Start: 2024-08-23 02:05:39 GMT [bookworm] 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 [bookworm-next] 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 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 --warn-on-usr-move fail --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz -d bookworm -d bookworm-next -B /srv/piuparts.debian.org/slave/refchroot/bookworm2next/reference-chroot-metadata.dat --apt macsyfinder=2.0-2+b1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.4.4~202408201642~1.4.3-11-g36a88c35 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --warn-on-usr-move fail --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz -d bookworm -d bookworm-next -B /srv/piuparts.debian.org/slave/refchroot/bookworm2next/reference-chroot-metadata.dat --apt macsyfinder=2.0-2+b1 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-32-amd64 #1 SMP Debian 5.10.223-1 (2024-08-10) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpodzd5te6 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpodzd5te6 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', '--auto-compress', '-xf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpodzd5te6/proc'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpodzd5te6/proc'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpodzd5te6/dev/pts'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpodzd5te6/dev/pts'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpodzd5te6/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpodzd5te6/dev/ptmx'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpodzd5te6/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpodzd5te6/dev/ptmx'] 0m0.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpodzd5te6/dev/console'] 0m0.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpodzd5te6/dev/console'] 0m0.4s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpodzd5te6/dev/shm'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpodzd5te6/dev/shm'] 0m0.4s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m0.4s DEBUG: Created policy-rc.d and chmodded it. 0m0.4s DEBUG: Created resolv.conf. 0m0.4s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpodzd5te6/tmp/scripts/ 0m0.4s INFO: Running scripts post_chroot_unpack 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'apt-get', 'update'] 0m1.4s DUMP: Hit:1 http://deb.debian.org/debian bookworm InRelease Reading package lists... 0m1.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'apt-get', 'update'] 0m1.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'apt-get', '-yf', 'dist-upgrade'] 0m1.8s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'apt-get', '-yf', 'dist-upgrade'] 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.3s DUMP: 913e17be84ed63a3110ce3137c1d003a - 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.3s INFO: Running scripts post_setup 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/post_setup_dummy_users'] 0m3.0s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/post_setup_dummy_users'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/post_setup_forbid_home'] 0m3.0s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/post_setup_forbid_home'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.0s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/post_setup_minimize'] 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/post_setup_minimize'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/post_setup_zz_backports'] 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/post_setup_zz_backports'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.1s DUMP: install ok installed adduser adduser 3.134 install ok installed apt apt 2.6.1 install ok installed base-files base-files 12.4+deb12u6 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b7 install ok installed bsdutils bsdutils 1:2.38.1-5+deb12u1 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.12-2 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.3+deb12u1 install ok installed debianutils debianutils 5.7-0.5~deb12u1 install ok installed diffutils diffutils 1:3.8-4 install ok installed dpkg dpkg 1.21.22 install ok installed e2fsprogs e2fsprogs 1.47.0-2 install ok installed findutils findutils 4.9.0-4 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-14 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.8-5 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu1 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.6.1 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.0.9-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.9-1 install ok installed libblkid1:amd64 libblkid1 2.38.1-5+deb12u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-9+deb12u7 install ok installed libc6:amd64 libc6 2.36-9+deb12u7 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3 install ok installed libcap2:amd64 libcap2 1:2.66-4 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.33-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.270 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-14 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-3 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.9-2+deb12u3 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.1-0.2 install ok installed libmd0:amd64 libmd0 1.0.4-2 install ok installed libmount1:amd64 libmount1 2.38.1-5+deb12u1 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-6+deb12u1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-6+deb12u1 install ok installed libpam-runtime libpam-runtime 1.5.2-6+deb12u1 install ok installed libpam0g:amd64 libpam0g 1.5.2-6+deb12u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-1 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+deb12u1 install ok installed libselinux1:amd64 libselinux1 3.4-1+b6 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b5 install ok installed libsepol2:amd64 libsepol2 3.4-2.1 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-5+deb12u1 install ok installed libss2:amd64 libss2 1.47.0-2 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-14 install ok installed libsystemd0:amd64 libsystemd0 252.26-1~deb12u2 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.4-4 install ok installed libudev1:amd64 libudev1 252.26-1~deb12u2 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+deb12u1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.4+dfsg2-5 install ok installed login login 1:4.13+dfsg1-1+b1 install ok installed logsave logsave 1.47.0-2 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mount mount 2.38.1-5+deb12u1 install ok installed ncurses-base ncurses-base 6.4-4 install ok installed ncurses-bin ncurses-bin 6.4-4 install ok installed passwd passwd 1:4.13+dfsg1-1+b1 install ok installed perl-base perl-base 5.36.0-7+deb12u1 install ok installed sed sed 4.9-1 install ok installed sysvinit-utils sysvinit-utils 3.06-4 install ok installed tar tar 1.34+dfsg-1.2+deb12u1 install ok installed tzdata tzdata 2024a-0+deb12u1 install ok installed usr-is-merged usr-is-merged 37~deb12u1 install ok installed util-linux util-linux 2.38.1-5+deb12u1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+deb12u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m3.1s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/bookworm2next/reference-chroot-metadata.dat 0m3.