (Reading database ... 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Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-3.1) ... Preparing to unpack .../02-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) over (10.0.0) ... Preparing to unpack .../03-tzdata_2024a-1_all.deb ... Unpacking tzdata (2024a-1) over (2024a-0+deb12u1) ... Preparing to unpack .../04-libsqlite3-0_3.45.1-1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.45.1-1) over (3.40.1-2) ... Selecting previously unselected package libpython3.12-stdlib:amd64. 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Setting up libkeyutils1:amd64 (1.6.3-3) ... Setting up libpsl5:amd64 (0.21.2-1+b1) ... Setting up fonts-lato (2.015-1) ... Setting up libicu72:amd64 (72.1-4+b1) ... Setting up liblerc4:amd64 (4.0.0+ds-4+b1) ... Setting up libdatrie1:amd64 (0.2.13-3) ... Setting up libmmdb2-0:amd64 (2.0.22-1+b1) ... Setting up libglvnd0:amd64 (1.7.0-1) ... Setting up libtirpc-common (1.3.4+ds-1.1) ... Setting up fonts-lyx (2.4.0~RC3-1) ... Setting up libargon2-1:amd64 (0~20190702+dfsg-4+b1) ... Setting up libbrotli1:amd64 (1.1.0-2+b3) ... Setting up libsqlite3-0:amd64 (3.45.1-1) ... Setting up libgdk-pixbuf2.0-common (2.42.10+dfsg-3) ... Setting up libpython3.12-minimal:amd64 (3.12.2-3) ... Setting up binutils-common:amd64 (2.42-3) ... Installing new version of config file /etc/gprofng.rc ... Setting up libsensors-config (1:3.6.0-9) ... Setting up libnghttp2-14:amd64 (1.59.0-1) ... Setting up libdeflate0:amd64 (1.19-1) ... Setting up linux-libc-dev (6.6.15-2) ... Setting up libctf-nobfd0:amd64 (2.42-3) ... Setting up libboost-thread1.83.0:amd64 (1.83.0-2.1) ... Setting up libqhull-r8.0:amd64 (2020.2-6+b1) ... Setting up xkb-data (2.41-2) ... Setting up libxcb-icccm4:amd64 (0.4.1-1.1+b1) ... Setting up libgomp1:amd64 (14-20240221-2.1) ... Setting up libjbig0:amd64 (2.1-6.1+b1) ... Setting up libpcre2-16-0:amd64 (10.42-4+b1) ... Setting up libaec0:amd64 (1.1.2-1) ... Setting up libsframe1:amd64 (2.42-3) ... Setting up libopengl0:amd64 (1.7.0-1) ... Setting up libelf1t64:amd64 (0.190-1.1) ... Setting up libjansson4:amd64 (2.14-2+b2) ... Setting up libxcb-image0:amd64 (0.4.0-2+b1) ... Setting up libkrb5support0:amd64 (1.20.1-5+b1) ... Setting up gcc-12-base:amd64 (12.3.0-15) ... Setting up tzdata (2024a-1) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Mar 2 04:43:50 UTC 2024. Universal Time is now: Sat Mar 2 04:43:50 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up unicode-data (15.1.0-1) ... Setting up libboost-numpy1.83.0 (1.83.0-2.1) ... Setting up libz3-4:amd64 (4.8.12-3.1+b2) ... Setting up libpcre2-32-0:amd64 (10.42-4+b1) ... Setting up libglib2.0-0t64:amd64 (2.78.4-2.1) ... Setting up libblas3:amd64 (3.12.0-3) ... Setting up gcc-13-base:amd64 (13.2.0-16.1) ... Setting up libjpeg62-turbo:amd64 (1:2.1.5-2+b2) ... Setting up libx11-data (2:1.8.7-1) ... Setting up libepoxy0:amd64 (1.5.10-1+b2) ... Setting up libmpfr6:amd64 (4.2.1-1+b1) ... Setting up libavahi-common-data:amd64 (0.8-13+b1) ... Setting up libdbus-1-3:amd64 (1.14.10-4) ... Setting up liblzf1:amd64 (3.6-4) ... Setting up libfribidi0:amd64 (1.0.13-3+b1) ... Setting up libquadmath0:amd64 (14-20240221-2.1) ... Setting up libimagequant0:amd64 (2.18.0-1) ... Setting up libproc2-0:amd64 (2:4.0.4-4) ... Setting up fonts-dejavu-mono (2.37-8) ... Setting up libpng16-16:amd64 (1.6.43-1) ... Setting up libmpc3:amd64 (1.3.1-1+b2) ... Setting up libatomic1:amd64 (14-20240221-2.1) ... Setting up libtcl8.6:amd64 (8.6.13+dfsg-2+b1) ... Setting up fonts-dejavu-core (2.37-8) ... Removing obsolete conffile /etc/fonts/conf.avail/20-unhint-small-dejavu-lgc-sans-mono.conf ... Removing obsolete conffile /etc/fonts/conf.avail/20-unhint-small-dejavu-sans-mono.conf ... Removing obsolete conffile /etc/fonts/conf.avail/57-dejavu-sans-mono.conf ... Removing obsolete conffile /etc/fonts/conf.avail/58-dejavu-lgc-sans-mono.conf ... Setting up xtl-dev (0.7.5-3) ... Setting up libsensors5:amd64 (1:3.6.0-9) ... Setting up libncursesw6:amd64 (6.4+20240113-1) ... Setting up libk5crypto3:amd64 (1.20.1-5+b1) ... Setting up libglapi-mesa:amd64 (24.0.2-1) ... Setting up libjs-sphinxdoc (7.2.6-4) ... Setting up logsave (1.47.0-2.3) ... Setting up libgfortran5:amd64 (14-20240221-2.1) ... Setting up libmtdev1:amd64 (1.1.6-1+b1) ... Setting up libvulkan1:amd64 (1.3.275.0-1) ... Setting up libwebp7:amd64 (1.3.2-0.4) ... Setting up libfdisk1:amd64 (2.39.3-7) ... Setting up libdb5.3t64:amd64 (5.3.28+dfsg2-5) ... Setting up libubsan1:amd64 (14-20240221-2.1) ... Setting up mount (2.39.3-7) ... Setting up libhwasan0:amd64 (14-20240221-2.1) ... Setting up at-spi2-common (2.51.90-1) ... Setting up libcrypt-dev:amd64 (1:4.4.36-4) ... Setting up libtiff6:amd64 (4.5.1+git230720-4) ... Setting up dbus-session-bus-common (1.14.10-4) ... Setting up libasan8:amd64 (14-20240221-2.1) ... Setting up procps (2:4.0.4-4) ... Installing new version of config file /etc/sysctl.conf ... Setting up libmd4c0:amd64 (0.4.8-1+b1) ... Setting up libopenjp2-7:amd64 (2.5.0-2+b2) ... Setting up libx11-6:amd64 (2:1.8.7-1) ... Setting up libthai-data (0.1.29-2) ... Setting up libssh2-1:amd64 (1.11.0-4) ... Setting up netbase (6.4) ... Setting up mawk (1.3.4.20240123-1) ... Setting up libatk1.0-0:amd64 (2.50.0-1+b1) ... Setting up libkrb5-3:amd64 (1.20.1-5+b1) ... Setting up libwayland-egl1:amd64 (1.22.0-2.1+b1) ... Setting up libtsan2:amd64 (14-20240221-2.1) ... Setting up libbinutils:amd64 (2.42-3) ... Setting up dbus-system-bus-common (1.14.10-4) ... Setting up libboost-python1.74.0 (1.74.0+ds1-23.1) ... Setting up libisl23:amd64 (0.26-3+b2) ... Setting up libc-dev-bin (2.37-15.1) ... Setting up openssl (3.1.5-1.1) ... Installing new version of config file /etc/ssl/openssl.cnf ... Setting up libwebpmux3:amd64 (1.3.2-0.4) ... Setting up libbsd0:amd64 (0.12.1-1) ... Setting up libdrm-common (2.4.120-2) ... Setting up libjson-c5:amd64 (0.17-1+b1) ... Setting up libevdev2:amd64 (1.13.1+dfsg-1) ... Setting up readline-common (8.2-3.1) ... Setting up libxml2:amd64 (2.9.14+dfsg-1.3+b2) ... Setting up sphinx-rtd-theme-common (2.0.0+dfsg-1) ... Setting up libcc1-0:amd64 (14-20240221-2.1) ... Setting up dbus-bin (1.14.10-4) ... Setting up libgudev-1.0-0:amd64 (238-3) ... Setting up liblsan0:amd64 (14-20240221-2.1) ... Setting up libsz2:amd64 (1.1.2-1) ... Setting up libitm1:amd64 (14-20240221-2.1) ... Setting up libkmod2:amd64 (31+20240202-2) ... Setting up libboost-thread1.74.0:amd64 (1.74.0+ds1-23.1) ... Setting up libboost-numpy1.74.0 (1.74.0+ds1-23.1) ... Setting up libwacom-common (2.10.0-1) ... Setting up libxkbcommon0:amd64 (1.6.0-1) ... Setting up libwayland-client0:amd64 (1.22.0-2.1+b1) ... Setting up libctf0:amd64 (2.42-3) ... Setting up python3.12-minimal (3.12.2-3) ... Setting up libx11-xcb1:amd64 (2:1.8.7-1) ... Setting up liblapack3:amd64 (3.12.0-3) ... Setting up cpp-12 (12.3.0-15) ... Setting up libopenblas0-pthread:amd64 (0.3.26+ds-1) ... Setting up libssm2:amd64 (1.4.0-2+b1) ... Setting up libxi6:amd64 (2:1.8.1-1) ... Setting up libwacom9:amd64 (2.10.0-1) ... Setting up cpp-13-x86-64-linux-gnu (13.2.0-16.1) ... Setting up fontconfig-config (2.15.0-1) ... Setting up libwebpdemux2:amd64 (1.3.2-0.4) ... Setting up libedit2:amd64 (3.1-20230828-1) ... Setting up libavahi-common3:amd64 (0.8-13+b1) ... Setting up libcloudproviders0:amd64 (0.3.5-1) ... Setting up e2fsprogs (1.47.0-2.3) ... Setting up dbus-daemon (1.14.10-4) ... Setting up libatspi2.0-0:amd64 (2.50.0-1+b1) ... Setting up libcolord2:amd64 (1.4.7-1) ... Setting up libinput-bin (1.25.0-1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg1-4+b1) ... Setting up libdconf1:amd64 (0.40.0-4+b1) ... Setting up libatk-bridge2.0-0:amd64 (2.50.0-1+b1) ... Setting up libthai0:amd64 (0.1.29-2) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 14 added, 8 removed; done. Setting up libxsimd-dev:amd64 (12.1.1-2) ... Setting up libgprofng0:amd64 (2.42-3) ... Setting up libfreetype6:amd64 (2.13.2+dfsg-1+b1) ... Setting up dbus (1.14.10-4) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libgcc-12-dev:amd64 (12.3.0-15) ... Setting up shared-mime-info (2.4-1) ... Setting up libxkbcommon-x11-0:amd64 (1.6.0-1) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-5+b1) ... Setting up libqt5core5a:amd64 (5.15.10+dfsg-7) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg1-4+b1) ... Setting up libreadline8t64:amd64 (8.2-3.1) ... Setting up libdrm2:amd64 (2.4.120-2) ... Setting up libgcc-13-dev:amd64 (13.2.0-16.1) ... Setting up libopenblas0:amd64 (0.3.26+ds-1) ... Setting up libqt5dbus5:amd64 (5.15.10+dfsg-7) ... Setting up libwayland-cursor0:amd64 (1.22.0-2.1+b1) ... Setting up libllvm15:amd64 (1:15.0.7-11) ... Setting up libpam-systemd:amd64 (255.4-1) ... Setting up libc6-dev:amd64 (2.37-15.1) ... Setting up libharfbuzz0b:amd64 (8.3.0-2) ... Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-3+b1) ... Setting up libfontconfig1:amd64 (2.15.0-1) ... Setting up libqt5test5:amd64 (5.15.10+dfsg-7) ... Setting up libllvm17:amd64 (1:17.0.6-5) ... Setting up libavahi-client3:amd64 (0.8-13+b1) ... Setting up libstdc++-13-dev:amd64 (13.2.0-16.1) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.4-1+b1) ... Setting up binutils-x86-64-linux-gnu (2.42-3) ... Setting up libdrm-amdgpu1:amd64 (2.4.120-2) ... Setting up cpp-x86-64-linux-gnu (4:13.2.0-7) ... Setting up libopenblas-pthread-dev:amd64 (0.3.26+ds-1) ... Setting up libinput10:amd64 (1.25.0-1) ... Setting up gtk-update-icon-cache (3.24.41-1.1) ... Setting up fontconfig (2.15.0-1) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.6-1+b1) ... Setting up libboost1.83-dev:amd64 (1.83.0-2.1) ... Setting up libdrm-nouveau2:amd64 (2.4.120-2) ... Setting up cpp-13 (13.2.0-16.1) ... Setting up libstdc++-12-dev:amd64 (12.3.0-15) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.1) ... Setting up libgbm1:amd64 (24.0.2-1) ... Setting up libdrm-radeon1:amd64 (2.4.120-2) ... Setting up gcc-13-x86-64-linux-gnu (13.2.0-16.1) ... Setting up libtk8.6:amd64 (8.6.13-2+b1) ... Setting up libpango-1.0-0:amd64 (1.52.0+ds-1) ... Setting up libdrm-intel1:amd64 (2.4.120-2) ... Setting up libgl1-mesa-dri:amd64 (24.0.2-1) ... Setting up binutils (2.42-3) ... Setting up libcairo2:amd64 (1.18.0-1+b1) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5+b3) ... Setting up libqt5network5:amd64 (5.15.10+dfsg-7) ... Setting up libqt5sql5:amd64 (5.15.10+dfsg-7) ... Setting up dbus-user-session (1.14.10-4) ... Setting up libopenblas-dev:amd64 (0.3.26+ds-1) ... Setting up libqt5xml5:amd64 (5.15.10+dfsg-7) ... Setting up libegl-mesa0:amd64 (24.0.2-1) ... Setting up libtirpc-dev:amd64 (1.3.4+ds-1.1) ... Setting up libexpat1-dev:amd64 (2.6.0-1) ... Setting up adwaita-icon-theme (46~beta-4) ... Setting up gcc-12 (12.3.0-15) ... Setting up libnotify4:amd64 (0.8.3-1) ... Setting up libraqm0:amd64 (0.10.1-1+b1) ... Setting up gcc-13 (13.2.0-16.1) ... Setting up libcups2:amd64 (2.4.7-1+b1) ... Setting up zlib1g-dev:amd64 (1:1.3.dfsg-3.1) ... Setting up cpp (4:13.2.0-7) ... Setting up libnsl2:amd64 (1.3.0-3) ... Setting up libegl1:amd64 (1.7.0-1) ... Setting up libcurl4:amd64 (8.6.0-3) ... Setting up libcairo-gobject2:amd64 (1.18.0-1+b1) ... Setting up libboost-dev:amd64 (1.83.0.2+b2) ... Setting up libpangoft2-1.0-0:amd64 (1.52.0+ds-1) ... Setting up libhdf5-103-1t64:amd64 (1.10.10+repack-3.1) ... Setting up libpangocairo-1.0-0:amd64 (1.52.0+ds-1) ... Setting up libhdf5-hl-100:amd64 (1.10.10+repack-3+b1) ... Setting up g++-12 (12.3.0-15) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-7) ... Setting up libglx-mesa0:amd64 (24.0.2-1) ... Setting up libcbf1t64:amd64 (0.9.7+dfsg1-3.1) ... Setting up libpython3.12-stdlib:amd64 (3.12.2-3) ... Setting up g++-13-x86-64-linux-gnu (13.2.0-16.1) ... Setting up gcc-x86-64-linux-gnu (4:13.2.0-7) ... Setting up libglx0:amd64 (1.7.0-1) ... Setting up blt (2.5.3+dfsg-7) ... Setting up libpython3.11-stdlib:amd64 (3.11.8-2) ... Setting up python3.12 (3.12.2-3) ... Setting up libpython3.11t64:amd64 (3.11.8-2) ... Setting up libcurl3-gnutls:amd64 (8.6.0-3) ... Setting up dconf-service (0.40.0-4+b1) ... Setting up libwxbase3.2-1:amd64 (3.2.4+dfsg-3) ... Setting up gcc (4:13.2.0-7) ... Setting up libpython3.12t64:amd64 (3.12.2-3) ... Setting up libgl1:amd64 (1.7.0-1) ... Setting up libpython3.11-dev:amd64 (3.11.8-2) ... Setting up libnetcdf19:amd64 (1:4.9.2-3+b1) ... Setting up libgl1-mesa-glx:amd64 (23.1.3-1) ... Setting up libnsl-dev:amd64 (1.3.0-3) ... Setting up g++-x86-64-linux-gnu (4:13.2.0-7) ... Setting up libpython3-stdlib:amd64 (3.11.6-1) ... Setting up libcctbx0 (2023.12+ds2+~3.17.0+ds1-4) ... Setting up g++-13 (13.2.0-16.1) ... Setting up python3.11 (3.11.8-2) ... Setting up libpython3-dev:amd64 (3.11.6-1) ... Setting up dconf-gsettings-backend:amd64 (0.40.0-4+b1) ... Setting up python3.11-dev (3.11.8-2) ... Setting up libqt5gui5:amd64 (5.15.10+dfsg-7) ... Setting up libqt5widgets5:amd64 (5.15.10+dfsg-7) ... Setting up python3 (3.11.6-1) ... Setting up libpython3.12-dev:amd64 (3.12.2-3) ... 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 libqt5help5:amd64 (5.15.10-6) ... Setting up python3-tz (2024.1-2) ... Setting up python3-orderedset (2.0.3+ds1-2) ... Setting up libqt5printsupport5:amd64 (5.15.10+dfsg-7) ... Setting up python3-pil:amd64 (10.2.0-1) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-packaging (23.2-1) ... Setting up python3-pyparsing (3.1.1-1) ... Setting up python3-certifi (2023.11.17-1) ... Setting up libpython3-all-dev:amd64 (3.11.6-1) ... Setting up python3-brotli (1.1.0-2+b3) ... Setting up python3-pycbf (0.9.7+dfsg1-3.1) ... Setting up python3-kiwisolver (1.4.4-1+b2) ... Setting up python3-idna (3.6-2) ... Setting up python3.12-dev (3.12.2-3) ... Setting up python3-urllib3 (1.26.18-2) ... Setting up python3-pyqt5.sip (12.13.0-1+b1) ... Setting up g++ (4:13.2.0-7) ... Setting up libqt5opengl5:amd64 (5.15.10+dfsg-7) ... Setting up python3-lxml:amd64 (5.1.0-1) ... Setting up python3-dateutil (2.8.2-3) ... Setting up python3-lib2to3 (3.11.5-1) ... Setting up python3-appdirs (1.4.4-4) ... Setting up python3-procrunner (2.3.3-1) ... Setting up libgtk-3-common (3.24.41-1.1) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-distutils (3.11.5-1) ... python3.12: can't get files for byte-compilation Setting up python3-sympy (1.12-7) ... Setting up python3-attr (23.2.0-2) ... Setting up python3-setuptools (68.1.2-2) ... Setting up libqt5designer5:amd64 (5.15.10-6) ... Setting up python3-lz4 (4.0.2+dfsg-1+b3) ... Setting up python3-charset-normalizer (3.3.2-1) ... Setting up libgtk-3-0:amd64 (3.24.41-1) ... Setting up python3-ply (3.11-6) ... Setting up python3-tqdm (4.64.1-2) ... Setting up python3-all (3.11.6-1) ... Setting up python3-tk:amd64 (3.11.5-1) ... Setting up python3-fs (2.4.16-3) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-pil.imagetk:amd64 (10.2.0-1) ... Setting up python3-dev (3.11.6-1) ... Setting up python3-requests (2.31.0+dfsg-1) ... Setting up libboost-python1.83-dev (1.83.0-2.1) ... Setting up python3-numpy (1:1.24.2-2) ... Setting up python3-contourpy (1.0.7-1+b2) ... Setting up python3-pyqt5 (5.15.10+dfsg-1) ... Setting up python3-all-dev (3.11.6-1) ... Setting up libwxgtk3.2-1:amd64 (3.2.4+dfsg-3) ... Setting up python3-pyqt5.qtopengl (5.15.10+dfsg-1) ... Setting up python3-scipy (1.11.4-6) ... Setting up libwxgtk-gl3.2-1:amd64 (3.2.4+dfsg-3) ... Setting up python3-wxgtk4.0 (4.2.1+dfsg-3) ... Setting up python3-h5py-serial (3.10.0-1) ... Setting up libboost-python-dev (1.83.0.2+b2) ... Setting up python3-h5py (3.10.0-1) ... Setting up python3-pythran (0.15.0+ds-2) ... Setting up python3-pymol (2.5.0+dfsg-1+b4) ... /usr/lib/python3/dist-packages/chempy/sdf.py:23: SyntaxWarning: invalid escape sequence '\s' getkee = re.compile("^>\s+<([^>]*)>") /usr/lib/python3/dist-packages/chempy/sdf.py:24: SyntaxWarning: invalid escape sequence '\s' gettag = re.compile("^>\s+<[^>]*>\s+\((.*)\)") /usr/lib/python3/dist-packages/pmg_tk/skins/normal/__init__.py:849: SyntaxWarning: invalid escape sequence '\.' g = re.search("(.*)(\..