Start: 2024-03-01 06:45:32 GMT [stable] Package: macsyfinder Source: macsyfinder (2.0~rc1-3) Version: 2.0~rc1-3+b1 Installed-Size: 33920 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3-colorlog, python3-networkx, python3-packaging, python3-yaml, python3:any, libjs-sphinxdoc (>= 2.4.3-5~), sphinx-rtd-theme-common (>= 0.5.1+dfsg), hmmer, ncbi-blast+, libjs-jquery, libjs-underscore Description: detection of macromolecular systems in protein datasets Homepage: https://github.com/gem-pasteur/macsyfinder Built-Using: sphinx (= 3.4.3-2) Description-md5: 0b9b635e7d46ea6cf9f81df42e76fb60 Section: science Priority: optional Filename: pool/main/m/macsyfinder/macsyfinder_2.0~rc1-3+b1_amd64.deb Size: 11591908 MD5sum: 5705068f9583ccb5f528b93e11f15b64 SHA256: fb0692ecc72e7b2707b4b2ec28e5c742f7302b6c656a64b92139f961d87b3e9e [testing] Package: macsyfinder Source: macsyfinder (2.0-2) Version: 2.0-2+b1 Installed-Size: 31261 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3-certifi, python3-colorama, python3-colorlog, python3-networkx, python3-packaging, python3-pandas, python3-yaml, python3:any, libjs-sphinxdoc (>= 5.2), sphinx-rtd-theme-common (>= 1.2.0+dfsg), hmmer, ncbi-blast+, libjs-jquery, libjs-underscore Description: detection of macromolecular systems in protein datasets Homepage: https://github.com/gem-pasteur/macsyfinder Built-Using: sphinx (= 5.3.0-4) Description-md5: 0b9b635e7d46ea6cf9f81df42e76fb60 Section: science Priority: optional Filename: pool/main/m/macsyfinder/macsyfinder_2.0-2+b1_amd64.deb Size: 12092624 MD5sum: eb2d3d59d82ebdf420a1f0583065830c SHA256: 4073d3a7cf9c56dc97a438914d67d8712235a6b16eb4dddc61b03e3da08013ea [sid] Package: macsyfinder Version: 2.1.3-1 Installed-Size: 37199 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3-certifi, python3-colorama, python3-colorlog, python3-networkx, python3-packaging, python3-pandas, python3-yaml, python3:any, libjs-jquery (>= 3.6.0), libjs-sphinxdoc (>= 7.2.2), sphinx-rtd-theme-common (>= 2.0.0+dfsg), hmmer, ncbi-blast+, libjs-underscore Description: detection of macromolecular systems in protein datasets Homepage: https://github.com/gem-pasteur/macsyfinder Built-Using: sphinx (= 7.2.6-4) Description-md5: 0b9b635e7d46ea6cf9f81df42e76fb60 Section: science Priority: optional Filename: pool/main/m/macsyfinder/macsyfinder_2.1.3-1_amd64.deb Size: 14458980 MD5sum: b21001e1e848e73816a612730f8abd39 SHA256: 4b7ebb0ed5059881a77729f0fb7689a764cd4315d59121253e662478c399e6b6 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/bullseye-merged-usr_amd64.tar.gz -d stable -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/stable22sid/reference-chroot-metadata.dat --apt macsyfinder=2.1.3-1 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 1.3.1~202401311821~1.3-2-g28295102 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz -d stable -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/stable22sid/reference-chroot-metadata.dat --apt macsyfinder=2.1.3-1 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-28-amd64 #1 SMP Debian 5.10.209-2 (2024-01-31) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmp9qz_sxh5 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp9qz_sxh5 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m0.5s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5/proc'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5/proc'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5/dev/pts'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5/dev/pts'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5/dev/ptmx'] 0m0.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5/dev/ptmx'] 0m0.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5/dev/console'] 0m0.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5/dev/console'] 0m0.5s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5/dev/shm'] 0m0.5s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5/dev/shm'] 0m0.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ bullseye main 0m0.5s DEBUG: Created policy-rc.d and chmodded it. 0m0.5s DEBUG: Created resolv.conf. 0m0.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp9qz_sxh5/tmp/scripts/ 0m0.5s INFO: Running scripts post_chroot_unpack 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-get', 'update'] 0m1.6s DUMP: Hit:1 http://deb.debian.org/debian bullseye InRelease Reading package lists... 0m1.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-get', 'update'] 0m1.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-get', '-yf', 'dist-upgrade'] 0m2.2s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-get', '-yf', 'dist-upgrade'] 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.5s DUMP: 29fcf27583012b383113cec2bf757015 - 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.5s INFO: Running scripts post_setup 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_setup_dummy_users'] 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_setup_dummy_users'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_setup_forbid_home'] 0m3.6s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_setup_forbid_home'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.7s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' dpkg-divert: warning: diverting file '/bin/sync' from an Essential package with rename is dangerous, use --no-rename '/bin/sync' -> 'true' 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_setup_minimize'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_setup_minimize'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_setup_zz_backports'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_setup_zz_backports'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.7s DUMP: install ok installed adduser adduser 3.118+deb11u1 install ok installed apt apt 2.2.4 install ok installed base-files base-files 11.1+deb11u9 install ok installed base-passwd base-passwd 3.5.51 install ok installed bash bash 5.1-2+deb11u1 install ok installed bsdutils bsdutils 1:2.36.1-8+deb11u1 install ok installed coreutils coreutils 8.32-4+b1 install ok installed dash dash 0.5.11+git20200708+dd9ef66-5 install ok installed debconf debconf 1.5.77 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1+deb11u1 install ok installed debianutils debianutils 4.11.2 install ok installed diffutils diffutils 1:3.7-5 install ok installed dpkg dpkg 1.20.13 install ok installed e2fsprogs e2fsprogs 1.46.2-2 install ok installed findutils findutils 4.8.0-1 install ok installed gcc-10-base:amd64 gcc-10-base 10.2.1-6 install ok installed gcc-9-base:amd64 gcc-9-base 9.3.0-22 install ok installed gpgv gpgv 2.2.27-2+deb11u2 install ok installed grep grep 3.6-1+deb11u1 install ok installed gzip gzip 1.10-4+deb11u1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.60 install ok installed libacl1:amd64 libacl1 2.2.53-10 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.2.4 install ok installed libattr1:amd64 libattr1 1:2.4.48-6 install ok installed libaudit-common libaudit-common 1:3.0-2 install ok installed libaudit1:amd64 libaudit1 1:3.0-2 install ok installed libblkid1:amd64 libblkid1 2.36.1-8+deb11u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4 install ok installed libc-bin libc-bin 2.31-13+deb11u8 install ok installed libc6:amd64 libc6 2.31-13+deb11u8 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2+b1 install ok installed libcom-err2:amd64 libcom-err2 1.46.2-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.18-4 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.8 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.260 install ok installed libext2fs2:amd64 libext2fs2 1.46.2-2 install ok installed libffi7:amd64 libffi7 3.3-6 install ok installed libgcc-s1:amd64 libgcc-s1 10.2.1-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.7-6 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg-1+deb11u1 install ok installed libgnutls30:amd64 libgnutls30 3.7.1-5+deb11u4 install ok installed libgpg-error0:amd64 libgpg-error0 1.38-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.18.3-6+deb11u4 install ok installed libhogweed6:amd64 libhogweed6 3.7.3-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.0-5 install ok installed libk5crypto3:amd64 libk5crypto3 1.18.3-6+deb11u4 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.18.3-6+deb11u4 install ok installed libkrb5support0:amd64 libkrb5support0 1.18.3-6+deb11u4 install ok installed liblz4-1:amd64 liblz4-1 1.9.3-2 install ok installed liblzma5:amd64 liblzma5 5.2.5-2.1~deb11u1 install ok installed libmount1:amd64 libmount1 2.36.1-8+deb11u1 install ok installed libnettle8:amd64 libnettle8 3.7.3-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.22-1 install ok installed libpam-modules:amd64 libpam-modules 1.4.0-9+deb11u1 install ok installed libpam-modules-bin libpam-modules-bin 1.4.0-9+deb11u1 install ok installed libpam-runtime libpam-runtime 1.4.0-9+deb11u1 install ok installed libpam0g:amd64 libpam0g 1.4.0-9+deb11u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.36-2+deb11u1 install ok installed libpcre3:amd64 libpcre3 2:8.39-13 install ok installed libseccomp2:amd64 libseccomp2 2.5.1-1+deb11u1 install ok installed libselinux1:amd64 libselinux1 3.1-3 install ok installed libsemanage-common libsemanage-common 3.1-1 install ok installed libsemanage1:amd64 libsemanage1 3.1-1+b2 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.36.1-8+deb11u1 install ok installed libss2:amd64 libss2 1.46.2-2 install ok installed libssl1.1:amd64 libssl1.1 1.1.1w-0+deb11u1 install ok installed libstdc++6:amd64 libstdc++6 10.2.1-6 install ok installed libsystemd0:amd64 libsystemd0 247.3-7+deb11u4 install ok installed libtasn1-6:amd64 libtasn1-6 4.16.0-2+deb11u1 install ok installed libtinfo6:amd64 libtinfo6 6.2+20201114-2+deb11u2 install ok installed libtirpc-common libtirpc-common 1.3.1-1+deb11u1 install ok installed libtirpc3:amd64 libtirpc3 1.3.1-1+deb11u1 install ok installed libudev1:amd64 libudev1 247.3-7+deb11u4 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed libuuid1:amd64 libuuid1 2.36.1-8+deb11u1 install ok installed libxxhash0:amd64 libxxhash0 0.8.0-2 install ok installed libzstd1:amd64 libzstd1 1.4.8+dfsg-2.1 install ok installed login login 1:4.8.1-1 install ok installed logsave logsave 1.46.2-2 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.4.20200120-2 install ok installed mount mount 2.36.1-8+deb11u1 install ok installed ncurses-base ncurses-base 6.2+20201114-2+deb11u2 install ok installed ncurses-bin ncurses-bin 6.2+20201114-2+deb11u2 install ok installed passwd passwd 1:4.8.1-1 install ok installed perl-base perl-base 5.32.1-4+deb11u3 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.96-7+deb11u1 install ok installed tar tar 1.34+dfsg-1+deb11u1 install ok installed tzdata tzdata 2024a-0+deb11u1 install ok installed util-linux util-linux 2.36.1-8+deb11u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2+deb11u2 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.7s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/stable22sid/reference-chroot-metadata.dat 0m3.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5'] 0m4.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5'] 0m4.3s INFO: Running scripts is_testable 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/is_testable_uninstallable'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/is_testable_uninstallable'] 0m4.3s INFO: Running scripts pre_test 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_test_exceptions'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_test_exceptions'] 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_test_root_password'] 0m4.4s DUMP: New password: Retype new password: passwd: password updated successfully 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_test_root_password'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-cache', 'show', '--no-all-versions', 'macsyfinder'] 0m4.6s DUMP: Package: macsyfinder Source: macsyfinder (2.0~rc1-3) Version: 2.0~rc1-3+b1 Installed-Size: 33920 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3-colorlog, python3-networkx, python3-packaging, python3-yaml, python3:any, libjs-sphinxdoc (>= 2.4.3-5~), sphinx-rtd-theme-common (>= 0.5.1+dfsg), hmmer, ncbi-blast+, libjs-jquery, libjs-underscore Description-en: detection of macromolecular systems in protein datasets MacSyFinder is a program to model and detect macromolecular systems, genetic pathways... in protein datasets. In prokaryotes, these systems have often evolutionarily conserved properties: they are made of conserved components, and are encoded in compact loci (conserved genetic architecture). The user models these systems with MacSyFinder to reflect these conserved features, and to allow their efficient detection . This package presents the Open Source Java API to biological databases and a series of mostly sequence-based algorithms. Description-md5: 0b9b635e7d46ea6cf9f81df42e76fb60 Homepage: https://github.com/gem-pasteur/macsyfinder Built-Using: sphinx (= 3.4.3-2) Section: science Priority: optional Filename: pool/main/m/macsyfinder/macsyfinder_2.0~rc1-3+b1_amd64.deb Size: 11591908 MD5sum: 5705068f9583ccb5f528b93e11f15b64 SHA256: fb0692ecc72e7b2707b4b2ec28e5c742f7302b6c656a64b92139f961d87b3e9e 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-cache', 'show', '--no-all-versions', 'macsyfinder'] 0m4.6s INFO: apt-cache knows about the following packages: macsyfinder 0m4.6s INFO: Running scripts pre_install 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_install_database-server'] 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_install_database-server'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_install_exceptions'] 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_install_exceptions'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_install_extras'] 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_install_extras'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-cache', 'policy'] 0m4.7s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.9,o=Debian,a=oldstable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-cache', 'policy'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-cache', 'policy', 'macsyfinder'] 0m4.7s DUMP: macsyfinder: Installed: (none) Candidate: 2.0~rc1-3+b1 Version table: 2.0~rc1-3+b1 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-cache', 'policy', 'macsyfinder'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-get', '-y', 'install', 'macsyfinder'] 0m19.8s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: fonts-font-awesome fonts-lato hmmer libdivsufsort3 libexpat1 libgdbm-compat4 libgdbm6 libgomp1 libjs-jquery libjs-sphinxdoc libjs-underscore liblmdb0 libmbedcrypto3 libmbedtls12 libmbedx509-0 libmpdec3 libncursesw6 libperl5.32 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libreadline8 libsqlite3-0 libyaml-0-2 media-types ncbi-blast+ ncbi-data perl perl-modules-5.32 python3 python3-colorlog python3-decorator python3-minimal python3-networkx python3-packaging python3-pkg-resources python3-pyparsing python3-yaml python3.9 python3.9-minimal readline-common sphinx-rtd-theme-common Suggested packages: hmmer-doc gdbm-l10n sensible-utils perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl python3-doc python3-tk python3-venv python-networkx-doc python3-setuptools python-pyparsing-doc python3.9-venv python3.9-doc binutils binfmt-support readline-doc Recommended packages: javascript-common libgpm2 ca-certificates netbase python3-gdal python3-matplotlib python3-numpy python3-pydot python3-pygraphviz python3-scipy The following NEW packages will be installed: fonts-font-awesome fonts-lato hmmer libdivsufsort3 libexpat1 libgdbm-compat4 libgdbm6 libgomp1 libjs-jquery libjs-sphinxdoc libjs-underscore liblmdb0 libmbedcrypto3 libmbedtls12 libmbedx509-0 libmpdec3 libncursesw6 libperl5.32 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libreadline8 libsqlite3-0 libyaml-0-2 macsyfinder media-types ncbi-blast+ ncbi-data perl perl-modules-5.32 python3 python3-colorlog python3-decorator python3-minimal python3-networkx python3-packaging python3-pkg-resources python3-pyparsing python3-yaml python3.9 python3.9-minimal readline-common sphinx-rtd-theme-common 0 upgraded, 43 newly installed, 0 to remove and 0 not upgraded. Need to get 48.2 MB of archives. After this operation, 212 MB of additional disk space will be used. 