Start: 2024-08-23 20:26:42 GMT [stable] Package: python3-pdb2pqr Source: pdb2pqr Version: 3.5.2+dfsg-3 Installed-Size: 1142 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-docutils, python3-numpy, python3-pdbx, python3-propka, python3-requests, python3:any Description: Preparation of protein structures for electrostatics calculations Homepage: https://www.poissonboltzmann.org Description-md5: c860a092fe2d8d53f9e1d87375d1389f Section: python Priority: optional Filename: pool/main/p/pdb2pqr/python3-pdb2pqr_3.5.2+dfsg-3_all.deb Size: 135524 MD5sum: f54258608c72050485494f09fbaaea7e SHA256: 189983bbf1783fe909044dc7bd31605a1f6e8f63a6fd2f7b0bbfb4f61bdd0f1a [testing] Package: python3-pdb2pqr Source: pdb2pqr Version: 3.6.1+dfsg-1 Installed-Size: 1142 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-docutils, python3-numpy, python3-pdbx, python3-propka, python3-requests, python3:any Description: Preparation of protein structures for electrostatics calculations Homepage: https://www.poissonboltzmann.org Description-md5: c860a092fe2d8d53f9e1d87375d1389f Section: python Priority: optional Filename: pool/main/p/pdb2pqr/python3-pdb2pqr_3.6.1+dfsg-1_all.deb Size: 135780 MD5sum: 88c06dde00c0c5e09df4501d308af446 SHA256: daa63e874e483893e2c18f888868ad1ca78194fbfaed1f561e79bff6e9833a5e [sid] Package: python3-pdb2pqr Source: pdb2pqr Version: 3.6.1+dfsg-1 Installed-Size: 1142 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-docutils, python3-numpy, python3-pdbx, python3-propka, python3-requests, python3:any Description: Preparation of protein structures for electrostatics calculations Homepage: https://www.poissonboltzmann.org Description-md5: c860a092fe2d8d53f9e1d87375d1389f Section: python Priority: optional Filename: pool/main/p/pdb2pqr/python3-pdb2pqr_3.6.1+dfsg-1_all.deb Size: 135780 MD5sum: 88c06dde00c0c5e09df4501d308af446 SHA256: daa63e874e483893e2c18f888868ad1ca78194fbfaed1f561e79bff6e9833a5e 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 stable -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/stable22sid/reference-chroot-metadata.dat --apt python3-pdb2pqr=3.6.1+dfsg-1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.4.4~202408201642~1.4.3-11-g36a88c35 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 stable -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/stable22sid/reference-chroot-metadata.dat --apt python3-pdb2pqr=3.6.1+dfsg-1 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-32-amd64 #1 SMP Debian 5.10.223-1 (2024-08-10) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpi9xwtaiv 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpi9xwtaiv 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m0.9s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m0.9s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv/proc'] 0m0.9s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv/proc'] 0m0.9s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv/dev/pts'] 0m1.0s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv/dev/pts'] 0m1.0s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv/dev/ptmx'] 0m1.0s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv/dev/ptmx'] 0m1.0s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv/dev/console'] 0m1.0s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv/dev/console'] 0m1.0s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv/dev/shm'] 0m1.0s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv/dev/shm'] 0m1.0s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m1.0s DEBUG: Created policy-rc.d and chmodded it. 0m1.0s DEBUG: Created resolv.conf. 0m1.0s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpi9xwtaiv/tmp/scripts/ 0m1.0s INFO: Running scripts post_chroot_unpack 0m1.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-get', 'update'] 0m2.2s DUMP: Hit:1 http://deb.debian.org/debian bookworm InRelease Reading package lists... 0m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-get', 'update'] 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-get', '-yf', 'dist-upgrade'] 0m2.6s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-get', '-yf', 'dist-upgrade'] 0m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.1s DUMP: 913e17be84ed63a3110ce3137c1d003a - 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.1s INFO: Running scripts post_setup 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_setup_dummy_users'] 0m4.4s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_setup_dummy_users'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_setup_forbid_home'] 0m4.4s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_setup_forbid_home'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.5s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_setup_minimize'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_setup_minimize'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_setup_zz_backports'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_setup_zz_backports'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.5s 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+deb12u6 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b7 install ok installed bsdutils bsdutils 1:2.38.1-5+deb12u1 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+deb12u1 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+deb12u7 install ok installed libc6:amd64 libc6 2.36-9+deb12u7 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+deb12u3 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+deb12u1 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+deb12u1 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+deb12u1 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 252.26-1~deb12u2 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 252.26-1~deb12u2 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+deb12u1 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+deb12u1 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+deb12u1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+deb12u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.5s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/stable22sid/reference-chroot-metadata.dat 0m4.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv'] 0m5.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv'] 0m5.1s INFO: Running scripts is_testable 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/is_testable_uninstallable'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/is_testable_uninstallable'] 0m5.1s INFO: Running scripts pre_test 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_test_exceptions'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_test_exceptions'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_test_root_password'] 0m5.1s DUMP: New password: Retype new password: passwd: password updated successfully 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_test_root_password'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-cache', 'show', '--no-all-versions', 'python3-pdb2pqr'] 0m5.4s DUMP: Package: python3-pdb2pqr Source: pdb2pqr Version: 3.5.2+dfsg-3 Installed-Size: 1142 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-docutils, python3-numpy, python3-pdbx, python3-propka, python3-requests, python3:any Description-en: Preparation of protein structures for electrostatics calculations PDB2PQR is a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations. It thus provides a platform-independent utility for converting protein files in PDB format to PQR format. These tasks include: * Adding a limited number of missing heavy atoms to biomolecular structures * Determining side-chain pKas * Placing missing hydrogens * Optimizing the protein for favorable hydrogen bonding * Assigning charge and radius parameters from a variety of force fields Description-md5: c860a092fe2d8d53f9e1d87375d1389f Homepage: https://www.poissonboltzmann.org Section: python Priority: optional Filename: pool/main/p/pdb2pqr/python3-pdb2pqr_3.5.2+dfsg-3_all.deb Size: 135524 MD5sum: f54258608c72050485494f09fbaaea7e SHA256: 189983bbf1783fe909044dc7bd31605a1f6e8f63a6fd2f7b0bbfb4f61bdd0f1a 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-cache', 'show', '--no-all-versions', 'python3-pdb2pqr'] 0m5.4s INFO: apt-cache knows about the following packages: python3-pdb2pqr 0m5.4s INFO: Running scripts pre_install 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_install_database-server'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_install_database-server'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_install_exceptions'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_install_exceptions'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_install_extras'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_install_extras'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-cache', 'policy'] 0m5.5s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.6,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-cache', 'policy'] 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-cache', 'policy', 'python3-pdb2pqr'] 0m5.5s DUMP: python3-pdb2pqr: Installed: (none) Candidate: 3.5.2+dfsg-3 Version table: 3.5.2+dfsg-3 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-cache', 'policy', 'python3-pdb2pqr'] 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-get', '-y', 'install', 'python3-pdb2pqr'] 0m20.7s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: ca-certificates docutils-common libblas3 libexpat1 libgfortran5 libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libncursesw6 libnsl2 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libquadmath0 libreadline8 libsqlite3-0 libssl3 libtirpc-common libtirpc3 media-types openssl python3 python3-certifi python3-chardet python3-charset-normalizer python3-docutils python3-idna python3-minimal python3-numpy python3-pdbx python3-pkg-resources python3-propka python3-requests python3-roman python3-six python3-urllib3 python3.11 python3.11-minimal readline-common sgml-base xml-core Suggested packages: krb5-doc krb5-user python3-doc python3-tk python3-venv docutils-doc fonts-linuxlibertine | ttf-linux-libertine texlive-lang-french texlive-latex-base texlive-latex-recommended gcc gfortran python3-dev python3-pytest python-pdbx-doc python3-setuptools python-propka-doc python3-cryptography python3-openssl python3-socks python-requests-doc python3-brotli python3.11-venv python3.11-doc binutils binfmt-support readline-doc sgml-base-doc debhelper Recommended packages: krb5-locales libgpm2 libpaper-utils python3-pil python3-pygments The following NEW packages will be installed: ca-certificates docutils-common libblas3 libexpat1 libgfortran5 libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libncursesw6 libnsl2 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libquadmath0 libreadline8 libsqlite3-0 libssl3 libtirpc-common libtirpc3 media-types openssl python3 python3-certifi python3-chardet python3-charset-normalizer python3-docutils python3-idna python3-minimal python3-numpy python3-pdb2pqr python3-pdbx python3-pkg-resources python3-propka python3-requests python3-roman python3-six python3-urllib3 python3.11 python3.11-minimal readline-common sgml-base xml-core 0 upgraded, 45 newly installed, 0 to remove and 0 not upgraded. Need to get 21.2 MB of archives. After this operation, 83.8 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 libssl3 amd64 3.0.13-1~deb12u1 [2022 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6+deb12u2 [814 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6+deb12u2 [2067 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get:6 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 libncursesw6 amd64 6.4-4 [134 kB] Get:8 http://deb.debian.org/debian bookworm/main amd64 libkrb5support0 amd64 1.20.1-2+deb12u1 [32.4 kB] Get:9 http://deb.debian.org/debian bookworm/main amd64 libk5crypto3 amd64 1.20.1-2+deb12u1 [78.9 kB] Get:10 http://deb.debian.org/debian bookworm/main amd64 libkeyutils1 amd64 1.6.3-2 [8808 B] Get:11 http://deb.debian.org/debian bookworm/main amd64 libkrb5-3 amd64 1.20.1-2+deb12u1 [332 kB] Get:12 http://deb.debian.org/debian bookworm/main amd64 libgssapi-krb5-2 amd64 1.20.1-2+deb12u1 [134 kB] Get:13 http://deb.debian.org/debian bookworm/main amd64 libtirpc-common all 1.3.3+ds-1 [14.0 kB] Get:14 http://deb.debian.org/debian