*)$", save_file) /usr/lib/python3/dist-packages/pmg_tk/skins/normal/__init__.py:889: SyntaxWarning: invalid escape sequence '\.' if re.search("\.pym*$|\.PYM*$",ofile): /usr/lib/python3/dist-packages/pymol/internal.py:252: SyntaxWarning: invalid escape sequence '\.' if re.search("[0-9]*\.png$",fname): # remove numbering, etc. /usr/lib/python3/dist-packages/pymol/internal.py:253: SyntaxWarning: invalid escape sequence '\.' fname = re.sub("[0-9]*\.png$","",fname) /usr/lib/python3/dist-packages/pymol/internal.py:254: SyntaxWarning: invalid escape sequence '\.' if re.search("[0-9]*\.ppm$",fname): /usr/lib/python3/dist-packages/pymol/internal.py:257: SyntaxWarning: invalid escape sequence '\.' fname = re.sub("[0-9]*\.ppm$","",fname) /usr/lib/python3/dist-packages/pymol/movie.py:818: SyntaxWarning: invalid escape sequence '\W' '''Return full path to executable or None. /usr/lib/python3/dist-packages/pymol/moving.py:733: SyntaxWarning: invalid escape sequence '\s' input = re.sub("\s"," ",specification) /usr/lib/python3/dist-packages/pymol/parser.py:48: SyntaxWarning: invalid escape sequence '\[' remove_lists_re = re.compile("\[[^\]]*\]") /usr/lib/python3/dist-packages/pymol/parser.py:408: SyntaxWarning: invalid escape sequence '\.' if re.search("\.py$|\.pym$",path) is not None: /usr/lib/python3/dist-packages/pymol/plugins/installation.py:23: SyntaxWarning: invalid escape sequence '\p' ''' /usr/lib/python3/dist-packages/pymol/viewing.py:899: SyntaxWarning: invalid escape sequence '\.' re_pat = re.compile("[0-9]+\.") /usr/lib/python3/dist-packages/pymol/viewing.py:912: SyntaxWarning: invalid escape sequence '\.' new_file = re.sub("\.pse$",".psw",new_file,re.I) /usr/lib/python3/dist-packages/pymol/viewing.py:914: SyntaxWarning: invalid escape sequence '\.' new_file = re.sub("\.psw$",".pse",new_file,re.I) /usr/lib/python3/dist-packages/pymol/wizard/pseudoatom.py:13: SyntaxWarning: invalid escape sequence '\8' self.prefix = 'Label text: \888' Setting up python3-nxmx (0.0.3-2) ... Setting up libcctbx-dev (2023.12+ds2+~3.17.0+ds1-4) ... Setting up python3-fonttools (4.46.0-1) ... Setting up python3-ufolib2 (0.16.0+dfsg1-1) ... Setting up libdevmapper1.02.1:amd64 (2:1.02.196-1) ... Setting up dmsetup (2:1.02.196-1) ... Setting up libcryptsetup12:amd64 (2:2.7.0-1) ... Setting up python3-matplotlib (3.6.3-1+b2) ... Setting up python3-cctbx (2023.12+ds2+~3.17.0+ds1-4) ... /usr/lib/python3/dist-packages/cctbx/command_line/find_reticular_twin_laws.py:37: SyntaxWarning: invalid escape sequence '\%' print(""" /usr/lib/python3/dist-packages/gltbx/util.py:61: SyntaxWarning: invalid escape sequence '\d' vers_pat = re.compile("^((\d+)\.(\d+))(?:\.(\d+))?(?: (.*))?$") /usr/lib/python3/dist-packages/iotbx/command_line/explore_metric_symmetry.py:339: SyntaxWarning: invalid escape sequence '\ ' print(" /%4i %4i %4i \ "%(mat[0][0],mat[0][1],mat[0][2]), file=log) /usr/lib/python3/dist-packages/iotbx/command_line/explore_metric_symmetry.py:341: SyntaxWarning: invalid escape sequence '\%' print(" \%4i %4i %4i / "%(mat[2][0],mat[2][1],mat[2][2]), file=log) /usr/lib/python3/dist-packages/iotbx/logfiles.py:19: SyntaxWarning: invalid escape sequence '\%' return float(re.sub("\%$", "", value)) /usr/lib/python3/dist-packages/iotbx/logfiles.py:474: SyntaxWarning: invalid escape sequence '\d' elif re.match("^\d", line): /usr/lib/python3/dist-packages/iotbx/pdb/utils.py:7: SyntaxWarning: invalid escape sequence '\{' """ Iterator to generate strings of length n_chars, using upper-case, /usr/lib/python3/dist-packages/iotbx/pdb/utils.py:45: SyntaxWarning: invalid escape sequence '\/' special_characters = """[]_,.;:"&<>()\/\{}'`~!@#$%*|+-""" /usr/lib/python3/dist-packages/iotbx/regression/ncs/tst_ncs_groups_preprocessing.py:409: SyntaxWarning: invalid escape sequence '\P' test_ncs_spec = '''\ /usr/lib/python3/dist-packages/libtbx/auto_build/bootstrap.py:455: SyntaxWarning: invalid escape sequence '\s' if re.match('remote\s*=', line.strip()): /usr/lib/python3/dist-packages/libtbx/auto_build/bootstrap.py:457: SyntaxWarning: invalid escape sequence '\s' if re.match('rebase\s*=', line.strip()): /usr/lib/python3/dist-packages/libtbx/auto_build/install_base_packages.py:840: SyntaxWarning: invalid escape sequence '\$' configure_args.append("LDFLAGS=-Wl,-rpath=\$$ORIGIN/../lib") /usr/lib/python3/dist-packages/libtbx/fastentrypoints.py:43: SyntaxWarning: invalid escape sequence '\.' TEMPLATE = '''\ /usr/lib/python3/dist-packages/libtbx/fastentrypoints.py:92: SyntaxWarning: invalid escape sequence '\.' filename = re.sub('\.pyc$', '.py', __file__) /usr/lib/python3/dist-packages/libtbx/file_clutter.py:12: SyntaxWarning: invalid escape sequence '\w' '^ from [ ]+ __future__ [ ]+ import [ \w,]+ division', re.VERBOSE) /usr/lib/python3/dist-packages/libtbx/file_clutter.py:14: SyntaxWarning: invalid escape sequence '\w' '^ from [ ]+ __future__ [ ]+ import [ \w,]+ absolute_import', re.VERBOSE) /usr/lib/python3/dist-packages/libtbx/file_clutter.py:16: SyntaxWarning: invalid escape sequence '\w' '^ from [ ]+ __future__ [ ]+ import [ \w,]+ print_function', re.VERBOSE) /usr/lib/python3/dist-packages/libtbx/queuing_system_utils/processing/polling.py:282: SyntaxWarning: invalid escape sequence '\?' pattern = "^.*?(?=<\?xml)", /usr/lib/python3/dist-packages/mmtbx/command_line/show_r_factors_by_shell.py:106: SyntaxWarning: invalid escape sequence '\(' first_label_non_anom = re.sub("\(.*", "", labels[0]) /usr/lib/python3/dist-packages/mmtbx/pdb_distances.py:777: SyntaxWarning: invalid escape sequence '\d' m=re.search('\d+', list[resid_count]) /usr/lib/python3/dist-packages/mmtbx/pdb_distances.py:779: SyntaxWarning: invalid escape sequence '\w' n=re.search('\w', list[resid_count + 1]) /usr/lib/python3/dist-packages/mmtbx/pdb_distances.py:816: SyntaxWarning: invalid escape sequence '\d' m=re.search('\d+', list[2 * a]) /usr/lib/python3/dist-packages/mmtbx/pdb_distances.py:823: SyntaxWarning: invalid escape sequence '\d' m=re.search('\d+', list[2 * a]) /usr/lib/python3/dist-packages/mmtbx/pdb_distances.py:1191: SyntaxWarning: invalid escape sequence '\d' m=re.search('\d+', MASTER_Basepairs_summary[i][j][2]) /usr/lib/python3/dist-packages/mmtbx/pdb_distances.py:1194: SyntaxWarning: invalid escape sequence '\d' m=re.search('\d+', MASTER_Basepairs_summary[i][j][4]) /usr/lib/python3/dist-packages/mmtbx/pdb_distances.py:1499: SyntaxWarning: invalid escape sequence '\d' m=re.search('\d+', MASTER_Basepairs[i][j][0]) /usr/lib/python3/dist-packages/mmtbx/pdb_distances.py:1501: SyntaxWarning: invalid escape sequence '\d' m=re.search('\d+', MASTER_Basepairs[i][j][3]) /usr/lib/python3/dist-packages/mmtbx/pdb_distances.py:1503: SyntaxWarning: invalid escape sequence '\S' m=re.search('\S+', MASTER_Basepairs[i][j][2]) /usr/lib/python3/dist-packages/mmtbx/pdb_distances.py:1505: SyntaxWarning: invalid escape sequence '\S' m=re.search('\S+', MASTER_Basepairs[i][j][5]) /usr/lib/python3/dist-packages/mmtbx/pdb_distances.py:1823: SyntaxWarning: invalid escape sequence '\d' m=re.search('\d+', LIST[r][s][2]) /usr/lib/python3/dist-packages/mmtbx/pdb_distances.py:1825: SyntaxWarning: invalid escape sequence '\d' m=re.search('\d+', LIST[r][s][4]) /usr/lib/python3/dist-packages/mmtbx/pdb_distances.py:1879: SyntaxWarning: invalid escape sequence '\/' ma=re.compile('\/+') /usr/lib/python3/dist-packages/mmtbx/pdb_distances.py:1988: SyntaxWarning: invalid escape sequence '\d' m=re.search('\d+', MASTER_Basepairs_summary_line[2]) /usr/lib/python3/dist-packages/mmtbx/pdb_distances.py:1991: SyntaxWarning: invalid escape sequence '\d' m=re.search('\d+', MASTER_Basepairs_summary_line[4]) /usr/lib/python3/dist-packages/mmtbx/pdb_distances.py:2318: SyntaxWarning: invalid escape sequence '\d' m=re.search('\d+', MASTER_Basepairs_summary[i][j][2]) /usr/lib/python3/dist-packages/mmtbx/pdb_distances.py:2324: SyntaxWarning: invalid escape sequence '\d' m=re.search('\d+', MASTER_Basepairs_summary[i][j][2]) /usr/lib/python3/dist-packages/mmtbx/pdb_distances.py:2892: SyntaxWarning: invalid escape sequence '\S' m=re.search('\S+', new_list_end[b][0]) /usr/lib/python3/dist-packages/mmtbx/pdb_distances.py:2979: SyntaxWarning: invalid escape sequence '\d' search = '\d+' /usr/lib/python3/dist-packages/mmtbx/pdb_distances.py:2981: SyntaxWarning: invalid escape sequence '\w' search = '\w+' /usr/lib/python3/dist-packages/prime/postrefine/mod_gui_frames.py:750: SyntaxWarning: invalid escape sequence '\A' self.bmult_axes.set_xlabel("Resolution ($\AA$)") /usr/lib/python3/dist-packages/scitbx/math/fliege_mayer_900_ylm.py:1: SyntaxWarning: invalid escape sequence '\i' """ /usr/lib/python3/dist-packages/wxtbx/info_panels.py:208: SyntaxWarning: invalid escape sequence '\s' str_value = re.sub("\s*\*\*\*", "", str_value) /usr/lib/python3/dist-packages/wxtbx/info_panels.py:418: SyntaxWarning: invalid escape sequence '\s' str_value = re.sub("\s*\*\*\*", "", str_value) /usr/lib/python3/dist-packages/wxtbx/phil_controls/choice.py:18: SyntaxWarning: invalid escape sequence '\*' choices = [ re.sub("\*", "", choice) for choice in choices ] /usr/lib/python3/dist-packages/xfel/command_line/cxi_stream_to_pickle.py:23: SyntaxWarning: invalid escape sequence '\s' re_energy = re.compile("photon_energy_eV\s=\s([0-9]+\.[0-9]+)") /usr/lib/python3/dist-packages/xfel/command_line/cxi_stream_to_pickle.py:24: SyntaxWarning: invalid escape sequence '\s' re_uc = re.compile("""Cell\sparameters\s /usr/lib/python3/dist-packages/xfel/command_line/cxi_stream_to_pickle.py:33: SyntaxWarning: invalid escape sequence '\s' re_miller = re.compile("""\s*(-?[0-9]{1,3}) /usr/lib/python3/dist-packages/xfel/command_line/cxi_stream_to_pickle.py:41: SyntaxWarning: invalid escape sequence '\s' re_lattice_type = re.compile("lattice_type\s=\s([a-zA-Z]+)") /usr/lib/python3/dist-packages/xfel/command_line/cxi_stream_to_pickle.py:42: SyntaxWarning: invalid escape sequence '\s' re_centering = re.compile("centering\s=\s([A-Z])") /usr/lib/python3/dist-packages/xfel/command_line/cxi_stream_to_pickle.py:45: SyntaxWarning: invalid escape sequence '\s' re_Astar = re.compile("""astar\s=\s*(-?\+?[0-9]+\.[0-9]+) /usr/lib/python3/dist-packages/xfel/command_line/cxi_stream_to_pickle.py:48: SyntaxWarning: invalid escape sequence '\s' re_Bstar = re.compile("""bstar\s=\s*(-?\+?[0-9]+\.[0-9]+) /usr/lib/python3/dist-packages/xfel/command_line/cxi_stream_to_pickle.py:51: SyntaxWarning: invalid escape sequence '\s' re_Cstar = re.compile("""cstar\s=\s*(-?\+?[0-9]+\.[0-9]+) /usr/lib/python3/dist-packages/xfel/command_line/detector_residuals.py:1124: SyntaxWarning: invalid escape sequence '\D' plt.title("2d histogram of $\Delta$ %s vs azimuthal angle"%caption) /usr/lib/python3/dist-packages/xfel/command_line/detector_residuals.py:1126: SyntaxWarning: invalid escape sequence '\D' plt.ylabel("$\Delta$ %s ($\mu$m)"%caption) /usr/lib/python3/dist-packages/xfel/command_line/detector_residuals.py:1266: SyntaxWarning: invalid escape sequence '\A' plt.title(u"%d: Ewald offset ($\AA^{-1}$) vs $2\\theta$ on %d spots"%(expt_id, len(two_thetas))) /usr/lib/python3/dist-packages/xfel/command_line/detector_residuals.py:1267: SyntaxWarning: invalid escape sequence '\c' plt.xlabel(u"$2\\theta (\circ)$") /usr/lib/python3/dist-packages/xfel/command_line/detector_residuals.py:1268: SyntaxWarning: invalid escape sequence '\A' plt.ylabel(u"Ewald offset ($\AA^{-1}$)") /usr/lib/python3/dist-packages/xfel/command_line/detector_residuals.py:1294: SyntaxWarning: invalid escape sequence '\s' plt.title(u"Binned $I/\sigma_I$ vs. Ewald offset") /usr/lib/python3/dist-packages/xfel/command_line/detector_residuals.py:1295: SyntaxWarning: invalid escape sequence '\A' plt.xlabel(u"Ewald offset ($\AA^{-1}$)") /usr/lib/python3/dist-packages/xfel/command_line/detector_residuals.py:1296: SyntaxWarning: invalid escape sequence '\s' plt.ylabel(u"Median $I/\sigma_I$") /usr/lib/python3/dist-packages/xfel/command_line/experiment_residuals.py:203: SyntaxWarning: invalid escape sequence '\D' cbar.ax.set_title("$\Delta \psi$") /usr/lib/python3/dist-packages/xfel/cxi/cspad_ana/mod_filter.py:52: SyntaxWarning: invalid escape sequence '\d' p_old = re.compile("\d{4}-\d{2}-\d{2}T\d{2}:\d{2}Z\d{2}\.\d{3}") /usr/lib/python3/dist-packages/xfel/cxi/cspad_ana/mod_filter.py:53: SyntaxWarning: invalid escape sequence '\d' p_new = re.compile("\d{17}") /usr/lib/python3/dist-packages/xfel/cxi/cxi_cc.py:132: SyntaxWarning: invalid escape sequence '\d' """Get the R1 factor according to this formula /usr/lib/python3/dist-packages/xfel/merging/application/statistics/intensity_resolution_statistics_cxi.py:350: SyntaxWarning: invalid escape sequence '\d' """Get the R1 factor according to this formula /usr/lib/python3/dist-packages/xfel/metrology/flatfile.py:1022: SyntaxWarning: invalid escape sequence '\s' re.compile('^\s*(#.*)?$') /usr/lib/python3/dist-packages/xfel/metrology/flatfile.py:1024: SyntaxWarning: invalid escape sequence '\s' re.compile('^\s*[Qq][Uu][Aa][Dd]\s+\d+\s*(#.*)?$') /usr/lib/python3/dist-packages/xfel/metrology/flatfile.py:1026: SyntaxWarning: invalid escape sequence '\s' re.compile('^\s*[Ss][Ee][Nn][Ss][Oo][Rr]\s+[Xx]\s+[Yy]\s+[Zz]\s*(#.*)?$') /usr/lib/python3/dist-packages/xfel/metrology/flatfile.py:1028: SyntaxWarning: invalid escape sequence '\s' re.compile('^\s*\d+\s+[+-]?\d+\s+[+-]?\d+\s+[+-]?\d+\s*(#.*)?$') /usr/lib/python3/dist-packages/xfel/ui/components/xfel_gui_plotter.py:393: SyntaxWarning: invalid escape sequence '\A' AA = "a-edge (%.2f +/- %.2f $\AA$)" % (flex.mean(a), /usr/lib/python3/dist-packages/xfel/ui/components/xfel_gui_plotter.py:395: SyntaxWarning: invalid escape sequence '\A' BB = "b-edge (%.2f +/- %.2f $\AA$)" % (flex.mean(b), /usr/lib/python3/dist-packages/xfel/ui/components/xfel_gui_plotter.py:397: SyntaxWarning: invalid escape sequence '\A' CC = "c-edge (%.2f +/- %.2f $\AA$)" % (flex.mean(c), /usr/lib/python3/dist-packages/xfel/ui/db/merging_log_scraper.py:106: SyntaxWarning: invalid escape sequence '\A' ax1.set_xlabel(u'Resolution ${\AA}$') /usr/lib/python3/dist-packages/xfel/ui/db/merging_log_scraper.py:189: SyntaxWarning: invalid escape sequence '\A' ax2.set_ylabel(u"Resolution ($\AA$") Processing triggers for libc-bin (2.37-15.1) ... Processing triggers for systemd (255.4-1) ... Processing triggers for debianutils (5.17) ... 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. 4m29.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'apt-get', '-yf', 'dist-upgrade'] 4m29.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 4m30.8s DUMP: 2e89ecccced98ef583aada8740b0cceb - 4m30.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 4m30.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'apt-cache', 'show', '--no-all-versions', 'python3-cctbx'] 4m31.1s DUMP: Package: python3-cctbx Source: cctbx Version: 2023.12+ds2+~3.17.0+ds1-4 Installed-Size: 501959 Maintainer: Debian Science Maintainers Architecture: amd64 Depends: ca-certificates, libcctbx-dev (= 2023.12+ds2+~3.17.0+ds1-4), libcctbx0 (= 2023.12+ds2+~3.17.0+ds1-4), python3-pycbf (>= 0.9.7+dfsg1-2~), python3 (<< 3.13), python3 (>= 3.11~), python3-h5py (>= 3), python3-matplotlib, python3-mrcfile, python3-numpy (>= 1:1.22.0), python3-numpy-abi9, python3-nxmx, python3-orderedset, 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-py311, libboost-numpy1.83.0-py312, libboost-python1.83.0 (>= 1.83.0), libboost-python1.83.0-py311, libboost-python1.83.0-py312, libboost-thread1.83.0 (>= 1.83.0), libc6 (>= 2.34), libcbf1t64 (>= 0.9.7+dfsg1-2~), libccp4c0 (>= 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 (>= 13.1) 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_2023.12+ds2+~3.17.0+ds1-4_amd64.deb Size: 50134860 MD5sum: 21abbf20e7beff55eaa010e9ec4923ae SHA256: c7f518562c87755b767b6de113da1cefbeb159cc5a0af722debc75e8e4674850 4m31.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'apt-cache', 'show', '--no-all-versions', 'python3-cctbx'] 4m31.1s INFO: apt-cache knows about the following packages: python3-cctbx 4m31.1s INFO: Running scripts pre_install 4m31.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_install_database-server'] 4m31.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_install_database-server'] 4m31.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_install_exceptions'] 4m31.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_install_exceptions'] 4m31.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_install_extras'] 4m31.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_install_extras'] 4m31.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_install_foreign_architecture'] 4m31.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_install_foreign_architecture'] 4m31.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_install_foreign_architecture_i386'] 4m31.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_install_foreign_architecture_i386'] 4m31.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'apt-cache', 'policy'] 4m31.1s 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: 4m31.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'apt-cache', 'policy'] 4m31.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'apt-cache', 'policy', 'python3-cctbx'] 4m31.2s DUMP: python3-cctbx: Installed: 2023.12+ds2+~3.17.0+ds1-4 Candidate: 2023.12+ds2+~3.17.0+ds1-4 Version table: *** 2023.12+ds2+~3.17.0+ds1-4 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 4m31.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'apt-cache', 'policy', 'python3-cctbx'] 4m31.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'apt-get', '-y', 'install', 'python3-cctbx'] 4m31.9s DUMP: Reading package lists... Building dependency tree... Reading state information... python3-cctbx is already the newest version (2023.12+ds2+~3.17.0+ds1-4). The following packages were automatically installed and are no longer required: libboost-dev libboost-numpy1.74.0 libboost-python1.74.0 libboost-thread1.74.0 libgl1-mesa-glx libllvm15 libnsl-dev libopenblas-dev libopenblas-pthread-dev libopenblas0 libpython3-all-dev libpython3.12-dev libpython3.12t64 libtirpc-dev libxsimd-dev python3-all-dev python3-beniget python3-gast python3-ply python3-pythran python3.12-dev xtl-dev Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 4m31.