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Setting up libgomp1:amd64 (10.2.1-6) ... Setting up libncursesw6:amd64 (6.2+20201114-2+deb11u2) ... Setting up libmpdec3:amd64 (2.5.1-1) ... Setting up libmbedcrypto3:amd64 (2.16.9-0.1) ... Setting up libjs-jquery (3.5.1+dfsg+~3.5.5-7) ... Setting up libdivsufsort3:amd64 (2.0.1-5) ... Setting up readline-common (8.1-1) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Setting up sphinx-rtd-theme-common (0.5.1+dfsg-1) ... Setting up libgdbm6:amd64 (1.19-2) ... Setting up libjs-underscore (1.9.1~dfsg-3) ... Setting up libmbedx509-0:amd64 (2.16.9-0.1) ... Setting up libreadline8:amd64 (8.1-1) ... Setting up libmbedtls12:amd64 (2.16.9-0.1) ... Setting up libgdbm-compat4:amd64 (1.19-2) ... Setting up libperl5.32:amd64 (5.32.1-4+deb11u3) ... Setting up libjs-sphinxdoc (3.4.3-2) ... Setting up hmmer (3.3.2+dfsg-1) ... Setting up libpython3.9-stdlib:amd64 (3.9.2-1) ... Setting up libpython3-stdlib:amd64 (3.9.2-3) ... Setting up perl (5.32.1-4+deb11u3) ... Setting up python3.9 (3.9.2-1) ... Setting up python3 (3.9.2-3) ... Setting up ncbi-blast+ (2.11.0+ds-1) ... Setting up python3-decorator (4.4.2-2) ... Setting up python3-pyparsing (2.4.7-1) ... Setting up python3-pkg-resources (52.0.0-4) ... Setting up python3-colorlog (4.7.2-1) ... Setting up python3-yaml (5.3.1-5) ... Setting up python3-networkx (2.5+ds-2) ... Setting up python3-packaging (20.9-2) ... Setting up macsyfinder (2.0~rc1-3+b1) ... Processing triggers for libc-bin (2.31-13+deb11u8) ... 0m19.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-get', '-y', 'install', 'macsyfinder'] 0m19.8s INFO: Running scripts post_install 0m19.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_install_exceptions'] 0m19.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_install_exceptions'] 0m19.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5'] 0m20.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5'] 0m20.5s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmp9qz_sxh5 to testing 0m20.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m20.5s INFO: Running scripts pre_distupgrade 0m20.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m20.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m20.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_distupgrade_exceptions'] 0m20.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_distupgrade_exceptions'] 0m20.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m20.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m20.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m20.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m20.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m20.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m20.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-get', 'update'] 0m24.3s DUMP: Get:1 http://deb.debian.org/debian bookworm InRelease [151 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 Packages [8786 kB] Get:3 http://deb.debian.org/debian bookworm/main Translation-en [6109 kB] Fetched 15.0 MB in 3s (5518 kB/s) Reading package lists... 0m24.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-get', 'update'] 0m24.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-get', '-yf', 'dist-upgrade'] 1m3.8s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libmbedcrypto3 libmbedtls12 libmbedx509-0 libmpdec3 libperl5.32 libpython3.9-minimal libpython3.9-stdlib perl-modules-5.32 python3-decorator python3-pyparsing python3.9 python3.9-minimal Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libsemanage1 The following NEW packages will be installed: ca-certificates gcc-12-base libblas3 libcap2 libffi8 libfile-find-rule-perl libgfortran5 liblapack3 libmbedcrypto7 libmbedtls14 libmbedx509-1 libmd0 libnumber-compare-perl libperl5.36 libpython3.11-minimal libpython3.11-stdlib libquadmath0 libsemanage2 libsepol2 libssl3 libtext-glob-perl openssl perl-modules-5.36 python3-certifi python3-colorama python3-dateutil python3-numpy python3-pandas python3-pandas-lib python3-six python3-tz python3.11 python3.11-minimal usrmerge util-linux-extra The following packages will be upgraded: adduser apt base-files base-passwd bash bsdutils coreutils dash debconf debian-archive-keyring debianutils diffutils dpkg e2fsprogs findutils gpgv grep gzip hostname init-system-helpers libacl1 libapt-pkg6.0 libattr1 libaudit-common libaudit1 libblkid1 libbz2-1.0 libc-bin libc6 libcap-ng0 libcom-err2 libcrypt1 libdb5.3 libdebconfclient0 libexpat1 libext2fs2 libgcc-s1 libgcrypt20 libgdbm-compat4 libgdbm6 libgmp10 libgnutls30 libgomp1 libgpg-error0 libgssapi-krb5-2 libhogweed6 libidn2-0 libjs-jquery libjs-sphinxdoc libjs-underscore libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblz4-1 liblzma5 libmount1 libncursesw6 libnettle8 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libpcre3 libpython3-stdlib libreadline8 libseccomp2 libselinux1 libsemanage-common libsmartcols1 libsqlite3-0 libss2 libstdc++6 libsystemd0 libtasn1-6 libtinfo6 libtirpc-common libtirpc3 libudev1 libunistring2 libuuid1 libxxhash0 libyaml-0-2 libzstd1 login logsave lsb-base macsyfinder mawk media-types mount ncbi-blast+ ncbi-data ncurses-base ncurses-bin passwd perl perl-base python3 python3-colorlog python3-decorator python3-minimal python3-networkx python3-packaging python3-pkg-resources python3-pyparsing python3-yaml readline-common sed sphinx-rtd-theme-common sysvinit-utils tar tzdata util-linux zlib1g 117 upgraded, 35 newly installed, 1 to remove and 0 not upgraded. Need to get 97.8 MB of archives. After this operation, 164 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 base-files amd64 12.4+deb12u5 [70.8 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 libc6 amd64 2.36-9+deb12u4 [2748 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libc-bin amd64 2.36-9+deb12u4 [606 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 gcc-12-base amd64 12.2.0-14 [37.5 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 libgcc-s1 amd64 12.2.0-14 [49.9 kB] Get:6 http://deb.debian.org/debian bookworm/main amd64 debianutils amd64 5.7-0.5~deb12u1 [103 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 bash amd64 5.2.15-2+b2 [1491 kB] Get:8 http://deb.debian.org/debian bookworm/main amd64 bsdutils amd64 1:2.38.1-5+b1 [94.4 kB] Get:9 http://deb.debian.org/debian bookworm/main amd64 libgmp10 amd64 2:6.2.1+dfsg1-1.1 [563 kB] Get:10 http://deb.debian.org/debian bookworm/main amd64 coreutils amd64 9.1-1 [2897 kB] Get:11 http://deb.debian.org/debian bookworm/main amd64 liblzma5 amd64 5.4.1-0.2 [205 kB] Get:12 http://deb.debian.org/debian bookworm/main amd64 libmd0 amd64 1.0.4-2 [29.5 kB] Get:13 http://deb.debian.org/debian bookworm/main amd64 libzstd1 amd64 1.5.4+dfsg2-5 [290 kB] Get:14 http://deb.debian.org/debian bookworm/main amd64 tar amd64 1.34+dfsg-1.2+deb12u1 [836 kB] Get:15 http://deb.debian.org/debian bookworm/main amd64 dpkg amd64 1.21.22 [1567 kB] Get:16 http://deb.debian.org/debian bookworm/main amd64 dash amd64 0.5.12-2 [91.8 kB] Get:17 http://deb.debian.org/debian bookworm/main amd64 diffutils amd64 1:3.8-4 [352 kB] Get:18 http://deb.debian.org/debian bookworm/main amd64 findutils amd64 4.9.0-4 [636 kB] Get:19 http://deb.debian.org/debian bookworm/main amd64 grep amd64 3.8-5 [421 kB] Get:20 http://deb.debian.org/debian bookworm/main amd64 gzip amd64 1.12-1 [140 kB] Get:21 http://deb.debian.org/debian bookworm/main amd64 hostname amd64 3.23+nmu1 [10.5 kB] Get:22 http://deb.debian.org/debian bookworm/main amd64 login amd64 1:4.13+dfsg1-1+b1 [616 kB] Get:23 http://deb.debian.org/debian bookworm/main amd64 libncursesw6 amd64 6.4-4 [134 kB] Get:24 http://deb.debian.org/debian bookworm/main amd64 libtinfo6 amd64 6.4-4 [331 kB] Get:25 http://deb.debian.org/debian bookworm/main amd64 ncurses-bin amd64 6.4-4 [421 kB] Get:26 http://deb.debian.org/debian bookworm/main amd64 perl-modules-5.36 all 5.36.0-7+deb12u1 [2815 kB] Get:27 http://deb.debian.org/debian bookworm/main amd64 libgdbm6 amd64 1.23-3 [72.2 kB] Get:28 http://deb.debian.org/debian bookworm/main amd64 libperl5.36 amd64 5.36.0-7+deb12u1 [4218 kB] Get:29 http://deb.debian.org/debian bookworm/main amd64 perl amd64 5.36.0-7+deb12u1 [239 kB] Get:30 http://deb.debian.org/debian bookworm/main amd64 perl-base amd64 5.36.0-7+deb12u1 [1608 kB] Get:31 http://deb.debian.org/debian bookworm/main amd64 libbz2-1.0 amd64 1.0.8-5+b1 [47.3 kB] Get:32 http://deb.debian.org/debian bookworm/main amd64 libaudit-common all 1:3.0.9-1 [10.4 kB] Get:33 http://deb.debian.org/debian bookworm/main amd64 libcap-ng0 amd64 0.8.3-1+b3 [17.1 kB] Get:34 http://deb.debian.org/debian bookworm/main amd64 libaudit1 amd64 1:3.0.9-1 [46.8 kB] Get:35 http://deb.debian.org/debian bookworm/main amd64 debconf all 1.5.82 [121 kB] Get:36 http://deb.debian.org/debian bookworm/main amd64 libpam0g amd64 1.5.2-6+deb12u1 [92.0 kB] Get:37 http://deb.debian.org/debian bookworm/main amd64 libcrypt1 amd64 1:4.4.33-2 [89.5 kB] Get:38 http://deb.debian.org/debian bookworm/main amd64 libdb5.3 amd64 5.3.28+dfsg2-1 [697 kB] Get:39 http://deb.debian.org/debian bookworm/main amd64 libgdbm-compat4 amd64 1.23-3 [48.2 kB] Get:40 http://deb.debian.org/debian bookworm/main amd64 zlib1g amd64 1:1.2.13.dfsg-1 [86.7 kB] Get:41 http://deb.debian.org/debian bookworm/main amd64 sed amd64 4.9-1 [329 kB] Get:42 http://deb.debian.org/debian bookworm/main amd64 libblkid1 amd64 2.38.1-5+b1 [147 kB] Get:43 http://deb.debian.org/debian bookworm/main amd64 libpcre2-8-0 amd64 10.42-1 [261 kB] Get:44 http://deb.debian.org/debian bookworm/main amd64 libselinux1 amd64 3.4-1+b6 [73.7 kB] Get:45 http://deb.debian.org/debian bookworm/main amd64 libmount1 amd64 2.38.1-5+b1 [166 kB] Get:46 http://deb.debian.org/debian bookworm/main amd64 libsmartcols1 amd64 2.38.1-5+b1 [107 kB] Get:47 http://deb.debian.org/debian bookworm/main amd64 util-linux-extra amd64 2.38.1-5+b1 [111 kB] Get:48 http://deb.debian.org/debian bookworm/main amd64 util-linux amd64 2.38.1-5+b1 [1177 kB] Get:49 http://deb.debian.org/debian bookworm/main amd64 libgpg-error0 amd64 1.46-1 [76.9 kB] Get:50 http://deb.debian.org/debian bookworm/main amd64 libgcrypt20 amd64 1.10.1-3 [696 kB] Get:51 http://deb.debian.org/debian bookworm/main amd64 libstdc++6 amd64 12.2.0-14 [614 kB] Get:52 http://deb.debian.org/debian bookworm/main amd64 liblz4-1 amd64 1.9.4-1 [62.9 kB] Get:53 http://deb.debian.org/debian bookworm/main amd64 libcap2 amd64 1:2.66-4 [27.0 kB] Get:54 http://deb.debian.org/debian bookworm/main amd64 libsystemd0 amd64 252.22-1~deb12u1 [331 kB] Get:55 http://deb.debian.org/debian bookworm/main amd64 libudev1 amd64 252.22-1~deb12u1 [108 kB] Get:56 http://deb.debian.org/debian bookworm/main amd64 libxxhash0 amd64 0.8.1-1 [27.6 kB] Get:57 http://deb.debian.org/debian bookworm/main amd64 libapt-pkg6.0 amd64 2.6.1 [907 kB] Get:58 http://deb.debian.org/debian bookworm/main amd64 libnettle8 amd64 3.8.1-2 [288 kB] Get:59 http://deb.debian.org/debian bookworm/main amd64 libhogweed6 amd64 3.8.1-2 [328 kB] Get:60 http://deb.debian.org/debian bookworm/main amd64 libunistring2 amd64 1.0-2 [437 kB] Get:61 http://deb.debian.org/debian bookworm/main amd64 libidn2-0 amd64 2.3.3-1+b1 [124 kB] Get:62 http://deb.debian.org/debian bookworm/main amd64 libffi8 amd64 3.4.4-1 [22.9 kB] Get:63 http://deb.debian.org/debian bookworm/main amd64 libp11-kit0 amd64 0.24.1-2 [345 kB] Get:64 http://deb.debian.org/debian bookworm/main amd64 libtasn1-6 amd64 4.19.0-2 [56.6 kB] Get:65 http://deb.debian.org/debian bookworm/main amd64 libgnutls30 amd64 3.7.9-2+deb12u2 [1404 kB] Get:66 http://deb.debian.org/debian bookworm/main amd64 libsemanage-common all 3.4-1 [21.6 kB] Get:67 http://deb.debian.org/debian bookworm/main amd64 libsepol2 amd64 3.4-2.1 [276 kB] Get:68 http://deb.debian.org/debian bookworm/main amd64 libsemanage2 amd64 3.4-1+b5 [89.9 kB] Get:69 http://deb.debian.org/debian bookworm/main amd64 passwd amd64 1:4.13+dfsg1-1+b1 [972 kB] Get:70 http://deb.debian.org/debian bookworm/main amd64 libpam-modules-bin amd64 1.5.2-6+deb12u1 [75.6 kB] Get:71 http://deb.debian.org/debian bookworm/main amd64 libpam-modules amd64 1.5.2-6+deb12u1 [291 kB] Get:72 http://deb.debian.org/debian bookworm/main amd64 adduser all 3.134 [183 kB] Get:73 http://deb.debian.org/debian bookworm/main amd64 gpgv amd64 2.2.40-1.1 [648 kB] Get:74 http://deb.debian.org/debian bookworm/main amd64 debian-archive-keyring all 2023.3+deb12u1 [161 kB] Get:75 http://deb.debian.org/debian bookworm/main amd64 libseccomp2 amd64 2.5.4-1+b3 [46.6 kB] Get:76 http://deb.debian.org/debian bookworm/main amd64 apt amd64 2.6.1 [1373 kB] Get:77 http://deb.debian.org/debian bookworm/main amd64 libdebconfclient0 amd64 0.270 [9900 B] Get:78 http://deb.debian.org/debian bookworm/main amd64 base-passwd amd64 3.6.1 [60.0 kB] Get:79 http://deb.debian.org/debian bookworm/main amd64 libnumber-compare-perl all 0.03-3 [6332 B] Get:80 http://deb.debian.org/debian bookworm/main amd64 libtext-glob-perl all 0.11-3 [7676 B] Get:81 http://deb.debian.org/debian bookworm/main amd64 libfile-find-rule-perl all 0.34-3 [26.6 kB] Get:82 http://deb.debian.org/debian bookworm/main amd64 usrmerge all 37~deb12u1 [13.3 kB] Get:83 http://deb.debian.org/debian bookworm/main amd64 init-system-helpers all 1.65.2 [49.8 kB] Get:84 http://deb.debian.org/debian bookworm/main amd64 ncurses-base all 6.4-4 [261 kB] Get:85 http://deb.debian.org/debian bookworm/main amd64 sysvinit-utils amd64 3.06-4 [31.0 kB] Get:86 http://deb.debian.org/debian bookworm/main amd64 lsb-base all 11.6 [4584 B] Get:87 http://deb.debian.org/debian bookworm/main amd64 logsave amd64 1.47.0-2 [19.6 kB] Get:88 http://deb.debian.org/debian bookworm/main amd64 libext2fs2 amd64 1.47.0-2 [205 kB] Get:89 http://deb.debian.org/debian bookworm/main amd64 e2fsprogs amd64 1.47.0-2 [571 kB] Get:90 http://deb.debian.org/debian bookworm/main amd64 mount amd64 2.38.1-5+b1 [134 kB] Get:91 http://deb.debian.org/debian bookworm/main amd64 libssl3 amd64 3.0.11-1~deb12u2 [2019 kB] Get:92 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6 [813 kB] Get:93 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get:94 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6 [2064 kB] Get:95 http://deb.debian.org/debian bookworm/main amd64 python3-yaml amd64 6.0-3+b2 [119 kB] Get:96 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get:97 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get:98 http://deb.debian.org/debian bookworm/main amd64 libyaml-0-2 amd64 0.2.5-1 [53.6 kB] Get:99 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get:100 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get:101 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get:102 http://deb.debian.org/debian bookworm/main amd64 libsqlite3-0 amd64 3.40.1-2 [837 kB] Get:103 http://deb.debian.org/debian bookworm/main amd64 libtirpc-common all 1.3.3+ds-1 [14.0 kB] Get:104 http://deb.debian.org/debian bookworm/main amd64 libgssapi-krb5-2 amd64 1.20.1-2+deb12u1 [134 kB] Get:105 http://deb.debian.org/debian bookworm/main amd64 libkrb5-3 amd64 1.20.1-2+deb12u1 [332 kB] Get:106 http://deb.debian.org/debian bookworm/main amd64 libk5crypto3 amd64 1.20.1-2+deb12u1 [78.9 kB] Get:107 http://deb.debian.org/debian bookworm/main amd64 libkrb5support0 amd64 1.20.1-2+deb12u1 [32.4 kB] Get:108 http://deb.debian.org/debian bookworm/main amd64 libcom-err2 amd64 1.47.0-2 [19.8 kB] Get:109 http://deb.debian.org/debian bookworm/main amd64 libkeyutils1 amd64 1.6.3-2 [8808 B] Get:110 http://deb.debian.org/debian bookworm/main amd64 libtirpc3 amd64 1.3.3+ds-1 [85.2 kB] Get:111 http://deb.debian.org/debian bookworm/main amd64 libuuid1 amd64 2.38.1-5+b1 [28.8 kB] Get:112 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6 [1796 kB] Get:113 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6 [572 kB] Get:114 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get:115 http://deb.debian.org/debian bookworm/main amd64 libpam-runtime all 1.5.2-6+deb12u1 [161 kB] Get:116 http://deb.debian.org/debian bookworm/main amd64 libacl1 amd64 