bookworm/main amd64 libtirpc3 amd64 1.3.3+ds-1 [85.2 kB] Get:15 http://deb.debian.org/debian bookworm/main amd64 libnsl2 amd64 1.3.0-2 [39.5 kB] Get:16 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get:17 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get:18 http://deb.debian.org/debian bookworm/main amd64 libsqlite3-0 amd64 3.40.1-2 [837 kB] Get:19 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6+deb12u2 [1799 kB] Get:20 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6+deb12u2 [573 kB] Get:21 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get:22 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get:23 http://deb.debian.org/debian bookworm/main amd64 sgml-base all 1.31 [15.4 kB] Get:24 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.13-1~deb12u1 [1418 kB] Get:25 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB] Get:26 http://deb.debian.org/debian bookworm/main amd64 xml-core all 0.18+nmu1 [23.8 kB] Get:27 http://deb.debian.org/debian bookworm/main amd64 docutils-common all 0.19+dfsg-6 [127 kB] Get:28 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB] Get:29 http://deb.debian.org/debian bookworm/main amd64 libquadmath0 amd64 12.2.0-14 [144 kB] Get:30 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get:31 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get:32 http://deb.debian.org/debian bookworm/main amd64 python3-certifi all 2022.9.24-1 [153 kB] Get:33 http://deb.debian.org/debian bookworm/main amd64 python3-pkg-resources all 66.1.1-1 [296 kB] Get:34 http://deb.debian.org/debian bookworm/main amd64 python3-chardet all 5.1.0+dfsg-2 [110 kB] Get:35 http://deb.debian.org/debian bookworm/main amd64 python3-charset-normalizer all 3.0.1-2 [49.3 kB] Get:36 http://deb.debian.org/debian bookworm/main amd64 python3-roman all 3.3-3 [9880 B] Get:37 http://deb.debian.org/debian bookworm/main amd64 python3-docutils all 0.19+dfsg-6 [382 kB] Get:38 http://deb.debian.org/debian bookworm/main amd64 python3-idna all 3.3-1+deb12u1 [41.0 kB] Get:39 http://deb.debian.org/debian bookworm/main amd64 python3-numpy amd64 1:1.24.2-1 [5209 kB] Get:40 http://deb.debian.org/debian bookworm/main amd64 python3-pdbx all 2.0.1-2 [17.4 kB] Get:41 http://deb.debian.org/debian bookworm/main amd64 python3-propka all 3.5.0-1 [65.6 kB] Get:42 http://deb.debian.org/debian bookworm/main amd64 python3-six all 1.16.0-4 [17.5 kB] Get:43 http://deb.debian.org/debian bookworm/main amd64 python3-urllib3 all 1.26.12-1 [117 kB] Get:44 http://deb.debian.org/debian bookworm/main amd64 python3-requests all 2.28.1+dfsg-1 [67.9 kB] Get:45 http://deb.debian.org/debian bookworm/main amd64 python3-pdb2pqr all 3.5.2+dfsg-3 [136 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 21.2 MB in 0s (87.2 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 ... 6093 files and directories currently installed.) Preparing to unpack .../libssl3_3.0.13-1~deb12u1_amd64.deb ... Unpacking libssl3:amd64 (3.0.13-1~deb12u1) ... Selecting previously unselected package libpython3.11-minimal:amd64. Preparing to unpack .../libpython3.11-minimal_3.11.2-6+deb12u2_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6+deb12u2) ... Selecting previously unselected package libexpat1:amd64. 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Selecting previously unselected package python3-urllib3. Preparing to unpack .../21-python3-urllib3_1.26.12-1_all.deb ... Unpacking python3-urllib3 (1.26.12-1) ... Selecting previously unselected package python3-requests. Preparing to unpack .../22-python3-requests_2.28.1+dfsg-1_all.deb ... Unpacking python3-requests (2.28.1+dfsg-1) ... Selecting previously unselected package python3-pdb2pqr. Preparing to unpack .../23-python3-pdb2pqr_3.5.2+dfsg-3_all.deb ... Unpacking python3-pdb2pqr (3.5.2+dfsg-3) ... Setting up media-types (10.0.0) ... Setting up libkeyutils1:amd64 (1.6.3-2) ... Setting up libtirpc-common (1.3.3+ds-1) ... Setting up libsqlite3-0:amd64 (3.40.1-2) ... Setting up libkrb5support0:amd64 (1.20.1-2+deb12u1) ... 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 libquadmath0:amd64 (12.2.0-14) ... Setting up libncursesw6:amd64 (6.4-4) ... Setting up libk5crypto3:amd64 (1.20.1-2+deb12u1) ... Setting up libgfortran5:amd64 (12.2.0-14) ... Setting up sgml-base (1.31) ... Setting up libkrb5-3:amd64 (1.20.1-2+deb12u1) ... Setting up openssl (3.0.13-1~deb12u1) ... Setting up readline-common (8.2-1.3) ... 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 libreadline8:amd64 (8.2-1.3) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libgssapi-krb5-2:amd64 (1.20.1-2+deb12u1) ... Setting up xml-core (0.18+nmu1) ... Setting up libtirpc3:amd64 (1.3.3+ds-1) ... Setting up libnsl2:amd64 (1.3.0-2) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6+deb12u2) ... Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6+deb12u2) ... Setting up python3 (3.11.2-1+b1) ... Setting up python3-six (1.16.0-4) ... Setting up python3-roman (3.3-3) ... Setting up python3-certifi (2022.9.24-1) ... Setting up python3-idna (3.3-1+deb12u1) ... Setting up python3-urllib3 (1.26.12-1) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-propka (3.5.0-1) ... Setting up python3-charset-normalizer (3.0.1-2) ... Setting up python3-pdbx (2.0.1-2) ... Setting up python3-chardet (5.1.0+dfsg-2) ... Setting up python3-requests (2.28.1+dfsg-1) ... Setting up python3-numpy (1:1.24.2-1) ... Processing triggers for libc-bin (2.36-9+deb12u7) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.19+dfsg-6) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.19+dfsg-6) ... Setting up python3-pdb2pqr (3.5.2+dfsg-3) ... 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. 0m20.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-get', '-y', 'install', 'python3-pdb2pqr'] 0m20.7s INFO: Running scripts post_install 0m20.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_install_exceptions'] 0m20.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_install_exceptions'] 0m20.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv'] 0m21.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv'] 0m21.6s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpi9xwtaiv to testing 0m21.6s DEBUG: sources.list: deb http://deb.debian.org/debian/ trixie main 0m21.6s INFO: Running scripts pre_distupgrade 0m21.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m21.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m21.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_distupgrade_exceptions'] 0m21.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_distupgrade_exceptions'] 0m21.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m21.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m21.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m21.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m21.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m21.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m21.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-get', 'update'] 0m24.9s DUMP: Get:1 http://deb.debian.org/debian trixie InRelease [169 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 Packages [9251 kB] Get:3 http://deb.debian.org/debian trixie/main Translation-en [6163 kB] Fetched 15.6 MB in 2s (7080 kB/s) Reading package lists... 0m24.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-get', 'update'] 0m24.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-get', '-yf', 'dist-upgrade'] 0m56.5s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libnsl2 libpython3.11-minimal libpython3.11-stdlib libquadmath0 libtirpc-common libtirpc3t64 python3-six python3.11 python3.11-minimal Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libapt-pkg6.0 libdb5.3 libext2fs2 libgnutls30 libhogweed6 libnettle8 libreadline8 libssl3 libtirpc3 The following NEW packages will be installed: gcc-14-base libapt-pkg6.0t64 libbsd0 libdb5.3t64 libext2fs2t64 libgnutls30t64 libhogweed6t64 libnettle8t64 libpython3.12-minimal libpython3.12-stdlib libreadline8t64 libssl3t64 libtirpc3t64 libunistring5 netbase python3.12 python3.12-minimal The following packages will be upgraded: adduser apt base-files base-passwd bash bsdutils ca-certificates coreutils dash debconf debian-archive-keyring debianutils diffutils docutils-common dpkg e2fsprogs findutils gcc-12-base gpgv grep gzip hostname init-system-helpers libacl1 libattr1 libaudit-common libaudit1 libblas3 libblkid1 libbz2-1.0 libc-bin libc6 libcap-ng0 libcap2 libcom-err2 libcrypt1 libdebconfclient0 libexpat1 libffi8 libgcc-s1 libgcrypt20 libgfortran5 libgmp10 libgpg-error0 libgssapi-krb5-2 libidn2-0 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblz4-1 liblzma5 libmd0 libmount1 libncursesw6 libnsl2 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libpython3-stdlib libquadmath0 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsmartcols1 libsqlite3-0 libss2 libstdc++6 libsystemd0 libtasn1-6 libtinfo6 libtirpc-common libudev1 libuuid1 libxxhash0 libzstd1 login logsave mawk media-types mount ncurses-base ncurses-bin openssl passwd perl-base python3 python3-certifi python3-chardet python3-charset-normalizer python3-docutils python3-idna python3-minimal python3-numpy python3-pdb2pqr python3-pkg-resources python3-propka python3-requests python3-six python3-urllib3 readline-common sed sysvinit-utils tar tzdata usr-is-merged util-linux util-linux-extra xml-core zlib1g 116 upgraded, 17 newly installed, 9 to remove and 0 not upgraded. Need to get 53.5 MB of archives. After this operation, 26.5 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian trixie/main amd64 base-files amd64 13.5 [72.8 kB] Get:2 http://deb.debian.org/debian trixie/main amd64 libc6 amd64 2.39-7 [2791 kB] Get:3 http://deb.debian.org/debian trixie/main amd64 libc-bin amd64 2.39-7 [610 kB] Get:4 http://deb.debian.org/debian trixie/main amd64 gcc-14-base amd64 14.2.0-1 [45.7 kB] Get:5 http://deb.debian.org/debian trixie/main amd64 libgcc-s1 amd64 14.2.0-1 [72.8 kB] Get:6 http://deb.debian.org/debian trixie/main amd64 debianutils amd64 5.20 [89.5 kB] Get:7 http://deb.debian.org/debian trixie/main amd64 bash amd64 5.2.21-2.1+b1 [1498 kB] Get:8 http://deb.debian.org/debian trixie/main amd64 libcap2 amd64 1:2.66-5 [27.4 kB] Get:9 http://deb.debian.org/debian trixie/main amd64 libsystemd0 amd64 256.5-1 [381 kB] Get:10 http://deb.debian.org/debian trixie/main amd64 bsdutils amd64 1:2.40.2-1 [104 kB] Get:11 http://deb.debian.org/debian trixie/main amd64 libgmp10 amd64 2:6.3.0+dfsg-2+b1 [559 kB] Get:12 http://deb.debian.org/debian trixie/main amd64 libzstd1 amd64 1.5.6+dfsg-1 [303 kB] Get:13 http://deb.debian.org/debian trixie/main amd64 openssl amd64 3.2.2-1 [1364 kB] Get:14 http://deb.debian.org/debian trixie/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get:15 http://deb.debian.org/debian trixie/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get:16 http://deb.debian.org/debian trixie/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get:17 http://deb.debian.org/debian trixie/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get:18 http://deb.debian.org/debian trixie/main amd64 libcom-err2 amd64 1.47.1-1 [22.9 kB] Get:19 http://deb.debian.org/debian trixie/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get:20 http://deb.debian.org/debian trixie/main amd64 libssl3t64 amd64 3.2.2-1 [2246 kB] Get:21 http://deb.debian.org/debian trixie/main amd64 zlib1g amd64 1:1.3.dfsg+really1.3.1-1 [87.9 kB] Get:22 http://deb.debian.org/debian trixie/main amd64 coreutils amd64 9.4-3.1 [2950 kB] Get:23 http://deb.debian.org/debian trixie/main amd64 dash amd64 0.5.12-9 [93.2 kB] Get:24 http://deb.debian.org/debian trixie/main amd64 diffutils amd64 1:3.10-1 [375 kB] Get:25 http://deb.debian.org/debian trixie/main amd64 libgpg-error0 amd64 1.50-3 [81.5 kB] Get:26 http://deb.debian.org/debian trixie/main amd64 libgcrypt20 amd64 1.11.0-6 [843 kB] Get:27 http://deb.debian.org/debian trixie/main amd64 libstdc++6 amd64 14.2.0-1 [713 kB] Get:28 http://deb.debian.org/debian trixie/main amd64 libnettle8t64 amd64 3.10-1 [303 kB] Get:29 http://deb.debian.org/debian trixie/main amd64 libhogweed6t64 amd64 3.10-1 [334 kB] Get:30 http://deb.debian.org/debian trixie/main amd64 libp11-kit0 amd64 0.25.5-2 [424 kB] Get:31 http://deb.debian.org/debian trixie/main amd64 libunistring5 amd64 1.2-1 [425 kB] Get:32 