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'apt-get', '-y', 'install', 'python3-cctbx'] 4m31.9s INFO: Running scripts post_install 4m31.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/post_install_exceptions'] 4m31.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/post_install_exceptions'] 4m31.9s INFO: Running scripts post_distupgrade 4m31.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/post_distupgrade_base_cleanup'] 4m31.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/post_distupgrade_base_cleanup'] 4m31.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/post_distupgrade_exceptions'] 4m31.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/post_distupgrade_exceptions'] 4m31.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 4m32.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 4m32.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/post_distupgrade_squeeze-backports'] 4m32.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/post_distupgrade_squeeze-backports'] 4m32.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/post_distupgrade_zz_backports'] 4m32.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/post_distupgrade_zz_backports'] 4m32.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv'] 4m35.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv'] 4m35.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv'] 4m40.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv'] 4m40.0s INFO: Running scripts pre_install 4m40.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_install_database-server'] 4m40.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_install_database-server'] 4m40.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_install_exceptions'] 4m40.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_install_exceptions'] 4m40.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_install_extras'] 4m40.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_install_extras'] 4m40.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_install_foreign_architecture'] 4m40.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_install_foreign_architecture'] 4m40.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_install_foreign_architecture_i386'] 4m40.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_install_foreign_architecture_i386'] 4m40.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'apt-cache', 'policy'] 4m40.1s 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: 4m40.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'apt-cache', 'policy'] 4m40.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'apt-cache', 'policy', 'python3-cctbx'] 4m40.2s DUMP: python3-cctbx: Installed: 2023.12+ds2+~3.17.0+ds1-4 Candidate: 2023.12+ds2+~3.17.0+ds1-4 Version table: *** 2023.12+ds2+~3.17.0+ds1-4 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 4m40.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'apt-cache', 'policy', 'python3-cctbx'] 4m40.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'apt-get', '-y', 'install', 'python3-cctbx=2023.12+ds2+~3.17.0+ds1-4'] 4m41.1s DUMP: Reading package lists... Building dependency tree... Reading state information... python3-cctbx is already the newest version (2023.12+ds2+~3.17.0+ds1-4). The following packages were automatically installed and are no longer required: libboost-dev libboost-numpy1.74.0 libboost-python1.74.0 libboost-thread1.74.0 libgl1-mesa-glx libllvm15 libnsl-dev libopenblas-dev libopenblas-pthread-dev libopenblas0 libpython3-all-dev libpython3.12-dev libpython3.12t64 libtirpc-dev libxsimd-dev python3-all-dev python3-beniget python3-gast python3-ply python3-pythran python3.12-dev xtl-dev Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 4m41.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'apt-get', '-y', 'install', 'python3-cctbx=2023.12+ds2+~3.17.0+ds1-4'] 4m41.1s INFO: Running scripts post_install 4m41.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/post_install_exceptions'] 4m41.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/post_install_exceptions'] 4m41.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv'] 4m45.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv'] 4m45.8s INFO: /bin converted to /usr/bin by /usr merge 4m45.8s INFO: /lib converted to /usr/lib by /usr merge 4m45.8s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 4m45.8s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 4m45.8s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 4m45.8s INFO: /lib64 converted to /usr/lib64 by /usr merge 4m45.8s INFO: /sbin converted to /usr/sbin by /usr merge 4m50.2s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', '-ac', '--ignore-obsolete'] 4m59.0s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', '-ac', '--ignore-obsolete'] 4m59.0s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 4m59.1s DUMP: 0.15.6 4m59.1s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 4m59.1s INFO: Running adequate version 0.15.6 now. 4m59.1s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'python3-cctbx'] 5m3.9s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'python3-cctbx'] 5m3.9s INFO: Running scripts pre_remove 5m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 5m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 5m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 5m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 5m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 5m25.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 5m25.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 5m25.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 5m25.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 5m25.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 5m25.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_remove_exceptions'] 5m25.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/pre_remove_exceptions'] 5m25.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 5m25.8s DUMP: install ok installed adduser adduser 3.137 install ok installed adwaita-icon-theme adwaita-icon-theme 46~beta-4 install ok installed apt apt 2.7.13+b1 install ok installed at-spi2-common at-spi2-common 2.51.90-1 install ok installed base-files base-files 13 install ok installed base-passwd base-passwd 3.6.3 install ok installed bash bash 5.2.21-2 install ok installed binutils binutils 2.42-3 install ok installed binutils-common:amd64 binutils-common 2.42-3 install ok installed binutils-x86-64-linux-gnu binutils-x86-64-linux-gnu 2.42-3 install ok installed blt blt 2.5.3+dfsg-7 install ok installed bsdutils bsdutils 1:2.39.3-7 install ok installed ca-certificates ca-certificates 20240203 install ok installed coreutils coreutils 9.4-3+b1 install ok installed cpp cpp 4:13.2.0-7 install ok installed cpp-12 cpp-12 12.3.0-15 install ok installed cpp-13 cpp-13 13.2.0-16.1 install ok installed cpp-13-x86-64-linux-gnu cpp-13-x86-64-linux-gnu 13.2.0-16.1 install ok installed cpp-x86-64-linux-gnu cpp-x86-64-linux-gnu 4:13.2.0-7 install ok installed dash dash 0.5.12-6 install ok installed dbus dbus 1.14.10-4 install ok installed dbus-bin dbus-bin 1.14.10-4 install ok installed dbus-daemon dbus-daemon 1.14.10-4 install ok installed dbus-session-bus-common dbus-session-bus-common 1.14.10-4 install ok installed dbus-system-bus-common dbus-system-bus-common 1.14.10-4 install ok installed dbus-user-session dbus-user-session 1.14.10-4 install ok installed dconf-gsettings-backend:amd64 dconf-gsettings-backend 0.40.0-4+b1 install ok installed dconf-service dconf-service 0.40.0-4+b1 install ok installed debconf debconf 1.5.86 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.17 install ok installed diffutils diffutils 1:3.10-1 install ok installed dmsetup dmsetup 2:1.02.196-1 install ok installed dpkg dpkg 1.22.5 install ok installed e2fsprogs e2fsprogs 1.47.0-2.3 install ok installed findutils findutils 4.9.0-5 install ok installed fontconfig fontconfig 2.15.0-1 install ok installed fontconfig-config fontconfig-config 2.15.0-1 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-8 install ok installed fonts-dejavu-mono fonts-dejavu-mono 2.37-8 install ok installed fonts-font-awesome fonts-font-awesome 5.0.10+really4.7.0~dfsg-4.1 install ok installed fonts-lato fonts-lato 2.015-1 install ok installed fonts-lyx fonts-lyx 2.4.0~RC3-1 install ok installed g++ g++ 4:13.2.0-7 install ok installed g++-12 g++-12 12.3.0-15 install ok installed g++-13 g++-13 13.2.0-16.1 install ok installed g++-13-x86-64-linux-gnu g++-13-x86-64-linux-gnu 13.2.0-16.1 install ok installed g++-x86-64-linux-gnu g++-x86-64-linux-gnu 4:13.2.0-7 install ok installed gcc gcc 4:13.2.0-7 install ok installed gcc-12 gcc-12 12.3.0-15 install ok installed gcc-12-base:amd64 gcc-12-base 12.3.0-15 install ok installed gcc-13 gcc-13 13.2.0-16.1 install ok installed gcc-13-base:amd64 gcc-13-base 13.2.0-16.1 install ok installed gcc-13-x86-64-linux-gnu gcc-13-x86-64-linux-gnu 13.2.0-16.1 install ok installed gcc-14-base:amd64 gcc-14-base 14-20240221-2.1 install ok installed gcc-x86-64-linux-gnu gcc-x86-64-linux-gnu 4:13.2.0-7 install ok installed gpgv gpgv 2.2.40-1.1+b1 install ok installed grep grep 3.11-4 install ok installed gtk-update-icon-cache gtk-update-icon-cache 3.24.41-1.1 install ok installed gzip gzip 1.12-1 install ok installed hicolor-icon-theme hicolor-icon-theme 0.17-2 install ok installed hostname hostname 3.23+nmu2 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed libacl1:amd64 libacl1 2.3.2-1 install ok installed libaec0:amd64 libaec0 1.1.2-1 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 install ok installed libapparmor1:amd64 libapparmor1 3.0.12-1+b2 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.7.13+b1 install ok installed libargon2-1:amd64 libargon2-1 0~20190702+dfsg-4+b1 install ok installed libasan8:amd64 libasan8 14-20240221-2.1 install ok installed libatk-bridge2.0-0:amd64 libatk-bridge2.0-0 2.50.0-1+b1 install ok installed libatk1.0-0:amd64 libatk1.0-0 2.50.0-1+b1 install ok installed libatomic1:amd64 libatomic1 14-20240221-2.1 install ok installed libatspi2.0-0:amd64 libatspi2.0-0 2.50.0-1+b1 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:3.1.2-2.1 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-2.1 install ok installed libavahi-client3:amd64 libavahi-client3 0.8-13+b1 install ok installed libavahi-common-data:amd64 libavahi-common-data 0.8-13+b1 install ok installed libavahi-common3:amd64 libavahi-common3 0.8-13+b1 install ok installed libbinutils:amd64 libbinutils 2.42-3 install ok installed libblas3:amd64 libblas3 3.12.0-3 install ok installed libblkid1:amd64 libblkid1 2.39.3-7 install ok installed libboost-dev:amd64 libboost-dev 1.83.0.2+b2 install ok installed libboost-numpy1.74.0 libboost-numpy1.74.0 1.74.0+ds1-23.1 install ok installed libboost-numpy1.83.0 libboost-numpy1.83.0 1.83.0-2.1 install ok installed libboost-python-dev libboost-python-dev 1.83.0.2+b2 install ok installed libboost-python1.74.0 libboost-python1.74.0 1.74.0+ds1-23.1 install ok installed libboost-python1.83-dev libboost-python1.83-dev 1.83.0-2.1 install ok installed libboost-python1.83.0 libboost-python1.83.0 1.83.0-2.1 install ok installed libboost-thread1.74.0:amd64 libboost-thread1.74.0 1.74.0+ds1-23.1 install ok installed libboost-thread1.83.0:amd64 libboost-thread1.83.0 1.83.0-2.1 install ok installed libboost1.83-dev:amd64 libboost1.83-dev 1.83.0-2.1 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b3 install ok installed libbsd0:amd64 libbsd0 0.12.1-1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b2 install ok installed libc-bin libc-bin 2.37-15.1 install ok installed libc-dev-bin libc-dev-bin 2.37-15.1 install ok installed libc6:amd64 libc6 2.37-15.1 install ok installed libc6-dev:amd64 libc6-dev 2.37-15.1 install ok installed libcairo-gobject2:amd64 libcairo-gobject2 1.18.0-1+b1 install ok installed libcairo2:amd64 libcairo2 1.18.0-1+b1 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.4-2 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libcbf1t64:amd64 libcbf1t64 0.9.7+dfsg1-3.1 install ok installed libcc1-0:amd64 libcc1-0 14-20240221-2.1 install ok installed libccp4-data libccp4-data 8.0.0-2 install ok installed libccp4-dev:amd64 libccp4-dev 8.0.0-2 install ok installed libccp4c0:amd64 libccp4c0 8.0.0-2 install ok installed libccp4f0:amd64 libccp4f0 8.0.0-2 install ok installed libcctbx-dev libcctbx-dev 2023.12+ds2+~3.17.0+ds1-4 install ok installed libcctbx0 libcctbx0 2023.12+ds2+~3.17.0+ds1-4 install ok installed libcloudproviders0:amd64 libcloudproviders0 0.3.5-1 install ok installed libcolord2:amd64 libcolord2 1.4.7-1 install ok installed libcom-err2t64:amd64 libcom-err2t64 1.47.0-2.3 install ok installed libcrypt-dev:amd64 libcrypt-dev 1:4.4.36-4 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-4 install ok installed libcryptsetup12:amd64 libcryptsetup12 2:2.7.0-1 install ok installed libctf-nobfd0:amd64 libctf-nobfd0 2.42-3 install ok installed libctf0:amd64 libctf0 2.42-3 install ok installed libcups2:amd64 libcups2 2.4.7-1+b1 install ok installed libcurl3-gnutls:amd64 libcurl3-gnutls 8.6.0-3 install ok installed libcurl4:amd64 libcurl4 8.6.0-3 install ok installed libdatrie1:amd64 libdatrie1 0.2.13-3 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-5 install ok installed libdbus-1-3:amd64 libdbus-1-3 1.14.10-4 install ok installed libdconf1:amd64 libdconf1 0.40.0-4+b1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.271+b1 install ok installed libdeflate0:amd64 libdeflate0 1.19-1 install ok installed libdevmapper1.02.1:amd64 libdevmapper1.02.1 2:1.02.196-1 install ok installed libdouble-conversion3:amd64 libdouble-conversion3 3.3.0-1+b1 install ok installed libdrm-amdgpu1:amd64 libdrm-amdgpu1 2.4.120-2 install ok installed libdrm-common libdrm-common 2.4.120-2 install ok installed libdrm-intel1:amd64 libdrm-intel1 2.4.120-2 install ok installed libdrm-nouveau2:amd64 libdrm-nouveau2 2.4.120-2 install ok installed libdrm-radeon1:amd64 libdrm-radeon1 2.4.120-2 install ok installed libdrm2:amd64 libdrm2 2.4.120-2 install ok installed libedit2:amd64 libedit2 3.1-20230828-1 install ok installed libegl-mesa0:amd64 libegl-mesa0 24.0.2-1 install ok installed libegl1:amd64 libegl1 1.7.0-1 install ok installed libelf1t64:amd64 libelf1t64 0.190-1.1 install ok installed libepoxy0:amd64 libepoxy0 1.5.10-1+b2 install ok installed libevdev2:amd64 libevdev2 1.13.1+dfsg-1 install ok installed libexpat1:amd64 libexpat1 2.6.0-1 install ok installed libexpat1-dev:amd64 libexpat1-dev 2.6.0-1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.0-2.3 install ok installed libfdisk1:amd64 libfdisk1 2.39.3-7 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libfontconfig1:amd64 libfontconfig1 2.15.0-1 install ok installed libfreetype6:amd64 libfreetype6 2.13.2+dfsg-1+b1 install ok installed libfribidi0:amd64 libfribidi0 1.0.13-3+b1 install ok installed libgbm1:amd64 libgbm1 24.0.2-1 install ok installed libgcc-12-dev:amd64 libgcc-12-dev 12.3.0-15 install ok installed libgcc-13-dev:amd64 libgcc-13-dev 13.2.0-16.1 install ok installed libgcc-s1:amd64 libgcc-s1 14-20240221-2.1 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.3-2 install ok installed libgdk-pixbuf-2.0-0:amd64 libgdk-pixbuf-2.0-0 2.42.10+dfsg-3+b1 install ok installed libgdk-pixbuf2.0-common libgdk-pixbuf2.0-common 2.42.10+dfsg-3 install ok installed libgfortran5:amd64 libgfortran5 14-20240221-2.1 install ok installed libgl1:amd64 libgl1 1.7.0-1 install ok installed libgl1-mesa-dri:amd64 libgl1-mesa-dri 24.0.2-1 install ok installed libgl1-mesa-glx:amd64 libgl1-mesa-glx 23.1.3-1 install ok installed libglapi-mesa:amd64 libglapi-mesa 24.0.2-1 install ok installed libglew2.2:amd64 libglew2.2 2.2.0-4+b1 deinstall ok config-files libglib2.0-0:amd64 libglib2.0-0 2.74.6-2 install ok installed libglib2.0-0t64:amd64 libglib2.0-0t64 2.78.4-2.1 install ok installed libglu1-mesa:amd64 libglu1-mesa 9.0.2-1.1 install ok installed libglvnd0:amd64 libglvnd0 1.7.0-1 install ok installed libglx-mesa0:amd64 libglx-mesa0 24.0.2-1 install ok installed libglx0:amd64 libglx0 1.7.0-1 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.3-1.1 install ok installed libgomp1:amd64 libgomp1 14-20240221-2.1 install ok installed libgpg-error0:amd64 libgpg-error0 1.47-3 install ok installed libgprofng0:amd64 libgprofng0 2.42-3 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.20.1-5+b1 install ok installed libgtk-3-0:amd64 libgtk-3-0 3.24.41-1 install ok installed libgtk-3-common libgtk-3-common 3.24.41-1.1 install ok installed libgudev-1.0-0:amd64 libgudev-1.0-0 238-3 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 8.3.0-2 install ok installed libhdf5-103-1t64:amd64 libhdf5-103-1t64 1.10.10+repack-3.1 install ok installed libhdf5-hl-100:amd64 libhdf5-hl-100 1.10.10+repack-3+b1 install ok installed libhogweed6:amd64 libhogweed6 