2.3.1-3 [31.5 kB] Get:117 http://deb.debian.org/debian bookworm/main amd64 libattr1 amd64 1:2.5.1-4 [22.2 kB] Get:118 http://deb.debian.org/debian bookworm/main amd64 libpcre3 amd64 2:8.39-15 [341 kB] Get:119 http://deb.debian.org/debian bookworm/main amd64 mawk amd64 1.3.4.20200120-3.1 [119 kB] Get:120 http://deb.debian.org/debian bookworm/main amd64 tzdata all 2024a-0+deb12u1 [297 kB] Get:121 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.11-1~deb12u2 [1419 kB] Get:122 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB] Get:123 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB] Get:124 http://deb.debian.org/debian bookworm/main amd64 libquadmath0 amd64 12.2.0-14 [144 kB] Get:125 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get:126 http://deb.debian.org/debian bookworm/main amd64 libgomp1 amd64 12.2.0-14 [116 kB] Get:127 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:128 http://deb.debian.org/debian bookworm/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get:129 http://deb.debian.org/debian bookworm/main amd64 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get:130 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get:131 http://deb.debian.org/debian bookworm/main amd64 libmbedcrypto7 amd64 2.28.3-1 [277 kB] Get:132 http://deb.debian.org/debian bookworm/main amd64 libmbedx509-1 amd64 2.28.3-1 [128 kB] Get:133 http://deb.debian.org/debian bookworm/main amd64 libmbedtls14 amd64 2.28.3-1 [163 kB] Get:134 http://deb.debian.org/debian bookworm/main amd64 libss2 amd64 1.47.0-2 [24.5 kB] Get:135 http://deb.debian.org/debian bookworm/main amd64 python3-certifi all 2022.9.24-1 [153 kB] Get:136 http://deb.debian.org/debian bookworm/main amd64 python3-colorama all 0.4.6-2 [36.8 kB] Get:137 http://deb.debian.org/debian bookworm/main amd64 python3-colorlog all 6.7.0-1 [26.5 kB] Get:138 http://deb.debian.org/debian bookworm/main amd64 python3-pkg-resources all 66.1.1-1 [296 kB] Get:139 http://deb.debian.org/debian bookworm/main amd64 python3-networkx all 2.8.8-1 [1425 kB] Get:140 http://deb.debian.org/debian bookworm/main amd64 python3-packaging all 23.0-1 [32.5 kB] Get:141 http://deb.debian.org/debian bookworm/main amd64 python3-six all 1.16.0-4 [17.5 kB] Get:142 http://deb.debian.org/debian bookworm/main amd64 python3-dateutil all 2.8.2-2 [78.3 kB] Get:143 http://deb.debian.org/debian bookworm/main amd64 python3-numpy amd64 1:1.24.2-1 [5209 kB] Get:144 http://deb.debian.org/debian bookworm/main amd64 python3-tz all 2022.7.1-4 [30.1 kB] Get:145 http://deb.debian.org/debian bookworm/main amd64 python3-pandas-lib amd64 1.5.3+dfsg-2 [3499 kB] Get:146 http://deb.debian.org/debian bookworm/main amd64 python3-pandas all 1.5.3+dfsg-2 [2885 kB] Get:147 http://deb.debian.org/debian bookworm/main amd64 sphinx-rtd-theme-common all 1.2.0+dfsg-1 [997 kB] Get:148 http://deb.debian.org/debian bookworm/main amd64 ncbi-data all 6.1.20170106+dfsg1-10 [3557 kB] Get:149 http://deb.debian.org/debian bookworm/main amd64 ncbi-blast+ amd64 2.12.0+ds-3+b1 [11.9 MB] Get:150 http://deb.debian.org/debian bookworm/main amd64 macsyfinder amd64 2.0-2+b1 [12.1 MB] Get:151 http://deb.debian.org/debian bookworm/main amd64 python3-decorator all 5.1.1-3 [14.9 kB] Get:152 http://deb.debian.org/debian bookworm/main amd64 python3-pyparsing all 3.0.9-1 [138 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 97.8 MB in 1s (141 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 ... 12818 files and directories currently installed.) Preparing to unpack .../libdb5.3_5.3.28+dfsg2-1_amd64.deb ... Unpacking libdb5.3:amd64 (5.3.28+dfsg2-1) over (5.3.28+dfsg1-0.8) ... Setting up libdb5.3:amd64 (5.3.28+dfsg2-1) ... (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 ... 12818 files and directories currently installed.) Preparing to unpack .../archives/sed_4.9-1_amd64.deb ... Unpacking sed (4.9-1) over (4.7-1) ... Setting up sed (4.9-1) ... (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 ... 12821 files and directories currently installed.) Preparing to unpack .../libpcre2-8-0_10.42-1_amd64.deb ... Unpacking libpcre2-8-0:amd64 (10.42-1) over (10.36-2+deb11u1) ... Setting up libpcre2-8-0:amd64 (10.42-1) ... (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 ... 12821 files and directories currently installed.) Preparing to unpack .../libselinux1_3.4-1+b6_amd64.deb ... Unpacking libselinux1:amd64 (3.4-1+b6) over (3.1-3) ... Setting up libselinux1:amd64 (3.4-1+b6) ... (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 ... 12822 files and directories currently installed.) Preparing to unpack .../libmount1_2.38.1-5+b1_amd64.deb ... Unpacking libmount1:amd64 (2.38.1-5+b1) over (2.36.1-8+deb11u1) ... Setting up libmount1:amd64 (2.38.1-5+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 ... 12824 files and directories currently installed.) Preparing to unpack .../libsmartcols1_2.38.1-5+b1_amd64.deb ... Unpacking libsmartcols1:amd64 (2.38.1-5+b1) over (2.36.1-8+deb11u1) ... Setting up libsmartcols1:amd64 (2.38.1-5+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 ... 12826 files and directories currently installed.) Preparing to unpack .../util-linux_2.38.1-5+b1_amd64.deb ... Unpacking util-linux (2.38.1-5+b1) over (2.36.1-8+deb11u1) ... 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 Selecting previously unselected package util-linux-extra. Preparing to unpack .../util-linux-extra_2.38.1-5+b1_amd64.deb ... Unpacking util-linux-extra (2.38.1-5+b1) ... Setting up util-linux-extra (2.38.1-5+b1) ... (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 ... 12840 files and directories currently installed.) Preparing to unpack .../libstdc++6_12.2.0-14_amd64.deb ... Unpacking libstdc++6:amd64 (12.2.0-14) over (10.2.1-6) ... Setting up libstdc++6:amd64 (12.2.0-14) ... (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 ... 12840 files and directories currently installed.) Preparing to unpack .../liblz4-1_1.9.4-1_amd64.deb ... Unpacking liblz4-1:amd64 (1.9.4-1) over (1.9.3-2) ... Setting up liblz4-1:amd64 (1.9.4-1) ... Selecting previously unselected package libcap2: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 ... 12840 files and directories currently installed.) Preparing to unpack .../libcap2_1%3a2.66-4_amd64.deb ... Unpacking libcap2:amd64 (1:2.66-4) ... Setting up libcap2:amd64 (1:2.66-4) ... (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 ... 12849 files and directories currently installed.) Preparing to unpack .../libudev1_252.22-1~deb12u1_amd64.deb ... Unpacking libudev1:amd64 (252.22-1~deb12u1) over (247.3-7+deb11u4) ... Setting up libudev1:amd64 (252.22-1~deb12u1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 12850 files and directories currently installed.) Preparing to unpack .../libxxhash0_0.8.1-1_amd64.deb ... Unpacking libxxhash0:amd64 (0.8.1-1) over (0.8.0-2) ... Setting up libxxhash0:amd64 (0.8.1-1) ... (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 ... 12850 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0_2.6.1_amd64.deb ... Unpacking libapt-pkg6.0:amd64 (2.6.1) over (2.2.4) ... Setting up libapt-pkg6.0:amd64 (2.6.1) ... (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 ... 12850 files and directories currently installed.) Preparing to unpack .../libnettle8_3.8.1-2_amd64.deb ... Unpacking libnettle8:amd64 (3.8.1-2) over (3.7.3-1) ... Setting up libnettle8:amd64 (3.8.1-2) ... (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 ... 12850 files and directories currently installed.) Preparing to unpack .../libhogweed6_3.8.1-2_amd64.deb ... Unpacking libhogweed6:amd64 (3.8.1-2) over (3.7.3-1) ... Setting up libhogweed6:amd64 (3.8.1-2) ... (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 ... 12850 files and directories currently installed.) Preparing to unpack .../libunistring2_1.0-2_amd64.deb ... Unpacking libunistring2:amd64 (1.0-2) over (0.9.10-4) ... Setting up libunistring2:amd64 (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 ... 12850 files and directories currently installed.) Preparing to unpack .../libidn2-0_2.3.3-1+b1_amd64.deb ... Unpacking libidn2-0:amd64 (2.3.3-1+b1) over (2.3.0-5) ... Setting up libidn2-0:amd64 (2.3.3-1+b1) ... Selecting previously unselected package libffi8: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 ... 12852 files and directories currently installed.) Preparing to unpack .../libffi8_3.4.4-1_amd64.deb ... Unpacking libffi8:amd64 (3.4.4-1) ... Setting up libffi8:amd64 (3.4.4-1) ... (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 ... 12857 files and directories currently installed.) Preparing to unpack .../libp11-kit0_0.24.1-2_amd64.deb ... Unpacking libp11-kit0:amd64 (0.24.1-2) over (0.23.22-1) ... Setting up libp11-kit0:amd64 (0.24.1-2) ... (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 ... 12857 files and directories currently installed.) Preparing to unpack .../libtasn1-6_4.19.0-2_amd64.deb ... Unpacking libtasn1-6:amd64 (4.19.0-2) over (4.16.0-2+deb11u1) ... Setting up libtasn1-6:amd64 (4.19.0-2) ... (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 ... 12857 files and directories currently installed.) Preparing to unpack .../libgnutls30_3.7.9-2+deb12u2_amd64.deb ... Unpacking libgnutls30:amd64 (3.7.9-2+deb12u2) over (3.7.1-5+deb11u4) ... Setting up libgnutls30:amd64 (3.7.9-2+deb12u2) ... (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 ... 12859 files and directories currently installed.) Preparing to unpack .../libsemanage-common_3.4-1_all.deb ... Unpacking libsemanage-common (3.4-1) over (3.1-1) ... Setting up libsemanage-common (3.4-1) ... Installing new version of config file /etc/selinux/semanage.conf ... Selecting previously unselected package libsepol2: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 ... 12859 files and directories currently installed.) Preparing to unpack .../libsepol2_3.4-2.1_amd64.deb ... Unpacking libsepol2:amd64 (3.4-2.1) ... Setting up libsepol2:amd64 (3.4-2.1) ... Selecting previously unselected package libsemanage2: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 ... 12863 files and directories currently installed.) Preparing to unpack .../libsemanage2_3.4-1+b5_amd64.deb ... Unpacking libsemanage2:amd64 (3.4-1+b5) ... Setting up libsemanage2:amd64 (3.4-1+b5) ... (Reading database ... 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Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-buster-stable.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bullseye-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bullseye-security-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bullseye-stable.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bookworm-stable.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bookworm-security-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-bookworm-automatic.gpg ... (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 ... 12872 files and directories currently installed.) Preparing to unpack .../libnumber-compare-perl_0.03-3_all.deb ... Unpacking libnumber-compare-perl (0.03-3) ... Setting up libnumber-compare-perl (0.03-3) ... Selecting previously unselected package libtext-glob-perl. (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 ... 12886 files and directories currently installed.) Preparing to unpack .../libfile-find-rule-perl_0.34-3_all.deb ... Unpacking libfile-find-rule-perl (0.34-3) ... Setting up perl-modules-5.36 (5.36.0-7+deb12u1) ... Setting up libgdbm6:amd64 (1.23-3) ... Setting up libgdbm-compat4:amd64 (1.23-3) ... Setting up libperl5.36:amd64 (5.36.0-7+deb12u1) ... Setting up perl (5.36.0-7+deb12u1) ... Setting up libfile-find-rule-perl (0.34-3) ... Selecting previously unselected package usrmerge. (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 ... 12901 files and directories currently installed.) Preparing to unpack .../usrmerge_37~deb12u1_all.deb ... Unpacking usrmerge (37~deb12u1) ... Setting up usrmerge (37~deb12u1) ... (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 ... 12909 files and directories currently installed.) Preparing to unpack .../0-e2fsprogs_1.47.0-2_amd64.deb ... Unpacking e2fsprogs (1.47.0-2) over (1.46.2-2) ... Preparing to unpack .../1-mount_2.38.1-5+b1_amd64.deb ... Unpacking mount (2.38.1-5+b1) over (2.36.1-8+deb11u1) ... Selecting previously unselected package libssl3:amd64. Preparing to unpack .../2-libssl3_3.0.11-1~deb12u2_amd64.deb ... Unpacking libssl3:amd64 (3.0.11-1~deb12u2) ... 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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 ... 13236 files and directories currently installed.) Preparing to unpack .../00-python3_3.11.2-1+b1_amd64.deb ... Unpacking python3 (3.11.2-1+b1) over (3.9.2-3) ... Preparing to unpack .../01-libyaml-0-2_0.2.5-1_amd64.deb ... Unpacking libyaml-0-2:amd64 (0.2.5-1) over (0.2.2-1) ... Preparing to unpack .../02-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) over (4.0.0) ... Preparing to unpack .../03-readline-common_8.2-1.3_all.deb ... 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Unpacking libkrb5support0:amd64 (1.20.1-2+deb12u1) over (1.18.3-6+deb11u4) ... Preparing to unpack .../11-libcom-err2_1.47.0-2_amd64.deb ... Unpacking libcom-err2:amd64 (1.47.0-2) over (1.46.2-2) ... Preparing to unpack .../12-libkeyutils1_1.6.3-2_amd64.deb ... Unpacking libkeyutils1:amd64 (1.6.3-2) over (1.6.1-2) ... Preparing to unpack .../13-libtirpc3_1.3.3+ds-1_amd64.deb ... Unpacking libtirpc3:amd64 (1.3.3+ds-1) over (1.3.1-1+deb11u1) ... Preparing to unpack .../14-libuuid1_2.38.1-5+b1_amd64.deb ... Unpacking libuuid1:amd64 (2.38.1-5+b1) over (2.36.1-8+deb11u1) ... Setting up libuuid1:amd64 (2.38.1-5+b1) ... Selecting previously unselected package libpython3.11-stdlib: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 ... 13243 files and directories currently installed.) Preparing to unpack .../libpython3.11-stdlib_3.11.2-6_amd64.deb ... Unpacking libpython3.11-stdlib:amd64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../python3.11_3.11.2-6_amd64.deb ... Unpacking python3.11 (3.11.2-6) ... Preparing to unpack .../libpython3-stdlib_3.11.2-1+b1_amd64.deb ... Unpacking libpython3-stdlib:amd64 (3.11.2-1+b1) over (3.9.2-3) ... 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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 ... 13618 files and directories currently installed.) Preparing to unpack .../libattr1_1%3a2.5.1-4_amd64.deb ... Unpacking libattr1:amd64 (1:2.5.1-4) over (1:2.4.48-6) ... Setting up libattr1:amd64 (1:2.5.1-4) ... Installing new version of config file /etc/xattr.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 ... 13619 files and directories currently installed.) Preparing to unpack .../libpcre3_2%3a8.39-15_amd64.deb ... Unpacking libpcre3:amd64 (2:8.39-15) over (2:8.39-13) ... Setting up libpcre3:amd64 (2:8.39-15) ... (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 ... 