http://deb.debian.org/debian trixie/main amd64 libgnutls30t64 amd64 3.8.6-2 [1444 kB] Get:33 http://deb.debian.org/debian trixie/main amd64 libffi8 amd64 3.4.6-1 [23.6 kB] Get:34 http://deb.debian.org/debian trixie/main amd64 libidn2-0 amd64 2.3.7-2 [128 kB] Get:35 http://deb.debian.org/debian trixie/main amd64 libtasn1-6 amd64 4.19.0-3+b2 [48.9 kB] Get:36 http://deb.debian.org/debian trixie/main amd64 libbz2-1.0 amd64 1.0.8-6 [37.9 kB] Get:37 http://deb.debian.org/debian trixie/main amd64 libxxhash0 amd64 0.8.2-2+b1 [26.6 kB] Get:38 http://deb.debian.org/debian trixie/main amd64 liblz4-1 amd64 1.9.4-3 [59.4 kB] Get:39 http://deb.debian.org/debian trixie/main amd64 liblzma5 amd64 5.6.2-2 [254 kB] Get:40 http://deb.debian.org/debian trixie/main amd64 libudev1 amd64 256.5-1 [144 kB] Get:41 http://deb.debian.org/debian trixie/main amd64 libapt-pkg6.0t64 amd64 2.9.8 [1045 kB] Get:42 http://deb.debian.org/debian trixie/main amd64 apt amd64 2.9.8 [1410 kB] Get:43 http://deb.debian.org/debian trixie/main amd64 tar amd64 1.35+dfsg-3 [813 kB] Get:44 http://deb.debian.org/debian trixie/main amd64 dpkg amd64 1.22.11 [1531 kB] Get:45 http://deb.debian.org/debian trixie/main amd64 findutils amd64 4.10.0-3 [700 kB] Get:46 http://deb.debian.org/debian trixie/main amd64 grep amd64 3.11-4 [431 kB] Get:47 http://deb.debian.org/debian trixie/main amd64 gzip amd64 1.12-1.1 [133 kB] Get:48 http://deb.debian.org/debian trixie/main amd64 hostname amd64 3.23+nmu2 [10.6 kB] Get:49 http://deb.debian.org/debian trixie/main amd64 libncursesw6 amd64 6.5-2 [135 kB] Get:50 http://deb.debian.org/debian trixie/main amd64 libtinfo6 amd64 6.5-2 [344 kB] Get:51 http://deb.debian.org/debian trixie/main amd64 ncurses-bin amd64 6.5-2 [433 kB] Get:52 http://deb.debian.org/debian trixie/main amd64 perl-base amd64 5.38.2-5 [1643 kB] Get:53 http://deb.debian.org/debian trixie/main amd64 sed amd64 4.9-2 [329 kB] Get:54 http://deb.debian.org/debian trixie/main amd64 libblkid1 amd64 2.40.2-1 [166 kB] Get:55 http://deb.debian.org/debian trixie/main amd64 libpcre2-8-0 amd64 10.42-4+b1 [262 kB] Get:56 http://deb.debian.org/debian trixie/main amd64 libselinux1 amd64 3.5-2+b4 [75.1 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[12.8 kB] Get:112 http://deb.debian.org/debian trixie/main amd64 tzdata all 2024a-4 [255 kB] Get:113 http://deb.debian.org/debian trixie/main amd64 libsqlite3-0 amd64 3.46.0-1 [902 kB] Get:114 http://deb.debian.org/debian trixie/main amd64 libpython3.12-stdlib amd64 3.12.4-3 [1950 kB] Get:115 http://deb.debian.org/debian trixie/main amd64 python3.12 amd64 3.12.4-3 [664 kB] Get:116 http://deb.debian.org/debian trixie/main amd64 libpython3-stdlib amd64 3.12.5-1 [9588 B] Get:117 http://deb.debian.org/debian trixie/main amd64 mawk amd64 1.3.4.20240622-2 [136 kB] Get:118 http://deb.debian.org/debian trixie/main amd64 ca-certificates all 20240203 [158 kB] Get:119 http://deb.debian.org/debian trixie/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get:120 http://deb.debian.org/debian trixie/main amd64 xml-core all 0.19 [20.1 kB] Get:121 http://deb.debian.org/debian trixie/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get:122 http://deb.debian.org/debian trixie/main amd64 libquadmath0 amd64 14.2.0-1 [145 kB] Get:123 http://deb.debian.org/debian trixie/main amd64 gcc-12-base amd64 12.4.0-2 [42.9 kB] Get:124 http://deb.debian.org/debian trixie/main amd64 libss2 amd64 1.47.1-1 [27.6 kB] Get:125 http://deb.debian.org/debian trixie/main amd64 python3-certifi all 2024.6.2-1 [157 kB] Get:126 http://deb.debian.org/debian trixie/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get:127 http://deb.debian.org/debian trixie/main amd64 python3-charset-normalizer amd64 3.3.2-2 [116 kB] Get:128 http://deb.debian.org/debian trixie/main amd64 python3-idna all 3.6-2.1 [38.6 kB] Get:129 http://deb.debian.org/debian trixie/main amd64 python3-propka all 3.5.1-1 [68.0 kB] Get:130 http://deb.debian.org/debian trixie/main amd64 python3-urllib3 all 2.0.7-2 [111 kB] Get:131 http://deb.debian.org/debian trixie/main amd64 python3-requests all 2.31.0+dfsg-2 [68.7 kB] Get:132 http://deb.debian.org/debian trixie/main amd64 python3-pdb2pqr all 3.6.1+dfsg-1 [136 kB] Get:133 http://deb.debian.org/debian trixie/main amd64 python3-six all 1.16.0-7 [16.4 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 53.5 MB in 0s (138 MB/s) (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 ... 9216 files and directories currently installed.) Preparing to unpack .../libzstd1_1.5.6+dfsg-1_amd64.deb ... Unpacking libzstd1:amd64 (1.5.6+dfsg-1) over (1.5.4+dfsg2-5) ... Setting up libzstd1:amd64 (1.5.6+dfsg-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 ... 9216 files and directories currently installed.) Preparing to unpack .../0-openssl_3.2.2-1_amd64.deb ... Unpacking openssl (3.2.2-1) over (3.0.13-1~deb12u1) ... Preparing to unpack .../1-libgssapi-krb5-2_1.21.3-3_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.21.3-3) over (1.20.1-2+deb12u1) ... Preparing to unpack .../2-libkrb5-3_1.21.3-3_amd64.deb ... Unpacking libkrb5-3:amd64 (1.21.3-3) over (1.20.1-2+deb12u1) ... Preparing to unpack .../3-libk5crypto3_1.21.3-3_amd64.deb ... Unpacking libk5crypto3:amd64 (1.21.3-3) over (1.20.1-2+deb12u1) ... Preparing to unpack .../4-libkrb5support0_1.21.3-3_amd64.deb ... Unpacking libkrb5support0:amd64 (1.21.3-3) over (1.20.1-2+deb12u1) ... Preparing to unpack .../5-libcom-err2_1.47.1-1_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.1-1) over (1.47.0-2) ... Preparing to unpack .../6-libkeyutils1_1.6.3-3_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-3) over (1.6.3-2) ... dpkg: libssl3:amd64: dependency problems, but removing anyway as you requested: libpython3.11-minimal:amd64 depends on libssl3 (>= 3.0.0). (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 ... 9237 files and directories currently installed.) Removing libssl3:amd64 (3.0.13-1~deb12u1) ... Selecting previously unselected package libssl3t64: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 ... 9225 files and directories currently installed.) Preparing to unpack .../libssl3t64_3.2.2-1_amd64.deb ... Unpacking libssl3t64:amd64 (3.2.2-1) ... Setting up libssl3t64:amd64 (3.2.2-1) ... (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 ... 9240 files and directories currently installed.) Preparing to unpack .../coreutils_9.4-3.1_amd64.deb ... Unpacking coreutils (9.4-3.1) over (9.1-1) ... Setting up coreutils (9.4-3.1) ... (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 ... 9245 files and directories currently installed.) Removing libhogweed6:amd64 (3.8.1-2) ... Selecting previously unselected package libhogweed6t64: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 ... 9239 files and directories currently installed.) Preparing to unpack .../libhogweed6t64_3.10-1_amd64.deb ... Unpacking libhogweed6t64:amd64 (3.10-1) ... Setting up libhogweed6t64:amd64 (3.10-1) ... (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 ... 9246 files and directories currently installed.) Preparing to unpack .../libp11-kit0_0.25.5-2_amd64.deb ... Unpacking libp11-kit0:amd64 (0.25.5-2) over (0.24.1-2) ... Setting up libp11-kit0:amd64 (0.25.5-2) ... Selecting previously unselected package libunistring5: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 ... 9246 files and directories currently installed.) Preparing to unpack .../libunistring5_1.2-1_amd64.deb ... Unpacking libunistring5:amd64 (1.2-1) ... Setting up libunistring5:amd64 (1.2-1) ... dpkg: libgnutls30:amd64: dependency problems, but removing anyway as you requested: apt depends on libgnutls30 (>= 3.7.5). (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 ... 9252 files and directories currently installed.) Removing libgnutls30:amd64 (3.7.9-2+deb12u3) ... Selecting previously unselected package libgnutls30t64: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 ... 9223 files and directories currently installed.) Preparing to unpack .../libgnutls30t64_3.8.6-2_amd64.deb ... Unpacking libgnutls30t64:amd64 (3.8.6-2) ... Setting up libgnutls30t64:amd64 (3.8.6-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9252 files and directories currently installed.) Preparing to unpack .../libffi8_3.4.6-1_amd64.deb ... Unpacking libffi8:amd64 (3.4.6-1) over (3.4.4-1) ... Setting up libffi8:amd64 (3.4.6-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9252 files and directories currently installed.) Preparing to unpack .../libidn2-0_2.3.7-2_amd64.deb ... Unpacking libidn2-0:amd64 (2.3.7-2) over (2.3.3-1+b1) ... Setting up libidn2-0:amd64 (2.3.7-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9252 files and directories currently installed.) Preparing to unpack .../libtasn1-6_4.19.0-3+b2_amd64.deb ... Unpacking libtasn1-6:amd64 (4.19.0-3+b2) over (4.19.0-2) ... Setting up libtasn1-6:amd64 (4.19.0-3+b2) ... (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 ... 9253 files and directories currently installed.) Preparing to unpack .../libbz2-1.0_1.0.8-6_amd64.deb ... Unpacking libbz2-1.0:amd64 (1.0.8-6) over (1.0.8-5+b1) ... Setting up libbz2-1.0:amd64 (1.0.8-6) ... (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 ... 9246 files and directories currently installed.) Preparing to unpack .../libcap-ng0_0.8.5-2_amd64.deb ... Unpacking libcap-ng0:amd64 (0.8.5-2) over (0.8.3-1+b3) ... Setting up libcap-ng0:amd64 (0.8.5-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9245 files and directories currently installed.) Preparing to unpack .../libaudit1_1%3a3.1.2-4+b1_amd64.deb ... Unpacking libaudit1:amd64 (1:3.1.2-4+b1) over (1:3.0.9-1) ... Setting up libaudit1:amd64 (1:3.1.2-4+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9246 files and directories currently installed.) Preparing to unpack .../util-linux_2.40.2-1_amd64.deb ... Unpacking util-linux (2.40.2-1) over (2.38.1-5+deb12u1) ... Setting up util-linux (2.40.2-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9220 files and directories currently installed.) Preparing to unpack .../util-linux-extra_2.40.2-1_amd64.deb ... Adding 'diversion of /sbin/ctrlaltdel to /sbin/ctrlaltdel.usr-is-merged by util-linux-extra' Adding 'diversion of /sbin/fsck.cramfs to /sbin/fsck.cramfs.usr-is-merged by util-linux-extra' Adding 'diversion of /sbin/fsck.minix to /sbin/fsck.minix.usr-is-merged by util-linux-extra' Adding 'diversion of /sbin/mkfs.bfs to /sbin/mkfs.bfs.usr-is-merged by util-linux-extra' Adding 'diversion of /sbin/mkfs.cramfs to /sbin/mkfs.cramfs.usr-is-merged by util-linux-extra' Adding 'diversion of /sbin/mkfs.minix to /sbin/mkfs.minix.usr-is-merged by util-linux-extra' Unpacking util-linux-extra (2.40.2-1) over (2.38.1-5+deb12u1) ... dpkg: warning: unable to delete old directory '/usr/lib/udev/rules.d': Directory not empty dpkg: warning: unable to delete old directory '/usr/lib/udev': Directory not empty dpkg: warning: unable to delete old directory '/etc/init.d': Directory not empty Setting up util-linux-extra (2.40.2-1) ... (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 ... 9259 files and directories currently installed.) Preparing to unpack .../libbsd0_0.12.2-1_amd64.deb ... Unpacking libbsd0:amd64 (0.12.2-1) ... Setting up libbsd0:amd64 (0.12.2-1) ... dpkg: libdb5.3:amd64: dependency problems, but removing anyway as you requested: libpython3.11-stdlib:amd64 depends on libdb5.3. libpam-modules:amd64 depends on libdb5.3. (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 ... 9266 files and directories currently installed.) Removing libdb5.3:amd64 (5.3.28+dfsg2-1) ... Selecting previously unselected package libdb5.3t64: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 ... 9260 files and directories currently installed.) Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-7_amd64.deb ... Unpacking libdb5.3t64:amd64 (5.3.28+dfsg2-7) ... Setting up libdb5.3t64:amd64 (5.3.28+dfsg2-7) ... (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 ... 9266 files and directories currently installed.) Preparing to unpack .../libcrypt1_1%3a4.4.36-5_amd64.deb ... Unpacking libcrypt1:amd64 (1:4.4.36-5) over (1:4.4.33-2) ... Setting up libcrypt1:amd64 (1:4.4.36-5) ... (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 ... 9264 files and directories currently installed.) Preparing to unpack .../libpam-modules-bin_1.5.3-7_amd64.deb ... Unpacking libpam-modules-bin (1.5.3-7) over (1.5.2-6+deb12u1) ... Setting up libpam-modules-bin (1.5.3-7) ... (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 ... 