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpodzd5te6'] 0m3.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpodzd5te6'] 0m3.5s INFO: Running scripts is_testable 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/is_testable_uninstallable'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/is_testable_uninstallable'] 0m3.5s INFO: Running scripts pre_test 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_test_exceptions'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_test_exceptions'] 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_test_root_password'] 0m3.6s DUMP: New password: Retype new password: passwd: password updated successfully 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_test_root_password'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'apt-cache', 'show', '--no-all-versions', 'macsyfinder'] 0m3.8s 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 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'apt-cache', 'show', '--no-all-versions', 'macsyfinder'] 0m3.8s INFO: apt-cache knows about the following packages: macsyfinder 0m3.8s INFO: Running scripts pre_install 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_install_database-server'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_install_database-server'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_install_exceptions'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_install_exceptions'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_install_extras'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_install_extras'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'apt-cache', 'policy'] 0m3.8s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.6,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'apt-cache', 'policy'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'apt-cache', 'policy', 'macsyfinder'] 0m3.9s DUMP: macsyfinder: Installed: (none) Candidate: 2.0-2+b1 Version table: 2.0-2+b1 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'apt-cache', 'policy', 'macsyfinder'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'apt-get', '-y', 'install', 'macsyfinder'] 0m26.3s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: ca-certificates fonts-font-awesome fonts-lato hmmer libblas3 libdivsufsort3 libexpat1 libgdbm-compat4 libgdbm6 libgfortran5 libgomp1 libgssapi-krb5-2 libjs-jquery libjs-sphinxdoc libjs-underscore libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblmdb0 libmbedcrypto7 libmbedtls14 libmbedx509-1 libncursesw6 libnsl2 libpcre3 libperl5.36 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libquadmath0 libreadline8 libsqlite3-0 libssl3 libtirpc-common libtirpc3 libyaml-0-2 media-types ncbi-blast+ ncbi-data openssl perl perl-modules-5.36 python3 python3-certifi python3-colorama python3-colorlog python3-dateutil python3-minimal python3-networkx python3-numpy python3-packaging python3-pandas python3-pandas-lib python3-pkg-resources python3-six python3-tz python3-yaml python3.11 python3.11-minimal readline-common sphinx-rtd-theme-common Suggested packages: hmmer-doc gdbm-l10n krb5-doc krb5-user sensible-utils perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl python3-doc python3-tk python3-venv gcc gfortran python3-dev python3-pytest python-pandas-doc python3-statsmodels python3-setuptools python3.11-venv python3.11-doc binutils binfmt-support readline-doc Recommended packages: javascript-common krb5-locales libgpm2 netbase python3-gdal python3-matplotlib python3-pydot python3-pygraphviz python3-scipy python3-bottleneck python3-numexpr python3-odf python3-openpyxl python3-bs4 python3-html5lib python3-lxml python3-tables python3-jinja2 python3-numba The following NEW packages will be installed: ca-certificates fonts-font-awesome fonts-lato hmmer libblas3 libdivsufsort3 libexpat1 libgdbm-compat4 libgdbm6 libgfortran5 libgomp1 libgssapi-krb5-2 libjs-jquery libjs-sphinxdoc libjs-underscore libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblmdb0 libmbedcrypto7 libmbedtls14 libmbedx509-1 libncursesw6 libnsl2 libpcre3 libperl5.36 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libquadmath0 libreadline8 libsqlite3-0 libssl3 libtirpc-common libtirpc3 libyaml-0-2 macsyfinder media-types ncbi-blast+ ncbi-data openssl perl perl-modules-5.36 python3 python3-certifi python3-colorama python3-colorlog python3-dateutil python3-minimal python3-networkx python3-numpy python3-packaging python3-pandas python3-pandas-lib python3-pkg-resources python3-six python3-tz python3-yaml python3.11 python3.11-minimal readline-common sphinx-rtd-theme-common 0 upgraded, 64 newly installed, 0 to remove and 0 not upgraded. Need to get 70.2 MB of archives. After this operation, 311 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 perl-modules-5.36 all 5.36.0-7+deb12u1 [2815 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 libgdbm6 amd64 1.23-3 [72.2 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libgdbm-compat4 amd64 1.23-3 [48.2 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 libperl5.36 amd64 5.36.0-7+deb12u1 [4218 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 perl amd64 5.36.0-7+deb12u1 [239 kB] Get:6 http://deb.debian.org/debian bookworm/main amd64 fonts-lato all 2.0-2.1 [2696 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 libssl3 amd64 3.0.13-1~deb12u1 [2022 kB] Get:8 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6+deb12u2 [814 kB] Get:9 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get:10 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6+deb12u2 [2067 kB] Get:11 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get:12 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get:13 http://deb.debian.org/debian bookworm/main amd64 libncursesw6 amd64 6.4-4 [134 kB] Get:14 http://deb.debian.org/debian bookworm/main amd64 libkrb5support0 amd64 1.20.1-2+deb12u1 [32.4 kB] Get:15 http://deb.debian.org/debian bookworm/main amd64 libk5crypto3 amd64 1.20.1-2+deb12u1 [78.9 kB] Get:16 http://deb.debian.org/debian bookworm/main amd64 libkeyutils1 amd64 1.6.3-2 [8808 B] Get:17 http://deb.debian.org/debian bookworm/main amd64 libkrb5-3 amd64 1.20.1-2+deb12u1 [332 kB] Get:18 http://deb.debian.org/debian bookworm/main amd64 libgssapi-krb5-2 amd64 1.20.1-2+deb12u1 [134 kB] Get:19 http://deb.debian.org/debian bookworm/main amd64 libtirpc-common all 1.3.3+ds-1 [14.0 kB] Get:20 http://deb.debian.org/debian bookworm/main amd64 libtirpc3 amd64 1.3.3+ds-1 [85.2 kB] Get:21 http://deb.debian.org/debian bookworm/main amd64 libnsl2 amd64 1.3.0-2 [39.5 kB] Get:22 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get:23 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get:24 http://deb.debian.org/debian bookworm/main amd64 libsqlite3-0 amd64 3.40.1-2 [837 kB] Get:25 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6+deb12u2 [1799 kB] Get:26 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6+deb12u2 [573 kB] Get:27 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get:28 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get:29 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.13-1~deb12u1 [1418 kB] Get:30 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB] Get:31 http://deb.debian.org/debian bookworm/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get:32 http://deb.debian.org/debian bookworm/main amd64 libdivsufsort3 amd64 2.0.1-5 [44.7 kB] Get:33 http://deb.debian.org/debian bookworm/main amd64 hmmer amd64 3.3.2+dfsg-1 [1153 kB] Get:34 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB] Get:35 http://deb.debian.org/debian bookworm/main amd64 libquadmath0 amd64 12.2.0-14 [144 kB] Get:36 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get:37 http://deb.debian.org/debian bookworm/main amd64 libgomp1 amd64 12.2.0-14 [116 kB] Get:38 http://deb.debian.org/debian bookworm/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get:39 http://deb.debian.org/debian bookworm/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get:40 http://deb.debian.org/debian bookworm/main amd64 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get:41 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get:42 http://deb.debian.org/debian bookworm/main amd64 liblmdb0 amd64 0.9.24-1 [45.0 kB] Get:43 http://deb.debian.org/debian bookworm/main amd64 libmbedcrypto7 amd64 2.28.3-1 [277 kB] Get:44 http://deb.debian.org/debian bookworm/main amd64 libmbedx509-1 amd64 2.28.3-1 [128 kB] Get:45 http://deb.debian.org/debian bookworm/main amd64 libmbedtls14 amd64 2.28.3-1 [163 kB] Get:46 http://deb.debian.org/debian bookworm/main amd64 libpcre3 amd64 2:8.39-15 [341 kB] Get:47 http://deb.debian.org/debian bookworm/main amd64 libyaml-0-2 amd64 0.2.5-1 [53.6 kB] Get:48 http://deb.debian.org/debian bookworm/main amd64 python3-certifi all 2022.9.24-1 [153 kB] Get:49 http://deb.debian.org/debian bookworm/main amd64 python3-colorama all 0.4.6-2 [36.8 kB] Get:50 http://deb.debian.org/debian bookworm/main amd64 python3-colorlog all 6.7.0-1 [26.5 kB] Get:51 http://deb.debian.org/debian bookworm/main amd64 python3-pkg-resources all 66.1.1-1 [296 kB] Get:52 http://deb.debian.org/debian bookworm/main amd64 python3-networkx all 2.8.8-1 [1425 kB] Get:53 http://deb.debian.org/debian bookworm/main amd64 python3-packaging all 23.0-1 [32.5 kB] Get:54 http://deb.debian.org/debian bookworm/main amd64 python3-six all 1.16.0-4 [17.5 kB] Get:55 http://deb.debian.org/debian bookworm/main amd64 python3-dateutil all 2.8.2-2 [78.3 kB] Get:56 http://deb.debian.org/debian bookworm/main amd64 python3-numpy amd64 1:1.24.2-1 [5209 kB] Get:57 http://deb.debian.org/debian bookworm/main amd64 python3-tz all 2022.7.1-4 [30.1 kB] Get:58 http://deb.debian.org/debian bookworm/main amd64 python3-pandas-lib amd64 1.5.3+dfsg-2 [3499 kB] Get:59 http://deb.debian.org/debian bookworm/main amd64 python3-pandas all 1.5.3+dfsg-2 [2885 kB] Get:60 http://deb.debian.org/debian bookworm/main amd64 python3-yaml amd64 6.0-3+b2 [119 kB] Get:61 http://deb.debian.org/debian bookworm/main amd64 sphinx-rtd-theme-common all 1.2.0+dfsg-1 [997 kB] Get:62 http://deb.debian.org/debian bookworm/main amd64 ncbi-data all 6.1.20170106+dfsg1-10 [3557 kB] Get:63 http://deb.debian.org/debian bookworm/main amd64 ncbi-blast+ amd64 2.12.0+ds-3+b1 [11.9 MB] Get:64 http://deb.debian.org/debian bookworm/main amd64 macsyfinder amd64 2.0-2+b1 [12.1 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 70.2 MB in 0s (148 MB/s) Selecting previously unselected package perl-modules-5.36. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6093 files and directories currently installed.) Preparing to unpack .../0-perl-modules-5.36_5.36.0-7+deb12u1_all.deb ... Unpacking perl-modules-5.36 (5.36.0-7+deb12u1) ... Selecting previously unselected package libgdbm6:amd64. Preparing to unpack .../1-libgdbm6_1.23-3_amd64.deb ... Unpacking libgdbm6:amd64 (1.23-3) ... Selecting previously unselected package libgdbm-compat4:amd64. 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Unpacking ca-certificates (20230311) ... Selecting previously unselected package fonts-font-awesome. Preparing to unpack .../03-fonts-font-awesome_5.0.10+really4.7.0~dfsg-4.1_all.deb ... Unpacking fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Selecting previously unselected package libdivsufsort3:amd64. Preparing to unpack .../04-libdivsufsort3_2.0.1-5_amd64.deb ... Unpacking libdivsufsort3:amd64 (2.0.1-5) ... Selecting previously unselected package hmmer. Preparing to unpack .../05-hmmer_3.3.2+dfsg-1_amd64.deb ... Unpacking hmmer (3.3.2+dfsg-1) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../06-libblas3_3.11.0-2_amd64.deb ... Unpacking libblas3:amd64 (3.11.0-2) ... Selecting previously unselected package libquadmath0:amd64. Preparing to unpack .../07-libquadmath0_12.2.0-14_amd64.deb ... Unpacking libquadmath0:amd64 (12.2.0-14) ... Selecting previously unselected package libgfortran5:amd64. 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Selecting previously unselected package liblmdb0:amd64. Preparing to unpack .../14-liblmdb0_0.9.24-1_amd64.deb ... Unpacking liblmdb0:amd64 (0.9.24-1) ... Selecting previously unselected package libmbedcrypto7:amd64. Preparing to unpack .../15-libmbedcrypto7_2.28.3-1_amd64.deb ... Unpacking libmbedcrypto7:amd64 (2.28.3-1) ... Selecting previously unselected package libmbedx509-1:amd64. Preparing to unpack .../16-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 .../17-libmbedtls14_2.28.3-1_amd64.deb ... Unpacking libmbedtls14:amd64 (2.28.3-1) ... Selecting previously unselected package libpcre3:amd64. Preparing to unpack .../18-libpcre3_2%3a8.39-15_amd64.deb ... Unpacking libpcre3:amd64 (2:8.39-15) ... Selecting previously unselected package libyaml-0-2:amd64. Preparing to unpack .../19-libyaml-0-2_0.2.5-1_amd64.deb ... Unpacking libyaml-0-2:amd64 (0.2.5-1) ... 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Unpacking python3-pandas (1.5.3+dfsg-2) ... Selecting previously unselected package python3-yaml. Preparing to unpack .../32-python3-yaml_6.0-3+b2_amd64.deb ... Unpacking python3-yaml (6.0-3+b2) ... Selecting previously unselected package sphinx-rtd-theme-common. Preparing to unpack .../33-sphinx-rtd-theme-common_1.2.0+dfsg-1_all.deb ... Unpacking sphinx-rtd-theme-common (1.2.0+dfsg-1) ... Selecting previously unselected package ncbi-data. Preparing to unpack .../34-ncbi-data_6.1.20170106+dfsg1-10_all.deb ... Unpacking ncbi-data (6.1.20170106+dfsg1-10) ... Selecting previously unselected package ncbi-blast+. Preparing to unpack .../35-ncbi-blast+_2.12.0+ds-3+b1_amd64.deb ... Unpacking ncbi-blast+ (2.12.0+ds-3+b1) ... Selecting previously unselected package macsyfinder. Preparing to unpack .../36-macsyfinder_2.0-2+b1_amd64.deb ... Unpacking macsyfinder (2.0-2+b1) ... Setting up media-types (10.0.0) ... Setting up liblmdb0:amd64 (0.9.24-1) ... Setting up ncbi-data (6.1.20170106+dfsg1-10) ... Setting up libkeyutils1:amd64 (1.6.3-2) ... Setting up fonts-lato (2.0-2.1) ... 