13619 files and directories currently installed.) Preparing to unpack .../00-mawk_1.3.4.20200120-3.1_amd64.deb ... Unpacking mawk (1.3.4.20200120-3.1) over (1.3.4.20200120-2) ... Preparing to unpack .../01-tzdata_2024a-0+deb12u1_all.deb ... Unpacking tzdata (2024a-0+deb12u1) over (2024a-0+deb11u1) ... Selecting previously unselected package openssl. Preparing to unpack .../02-openssl_3.0.11-1~deb12u2_amd64.deb ... Unpacking openssl (3.0.11-1~deb12u2) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../03-ca-certificates_20230311_all.deb ... Unpacking ca-certificates (20230311) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../04-libblas3_3.11.0-2_amd64.deb ... Unpacking libblas3:amd64 (3.11.0-2) ... Selecting previously unselected package libquadmath0:amd64. Preparing to unpack .../05-libquadmath0_12.2.0-14_amd64.deb ... Unpacking libquadmath0:amd64 (12.2.0-14) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../06-libgfortran5_12.2.0-14_amd64.deb ... Unpacking libgfortran5:amd64 (12.2.0-14) ... Preparing to unpack .../07-libgomp1_12.2.0-14_amd64.deb ... Unpacking libgomp1:amd64 (12.2.0-14) over (10.2.1-6) ... Preparing to unpack .../08-libjs-jquery_3.6.1+dfsg+~3.5.14-1_all.deb ... Unpacking libjs-jquery (3.6.1+dfsg+~3.5.14-1) over (3.5.1+dfsg+~3.5.5-7) ... Preparing to unpack .../09-libjs-underscore_1.13.4~dfsg+~1.11.4-3_all.deb ... Unpacking libjs-underscore (1.13.4~dfsg+~1.11.4-3) over (1.9.1~dfsg-3) ... Preparing to unpack .../10-libjs-sphinxdoc_5.3.0-4_all.deb ... Unpacking libjs-sphinxdoc (5.3.0-4) over (3.4.3-2) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../11-liblapack3_3.11.0-2_amd64.deb ... Unpacking liblapack3:amd64 (3.11.0-2) ... Selecting previously unselected package libmbedcrypto7:amd64. Preparing to unpack .../12-libmbedcrypto7_2.28.3-1_amd64.deb ... Unpacking libmbedcrypto7:amd64 (2.28.3-1) ... Selecting previously unselected package libmbedx509-1:amd64. Preparing to unpack .../13-libmbedx509-1_2.28.3-1_amd64.deb ... Unpacking libmbedx509-1:amd64 (2.28.3-1) ... Selecting previously unselected package libmbedtls14:amd64. Preparing to unpack .../14-libmbedtls14_2.28.3-1_amd64.deb ... Unpacking libmbedtls14:amd64 (2.28.3-1) ... Preparing to unpack .../15-libss2_1.47.0-2_amd64.deb ... Unpacking libss2:amd64 (1.47.0-2) over (1.46.2-2) ... Selecting previously unselected package python3-certifi. Preparing to unpack .../16-python3-certifi_2022.9.24-1_all.deb ... Unpacking python3-certifi (2022.9.24-1) ... Selecting previously unselected package python3-colorama. Preparing to unpack .../17-python3-colorama_0.4.6-2_all.deb ... Unpacking python3-colorama (0.4.6-2) ... Preparing to unpack .../18-python3-colorlog_6.7.0-1_all.deb ... Unpacking python3-colorlog (6.7.0-1) over (4.7.2-1) ... Preparing to unpack .../19-python3-pkg-resources_66.1.1-1_all.deb ... Unpacking python3-pkg-resources (66.1.1-1) over (52.0.0-4) ... Preparing to unpack .../20-python3-networkx_2.8.8-1_all.deb ... Unpacking python3-networkx (2.8.8-1) over (2.5+ds-2) ... Preparing to unpack .../21-python3-packaging_23.0-1_all.deb ... Unpacking python3-packaging (23.0-1) over (20.9-2) ... Selecting previously unselected package python3-six. Preparing to unpack .../22-python3-six_1.16.0-4_all.deb ... Unpacking python3-six (1.16.0-4) ... Selecting previously unselected package python3-dateutil. Preparing to unpack .../23-python3-dateutil_2.8.2-2_all.deb ... Unpacking python3-dateutil (2.8.2-2) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../24-python3-numpy_1%3a1.24.2-1_amd64.deb ... Unpacking python3-numpy (1:1.24.2-1) ... Selecting previously unselected package python3-tz. Preparing to unpack .../25-python3-tz_2022.7.1-4_all.deb ... Unpacking python3-tz (2022.7.1-4) ... Selecting previously unselected package python3-pandas-lib:amd64. Preparing to unpack .../26-python3-pandas-lib_1.5.3+dfsg-2_amd64.deb ... Unpacking python3-pandas-lib:amd64 (1.5.3+dfsg-2) ... Selecting previously unselected package python3-pandas. Preparing to unpack .../27-python3-pandas_1.5.3+dfsg-2_all.deb ... Unpacking python3-pandas (1.5.3+dfsg-2) ... Preparing to unpack .../28-sphinx-rtd-theme-common_1.2.0+dfsg-1_all.deb ... Unpacking sphinx-rtd-theme-common (1.2.0+dfsg-1) over (0.5.1+dfsg-1) ... Preparing to unpack .../29-ncbi-data_6.1.20170106+dfsg1-10_all.deb ... Unpacking ncbi-data (6.1.20170106+dfsg1-10) over (6.1.20170106+dfsg1-9) ... Preparing to unpack .../30-ncbi-blast+_2.12.0+ds-3+b1_amd64.deb ... Unpacking ncbi-blast+ (2.12.0+ds-3+b1) over (2.11.0+ds-1) ... Preparing to unpack .../31-macsyfinder_2.0-2+b1_amd64.deb ... Unpacking macsyfinder (2.0-2+b1) over (2.0~rc1-3+b1) ... dpkg: warning: unable to delete old directory '/etc/macsyfinder': Directory not empty Preparing to unpack .../32-python3-decorator_5.1.1-3_all.deb ... Unpacking python3-decorator (5.1.1-3) over (4.4.2-2) ... Preparing to unpack .../33-python3-pyparsing_3.0.9-1_all.deb ... Unpacking python3-pyparsing (3.0.9-1) over (2.4.7-1) ... Setting up media-types (10.0.0) ... Installing new version of config file /etc/mime.types ... Setting up ncbi-data (6.1.20170106+dfsg1-10) ... Installing new version of config file /etc/ncbi/.ncbirc ... Setting up lsb-base (11.6) ... Setting up libkeyutils1:amd64 (1.6.3-2) ... Setting up libyaml-0-2:amd64 (0.2.5-1) ... Setting up libtirpc-common (1.3.3+ds-1) ... Setting up libsqlite3-0:amd64 (3.40.1-2) ... Setting up libcom-err2:amd64 (1.47.0-2) ... Setting up libgomp1:amd64 (12.2.0-14) ... Setting up libkrb5support0:amd64 (1.20.1-2+deb12u1) ... Setting up tzdata (2024a-0+deb12u1) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Mar 1 06:46:22 UTC 2024. Universal Time is now: Fri Mar 1 06:46:22 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. 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 libmbedcrypto7:amd64 (2.28.3-1) ... Setting up libquadmath0:amd64 (12.2.0-14) ... Setting up libss2:amd64 (1.47.0-2) ... Setting up util-linux (2.38.1-5+b1) ... Setting up libncursesw6:amd64 (6.4-4) ... Setting up libk5crypto3:amd64 (1.20.1-2+deb12u1) ... Setting up logsave (1.47.0-2) ... Setting up libgfortran5:amd64 (12.2.0-14) ... Setting up mount (2.38.1-5+b1) ... Setting up mawk (1.3.4.20200120-3.1) ... Setting up libkrb5-3:amd64 (1.20.1-2+deb12u1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up openssl (3.0.11-1~deb12u2) ... Setting up readline-common (8.2-1.3) ... Setting up sphinx-rtd-theme-common (1.2.0+dfsg-1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... 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 libmbedx509-1:amd64 (2.28.3-1) ... Setting up libmbedtls14:amd64 (2.28.3-1) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up e2fsprogs (1.47.0-2) ... Installing new version of config file /etc/mke2fs.conf ... 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 libjs-sphinxdoc (5.3.0-4) ... Setting up libtirpc3:amd64 (1.3.3+ds-1) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6) ... Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6) ... Setting up python3 (3.11.2-1+b1) ... Setting up python3-tz (2022.7.1-4) ... Setting up ncbi-blast+ (2.12.0+ds-3+b1) ... Setting up python3-six (1.16.0-4) ... Setting up python3-decorator (5.1.1-3) ... Setting up python3-packaging (23.0-1) ... Setting up python3-pyparsing (3.0.9-1) ... Setting up python3-certifi (2022.9.24-1) ... Setting up python3-dateutil (2.8.2-2) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-colorama (0.4.6-2) ... Setting up python3-colorlog (6.7.0-1) ... Setting up python3-yaml (6.0-3+b2) ... Setting up python3-networkx (2.8.8-1) ... Setting up python3-numpy (1:1.24.2-1) ... Setting up python3-pandas-lib:amd64 (1.5.3+dfsg-2) ... Setting up python3-pandas (1.5.3+dfsg-2) ... Setting up macsyfinder (2.0-2+b1) ... Processing triggers for libc-bin (2.36-9+deb12u4) ... Processing triggers for debianutils (5.7-0.5~deb12u1) ... Processing triggers for ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 1m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-get', '-yf', 'dist-upgrade'] 1m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m5.0s DUMP: 0942a352c5bc637c4fdbc12bf31cd5ba - 1m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-cache', 'show', '--no-all-versions', 'macsyfinder'] 1m5.3s DUMP: Package: macsyfinder Source: macsyfinder (2.0-2) Version: 2.0-2+b1 Installed-Size: 31261 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3-certifi, python3-colorama, python3-colorlog, python3-networkx, python3-packaging, python3-pandas, python3-yaml, python3:any, libjs-sphinxdoc (>= 5.2), sphinx-rtd-theme-common (>= 1.2.0+dfsg), hmmer, ncbi-blast+, libjs-jquery, libjs-underscore Description-en: detection of macromolecular systems in protein datasets MacSyFinder is a program to model and detect macromolecular systems, genetic pathways... in protein datasets. In prokaryotes, these systems have often evolutionarily conserved properties: they are made of conserved components, and are encoded in compact loci (conserved genetic architecture). The user models these systems with MacSyFinder to reflect these conserved features, and to allow their efficient detection . This package presents the Open Source Java API to biological databases and a series of mostly sequence-based algorithms. Description-md5: 0b9b635e7d46ea6cf9f81df42e76fb60 Homepage: https://github.com/gem-pasteur/macsyfinder Built-Using: sphinx (= 5.3.0-4) Section: science Priority: optional Filename: pool/main/m/macsyfinder/macsyfinder_2.0-2+b1_amd64.deb Size: 12092624 MD5sum: eb2d3d59d82ebdf420a1f0583065830c SHA256: 4073d3a7cf9c56dc97a438914d67d8712235a6b16eb4dddc61b03e3da08013ea 1m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-cache', 'show', '--no-all-versions', 'macsyfinder'] 1m5.3s INFO: apt-cache knows about the following packages: macsyfinder 1m5.3s INFO: Running scripts pre_install 1m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_install_database-server'] 1m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_install_database-server'] 1m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_install_exceptions'] 1m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_install_exceptions'] 1m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_install_extras'] 1m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_install_extras'] 1m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_install_foreign_architecture'] 1m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_install_foreign_architecture'] 1m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-cache', 'policy'] 1m5.4s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.5,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 1m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-cache', 'policy'] 1m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-cache', 'policy', 'macsyfinder'] 1m5.4s DUMP: macsyfinder: Installed: 2.0-2+b1 Candidate: 2.0-2+b1 Version table: *** 2.0-2+b1 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 100 /var/lib/dpkg/status 1m5.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-cache', 'policy', 'macsyfinder'] 1m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-get', '-y', 'install', 'macsyfinder'] 1m6.0s DUMP: Reading package lists... Building dependency tree... Reading state information... macsyfinder is already the newest version (2.0-2+b1). The following packages were automatically installed and are no longer required: libmbedcrypto3 libmbedtls12 libmbedx509-0 libmpdec3 libperl5.32 libpython3.9-minimal libpython3.9-stdlib perl-modules-5.32 python3-decorator python3-pyparsing python3.9 python3.9-minimal Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-get', '-y', 'install', 'macsyfinder'] 1m6.0s INFO: Running scripts post_install 1m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_install_exceptions'] 1m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_install_exceptions'] 1m6.0s INFO: Running scripts post_distupgrade 1m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_distupgrade_exceptions'] 1m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_distupgrade_exceptions'] 1m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_distupgrade_zz_backports'] 1m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_distupgrade_zz_backports'] 1m6.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5'] 1m7.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5'] 1m7.2s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmp9qz_sxh5 to sid 1m7.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 1m7.2s INFO: Running scripts pre_distupgrade 1m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 1m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 1m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_distupgrade_exceptions'] 1m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_distupgrade_exceptions'] 1m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 1m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 1m7.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_distupgrade_zz_database-server'] 1m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_distupgrade_zz_database-server'] 1m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 1m7.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 1m7.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-get', 'update'] 1m11.8s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [198 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9874 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7210 kB] Fetched 17.3 MB in 4s (4840 kB/s) Reading package lists... 1m11.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-get', 'update'] 1m11.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-get', '-yf', 'dist-upgrade'] 1m58.7s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: gcc-12-base libmbedcrypto3 libmbedtls12 libmbedx509-0 libmpdec3 libperl5.32 libperl5.36 libpython3.9-minimal libpython3.9-stdlib libquadmath0 perl-modules-5.32 perl-modules-5.36 python3-decorator python3-pyparsing python3.9 python3.9-minimal Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libapt-pkg6.0 libcom-err2 libdb5.3 libss2 libssl3 libuuid1 The following NEW packages will be installed: gcc-14-base libapt-pkg6.0t64 libcom-err2t64 libdb5.3t64 libperl5.38 libpython3.12-minimal libpython3.12-stdlib libss2t64 libssl3t64 libunistring5 libuuid1t64 netbase perl-modules-5.38 python3.12 python3.12-minimal The following packages have been kept back: e2fsprogs libext2fs2 util-linux The following packages will be upgraded: adduser apt base-files base-passwd bash bsdutils ca-certificates coreutils dash debconf debian-archive-keyring debianutils diffutils dpkg findutils fonts-lato gcc-10-base gcc-12-base gcc-9-base gpgv grep hmmer hostname init-system-helpers libacl1 libattr1 libaudit-common libaudit1 libblas3 libblkid1 libbz2-1.0 libc-bin libc6 libcap-ng0 libcap2 libcrypt1 libdebconfclient0 libdivsufsort3 libexpat1 libffi8 libgcc-s1 libgcrypt20 libgdbm-compat4 libgdbm6 libgfortran5 libgmp10 libgnutls30 libgomp1 libgpg-error0 libgssapi-krb5-2 libhogweed6 libidn2-0 libjs-sphinxdoc libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblmdb0 liblz4-1 liblzma5 libmbedcrypto7 libmbedtls14 libmbedx509-1 libmd0 libmount1 libmpdec3 libncursesw6 libnettle8 libnsl2 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpcre2-8-0 libpcre3 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libquadmath0 libreadline8 libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsmartcols1 libsqlite3-0 libstdc++6 libsystemd0 libtasn1-6 libtinfo6 libtirpc-common libtirpc3 libudev1 libxxhash0 libzstd1 login logsave macsyfinder mawk media-types mount ncbi-blast+ ncurses-base ncurses-bin openssl passwd perl perl-base python3 python3-certifi python3-colorama python3-colorlog python3-dateutil python3-decorator python3-minimal python3-numpy python3-packaging python3-pandas python3-pandas-lib python3-pkg-resources python3-pyparsing python3-tz python3-yaml python3.11 python3.11-minimal readline-common sed sphinx-rtd-theme-common sysvinit-utils tar tzdata usrmerge util-linux-extra zlib1g 137 upgraded, 15 newly installed, 6 to remove and 3 not upgraded. Need to get 109 MB of archives. After this operation, 124 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 base-files amd64 13 [70.6 kB] Get:2 http://deb.debian.org/debian sid/main amd64 debianutils amd64 5.16 [88.9 kB] Get:3 http://deb.debian.org/debian sid/main amd64 bash amd64 5.2.21-2 [1492 kB] Get:4 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.39.3-6.1 [97.0 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libc6 amd64 2.37-15 [2750 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libc-bin amd64 2.37-15 [602 kB] Get:7 http://deb.debian.org/debian sid/main amd64 gcc-14-base amd64 14-20240221-2.1 [42.8 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 14-20240221-2.1 [72.2 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libgmp10 amd64 2:6.3.0+dfsg-2+b1 [559 kB] Get:10 http://deb.debian.org/debian sid/main amd64 coreutils amd64 9.4-3+b1 [2950 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libzstd1 amd64 1.5.5+dfsg2-2 [295 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 14-20240221-2.1 [713 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libbz2-1.0 amd64 1.0.8-5+b2 [38.2 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libgpg-error0 amd64 1.47-3 [77.8 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libgcrypt20 amd64 1.10.3-2 [708 kB] Get:16 http://deb.debian.org/debian sid/main amd64 liblz4-1 amd64 1.9.4-1+b2 [61.6 kB] Get:17 http://deb.debian.org/debian