9263 files and directories currently installed.) Preparing to unpack .../libpam-modules_1.5.3-7_amd64.deb ... Unpacking libpam-modules:amd64 (1.5.3-7) over (1.5.2-6+deb12u1) ... dpkg: warning: unable to delete old directory '/lib/x86_64-linux-gnu/security': Directory not empty Setting up libpam-modules:amd64 (1.5.3-7) ... Installing new version of config file /etc/security/namespace.init ... (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 ... 9262 files and directories currently installed.) Preparing to unpack .../login_1%3a4.15.3-2_amd64.deb ... Unpacking login (1:4.15.3-2) over (1:4.13+dfsg1-1+b1) ... Setting up login (1:4.15.3-2) ... Installing new version of config file /etc/login.defs ... Installing new version of config file /etc/pam.d/login ... (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 ... 9224 files and directories currently installed.) Preparing to unpack .../libattr1_1%3a2.5.2-1_amd64.deb ... Unpacking libattr1:amd64 (1:2.5.2-1) over (1:2.5.1-4) ... Setting up libattr1:amd64 (1:2.5.2-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9224 files and directories currently installed.) Preparing to unpack .../libsemanage-common_3.5-1_all.deb ... Unpacking libsemanage-common (3.5-1) over (3.4-1) ... Setting up libsemanage-common (3.5-1) ... (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 ... 9224 files and directories currently installed.) Preparing to unpack .../libsepol2_3.7-1_amd64.deb ... Unpacking libsepol2:amd64 (3.7-1) over (3.4-2.1) ... Setting up libsepol2:amd64 (3.7-1) ... (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 ... 9224 files and directories currently installed.) Preparing to unpack .../libsemanage2_3.5-1+b4_amd64.deb ... Unpacking libsemanage2:amd64 (3.5-1+b4) over (3.4-1+b5) ... Setting up libsemanage2:amd64 (3.5-1+b4) ... (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 ... 9224 files and directories currently installed.) Preparing to unpack .../passwd_1%3a4.15.3-2_amd64.deb ... Unpacking passwd (1:4.15.3-2) over (1:4.13+dfsg1-1+b1) ... Setting up passwd (1:4.15.3-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9217 files and directories currently installed.) Preparing to unpack .../archives/adduser_3.137_all.deb ... Unpacking adduser (3.137) over (3.134) ... Setting up adduser (3.137) ... Installing new version of config file /etc/adduser.conf ... (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 ... 9211 files and directories currently installed.) Preparing to unpack .../gpgv_2.2.43-8_amd64.deb ... Unpacking gpgv (2.2.43-8) over (2.2.40-1.1) ... Setting up gpgv (2.2.43-8) ... (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 ... 9211 files and directories currently installed.) Preparing to unpack .../debian-archive-keyring_2023.4_all.deb ... Unpacking debian-archive-keyring (2023.4) over (2023.3+deb12u1) ... Setting up debian-archive-keyring (2023.4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9211 files and directories currently installed.) Preparing to unpack .../libseccomp2_2.5.5-1+b1_amd64.deb ... Unpacking libseccomp2:amd64 (2.5.5-1+b1) over (2.5.4-1+deb12u1) ... Setting up libseccomp2:amd64 (2.5.5-1+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9212 files and directories currently installed.) Preparing to unpack .../usr-is-merged_39_all.deb ... Unpacking usr-is-merged (39) over (37~deb12u1) ... Setting up usr-is-merged (39) ... (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 ... 9212 files and directories currently installed.) Preparing to unpack .../init-system-helpers_1.66_all.deb ... Unpacking init-system-helpers (1.66) over (1.65.2) ... Setting up init-system-helpers (1.66) ... (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 ... 9212 files and directories currently installed.) Preparing to unpack .../ncurses-base_6.5-2_all.deb ... Unpacking ncurses-base (6.5-2) over (6.4-4) ... Setting up ncurses-base (6.5-2) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9210 files and directories currently installed.) Preparing to unpack .../sysvinit-utils_3.10-1_amd64.deb ... Unpacking sysvinit-utils (3.10-1) over (3.06-4) ... dpkg: warning: unable to delete old directory '/lib/lsb/init-functions.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/lsb': Directory not empty dpkg: warning: unable to delete old directory '/lib/init': Directory not empty Setting up sysvinit-utils (3.10-1) ... (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 ... 9210 files and directories currently installed.) Preparing to unpack .../logsave_1.47.1-1_amd64.deb ... Unpacking logsave (1.47.1-1) over (1.47.0-2) ... dpkg: libext2fs2:amd64: dependency problems, but removing anyway as you requested: e2fsprogs depends on libext2fs2 (= 1.47.0-2). (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9210 files and directories currently installed.) Removing libext2fs2:amd64 (1.47.0-2) ... Selecting previously unselected package libext2fs2t64: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 ... 9203 files and directories currently installed.) Preparing to unpack .../libext2fs2t64_1.47.1-1_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64' Adding 'diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64' Adding 'diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64' Adding 'diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64' Unpacking libext2fs2t64:amd64 (1.47.1-1) ... Setting up libcom-err2:amd64 (1.47.1-1) ... Setting up libext2fs2t64:amd64 (1.47.1-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9219 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.47.1-1_amd64.deb ... Unpacking e2fsprogs (1.47.1-1) over (1.47.0-2) ... dpkg: warning: unable to delete old directory '/lib/udev/rules.d': Directory not empty dpkg: warning: unable to delete old directory '/lib/udev': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd/system': Directory not empty dpkg: warning: unable to delete old directory '/lib/systemd': Directory not empty Preparing to unpack .../readline-common_8.2-4_all.deb ... Unpacking readline-common (8.2-4) over (8.2-1.3) ... dpkg: libreadline8:amd64: dependency problems, but removing anyway as you requested: libpython3.11-stdlib:amd64 depends on libreadline8 (>= 7.0~beta). (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 ... 9217 files and directories currently installed.) Removing libreadline8:amd64 (8.2-1.3) ... Selecting previously unselected package libreadline8t64: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 ... 9204 files and directories currently installed.) Preparing to unpack .../libreadline8t64_8.2-4_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Adding 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Unpacking libreadline8t64:amd64 (8.2-4) ... Preparing to unpack .../libtirpc-common_1.3.4+ds-1.3_all.deb ... Unpacking libtirpc-common (1.3.4+ds-1.3) over (1.3.3+ds-1) ... Preparing to unpack .../libnsl2_1.3.0-3+b2_amd64.deb ... Unpacking libnsl2:amd64 (1.3.0-3+b2) over (1.3.0-2) ... dpkg: libtirpc3:amd64: dependency problems, but removing anyway as you requested: libpython3.11-stdlib:amd64 depends on libtirpc3 (>= 1.0.2). (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9226 files and directories currently installed.) Removing libtirpc3:amd64 (1.3.3+ds-1) ... Selecting previously unselected package libtirpc3t64: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 ... 9219 files and directories currently installed.) Preparing to unpack .../0-libtirpc3t64_1.3.4+ds-1.3_amd64.deb ... Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Adding 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Unpacking libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Preparing to unpack .../1-mount_2.40.2-1_amd64.deb ... Unpacking mount (2.40.2-1) over (2.38.1-5+deb12u1) ... Selecting previously unselected package libpython3.12-minimal:amd64. Preparing to unpack .../2-libpython3.12-minimal_3.12.4-3_amd64.deb ... Unpacking libpython3.12-minimal:amd64 (3.12.4-3) ... Preparing to unpack .../3-libexpat1_2.6.2-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.2-1) over (2.5.0-1) ... Selecting previously unselected package python3.12-minimal. Preparing to unpack .../4-python3.12-minimal_3.12.4-3_amd64.deb ... Unpacking python3.12-minimal (3.12.4-3) ... Preparing to unpack .../5-python3-numpy_1%3a1.26.4+ds-11_amd64.deb ... Unpacking python3-numpy (1:1.26.4+ds-11) over (1:1.24.2-1) ... Setting up libpython3.12-minimal:amd64 (3.12.4-3) ... Setting up libexpat1:amd64 (2.6.2-1) ... Setting up python3.12-minimal (3.12.4-3) ... (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 ... 9448 files and directories currently installed.) Preparing to unpack .../python3-minimal_3.12.5-1_amd64.deb ... Unpacking python3-minimal (3.12.5-1) over (3.11.2-1+b1) ... Setting up python3-minimal (3.12.5-1) ... (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 ... 9447 files and directories currently installed.) Preparing to unpack .../00-python3_3.12.5-1_amd64.deb ... Unpacking python3 (3.12.5-1) over (3.11.2-1+b1) ... Preparing to unpack .../01-libblas3_3.12.0-3_amd64.deb ... Unpacking libblas3:amd64 (3.12.0-3) over (3.11.0-2) ... Preparing to unpack .../02-libgfortran5_14.2.0-1_amd64.deb ... Unpacking libgfortran5:amd64 (14.2.0-1) over (12.2.0-14) ... Preparing to unpack .../03-liblapack3_3.12.0-3_amd64.deb ... Unpacking liblapack3:amd64 (3.12.0-3) over (3.11.0-2) ... Preparing to unpack .../04-python3-pkg-resources_70.3.0-2_all.deb ... Unpacking python3-pkg-resources (70.3.0-2) over (66.1.1-1) ... Preparing to unpack .../05-media-types_10.1.0_all.deb ... Unpacking media-types (10.1.0) over (10.0.0) ... Selecting previously unselected package netbase. Preparing to unpack .../06-netbase_6.4_all.deb ... Unpacking netbase (6.4) ... Preparing to unpack .../07-tzdata_2024a-4_all.deb ... Unpacking tzdata (2024a-4) over (2024a-0+deb12u1) ... Preparing to unpack .../08-libsqlite3-0_3.46.0-1_amd64.deb ... Unpacking libsqlite3-0:amd64 (3.46.0-1) over (3.40.1-2) ... Selecting previously unselected package libpython3.12-stdlib:amd64. Preparing to unpack .../09-libpython3.12-stdlib_3.12.4-3_amd64.deb ... Unpacking libpython3.12-stdlib:amd64 (3.12.4-3) ... Selecting previously unselected package python3.12. Preparing to unpack .../10-python3.12_3.12.4-3_amd64.deb ... Unpacking python3.12 (3.12.4-3) ... Preparing to unpack .../11-libpython3-stdlib_3.12.5-1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.12.5-1) over (3.11.2-1+b1) ... Preparing to unpack .../12-mawk_1.3.4.20240622-2_amd64.deb ... Unpacking mawk (1.3.4.20240622-2) over (1.3.4.20200120-3.1) ... Preparing to unpack .../13-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) over (20230311) ... Preparing to unpack .../14-python3-docutils_0.21.2+dfsg-2_all.deb ... Unpacking python3-docutils (0.21.2+dfsg-2) over (0.19+dfsg-6) ... Preparing to unpack .../15-xml-core_0.19_all.deb ... Unpacking xml-core (0.19) over (0.18+nmu1) ... Preparing to unpack .../16-docutils-common_0.21.2+dfsg-2_all.deb ... Unpacking docutils-common (0.21.2+dfsg-2) over (0.19+dfsg-6) ... Preparing to unpack .../17-libquadmath0_14.2.0-1_amd64.deb ... Unpacking libquadmath0:amd64 (14.2.0-1) over (12.2.0-14) ... Preparing to unpack .../18-gcc-12-base_12.4.0-2_amd64.deb ... Unpacking gcc-12-base:amd64 (12.4.0-2) over (12.2.0-14) ... Preparing to unpack .../19-libss2_1.47.1-1_amd64.deb ... Unpacking libss2:amd64 (1.47.1-1) over (1.47.0-2) ... dpkg: warning: unable to delete old directory '/lib/x86_64-linux-gnu': Directory not empty Preparing to unpack .../20-python3-certifi_2024.6.2-1_all.deb ... Unpacking python3-certifi (2024.6.2-1) over (2022.9.24-1) ... Preparing to unpack .../21-python3-chardet_5.2.0+dfsg-1_all.deb ... Unpacking python3-chardet (5.2.0+dfsg-1) over (5.1.0+dfsg-2) ... Preparing to unpack .../22-python3-charset-normalizer_3.3.2-2_amd64.deb ... Unpacking python3-charset-normalizer (3.3.2-2) over (3.0.1-2) ... Preparing to unpack .../23-python3-idna_3.6-2.1_all.deb ... Unpacking python3-idna (3.6-2.1) over (3.3-1+deb12u1) ... Preparing to unpack .../24-python3-propka_3.5.1-1_all.deb ... Unpacking python3-propka (3.5.1-1) over (3.5.0-1) ... Preparing to unpack .../25-python3-urllib3_2.0.7-2_all.deb ... Unpacking python3-urllib3 (2.0.7-2) over (1.26.12-1) ... Preparing to unpack .../26-python3-requests_2.31.0+dfsg-2_all.deb ... Unpacking python3-requests (2.31.0+dfsg-2) over (2.28.1+dfsg-1) ... Preparing to unpack .../27-python3-pdb2pqr_3.6.1+dfsg-1_all.deb ... Unpacking python3-pdb2pqr (3.6.1+dfsg-1) over (3.5.2+dfsg-3) ... Preparing to unpack .../28-python3-six_1.16.0-7_all.deb ... Unpacking python3-six (1.16.0-7) over (1.16.0-4) ... Setting up media-types (10.1.0) ... Installing new version of config file /etc/mime.types ... Setting up libkeyutils1:amd64 (1.6.3-3) ... Setting up libtirpc-common (1.3.4+ds-1.3) ... Setting up libsqlite3-0:amd64 (3.46.0-1) ... Setting up libkrb5support0:amd64 (1.21.3-3) ... Setting up gcc-12-base:amd64 (12.4.0-2) ... Setting up tzdata (2024a-4) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Aug 23 20:27:26 UTC 2024. Universal Time is now: Fri Aug 23 20:27:26 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libblas3:amd64 (3.12.0-3) ... Setting up libquadmath0:amd64 (14.2.0-1) ... Setting up libss2:amd64 (1.47.1-1) ... Setting up libncursesw6:amd64 (6.5-2) ... Setting up libk5crypto3:amd64 (1.21.3-3) ... Setting up logsave (1.47.1-1) ... Setting up libgfortran5:amd64 (14.2.0-1) ... Setting up mount (2.40.2-1) ... Setting up xml-core (0.19) ... Setting up netbase (6.4) ... Setting up mawk (1.3.4.20240622-2) ... Setting up libkrb5-3:amd64 (1.21.3-3) ... Setting up openssl (3.2.2-1) ... Installing new version of config file /etc/ssl/openssl.cnf ... Setting up readline-common (8.2-4) ... Setting up liblapack3:amd64 (3.12.0-3) ... Setting up e2fsprogs (1.47.1-1) ... Installing new version of config file /etc/cron.d/e2scrub_all ... Installing new version of config file /etc/mke2fs.conf ... 