3.9.1-2+b1 install ok installed libhwasan0:amd64 libhwasan0 14-20240221-2.1 install ok installed libice6:amd64 libice6 2:1.0.10-1 install ok installed libicu72:amd64 libicu72 72.1-4+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed libimagequant0:amd64 libimagequant0 2.18.0-1 install ok installed libinput-bin libinput-bin 1.25.0-1 install ok installed libinput10:amd64 libinput10 1.25.0-1 install ok installed libip4tc2:amd64 libip4tc2 1.8.10-3 install ok installed libisl23:amd64 libisl23 0.26-3+b2 install ok installed libitm1:amd64 libitm1 14-20240221-2.1 install ok installed libjansson4:amd64 libjansson4 2.14-2+b2 install ok installed libjbig0:amd64 libjbig0 2.1-6.1+b1 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-2+b2 install ok installed libjs-jquery libjs-jquery 3.6.1+dfsg+~3.5.14-1 install ok installed libjs-jquery-ui libjs-jquery-ui 1.13.2+dfsg-1 install ok installed libjs-sphinxdoc libjs-sphinxdoc 7.2.6-4 install ok installed libjs-underscore libjs-underscore 1.13.4~dfsg+~1.11.4-3 install ok installed libjson-c5:amd64 libjson-c5 0.17-1+b1 install ok installed libk5crypto3:amd64 libk5crypto3 1.20.1-5+b1 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-3 install ok installed libkmod2:amd64 libkmod2 31+20240202-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.20.1-5+b1 install ok installed libkrb5support0:amd64 libkrb5support0 1.20.1-5+b1 install ok installed liblapack3:amd64 liblapack3 3.12.0-3 install ok installed liblbfgsb0:amd64 liblbfgsb0 3.0+dfsg.4-1+b1 install ok installed liblcms2-2:amd64 liblcms2-2 2.14-2+b1 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.13+dfsg-5+b3 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-4+b1 install ok installed libllvm15:amd64 libllvm15 1:15.0.7-11 install ok installed libllvm17:amd64 libllvm17 1:17.0.6-5 install ok installed liblsan0:amd64 liblsan0 14-20240221-2.1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1+b2 install ok installed liblzf1:amd64 liblzf1 3.6-4 install ok installed liblzma5:amd64 liblzma5 5.6.0-0.2 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmd4c0:amd64 libmd4c0 0.4.8-1+b1 install ok installed libmmdb2-0:amd64 libmmdb2-0 2.0.22-1+b1 install ok installed libmount1:amd64 libmount1 2.39.3-7 install ok installed libmpc3:amd64 libmpc3 1.3.1-1+b2 install ok installed libmpfr6:amd64 libmpfr6 4.2.1-1+b1 install ok installed libmtdev1:amd64 libmtdev1 1.1.6-1+b1 install ok installed libncursesw6:amd64 libncursesw6 6.4+20240113-1 install ok installed libnetcdf19:amd64 libnetcdf19 1:4.9.2-3+b1 install ok installed libnettle8:amd64 libnettle8 3.9.1-2+b1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.59.0-1 install ok installed libnotify4:amd64 libnotify4 0.8.3-1 install ok installed libnsl-dev:amd64 libnsl-dev 1.3.0-3 install ok installed libnsl2:amd64 libnsl2 1.3.0-3 install ok installed libopenblas-dev:amd64 libopenblas-dev 0.3.26+ds-1 install ok installed libopenblas-pthread-dev:amd64 libopenblas-pthread-dev 0.3.26+ds-1 install ok installed libopenblas0:amd64 libopenblas0 0.3.26+ds-1 install ok installed libopenblas0-pthread:amd64 libopenblas0-pthread 0.3.26+ds-1 install ok installed libopengl0:amd64 libopengl0 1.7.0-1 install ok installed libopenjp2-7:amd64 libopenjp2-7 2.5.0-2+b2 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.3-4 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-6 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-6 install ok installed libpam-runtime libpam-runtime 1.5.3-6 install ok installed libpam-systemd:amd64 libpam-systemd 255.4-1 install ok installed libpam0g:amd64 libpam0g 1.5.3-6 install ok installed libpango-1.0-0:amd64 libpango-1.0-0 1.52.0+ds-1 install ok installed libpangocairo-1.0-0:amd64 libpangocairo-1.0-0 1.52.0+ds-1 install ok installed libpangoft2-1.0-0:amd64 libpangoft2-1.0-0 1.52.0+ds-1 install ok installed libpciaccess0:amd64 libpciaccess0 0.17-3 install ok installed libpcre2-16-0:amd64 libpcre2-16-0 10.42-4+b1 install ok installed libpcre2-32-0:amd64 libpcre2-32-0 10.42-4+b1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b1 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.42.2-1+b1 install ok installed libpng16-16:amd64 libpng16-16 1.6.43-1 install ok installed libproc2-0:amd64 libproc2-0 2:4.0.4-4 install ok installed libpsl5:amd64 libpsl5 0.21.2-1+b1 install ok installed libpython3-all-dev:amd64 libpython3-all-dev 3.11.6-1 install ok installed libpython3-dev:amd64 libpython3-dev 3.11.6-1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.11.6-1 install ok installed libpython3.11-dev:amd64 libpython3.11-dev 3.11.8-2 install ok installed libpython3.11-minimal:amd64 libpython3.11-minimal 3.11.8-2 install ok installed libpython3.11-stdlib:amd64 libpython3.11-stdlib 3.11.8-2 install ok installed libpython3.11t64:amd64 libpython3.11t64 3.11.8-2 install ok installed libpython3.12-dev:amd64 libpython3.12-dev 3.12.2-3 install ok installed libpython3.12-minimal:amd64 libpython3.12-minimal 3.12.2-3 install ok installed libpython3.12-stdlib:amd64 libpython3.12-stdlib 3.12.2-3 install ok installed libpython3.12t64:amd64 libpython3.12t64 3.12.2-3 install ok installed libqhull-r8.0:amd64 libqhull-r8.0 2020.2-6+b1 install ok installed libqt5core5a:amd64 libqt5core5a 5.15.10+dfsg-7 install ok installed libqt5dbus5:amd64 libqt5dbus5 5.15.10+dfsg-7 install ok installed libqt5designer5:amd64 libqt5designer5 5.15.10-6 install ok installed libqt5gui5:amd64 libqt5gui5 5.15.10+dfsg-7 install ok installed libqt5help5:amd64 libqt5help5 5.15.10-6 install ok installed libqt5network5:amd64 libqt5network5 5.15.10+dfsg-7 install ok installed libqt5opengl5:amd64 libqt5opengl5 5.15.10+dfsg-7 install ok installed libqt5printsupport5:amd64 libqt5printsupport5 5.15.10+dfsg-7 install ok installed libqt5sql5:amd64 libqt5sql5 5.15.10+dfsg-7 install ok installed libqt5test5:amd64 libqt5test5 5.15.10+dfsg-7 install ok installed libqt5widgets5:amd64 libqt5widgets5 5.15.10+dfsg-7 install ok installed libqt5xml5:amd64 libqt5xml5 5.15.10+dfsg-7 install ok installed libquadmath0:amd64 libquadmath0 14-20240221-2.1 install ok installed libraqm0:amd64 libraqm0 0.10.1-1+b1 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-3.1 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b2 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-4+b1 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-4+b1 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1 install ok installed libselinux1:amd64 libselinux1 3.5-2 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b2 install ok installed libsensors-config libsensors-config 1:3.6.0-9 install ok installed libsensors5:amd64 libsensors5 1:3.6.0-9 install ok installed libsepol2:amd64 libsepol2 3.5-2 install ok installed libsframe1:amd64 libsframe1 2.42-3 install ok installed libsharpyuv0:amd64 libsharpyuv0 1.3.2-0.4 install ok installed libsm6:amd64 libsm6 2:1.2.3-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.39.3-7 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.45.1-1 install ok installed libss2t64:amd64 libss2t64 1.47.0-2.3 install ok installed libssh2-1:amd64 libssh2-1 1.11.0-4 install ok installed libssl3t64:amd64 libssl3t64 3.1.5-1.1 install ok installed libssm2:amd64 libssm2 1.4.0-2+b1 install ok installed libstdc++-12-dev:amd64 libstdc++-12-dev 12.3.0-15 install ok installed libstdc++-13-dev:amd64 libstdc++-13-dev 13.2.0-16.1 install ok installed libstdc++6:amd64 libstdc++6 14-20240221-2.1 install ok installed libsystemd-shared:amd64 libsystemd-shared 255.4-1 install ok installed libsystemd0:amd64 libsystemd0 255.4-1 install ok installed libsz2:amd64 libsz2 1.1.2-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.13+dfsg-2+b1 install ok installed libthai-data libthai-data 0.1.29-2 install ok installed libthai0:amd64 libthai0 0.1.29-2 install ok installed libtiff6:amd64 libtiff6 4.5.1+git230720-4 install ok installed libtinfo6:amd64 libtinfo6 6.4+20240113-1 install ok installed libtirpc-common libtirpc-common 1.3.4+ds-1.1 install ok installed libtirpc-dev:amd64 libtirpc-dev 1.3.4+ds-1.1 install ok installed libtirpc3t64:amd64 libtirpc3t64 1.3.4+ds-1.1 install ok installed libtk8.6:amd64 libtk8.6 8.6.13-2+b1 install ok installed libtsan2:amd64 libtsan2 14-20240221-2.1 install ok installed libubsan1:amd64 libubsan1 14-20240221-2.1 install ok installed libudev1:amd64 libudev1 255.4-1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libunistring5:amd64 libunistring5 1.1-2 install ok installed libuuid1:amd64 libuuid1 2.39.3-7 install ok installed libuuid1t64:amd64 libuuid1t64 2.39.3-6.1 install ok installed libvulkan1:amd64 libvulkan1 1.3.275.0-1 install ok installed libwacom-common libwacom-common 2.10.0-1 install ok installed libwacom9:amd64 libwacom9 2.10.0-1 install ok installed libwayland-client0:amd64 libwayland-client0 1.22.0-2.1+b1 install ok installed libwayland-cursor0:amd64 libwayland-cursor0 1.22.0-2.1+b1 install ok installed libwayland-egl1:amd64 libwayland-egl1 1.22.0-2.1+b1 install ok installed libwayland-server0:amd64 libwayland-server0 1.22.0-2.1+b1 install ok installed libwebp7:amd64 libwebp7 1.3.2-0.4 install ok installed libwebpdemux2:amd64 libwebpdemux2 1.3.2-0.4 install ok installed libwebpmux3:amd64 libwebpmux3 1.3.2-0.4 install ok installed libwxbase3.2-1:amd64 libwxbase3.2-1 3.2.4+dfsg-3 install ok installed libwxgtk-gl3.2-1:amd64 libwxgtk-gl3.2-1 3.2.4+dfsg-3 install ok installed libwxgtk3.2-1:amd64 libwxgtk3.2-1 3.2.4+dfsg-3 install ok installed libx11-6:amd64 libx11-6 2:1.8.7-1 install ok installed libx11-data libx11-data 2:1.8.7-1 install ok installed libx11-xcb1:amd64 libx11-xcb1 2:1.8.7-1 install ok installed libxau6:amd64 libxau6 1:1.0.9-1 install ok installed libxcb-dri2-0:amd64 libxcb-dri2-0 1.15-1 install ok installed libxcb-dri3-0:amd64 libxcb-dri3-0 1.15-1 install ok installed libxcb-glx0:amd64 libxcb-glx0 1.15-1 install ok installed libxcb-icccm4:amd64 libxcb-icccm4 0.4.1-1.1+b1 install ok installed libxcb-image0:amd64 libxcb-image0 0.4.0-2+b1 install ok installed libxcb-keysyms1:amd64 libxcb-keysyms1 0.4.0-1+b2 install ok installed libxcb-present0:amd64 libxcb-present0 1.15-1 install ok installed libxcb-randr0:amd64 libxcb-randr0 1.15-1 install ok installed libxcb-render-util0:amd64 libxcb-render-util0 0.3.9-1+b1 install ok installed libxcb-render0:amd64 libxcb-render0 1.15-1 install ok installed libxcb-shape0:amd64 libxcb-shape0 1.15-1 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.15-1 install ok installed libxcb-sync1:amd64 libxcb-sync1 1.15-1 install ok installed libxcb-util1:amd64 libxcb-util1 0.4.0-1+b1 install ok installed libxcb-xfixes0:amd64 libxcb-xfixes0 1.15-1 install ok installed libxcb-xinerama0:amd64 libxcb-xinerama0 1.15-1 install ok installed libxcb-xinput0:amd64 libxcb-xinput0 1.15-1 install ok installed libxcb-xkb1:amd64 libxcb-xkb1 1.15-1 install ok installed libxcb1:amd64 libxcb1 1.15-1 install ok installed libxcomposite1:amd64 libxcomposite1 1:0.4.5-1 install ok installed libxcursor1:amd64 libxcursor1 1:1.2.1-1 install ok installed libxdamage1:amd64 libxdamage1 1:1.1.6-1 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b1 install ok installed libxfixes3:amd64 libxfixes3 1:6.0.0-2 install ok installed libxft2:amd64 libxft2 2.3.6-1+b1 install ok installed libxi6:amd64 libxi6 2:1.8.1-1 install ok installed libxinerama1:amd64 libxinerama1 2:1.1.4-3 install ok installed libxkbcommon-x11-0:amd64 libxkbcommon-x11-0 1.6.0-1 install ok installed libxkbcommon0:amd64 libxkbcommon0 1.6.0-1 install ok installed libxml2:amd64 libxml2 2.9.14+dfsg-1.3+b2 install ok installed libxrandr2:amd64 libxrandr2 2:1.5.2-2+b1 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1.1 install ok installed libxshmfence1:amd64 libxshmfence1 1.3-1 install ok installed libxsimd-dev:amd64 libxsimd-dev 12.1.1-2 install ok installed libxslt1.1:amd64 libxslt1.1 1.1.35-1 install ok installed libxss1:amd64 libxss1 1:1.2.3-1 install ok installed libxtst6:amd64 libxtst6 2:1.2.3-1.1 install ok installed libxxf86vm1:amd64 libxxf86vm1 1:1.1.4-1+b2 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libz3-4:amd64 libz3-4 4.8.12-3.1+b2 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-2 install ok installed linux-libc-dev linux-libc-dev 6.6.15-2 install ok installed login login 1:4.13+dfsg1-4 install ok installed logsave logsave 1.47.0-2.3 install ok installed mawk mawk 1.3.4.20240123-1 install ok installed media-types media-types 10.1.0 install ok installed mount mount 2.39.3-7 install ok installed ncurses-base ncurses-base 6.4+20240113-1 install ok installed ncurses-bin ncurses-bin 6.4+20240113-1 install ok installed netbase netbase 6.4 install ok installed openssl openssl 3.1.5-1.1 install ok installed passwd passwd 1:4.13+dfsg1-4 install ok installed perl-base perl-base 5.38.2-3 install ok installed procps procps 2:4.0.4-4 install ok installed pymol-data pymol-data 2.5.0+dfsg-1 install ok installed python-matplotlib-data python-matplotlib-data 3.6.3-1 install ok installed python3 python3 3.11.6-1 install ok installed python3-all python3-all 3.11.6-1 install ok installed python3-all-dev python3-all-dev 3.11.6-1 install ok installed python3-appdirs python3-appdirs 1.4.4-4 install ok installed python3-attr python3-attr 23.2.0-2 install ok installed python3-beniget python3-beniget 0.4.1-3 install ok installed python3-brotli python3-brotli 1.1.0-2+b3 install ok installed python3-cctbx python3-cctbx 2023.12+ds2+~3.17.0+ds1-4 install ok installed python3-certifi python3-certifi 2023.11.17-1 install ok installed python3-chardet python3-chardet 5.2.0+dfsg-1 install ok installed python3-charset-normalizer python3-charset-normalizer 3.3.2-1 install ok installed python3-contourpy python3-contourpy 1.0.7-1+b2 install ok installed python3-cycler python3-cycler 0.11.0-1 install ok installed python3-dateutil python3-dateutil 2.8.2-3 install ok installed python3-decorator python3-decorator 5.1.1-5 install ok installed python3-dev python3-dev 3.11.6-1 install ok installed python3-distutils python3-distutils 3.11.5-1 install ok installed python3-fonttools python3-fonttools 4.46.0-1 install ok installed python3-fs python3-fs 2.4.16-3 install ok installed python3-gast python3-gast 0.5.2-2 install ok installed python3-h5py python3-h5py 3.10.0-1 install ok installed python3-h5py-serial python3-h5py-serial 3.10.0-1 install ok installed python3-idna python3-idna 3.6-2 install ok installed python3-kiwisolver python3-kiwisolver 1.4.4-1+b2 install ok installed python3-lib2to3 python3-lib2to3 3.11.5-1 install ok installed python3-lxml:amd64 python3-lxml 5.1.0-1 install ok installed python3-lz4 python3-lz4 4.0.2+dfsg-1+b3 install ok installed python3-matplotlib python3-matplotlib 3.6.3-1+b2 install ok installed python3-minimal python3-minimal 3.11.6-1 install ok installed python3-mpmath python3-mpmath 1.2.1-2 install ok installed python3-mrcfile python3-mrcfile 1.4.3-3 install ok installed python3-numpy python3-numpy 1:1.24.2-2 install ok installed python3-nxmx python3-nxmx 0.0.3-2 install ok installed python3-opengl python3-opengl 3.1.7+dfsg-1 install ok installed python3-orderedset python3-orderedset 2.0.3+ds1-2 install ok installed python3-packaging python3-packaging 23.2-1 install ok installed python3-pil:amd64 python3-pil 10.2.0-1 install ok installed python3-pil.imagetk:amd64 python3-pil.imagetk 10.2.0-1 install ok installed python3-pint python3-pint 0.19.2-1 install ok installed python3-pkg-resources python3-pkg-resources 68.1.2-2 install ok installed python3-ply python3-ply 3.11-6 install ok installed python3-procrunner python3-procrunner 2.3.3-1 install ok installed python3-pycbf python3-pycbf 0.9.7+dfsg1-3.1 install ok installed python3-pymol python3-pymol 2.5.0+dfsg-1+b4 install ok installed python3-pyparsing python3-pyparsing 3.1.1-1 install ok installed python3-pyqt5 python3-pyqt5 5.15.10+dfsg-1 install ok installed python3-pyqt5.qtopengl python3-pyqt5.qtopengl 5.15.10+dfsg-1 install ok installed python3-pyqt5.sip python3-pyqt5.sip 12.13.0-1+b1 install ok installed python3-pythran python3-pythran 0.15.0+ds-2 install ok installed python3-requests python3-requests 2.31.0+dfsg-1 install ok installed python3-scipy python3-scipy 1.11.4-6 install ok installed python3-setuptools python3-setuptools 68.1.2-2 install ok installed python3-six python3-six 1.16.0-4 install ok installed python3-sympy python3-sympy 1.12-7 install ok installed python3-tk:amd64 python3-tk 3.11.5-1 install ok installed python3-tqdm python3-tqdm 4.64.1-2 install ok installed python3-tz python3-tz 2024.1-2 install ok installed python3-ufolib2 python3-ufolib2 0.16.0+dfsg1-1 install ok installed python3-urllib3 python3-urllib3 1.26.18-2 install ok installed python3-wxgtk4.0 python3-wxgtk4.0 4.2.1+dfsg-3 install ok installed python3.11 python3.11 3.11.8-2 install ok installed python3.11-dev python3.11-dev 3.11.8-2 install ok installed python3.11-minimal python3.11-minimal 3.11.8-2 install ok installed python3.12 python3.12 3.12.2-3 install ok installed python3.12-dev python3.12-dev 3.12.2-3 install ok installed python3.12-minimal python3.12-minimal 3.12.2-3 install ok installed readline-common readline-common 8.2-3.1 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 2.4-1 install ok installed sphinx-rtd-theme-common sphinx-rtd-theme-common 2.0.0+dfsg-1 install ok installed systemd systemd 255.4-1 install ok installed systemd-dev systemd-dev 255.4-1 install ok installed systemd-sysv systemd-sysv 255.4-1 install ok installed sysvinit-utils sysvinit-utils 3.08-7 install ok installed tar tar 1.35+dfsg-3 install ok installed tk8.6-blt2.5 tk8.6-blt2.5 2.5.3+dfsg-7 install ok installed tzdata tzdata 2024a-1 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 2.39.3-7 install ok installed util-linux-extra util-linux-extra 2.39.3-7 install ok installed x11-common x11-common 1:7.7+23 install ok installed xkb-data xkb-data 2.41-2 install ok installed xtl-dev xtl-dev 0.7.5-3 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg-3.1 install ok installed zlib1g-dev:amd64 zlib1g-dev 1:1.3.dfsg-3.1 5m25.