sid/main amd64 liblzma5 amd64 5.6.0-0.2 [250 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libcap2 amd64 1:2.66-5 [27.4 kB] Get:19 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 255.4-1 [364 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 255.4-1 [125 kB] Get:21 http://deb.debian.org/debian sid/main amd64 libxxhash0 amd64 0.8.2-2+b1 [26.6 kB] Get:22 http://deb.debian.org/debian sid/main amd64 zlib1g amd64 1:1.3.dfsg-3+b1 [87.8 kB] Get:23 http://deb.debian.org/debian sid/main amd64 libnettle8 amd64 3.9.1-2+b1 [296 kB] Get:24 http://deb.debian.org/debian sid/main amd64 libp11-kit0 amd64 0.25.3-4 [418 kB] Get:25 http://deb.debian.org/debian sid/main amd64 libunistring5 amd64 1.1-2 [421 kB] Get:26 http://deb.debian.org/debian sid/main amd64 libgnutls30 amd64 3.8.3-1 [1425 kB] Get:27 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0t64 amd64 2.7.13 [984 kB] Get:28 http://deb.debian.org/debian sid/main amd64 apt amd64 2.7.13 [1367 kB] Get:29 http://deb.debian.org/debian sid/main amd64 tar amd64 1.35+dfsg-3 [813 kB] Get:30 http://deb.debian.org/debian sid/main amd64 dpkg amd64 1.22.5 [1510 kB] Get:31 http://deb.debian.org/debian sid/main amd64 dash amd64 0.5.12-6 [92.1 kB] Get:32 http://deb.debian.org/debian sid/main amd64 diffutils amd64 1:3.10-1 [375 kB] Get:33 http://deb.debian.org/debian sid/main amd64 findutils amd64 4.9.0-5 [636 kB] Get:34 http://deb.debian.org/debian sid/main amd64 grep amd64 3.11-4 [431 kB] Get:35 http://deb.debian.org/debian sid/main amd64 hostname amd64 3.23+nmu2 [10.6 kB] Get:36 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.13+dfsg1-4 [616 kB] Get:37 http://deb.debian.org/debian sid/main amd64 libncursesw6 amd64 6.4+20240113-1 [135 kB] Get:38 http://deb.debian.org/debian sid/main amd64 libtinfo6 amd64 6.4+20240113-1 [342 kB] Get:39 http://deb.debian.org/debian sid/main amd64 ncurses-bin amd64 6.4+20240113-1 [431 kB] Get:40 http://deb.debian.org/debian sid/main amd64 perl-modules-5.38 all 5.38.2-3 [2899 kB] Get:41 http://deb.debian.org/debian sid/main amd64 libperl5.38 amd64 5.38.2-3 [4275 kB] Get:42 http://deb.debian.org/debian sid/main amd64 perl amd64 5.38.2-3 [236 kB] Get:43 http://deb.debian.org/debian sid/main amd64 perl-base amd64 5.38.2-3 [1643 kB] Get:44 http://deb.debian.org/debian sid/main amd64 libcrypt1 amd64 1:4.4.36-4 [89.8 kB] Get:45 http://deb.debian.org/debian sid/main amd64 media-types all 10.1.0 [26.9 kB] Get:46 http://deb.debian.org/debian sid/main amd64 python3.11 amd64 3.11.8-2 [597 kB] Get:47 http://deb.debian.org/debian sid/main amd64 libexpat1 amd64 2.6.0-1 [101 kB] Get:48 http://deb.debian.org/debian sid/main amd64 python3.11-minimal amd64 3.11.8-2 [2037 kB] Get:49 http://deb.debian.org/debian sid/main amd64 openssl amd64 3.1.5-1.1 [1241 kB] Get:50 http://deb.debian.org/debian sid/main amd64 libgssapi-krb5-2 amd64 1.20.1-5+b1 [135 kB] Get:51 http://deb.debian.org/debian sid/main amd64 libkrb5-3 amd64 1.20.1-5+b1 [333 kB] Get:52 http://deb.debian.org/debian sid/main amd64 libk5crypto3 amd64 1.20.1-5+b1 [80.0 kB] Get:53 http://deb.debian.org/debian sid/main amd64 libkrb5support0 amd64 1.20.1-5+b1 [33.2 kB] Get:54 http://deb.debian.org/debian sid/main amd64 libss2t64 amd64 1.47.0-2.2 [24.8 kB] Get:55 http://deb.debian.org/debian sid/main amd64 libcom-err2t64 amd64 1.47.0-2.2 [20.1 kB] Get:56 http://deb.debian.org/debian sid/main amd64 libkeyutils1 amd64 1.6.3-3 [8952 B] Get:57 http://deb.debian.org/debian sid/main amd64 libssl3t64 amd64 3.1.5-1.1 [2058 kB] Get:58 http://deb.debian.org/debian sid/main amd64 libpython3.11-stdlib amd64 3.11.8-2 [1827 kB] Get:59 http://deb.debian.org/debian sid/main amd64 libpython3.11-minimal amd64 3.11.8-2 [817 kB] Get:60 http://deb.debian.org/debian sid/main amd64 netbase all 6.4 [12.8 kB] Get:61 http://deb.debian.org/debian sid/main amd64 debconf all 1.5.86 [119 kB] Get:62 http://deb.debian.org/debian sid/main amd64 tzdata all 2024a-1 [255 kB] Get:63 http://deb.debian.org/debian sid/main amd64 libffi8 amd64 3.4.6-1 [23.6 kB] Get:64 http://deb.debian.org/debian sid/main amd64 libtirpc-common all 1.3.4+ds-1.1 [10.8 kB] Get:65 http://deb.debian.org/debian sid/main amd64 libtirpc3 amd64 1.3.4+ds-1 [82.1 kB] Get:66 http://deb.debian.org/debian sid/main amd64 libnsl2 amd64 1.3.0-3 [40.0 kB] Get:67 http://deb.debian.org/debian sid/main amd64 readline-common all 8.2-3 [69.1 kB] Get:68 http://deb.debian.org/debian sid/main amd64 libreadline8 amd64 8.2-3+b1 [167 kB] Get:69 http://deb.debian.org/debian sid/main amd64 libsqlite3-0 amd64 3.45.1-1 [894 kB] Get:70 http://deb.debian.org/debian sid/main amd64 libuuid1t64 amd64 2.39.3-6.1 [30.0 kB] Get:71 http://deb.debian.org/debian sid/main amd64 libaudit-common all 1:3.1.2-2.1 [11.4 kB] Get:72 http://deb.debian.org/debian sid/main amd64 libcap-ng0 amd64 0.8.4-2 [16.9 kB] Get:73 http://deb.debian.org/debian sid/main amd64 libaudit1 amd64 1:3.1.2-2.1 [48.5 kB] Get:74 http://deb.debian.org/debian sid/main amd64 libpam0g amd64 1.5.3-6 [67.7 kB] Get:75 http://deb.debian.org/debian sid/main amd64 libpcre2-8-0 amd64 10.42-4+b1 [262 kB] Get:76 http://deb.debian.org/debian sid/main amd64 libselinux1 amd64 3.5-2 [74.8 kB] Get:77 http://deb.debian.org/debian sid/main amd64 libpam-modules-bin amd64 1.5.3-6 [54.2 kB] Get:78 http://deb.debian.org/debian sid/main amd64 libpam-modules amd64 1.5.3-6 [260 kB] Get:79 http://deb.debian.org/debian sid/main amd64 libdb5.3t64 amd64 5.3.28+dfsg2-5 [697 kB] Get:80 http://deb.debian.org/debian sid/main amd64 libgdbm6 amd64 1.23-5+b1 [72.8 kB] Get:81 http://deb.debian.org/debian sid/main amd64 libgdbm-compat4 amd64 1.23-5+b1 [48.5 kB] Get:82 http://deb.debian.org/debian sid/main amd64 sed amd64 4.9-2 [329 kB] Get:83 http://deb.debian.org/debian sid/main amd64 libhogweed6 amd64 3.9.1-2+b1 [328 kB] Get:84 http://deb.debian.org/debian sid/main amd64 libidn2-0 amd64 2.3.7-2 [128 kB] Get:85 http://deb.debian.org/debian sid/main amd64 libtasn1-6 amd64 4.19.0-3+b2 [48.9 kB] Get:86 http://deb.debian.org/debian sid/main amd64 libdebconfclient0 amd64 0.271+b1 [10.2 kB] Get:87 http://deb.debian.org/debian sid/main amd64 base-passwd amd64 3.6.3 [50.8 kB] Get:88 http://deb.debian.org/debian sid/main amd64 libsemanage-common all 3.5-1 [9908 B] Get:89 http://deb.debian.org/debian sid/main amd64 libsepol2 amd64 3.5-2 [277 kB] Get:90 http://deb.debian.org/debian sid/main amd64 libsemanage2 amd64 3.5-1+b2 [90.3 kB] Get:91 http://deb.debian.org/debian sid/main amd64 passwd amd64 1:4.13+dfsg1-4 [973 kB] Get:92 http://deb.debian.org/debian sid/main amd64 adduser all 3.137 [140 kB] Get:93 http://deb.debian.org/debian sid/main amd64 gpgv amd64 2.2.40-1.1+b1 [649 kB] Get:94 http://deb.debian.org/debian sid/main amd64 debian-archive-keyring all 2023.4 [161 kB] Get:95 http://deb.debian.org/debian sid/main amd64 libseccomp2 amd64 2.5.5-1 [47.0 kB] Get:96 http://deb.debian.org/debian sid/main amd64 usrmerge all 39 [13.1 kB] Get:97 http://deb.debian.org/debian sid/main amd64 init-system-helpers all 1.66 [39.0 kB] Get:98 http://deb.debian.org/debian sid/main amd64 ncurses-base all 6.4+20240113-1 [268 kB] Get:99 http://deb.debian.org/debian sid/main amd64 sysvinit-utils amd64 3.08-7 [32.2 kB] Get:100 http://deb.debian.org/debian sid/main amd64 libblkid1 amd64 2.39.3-6.1 [159 kB] Get:101 http://deb.debian.org/debian sid/main amd64 libmount1 amd64 2.39.3-6.1 [191 kB] Get:102 http://deb.debian.org/debian sid/main amd64 mount amd64 2.39.3-6.1 [143 kB] Get:103 http://deb.debian.org/debian sid/main amd64 fonts-lato all 2.015-1 [2780 kB] Get:104 http://deb.debian.org/debian sid/main amd64 python3-pandas all 2.1.4+dfsg-5 [3015 kB] Get:105 http://deb.debian.org/debian sid/main amd64 python3-minimal amd64 3.11.6-1 [26.2 kB] Get:106 http://deb.debian.org/debian sid/main amd64 python3 amd64 3.11.6-1 [26.2 kB] Get:107 http://deb.debian.org/debian sid/main amd64 python3-dateutil all 2.8.2-3 [78.4 kB] Get:108 http://deb.debian.org/debian sid/main amd64 python3-pkg-resources all 68.1.2-2 [241 kB] Get:109 http://deb.debian.org/debian sid/main amd64 libpython3.12-minimal amd64 3.12.2-1 [807 kB] Get:110 http://deb.debian.org/debian sid/main amd64 python3.12-minimal amd64 3.12.2-1 [2186 kB] Get:111 http://deb.debian.org/debian sid/main amd64 libpython3.12-stdlib amd64 3.12.2-1 [1929 kB] Get:112 http://deb.debian.org/debian sid/main amd64 python3.12 amd64 3.12.2-1 [653 kB] Get:113 http://deb.debian.org/debian sid/main amd64 libblas3 amd64 3.12.0-3 [148 kB] Get:114 http://deb.debian.org/debian sid/main amd64 libgfortran5 amd64 14-20240221-2.1 [836 kB] Get:115 http://deb.debian.org/debian sid/main amd64 liblapack3 amd64 3.12.0-3 [2407 kB] Get:116 http://deb.debian.org/debian sid/main amd64 python3-numpy amd64 1:1.24.2-2 [6299 kB] Get:117 http://deb.debian.org/debian sid/main amd64 python3-tz all 2024.1-2 [30.9 kB] Get:118 http://deb.debian.org/debian sid/main amd64 python3-pandas-lib amd64 2.1.4+dfsg-5 [7883 kB] Get:119 http://deb.debian.org/debian sid/main amd64 libpython3-stdlib amd64 3.11.6-1 [9224 B] Get:120 http://deb.debian.org/debian sid/main amd64 libpam-runtime all 1.5.3-6 [140 kB] Get:121 http://deb.debian.org/debian sid/main amd64 libsmartcols1 amd64 2.39.3-6.1 [116 kB] Get:122 http://deb.debian.org/debian sid/main amd64 util-linux-extra amd64 2.39.3-6.1 [155 kB] Get:123 http://deb.debian.org/debian sid/main amd64 libacl1 amd64 2.3.2-1 [32.4 kB] Get:124 http://deb.debian.org/debian sid/main amd64 libattr1 amd64 1:2.5.2-1 [22.5 kB] Get:125 http://deb.debian.org/debian sid/main amd64 libmd0 amd64 1.1.0-2 [35.8 kB] Get:126 http://deb.debian.org/debian sid/main amd64 mawk amd64 1.3.4.20240123-1 [136 kB] Get:127 http://deb.debian.org/debian sid/main amd64 ca-certificates all 20240203 [158 kB] Get:128 http://deb.debian.org/debian sid/main amd64 gcc-10-base amd64 10.5.0-3 [36.6 kB] Get:129 http://deb.debian.org/debian sid/main amd64 libquadmath0 amd64 14-20240221-2.1 [147 kB] Get:130 http://deb.debian.org/debian sid/main amd64 libgomp1 amd64 14-20240221-2.1 [136 kB] Get:131 http://deb.debian.org/debian sid/main amd64 gcc-12-base amd64 12.3.0-14 [41.2 kB] Get:132 http://deb.debian.org/debian sid/main amd64 gcc-9-base amd64 9.5.0-5 [28.8 kB] Get:133 http://deb.debian.org/debian sid/main amd64 libdivsufsort3 amd64 2.0.1-6 [45.6 kB] Get:134 http://deb.debian.org/debian sid/main amd64 hmmer amd64 3.4+dfsg-2 [1062 kB] Get:135 http://deb.debian.org/debian sid/main amd64 libjs-sphinxdoc all 7.2.6-4 [150 kB] Get:136 http://deb.debian.org/debian sid/main amd64 liblmdb0 amd64 0.9.31-1+b1 [44.8 kB] Get:137 http://deb.debian.org/debian sid/main amd64 libmbedcrypto7 amd64 2.28.7-1 [280 kB] Get:138 http://deb.debian.org/debian sid/main amd64 libmbedx509-1 amd64 2.28.7-1 [130 kB] Get:139 http://deb.debian.org/debian sid/main amd64 libmbedtls14 amd64 2.28.7-1 [165 kB] Get:140 http://deb.debian.org/debian sid/main amd64 libmpdec3 amd64 2.5.1-2 [87.8 kB] Get:141 http://deb.debian.org/debian sid/main amd64 libpcre3 amd64 2:8.39-15+b1 [342 kB] Get:142 http://deb.debian.org/debian sid/main amd64 logsave amd64 1.47.0-2.2 [19.8 kB] Get:143 http://deb.debian.org/debian sid/main amd64 python3-certifi all 2023.11.17-1 [155 kB] Get:144 http://deb.debian.org/debian sid/main amd64 python3-colorama all 0.4.6-4 [36.2 kB] Get:145 http://deb.debian.org/debian sid/main amd64 python3-colorlog all 6.8.0-1 [26.6 kB] Get:146 http://deb.debian.org/debian sid/main amd64 python3-packaging all 23.2-1 [44.8 kB] Get:147 http://deb.debian.org/debian sid/main amd64 python3-yaml amd64 6.0.1-2 [177 kB] Get:148 http://deb.debian.org/debian sid/main amd64 sphinx-rtd-theme-common all 2.0.0+dfsg-1 [1021 kB] Get:149 http://deb.debian.org/debian sid/main amd64 ncbi-blast+ amd64 2.12.0+ds-4 [12.5 MB] Get:150 http://deb.debian.org/debian sid/main amd64 macsyfinder amd64 2.1.3-1 [14.5 MB] Get:151 http://deb.debian.org/debian sid/main amd64 python3-decorator all 5.1.1-5 [15.1 kB] Get:152 http://deb.debian.org/debian sid/main amd64 python3-pyparsing all 3.1.1-1 [145 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 109 MB in 1s (146 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 ... 16692 files and directories currently installed.) Preparing to unpack .../libapt-pkg6.0t64_2.7.13_amd64.deb ... Unpacking libapt-pkg6.0t64:amd64 (2.7.13) ... Setting up libapt-pkg6.0t64:amd64 (2.7.13) ... (Reading database ... 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Installing new version of config file /etc/security/namespace.init ... dpkg: libdb5.3:amd64: dependency problems, but removing anyway as you requested: libpython3.9-stdlib:amd64 depends on libdb5.3. libperl5.38:amd64 depends on libdb5.3. libperl5.36:amd64 depends on libdb5.3. libperl5.32: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 ... 17909 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 ... 17903 files and directories currently installed.) Preparing to unpack .../libdb5.3t64_5.3.28+dfsg2-5_amd64.deb ... Unpacking libdb5.3t64:amd64 (5.3.28+dfsg2-5) ... Preparing to unpack .../libgdbm6_1.23-5+b1_amd64.deb ... Unpacking libgdbm6:amd64 (1.23-5+b1) over (1.23-3) ... Preparing to unpack .../libgdbm-compat4_1.23-5+b1_amd64.deb ... 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(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 17907 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 ... 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(Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 17905 files and directories currently installed.) Preparing to unpack .../libblkid1_2.39.3-6.1_amd64.deb ... Unpacking libblkid1:amd64 (2.39.3-6.1) over (2.38.1-5+b1) ... Setting up libblkid1:amd64 (2.39.3-6.1) ... (Reading database ... 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Setting up libpython3.11-minimal:amd64 (3.11.8-2) ... Setting up libexpat1:amd64 (2.6.0-1) ... Setting up python3.11-minimal (3.11.8-2) ... (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 ... 17902 files and directories currently installed.) Preparing to unpack .../python3-minimal_3.11.6-1_amd64.deb ... Unpacking python3-minimal (3.11.6-1) over (3.11.2-1+b1) ... Setting up python3-minimal (3.11.6-1) ... (Reading database ... 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Unpacking util-linux-extra (2.39.3-6.1) over (2.38.1-5+b1) ... 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 (2.39.3-6.1) ... (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 ... 18679 files and directories currently installed.) Preparing to unpack .../libacl1_2.3.2-1_amd64.deb ... Unpacking libacl1:amd64 (2.3.2-1) over (2.3.1-3) ... Setting up libacl1:amd64 (2.3.2-1) ... (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 ... 18679 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 ... 18679 files and directories currently installed.) Preparing to unpack .../libmd0_1.1.0-2_amd64.deb ... Unpacking libmd0:amd64 (1.1.0-2) over (1.0.4-2) ... Setting up libmd0:amd64 (1.1.0-2) ... (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 ... 