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 libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libreadline8t64:amd64 (8.2-4) ... Setting up libpython3.12-stdlib:amd64 (3.12.4-3) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Setting up python3.12 (3.12.4-3) ... Setting up libnsl2:amd64 (1.3.0-3+b2) ... Setting up libpython3-stdlib:amd64 (3.12.5-1) ... Setting up python3 (3.12.5-1) ... Setting up python3-six (1.16.0-7) ... Setting up python3-certifi (2024.6.2-1) ... Setting up python3-idna (3.6-2.1) ... Setting up python3-urllib3 (2.0.7-2) ... Setting up python3-pkg-resources (70.3.0-2) ... Setting up python3-propka (3.5.1-1) ... Setting up python3-charset-normalizer (3.3.2-2) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up python3-requests (2.31.0+dfsg-2) ... Setting up python3-numpy (1:1.26.4+ds-11) ... Processing triggers for sgml-base (1.31) ... Processing triggers for debianutils (5.20) ... Processing triggers for libc-bin (2.39-7) ... Setting up docutils-common (0.21.2+dfsg-2) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.21.2+dfsg-2) ... Setting up python3-pdb2pqr (3.6.1+dfsg-1) ... 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. 0m56.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-get', '-yf', 'dist-upgrade'] 0m56.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m57.6s DUMP: 7e6a2b13f9a36fe50b12d30d67e22c7e - 0m57.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m57.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-cache', 'show', '--no-all-versions', 'python3-pdb2pqr'] 0m57.9s DUMP: Package: python3-pdb2pqr Source: pdb2pqr Version: 3.6.1+dfsg-1 Installed-Size: 1142 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-docutils, python3-numpy, python3-pdbx, python3-propka, python3-requests, python3:any Description-en: Preparation of protein structures for electrostatics calculations PDB2PQR is a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations. It thus provides a platform-independent utility for converting protein files in PDB format to PQR format. These tasks include: * Adding a limited number of missing heavy atoms to biomolecular structures * Determining side-chain pKas * Placing missing hydrogens * Optimizing the protein for favorable hydrogen bonding * Assigning charge and radius parameters from a variety of force fields Description-md5: c860a092fe2d8d53f9e1d87375d1389f Homepage: https://www.poissonboltzmann.org Section: python Priority: optional Filename: pool/main/p/pdb2pqr/python3-pdb2pqr_3.6.1+dfsg-1_all.deb Size: 135780 MD5sum: 88c06dde00c0c5e09df4501d308af446 SHA256: daa63e874e483893e2c18f888868ad1ca78194fbfaed1f561e79bff6e9833a5e 0m57.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-cache', 'show', '--no-all-versions', 'python3-pdb2pqr'] 0m57.9s INFO: apt-cache knows about the following packages: python3-pdb2pqr 0m57.9s INFO: Running scripts pre_install 0m57.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_install_database-server'] 0m57.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_install_database-server'] 0m57.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_install_exceptions'] 0m57.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_install_exceptions'] 0m57.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_install_extras'] 0m58.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_install_extras'] 0m58.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_install_foreign_architecture'] 0m58.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_install_foreign_architecture'] 0m58.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m58.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m58.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-cache', 'policy'] 0m58.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian trixie/main amd64 Packages release o=Debian,a=testing,n=trixie,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m58.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-cache', 'policy'] 0m58.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-cache', 'policy', 'python3-pdb2pqr'] 0m58.0s DUMP: python3-pdb2pqr: Installed: 3.6.1+dfsg-1 Candidate: 3.6.1+dfsg-1 Version table: *** 3.6.1+dfsg-1 500 500 http://deb.debian.org/debian trixie/main amd64 Packages 100 /var/lib/dpkg/status 0m58.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-cache', 'policy', 'python3-pdb2pqr'] 0m58.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-get', '-y', 'install', 'python3-pdb2pqr'] 0m58.6s DUMP: Reading package lists... Building dependency tree... Reading state information... python3-pdb2pqr is already the newest version (3.6.1+dfsg-1). The following packages were automatically installed and are no longer required: libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libnsl2 libpython3.11-minimal libpython3.11-stdlib libquadmath0 libtirpc-common libtirpc3t64 python3-six python3.11 python3.11-minimal Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m58.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-get', '-y', 'install', 'python3-pdb2pqr'] 0m58.6s INFO: Running scripts post_install 0m58.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_install_exceptions'] 0m58.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_install_exceptions'] 0m58.6s INFO: Running scripts post_distupgrade 0m58.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m58.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m58.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_distupgrade_exceptions'] 0m58.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_distupgrade_exceptions'] 0m58.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m58.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m58.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m58.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m58.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_distupgrade_zz_backports'] 0m58.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_distupgrade_zz_backports'] 0m58.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv'] 0m59.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv'] 0m59.4s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpi9xwtaiv to sid 0m59.4s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m59.4s INFO: Running scripts pre_distupgrade 0m59.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m59.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m59.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_distupgrade_exceptions'] 0m59.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_distupgrade_exceptions'] 0m59.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m59.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m59.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m59.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m59.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m59.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m59.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-get', 'update'] 1m2.8s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [198 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9953 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7301 kB] Fetched 17.5 MB in 2s (7377 kB/s) Reading package lists... 1m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-get', 'update'] 1m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-get', '-yf', 'dist-upgrade'] 1m12.7s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libpython3.11-minimal libpython3.11-stdlib libquadmath0 python3-six python3.11 python3.11-minimal Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: login.defs openssl-provider-legacy python3-autocommand python3-inflect python3-jaraco.context python3-jaraco.functools python3-more-itertools python3-typeguard python3-typing-extensions The following packages will be upgraded: bash bsdutils gcc-14-base libaudit-common libaudit1 libblkid1 libgcc-s1 libgfortran5 libmount1 libpython3.11-minimal libpython3.11-stdlib libpython3.12-minimal libpython3.12-stdlib libquadmath0 libreadline8t64 libselinux1 libsmartcols1 libsqlite3-0 libssl3t64 libstdc++6 libuuid1 login mawk mount openssl passwd python3-pkg-resources python3-requests python3.11 python3.11-minimal python3.12 python3.12-minimal readline-common util-linux util-linux-extra 35 upgraded, 9 newly installed, 0 to remove and 0 not upgraded. Need to get 23.7 MB of archives. After this operation, 1635 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 bash amd64 5.2.32-1 [1499 kB] Get:2 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.40.2-7 [105 kB] Get:3 http://deb.debian.org/debian sid/main amd64 libaudit-common all 1:4.0.1-1 [12.3 kB] Get:4 http://deb.debian.org/debian sid/main amd64 libaudit1 amd64 1:4.0.1-1 [54.5 kB] Get:5 http://deb.debian.org/debian sid/main amd64 util-linux-extra amd64 2.40.2-7 [265 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libuuid1 amd64 2.40.2-7 [35.3 kB] Get:7 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.40.2-7 [167 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.40.2-7 [199 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.40.2-7 [139 kB] Get:10 http://deb.debian.org/debian sid/main amd64 util-linux amd64 2.40.2-7 [1217 kB] Get:11 http://deb.debian.org/debian sid/main amd64 mount amd64 2.40.2-7 [154 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libselinux1 amd64 3.7-1+b1 [76.6 kB] Get:13 http://deb.debian.org/debian sid/main amd64 login.defs all 1:4.16.0-4 [185 kB] Get:14 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.16.0-2+really2.40.2-7 [57.7 kB] Get:15 http://deb.debian.org/debian sid/main amd64 openssl-provider-legacy amd64 3.3.1-7 [298 kB] Get:16 http://deb.debian.org/debian sid/main amd64 libssl3t64 amd64 3.3.1-7 [2269 kB] Get:17 http://deb.debian.org/debian sid/main amd64 python3.11 amd64 3.11.9-1 [602 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libpython3.11-stdlib amd64 3.11.9-1 [1792 kB] Get:19 http://deb.debian.org/debian sid/main amd64 python3.11-minimal amd64 3.11.9-1 [1879 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libpython3.11-minimal amd64 3.11.9-1 [817 kB] Get:21 http://deb.debian.org/debian sid/main amd64 readline-common all 8.2-5 [69.3 kB] Get:22 http://deb.debian.org/debian sid/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get:23 http://deb.debian.org/debian sid/main amd64 libsqlite3-0 amd64 3.46.1-1 [913 kB] Get:24 http://deb.debian.org/debian sid/main amd64 python3.12 amd64 3.12.5-4 [667 kB] Get:25 http://deb.debian.org/debian sid/main amd64 libpython3.12-stdlib amd64 3.12.5-4 [1960 kB] Get:26 http://deb.debian.org/debian sid/main amd64 python3.12-minimal amd64 3.12.5-4 [2168 kB] Get:27 http://deb.debian.org/debian sid/main amd64 libpython3.12-minimal amd64 3.12.5-4 [812 kB] Get:28 http://deb.debian.org/debian sid/main amd64 passwd amd64 1:4.16.0-4 [1232 kB] Get:29 http://deb.debian.org/debian sid/main amd64 gcc-14-base amd64 14.2.0-3 [46.2 kB] Get:30 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 14.2.0-3 [713 kB] Get:31 http://deb.debian.org/debian sid/main amd64 libquadmath0 amd64 14.2.0-3 [145 kB] Get:32 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14.2.0-3 [837 kB] Get:33 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 14.2.0-3 [72.8 kB] Get:34 http://deb.debian.org/debian sid/main amd64 mawk amd64 1.3.4.20240819-2 [138 kB] Get:35 http://deb.debian.org/debian sid/main amd64 openssl amd64 3.3.1-7 [1381 kB] Get:36 http://deb.debian.org/debian sid/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get:37 http://deb.debian.org/debian sid/main amd64 python3-more-itertools all 10.3.0-1 [62.0 kB] Get:38 http://deb.debian.org/debian sid/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get:39 http://deb.debian.org/debian sid/main amd64 python3-typeguard all 4.3.0-1 [36.5 kB] Get:40 http://deb.debian.org/debian sid/main amd64 python3-inflect all 7.3.1-1 [42.2 kB] Get:41 http://deb.debian.org/debian sid/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get:42 http://deb.debian.org/debian sid/main amd64 python3-jaraco.functools all 4.0.2-1 [11.7 kB] Get:43 http://deb.debian.org/debian sid/main amd64 python3-pkg-resources all 73.0.1-1 [212 kB] Get:44 http://deb.debian.org/debian sid/main amd64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 23.7 MB in 0s (110 MB/s) (Reading database ... 