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 5m25.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'apt-get', '-y', '--no-install-recommends', '--force-yes', 'install', 'libdb5.3:amd64=5.3.28+dfsg2-4+b1', 'libssl3:amd64=3.1.5-1', 'adwaita-icon-theme-', 'at-spi2-common-', 'binutils-', 'binutils-common:amd64-', 'binutils-x86-64-linux-gnu-', 'blt-', 'ca-certificates-', 'cpp-', 'cpp-12-', 'cpp-13-', 'cpp-13-x86-64-linux-gnu-', 'cpp-x86-64-linux-gnu-', 'dbus-', 'dbus-bin-', 'dbus-daemon-', 'dbus-session-bus-common-', 'dbus-system-bus-common-', 'dbus-user-session-', 'dconf-gsettings-backend:amd64-', 'dconf-service-', 'dmsetup-', 'fontconfig-', 'fontconfig-config-', 'fonts-dejavu-core-', 'fonts-dejavu-mono-', 'fonts-font-awesome-', 'fonts-lato-', 'fonts-lyx-', 'g++-', 'g++-12-', 'g++-13-', 'g++-13-x86-64-linux-gnu-', 'g++-x86-64-linux-gnu-', 'gcc-', 'gcc-12-', 'gcc-13-', 'gcc-13-base:amd64-', 'gcc-13-x86-64-linux-gnu-', 'gcc-x86-64-linux-gnu-', 'gtk-update-icon-cache-', 'hicolor-icon-theme-', 'libaec0:amd64-', 'libann-cctbx-dev-', 'libann-cctbx0-', 'libantlr3c-3.4-0:amd64-', 'libapparmor1:amd64-', 'libargon2-1:amd64-', 'libasan8:amd64-', 'libatk-bridge2.0-0:amd64-', 'libatk1.0-0:amd64-', 'libatomic1:amd64-', 'libatspi2.0-0:amd64-', 'libavahi-client3:amd64-', 'libavahi-common-data:amd64-', 'libavahi-common3:amd64-', 'libbinutils:amd64-', 'libblas3:amd64-', 'libboost-dev:amd64-', 'libboost-numpy1.74.0-', 'libboost-numpy1.83.0-', 'libboost-python-dev-', 'libboost-python1.74.0-', 'libboost-python1.83-dev-', 'libboost-python1.83.0-', 'libboost-thread1.74.0:amd64-', 'libboost-thread1.83.0:amd64-', 'libboost1.83-dev:amd64-', 'libbrotli1:amd64-', 'libbsd0:amd64-', 'libc-dev-bin-', 'libc6-dev:amd64-', 'libcairo-gobject2:amd64-', 'libcairo2:amd64-', 'libcbf1t64:amd64-', 'libcc1-0:amd64-', 'libccp4-data-', 'libccp4-dev:amd64-', 'libccp4c0:amd64-', 'libccp4f0:amd64-', 'libcctbx-dev-', 'libcctbx0-', 'libcloudproviders0:amd64-', 'libcolord2:amd64-', 'libcrypt-dev:amd64-', 'libcryptsetup12:amd64-', 'libctf-nobfd0:amd64-', 'libctf0:amd64-', 'libcups2:amd64-', 'libcurl3-gnutls:amd64-', 'libcurl4:amd64-', 'libdatrie1:amd64-', 'libdb5.3t64:amd64-', 'libdbus-1-3:amd64-', 'libdconf1:amd64-', 'libdeflate0:amd64-', 'libdevmapper1.02.1:amd64-', 'libdouble-conversion3:amd64-', 'libdrm-amdgpu1:amd64-', 'libdrm-common-', 'libdrm-intel1:amd64-', 'libdrm-nouveau2:amd64-', 'libdrm-radeon1:amd64-', 'libdrm2:amd64-', 'libedit2:amd64-', 'libegl-mesa0:amd64-', 'libegl1:amd64-', 'libelf1t64:amd64-', 'libepoxy0:amd64-', 'libevdev2:amd64-', 'libexpat1:amd64-', 'libexpat1-dev:amd64-', 'libfdisk1:amd64-', 'libfontconfig1:amd64-', 'libfreetype6:amd64-', 'libfribidi0:amd64-', 'libgbm1:amd64-', 'libgcc-12-dev:amd64-', 'libgcc-13-dev:amd64-', 'libgdk-pixbuf-2.0-0:amd64-', 'libgdk-pixbuf2.0-common-', 'libgfortran5:amd64-', 'libgl1:amd64-', 'libgl1-mesa-dri:amd64-', 'libgl1-mesa-glx:amd64-', 'libglapi-mesa:amd64-', 'libglew2.2:amd64-', 'libglib2.0-0:amd64-', 'libglib2.0-0t64:amd64-', 'libglu1-mesa:amd64-', 'libglvnd0:amd64-', 'libglx-mesa0:amd64-', 'libglx0:amd64-', 'libgomp1:amd64-', 'libgprofng0:amd64-', 'libgraphite2-3:amd64-', 'libgssapi-krb5-2:amd64-', 'libgtk-3-0:amd64-', 'libgtk-3-common-', 'libgudev-1.0-0:amd64-', 'libharfbuzz0b:amd64-', 'libhdf5-103-1t64:amd64-', 'libhdf5-hl-100:amd64-', 'libhwasan0:amd64-', 'libice6:amd64-', 'libicu72:amd64-', 'libimagequant0:amd64-', 'libinput-bin-', 'libinput10:amd64-', 'libip4tc2:amd64-', 'libisl23:amd64-', 'libitm1:amd64-', 'libjansson4:amd64-', 'libjbig0:amd64-', 'libjpeg62-turbo:amd64-', 'libjs-jquery-', 'libjs-jquery-ui-', 'libjs-sphinxdoc-', 'libjs-underscore-', 'libjson-c5:amd64-', 'libk5crypto3:amd64-', 'libkeyutils1:amd64-', 'libkmod2:amd64-', 'libkrb5-3:amd64-', 'libkrb5support0:amd64-', 'liblapack3:amd64-', 'liblbfgsb0:amd64-', 'liblcms2-2:amd64-', 'libldap-2.5-0:amd64-', 'liblerc4:amd64-', 'libllvm15:amd64-', 'libllvm17:amd64-', 'liblsan0:amd64-', 'liblzf1:amd64-', 'libmd4c0:amd64-', 'libmmdb2-0:amd64-', 'libmpc3:amd64-', 'libmpfr6:amd64-', 'libmtdev1:amd64-', 'libncursesw6:amd64-', 'libnetcdf19:amd64-', 'libnghttp2-14:amd64-', 'libnotify4:amd64-', 'libnsl-dev:amd64-', 'libnsl2:amd64-', 'libopenblas-dev:amd64-', 'libopenblas-pthread-dev:amd64-', 'libopenblas0:amd64-', 'libopenblas0-pthread: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-', 'libpng16-16:amd64-', 'libproc2-0:amd64-', 'libpsl5:amd64-', 'libpython3-all-dev:amd64-', 'libpython3-dev:amd64-', 'libpython3-stdlib:amd64-', 'libpython3.11-dev:amd64-', 'libpython3.11-minimal:amd64-', 'libpython3.11-stdlib:amd64-', 'libpython3.11t64:amd64-', 'libpython3.12-dev:amd64-', 'libpython3.12-minimal:amd64-', 'libpython3.12-stdlib:amd64-', 'libpython3.12t64:amd64-', 'libqhull-r8.0:amd64-', 'libqt5core5a:amd64-', 'libqt5dbus5:amd64-', 'libqt5designer5:amd64-', 'libqt5gui5:amd64-', 'libqt5help5:amd64-', 'libqt5network5:amd64-', 'libqt5opengl5:amd64-', 'libqt5printsupport5:amd64-', 'libqt5sql5:amd64-', 'libqt5test5:amd64-', 'libqt5widgets5:amd64-', 'libqt5xml5:amd64-', 'libquadmath0:amd64-', 'libraqm0:amd64-', 'libreadline8t64:amd64-', 'librtmp1:amd64-', 'libsasl2-2:amd64-', 'libsasl2-modules-db:amd64-', 'libsensors-config-', 'libsensors5:amd64-', 'libsframe1:amd64-', 'libsharpyuv0:amd64-', 'libsm6:amd64-', 'libsqlite3-0:amd64-', 'libssh2-1:amd64-', 'libssl3t64:amd64-', 'libssm2:amd64-', 'libstdc++-12-dev:amd64-', 'libstdc++-13-dev:amd64-', 'libsystemd-shared:amd64-', 'libsz2:amd64-', 'libtcl8.6:amd64-', 'libthai-data-', 'libthai0:amd64-', 'libtiff6:amd64-', 'libtirpc-common-', 'libtirpc-dev:amd64-', '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-', 'libwxbase3.2-1:amd64-', 'libwxgtk-gl3.2-1:amd64-', 'libwxgtk3.2-1: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-', 'libxsimd-dev:amd64-', 'libxslt1.1:amd64-', 'libxss1:amd64-', 'libxtst6:amd64-', 'libxxf86vm1:amd64-', 'libz3-4:amd64-', 'linux-libc-dev-', 'media-types-', 'netbase-', 'openssl-', 'procps-', 'pymol-data-', 'python-matplotlib-data-', 'python3-', 'python3-all-', 'python3-all-dev-', 'python3-appdirs-', 'python3-attr-', 'python3-beniget-', 'python3-brotli-', 'python3-certifi-', 'python3-chardet-', 'python3-charset-normalizer-', 'python3-contourpy-', 'python3-cycler-', 'python3-dateutil-', 'python3-decorator-', 'python3-dev-', 'python3-distutils-', 'python3-fonttools-', 'python3-fs-', 'python3-gast-', 'python3-h5py-', 'python3-h5py-serial-', 'python3-idna-', 'python3-kiwisolver-', 'python3-lib2to3-', 'python3-lxml:amd64-', 'python3-lz4-', 'python3-matplotlib-', 'python3-minimal-', 'python3-mpmath-', 'python3-mrcfile-', 'python3-numpy-', 'python3-nxmx-', 'python3-opengl-', 'python3-orderedset-', 'python3-packaging-', 'python3-pil:amd64-', 'python3-pil.imagetk:amd64-', 'python3-pint-', 'python3-pkg-resources-', 'python3-ply-', 'python3-procrunner-', 'python3-pycbf-', 'python3-pymol-', 'python3-pyparsing-', 'python3-pyqt5-', 'python3-pyqt5.qtopengl-', 'python3-pyqt5.sip-', 'python3-pythran-', 'python3-requests-', 'python3-scipy-', 'python3-setuptools-', 'python3-six-', 'python3-sympy-', 'python3-tk:amd64-', 'python3-tqdm-', 'python3-tz-', 'python3-ufolib2-', 'python3-urllib3-', 'python3-wxgtk4.0-', 'python3.11-', 'python3.11-dev-', 'python3.11-minimal-', 'python3.12-', 'python3.12-dev-', 'python3.12-minimal-', 'readline-common-', 'rpcsvc-proto-', 'shared-mime-info-', 'sphinx-rtd-theme-common-', 'systemd-', 'systemd-dev-', 'systemd-sysv-', 'tk8.6-blt2.5-', 'unicode-data-', 'x11-common-', 'xkb-data-', 'xtl-dev-', 'zlib1g-dev:amd64-', 'python3-cctbx-'] 5m44.5s DUMP: Reading package lists... Building dependency tree... Reading state information... Package 'libglib2.0-0' is not installed, so not removed The following packages will be REMOVED: adwaita-icon-theme at-spi2-common binutils binutils-common binutils-x86-64-linux-gnu blt ca-certificates cpp cpp-12 cpp-13 cpp-13-x86-64-linux-gnu cpp-x86-64-linux-gnu dbus dbus-bin dbus-daemon dbus-session-bus-common dbus-system-bus-common dbus-user-session dconf-gsettings-backend dconf-service dmsetup fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono fonts-font-awesome fonts-lato fonts-lyx g++ g++-12 g++-13 g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu gcc gcc-12 gcc-13 gcc-13-base gcc-13-x86-64-linux-gnu gcc-x86-64-linux-gnu gtk-update-icon-cache hicolor-icon-theme libaec0 libann-cctbx-dev libann-cctbx0 libantlr3c-3.4-0 libapparmor1 libargon2-1 libasan8 libatk-bridge2.0-0 libatk1.0-0 libatomic1 libatspi2.0-0 libavahi-client3 libavahi-common-data libavahi-common3 libbinutils libblas3 libboost-dev libboost-numpy1.74.0 libboost-numpy1.83.0 libboost-python-dev libboost-python1.74.0 libboost-python1.83-dev libboost-python1.83.0 libboost-thread1.74.0 libboost-thread1.83.0 libboost1.83-dev libbrotli1 libbsd0 libc-dev-bin libc6-dev libcairo-gobject2 libcairo2 libcbf1t64 libcc1-0 libccp4-data libccp4-dev libccp4c0 libccp4f0 libcctbx-dev libcctbx0 libcloudproviders0 libcolord2 libcrypt-dev libcryptsetup12 libctf-nobfd0 libctf0 libcups2 libcurl3-gnutls libcurl4 libdatrie1 libdb5.3t64 libdbus-1-3 libdconf1 libdeflate0 libdevmapper1.02.1 libdouble-conversion3 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libegl-mesa0 libegl1 libelf1t64 libepoxy0 libevdev2 libexpat1 libexpat1-dev libfdisk1 libfontconfig1 libfreetype6 libfribidi0 libgbm1 libgcc-12-dev libgcc-13-dev libgdk-pixbuf-2.0-0 libgdk-pixbuf2.0-common libgfortran5 libgl1 libgl1-mesa-dri libgl1-mesa-glx libglapi-mesa libglew2.2 libglib2.0-0t64 libglu1-mesa libglvnd0 libglx-mesa0 libglx0 libgomp1 libgprofng0 libgraphite2-3 libgssapi-krb5-2 libgtk-3-0 libgtk-3-common libgudev-1.0-0 libharfbuzz0b libhdf5-103-1t64 libhdf5-hl-100 libhwasan0 libice6 libicu72 libimagequant0 libinput-bin libinput10 libip4tc2 libisl23 libitm1 libjansson4 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libjs-sphinxdoc libjs-underscore libjson-c5 libk5crypto3 libkeyutils1 libkmod2 libkrb5-3 libkrb5support0 liblapack3 liblbfgsb0 liblcms2-2 libldap-2.5-0 liblerc4 libllvm15 libllvm17 liblsan0 liblzf1 libmd4c0 libmmdb2-0 libmpc3 libmpfr6 libmtdev1 libncursesw6 libnetcdf19 libnghttp2-14 libnotify4 libnsl-dev libnsl2 libopenblas-dev libopenblas-pthread-dev libopenblas0 libopenblas0-pthread 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 libpng16-16 libproc2-0 libpsl5 libpython3-all-dev libpython3-dev libpython3-stdlib libpython3.11-dev libpython3.11-minimal libpython3.11-stdlib libpython3.11t64 libpython3.12-dev libpython3.12-minimal libpython3.12-stdlib libpython3.12t64 libqhull-r8.0 libqt5core5a libqt5dbus5 libqt5designer5 libqt5gui5 libqt5help5 libqt5network5 libqt5opengl5 libqt5printsupport5 libqt5sql5 libqt5test5 libqt5widgets5 libqt5xml5 libquadmath0 libraqm0 libreadline8t64 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libsframe1 libsharpyuv0 libsm6 libsqlite3-0 libssh2-1 libssl3t64 libssm2 libstdc++-12-dev libstdc++-13-dev libsystemd-shared libsz2 libtcl8.6 libthai-data libthai0 libtiff6 libtirpc-common libtirpc-dev libtirpc3t64 libtk8.6 libtsan2 libubsan1 libvulkan1 libwacom-common libwacom9 libwayland-client0 libwayland-cursor0 libwayland-egl1 libwayland-server0 libwebp7 libwebpdemux2 libwebpmux3 libwxbase3.2-1 libwxgtk-gl3.2-1 libwxgtk3.2-1 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 libxsimd-dev libxslt1.1 libxss1 libxtst6 libxxf86vm1 libz3-4 linux-libc-dev media-types netbase openssl procps pymol-data python-matplotlib-data python3 python3-all python3-all-dev python3-appdirs python3-attr python3-beniget python3-brotli python3-cctbx python3-certifi python3-chardet python3-charset-normalizer python3-contourpy python3-cycler python3-dateutil python3-decorator python3-dev python3-distutils python3-fonttools python3-fs python3-gast python3-h5py python3-h5py-serial python3-idna python3-kiwisolver python3-lib2to3 python3-lxml python3-lz4 python3-matplotlib python3-minimal python3-mpmath python3-mrcfile python3-numpy python3-nxmx python3-opengl python3-orderedset python3-packaging python3-pil python3-pil.imagetk python3-pint python3-pkg-resources python3-ply python3-procrunner python3-pycbf python3-pymol python3-pyparsing python3-pyqt5 python3-pyqt5.qtopengl python3-pyqt5.sip python3-pythran python3-requests python3-scipy python3-setuptools python3-six python3-sympy python3-tk python3-tqdm python3-tz python3-ufolib2 python3-urllib3 python3-wxgtk4.0 python3.11 python3.11-dev python3.11-minimal python3.12 python3.12-dev python3.12-minimal readline-common rpcsvc-proto shared-mime-info sphinx-rtd-theme-common systemd systemd-dev systemd-sysv tk8.6-blt2.5 unicode-data x11-common xkb-data xtl-dev zlib1g-dev The following NEW packages will be installed: libdb5.3 libssl3 0 upgraded, 2 newly installed, 396 to remove and 0 not upgraded. Need to get 2760 kB of archives. After this operation, 2438 MB disk space will be freed. Get:1 http://deb.debian.org/debian sid/main amd64 libssl3 amd64 3.1.5-1 [2063 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libdb5.3 amd64 5.3.28+dfsg2-4+b1 [697 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 2760 kB in 0s (39.2 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 58631 files and directories currently installed.) Removing python3-cctbx (2023.12+ds2+~3.17.0+ds1-4) ... Removing python3-wxgtk4.0 (4.2.1+dfsg-3) ... Removing libwxgtk-gl3.2-1:amd64 (3.2.4+dfsg-3) ... Removing libwxgtk3.2-1:amd64 (3.2.4+dfsg-3) ... Removing libgtk-3-0:amd64 (3.24.41-1) ... Removing adwaita-icon-theme (46~beta-4) ... Removing libatk-bridge2.0-0:amd64 (2.50.0-1+b1) ... Removing libatk1.0-0:amd64 (2.50.0-1+b1) ... Removing at-spi2-common (2.51.90-1) ... Removing python3-pythran (0.15.0+ds-2) ... Removing g++ (4:13.2.0-7) ... Removing gcc (4:13.2.0-7) ... Removing g++-12 (12.3.0-15) ... Removing gcc-12 (12.3.0-15) ... Removing g++-x86-64-linux-gnu (4:13.2.0-7) ... Removing gcc-x86-64-linux-gnu (4:13.2.0-7) ... Removing g++-13 (13.2.0-16.1) ... Removing g++-13-x86-64-linux-gnu (13.2.0-16.1) ... Removing python3-matplotlib (3.6.3-1+b2) ... Removing python3-pil.imagetk:amd64 (10.2.0-1) ... Removing python3-pil:amd64 (10.2.0-1) ... Removing python3-tk:amd64 (3.11.5-1) ... Removing blt (2.5.3+dfsg-7) ... Removing python3-requests (2.31.0+dfsg-1) ... Removing python3-certifi (2023.11.17-1) ... Removing ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing cpp (4:13.2.0-7) ... Removing cpp-12 (12.3.0-15) ... Removing cpp-13 (13.2.0-16.1) ... Removing cpp-x86-64-linux-gnu (4:13.2.0-7) ... Removing libgtk-3-common (3.24.41-1.1) ... Removing dconf-gsettings-backend:amd64 (0.40.0-4+b1) ... Removing dconf-service (0.40.0-4+b1) ... Removing dbus-user-session (1.14.10-4) ... Removing libpam-systemd:amd64 (255.4-1) ... Removing dbus (1.14.10-4) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of stop. Removing dbus-daemon (1.14.10-4) ... Removing dbus-bin (1.14.10-4) ... Removing dbus-session-bus-common (1.14.10-4) ... Removing dbus-system-bus-common (1.14.10-4) ... Removing systemd-sysv (255.4-1) ... Removing systemd (255.4-1) ... Removing libcryptsetup12:amd64 (2:2.7.0-1) ... Removing python3-pymol (2.5.0+dfsg-1+b4) ... Removing python3-pyqt5.qtopengl (5.15.10+dfsg-1) ... Removing python3-pyqt5 (5.15.10+dfsg-1) ... Removing libqt5help5:amd64 (5.15.10-6) ... Removing libqt5designer5:amd64 (5.15.10-6) ... Removing libpangocairo-1.0-0:amd64 (1.52.0+ds-1) ... Removing libpangoft2-1.0-0:amd64 (1.52.0+ds-1) ... Removing libpango-1.0-0:amd64 (1.52.0+ds-1) ... Removing tk8.6-blt2.5 (2.5.3+dfsg-7) ... Removing libtk8.6:amd64 (8.6.13-2+b1) ... Removing libxft2:amd64 (2.3.6-1+b1) ... Removing libcairo-gobject2:amd64 (1.18.0-1+b1) ... Removing libcairo2:amd64 (1.18.0-1+b1) ... Removing python-matplotlib-data (3.6.3-1) ... Removing python3-mrcfile (1.4.3-3) ... Removing sphinx-rtd-theme-common (2.0.0+dfsg-1) ... Removing fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Removing fonts-lato (2.015-1) ... Removing fonts-lyx (2.4.0~RC3-1) ... Removing libcctbx-dev (2023.12+ds2+~3.17.0+ds1-4) ... Removing libboost-python-dev (1.83.0.2+b2) ... Removing libboost-python1.83-dev (1.83.0-2.1) ... Removing libboost-dev:amd64 (1.83.0.2+b2) ... Removing libboost1.83-dev:amd64 (1.83.0-2.1) ... Removing libstdc++-13-dev:amd64 (13.2.0-16.1) ... Removing gtk-update-icon-cache (3.24.41-1.1) ... Removing hicolor-icon-theme (0.17-2) ... Removing libnetcdf19:amd64 (1:4.9.2-3+b1) ... Removing python3-nxmx (0.0.3-2) ... Removing python3-h5py (3.10.0-1) ... Removing python3-h5py-serial (3.10.0-1) ... Removing libhdf5-hl-100:amd64 (1.10.10+repack-3+b1) ... Removing libann-cctbx-dev (1.1.2+doc-9+b1) ... Removing libcctbx0 (2023.12+ds2+~3.17.0+ds1-4) ... Removing libann-cctbx0 (1.1.2+doc-9+b1) ... Removing libantlr3c-3.4-0:amd64 (3.4+dfsg-4) ... Removing libsystemd-shared:amd64 (255.4-1) ... Removing libapparmor1:amd64 (3.0.12-1+b2) ... Removing libargon2-1:amd64 (0~20190702+dfsg-4+b1) ... Removing libstdc++-12-dev:amd64 (12.3.0-15) ... Removing libgcc-12-dev:amd64 (12.3.0-15) ... Removing libatspi2.0-0:amd64 (2.50.0-1+b1) ... Removing libqt5printsupport5:amd64 (5.15.10+dfsg-7) ... Removing libcups2:amd64 (2.4.7-1+b1) ... Removing libavahi-client3:amd64 (0.8-13+b1) ... Removing libavahi-common3:amd64 (0.8-13+b1) ... Removing libavahi-common-data:amd64 (0.8-13+b1) ... Removing python3-contourpy (1.0.7-1+b2) ... Removing liblapack3:amd64 (3.12.0-3) ... Removing libblas3:amd64 (3.12.0-3) ... Removing libboost-numpy1.74.0 (1.74.0+ds1-23.1) ... Removing libboost-numpy1.83.0 (1.83.0-2.1) ... Removing libboost-python1.74.0 (1.74.0+ds1-23.1) ... Removing libboost-python1.83.0 (1.83.0-2.1) ... Removing libboost-thread1.74.0:amd64 (1.74.0+ds1-23.1) ... Removing libboost-thread1.83.0:amd64 (1.83.0-2.1) ... Removing libraqm0:amd64 (0.10.1-1+b1) ... Removing libwxbase3.2-1:amd64 (3.2.4+dfsg-3) ... Removing python3-all-dev (3.11.6-1) ... Removing python3.12-dev (3.12.2-3) ... Removing libpython3-all-dev:amd64 (3.11.6-1) ... Removing libpython3.12-dev:amd64 (3.12.2-3) ... Removing python3-dev (3.11.6-1) ... Removing python3.11-dev (3.11.8-2) ... Removing python3-pycbf (0.9.7+dfsg1-3.1) ... Removing libcbf1t64:amd64 (0.9.7+dfsg1-3.1) ... Removing libccp4-dev:amd64 (8.0.0-2) ... Removing libccp4f0:amd64 (8.0.0-2) ... Removing libccp4c0:amd64 (8.0.0-2) ... Removing libccp4-data (8.0.0-2) ... Removing libcloudproviders0:amd64 (0.3.5-1) ... Removing libcolord2:amd64 (1.4.7-1) ... Removing libcurl3-gnutls:amd64 (8.6.0-3) ... Removing libthai0:amd64 (0.1.29-2) ... Removing libdatrie1:amd64 (0.2.13-3) ... Removing libpython3.12t64:amd64 (3.12.2-3) ... Removing python3-orderedset (2.0.3+ds1-2) ... Removing python3-setuptools (68.1.2-2) ... Removing python3-tqdm (4.64.1-2) ... Removing libdconf1:amd64 (0.40.0-4+b1) ... Removing libnotify4:amd64 (0.8.3-1) ... Removing libgdk-pixbuf-2.0-0:amd64 (2.42.10+dfsg-3+b1) ... Removing libtiff6:amd64 (4.5.1+git230720-4) ... Removing libdeflate0:amd64 (1.19-1) ... Removing libqt5xml5:amd64 (5.15.10+dfsg-7) ... Removing libqt5opengl5:amd64 (5.15.10+dfsg-7) ... Removing libqt5widgets5:amd64 (5.15.10+dfsg-7) ... Removing libqt5test5:amd64 (5.15.10+dfsg-7) ... Removing python3-opengl (3.1.7+dfsg-1) ... Removing libgl1-mesa-glx:amd64 (23.1.3-1) ... Removing libllvm15:amd64 (1:15.0.7-11) ... Removing libepoxy0:amd64 (1.5.10-1+b2) ... Removing libfdisk1:amd64 (2.39.3-7) ... Removing libfribidi0:amd64 (1.0.13-3+b1) ... Removing libgdk-pixbuf2.0-common (2.42.10+dfsg-3) ... Removing libopenblas-dev:amd64 (0.3.26+ds-1) ... Removing libopenblas-pthread-dev:amd64 (0.3.26+ds-1) ... Removing libopenblas0:amd64 (0.3.26+ds-1) ... Removing libglew2.2:amd64 (2.2.0-4+b1) ... Removing libglu1-mesa:amd64 (9.0.2-1.1) ... Removing libopengl0:amd64 (1.7.0-1) ... Removing libimagequant0:amd64 (2.18.0-1) ... Removing libnsl-dev:amd64 (1.3.0-3) ... Removing libtirpc-dev:amd64 (1.3.4+ds-1.1) ... Removing libip4tc2:amd64 (1.8.10-3) ... Removing libjbig0:amd64 (2.1-6.1+b1) ... Removing libjs-sphinxdoc (7.2.6-4) ... 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 libjson-c5:amd64 (0.17-1+b1) ... Removing libkmod2:amd64 (31+20240202-2) ... Removing liblcms2-2:amd64 (2.14-2+b1) ... Removing liblerc4:amd64 (4.0.0+ds-4+b1) ... Removing liblzf1:amd64 (3.6-4) ... Removing libssm2:amd64 (1.4.0-2+b1) ... Removing libmmdb2-0:amd64 (2.0.22-1+b1) ... Removing procps (2:4.0.4-4) ... Removing libopenjp2-7:amd64 (2.5.0-2+b2) ... Removing libpcre2-32-0:amd64 (10.42-4+b1) ... Removing libpixman-1-0:amd64 (0.42.2-1+b1) ... Removing libproc2-0:amd64 (2:4.0.4-4) ... Removing libpython3-dev:amd64 (3.11.6-1) ... Removing libqhull-r8.0:amd64 (2020.2-6+b1) ... Removing libqt5sql5:amd64 (5.15.10+dfsg-7) ... Removing libwebpmux3:amd64 (1.3.2-0.4) ... Removing libwebpdemux2:amd64 (1.3.2-0.4) ... Removing libwebp7:amd64 (1.3.2-0.4) ... Removing libsharpyuv0:amd64 (1.3.2-0.4) ... Removing openssl (3.1.5-1.1) ... Removing gcc-13 (13.2.0-16.1) ... Removing binutils (2.42-3) ... Removing gcc-13-x86-64-linux-gnu (13.2.0-16.1) ... Removing binutils-x86-64-linux-gnu (2.42-3) ... Removing libgprofng0:amd64 (2.42-3) ... Removing libctf0:amd64 (2.42-3) ... Removing libbinutils:amd64 (2.42-3) ... Removing binutils-common:amd64 (2.42-3) ... Removing cpp-13-x86-64-linux-gnu (13.2.0-16.1) ... Removing libqt5gui5:amd64 (5.15.10+dfsg-7) ... Removing fontconfig (2.15.0-1) ... Removing libfontconfig1:amd64 (2.15.0-1) ... Removing fontconfig-config (2.15.0-1) ... Removing fonts-dejavu-core (2.37-8) ... Removing fonts-dejavu-mono (2.37-8) ... Removing libgcc-13-dev:amd64 (13.2.0-16.1) ... Removing gcc-13-base:amd64 (13.2.0-16.1) ... Removing libhdf5-103-1t64:amd64 (1.10.10+repack-3.1) ... Removing libsz2:amd64 (1.1.2-1) ... Removing libaec0:amd64 (1.1.2-1) ... Removing libasan8:amd64 (14-20240221-2.1) ... Removing libatomic1:amd64 (14-20240221-2.1) ... Removing libharfbuzz0b:amd64 (8.3.0-2) ... Removing libfreetype6:amd64 (2.13.2+dfsg-1+b1) ... Removing libcurl4:amd64 (8.6.0-3) ... Removing libbrotli1:amd64 (1.1.0-2+b3) ... Removing libxcb-icccm4:amd64 (0.4.1-1.1+b1) ... Removing libxcb-render-util0:amd64 (0.3.9-1+b1) ... Removing libsm6:amd64 (2:1.2.3-1) ... Removing libice6:amd64 (2:1.0.10-1) ... Removing libpython3.11-dev:amd64 (3.11.8-2) ... Removing zlib1g-dev:amd64 (1:1.3.dfsg-3.1) ... Removing libexpat1-dev:amd64 (2.6.0-1) ... Removing libc6-dev:amd64 (2.37-15.1) ... Removing libc-dev-bin (2.37-15.1) ... Removing libcc1-0:amd64 (14-20240221-2.1) ... Removing libcrypt-dev:amd64 (1:4.4.36-4) ... Removing libctf-nobfd0:amd64 (2.42-3) ... Removing libldap-2.5-0:amd64 (2.5.13+dfsg-5+b3) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-4+b1) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-4+b1) ... Removing libqt5network5:amd64 (5.15.10+dfsg-7) ... Removing libqt5dbus5:amd64 (5.15.10+dfsg-7) ... Removing libdbus-1-3:amd64 (1.14.10-4) ... Removing libqt5core5a:amd64 (5.15.10+dfsg-7) ... Removing libdouble-conversion3:amd64 (3.3.0-1+b1) ... Removing libgl1:amd64 (1.7.0-1) ... Removing libglx0:amd64 (1.7.0-1) ... Removing libglx-mesa0:amd64 (24.0.2-1) ... Removing libgl1-mesa-dri:amd64 (24.0.2-1) ... Removing libdrm-amdgpu1:amd64 (2.4.120-2) ... Removing libegl1:amd64 (1.7.0-1) ... Removing libegl-mesa0:amd64 (24.0.2-1) ... Removing libgbm1:amd64 (24.0.2-1) ... Removing libdrm-intel1:amd64 (2.4.120-2) ... Removing libdrm-nouveau2:amd64 (2.4.120-2) ... Removing libdrm-radeon1:amd64 (2.4.120-2) ... Removing libllvm17:amd64 (1:17.0.6-5) ... Removing libedit2:amd64 (3.1-20230828-1) ... Removing libelf1t64:amd64 (0.190-1.1) ... Removing libinput10:amd64 (1.25.0-1) ... Removing libinput-bin (1.25.0-1) ... dpkg: warning: while removing libinput-bin, directory '/lib/udev/rules.d' not empty so not removed Removing libwacom9:amd64 (2.10.0-1) ... Removing libevdev2:amd64 (1.13.1+dfsg-1) ... Removing libglapi-mesa:amd64 (24.0.2-1) ... Removing shared-mime-info (2.4-1) ... Removing libgudev-1.0-0:amd64 (238-3) ... Removing libglib2.0-0t64:amd64 (2.78.4-2.1) ... Removing libglvnd0:amd64 (1.7.0-1) ... Removing libgomp1:amd64 (14-20240221-2.1) ... Removing libgraphite2-3:amd64 (1.3.14-2) ... Removing libhwasan0:amd64 (14-20240221-2.1) ... Removing libisl23:amd64 (0.26-3+b2) ... Removing libitm1:amd64 (14-20240221-2.1) ... Removing libjansson4:amd64 (2.14-2+b2) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-2+b2) ... Removing liblsan0:amd64 (14-20240221-2.1) ... Removing libmd4c0:amd64 (0.4.8-1+b1) ... Removing libmpc3:amd64 (1.3.1-1+b2) ... Removing libmpfr6:amd64 (4.2.1-1+b1) ... Removing libmtdev1:amd64 (1.1.6-1+b1) ... Removing libnghttp2-14:amd64 (1.59.0-1) ... Removing libpciaccess0:amd64 (0.17-3) ... Removing libpcre2-16-0:amd64 (10.42-4+b1) ... Removing libpng16-16:amd64 (1.6.43-1) ... Removing libpsl5:amd64 (0.21.2-1+b1) ... Removing libpython3.11t64:amd64 (3.11.8-2) ... Removing libquadmath0:amd64 (14-20240221-2.1) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Removing libsensors5:amd64 (1:3.6.0-9) ... Removing libsensors-config (1:3.6.0-9) ... Removing libsframe1:amd64 (2.42-3) ... Removing libssh2-1:amd64 (1.11.0-4) ... Removing libdrm2:amd64 (2.4.120-2) ... Removing libdrm-common (2.4.120-2) ... Removing dmsetup (2:1.02.196-1) ... Removing libdevmapper1.02.1:amd64 (2:1.02.196-1) ... Removing python3-fonttools (4.46.0-1) ... Removing python3-scipy (1.11.4-6) ... Removing python3-numpy (1:1.24.2-2) ... Removing liblbfgsb0:amd64 (3.0+dfsg.4-1+b1) ... Removing python3-all (3.11.6-1) ... Removing python3.12 (3.12.2-3) ... Removing libpython3.12-stdlib:amd64 (3.12.2-3) ... Removing python3-distutils (3.11.5-1) ... Removing python3.12-minimal (3.12.2-3) ... Removing libopenblas0-pthread:amd64 (0.3.26+ds-1) ... Removing libgfortran5:amd64 (14-20240221-2.1) ... Removing python3-lxml:amd64 (5.1.0-1) ... Removing libxslt1.1:amd64 (1.1.35-1) ... Removing libxml2:amd64 (2.9.14+dfsg-1.3+b2) ... Removing libicu72:amd64 (72.1-4+b1) ... Removing libpython3.12-minimal:amd64 (3.12.2-3) ... Removing python3-ufolib2 (0.16.0+dfsg1-1) ... dpkg: python3: dependency problems, but removing anyway as you requested: python3-urllib3 depends on python3:any. python3-tz depends on python3:any. python3-sympy depends on python3:any. python3-six depends on python3:any. python3-pyqt5.sip depends on python3 (<< 3.13). python3-pyqt5.sip depends on python3 (>= 3.11~). python3-pyqt5.sip depends on python3 (<< 3.13). python3-pyqt5.sip depends on python3 (>= 3.11~). python3-pyparsing depends on python3:any. python3-procrunner depends on python3:any. python3-ply depends on python3:any. python3-pkg-resources depends on python3:any. python3-pint depends on python3:any. python3-packaging depends on python3:any. python3-mpmath depends on python3:any. python3-lz4 depends on python3 (<< 3.13). python3-lz4 depends on python3 (>= 3.11~). python3-lz4 depends on python3:any. python3-lz4 depends on python3 (<< 3.13). python3-lz4 depends on python3 (>= 3.11~). python3-lz4 depends on python3:any. python3-lz4 depends on python3 (<< 3.13). python3-lz4 depends on python3 (>= 3.11~). python3-lz4 depends on python3:any. python3-lib2to3 depends on python3:any (>= 3.11.2-0~). python3-lib2to3 depends on python3:any (<< 3.13). python3-lib2to3 depends on python3:any (>= 3.11.2-0~). python3-lib2to3 depends on python3:any (<< 3.13). python3-kiwisolver depends on python3 (<< 3.13). python3-kiwisolver depends on python3 (>= 3.11~). python3-kiwisolver depends on python3-typing-extensions | python3-supported-min (>= 3.8); however: Package python3-typing-extensions is not installed. Package python3-supported-min is not installed. Package python3 which provides python3-supported-min is to be removed. python3-kiwisolver depends on python3:any. python3-kiwisolver depends on python3 (<< 3.13). python3-kiwisolver depends on python3 (>= 3.11~). python3-kiwisolver depends on python3-typing-extensions | python3-supported-min (>= 3.8); however: Package python3-typing-extensions is not installed. Package python3-supported-min is not installed. Package python3 which provides python3-supported-min is to be removed. python3-kiwisolver depends on python3:any. python3-kiwisolver depends on python3 (<< 3.13). python3-kiwisolver depends on python3 (>= 3.11~). python3-kiwisolver depends on python3-typing-extensions | python3-supported-min (>= 3.8); however: Package python3-typing-extensions is not installed. Package python3-supported-min is not installed. Package python3 which provides python3-supported-min is to be removed. python3-kiwisolver depends on python3:any. python3-idna depends on python3:any. python3-gast depends on python3:any. python3-fs depends on python3:any. python3-decorator depends on python3:any. python3-dateutil depends on python3:any. python3-cycler depends on python3:any. python3-charset-normalizer depends on python3:any. python3-chardet depends on python3:any. python3-brotli depends on python3 (<< 3.13). python3-brotli depends on python3 (>= 3.11~). python3-brotli depends on python3:any. python3-brotli depends on python3 (<< 3.13). python3-brotli depends on python3 (>= 3.11~). python3-brotli depends on python3:any. python3-brotli depends on python3 (<< 3.13). python3-brotli depends on python3 (>= 3.11~). python3-brotli depends on python3:any. python3-beniget depends on python3:any. python3-attr depends on python3-importlib-metadata | python3-supported-min (>= 3.8); however: Package python3-importlib-metadata is not installed. Package python3-supported-min is not installed. Package python3 which provides python3-supported-min is to be removed. python3-attr depends on python3:any. python3-appdirs depends on python3:any. python3-kiwisolver depends on python3 (<< 3.13). python3-kiwisolver depends on python3 (>= 3.11~). python3-kiwisolver depends on python3-typing-extensions | python3-supported-min (>= 3.8); however: Package python3-typing-extensions is not installed. Package python3-supported-min is not installed. Package python3 which provides python3-supported-min is to be removed. python3-kiwisolver depends on python3:any. python3-attr depends on python3-importlib-metadata | python3-supported-min (>= 3.8); however: Package python3-importlib-metadata is not installed. Package python3-supported-min is not installed. Package python3 which provides python3-supported-min is to be removed. python3-attr depends on python3:any. Removing python3 (3.11.6-1) ... Removing python3.11 (3.11.8-2) ... dpkg: libpython3.11-stdlib:amd64: dependency problems, but removing anyway as you requested: libpython3-stdlib:amd64 depends on libpython3.11-stdlib (>= 3.11.6-1~). Removing libpython3.11-stdlib:amd64 (3.11.8-2) ... Removing libdb5.3t64:amd64 (5.3.28+dfsg2-5) ... Removing python3-minimal (3.11.6-1) ... Removing python3.11-minimal (3.11.8-2) ... Removing libexpat1:amd64 (2.6.0-1) ... Removing libnsl2:amd64 (1.3.0-3) ... Removing libtirpc3t64:amd64 (1.3.4+ds-1.1) ... 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 (1.20.1-5+b1) ... Removing libkrb5-3:amd64 (1.20.1-5+b1) ... Removing libk5crypto3:amd64 (1.20.1-5+b1) ... Removing libkeyutils1:amd64 (1.6.3-3) ... Removing libkrb5support0:amd64 (1.20.1-5+b1) ... Removing libncursesw6:amd64 (6.4+20240113-1) ... Removing libpython3-stdlib:amd64 (3.11.6-1) ... Removing libpython3.11-minimal:amd64 (3.11.8-2) ... Removing libreadline8t64:amd64 (8.2-3.1) ... Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Removing libsqlite3-0:amd64 (3.45.1-1) ... dpkg: libssl3t64:amd64: dependency problems, but removing anyway as you requested: coreutils depends on libssl3 (>= 3.0.0); however: Package libssl3 is not installed. Package libssl3t64:amd64 which provides libssl3 is to be removed. Removing libssl3t64:amd64 (3.1.5-1.1) ... dpkg: libxcb1:amd64: dependency problems, but removing anyway as you requested: libxkbcommon-x11-0:amd64 depends on libxcb1 (>= 1.6). libxcb-xkb1:amd64 depends on libxcb1. libxcb-xinput0:amd64 depends on libxcb1 (>= 1.8). libxcb-xinerama0:amd64 depends on libxcb1. libxcb-xfixes0:amd64 depends on libxcb1. libxcb-util1:amd64 depends on libxcb1. libxcb-sync1:amd64 depends on libxcb1. libxcb-shm0:amd64 depends on libxcb1 (>= 1.12). libxcb-shape0:amd64 depends on libxcb1. libxcb-render0:amd64 depends on libxcb1 (>= 1.8). libxcb-randr0:amd64 depends on libxcb1 (>= 1.9.2). libxcb-present0:amd64 depends on libxcb1. libxcb-keysyms1:amd64 depends on libxcb1. libxcb-image0:amd64 depends on libxcb1. libxcb-glx0:amd64 depends on libxcb1. libxcb-dri3-0:amd64 depends on libxcb1 (>= 1.12). libxcb-dri2-0:amd64 depends on libxcb1. libx11-6:amd64 depends on libxcb1 (>= 1.11.1). Removing libxcb1:amd64 (1.15-1) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libbsd0:amd64 (0.12.1-1) ... Selecting previously unselected package libssl3: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 ... 