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 libgomp1:amd64 (12.2.0-14) ... Setting up libkrb5support0:amd64 (1.20.1-2+deb12u1) ... Setting up libpcre3:amd64 (2:8.39-15) ... Setting up perl-modules-5.36 (5.36.0-7+deb12u1) ... Setting up libblas3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libmbedcrypto7:amd64 (2.28.3-1) ... Setting up libquadmath0:amd64 (12.2.0-14) ... Setting up libncursesw6:amd64 (6.4-4) ... Setting up libk5crypto3:amd64 (1.20.1-2+deb12u1) ... Setting up libgfortran5:amd64 (12.2.0-14) ... Setting up libkrb5-3:amd64 (1.20.1-2+deb12u1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libdivsufsort3:amd64 (2.0.1-5) ... Setting up openssl (3.0.13-1~deb12u1) ... Setting up readline-common (8.2-1.3) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Setting up sphinx-rtd-theme-common (1.2.0+dfsg-1) ... Setting up libgdbm6:amd64 (1.23-3) ... 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 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 libgdbm-compat4:amd64 (1.23-3) ... Setting up libjs-sphinxdoc (5.3.0-4) ... Setting up hmmer (3.3.2+dfsg-1) ... Setting up libperl5.36:amd64 (5.36.0-7+deb12u1) ... Setting up libtirpc3:amd64 (1.3.3+ds-1) ... Setting up perl (5.36.0-7+deb12u1) ... Setting up libnsl2:amd64 (1.3.0-2) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6+deb12u2) ... Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6+deb12u2) ... Setting up python3 (3.11.2-1+b1) ... Setting up python3-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-packaging (23.0-1) ... 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+deb12u7) ... 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. 0m26.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'apt-get', '-y', 'install', 'macsyfinder'] 0m26.3s INFO: Running scripts post_install 0m26.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/post_install_exceptions'] 0m26.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/post_install_exceptions'] 0m26.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpodzd5te6'] 0m27.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpodzd5te6'] 0m27.2s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpodzd5te6 to bookworm-next 0m27.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main deb http://security.debian.org bookworm-security main deb http://deb.debian.org/debian/ bookworm-updates main deb http://deb.debian.org/debian/ bookworm-proposed-updates main 0m27.2s INFO: Running scripts pre_distupgrade 0m27.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m27.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m27.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_distupgrade_exceptions'] 0m27.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_distupgrade_exceptions'] 0m27.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m27.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m27.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m27.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m27.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m27.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m27.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'apt-get', 'update'] 0m28.8s DUMP: Get:1 http://security.debian.org bookworm-security InRelease [48.0 kB] Hit:2 http://deb.debian.org/debian bookworm InRelease Get:3 http://deb.debian.org/debian bookworm-updates InRelease [55.4 kB] Get:4 http://deb.debian.org/debian bookworm-proposed-updates InRelease [59.5 kB] Get:5 http://security.debian.org bookworm-security/main amd64 Packages [176 kB] Get:6 http://security.debian.org bookworm-security/main Translation-en [106 kB] Get:7 http://deb.debian.org/debian bookworm-updates/main amd64 Packages [13.8 kB] Get:8 http://deb.debian.org/debian bookworm-updates/main Translation-en [16.0 kB] Get:9 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 Packages [111 kB] Get:10 http://deb.debian.org/debian bookworm-proposed-updates/main Translation-en [64.2 kB] Fetched 649 kB in 1s (1016 kB/s) Reading package lists... 0m28.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'apt-get', 'update'] 0m28.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'apt-get', '-yf', 'dist-upgrade'] 0m33.3s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: libc-bin libc6 libgssapi-krb5-2 libk5crypto3 libkrb5-3 libkrb5support0 libssl3 libsystemd0 libudev1 openssl python3-numpy 11 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 12.8 MB of archives. After this operation, 1627 kB disk space will be freed. Get:1 http://security.debian.org bookworm-security/main amd64 libgssapi-krb5-2 amd64 1.20.1-2+deb12u2 [135 kB] Get:2 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libc6 amd64 2.36-9+deb12u8 [2754 kB] Get:3 http://security.debian.org bookworm-security/main amd64 libkrb5-3 amd64 1.20.1-2+deb12u2 [332 kB] Get:4 http://security.debian.org bookworm-security/main amd64 libkrb5support0 amd64 1.20.1-2+deb12u2 [32.6 kB] Get:5 http://security.debian.org bookworm-security/main amd64 libk5crypto3 amd64 1.20.1-2+deb12u2 [78.7 kB] Get:6 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libc-bin amd64 2.36-9+deb12u8 [608 kB] Get:7 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libsystemd0 amd64 252.29-1~deb12u1 [332 kB] Get:8 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libudev1 amd64 252.29-1~deb12u1 [108 kB] Get:9 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libssl3 amd64 3.0.14-1~deb12u1 [2024 kB] Get:10 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 openssl amd64 3.0.14-1~deb12u1 [1423 kB] Get:11 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 python3-numpy amd64 1:1.24.2-1+deb12u1 [4960 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 12.8 MB in 0s (117 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 ... 14060 files and directories currently installed.) Preparing to unpack .../libc6_2.36-9+deb12u8_amd64.deb ... Unpacking libc6:amd64 (2.36-9+deb12u8) over (2.36-9+deb12u7) ... Setting up libc6:amd64 (2.36-9+deb12u8) ... (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 ... 14060 files and directories currently installed.) Preparing to unpack .../libsystemd0_252.29-1~deb12u1_amd64.deb ... Unpacking libsystemd0:amd64 (252.29-1~deb12u1) over (252.26-1~deb12u2) ... Setting up libsystemd0:amd64 (252.29-1~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 ... 14060 files and directories currently installed.) Preparing to unpack .../libudev1_252.29-1~deb12u1_amd64.deb ... Unpacking libudev1:amd64 (252.29-1~deb12u1) over (252.26-1~deb12u2) ... Setting up libudev1:amd64 (252.29-1~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 ... 