18679 files and directories currently installed.) Preparing to unpack .../00-mawk_1.3.4.20240123-1_amd64.deb ... Unpacking mawk (1.3.4.20240123-1) over (1.3.4.20200120-3.1) ... Preparing to unpack .../01-ca-certificates_20240203_all.deb ... Unpacking ca-certificates (20240203) over (20230311) ... Preparing to unpack .../02-gcc-10-base_10.5.0-3_amd64.deb ... Unpacking gcc-10-base:amd64 (10.5.0-3) over (10.2.1-6) ... Preparing to unpack .../03-libquadmath0_14-20240221-2.1_amd64.deb ... Unpacking libquadmath0:amd64 (14-20240221-2.1) over (12.2.0-14) ... Preparing to unpack .../04-libgomp1_14-20240221-2.1_amd64.deb ... Unpacking libgomp1:amd64 (14-20240221-2.1) over (12.2.0-14) ... Preparing to unpack .../05-gcc-12-base_12.3.0-14_amd64.deb ... Unpacking gcc-12-base:amd64 (12.3.0-14) over (12.2.0-14) ... Preparing to unpack .../06-gcc-9-base_9.5.0-5_amd64.deb ... Unpacking gcc-9-base:amd64 (9.5.0-5) over (9.3.0-22) ... Preparing to unpack .../07-libdivsufsort3_2.0.1-6_amd64.deb ... Unpacking libdivsufsort3:amd64 (2.0.1-6) over (2.0.1-5) ... Preparing to unpack .../08-hmmer_3.4+dfsg-2_amd64.deb ... Unpacking hmmer (3.4+dfsg-2) over (3.3.2+dfsg-1) ... Preparing to unpack .../09-libjs-sphinxdoc_7.2.6-4_all.deb ... Unpacking libjs-sphinxdoc (7.2.6-4) over (5.3.0-4) ... Preparing to unpack .../10-liblmdb0_0.9.31-1+b1_amd64.deb ... Unpacking liblmdb0:amd64 (0.9.31-1+b1) over (0.9.24-1) ... Preparing to unpack .../11-libmbedcrypto7_2.28.7-1_amd64.deb ... Unpacking libmbedcrypto7:amd64 (2.28.7-1) over (2.28.3-1) ... Preparing to unpack .../12-libmbedx509-1_2.28.7-1_amd64.deb ... Unpacking libmbedx509-1:amd64 (2.28.7-1) over (2.28.3-1) ... Preparing to unpack .../13-libmbedtls14_2.28.7-1_amd64.deb ... Unpacking libmbedtls14:amd64 (2.28.7-1) over (2.28.3-1) ... Preparing to unpack .../14-libmpdec3_2.5.1-2_amd64.deb ... Unpacking libmpdec3:amd64 (2.5.1-2) over (2.5.1-1) ... Preparing to unpack .../15-libpcre3_2%3a8.39-15+b1_amd64.deb ... Unpacking libpcre3:amd64 (2:8.39-15+b1) over (2:8.39-15) ... Preparing to unpack .../16-logsave_1.47.0-2.2_amd64.deb ... Unpacking logsave (1.47.0-2.2) over (1.47.0-2) ... Preparing to unpack .../17-python3-certifi_2023.11.17-1_all.deb ... Unpacking python3-certifi (2023.11.17-1) over (2022.9.24-1) ... Preparing to unpack .../18-python3-colorama_0.4.6-4_all.deb ... Unpacking python3-colorama (0.4.6-4) over (0.4.6-2) ... Preparing to unpack .../19-python3-colorlog_6.8.0-1_all.deb ... Unpacking python3-colorlog (6.8.0-1) over (6.7.0-1) ... Preparing to unpack .../20-python3-packaging_23.2-1_all.deb ... Unpacking python3-packaging (23.2-1) over (23.0-1) ... Preparing to unpack .../21-python3-yaml_6.0.1-2_amd64.deb ... Unpacking python3-yaml (6.0.1-2) over (6.0-3+b2) ... Preparing to unpack .../22-sphinx-rtd-theme-common_2.0.0+dfsg-1_all.deb ... Unpacking sphinx-rtd-theme-common (2.0.0+dfsg-1) over (1.2.0+dfsg-1) ... Preparing to unpack .../23-ncbi-blast+_2.12.0+ds-4_amd64.deb ... Unpacking ncbi-blast+ (2.12.0+ds-4) over (2.12.0+ds-3+b1) ... Preparing to unpack .../24-macsyfinder_2.1.3-1_amd64.deb ... Unpacking macsyfinder (2.1.3-1) over (2.0-2+b1) ... Preparing to unpack .../25-python3-decorator_5.1.1-5_all.deb ... Unpacking python3-decorator (5.1.1-5) over (5.1.1-3) ... Preparing to unpack .../26-python3-pyparsing_3.1.1-1_all.deb ... Unpacking python3-pyparsing (3.1.1-1) over (3.0.9-1) ... Setting up media-types (10.1.0) ... Installing new version of config file /etc/mime.types ... Setting up liblmdb0:amd64 (0.9.31-1+b1) ... Setting up libkeyutils1:amd64 (1.6.3-3) ... Setting up fonts-lato (2.015-1) ... Setting up libtirpc-common (1.3.4+ds-1.1) ... Setting up libsqlite3-0:amd64 (3.45.1-1) ... Setting up libpython3.12-minimal:amd64 (3.12.2-1) ... Setting up libgomp1:amd64 (14-20240221-2.1) ... Setting up libkrb5support0:amd64 (1.20.1-5+b1) ... Setting up gcc-12-base:amd64 (12.3.0-14) ... Setting up tzdata (2024a-1) ... Current default time zone: 'Etc/UTC' Local time is now: Fri Mar 1 06:47:09 UTC 2024. Universal Time is now: Fri Mar 1 06:47:09 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up gcc-10-base:amd64 (10.5.0-3) ... Setting up libpcre3:amd64 (2:8.39-15+b1) ... Setting up libblas3:amd64 (3.12.0-3) ... Setting up libcom-err2t64:amd64 (1.47.0-2.2) ... Setting up libmbedcrypto7:amd64 (2.28.7-1) ... Setting up libquadmath0:amd64 (14-20240221-2.1) ... Setting up libncursesw6:amd64 (6.4+20240113-1) ... Setting up libk5crypto3:amd64 (1.20.1-5+b1) ... Setting up libjs-sphinxdoc (7.2.6-4) ... Setting up logsave (1.47.0-2.2) ... Setting up libgfortran5:amd64 (14-20240221-2.1) ... Setting up mount (2.39.3-6.1) ... Setting up libmpdec3:amd64 (2.5.1-2) ... Setting up netbase (6.4) ... Setting up mawk (1.3.4.20240123-1) ... Setting up libkrb5-3:amd64 (1.20.1-5+b1) ... Setting up libdivsufsort3:amd64 (2.0.1-6) ... Setting up openssl (3.1.5-1.1) ... Installing new version of config file /etc/ssl/openssl.cnf ... Setting up readline-common (8.2-3) ... Setting up sphinx-rtd-theme-common (2.0.0+dfsg-1) ... Setting up gcc-9-base:amd64 (9.5.0-5) ... Setting up python3.12-minimal (3.12.2-1) ... Setting up liblapack3:amd64 (3.12.0-3) ... Setting up libmbedx509-1:amd64 (2.28.7-1) ... Setting up libmbedtls14:amd64 (2.28.7-1) ... Setting up libreadline8:amd64 (8.2-3+b1) ... Setting up libss2t64:amd64 (1.47.0-2.2) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... rehash: warning: skipping ca-certificates.crt,it does not contain exactly one certificate or CRL 14 added, 8 removed; done. Setting up libgssapi-krb5-2:amd64 (1.20.1-5+b1) ... Setting up hmmer (3.4+dfsg-2) ... Setting up libtirpc3:amd64 (1.3.4+ds-1) ... Setting up libnsl2:amd64 (1.3.0-3) ... Setting up libpython3.12-stdlib:amd64 (3.12.2-1) ... Setting up libpython3.11-stdlib:amd64 (3.11.8-2) ... Setting up python3.12 (3.12.2-1) ... Setting up libpython3-stdlib:amd64 (3.11.6-1) ... Setting up python3.11 (3.11.8-2) ... Setting up python3 (3.11.6-1) ... Setting up python3-tz (2024.1-2) ... Setting up ncbi-blast+ (2.12.0+ds-4) ... Setting up python3-decorator (5.1.1-5) ... Setting up python3-packaging (23.2-1) ... Setting up python3-pyparsing (3.1.1-1) ... Setting up python3-certifi (2023.11.17-1) ... Setting up python3-dateutil (2.8.2-3) ... Setting up python3-pkg-resources (68.1.2-2) ... Setting up python3-colorama (0.4.6-4) ... Setting up python3-colorlog (6.8.0-1) ... Setting up python3-yaml (6.0.1-2) ... Setting up python3-numpy (1:1.24.2-2) ... Setting up python3-pandas-lib:amd64 (2.1.4+dfsg-5) ... Setting up python3-pandas (2.1.4+dfsg-5) ... Setting up macsyfinder (2.1.3-1) ... /usr/lib/python3/dist-packages/macsypy/scripts/macsyconfig.py:282: SyntaxWarning: invalid escape sequence '\_' """ Processing triggers for libc-bin (2.37-15) ... Processing triggers for debianutils (5.16) ... 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. 1m58.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-get', '-yf', 'dist-upgrade'] 1m58.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 2m0.1s DUMP: 3545097c7221f1b7eec7078f0200dd2c - 2m0.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 2m0.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-cache', 'show', '--no-all-versions', 'macsyfinder'] 2m0.4s DUMP: Package: macsyfinder Version: 2.1.3-1 Installed-Size: 37199 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3-certifi, python3-colorama, python3-colorlog, python3-networkx, python3-packaging, python3-pandas, python3-yaml, python3:any, libjs-jquery (>= 3.6.0), libjs-sphinxdoc (>= 7.2.2), sphinx-rtd-theme-common (>= 2.0.0+dfsg), hmmer, ncbi-blast+, libjs-underscore Description-en: detection of macromolecular systems in protein datasets MacSyFinder is a program to model and detect macromolecular systems, genetic pathways... in protein datasets. In prokaryotes, these systems have often evolutionarily conserved properties: they are made of conserved components, and are encoded in compact loci (conserved genetic architecture). The user models these systems with MacSyFinder to reflect these conserved features, and to allow their efficient detection . This package presents the Open Source Java API to biological databases and a series of mostly sequence-based algorithms. Description-md5: 0b9b635e7d46ea6cf9f81df42e76fb60 Homepage: https://github.com/gem-pasteur/macsyfinder Built-Using: sphinx (= 7.2.6-4) Section: science Priority: optional Filename: pool/main/m/macsyfinder/macsyfinder_2.1.3-1_amd64.deb Size: 14458980 MD5sum: b21001e1e848e73816a612730f8abd39 SHA256: 4b7ebb0ed5059881a77729f0fb7689a764cd4315d59121253e662478c399e6b6 2m0.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-cache', 'show', '--no-all-versions', 'macsyfinder'] 2m0.4s INFO: apt-cache knows about the following packages: macsyfinder 2m0.4s INFO: Running scripts pre_install 2m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_install_database-server'] 2m0.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_install_database-server'] 2m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_install_exceptions'] 2m0.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_install_exceptions'] 2m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_install_extras'] 2m0.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_install_extras'] 2m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_install_foreign_architecture'] 2m0.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_install_foreign_architecture'] 2m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m0.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-cache', 'policy'] 2m0.5s 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: 2m0.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-cache', 'policy'] 2m0.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-cache', 'policy', 'macsyfinder'] 2m0.5s DUMP: macsyfinder: Installed: 2.1.3-1 Candidate: 2.1.3-1 Version table: *** 2.1.3-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 2m0.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-cache', 'policy', 'macsyfinder'] 2m0.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-get', '-y', 'install', 'macsyfinder'] 2m1.1s DUMP: Reading package lists... Building dependency tree... Reading state information... macsyfinder is already the newest version (2.1.3-1). The following packages were automatically installed and are no longer required: gcc-12-base libmbedcrypto3 libmbedtls12 libmbedx509-0 libmpdec3 libperl5.32 libperl5.36 libpython3.9-minimal libpython3.9-stdlib libquadmath0 perl-modules-5.32 perl-modules-5.36 python3-decorator python3-pyparsing python3.9 python3.9-minimal Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded. 2m1.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-get', '-y', 'install', 'macsyfinder'] 2m1.1s INFO: Running scripts post_install 2m1.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_install_exceptions'] 2m1.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_install_exceptions'] 2m1.1s INFO: Running scripts post_distupgrade 2m1.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_distupgrade_base_cleanup'] 2m1.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_distupgrade_base_cleanup'] 2m1.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_distupgrade_exceptions'] 2m1.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_distupgrade_exceptions'] 2m1.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 2m1.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 2m1.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_distupgrade_squeeze-backports'] 2m1.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_distupgrade_squeeze-backports'] 2m1.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_distupgrade_zz_backports'] 2m1.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_distupgrade_zz_backports'] 2m1.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5'] 2m2.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5'] 2m2.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5'] 2m4.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5'] 2m4.1s INFO: Running scripts pre_install 2m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_install_database-server'] 2m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_install_database-server'] 2m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_install_exceptions'] 2m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_install_exceptions'] 2m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_install_extras'] 2m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_install_extras'] 2m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_install_foreign_architecture'] 2m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_install_foreign_architecture'] 2m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-cache', 'policy'] 2m4.2s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 2m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-cache', 'policy'] 2m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-cache', 'policy', 'macsyfinder'] 2m4.2s DUMP: macsyfinder: Installed: 2.1.3-1 Candidate: 2.1.3-1 Version table: *** 2.1.3-1 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 2m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-cache', 'policy', 'macsyfinder'] 2m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-get', '-y', 'install', 'macsyfinder=2.1.3-1'] 2m5.0s DUMP: Reading package lists... Building dependency tree... Reading state information... macsyfinder is already the newest version (2.1.3-1). The following packages were automatically installed and are no longer required: gcc-12-base libmbedcrypto3 libmbedtls12 libmbedx509-0 libmpdec3 libperl5.32 libperl5.36 libpython3.9-minimal libpython3.9-stdlib libquadmath0 perl-modules-5.32 perl-modules-5.36 python3-decorator python3-pyparsing python3.9 python3.9-minimal Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded. 2m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-get', '-y', 'install', 'macsyfinder=2.1.3-1'] 2m5.0s INFO: Running scripts post_install 2m5.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_install_exceptions'] 2m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_install_exceptions'] 2m5.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5'] 2m6.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5'] 2m6.4s INFO: /bin converted to /usr/bin by /usr merge 2m6.4s INFO: /lib converted to /usr/lib by /usr merge 2m6.4s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 2m6.4s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 2m6.4s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 2m6.4s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 2m6.4s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 2m6.4s INFO: /lib64 converted to /usr/lib64 by /usr merge 2m6.4s INFO: /sbin converted to /usr/sbin by /usr merge 2m7.9s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', '-ac', '--ignore-obsolete'] 2m10.9s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', '-ac', '--ignore-obsolete'] 2m10.9s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 2m10.9s DUMP: 0.15.6 2m10.9s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 2m10.9s INFO: Running adequate version 0.15.6 now. 2m10.9s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'macsyfinder'] 2m11.1s DUMP: macsyfinder: obsolete-conffile /etc/macsyfinder/macsyfinder.conf 2m11.1s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'macsyfinder'] 2m11.1s ERROR: WARN: Inadequate results from running adequate! macsyfinder: obsolete-conffile /etc/macsyfinder/macsyfinder.conf 2m11.1s ERROR: WARN: Running adequate resulted in less interesting tags found: obsolete-conffile 2m11.1s INFO: Running scripts pre_remove 2m11.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 2m11.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 2m11.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 2m11.2s DUMP: OBSOLETE CONFFILE /etc/macsyfinder/macsyfinder.conf REGISTERED BY macsyfinder 2m11.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 2m11.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 2m13.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 2m13.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 2m13.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 2m13.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 2m13.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 2m13.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_remove_exceptions'] 2m13.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/pre_remove_exceptions'] 2m13.