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Leaving 'diversion of /sbin/ctrlaltdel to /sbin/ctrlaltdel.usr-is-merged by util-linux-extra' Leaving 'diversion of /sbin/fsck.cramfs to /sbin/fsck.cramfs.usr-is-merged by util-linux-extra' Leaving 'diversion of /sbin/fsck.minix to /sbin/fsck.minix.usr-is-merged by util-linux-extra' Leaving 'diversion of /sbin/mkfs.bfs to /sbin/mkfs.bfs.usr-is-merged by util-linux-extra' Leaving 'diversion of /sbin/mkfs.cramfs to /sbin/mkfs.cramfs.usr-is-merged by util-linux-extra' Leaving 'diversion of /sbin/mkfs.minix to /sbin/mkfs.minix.usr-is-merged by util-linux-extra' Unpacking util-linux-extra (2.40.2-7) over (2.40.2-1) ... Preparing to unpack .../libuuid1_2.40.2-7_amd64.deb ... Unpacking libuuid1:amd64 (2.40.2-7) over (2.40.2-1) ... Setting up libuuid1:amd64 (2.40.2-7) ... (Reading database ... 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Unpacking python3-autocommand (2.2.2-3) ... Selecting previously unselected package python3-more-itertools. Preparing to unpack .../03-python3-more-itertools_10.3.0-1_all.deb ... Unpacking python3-more-itertools (10.3.0-1) ... Selecting previously unselected package python3-typing-extensions. Preparing to unpack .../04-python3-typing-extensions_4.12.2-2_all.deb ... Unpacking python3-typing-extensions (4.12.2-2) ... Selecting previously unselected package python3-typeguard. Preparing to unpack .../05-python3-typeguard_4.3.0-1_all.deb ... Unpacking python3-typeguard (4.3.0-1) ... Selecting previously unselected package python3-inflect. Preparing to unpack .../06-python3-inflect_7.3.1-1_all.deb ... Unpacking python3-inflect (7.3.1-1) ... Selecting previously unselected package python3-jaraco.context. Preparing to unpack .../07-python3-jaraco.context_6.0.0-1_all.deb ... Unpacking python3-jaraco.context (6.0.0-1) ... Selecting previously unselected package python3-jaraco.functools. Preparing to unpack .../08-python3-jaraco.functools_4.0.2-1_all.deb ... Unpacking python3-jaraco.functools (4.0.2-1) ... Preparing to unpack .../09-python3-pkg-resources_73.0.1-1_all.deb ... Unpacking python3-pkg-resources (73.0.1-1) over (70.3.0-2) ... Preparing to unpack .../10-python3-requests_2.32.3+dfsg-1_all.deb ... Unpacking python3-requests (2.32.3+dfsg-1) over (2.31.0+dfsg-2) ... Setting up python3-more-itertools (10.3.0-1) ... Setting up python3-jaraco.functools (4.0.2-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up libsqlite3-0:amd64 (3.46.1-1) ... Setting up libpython3.12-minimal:amd64 (3.12.5-4) ... Setting up python3-autocommand (2.2.2-3) ... Setting up libquadmath0:amd64 (14.2.0-3) ... Setting up python3-requests (2.32.3+dfsg-1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up libgfortran5:amd64 (14.2.0-3) ... Setting up mount (2.40.2-7) ... Setting up mawk (1.3.4.20240819-2) ... Setting up libpython3.11-minimal:amd64 (3.11.9-1) ... Setting up openssl (3.3.1-7) ... Installing new version of config file /etc/ssl/openssl.cnf ... Setting up readline-common (8.2-5) ... Setting up util-linux-extra (2.40.2-7) ... Setting up login (1:4.16.0-2+really2.40.2-7) ... Setting up python3.11-minimal (3.11.9-1) ... Setting up python3.12-minimal (3.12.5-4) ... Setting up python3-typeguard (4.3.0-1) ... Setting up python3-inflect (7.3.1-1) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up python3-pkg-resources (73.0.1-1) ... Setting up libpython3.12-stdlib:amd64 (3.12.5-4) ... Setting up libpython3.11-stdlib:amd64 (3.11.9-1) ... Setting up python3.12 (3.12.5-4) ... Setting up python3.11 (3.11.9-1) ... Processing triggers for debianutils (5.20) ... Processing triggers for libc-bin (2.39-7) ... 1m12.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-get', '-yf', 'dist-upgrade'] 1m12.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m13.0s DUMP: ca471e2c897513b29c31c8c4eb406e89 - 1m13.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m13.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-cache', 'show', '--no-all-versions', 'python3-pdb2pqr'] 1m13.2s DUMP: Package: python3-pdb2pqr Source: pdb2pqr Version: 3.6.1+dfsg-1 Installed-Size: 1142 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-docutils, python3-numpy, python3-pdbx, python3-propka, python3-requests, python3:any Description-en: Preparation of protein structures for electrostatics calculations PDB2PQR is a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations. It thus provides a platform-independent utility for converting protein files in PDB format to PQR format. These tasks include: * Adding a limited number of missing heavy atoms to biomolecular structures * Determining side-chain pKas * Placing missing hydrogens * Optimizing the protein for favorable hydrogen bonding * Assigning charge and radius parameters from a variety of force fields Description-md5: c860a092fe2d8d53f9e1d87375d1389f Homepage: https://www.poissonboltzmann.org Section: python Priority: optional Filename: pool/main/p/pdb2pqr/python3-pdb2pqr_3.6.1+dfsg-1_all.deb Size: 135780 MD5sum: 88c06dde00c0c5e09df4501d308af446 SHA256: daa63e874e483893e2c18f888868ad1ca78194fbfaed1f561e79bff6e9833a5e 1m13.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-cache', 'show', '--no-all-versions', 'python3-pdb2pqr'] 1m13.2s INFO: apt-cache knows about the following packages: python3-pdb2pqr 1m13.2s INFO: Running scripts pre_install 1m13.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_install_database-server'] 1m13.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_install_database-server'] 1m13.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_install_exceptions'] 1m13.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_install_exceptions'] 1m13.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_install_extras'] 1m13.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_install_extras'] 1m13.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_install_foreign_architecture'] 1m13.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_install_foreign_architecture'] 1m13.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m13.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m13.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-cache', 'policy'] 1m13.4s 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: 1m13.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-cache', 'policy'] 1m13.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-cache', 'policy', 'python3-pdb2pqr'] 1m13.4s DUMP: python3-pdb2pqr: Installed: 3.6.1+dfsg-1 Candidate: 3.6.1+dfsg-1 Version table: *** 3.6.1+dfsg-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 1m13.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-cache', 'policy', 'python3-pdb2pqr'] 1m13.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-get', '-y', 'install', 'python3-pdb2pqr'] 1m14.2s DUMP: Reading package lists... Building dependency tree... Reading state information... python3-pdb2pqr is already the newest version (3.6.1+dfsg-1). The following packages were automatically installed and are no longer required: libpython3.11-minimal libpython3.11-stdlib libquadmath0 python3-six python3.11 python3.11-minimal Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m14.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-get', '-y', 'install', 'python3-pdb2pqr'] 1m14.2s INFO: Running scripts post_install 1m14.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_install_exceptions'] 1m14.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_install_exceptions'] 1m14.2s INFO: Running scripts post_distupgrade 1m14.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m14.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m14.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_distupgrade_exceptions'] 1m14.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_distupgrade_exceptions'] 1m14.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m14.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m14.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m14.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m14.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_distupgrade_zz_backports'] 1m14.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_distupgrade_zz_backports'] 1m14.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv'] 1m14.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv'] 1m14.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv'] 1m15.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv'] 1m15.8s INFO: Running scripts pre_install 1m15.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_install_database-server'] 1m15.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_install_database-server'] 1m15.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_install_exceptions'] 1m15.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_install_exceptions'] 1m15.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_install_extras'] 1m15.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_install_extras'] 1m15.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_install_foreign_architecture'] 1m15.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_install_foreign_architecture'] 1m15.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m15.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m15.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-cache', 'policy'] 1m16.0s 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: 1m16.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-cache', 'policy'] 1m16.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-cache', 'policy', 'python3-pdb2pqr'] 1m16.1s DUMP: python3-pdb2pqr: Installed: 3.6.1+dfsg-1 Candidate: 3.6.1+dfsg-1 Version table: *** 3.6.1+dfsg-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 1m16.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-cache', 'policy', 'python3-pdb2pqr'] 1m16.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-get', '-y', 'install', 'python3-pdb2pqr=3.6.1+dfsg-1'] 1m16.9s DUMP: Reading package lists... Building dependency tree... Reading state information... python3-pdb2pqr is already the newest version (3.6.1+dfsg-1). The following packages were automatically installed and are no longer required: libpython3.11-minimal libpython3.11-stdlib libquadmath0 python3-six python3.11 python3.11-minimal Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m16.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-get', '-y', 'install', 'python3-pdb2pqr=3.6.1+dfsg-1'] 1m16.9s INFO: Running scripts post_install 1m16.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_install_exceptions'] 1m16.