14060 files and directories currently installed.) Preparing to unpack .../0-libgssapi-krb5-2_1.20.1-2+deb12u2_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.20.1-2+deb12u2) over (1.20.1-2+deb12u1) ... Preparing to unpack .../1-libkrb5-3_1.20.1-2+deb12u2_amd64.deb ... Unpacking libkrb5-3:amd64 (1.20.1-2+deb12u2) over (1.20.1-2+deb12u1) ... Preparing to unpack .../2-libkrb5support0_1.20.1-2+deb12u2_amd64.deb ... Unpacking libkrb5support0:amd64 (1.20.1-2+deb12u2) over (1.20.1-2+deb12u1) ... Preparing to unpack .../3-libk5crypto3_1.20.1-2+deb12u2_amd64.deb ... Unpacking libk5crypto3:amd64 (1.20.1-2+deb12u2) over (1.20.1-2+deb12u1) ... Preparing to unpack .../4-libssl3_3.0.14-1~deb12u1_amd64.deb ... Unpacking libssl3:amd64 (3.0.14-1~deb12u1) over (3.0.13-1~deb12u1) ... Preparing to unpack .../5-openssl_3.0.14-1~deb12u1_amd64.deb ... Unpacking openssl (3.0.14-1~deb12u1) over (3.0.13-1~deb12u1) ... Preparing to unpack .../6-python3-numpy_1%3a1.24.2-1+deb12u1_amd64.deb ... Unpacking python3-numpy (1:1.24.2-1+deb12u1) over (1:1.24.2-1) ... Setting up libssl3:amd64 (3.0.14-1~deb12u1) ... Setting up libkrb5support0:amd64 (1.20.1-2+deb12u2) ... Setting up libk5crypto3:amd64 (1.20.1-2+deb12u2) ... Setting up python3-numpy (1:1.24.2-1+deb12u1) ... Setting up libkrb5-3:amd64 (1.20.1-2+deb12u2) ... Setting up openssl (3.0.14-1~deb12u1) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-2+deb12u2) ... Processing triggers for libc-bin (2.36-9+deb12u8) ... 0m33.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'apt-get', '-yf', 'dist-upgrade'] 0m33.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m33.6s DUMP: a7383adc5fdea12f93db4552c396e73a - 0m33.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m33.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'apt-cache', 'show', '--no-all-versions', 'macsyfinder'] 0m33.8s 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 0m33.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'apt-cache', 'show', '--no-all-versions', 'macsyfinder'] 0m33.8s INFO: apt-cache knows about the following packages: macsyfinder 0m33.8s INFO: Running scripts pre_install 0m33.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_install_database-server'] 0m33.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_install_database-server'] 0m33.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_install_exceptions'] 0m33.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_install_exceptions'] 0m33.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_install_extras'] 0m33.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_install_extras'] 0m33.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_install_foreign_architecture'] 0m33.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_install_foreign_architecture'] 0m33.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m33.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m33.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'apt-cache', 'policy'] 0m33.8s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 Packages release v=12-updates,o=Debian,a=proposed-updates,n=bookworm-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian bookworm-updates/main amd64 Packages release v=12-updates,o=Debian,a=stable-updates,n=bookworm-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org bookworm-security/main amd64 Packages release v=12,o=Debian,a=stable-security,n=bookworm-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.6,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m33.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'apt-cache', 'policy'] 0m33.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'apt-cache', 'policy', 'macsyfinder'] 0m33.9s 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 0m33.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'apt-cache', 'policy', 'macsyfinder'] 0m33.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'apt-get', '-y', 'install', 'macsyfinder'] 0m34.2s DUMP: Reading package lists... Building dependency tree... Reading state information... macsyfinder is already the newest version (2.0-2+b1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m34.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'apt-get', '-y', 'install', 'macsyfinder'] 0m34.2s INFO: Running scripts post_install 0m34.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/post_install_exceptions'] 0m34.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/post_install_exceptions'] 0m34.2s INFO: Running scripts post_distupgrade 0m34.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m34.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m34.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/post_distupgrade_exceptions'] 0m34.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/post_distupgrade_exceptions'] 0m34.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m34.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m34.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m34.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m34.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/post_distupgrade_zz_backports'] 0m34.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/post_distupgrade_zz_backports'] 0m34.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpodzd5te6'] 0m35.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpodzd5te6'] 0m35.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpodzd5te6'] 0m36.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpodzd5te6'] 0m36.0s INFO: Running scripts pre_install 0m36.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_install_database-server'] 0m36.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_install_database-server'] 0m36.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_install_exceptions'] 0m36.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_install_exceptions'] 0m36.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_install_extras'] 0m36.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_install_extras'] 0m36.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_install_foreign_architecture'] 0m36.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_install_foreign_architecture'] 0m36.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m36.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m36.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'apt-cache', 'policy'] 0m36.1s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 Packages release v=12-updates,o=Debian,a=proposed-updates,n=bookworm-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian bookworm-updates/main amd64 Packages release v=12-updates,o=Debian,a=stable-updates,n=bookworm-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org bookworm-security/main amd64 Packages release v=12,o=Debian,a=stable-security,n=bookworm-security,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.6,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m36.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'apt-cache', 'policy'] 0m36.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'apt-cache', 'policy', 'macsyfinder'] 0m36.1s 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 0m36.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'apt-cache', 'policy', 'macsyfinder'] 0m36.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'apt-get', '-y', 'install', 'macsyfinder=2.0-2+b1'] 0m36.4s DUMP: Reading package lists... Building dependency tree... Reading state information... macsyfinder is already the newest version (2.0-2+b1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m36.