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 2m13.4s DUMP: install ok installed adduser adduser 3.137 install ok installed apt apt 2.7.13 install ok installed base-files base-files 13 install ok installed base-passwd base-passwd 3.6.3 install ok installed bash bash 5.2.21-2 install ok installed bsdutils bsdutils 1:2.39.3-6.1 install ok installed ca-certificates ca-certificates 20240203 install ok installed coreutils coreutils 9.4-3+b1 install ok installed dash dash 0.5.12-6 install ok installed debconf debconf 1.5.86 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.16 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.5 install ok installed e2fsprogs e2fsprogs 1.47.0-2 install ok installed findutils findutils 4.9.0-5 install ok installed fonts-font-awesome fonts-font-awesome 5.0.10+really4.7.0~dfsg-4.1 install ok installed fonts-lato fonts-lato 2.015-1 install ok installed gcc-10-base:amd64 gcc-10-base 10.5.0-3 install ok installed gcc-12-base:amd64 gcc-12-base 12.3.0-14 install ok installed gcc-14-base:amd64 gcc-14-base 14-20240221-2.1 install ok installed gcc-9-base:amd64 gcc-9-base 9.5.0-5 install ok installed gpgv gpgv 2.2.40-1.1+b1 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1 install ok installed hmmer hmmer 3.4+dfsg-2 install ok installed hostname hostname 3.23+nmu2 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed libacl1:amd64 libacl1 2.3.2-1 install ok installed libapt-pkg6.0t64:amd64 libapt-pkg6.0t64 2.7.13 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:3.1.2-2.1 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-2.1 install ok installed libblas3:amd64 libblas3 3.12.0-3 install ok installed libblkid1:amd64 libblkid1 2.39.3-6.1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b2 install ok installed libc-bin libc-bin 2.37-15 install ok installed libc6:amd64 libc6 2.37-15 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.4-2 install ok installed libcap2:amd64 libcap2 1:2.66-5 install ok installed libcom-err2t64:amd64 libcom-err2t64 1.47.0-2.2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-4 install ok installed libdb5.3t64:amd64 libdb5.3t64 5.3.28+dfsg2-5 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.271+b1 install ok installed libdivsufsort3:amd64 libdivsufsort3 2.0.1-6 install ok installed libexpat1:amd64 libexpat1 2.6.0-1 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2 install ok installed libffi7:amd64 libffi7 3.3-6 install ok installed libffi8:amd64 libffi8 3.4.6-1 install ok installed libfile-find-rule-perl libfile-find-rule-perl 0.34-3 install ok installed libgcc-s1:amd64 libgcc-s1 14-20240221-2.1 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.3-2 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.23-5+b1 install ok installed libgdbm6:amd64 libgdbm6 1.23-5+b1 install ok installed libgfortran5:amd64 libgfortran5 14-20240221-2.1 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2+b1 install ok installed libgnutls30:amd64 libgnutls30 3.8.3-1 install ok installed libgomp1:amd64 libgomp1 14-20240221-2.1 install ok installed libgpg-error0:amd64 libgpg-error0 1.47-3 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.20.1-5+b1 install ok installed libhogweed6:amd64 libhogweed6 3.9.1-2+b1 install ok installed libidn2-0:amd64 libidn2-0 2.3.7-2 install ok installed libjs-jquery libjs-jquery 3.6.1+dfsg+~3.5.14-1 install ok installed libjs-sphinxdoc libjs-sphinxdoc 7.2.6-4 install ok installed libjs-underscore libjs-underscore 1.13.4~dfsg+~1.11.4-3 install ok installed libk5crypto3:amd64 libk5crypto3 1.20.1-5+b1 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-3 install ok installed libkrb5-3:amd64 libkrb5-3 1.20.1-5+b1 install ok installed libkrb5support0:amd64 libkrb5support0 1.20.1-5+b1 install ok installed liblapack3:amd64 liblapack3 3.12.0-3 install ok installed liblmdb0:amd64 liblmdb0 0.9.31-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1+b2 install ok installed liblzma5:amd64 liblzma5 5.6.0-0.2 install ok installed libmbedcrypto3:amd64 libmbedcrypto3 2.16.9-0.1 install ok installed libmbedcrypto7:amd64 libmbedcrypto7 2.28.7-1 install ok installed libmbedtls12:amd64 libmbedtls12 2.16.9-0.1 install ok installed libmbedtls14:amd64 libmbedtls14 2.28.7-1 install ok installed libmbedx509-0:amd64 libmbedx509-0 2.16.9-0.1 install ok installed libmbedx509-1:amd64 libmbedx509-1 2.28.7-1 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmount1:amd64 libmount1 2.39.3-6.1 install ok installed libmpdec3:amd64 libmpdec3 2.5.1-2 install ok installed libncursesw6:amd64 libncursesw6 6.4+20240113-1 install ok installed libnettle8:amd64 libnettle8 3.9.1-2+b1 install ok installed libnsl2:amd64 libnsl2 1.3.0-3 install ok installed libnumber-compare-perl libnumber-compare-perl 0.03-3 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.3-4 install ok installed libpam-modules:amd64 libpam-modules 1.5.3-6 install ok installed libpam-modules-bin libpam-modules-bin 1.5.3-6 install ok installed libpam-runtime libpam-runtime 1.5.3-6 install ok installed libpam0g:amd64 libpam0g 1.5.3-6 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4+b1 install ok installed libpcre3:amd64 libpcre3 2:8.39-15+b1 install ok installed libperl5.32:amd64 libperl5.32 5.32.1-4+deb11u3 install ok installed libperl5.36:amd64 libperl5.36 5.36.0-7+deb12u1 install ok installed libperl5.38:amd64 libperl5.38 5.38.2-3 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.11.6-1 install ok installed libpython3.11-minimal:amd64 libpython3.11-minimal 3.11.8-2 install ok installed libpython3.11-stdlib:amd64 libpython3.11-stdlib 3.11.8-2 install ok installed libpython3.12-minimal:amd64 libpython3.12-minimal 3.12.2-1 install ok installed libpython3.12-stdlib:amd64 libpython3.12-stdlib 3.12.2-1 install ok installed libpython3.9-minimal:amd64 libpython3.9-minimal 3.9.2-1 install ok installed libpython3.9-stdlib:amd64 libpython3.9-stdlib 3.9.2-1 install ok installed libquadmath0:amd64 libquadmath0 14-20240221-2.1 install ok installed libreadline8:amd64 libreadline8 8.2-3+b1 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1 install ok installed libselinux1:amd64 libselinux1 3.5-2 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b2 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsepol2:amd64 libsepol2 3.5-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.39.3-6.1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.45.1-1 install ok installed libss2t64:amd64 libss2t64 1.47.0-2.2 install ok installed libssl1.1:amd64 libssl1.1 1.1.1w-0+deb11u1 install ok installed libssl3t64:amd64 libssl3t64 3.1.5-1.1 install ok installed libstdc++6:amd64 libstdc++6 14-20240221-2.1 install ok installed libsystemd0:amd64 libsystemd0 255.4-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtext-glob-perl libtext-glob-perl 0.11-3 install ok installed libtinfo6:amd64 libtinfo6 6.4+20240113-1 install ok installed libtirpc-common libtirpc-common 1.3.4+ds-1.1 install ok installed libtirpc3:amd64 libtirpc3 1.3.4+ds-1 install ok installed libudev1:amd64 libudev1 255.4-1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libunistring5:amd64 libunistring5 1.1-2 install ok installed libuuid1t64:amd64 libuuid1t64 2.39.3-6.1 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2+b1 install ok installed libyaml-0-2:amd64 libyaml-0-2 0.2.5-1 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-2 install ok installed login login 1:4.13+dfsg1-4 install ok installed logsave logsave 1.47.0-2.2 install ok installed lsb-base lsb-base 11.6 install ok installed macsyfinder macsyfinder 2.1.3-1 install ok installed mawk mawk 1.3.4.20240123-1 install ok installed media-types media-types 10.1.0 install ok installed mount mount 2.39.3-6.1 install ok installed ncbi-blast+ ncbi-blast+ 2.12.0+ds-4 install ok installed ncbi-data ncbi-data 6.1.20170106+dfsg1-10 install ok installed ncurses-base ncurses-base 6.4+20240113-1 install ok installed ncurses-bin ncurses-bin 6.4+20240113-1 install ok installed netbase netbase 6.4 install ok installed openssl openssl 3.1.5-1.1 install ok installed passwd passwd 1:4.13+dfsg1-4 install ok installed perl perl 5.38.2-3 install ok installed perl-base perl-base 5.38.2-3 install ok installed perl-modules-5.32 perl-modules-5.32 5.32.1-4+deb11u3 install ok installed perl-modules-5.36 perl-modules-5.36 5.36.0-7+deb12u1 install ok installed perl-modules-5.38 perl-modules-5.38 5.38.2-3 install ok installed python3 python3 3.11.6-1 install ok installed python3-certifi python3-certifi 2023.11.17-1 install ok installed python3-colorama python3-colorama 0.4.6-4 install ok installed python3-colorlog python3-colorlog 6.8.0-1 install ok installed python3-dateutil python3-dateutil 2.8.2-3 install ok installed python3-decorator python3-decorator 5.1.1-5 install ok installed python3-minimal python3-minimal 3.11.6-1 install ok installed python3-networkx python3-networkx 2.8.8-1 install ok installed python3-numpy python3-numpy 1:1.24.2-2 install ok installed python3-packaging python3-packaging 23.2-1 install ok installed python3-pandas python3-pandas 2.1.4+dfsg-5 install ok installed python3-pandas-lib:amd64 python3-pandas-lib 2.1.4+dfsg-5 install ok installed python3-pkg-resources python3-pkg-resources 68.1.2-2 install ok installed python3-pyparsing python3-pyparsing 3.1.1-1 install ok installed python3-six python3-six 1.16.0-4 install ok installed python3-tz python3-tz 2024.1-2 install ok installed python3-yaml python3-yaml 6.0.1-2 install ok installed python3.11 python3.11 3.11.8-2 install ok installed python3.11-minimal python3.11-minimal 3.11.8-2 install ok installed python3.12 python3.12 3.12.2-1 install ok installed python3.12-minimal python3.12-minimal 3.12.2-1 install ok installed python3.9 python3.9 3.9.2-1 install ok installed python3.9-minimal python3.9-minimal 3.9.2-1 install ok installed readline-common readline-common 8.2-3 install ok installed sed sed 4.9-2 install ok installed sphinx-rtd-theme-common sphinx-rtd-theme-common 2.0.0+dfsg-1 install ok installed sysvinit-utils sysvinit-utils 3.08-7 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2024a-1 install ok installed usrmerge usrmerge 39 install ok installed util-linux util-linux 2.38.1-5+b1 install ok installed util-linux-extra util-linux-extra 2.39.3-6.1 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg-3+b1 2m13.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 2m13.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-get', '-y', '--no-install-recommends', '--force-yes', 'install', 'libdb5.3:amd64=5.3.28+dfsg2-4+b1', 'libssl3:amd64=3.1.5-1', 'ca-certificates-', 'fonts-font-awesome-', 'fonts-lato-', 'hmmer-', 'libblas3:amd64-', 'libdb5.3t64:amd64-', 'libdivsufsort3:amd64-', 'libexpat1:amd64-', 'libgfortran5:amd64-', 'libgomp1:amd64-', 'libjs-jquery-', 'libjs-sphinxdoc-', 'libjs-underscore-', 'liblapack3:amd64-', 'liblmdb0:amd64-', 'libmbedcrypto3:amd64-', 'libmbedcrypto7:amd64-', 'libmbedtls12:amd64-', 'libmbedtls14:amd64-', 'libmbedx509-0:amd64-', 'libmbedx509-1:amd64-', 'libmpdec3:amd64-', 'libncursesw6:amd64-', 'libperl5.32:amd64-', 'libpython3-stdlib:amd64-', 'libpython3.11-minimal:amd64-', 'libpython3.11-stdlib:amd64-', 'libpython3.12-minimal:amd64-', 'libpython3.12-stdlib:amd64-', 'libpython3.9-minimal:amd64-', 'libpython3.9-stdlib:amd64-', 'libquadmath0:amd64-', 'libreadline8:amd64-', 'libsqlite3-0:amd64-', 'libssl3t64:amd64-', 'libyaml-0-2:amd64-', 'media-types-', 'ncbi-blast+-', 'ncbi-data-', 'netbase-', 'openssl-', 'perl-modules-5.32-', 'python3-', 'python3-certifi-', 'python3-colorama-', 'python3-colorlog-', 'python3-dateutil-', 'python3-decorator-', 'python3-minimal-', 'python3-networkx-', 'python3-numpy-', 'python3-packaging-', 'python3-pandas-', 'python3-pandas-lib:amd64-', 'python3-pkg-resources-', 'python3-pyparsing-', 'python3-six-', 'python3-tz-', 'python3-yaml-', 'python3.11-', 'python3.11-minimal-', 'python3.12-', 'python3.12-minimal-', 'python3.9-', 'python3.9-minimal-', 'readline-common-', 'sphinx-rtd-theme-common-', 'macsyfinder-'] 2m18.6s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: gcc-12-base libperl5.36 perl-modules-5.36 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: ca-certificates fonts-font-awesome fonts-lato hmmer libblas3 libdb5.3t64 libdivsufsort3 libexpat1 libgfortran5 libgomp1 libjs-jquery libjs-sphinxdoc libjs-underscore liblapack3 liblmdb0 libmbedcrypto3 libmbedcrypto7 libmbedtls12 libmbedtls14 libmbedx509-0 libmbedx509-1 libmpdec3 libncursesw6 libperl5.32 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libpython3.12-minimal libpython3.12-stdlib libpython3.9-minimal libpython3.9-stdlib libquadmath0 libreadline8 libsqlite3-0 libssl3t64 libyaml-0-2 macsyfinder media-types ncbi-blast+ ncbi-data netbase openssl perl-modules-5.32 python3 python3-certifi python3-colorama python3-colorlog python3-dateutil python3-decorator python3-minimal python3-networkx python3-numpy python3-packaging python3-pandas python3-pandas-lib python3-pkg-resources python3-pyparsing python3-six python3-tz python3-yaml python3.11 python3.11-minimal python3.12 python3.12-minimal python3.9 python3.9-minimal readline-common sphinx-rtd-theme-common The following NEW packages will be installed: libdb5.3 libssl3 0 upgraded, 2 newly installed, 68 to remove and 3 not upgraded. Need to get 2760 kB of archives. After this operation, 391 MB disk space will be freed. Get:1 http://deb.debian.org/debian sid/main amd64 libdb5.3 amd64 5.3.28+dfsg2-4+b1 [697 kB] Get:2 http://deb.debian.org/debian sid/main amd64 libssl3 amd64 3.1.5-1 [2063 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 2760 kB in 0s (42.3 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 18687 files and directories currently installed.) Removing macsyfinder (2.1.3-1) ... Removing python3-certifi (2023.11.17-1) ... Removing ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing sphinx-rtd-theme-common (2.0.0+dfsg-1) ... Removing fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Removing fonts-lato (2.015-1) ... Removing hmmer (3.4+dfsg-2) ... Removing python3-pandas (2.1.4+dfsg-5) ... Removing python3-pandas-lib:amd64 (2.1.4+dfsg-5) ... Removing python3-numpy (1:1.24.2-2) ... Removing liblapack3:amd64 (3.12.0-3) ... Removing libblas3:amd64 (3.12.0-3) ... Removing python3-yaml (6.0.1-2) ... Removing python3-dateutil (2.8.2-3) ... Removing python3-six (1.16.0-4) ... Removing ncbi-blast+ (2.12.0+ds-4) ... Removing python3-networkx (2.8.8-1) ... Removing python3-pkg-resources (68.1.2-2) ... Removing python3.9 (3.9.2-1) ... Removing libpython3.9-stdlib:amd64 (3.9.2-1) ... dpkg: python3: dependency problems, but removing anyway as you requested: python3-tz depends on python3:any. python3-pyparsing depends on python3:any. python3-packaging depends on python3:any. python3-decorator depends on python3:any. python3-colorlog depends on python3:any. python3-colorama depends on python3:any. Removing python3 (3.11.6-1) ... Removing python3.11 (3.11.8-2) ... Removing libpython3-stdlib:amd64 (3.11.6-1) ... Removing libpython3.11-stdlib:amd64 (3.11.8-2) ... Selecting previously unselected package libdb5.3:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 13371 files and directories currently installed.) Preparing to unpack .../libdb5.3_5.3.28+dfsg2-4+b1_amd64.deb ... Unpacking libdb5.3:amd64 (5.3.28+dfsg2-4+b1) ... Replaced by files in installed package libdb5.3t64:amd64 (5.3.28+dfsg2-5) ... (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 ... 13377 files and directories currently installed.) Removing libperl5.32:amd64 (5.32.1-4+deb11u3) ... Removing libdivsufsort3:amd64 (2.0.1-6) ... Removing python3.9-minimal (3.9.2-1) ... Removing python3.12 (3.12.2-1) ... Removing python3.12-minimal (3.12.2-1) ... Removing libgfortran5:amd64 (14-20240221-2.1) ... Removing libgomp1:amd64 (14-20240221-2.1) ... Removing libjs-sphinxdoc (7.2.6-4) ... Removing libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Removing libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Removing liblmdb0:amd64 (0.9.31-1+b1) ... Removing libmbedtls12:amd64 (2.16.9-0.1) ... Removing libmbedx509-0:amd64 (2.16.9-0.1) ... Removing libmbedcrypto3:amd64 (2.16.9-0.1) ... Removing libmbedtls14:amd64 (2.28.7-1) ... Removing libmbedx509-1:amd64 (2.28.7-1) ... Removing libmbedcrypto7:amd64 (2.28.7-1) ... Removing libmpdec3:amd64 (2.5.1-2) ... Removing libpython3.12-stdlib:amd64 (3.12.2-1) ... Removing libncursesw6:amd64 (6.4+20240113-1) ... Removing python3-minimal (3.11.6-1) ... Removing python3.11-minimal (3.11.8-2) ... Removing libpython3.11-minimal:amd64 (3.11.8-2) ... Removing libpython3.12-minimal:amd64 (3.12.2-1) ... Removing libpython3.9-minimal:amd64 (3.9.2-1) ... Removing libquadmath0:amd64 (14-20240221-2.1) ... Removing libreadline8:amd64 (8.2-3+b1) ... Removing libsqlite3-0:amd64 (3.45.1-1) ... Removing openssl (3.1.5-1.1) ... Removing libexpat1:amd64 (2.6.0-1) ... dpkg: libssl3t64:amd64: dependency problems, but removing anyway as you requested: libkrb5-3:amd64 depends on libssl3 (>= 3.0.0); however: Package libssl3 is not installed. Package libssl3t64:amd64 which provides libssl3 is to be removed. coreutils depends on libssl3 (>= 3.0.0); however: Package libssl3 is not installed. Package libssl3t64:amd64 which provides libssl3 is to be removed. Removing libssl3t64:amd64 (3.1.5-1.1) ... dpkg: libdb5.3t64:amd64: dependency problems, but removing anyway as you requested: libperl5.38:amd64 depends on libdb5.3; however: Package libdb5.3:amd64 is not configured yet. Package libdb5.3t64:amd64 which provides libdb5.3 is to be removed. libperl5.36:amd64 depends on libdb5.3; however: Package libdb5.3:amd64 is not configured yet. Package libdb5.3t64:amd64 which provides libdb5.3 is to be removed. Removing libdb5.3t64:amd64 (5.3.28+dfsg2-5) ... 