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_install_exceptions'] 1m16.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv'] 1m17.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv'] 1m18.3s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', '-ac', '--ignore-obsolete'] 1m19.4s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', '-ac', '--ignore-obsolete'] 1m19.4s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m19.4s DUMP: 0.15.6 1m19.4s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m19.4s INFO: Running adequate version 0.15.6 now. 1m19.4s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'python3-pdb2pqr'] 1m19.6s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'python3-pdb2pqr'] 1m19.6s INFO: Running scripts pre_remove 1m19.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m19.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m19.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m19.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m19.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m20.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m20.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m20.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m20.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m20.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m20.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_remove_exceptions'] 1m20.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/pre_remove_exceptions'] 1m20.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m20.7s DUMP: install ok installed adduser adduser 3.137 install ok installed apt apt 2.9.8 install ok installed base-files base-files 13.5 install ok installed base-passwd base-passwd 3.6.4 install ok installed bash bash 5.2.32-1 install ok installed bsdutils bsdutils 1:2.40.2-7 install ok installed ca-certificates ca-certificates 20240203 install ok installed coreutils coreutils 9.4-3.1 install ok installed dash dash 0.5.12-9 install ok installed debconf debconf 1.5.87 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.20 install ok installed diffutils diffutils 1:3.10-1 install ok installed docutils-common docutils-common 0.21.2+dfsg-2 install ok installed dpkg dpkg 1.22.11 install ok installed e2fsprogs e2fsprogs 1.47.1-1 install ok installed findutils findutils 4.10.0-3 install ok installed gcc-12-base:amd64 gcc-12-base 12.4.0-2 install ok installed gcc-14-base:amd64 gcc-14-base 14.2.0-3 install ok installed gpgv gpgv 2.2.43-8 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1.1 install ok installed hostname hostname 3.23+nmu2 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed libacl1:amd64 libacl1 2.3.2-2 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.9.8 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:4.0.1-1 install ok installed libaudit1:amd64 libaudit1 1:4.0.1-1 install ok installed libblas3:amd64 libblas3 3.12.0-3 install ok installed libblkid1:amd64 libblkid1 2.40.2-7 install ok installed libbsd0:amd64 libbsd0 0.12.2-1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-6 install ok installed libc-bin libc-bin 2.39-7 install ok installed libc6:amd64 libc6 2.39-7 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.5-2 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libcom-err2:amd64 libcom-err2 1.47.1-1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-5 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-7 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.272 install ok installed libexpat1:amd64 libexpat1 2.6.2-1 install ok installed libext2fs2t64:amd64 libext2fs2t64 1.47.1-1 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libgcc-s1:amd64 libgcc-s1 14.2.0-3 install ok installed libgcrypt20:amd64 libgcrypt20 1.11.0-6 install ok installed libgfortran5:amd64 libgfortran5 14.2.0-3 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30t64:amd64 libgnutls30t64 3.8.6-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.50-3 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.21.3-3 install ok installed libhogweed6t64:amd64 libhogweed6t64 3.10-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed libk5crypto3:amd64 libk5crypto3 1.21.3-3 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-3 install ok installed libkrb5-3:amd64 libkrb5-3 1.21.3-3 install ok installed libkrb5support0:amd64 libkrb5support0 1.21.3-3 install ok installed liblapack3:amd64 liblapack3 3.12.0-3 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-3 install ok installed liblzma5:amd64 liblzma5 5.6.2-2 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.40.2-7 install ok installed libncursesw6:amd64 libncursesw6 6.5-2 install ok installed libnettle8t64:amd64 libnettle8t64 3.10-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-3+b2 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.5-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-7 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-7 install ok installed libpam-runtime libpam-runtime 1.5.3-7 install ok installed libpam0g:amd64 libpam0g 1.5.3-7 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.12.5-1 install ok installed libpython3.11-minimal:amd64 libpython3.11-minimal 3.11.9-1 install ok installed libpython3.11-stdlib:amd64 libpython3.11-stdlib 3.11.9-1 install ok installed libpython3.12-minimal:amd64 libpython3.12-minimal 3.12.5-4 install ok installed libpython3.12-stdlib:amd64 libpython3.12-stdlib 3.12.5-4 install ok installed libquadmath0:amd64 libquadmath0 14.2.0-3 install ok installed libreadline8t64:amd64 libreadline8t64 8.2-5 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1+b1 install ok installed libselinux1:amd64 libselinux1 3.7-1+b1 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b4 install ok installed libsepol2:amd64 libsepol2 3.7-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.40.2-7 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.46.1-1 install ok installed libss2:amd64 libss2 1.47.1-1 install ok installed libssl3t64:amd64 libssl3t64 3.3.1-7 install ok installed libstdc++6:amd64 libstdc++6 14.2.0-3 install ok installed libsystemd0:amd64 libsystemd0 256.5-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtinfo6:amd64 libtinfo6 6.5-2 install ok installed libtirpc-common libtirpc-common 1.3.4+ds-1.3 install ok installed libtirpc3t64:amd64 libtirpc3t64 1.3.4+ds-1.3 install ok installed libudev1:amd64 libudev1 256.5-1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libunistring5:amd64 libunistring5 1.2-1 install ok installed libuuid1:amd64 libuuid1 2.40.2-7 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libzstd1:amd64 libzstd1 1.5.6+dfsg-1 install ok installed login login 1:4.16.0-2+really2.40.2-7 install ok installed login.defs login.defs 1:4.16.0-4 install ok installed logsave logsave 1.47.1-1 install ok installed mawk mawk 1.3.4.20240819-2 install ok installed media-types media-types 10.1.0 install ok installed mount mount 2.40.2-7 install ok installed ncurses-base ncurses-base 6.5-2 install ok installed ncurses-bin ncurses-bin 6.5-2 install ok installed netbase netbase 6.4 install ok installed openssl openssl 3.3.1-7 install ok installed openssl-provider-legacy openssl-provider-legacy 3.3.1-7 install ok installed passwd passwd 1:4.16.0-4 install ok installed perl-base perl-base 5.38.2-5 install ok installed python3 python3 3.12.5-1 install ok installed python3-autocommand python3-autocommand 2.2.2-3 install ok installed python3-certifi python3-certifi 2024.6.2-1 install ok installed python3-chardet python3-chardet 5.2.0+dfsg-1 install ok installed python3-charset-normalizer python3-charset-normalizer 3.3.2-2 install ok installed python3-docutils python3-docutils 0.21.2+dfsg-2 install ok installed python3-idna python3-idna 3.6-2.1 install ok installed python3-inflect python3-inflect 7.3.1-1 install ok installed python3-jaraco.context python3-jaraco.context 6.0.0-1 install ok installed python3-jaraco.functools python3-jaraco.functools 4.0.2-1 install ok installed python3-minimal python3-minimal 3.12.5-1 install ok installed python3-more-itertools python3-more-itertools 10.3.0-1 install ok installed python3-numpy python3-numpy 1:1.26.4+ds-11 install ok installed python3-pdb2pqr python3-pdb2pqr 3.6.1+dfsg-1 install ok installed python3-pdbx python3-pdbx 2.0.1-2 install ok installed python3-pkg-resources python3-pkg-resources 73.0.1-1 install ok installed python3-propka python3-propka 3.5.1-1 install ok installed python3-requests python3-requests 2.32.3+dfsg-1 install ok installed python3-roman python3-roman 3.3-3 install ok installed python3-six python3-six 1.16.0-7 install ok installed python3-typeguard python3-typeguard 4.3.0-1 install ok installed python3-typing-extensions python3-typing-extensions 4.12.2-2 install ok installed python3-urllib3 python3-urllib3 2.0.7-2 install ok installed python3.11 python3.11 3.11.9-1 install ok installed python3.11-minimal python3.11-minimal 3.11.9-1 install ok installed python3.12 python3.12 3.12.5-4 install ok installed python3.12-minimal python3.12-minimal 3.12.5-4 install ok installed readline-common readline-common 8.2-5 install ok installed sed sed 4.9-2 install ok installed sgml-base sgml-base 1.31 install ok installed sysvinit-utils sysvinit-utils 3.10-1 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024a-4 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.40.2-7 install ok installed util-linux-extra util-linux-extra 2.40.2-7 install ok installed xml-core xml-core 0.19 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg+really1.3.1-1 1m20.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m20.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-get', 'remove', 'ca-certificates', 'docutils-common', 'libblas3:amd64', 'libexpat1:amd64', 'libgfortran5:amd64', 'libgssapi-krb5-2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8t64:amd64', 'libsqlite3-0:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'media-types', 'netbase', 'openssl', 'python3', 'python3-autocommand', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-docutils', 'python3-idna', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-minimal', 'python3-more-itertools', 'python3-numpy', 'python3-pdbx', 'python3-pkg-resources', 'python3-propka', 'python3-requests', 'python3-roman', 'python3-six', 'python3-typeguard', 'python3-typing-extensions', 'python3-urllib3', 'python3.11', 'python3.11-minimal', 'python3.12', 'python3.12-minimal', 'readline-common', 'sgml-base', 'xml-core', 'python3-pdb2pqr'] 1m24.7s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: ca-certificates docutils-common libblas3 libexpat1 libgfortran5 libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libncursesw6 libnsl2 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libpython3.12-minimal libpython3.12-stdlib libquadmath0 libreadline8t64 libsqlite3-0 libtirpc-common libtirpc3t64 media-types netbase openssl python3 python3-autocommand python3-certifi python3-chardet python3-charset-normalizer python3-docutils python3-idna python3-inflect python3-jaraco.context python3-jaraco.functools python3-minimal python3-more-itertools python3-numpy python3-pdb2pqr python3-pdbx python3-pkg-resources python3-propka python3-requests python3-roman python3-six python3-typeguard python3-typing-extensions python3-urllib3 python3.11 python3.11-minimal python3.12 python3.12-minimal readline-common sgml-base xml-core 0 upgraded, 0 newly installed, 56 to remove and 0 not upgraded. After this operation, 99.5 MB disk space will be freed. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9182 files and directories currently installed.) Removing python3-pdb2pqr (3.6.1+dfsg-1) ... Removing python3-requests (2.32.3+dfsg-1) ... Removing python3-certifi (2024.6.2-1) ... Removing ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing python3-docutils (0.21.2+dfsg-2) ... Removing docutils-common (0.21.2+dfsg-2) ... Removing python3-numpy (1:1.26.4+ds-11) ... Removing liblapack3:amd64 (3.12.0-3) ... Removing libblas3:amd64 (3.12.0-3) ... Removing python3-charset-normalizer (3.3.2-2) ... Removing python3-six (1.16.0-7) ... Removing python3-chardet (5.2.0+dfsg-1) ... Removing python3-pkg-resources (73.0.1-1) ... Removing python3-urllib3 (2.0.7-2) ... Removing python3-inflect (7.3.1-1) ... Removing python3-typeguard (4.3.0-1) ... Removing python3.11 (3.11.9-1) ... Removing python3.11-minimal (3.11.9-1) ... Removing libgfortran5:amd64 (14.2.0-3) ... Removing libpython3.11-stdlib:amd64 (3.11.9-1) ... Removing libpython3.11-minimal:amd64 (3.11.9-1) ... Removing libquadmath0:amd64 (14.2.0-3) ... Removing openssl (3.3.1-7) ... Removing python3-autocommand (2.2.2-3) ... Removing python3-idna (3.6-2.1) ... Removing python3-jaraco.context (6.0.0-1) ... Removing python3-jaraco.functools (4.0.2-1) ... Removing python3-more-itertools (10.3.0-1) ... Removing python3-pdbx (2.0.1-2) ... Removing python3-propka (3.5.1-1) ... Removing python3-roman (3.3-3) ... Removing python3-typing-extensions (4.12.2-2) ... Removing xml-core (0.19) ... Removing sgml-base (1.31) ... Removing python3 (3.12.5-1) ... Removing python3.12 (3.12.5-4) ... Removing python3-minimal (3.12.5-1) ... Removing python3.12-minimal (3.12.5-4) ... Removing libexpat1:amd64 (2.6.2-1) ... Removing libpython3-stdlib:amd64 (3.12.5-1) ... Removing libpython3.12-stdlib:amd64 (3.12.5-4) ... find: '/usr/lib/python3': No such file or directory Removing libnsl2:amd64 (1.3.0-3+b2) ... Removing libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3 to /lib/x86_64-linux-gnu/libtirpc.so.3.usr-is-merged by libtirpc3t64' Removing 'diversion of /lib/x86_64-linux-gnu/libtirpc.so.3.0.0 to /lib/x86_64-linux-gnu/libtirpc.so.3.0.0.usr-is-merged by libtirpc3t64' Removing libgssapi-krb5-2:amd64 (1.21.3-3) ... Removing libkrb5-3:amd64 (1.21.3-3) ... Removing libk5crypto3:amd64 (1.21.3-3) ... Removing libkeyutils1:amd64 (1.6.3-3) ... Removing libkrb5support0:amd64 (1.21.3-3) ... Removing libncursesw6:amd64 (6.5-2) ... Removing libpython3.12-minimal:amd64 (3.12.5-4) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8t64:amd64 (8.2-5) ... Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8 to /lib/x86_64-linux-gnu/libhistory.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libhistory.so.8.2 to /lib/x86_64-linux-gnu/libhistory.so.8.2.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8 to /lib/x86_64-linux-gnu/libreadline.so.8.usr-is-merged by libreadline8t64' Removing 'diversion of /lib/x86_64-linux-gnu/libreadline.so.8.2 to /lib/x86_64-linux-gnu/libreadline.so.8.2.usr-is-merged by libreadline8t64' Removing libsqlite3-0:amd64 (3.46.1-1) ... Removing libtirpc-common (1.3.4+ds-1.3) ... Removing media-types (10.1.0) ... Removing netbase (6.4) ... Removing readline-common (8.2-5) ... Processing triggers for libc-bin (2.39-7) ... 1m24.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-get', 'remove', 'ca-certificates', 'docutils-common', 'libblas3:amd64', 'libexpat1:amd64', 'libgfortran5:amd64', 'libgssapi-krb5-2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8t64:amd64', 'libsqlite3-0:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'media-types', 'netbase', 'openssl', 'python3', 'python3-autocommand', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-docutils', 'python3-idna', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-minimal', 'python3-more-itertools', 'python3-numpy', 'python3-pdbx', 'python3-pkg-resources', 'python3-propka', 'python3-requests', 'python3-roman', 'python3-six', 'python3-typeguard', 'python3-typing-extensions', 'python3-urllib3', 'python3.11', 'python3.11-minimal', 'python3.12', 'python3.12-minimal', 'readline-common', 'sgml-base', 'xml-core', 'python3-pdb2pqr'] 1m24.7s INFO: Running scripts post_remove 1m24.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_remove_exceptions'] 1m24.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_remove_exceptions'] 1m24.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'dpkg', '--purge', 'ca-certificates', 'docutils-common', 'libblas3:amd64', 'libexpat1:amd64', 'libgfortran5:amd64', 'libgssapi-krb5-2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8t64:amd64', 'libsqlite3-0:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'media-types', 'netbase', 'openssl', 'python3', 'python3-autocommand', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-docutils', 'python3-idna', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-minimal', 'python3-more-itertools', 'python3-numpy', 'python3-pdbx', 'python3-pkg-resources', 'python3-propka', 'python3-requests', 'python3-roman', 'python3-six', 'python3-typeguard', 'python3-typing-extensions', 'python3-urllib3', 'python3.11', 'python3.11-minimal', 'python3.12', 'python3.12-minimal', 'readline-common', 'sgml-base', 'xml-core'] 1m24.9s DUMP: (Reading database ... 5298 files and directories currently installed.) Purging configuration files for ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Purging configuration files for docutils-common (0.21.2+dfsg-2) ... dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.21.3-3) ... dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libnsl2 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.11-minimal:amd64 (3.11.9-1) ... dpkg: warning: ignoring request to remove libpython3.11-stdlib which isn't installed Purging configuration files for libpython3.12-minimal:amd64 (3.12.5-4) ... dpkg: warning: ignoring request to remove libpython3.12-stdlib which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed Purging configuration files for libreadline8t64:amd64 (8.2-5) ... dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed Purging configuration files for libtirpc-common (1.3.4+ds-1.3) ... Purging configuration files for libtirpc3t64:amd64 (1.3.4+ds-1.3) ... Purging configuration files for media-types (10.1.0) ... Purging configuration files for netbase (6.4) ... Purging configuration files for openssl (3.3.1-7) ... Purging configuration files for python3 (3.12.5-1) ... dpkg: warning: ignoring request to remove python3-autocommand 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-docutils which isn't installed dpkg: warning: ignoring request to remove python3-idna which isn't installed dpkg: warning: ignoring request to remove python3-inflect which isn't installed dpkg: warning: ignoring request to remove python3-jaraco.context which isn't installed dpkg: warning: ignoring request to remove python3-jaraco.functools which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-more-itertools which isn't installed dpkg: warning: ignoring request to remove python3-numpy which isn't installed dpkg: warning: ignoring request to remove python3-pdbx which isn't installed dpkg: warning: ignoring request to remove python3-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python3-propka which isn't installed dpkg: warning: ignoring request to remove python3-requests which isn't installed dpkg: warning: ignoring request to remove python3-roman which isn't installed dpkg: warning: ignoring request to remove python3-six which isn't installed dpkg: warning: ignoring request to remove python3-typeguard which isn't installed dpkg: warning: ignoring request to remove python3-typing-extensions which isn't installed dpkg: warning: ignoring request to remove python3-urllib3 which isn't installed dpkg: warning: ignoring request to remove python3.11 which isn't installed Purging configuration files for python3.11-minimal (3.11.9-1) ... dpkg: warning: ignoring request to remove python3.12 which isn't installed Purging configuration files for python3.12-minimal (3.12.5-4) ... Purging configuration files for readline-common (8.2-5) ... Purging configuration files for sgml-base (1.31) ... Purging configuration files for xml-core (0.19) ... 1m24.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'dpkg', '--purge', 'ca-certificates', 'docutils-common', 'libblas3:amd64', 'libexpat1:amd64', 'libgfortran5:amd64', 'libgssapi-krb5-2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8t64:amd64', 'libsqlite3-0:amd64', 'libtirpc-common', 'libtirpc3t64:amd64', 'media-types', 'netbase', 'openssl', 'python3', 'python3-autocommand', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-docutils', 'python3-idna', 'python3-inflect', 'python3-jaraco.context', 'python3-jaraco.functools', 'python3-minimal', 'python3-more-itertools', 'python3-numpy', 'python3-pdbx', 'python3-pkg-resources', 'python3-propka', 'python3-requests', 'python3-roman', 'python3-six', 'python3-typeguard', 'python3-typing-extensions', 'python3-urllib3', 'python3.11', 'python3.11-minimal', 'python3.12', 'python3.12-minimal', 'readline-common', 'sgml-base', 'xml-core'] 1m24.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'dpkg', '--purge', 'python3-pdb2pqr'] 1m24.9s DUMP: dpkg: warning: ignoring request to remove python3-pdb2pqr which isn't installed 1m24.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'dpkg', '--purge', 'python3-pdb2pqr'] 1m24.9s INFO: Running scripts post_purge 1m24.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_purge_exceptions'] 1m24.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_purge_exceptions'] 1m24.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'dpkg', '--purge', '--pending'] 1m24.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'dpkg', '--purge', '--pending'] 1m24.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'dpkg', '--remove', '--pending'] 1m25.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'dpkg', '--remove', '--pending'] 1m25.0s INFO: Running scripts post_test 1m25.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_test_exceptions'] 1m25.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'tmp/scripts/post_test_exceptions'] 1m25.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv'] 1m25.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv'] 1m25.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'dpkg-divert', '--list'] 1m25.3s DUMP: diversion of /sbin/mkfs.bfs to /sbin/mkfs.bfs.usr-is-merged by util-linux-extra diversion of /lib/x86_64-linux-gnu/libe2p.so.2 to /lib/x86_64-linux-gnu/libe2p.so.2.usr-is-merged by libext2fs2t64 local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /sbin/mkfs.minix to /sbin/mkfs.minix.usr-is-merged by util-linux-extra diversion of /lib/x86_64-linux-gnu/libext2fs.so.2.4 to /lib/x86_64-linux-gnu/libext2fs.so.2.4.usr-is-merged by libext2fs2t64 diversion of /sbin/mkfs.cramfs to /sbin/mkfs.cramfs.usr-is-merged by util-linux-extra local diversion of /home to /home.distrib diversion of /lib64/ld-linux-x86-64.so.2 to /lib64/ld-linux-x86-64.so.2.usr-is-merged by libc6 diversion of /lib/x86_64-linux-gnu/libext2fs.so.2 to /lib/x86_64-linux-gnu/libext2fs.so.2.usr-is-merged by libext2fs2t64 diversion of /lib/x86_64-linux-gnu/libe2p.so.2.3 to /lib/x86_64-linux-gnu/libe2p.so.2.3.usr-is-merged by libext2fs2t64 diversion of /libx32 to /.libx32.usr-is-merged by base-files local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /sbin/ctrlaltdel to /sbin/ctrlaltdel.usr-is-merged by util-linux-extra diversion of /sbin/fsck.minix to /sbin/fsck.minix.usr-is-merged by util-linux-extra diversion of /lib32 to /.lib32.usr-is-merged by base-files diversion of /libo32 to /.libo32.usr-is-merged by base-files diversion of /sbin/fsck.cramfs to /sbin/fsck.cramfs.usr-is-merged by util-linux-extra 1m25.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'dpkg-divert', '--list'] 1m25.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-get', 'clean'] 1m25.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv', 'apt-get', 'clean'] 1m25.3s DEBUG: Recording chroot state 1m26.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv/dev/shm'] 1m26.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv/dev/shm'] 1m26.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv/dev/console'] 1m26.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv/dev/console'] 1m26.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv/dev/ptmx'] 1m26.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv/dev/ptmx'] 1m26.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv/dev/pts'] 1m26.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv/dev/pts'] 1m26.3s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv/proc'] 1m26.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv/proc'] 1m26.3s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv'] 1m26.4s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpi9xwtaiv'] 1m26.4s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpi9xwtaiv 1m26.4s INFO: PASS: Upgrading between Debian distributions. 1m26.4s INFO: PASS: All tests. 1m26.4s INFO: piuparts run ends. ret=0 End: 2024-08-23 20:28:09 GMT