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'apt-get', '-y', 'install', 'macsyfinder=2.0-2+b1'] 0m36.4s INFO: Running scripts post_install 0m36.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/post_install_exceptions'] 0m36.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/post_install_exceptions'] 0m36.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpodzd5te6'] 0m37.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpodzd5te6'] 0m37.7s DEBUG: No file moved between /{bin|sbin|lib*} and /usr/{bin|sbin|lib*}. 0m37.7s INFO: /bin converted to /usr/bin by /usr merge 0m37.7s INFO: /lib converted to /usr/lib by /usr merge 0m37.7s INFO: /lib/init converted to /usr/lib/init by /usr merge 0m37.7s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 0m37.7s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 0m37.7s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 0m37.7s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 0m37.7s INFO: /lib/terminfo converted to /usr/lib/terminfo by /usr merge 0m37.7s INFO: /lib/terminfo/E converted to /usr/lib/terminfo/E by /usr merge 0m37.7s INFO: /lib/terminfo/a converted to /usr/lib/terminfo/a by /usr merge 0m37.7s INFO: /lib/terminfo/c converted to /usr/lib/terminfo/c by /usr merge 0m37.7s INFO: /lib/terminfo/d converted to /usr/lib/terminfo/d by /usr merge 0m37.7s INFO: /lib/terminfo/h converted to /usr/lib/terminfo/h by /usr merge 0m37.7s INFO: /lib/terminfo/l converted to /usr/lib/terminfo/l by /usr merge 0m37.7s INFO: /lib/terminfo/m converted to /usr/lib/terminfo/m by /usr merge 0m37.7s INFO: /lib/terminfo/p converted to /usr/lib/terminfo/p by /usr merge 0m37.7s INFO: /lib/terminfo/r converted to /usr/lib/terminfo/r by /usr merge 0m37.7s INFO: /lib/terminfo/s converted to /usr/lib/terminfo/s by /usr merge 0m37.7s INFO: /lib/terminfo/t converted to /usr/lib/terminfo/t by /usr merge 0m37.7s INFO: /lib/terminfo/v converted to /usr/lib/terminfo/v by /usr merge 0m37.7s INFO: /lib/terminfo/w converted to /usr/lib/terminfo/w by /usr merge 0m37.7s INFO: /lib/terminfo/x converted to /usr/lib/terminfo/x by /usr merge 0m37.7s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 0m37.7s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 0m37.7s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 0m37.7s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 0m37.7s INFO: /lib64 converted to /usr/lib64 by /usr merge 0m37.7s INFO: /sbin converted to /usr/sbin by /usr merge 0m38.5s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', '-ac', '--ignore-obsolete'] 0m40.0s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', '-ac', '--ignore-obsolete'] 0m40.0s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m40.0s DUMP: 0.15.6 0m40.0s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m40.0s INFO: Running adequate version 0.15.6 now. 0m40.0s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'macsyfinder'] 0m40.2s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'macsyfinder'] 0m40.2s INFO: Running scripts pre_remove 0m40.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m40.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m40.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m40.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m40.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m41.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m41.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m41.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m41.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m41.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m41.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_remove_exceptions'] 0m41.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/pre_remove_exceptions'] 0m41.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m41.9s DUMP: install ok installed adduser adduser 3.134 install ok installed apt apt 2.6.1 install ok installed base-files base-files 12.4+deb12u6 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b7 install ok installed bsdutils bsdutils 1:2.38.1-5+deb12u1 install ok installed ca-certificates ca-certificates 20230311 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.12-2 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.3+deb12u1 install ok installed debianutils debianutils 5.7-0.5~deb12u1 install ok installed diffutils diffutils 1:3.8-4 install ok installed dpkg dpkg 1.21.22 install ok installed e2fsprogs e2fsprogs 1.47.0-2 install ok installed findutils findutils 4.9.0-4 install ok installed fonts-font-awesome fonts-font-awesome 5.0.10+really4.7.0~dfsg-4.1 install ok installed fonts-lato fonts-lato 2.0-2.1 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-14 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.8-5 install ok installed gzip gzip 1.12-1 install ok installed hmmer hmmer 3.3.2+dfsg-1 install ok installed hostname hostname 3.23+nmu1 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.6.1 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.0.9-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.9-1 install ok installed libblas3:amd64 libblas3 3.11.0-2 install ok installed libblkid1:amd64 libblkid1 2.38.1-5+deb12u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-9+deb12u8 install ok installed libc6:amd64 libc6 2.36-9+deb12u8 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3 install ok installed libcap2:amd64 libcap2 1:2.66-4 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.33-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.270 install ok installed libdivsufsort3:amd64 libdivsufsort3 2.0.1-5 install ok installed libexpat1:amd64 libexpat1 2.5.0-1 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-14 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-3 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.23-3 install ok installed libgdbm6:amd64 libgdbm6 1.23-3 install ok installed libgfortran5:amd64 libgfortran5 12.2.0-14 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.9-2+deb12u3 install ok installed libgomp1:amd64 libgomp1 12.2.0-14 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.20.1-2+deb12u2 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed libjs-jquery libjs-jquery 3.6.1+dfsg+~3.5.14-1 install ok installed libjs-sphinxdoc libjs-sphinxdoc 5.3.0-4 install ok installed libjs-underscore libjs-underscore 1.13.4~dfsg+~1.11.4-3 install ok installed libk5crypto3:amd64 libk5crypto3 1.20.1-2+deb12u2 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.20.1-2+deb12u2 install ok installed libkrb5support0:amd64 libkrb5support0 1.20.1-2+deb12u2 install ok installed liblapack3:amd64 liblapack3 3.11.0-2 install ok installed liblmdb0:amd64 liblmdb0 0.9.24-1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.1-0.2 install ok installed libmbedcrypto7:amd64 libmbedcrypto7 2.28.3-1 install ok installed libmbedtls14:amd64 libmbedtls14 2.28.3-1 install ok installed libmbedx509-1:amd64 libmbedx509-1 