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 ... 11086 files and directories currently installed.) Preparing to unpack .../libssl3_3.1.5-1_amd64.deb ... Unpacking libssl3:amd64 (3.1.5-1) ... Setting up libssl3:amd64 (3.1.5-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 11099 files and directories currently installed.) Removing libyaml-0-2:amd64 (0.2.5-1) ... Removing media-types (10.1.0) ... Removing ncbi-data (6.1.20170106+dfsg1-10) ... Removing netbase (6.4) ... Removing perl-modules-5.32 (5.32.1-4+deb11u3) ... Removing python3-colorama (0.4.6-4) ... rm: cannot remove '/usr/share/doc/python3-colorama/examples/__pycache__/demo01.*': No such file or directory rm: cannot remove '/usr/share/doc/python3-colorama/examples/__pycache__/demo02.*': No such file or directory rm: cannot remove '/usr/share/doc/python3-colorama/examples/__pycache__/demo03.*': No such file or directory rm: cannot remove '/usr/share/doc/python3-colorama/examples/__pycache__/demo04.*': No such file or directory rm: cannot remove '/usr/share/doc/python3-colorama/examples/__pycache__/demo05.*': No such file or directory rm: cannot remove '/usr/share/doc/python3-colorama/examples/__pycache__/demo06.*': No such file or directory rm: cannot remove '/usr/share/doc/python3-colorama/examples/__pycache__/demo07.*': No such file or directory rm: cannot remove '/usr/share/doc/python3-colorama/examples/__pycache__/demo08.*': No such file or directory rm: cannot remove '/usr/share/doc/python3-colorama/examples/__pycache__/demo09.*': No such file or directory rm: cannot remove '/usr/share/doc/python3-colorama/examples/__pycache__/fixpath.*': No such file or directory Removing python3-colorlog (6.8.0-1) ... rm: cannot remove '/usr/share/doc/python3-colorlog/examples/__pycache__/colors.*': No such file or directory rm: cannot remove '/usr/share/doc/python3-colorlog/examples/__pycache__/custom_level.*': No such file or directory rm: cannot remove '/usr/share/doc/python3-colorlog/examples/__pycache__/example.*': No such file or directory rm: cannot remove '/usr/share/doc/python3-colorlog/examples/__pycache__/yaml_example.*': No such file or directory Removing python3-decorator (5.1.1-5) ... Removing python3-packaging (23.2-1) ... Removing python3-pyparsing (3.1.1-1) ... Removing python3-tz (2024.1-2) ... Removing readline-common (8.2-3) ... Setting up libdb5.3:amd64 (5.3.28+dfsg2-4+b1) ... Processing triggers for libc-bin (2.37-15) ... W: --force-yes is deprecated, use one of the options starting with --allow instead. 2m18.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-get', '-y', '--no-install-recommends', '--force-yes', 'install', 'libdb5.3:amd64=5.3.28+dfsg2-4+b1', 'libssl3:amd64=3.1.5-1', 'ca-certificates-', 'fonts-font-awesome-', 'fonts-lato-', 'hmmer-', 'libblas3:amd64-', 'libdb5.3t64:amd64-', 'libdivsufsort3:amd64-', 'libexpat1:amd64-', 'libgfortran5:amd64-', 'libgomp1:amd64-', 'libjs-jquery-', 'libjs-sphinxdoc-', 'libjs-underscore-', 'liblapack3:amd64-', 'liblmdb0:amd64-', 'libmbedcrypto3:amd64-', 'libmbedcrypto7:amd64-', 'libmbedtls12:amd64-', 'libmbedtls14:amd64-', 'libmbedx509-0:amd64-', 'libmbedx509-1:amd64-', 'libmpdec3:amd64-', 'libncursesw6:amd64-', 'libperl5.32:amd64-', 'libpython3-stdlib:amd64-', 'libpython3.11-minimal:amd64-', 'libpython3.11-stdlib:amd64-', 'libpython3.12-minimal:amd64-', 'libpython3.12-stdlib:amd64-', 'libpython3.9-minimal:amd64-', 'libpython3.9-stdlib:amd64-', 'libquadmath0:amd64-', 'libreadline8:amd64-', 'libsqlite3-0:amd64-', 'libssl3t64:amd64-', 'libyaml-0-2:amd64-', 'media-types-', 'ncbi-blast+-', 'ncbi-data-', 'netbase-', 'openssl-', 'perl-modules-5.32-', 'python3-', 'python3-certifi-', 'python3-colorama-', 'python3-colorlog-', 'python3-dateutil-', 'python3-decorator-', 'python3-minimal-', 'python3-networkx-', 'python3-numpy-', 'python3-packaging-', 'python3-pandas-', 'python3-pandas-lib:amd64-', 'python3-pkg-resources-', 'python3-pyparsing-', 'python3-six-', 'python3-tz-', 'python3-yaml-', 'python3.11-', 'python3.11-minimal-', 'python3.12-', 'python3.12-minimal-', 'python3.9-', 'python3.9-minimal-', 'readline-common-', 'sphinx-rtd-theme-common-', 'macsyfinder-'] 2m18.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-get', '-y', '--no-install-recommends', '--reinstall', 'install', 'libdb5.3:amd64=5.3.28+dfsg2-4+b1', 'libssl3:amd64=3.1.5-1'] 2m19.9s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages were automatically installed and are no longer required: gcc-12-base libperl5.36 perl-modules-5.36 Use 'sudo apt autoremove' to remove them. debconf: delaying package configuration, since apt-utils is not installed 0 upgraded, 0 newly installed, 2 reinstalled, 0 to remove and 3 not upgraded. Need to get 0 B/2760 kB of archives. After this operation, 0 B of additional disk space will be used. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9427 files and directories currently installed.) Preparing to unpack .../libssl3_3.1.5-1_amd64.deb ... Unpacking libssl3:amd64 (3.1.5-1) over (3.1.5-1) ... Setting up libssl3:amd64 (3.1.5-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 9427 files and directories currently installed.) Preparing to unpack .../libdb5.3_5.3.28+dfsg2-4+b1_amd64.deb ... Unpacking libdb5.3:amd64 (5.3.28+dfsg2-4+b1) over (5.3.28+dfsg2-4+b1) ... Setting up libdb5.3:amd64 (5.3.28+dfsg2-4+b1) ... Processing triggers for libc-bin (2.37-15) ... 2m19.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-get', '-y', '--no-install-recommends', '--reinstall', 'install', 'libdb5.3:amd64=5.3.28+dfsg2-4+b1', 'libssl3:amd64=3.1.5-1'] 2m19.9s INFO: Running scripts post_remove 2m19.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_remove_exceptions'] 2m19.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_remove_exceptions'] 2m19.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'dpkg', '--purge', 'ca-certificates', 'fonts-font-awesome', 'fonts-lato', 'hmmer', 'libblas3:amd64', 'libdb5.3t64:amd64', 'libdivsufsort3:amd64', 'libexpat1:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libjs-jquery', 'libjs-sphinxdoc', 'libjs-underscore', 'liblapack3:amd64', 'liblmdb0:amd64', 'libmbedcrypto3:amd64', 'libmbedcrypto7:amd64', 'libmbedtls12:amd64', 'libmbedtls14:amd64', 'libmbedx509-0:amd64', 'libmbedx509-1:amd64', 'libmpdec3:amd64', 'libncursesw6:amd64', 'libperl5.32:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libssl3t64:amd64', 'libyaml-0-2:amd64', 'media-types', 'ncbi-blast+', 'ncbi-data', 'netbase', 'openssl', 'perl-modules-5.32', 'python3', 'python3-certifi', 'python3-colorama', 'python3-colorlog', 'python3-dateutil', 'python3-decorator', 'python3-minimal', 'python3-networkx', 'python3-numpy', 'python3-packaging', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-pkg-resources', 'python3-pyparsing', 'python3-six', 'python3-tz', 'python3-yaml', 'python3.11', 'python3.11-minimal', 'python3.12', 'python3.12-minimal', 'python3.9', 'python3.9-minimal', 'readline-common', 'sphinx-rtd-theme-common'] 2m20.1s DUMP: (Reading database ... 9428 files and directories currently installed.) Purging configuration files for ca-certificates (20240203) ... Removing dangling symlinks from /etc/ssl/certs... done. Purging configuration files for fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... dpkg: warning: ignoring request to remove fonts-lato which isn't installed dpkg: warning: ignoring request to remove hmmer which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libdb5.3t64 which isn't installed dpkg: warning: ignoring request to remove libdivsufsort3 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 dpkg: warning: ignoring request to remove libgomp1 which isn't installed Purging configuration files for libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... dpkg: warning: ignoring request to remove libjs-sphinxdoc which isn't installed dpkg: warning: ignoring request to remove libjs-underscore which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove liblmdb0 which isn't installed dpkg: warning: ignoring request to remove libmbedcrypto3 which isn't installed dpkg: warning: ignoring request to remove libmbedcrypto7 which isn't installed dpkg: warning: ignoring request to remove libmbedtls12 which isn't installed dpkg: warning: ignoring request to remove libmbedtls14 which isn't installed dpkg: warning: ignoring request to remove libmbedx509-0 which isn't installed dpkg: warning: ignoring request to remove libmbedx509-1 which isn't installed dpkg: warning: ignoring request to remove libmpdec3 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libperl5.32 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.11-minimal:amd64 (3.11.8-2) ... dpkg: warning: ignoring request to remove libpython3.11-stdlib which isn't installed Purging configuration files for libpython3.12-minimal:amd64 (3.12.2-1) ... dpkg: warning: ignoring request to remove libpython3.12-stdlib which isn't installed Purging configuration files for libpython3.9-minimal:amd64 (3.9.2-1) ... dpkg: warning: ignoring request to remove libpython3.9-stdlib which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed dpkg: warning: ignoring request to remove libreadline8 which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libssl3t64 which isn't installed dpkg: warning: ignoring request to remove libyaml-0-2 which isn't installed Purging configuration files for media-types (10.1.0) ... dpkg: warning: ignoring request to remove ncbi-blast+ which isn't installed Purging configuration files for ncbi-data (6.1.20170106+dfsg1-10) ... Purging configuration files for netbase (6.4) ... Purging configuration files for openssl (3.1.5-1.1) ... dpkg: warning: ignoring request to remove perl-modules-5.32 which isn't installed Purging configuration files for python3 (3.11.6-1) ... dpkg: warning: ignoring request to remove python3-certifi which isn't installed dpkg: warning: ignoring request to remove python3-colorama which isn't installed dpkg: warning: ignoring request to remove python3-colorlog which isn't installed dpkg: warning: ignoring request to remove python3-dateutil which isn't installed dpkg: warning: ignoring request to remove python3-decorator which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-networkx which isn't installed dpkg: warning: ignoring request to remove python3-numpy which isn't installed dpkg: warning: ignoring request to remove python3-packaging which isn't installed dpkg: warning: ignoring request to remove python3-pandas which isn't installed dpkg: warning: ignoring request to remove python3-pandas-lib which isn't installed dpkg: warning: ignoring request to remove python3-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python3-pyparsing which isn't installed dpkg: warning: ignoring request to remove python3-six which isn't installed dpkg: warning: ignoring request to remove python3-tz which isn't installed dpkg: warning: ignoring request to remove python3-yaml which isn't installed dpkg: warning: ignoring request to remove python3.11 which isn't installed Purging configuration files for python3.11-minimal (3.11.8-2) ... dpkg: warning: ignoring request to remove python3.12 which isn't installed Purging configuration files for python3.12-minimal (3.12.2-1) ... dpkg: warning: ignoring request to remove python3.9 which isn't installed Purging configuration files for python3.9-minimal (3.9.2-1) ... Purging configuration files for readline-common (8.2-3) ... dpkg: warning: ignoring request to remove sphinx-rtd-theme-common which isn't installed 2m20.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'dpkg', '--purge', 'ca-certificates', 'fonts-font-awesome', 'fonts-lato', 'hmmer', 'libblas3:amd64', 'libdb5.3t64:amd64', 'libdivsufsort3:amd64', 'libexpat1:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libjs-jquery', 'libjs-sphinxdoc', 'libjs-underscore', 'liblapack3:amd64', 'liblmdb0:amd64', 'libmbedcrypto3:amd64', 'libmbedcrypto7:amd64', 'libmbedtls12:amd64', 'libmbedtls14:amd64', 'libmbedx509-0:amd64', 'libmbedx509-1:amd64', 'libmpdec3:amd64', 'libncursesw6:amd64', 'libperl5.32:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libpython3.12-minimal:amd64', 'libpython3.12-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libssl3t64:amd64', 'libyaml-0-2:amd64', 'media-types', 'ncbi-blast+', 'ncbi-data', 'netbase', 'openssl', 'perl-modules-5.32', 'python3', 'python3-certifi', 'python3-colorama', 'python3-colorlog', 'python3-dateutil', 'python3-decorator', 'python3-minimal', 'python3-networkx', 'python3-numpy', 'python3-packaging', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-pkg-resources', 'python3-pyparsing', 'python3-six', 'python3-tz', 'python3-yaml', 'python3.11', 'python3.11-minimal', 'python3.12', 'python3.12-minimal', 'python3.9', 'python3.9-minimal', 'readline-common', 'sphinx-rtd-theme-common'] 2m20.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'dpkg', '--purge', 'macsyfinder'] 2m20.1s DUMP: (Reading database ... 9411 files and directories currently installed.) Purging configuration files for macsyfinder (2.1.3-1) ... 2m20.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'dpkg', '--purge', 'macsyfinder'] 2m20.1s INFO: Running scripts post_purge 2m20.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_purge_exceptions'] 2m20.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_purge_exceptions'] 2m20.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'dpkg', '--purge', '--pending'] 2m20.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'dpkg', '--purge', '--pending'] 2m20.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'dpkg', '--remove', '--pending'] 2m20.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'dpkg', '--remove', '--pending'] 2m20.2s INFO: Running scripts post_test 2m20.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_test_exceptions'] 2m20.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'tmp/scripts/post_test_exceptions'] 2m20.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5'] 2m20.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5'] 2m20.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'dpkg-divert', '--list'] 2m20.9s DUMP: local diversion of /bin/sync to /bin/sync.distrib local diversion of /home to /home.distrib 2m20.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'dpkg-divert', '--list'] 2m20.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-get', 'clean'] 2m20.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5', 'apt-get', 'clean'] 2m20.9s DEBUG: Recording chroot state 2m21.8s INFO: Warning: Package purging left files on system: /etc/macsyfinder/ not owned 2m22.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5/dev/shm'] 2m22.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5/dev/shm'] 2m22.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5/dev/console'] 2m22.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5/dev/console'] 2m22.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5/dev/ptmx'] 2m22.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5/dev/ptmx'] 2m22.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5/dev/pts'] 2m22.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5/dev/pts'] 2m22.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5/proc'] 2m22.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5/proc'] 2m22.6s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5'] 2m22.7s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp9qz_sxh5'] 2m22.7s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp9qz_sxh5 2m22.7s INFO: PASS: Upgrading between Debian distributions. 2m22.7s INFO: PASS: All tests. 2m22.7s INFO: piuparts run ends. ret=0 End: 2024-03-01 06:47:55 GMT