12936 files and directories currently installed.) Preparing to unpack .../libssl3_3.1.5-1_amd64.deb ... Unpacking libssl3:amd64 (3.1.5-1) ... Setting up libssl3:amd64 (3.1.5-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12948 files and directories currently installed.) Removing libtcl8.6:amd64 (8.6.13+dfsg-2+b1) ... Removing libthai-data (0.1.29-2) ... Removing libtirpc-common (1.3.4+ds-1.1) ... Removing libtsan2:amd64 (14-20240221-2.1) ... Removing libubsan1:amd64 (14-20240221-2.1) ... Removing libvulkan1:amd64 (1.3.275.0-1) ... Removing libwacom-common (2.10.0-1) ... Removing libwayland-cursor0:amd64 (1.22.0-2.1+b1) ... Removing libwayland-client0:amd64 (1.22.0-2.1+b1) ... Removing libwayland-egl1:amd64 (1.22.0-2.1+b1) ... Removing libwayland-server0:amd64 (1.22.0-2.1+b1) ... Removing libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Removing libxtst6:amd64 (2:1.2.3-1.1) ... Removing libx11-xcb1:amd64 (2:1.8.7-1) ... Removing libxau6:amd64 (1:1.0.9-1) ... Removing libxcb-dri2-0:amd64 (1.15-1) ... Removing libxcb-dri3-0:amd64 (1.15-1) ... Removing libxcb-glx0:amd64 (1.15-1) ... Removing libxcb-image0:amd64 (0.4.0-2+b1) ... Removing libxcb-keysyms1:amd64 (0.4.0-1+b2) ... Removing libxcb-present0:amd64 (1.15-1) ... Removing libxcb-randr0:amd64 (1.15-1) ... Removing libxcb-render0:amd64 (1.15-1) ... Removing libxcb-shape0:amd64 (1.15-1) ... Removing libxcb-shm0:amd64 (1.15-1) ... Removing libxcb-sync1:amd64 (1.15-1) ... Removing libxcb-util1:amd64 (0.4.0-1+b1) ... Removing libxcb-xfixes0:amd64 (1.15-1) ... Removing libxcb-xinerama0:amd64 (1.15-1) ... Removing libxcb-xinput0:amd64 (1.15-1) ... Removing libxkbcommon-x11-0:amd64 (1.6.0-1) ... Removing libxcb-xkb1:amd64 (1.15-1) ... Removing libxcomposite1:amd64 (1:0.4.5-1) ... Removing libxcursor1:amd64 (1:1.2.1-1) ... Removing libxdamage1:amd64 (1:1.1.6-1) ... Removing libxss1:amd64 (1:1.2.3-1) ... Removing libxfixes3:amd64 (1:6.0.0-2) ... Removing libxi6:amd64 (2:1.8.1-1) ... Removing libxinerama1:amd64 (2:1.1.4-3) ... Removing libxkbcommon0:amd64 (1.6.0-1) ... Removing libxrandr2:amd64 (2:1.5.2-2+b1) ... Removing libxrender1:amd64 (1:0.9.10-1.1) ... Removing libxshmfence1:amd64 (1.3-1) ... Removing libxsimd-dev:amd64 (12.1.1-2) ... Removing libz3-4:amd64 (4.8.12-3.1+b2) ... Removing linux-libc-dev (6.6.15-2) ... Removing media-types (10.1.0) ... Removing netbase (6.4) ... Removing pymol-data (2.5.0+dfsg-1) ... Removing python3-fs (2.4.16-3) ... Removing python3-appdirs (1.4.4-4) ... Removing python3-attr (23.2.0-2) ... Removing python3-beniget (0.4.1-3) ... Removing python3-brotli (1.1.0-2+b3) ... Removing python3-chardet (5.2.0+dfsg-1) ... Removing python3-charset-normalizer (3.3.2-1) ... Removing python3-cycler (0.11.0-1) ... Removing python3-dateutil (2.8.2-3) ... Removing python3-decorator (5.1.1-5) ... Removing python3-gast (0.5.2-2) ... Removing python3-idna (3.6-2) ... Removing python3-kiwisolver (1.4.4-1+b2) ... Removing python3-lib2to3 (3.11.5-1) ... Removing python3-lz4 (4.0.2+dfsg-1+b3) ... Removing python3-sympy (1.12-7) ... Removing python3-mpmath (1.2.1-2) ... Removing python3-packaging (23.2-1) ... Removing python3-pint (0.19.2-1) ... Removing python3-pkg-resources (68.1.2-2) ... Removing python3-ply (3.11-6) ... Removing python3-procrunner (2.3.3-1) ... Removing python3-pyparsing (3.1.1-1) ... Removing python3-pyqt5.sip (12.13.0-1+b1) ... Removing python3-urllib3 (1.26.18-2) ... Removing python3-six (1.16.0-4) ... Removing python3-tz (2024.1-2) ... Removing readline-common (8.2-3.1) ... Removing rpcsvc-proto (1.4.3-1) ... Removing systemd-dev (255.4-1) ... Removing unicode-data (15.1.0-1) ... Removing x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing xkb-data (2.41-2) ... Removing xtl-dev (0.7.5-3) ... Removing libxext6:amd64 (2:1.3.4-1+b1) ... Removing libx11-6:amd64 (2:1.8.7-1) ... Removing libx11-data (2:1.8.7-1) ... Selecting previously unselected package libdb5.3: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 ... 5412 files and directories currently installed.) Preparing to unpack .../libdb5.3_5.3.28+dfsg2-4+b1_amd64.deb ... Unpacking libdb5.3:amd64 (5.3.28+dfsg2-4+b1) ... Setting up libdb5.3:amd64 (5.3.28+dfsg2-4+b1) ... Processing triggers for libc-bin (2.37-15.1) ... W: --force-yes is deprecated, use one of the options starting with --allow instead. 5m44.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'apt-get', '-y', '--no-install-recommends', '--force-yes', 'install', 'libdb5.3:amd64=5.3.28+dfsg2-4+b1', 'libssl3:amd64=3.1.5-1', 'adwaita-icon-theme-', 'at-spi2-common-', 'binutils-', 'binutils-common:amd64-', 'binutils-x86-64-linux-gnu-', 'blt-', 'ca-certificates-', 'cpp-', 'cpp-12-', 'cpp-13-', 'cpp-13-x86-64-linux-gnu-', 'cpp-x86-64-linux-gnu-', 'dbus-', 'dbus-bin-', 'dbus-daemon-', 'dbus-session-bus-common-', 'dbus-system-bus-common-', 'dbus-user-session-', 'dconf-gsettings-backend:amd64-', 'dconf-service-', 'dmsetup-', 'fontconfig-', 'fontconfig-config-', 'fonts-dejavu-core-', 'fonts-dejavu-mono-', 'fonts-font-awesome-', 'fonts-lato-', 'fonts-lyx-', 'g++-', 'g++-12-', 'g++-13-', 'g++-13-x86-64-linux-gnu-', 'g++-x86-64-linux-gnu-', 'gcc-', 'gcc-12-', 'gcc-13-', 'gcc-13-base:amd64-', 'gcc-13-x86-64-linux-gnu-', 'gcc-x86-64-linux-gnu-', 'gtk-update-icon-cache-', 'hicolor-icon-theme-', 'libaec0:amd64-', 'libann-cctbx-dev-', 'libann-cctbx0-', 'libantlr3c-3.4-0:amd64-', 'libapparmor1:amd64-', 'libargon2-1:amd64-', 'libasan8:amd64-', 'libatk-bridge2.0-0:amd64-', 'libatk1.0-0:amd64-', 'libatomic1:amd64-', 'libatspi2.0-0:amd64-', 'libavahi-client3:amd64-', 'libavahi-common-data:amd64-', 'libavahi-common3:amd64-', 'libbinutils:amd64-', 'libblas3:amd64-', 'libboost-dev:amd64-', 'libboost-numpy1.74.0-', 'libboost-numpy1.83.0-', 'libboost-python-dev-', 'libboost-python1.74.0-', 'libboost-python1.83-dev-', 'libboost-python1.83.0-', 'libboost-thread1.74.0:amd64-', 'libboost-thread1.83.0:amd64-', 'libboost1.83-dev:amd64-', 'libbrotli1:amd64-', 'libbsd0:amd64-', 'libc-dev-bin-', 'libc6-dev:amd64-', 'libcairo-gobject2:amd64-', 'libcairo2:amd64-', 'libcbf1t64:amd64-', 'libcc1-0:amd64-', 'libccp4-data-', 'libccp4-dev:amd64-', 'libccp4c0:amd64-', 'libccp4f0:amd64-', 'libcctbx-dev-', 'libcctbx0-', 'libcloudproviders0:amd64-', 'libcolord2:amd64-', 'libcrypt-dev:amd64-', 'libcryptsetup12:amd64-', 'libctf-nobfd0:amd64-', 'libctf0:amd64-', 'libcups2:amd64-', 'libcurl3-gnutls:amd64-', 'libcurl4:amd64-', 'libdatrie1:amd64-', 'libdb5.3t64:amd64-', 'libdbus-1-3:amd64-', 'libdconf1:amd64-', 'libdeflate0:amd64-', 'libdevmapper1.02.1:amd64-', 'libdouble-conversion3:amd64-', 'libdrm-amdgpu1:amd64-', 'libdrm-common-', 'libdrm-intel1:amd64-', 'libdrm-nouveau2:amd64-', 'libdrm-radeon1:amd64-', 'libdrm2:amd64-', 'libedit2:amd64-', 'libegl-mesa0:amd64-', 'libegl1:amd64-', 'libelf1t64:amd64-', 'libepoxy0:amd64-', 'libevdev2:amd64-', 'libexpat1:amd64-', 'libexpat1-dev:amd64-', 'libfdisk1:amd64-', 'libfontconfig1:amd64-', 'libfreetype6:amd64-', 'libfribidi0:amd64-', 'libgbm1:amd64-', 'libgcc-12-dev:amd64-', 'libgcc-13-dev:amd64-', 'libgdk-pixbuf-2.0-0:amd64-', 'libgdk-pixbuf2.0-common-', 'libgfortran5:amd64-', 'libgl1:amd64-', 'libgl1-mesa-dri:amd64-', 'libgl1-mesa-glx:amd64-', 'libglapi-mesa:amd64-', 'libglew2.2:amd64-', 'libglib2.0-0:amd64-', 'libglib2.0-0t64:amd64-', 'libglu1-mesa:amd64-', 'libglvnd0:amd64-', 'libglx-mesa0:amd64-', 'libglx0:amd64-', 'libgomp1:amd64-', 'libgprofng0:amd64-', 'libgraphite2-3:amd64-', 'libgssapi-krb5-2:amd64-', 'libgtk-3-0:amd64-', 'libgtk-3-common-', 'libgudev-1.0-0:amd64-', 'libharfbuzz0b:amd64-', 'libhdf5-103-1t64:amd64-', 'libhdf5-hl-100:amd64-', 'libhwasan0:amd64-', 'libice6:amd64-', 'libicu72:amd64-', 'libimagequant0:amd64-', 'libinput-bin-', 'libinput10:amd64-', 'libip4tc2:amd64-', 'libisl23:amd64-', 'libitm1:amd64-', 'libjansson4:amd64-', 'libjbig0:amd64-', 'libjpeg62-turbo:amd64-', 'libjs-jquery-', 'libjs-jquery-ui-', 'libjs-sphinxdoc-', 'libjs-underscore-', 'libjson-c5:amd64-', 'libk5crypto3:amd64-', 'libkeyutils1:amd64-', 'libkmod2:amd64-', 'libkrb5-3:amd64-', 'libkrb5support0:amd64-', 'liblapack3:amd64-', 'liblbfgsb0:amd64-', 'liblcms2-2:amd64-', 'libldap-2.5-0:amd64-', 'liblerc4:amd64-', 'libllvm15:amd64-', 'libllvm17:amd64-', 'liblsan0:amd64-', 'liblzf1:amd64-', 'libmd4c0:amd64-', 'libmmdb2-0:amd64-', 'libmpc3:amd64-', 'libmpfr6:amd64-', 'libmtdev1:amd64-', 'libncursesw6:amd64-', 'libnetcdf19:amd64-', 'libnghttp2-14:amd64-', 'libnotify4:amd64-', 'libnsl-dev:amd64-', 'libnsl2:amd64-', 'libopenblas-dev:amd64-', 'libopenblas-pthread-dev:amd64-', 'libopenblas0:amd64-', 'libopenblas0-pthread: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-', 'libpng16-16:amd64-', 'libproc2-0:amd64-', 'libpsl5:amd64-', 'libpython3-all-dev:amd64-', 'libpython3-dev:amd64-', 'libpython3-stdlib:amd64-', 'libpython3.11-dev:amd64-', 'libpython3.11-minimal:amd64-', 'libpython3.11-stdlib:amd64-', 'libpython3.11t64:amd64-', 'libpython3.12-dev:amd64-', 'libpython3.12-minimal:amd64-', 'libpython3.12-stdlib:amd64-', 'libpython3.12t64:amd64-', 'libqhull-r8.0:amd64-', 'libqt5core5a:amd64-', 'libqt5dbus5:amd64-', 'libqt5designer5:amd64-', 'libqt5gui5:amd64-', 'libqt5help5:amd64-', 'libqt5network5:amd64-', 'libqt5opengl5:amd64-', 'libqt5printsupport5:amd64-', 'libqt5sql5:amd64-', 'libqt5test5:amd64-', 'libqt5widgets5:amd64-', 'libqt5xml5:amd64-', 'libquadmath0:amd64-', 'libraqm0:amd64-', 'libreadline8t64:amd64-', 'librtmp1:amd64-', 'libsasl2-2:amd64-', 'libsasl2-modules-db:amd64-', 'libsensors-config-', 'libsensors5:amd64-', 'libsframe1:amd64-', 'libsharpyuv0:amd64-', 'libsm6:amd64-', 'libsqlite3-0:amd64-', 'libssh2-1:amd64-', 'libssl3t64:amd64-', 'libssm2:amd64-', 'libstdc++-12-dev:amd64-', 'libstdc++-13-dev:amd64-', 'libsystemd-shared:amd64-', 'libsz2:amd64-', 'libtcl8.6:amd64-', 'libthai-data-', 'libthai0:amd64-', 'libtiff6:amd64-', 'libtirpc-common-', 'libtirpc-dev:amd64-', '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-', 'libwxbase3.2-1:amd64-', 'libwxgtk-gl3.2-1:amd64-', 'libwxgtk3.2-1: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-', 'libxsimd-dev:amd64-', 'libxslt1.1:amd64-', 'libxss1:amd64-', 'libxtst6:amd64-', 'libxxf86vm1:amd64-', 'libz3-4:amd64-', 'linux-libc-dev-', 'media-types-', 'netbase-', 'openssl-', 'procps-', 'pymol-data-', 'python-matplotlib-data-', 'python3-', 'python3-all-', 'python3-all-dev-', 'python3-appdirs-', 'python3-attr-', 'python3-beniget-', 'python3-brotli-', 'python3-certifi-', 'python3-chardet-', 'python3-charset-normalizer-', 'python3-contourpy-', 'python3-cycler-', 'python3-dateutil-', 'python3-decorator-', 'python3-dev-', 'python3-distutils-', 'python3-fonttools-', 'python3-fs-', 'python3-gast-', 'python3-h5py-', 'python3-h5py-serial-', 'python3-idna-', 'python3-kiwisolver-', 'python3-lib2to3-', 'python3-lxml:amd64-', 'python3-lz4-', 'python3-matplotlib-', 'python3-minimal-', 'python3-mpmath-', 'python3-mrcfile-', 'python3-numpy-', 'python3-nxmx-', 'python3-opengl-', 'python3-orderedset-', 'python3-packaging-', 'python3-pil:amd64-', 'python3-pil.imagetk:amd64-', 'python3-pint-', 'python3-pkg-resources-', 'python3-ply-', 'python3-procrunner-', 'python3-pycbf-', 'python3-pymol-', 'python3-pyparsing-', 'python3-pyqt5-', 'python3-pyqt5.qtopengl-', 'python3-pyqt5.sip-', 'python3-pythran-', 'python3-requests-', 'python3-scipy-', 'python3-setuptools-', 'python3-six-', 'python3-sympy-', 'python3-tk:amd64-', 'python3-tqdm-', 'python3-tz-', 'python3-ufolib2-', 'python3-urllib3-', 'python3-wxgtk4.0-', 'python3.11-', 'python3.11-dev-', 'python3.11-minimal-', 'python3.12-', 'python3.12-dev-', 'python3.12-minimal-', 'readline-common-', 'rpcsvc-proto-', 'shared-mime-info-', 'sphinx-rtd-theme-common-', 'systemd-', 'systemd-dev-', 'systemd-sysv-', 'tk8.6-blt2.5-', 'unicode-data-', 'x11-common-', 'xkb-data-', 'xtl-dev-', 'zlib1g-dev:amd64-', 'python3-cctbx-'] 5m44.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'apt-get', '-y', '--no-install-recommends', '--reinstall', 'install', 'libdb5.3:amd64=5.3.28+dfsg2-4+b1', 'libssl3:amd64=3.1.5-1'] 5m45.9s DUMP: Reading package lists... Building dependency tree... Reading state information... debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 0 newly installed, 2 reinstalled, 0 to remove and 0 not upgraded. Need to get 0 B/2760 kB of archives. After this operation, 0 B of additional disk space will be used. (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 ... 5419 files and directories currently installed.) Preparing to unpack .../libssl3_3.1.5-1_amd64.deb ... Unpacking libssl3:amd64 (3.1.5-1) over (3.1.5-1) ... Setting up libssl3:amd64 (3.1.5-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5419 files and directories currently installed.) Preparing to unpack .../libdb5.3_5.3.28+dfsg2-4+b1_amd64.deb ... Unpacking libdb5.3:amd64 (5.3.28+dfsg2-4+b1) over (5.3.28+dfsg2-4+b1) ... Setting up libdb5.3:amd64 (5.3.28+dfsg2-4+b1) ... Processing triggers for libc-bin (2.37-15.1) ... 5m45.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'apt-get', '-y', '--no-install-recommends', '--reinstall', 'install', 'libdb5.3:amd64=5.3.28+dfsg2-4+b1', 'libssl3:amd64=3.1.5-1'] 5m45.9s INFO: Running scripts post_remove 5m45.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/post_remove_exceptions'] 5m45.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/post_remove_exceptions'] 5m45.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'dpkg', '--purge', 'adwaita-icon-theme', 'at-spi2-common', 'binutils', 'binutils-common:amd64', 'binutils-x86-64-linux-gnu', 'blt', 'ca-certificates', 'cpp', 'cpp-12', 'cpp-13', 'cpp-13-x86-64-linux-gnu', 'cpp-x86-64-linux-gnu', 'dbus', 'dbus-bin', 'dbus-daemon', 'dbus-session-bus-common', 'dbus-system-bus-common', 'dbus-user-session', 'dconf-gsettings-backend:amd64', 'dconf-service', 'dmsetup', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-font-awesome', 'fonts-lato', 'fonts-lyx', 'g++', 'g++-12', 'g++-13', 'g++-13-x86-64-linux-gnu', 'g++-x86-64-linux-gnu', 'gcc', 'gcc-12', 'gcc-13', 'gcc-13-base:amd64', 'gcc-13-x86-64-linux-gnu', 'gcc-x86-64-linux-gnu', 'gtk-update-icon-cache', 'hicolor-icon-theme', 'libaec0:amd64', 'libann-cctbx-dev', 'libann-cctbx0', 'libantlr3c-3.4-0:amd64', 'libapparmor1:amd64', 'libargon2-1:amd64', 'libasan8:amd64', 'libatk-bridge2.0-0:amd64', 'libatk1.0-0:amd64', 'libatomic1:amd64', 'libatspi2.0-0:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbinutils:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost-numpy1.74.0', 'libboost-numpy1.83.0', 'libboost-python-dev', 'libboost-python1.74.0', 'libboost-python1.83-dev', 'libboost-python1.83.0', 'libboost-thread1.74.0:amd64', 'libboost-thread1.83.0:amd64', 'libboost1.83-dev:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo-gobject2:amd64', 'libcairo2:amd64', 'libcbf1t64:amd64', 'libcc1-0:amd64', 'libccp4-data', 'libccp4-dev:amd64', 'libccp4c0:amd64', 'libccp4f0:amd64', 'libcctbx-dev', 'libcctbx0', 'libcloudproviders0:amd64', 'libcolord2:amd64', 'libcrypt-dev:amd64', 'libcryptsetup12:amd64', 'libctf-nobfd0:amd64', 'libctf0:amd64', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdatrie1:amd64', 'libdb5.3t64:amd64', 'libdbus-1-3:amd64', 'libdconf1:amd64', 'libdeflate0:amd64', 'libdevmapper1.02.1:amd64', 'libdouble-conversion3:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm-nouveau2:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libedit2:amd64', 'libegl-mesa0:amd64', 'libegl1:amd64', 'libelf1t64:amd64', 'libepoxy0:amd64', 'libevdev2:amd64', 'libexpat1:amd64', 'libexpat1-dev:amd64', 'libfdisk1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgbm1:amd64', 'libgcc-12-dev:amd64', 'libgcc-13-dev:amd64', 'libgdk-pixbuf-2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgfortran5:amd64', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libgl1-mesa-glx:amd64', 'libglapi-mesa:amd64', 'libglew2.2:amd64', 'libglib2.0-0:amd64', 'libglib2.0-0t64:amd64', 'libglu1-mesa:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgprofng0:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libgtk-3-0:amd64', 'libgtk-3-common', 'libgudev-1.0-0:amd64', 'libharfbuzz0b:amd64', 'libhdf5-103-1t64:amd64', 'libhdf5-hl-100:amd64', 'libhwasan0:amd64', 'libice6:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libinput-bin', 'libinput10:amd64', 'libip4tc2:amd64', 'libisl23:amd64', 'libitm1:amd64', 'libjansson4:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libjs-sphinxdoc', 'libjs-underscore', 'libjson-c5:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkmod2:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libllvm15:amd64', 'libllvm17:amd64', 'liblsan0:amd64', 'liblzf1:amd64', 'libmd4c0:amd64', 'libmmdb2-0:amd64', 'libmpc3:amd64', 'libmpfr6:amd64', 'libmtdev1:amd64', 'libncursesw6:amd64', 'libnetcdf19:amd64', 'libnghttp2-14:amd64', 'libnotify4:amd64', 'libnsl-dev:amd64', 'libnsl2:amd64', 'libopenblas-dev:amd64', 'libopenblas-pthread-dev:amd64', 'libopenblas0:amd64', 'libopenblas0-pthread: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', 'libpng16-16:amd64', 'libproc2-0:amd64', 'libpsl5:amd64', 'libpython3-all-dev:amd64', 'libpython3-dev:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-dev:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.11t64:amd64', 'libpython3.12-dev:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libpython3.12t64:amd64', 'libqhull-r8.0:amd64', 'libqt5core5a:amd64', 'libqt5dbus5:amd64', 'libqt5designer5:amd64', 'libqt5gui5:amd64', 'libqt5help5:amd64', 'libqt5network5:amd64', 'libqt5opengl5:amd64', 'libqt5printsupport5:amd64', 'libqt5sql5:amd64', 'libqt5test5:amd64', 'libqt5widgets5:amd64', 'libqt5xml5:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libsframe1:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl3t64:amd64', 'libssm2:amd64', 'libstdc++-12-dev:amd64', 'libstdc++-13-dev:amd64', 'libsystemd-shared:amd64', 'libsz2:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc-dev:amd64', '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', 'libwxbase3.2-1:amd64', 'libwxgtk-gl3.2-1:amd64', 'libwxgtk3.2-1: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', 'libxsimd-dev:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libz3-4:amd64', 'linux-libc-dev', 'media-types', 'netbase', 'openssl', 'procps', 'pymol-data', 'python-matplotlib-data', 'python3', 'python3-all', 'python3-all-dev', 'python3-appdirs', 'python3-attr', 'python3-beniget', 'python3-brotli', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-dev', 'python3-distutils', 'python3-fonttools', 'python3-fs', 'python3-gast', 'python3-h5py', 'python3-h5py-serial', 'python3-idna', 'python3-kiwisolver', 'python3-lib2to3', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-minimal', 'python3-mpmath', 'python3-mrcfile', 'python3-numpy', 'python3-nxmx', 'python3-opengl', 'python3-orderedset', 'python3-packaging', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pint', 'python3-pkg-resources', 'python3-ply', 'python3-procrunner', 'python3-pycbf', 'python3-pymol', 'python3-pyparsing', 'python3-pyqt5', 'python3-pyqt5.qtopengl', 'python3-pyqt5.sip', 'python3-pythran', 'python3-requests', 'python3-scipy', 'python3-setuptools', 'python3-six', 'python3-sympy', 'python3-tk:amd64', 'python3-tqdm', 'python3-tz', 'python3-ufolib2', 'python3-urllib3', 'python3-wxgtk4.0', 'python3.11', 'python3.11-dev', 'python3.11-minimal', 'python3.12', 'python3.12-dev', 'python3.12-minimal', 'readline-common', 'rpcsvc-proto', 'shared-mime-info', 'sphinx-rtd-theme-common', 'systemd', 'systemd-dev', 'systemd-sysv', 'tk8.6-blt2.5', 'unicode-data', 'x11-common', 'xkb-data', 'xtl-dev', 'zlib1g-dev:amd64'] 5m46.5s DUMP: (Reading database ... 5418 files and directories currently installed.) Purging configuration files for adwaita-icon-theme (46~beta-4) ... dpkg: warning: ignoring request to remove at-spi2-common which isn't installed dpkg: warning: ignoring request to remove binutils which isn't installed Purging configuration files for binutils-common:amd64 (2.42-3) ... dpkg: warning: ignoring request to remove binutils-x86-64-linux-gnu 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. 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which isn't installed dpkg: warning: ignoring request to remove libmtdev1 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libnetcdf19 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libnotify4 which isn't installed dpkg: warning: ignoring request to remove libnsl-dev which isn't installed dpkg: warning: ignoring request to remove libnsl2 which isn't installed dpkg: warning: ignoring request to remove libopenblas-dev which isn't installed dpkg: warning: ignoring request to remove libopenblas-pthread-dev which isn't installed dpkg: warning: ignoring request to remove libopenblas0 which isn't installed dpkg: warning: ignoring request to remove libopenblas0-pthread 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 libpng16-16 which isn't installed dpkg: warning: ignoring request to remove libproc2-0 which isn't installed dpkg: warning: ignoring request to remove libpsl5 which isn't installed dpkg: warning: ignoring request to remove libpython3-all-dev which isn't installed dpkg: warning: ignoring 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isn't installed dpkg: warning: ignoring request to remove libqt5designer5 which isn't installed dpkg: warning: ignoring request to remove libqt5gui5 which isn't installed dpkg: warning: ignoring request to remove libqt5help5 which isn't installed dpkg: warning: ignoring request to remove libqt5network5 which isn't installed dpkg: warning: ignoring request to remove libqt5opengl5 which isn't installed dpkg: warning: ignoring request to remove libqt5printsupport5 which isn't installed dpkg: warning: ignoring request to remove libqt5sql5 which isn't installed dpkg: warning: ignoring request to remove libqt5test5 which isn't installed dpkg: warning: ignoring request to remove libqt5widgets5 which isn't installed dpkg: warning: ignoring request to remove libqt5xml5 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 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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 libxsimd-dev 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) ... Purging configuration files for netbase (6.4) ... Purging configuration files for openssl (3.1.5-1.1) ... Purging configuration files for procps (2:4.0.4-4) ... dpkg: warning: ignoring request to remove pymol-data which isn't installed Purging configuration files for python-matplotlib-data (3.6.3-1) ... Purging configuration files for python3 (3.11.6-1) ... dpkg: warning: ignoring request to remove python3-all which isn't installed dpkg: warning: ignoring request to remove python3-all-dev which isn't installed 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-beniget 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-distutils 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-gast 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-idna which isn't installed dpkg: warning: ignoring request to remove python3-kiwisolver which isn't installed dpkg: warning: ignoring request to remove python3-lib2to3 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-mpmath which isn't installed dpkg: warning: ignoring request to remove python3-mrcfile 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-orderedset 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-ply 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-pythran 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-setuptools which isn't installed dpkg: warning: ignoring request to remove python3-six which isn't installed Purging configuration files for python3-sympy (1.12-7) ... dpkg: warning: ignoring request to remove python3-tk which isn't installed dpkg: warning: ignoring request to remove python3-tqdm which isn't installed dpkg: warning: ignoring request to remove python3-tz which isn't installed dpkg: warning: ignoring request to remove python3-ufolib2 which isn't installed dpkg: warning: ignoring request to remove python3-urllib3 which isn't installed dpkg: warning: ignoring request to remove python3-wxgtk4.0 which isn't installed dpkg: warning: ignoring request to remove python3.11 which isn't installed dpkg: warning: ignoring request to remove python3.11-dev which isn't installed Purging configuration files for python3.11-minimal (3.11.8-2) ... 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 (3.12.2-3) ... Purging configuration files for readline-common (8.2-3.1) ... dpkg: warning: ignoring request to remove rpcsvc-proto which isn't installed Purging configuration files for shared-mime-info (2.4-1) ... dpkg: warning: ignoring request to remove sphinx-rtd-theme-common which isn't installed Purging configuration files for systemd (255.4-1) ... dpkg: warning: ignoring request to remove systemd-dev which isn't installed 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) ... dpkg: warning: while removing x11-common, directory '/etc/init.d' not empty so not removed dpkg: warning: ignoring request to remove xkb-data which isn't installed dpkg: warning: ignoring request to remove xtl-dev which isn't installed dpkg: warning: ignoring request to remove zlib1g-dev which isn't installed 5m46.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'dpkg', '--purge', 'adwaita-icon-theme', 'at-spi2-common', 'binutils', 'binutils-common:amd64', 'binutils-x86-64-linux-gnu', 'blt', 'ca-certificates', 'cpp', 'cpp-12', 'cpp-13', 'cpp-13-x86-64-linux-gnu', 'cpp-x86-64-linux-gnu', 'dbus', 'dbus-bin', 'dbus-daemon', 'dbus-session-bus-common', 'dbus-system-bus-common', 'dbus-user-session', 'dconf-gsettings-backend:amd64', 'dconf-service', 'dmsetup', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'fonts-font-awesome', 'fonts-lato', 'fonts-lyx', 'g++', 'g++-12', 'g++-13', 'g++-13-x86-64-linux-gnu', 'g++-x86-64-linux-gnu', 'gcc', 'gcc-12', 'gcc-13', 'gcc-13-base:amd64', 'gcc-13-x86-64-linux-gnu', 'gcc-x86-64-linux-gnu', 'gtk-update-icon-cache', 'hicolor-icon-theme', 'libaec0:amd64', 'libann-cctbx-dev', 'libann-cctbx0', 'libantlr3c-3.4-0:amd64', 'libapparmor1:amd64', 'libargon2-1:amd64', 'libasan8:amd64', 'libatk-bridge2.0-0:amd64', 'libatk1.0-0:amd64', 'libatomic1:amd64', 'libatspi2.0-0:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbinutils:amd64', 'libblas3:amd64', 'libboost-dev:amd64', 'libboost-numpy1.74.0', 'libboost-numpy1.83.0', 'libboost-python-dev', 'libboost-python1.74.0', 'libboost-python1.83-dev', 'libboost-python1.83.0', 'libboost-thread1.74.0:amd64', 'libboost-thread1.83.0:amd64', 'libboost1.83-dev:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcairo-gobject2:amd64', 'libcairo2:amd64', 'libcbf1t64:amd64', 'libcc1-0:amd64', 'libccp4-data', 'libccp4-dev:amd64', 'libccp4c0:amd64', 'libccp4f0:amd64', 'libcctbx-dev', 'libcctbx0', 'libcloudproviders0:amd64', 'libcolord2:amd64', 'libcrypt-dev:amd64', 'libcryptsetup12:amd64', 'libctf-nobfd0:amd64', 'libctf0:amd64', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdatrie1:amd64', 'libdb5.3t64:amd64', 'libdbus-1-3:amd64', 'libdconf1:amd64', 'libdeflate0:amd64', 'libdevmapper1.02.1:amd64', 'libdouble-conversion3:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm-nouveau2:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libedit2:amd64', 'libegl-mesa0:amd64', 'libegl1:amd64', 'libelf1t64:amd64', 'libepoxy0:amd64', 'libevdev2:amd64', 'libexpat1:amd64', 'libexpat1-dev:amd64', 'libfdisk1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgbm1:amd64', 'libgcc-12-dev:amd64', 'libgcc-13-dev:amd64', 'libgdk-pixbuf-2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgfortran5:amd64', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libgl1-mesa-glx:amd64', 'libglapi-mesa:amd64', 'libglew2.2:amd64', 'libglib2.0-0:amd64', 'libglib2.0-0t64:amd64', 'libglu1-mesa:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgprofng0:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libgtk-3-0:amd64', 'libgtk-3-common', 'libgudev-1.0-0:amd64', 'libharfbuzz0b:amd64', 'libhdf5-103-1t64:amd64', 'libhdf5-hl-100:amd64', 'libhwasan0:amd64', 'libice6:amd64', 'libicu72:amd64', 'libimagequant0:amd64', 'libinput-bin', 'libinput10:amd64', 'libip4tc2:amd64', 'libisl23:amd64', 'libitm1:amd64', 'libjansson4:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libjs-sphinxdoc', 'libjs-underscore', 'libjson-c5:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkmod2:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libllvm15:amd64', 'libllvm17:amd64', 'liblsan0:amd64', 'liblzf1:amd64', 'libmd4c0:amd64', 'libmmdb2-0:amd64', 'libmpc3:amd64', 'libmpfr6:amd64', 'libmtdev1:amd64', 'libncursesw6:amd64', 'libnetcdf19:amd64', 'libnghttp2-14:amd64', 'libnotify4:amd64', 'libnsl-dev:amd64', 'libnsl2:amd64', 'libopenblas-dev:amd64', 'libopenblas-pthread-dev:amd64', 'libopenblas0:amd64', 'libopenblas0-pthread: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', 'libpng16-16:amd64', 'libproc2-0:amd64', 'libpsl5:amd64', 'libpython3-all-dev:amd64', 'libpython3-dev:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-dev:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.11t64:amd64', 'libpython3.12-dev:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libpython3.12t64:amd64', 'libqhull-r8.0:amd64', 'libqt5core5a:amd64', 'libqt5dbus5:amd64', 'libqt5designer5:amd64', 'libqt5gui5:amd64', 'libqt5help5:amd64', 'libqt5network5:amd64', 'libqt5opengl5:amd64', 'libqt5printsupport5:amd64', 'libqt5sql5:amd64', 'libqt5test5:amd64', 'libqt5widgets5:amd64', 'libqt5xml5:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8t64:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libsframe1:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl3t64:amd64', 'libssm2:amd64', 'libstdc++-12-dev:amd64', 'libstdc++-13-dev:amd64', 'libsystemd-shared:amd64', 'libsz2:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc-dev:amd64', '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', 'libwxbase3.2-1:amd64', 'libwxgtk-gl3.2-1:amd64', 'libwxgtk3.2-1: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', 'libxsimd-dev:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'libz3-4:amd64', 'linux-libc-dev', 'media-types', 'netbase', 'openssl', 'procps', 'pymol-data', 'python-matplotlib-data', 'python3', 'python3-all', 'python3-all-dev', 'python3-appdirs', 'python3-attr', 'python3-beniget', 'python3-brotli', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-contourpy', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-dev', 'python3-distutils', 'python3-fonttools', 'python3-fs', 'python3-gast', 'python3-h5py', 'python3-h5py-serial', 'python3-idna', 'python3-kiwisolver', 'python3-lib2to3', 'python3-lxml:amd64', 'python3-lz4', 'python3-matplotlib', 'python3-minimal', 'python3-mpmath', 'python3-mrcfile', 'python3-numpy', 'python3-nxmx', 'python3-opengl', 'python3-orderedset', 'python3-packaging', 'python3-pil:amd64', 'python3-pil.imagetk:amd64', 'python3-pint', 'python3-pkg-resources', 'python3-ply', 'python3-procrunner', 'python3-pycbf', 'python3-pymol', 'python3-pyparsing', 'python3-pyqt5', 'python3-pyqt5.qtopengl', 'python3-pyqt5.sip', 'python3-pythran', 'python3-requests', 'python3-scipy', 'python3-setuptools', 'python3-six', 'python3-sympy', 'python3-tk:amd64', 'python3-tqdm', 'python3-tz', 'python3-ufolib2', 'python3-urllib3', 'python3-wxgtk4.0', 'python3.11', 'python3.11-dev', 'python3.11-minimal', 'python3.12', 'python3.12-dev', 'python3.12-minimal', 'readline-common', 'rpcsvc-proto', 'shared-mime-info', 'sphinx-rtd-theme-common', 'systemd', 'systemd-dev', 'systemd-sysv', 'tk8.6-blt2.5', 'unicode-data', 'x11-common', 'xkb-data', 'xtl-dev', 'zlib1g-dev:amd64'] 5m46.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'dpkg', '--purge', 'python3-cctbx'] 5m46.5s DUMP: dpkg: warning: ignoring request to remove python3-cctbx which isn't installed 5m46.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'dpkg', '--purge', 'python3-cctbx'] 5m46.5s INFO: Running scripts post_purge 5m46.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/post_purge_exceptions'] 5m46.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/post_purge_exceptions'] 5m46.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'dpkg', '--purge', '--pending'] 5m46.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'dpkg', '--purge', '--pending'] 5m46.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'dpkg', '--remove', '--pending'] 5m46.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'dpkg', '--remove', '--pending'] 5m46.5s INFO: Running scripts post_test 5m46.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/post_test_exceptions'] 5m46.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'tmp/scripts/post_test_exceptions'] 5m46.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv'] 5m46.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv'] 5m46.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'dpkg-divert', '--list'] 5m47.0s DUMP: local diversion of /bin/sync to /bin/sync.distrib local diversion of /home to /home.distrib 5m47.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'dpkg-divert', '--list'] 5m47.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'apt-get', 'clean'] 5m47.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv', 'apt-get', 'clean'] 5m47.1s DEBUG: Recording chroot state 5m47.9s INFO: Warning: Package purging left files on system: /etc/default/locale -> ../locale.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/lib/systemd/coredump/ not owned /var/lib/systemd/ephemeral-trees/ not owned /var/lib/systemd/pstore/ not owned /var/log/private/ not owned 5m48.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv/dev/shm'] 5m48.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv/dev/shm'] 5m48.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv/dev/console'] 5m48.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv/dev/console'] 5m48.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv/dev/ptmx'] 5m48.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv/dev/ptmx'] 5m48.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv/dev/pts'] 5m48.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv/dev/pts'] 5m48.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv/proc'] 5m48.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv/proc'] 5m48.5s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv'] 5m48.6s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmprx0kbrwv'] 5m48.6s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmprx0kbrwv 5m48.6s INFO: PASS: Upgrading between Debian distributions. 5m48.6s INFO: PASS: All tests. 5m48.6s INFO: piuparts run ends. ret=0 End: 2024-03-02 04:46:32 GMT