2.28.3-1 install ok installed libmd0:amd64 libmd0 1.0.4-2 install ok installed libmount1:amd64 libmount1 2.38.1-5+deb12u1 install ok installed libncursesw6:amd64 libncursesw6 6.4-4 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-6+deb12u1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-6+deb12u1 install ok installed libpam-runtime libpam-runtime 1.5.2-6+deb12u1 install ok installed libpam0g:amd64 libpam0g 1.5.2-6+deb12u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-1 install ok installed libpcre3:amd64 libpcre3 2:8.39-15 install ok installed libperl5.36:amd64 libperl5.36 5.36.0-7+deb12u1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.11.2-1+b1 install ok installed libpython3.11-minimal:amd64 libpython3.11-minimal 3.11.2-6+deb12u2 install ok installed libpython3.11-stdlib:amd64 libpython3.11-stdlib 3.11.2-6+deb12u2 install ok installed libquadmath0:amd64 libquadmath0 12.2.0-14 install ok installed libreadline8:amd64 libreadline8 8.2-1.3 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+deb12u1 install ok installed libselinux1:amd64 libselinux1 3.4-1+b6 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b5 install ok installed libsepol2:amd64 libsepol2 3.4-2.1 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-5+deb12u1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.40.1-2 install ok installed libss2:amd64 libss2 1.47.0-2 install ok installed libssl3:amd64 libssl3 3.0.14-1~deb12u1 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-14 install ok installed libsystemd0:amd64 libsystemd0 252.29-1~deb12u1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.4-4 install ok installed libtirpc-common libtirpc-common 1.3.3+ds-1 install ok installed libtirpc3:amd64 libtirpc3 1.3.3+ds-1 install ok installed libudev1:amd64 libudev1 252.29-1~deb12u1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+deb12u1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libyaml-0-2:amd64 libyaml-0-2 0.2.5-1 install ok installed libzstd1:amd64 libzstd1 1.5.4+dfsg2-5 install ok installed login login 1:4.13+dfsg1-1+b1 install ok installed logsave logsave 1.47.0-2 install ok installed macsyfinder macsyfinder 2.0-2+b1 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed media-types media-types 10.0.0 install ok installed mount mount 2.38.1-5+deb12u1 install ok installed ncbi-blast+ ncbi-blast+ 2.12.0+ds-3+b1 install ok installed ncbi-data ncbi-data 6.1.20170106+dfsg1-10 install ok installed ncurses-base ncurses-base 6.4-4 install ok installed ncurses-bin ncurses-bin 6.4-4 install ok installed openssl openssl 3.0.14-1~deb12u1 install ok installed passwd passwd 1:4.13+dfsg1-1+b1 install ok installed perl perl 5.36.0-7+deb12u1 install ok installed perl-base perl-base 5.36.0-7+deb12u1 install ok installed perl-modules-5.36 perl-modules-5.36 5.36.0-7+deb12u1 install ok installed python3 python3 3.11.2-1+b1 install ok installed python3-certifi python3-certifi 2022.9.24-1 install ok installed python3-colorama python3-colorama 0.4.6-2 install ok installed python3-colorlog python3-colorlog 6.7.0-1 install ok installed python3-dateutil python3-dateutil 2.8.2-2 install ok installed python3-minimal python3-minimal 3.11.2-1+b1 install ok installed python3-networkx python3-networkx 2.8.8-1 install ok installed python3-numpy python3-numpy 1:1.24.2-1+deb12u1 install ok installed python3-packaging python3-packaging 23.0-1 install ok installed python3-pandas python3-pandas 1.5.3+dfsg-2 install ok installed python3-pandas-lib:amd64 python3-pandas-lib 1.5.3+dfsg-2 install ok installed python3-pkg-resources python3-pkg-resources 66.1.1-1 install ok installed python3-six python3-six 1.16.0-4 install ok installed python3-tz python3-tz 2022.7.1-4 install ok installed python3-yaml python3-yaml 6.0-3+b2 install ok installed python3.11 python3.11 3.11.2-6+deb12u2 install ok installed python3.11-minimal python3.11-minimal 3.11.2-6+deb12u2 install ok installed readline-common readline-common 8.2-1.3 install ok installed sed sed 4.9-1 install ok installed sphinx-rtd-theme-common sphinx-rtd-theme-common 1.2.0+dfsg-1 install ok installed sysvinit-utils sysvinit-utils 3.06-4 install ok installed tar tar 1.34+dfsg-1.2+deb12u1 install ok installed tzdata tzdata 2024a-0+deb12u1 install ok installed usr-is-merged usr-is-merged 37~deb12u1 install ok installed util-linux util-linux 2.38.1-5+deb12u1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+deb12u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m41.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m41.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'apt-get', 'remove', 'ca-certificates', 'fonts-font-awesome', 'fonts-lato', 'hmmer', 'libblas3:amd64', 'libdivsufsort3:amd64', 'libexpat1:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libjs-jquery', 'libjs-sphinxdoc', 'libjs-underscore', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblmdb0:amd64', 'libmbedcrypto7:amd64', 'libmbedtls14:amd64', 'libmbedx509-1:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libpcre3:amd64', 'libperl5.36:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libssl3:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libyaml-0-2:amd64', 'media-types', 'ncbi-blast+-', 'ncbi-data', 'openssl', 'perl', 'perl-modules-5.36', 'python3', 'python3-certifi', 'python3-colorama', 'python3-colorlog', 'python3-dateutil', 'python3-minimal', 'python3-networkx', 'python3-numpy', 'python3-packaging', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-pkg-resources', 'python3-six', 'python3-tz', 'python3-yaml', 'python3.11', 'python3.11-minimal', 'readline-common', 'sphinx-rtd-theme-common', 'macsyfinder'] 0m44.4s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: ca-certificates fonts-font-awesome fonts-lato hmmer libblas3 libdivsufsort3 libexpat1 libgdbm-compat4 libgdbm6 libgfortran5 libgomp1 libgssapi-krb5-2 libjs-jquery libjs-sphinxdoc libjs-underscore libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblmdb0 libmbedcrypto7 libmbedtls14 libmbedx509-1 libncursesw6 libnsl2 libpcre3 libperl5.36 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libquadmath0 libreadline8 libsqlite3-0 libssl3 libtirpc-common libtirpc3 libyaml-0-2 macsyfinder media-types ncbi-blast+ ncbi-data openssl perl perl-modules-5.36 python3 python3-certifi python3-colorama python3-colorlog python3-dateutil python3-minimal python3-networkx python3-numpy python3-packaging python3-pandas python3-pandas-lib python3-pkg-resources python3-six python3-tz python3-yaml python3.11 python3.11-minimal readline-common sphinx-rtd-theme-common 0 upgraded, 0 newly installed, 64 to remove and 0 not upgraded. After this operation, 309 MB disk space will be freed. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 14059 files and directories currently installed.) Removing macsyfinder (2.0-2+b1) ... Removing python3-certifi (2022.9.24-1) ... Removing ca-certificates (20230311) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing sphinx-rtd-theme-common (1.2.0+dfsg-1) ... Removing fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Removing fonts-lato (2.0-2.1) ... Removing hmmer (3.3.2+dfsg-1) ... Removing python3-pandas (1.5.3+dfsg-2) ... Removing python3-pandas-lib:amd64 (1.5.3+dfsg-2) ... Removing python3-numpy (1:1.24.2-1+deb12u1) ... Removing liblapack3:amd64 (3.11.0-2) ... Removing libblas3:amd64 (3.11.0-2) ... Removing libdivsufsort3:amd64 (2.0.1-5) ... Removing python3-yaml (6.0-3+b2) ... Removing python3-dateutil (2.8.2-2) ... Removing python3-six (1.16.0-4) ... Removing ncbi-blast+ (2.12.0+ds-3+b1) ... Removing python3-networkx (2.8.8-1) ... Removing python3-pkg-resources (66.1.1-1) ... Removing perl (5.36.0-7+deb12u1) ... Removing libperl5.36:amd64 (5.36.0-7+deb12u1) ... Removing libgdbm-compat4:amd64 (1.23-3) ... Removing libgdbm6:amd64 (1.23-3) ... Removing libgfortran5:amd64 (12.2.0-14) ... Removing libgomp1:amd64 (12.2.0-14) ... Removing libjs-sphinxdoc (5.3.0-4) ... 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 (0.9.24-1) ... Removing libmbedtls14:amd64 (2.28.3-1) ... Removing libmbedx509-1:amd64 (2.28.3-1) ... Removing libmbedcrypto7:amd64 (2.28.3-1) ... Removing libpcre3:amd64 (2:8.39-15) ... Removing libquadmath0:amd64 (12.2.0-14) ... Removing openssl (3.0.14-1~deb12u1) ... Removing libyaml-0-2:amd64 (0.2.5-1) ... Removing ncbi-data (6.1.20170106+dfsg1-10) ... Removing perl-modules-5.36 (5.36.0-7+deb12u1) ... Removing python3-colorama (0.4.6-2) ... Removing python3-colorlog (6.7.0-1) ... Removing python3-packaging (23.0-1) ... Removing python3-tz (2022.7.1-4) ... Removing python3 (3.11.2-1+b1) ... Removing python3.11 (3.11.2-6+deb12u2) ... Removing python3-minimal (3.11.2-1+b1) ... Removing python3.11-minimal (3.11.2-6+deb12u2) ... Removing libexpat1:amd64 (2.5.0-1) ... Removing libpython3-stdlib:amd64 (3.11.2-1+b1) ... Removing libpython3.11-stdlib:amd64 (3.11.2-6+deb12u2) ... find: '/usr/lib/python3': No such file or directory Removing libnsl2:amd64 (1.3.0-2) ... Removing libtirpc3:amd64 (1.3.3+ds-1) ... Removing libgssapi-krb5-2:amd64 (1.20.1-2+deb12u2) ... Removing libkrb5-3:amd64 (1.20.1-2+deb12u2) ... Removing libk5crypto3:amd64 (1.20.1-2+deb12u2) ... Removing libkeyutils1:amd64 (1.6.3-2) ... Removing libkrb5support0:amd64 (1.20.1-2+deb12u2) ... Removing libncursesw6:amd64 (6.4-4) ... Removing libpython3.11-minimal:amd64 (3.11.2-6+deb12u2) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8:amd64 (8.2-1.3) ... Removing libsqlite3-0:amd64 (3.40.1-2) ... Removing libssl3:amd64 (3.0.14-1~deb12u1) ... Removing libtirpc-common (1.3.3+ds-1) ... Removing media-types (10.0.0) ... Removing readline-common (8.2-1.3) ... Processing triggers for libc-bin (2.36-9+deb12u8) ... 0m44.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'apt-get', 'remove', 'ca-certificates', 'fonts-font-awesome', 'fonts-lato', 'hmmer', 'libblas3:amd64', 'libdivsufsort3:amd64', 'libexpat1:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libjs-jquery', 'libjs-sphinxdoc', 'libjs-underscore', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblmdb0:amd64', 'libmbedcrypto7:amd64', 'libmbedtls14:amd64', 'libmbedx509-1:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libpcre3:amd64', 'libperl5.36:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libssl3:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libyaml-0-2:amd64', 'media-types', 'ncbi-blast+-', 'ncbi-data', 'openssl', 'perl', 'perl-modules-5.36', 'python3', 'python3-certifi', 'python3-colorama', 'python3-colorlog', 'python3-dateutil', 'python3-minimal', 'python3-networkx', 'python3-numpy', 'python3-packaging', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-pkg-resources', 'python3-six', 'python3-tz', 'python3-yaml', 'python3.11', 'python3.11-minimal', 'readline-common', 'sphinx-rtd-theme-common', 'macsyfinder'] 0m44.4s INFO: Running scripts post_remove 0m44.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/post_remove_exceptions'] 0m44.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/post_remove_exceptions'] 0m44.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'dpkg', '--purge', 'ca-certificates', 'fonts-font-awesome', 'fonts-lato', 'hmmer', 'libblas3:amd64', 'libdivsufsort3:amd64', 'libexpat1:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libjs-jquery', 'libjs-sphinxdoc', 'libjs-underscore', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblmdb0:amd64', 'libmbedcrypto7:amd64', 'libmbedtls14:amd64', 'libmbedx509-1:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libpcre3:amd64', 'libperl5.36:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libssl3:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libyaml-0-2:amd64', 'media-types', 'ncbi-blast+', 'ncbi-data', 'openssl', 'perl', 'perl-modules-5.36', 'python3', 'python3-certifi', 'python3-colorama', 'python3-colorlog', 'python3-dateutil', 'python3-minimal', 'python3-networkx', 'python3-numpy', 'python3-packaging', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-pkg-resources', 'python3-six', 'python3-tz', 'python3-yaml', 'python3.11', 'python3.11-minimal', 'readline-common', 'sphinx-rtd-theme-common'] 0m44.5s DUMP: (Reading database ... 6107 files and directories currently installed.) Purging configuration files for ca-certificates (20230311) ... 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 libdivsufsort3 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libgdbm-compat4 which isn't installed dpkg: warning: ignoring request to remove libgdbm6 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 libgssapi-krb5-2:amd64 (1.20.1-2+deb12u2) ... 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 libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove liblmdb0 which isn't installed dpkg: warning: ignoring request to remove libmbedcrypto7 which isn't installed dpkg: warning: ignoring request to remove libmbedtls14 which isn't installed dpkg: warning: ignoring request to remove libmbedx509-1 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libnsl2 which isn't installed dpkg: warning: ignoring request to remove libpcre3 which isn't installed dpkg: warning: ignoring request to remove libperl5.36 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.11-minimal:amd64 (3.11.2-6+deb12u2) ... dpkg: warning: ignoring request to remove libpython3.11-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 libssl3 which isn't installed Purging configuration files for libtirpc-common (1.3.3+ds-1) ... dpkg: warning: ignoring request to remove libtirpc3 which isn't installed dpkg: warning: ignoring request to remove libyaml-0-2 which isn't installed Purging configuration files for media-types (10.0.0) ... 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 openssl (3.0.14-1~deb12u1) ... Purging configuration files for perl (5.36.0-7+deb12u1) ... dpkg: warning: ignoring request to remove perl-modules-5.36 which isn't installed Purging configuration files for python3 (3.11.2-1+b1) ... 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-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-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 (3.11.2-6+deb12u2) ... Purging configuration files for readline-common (8.2-1.3) ... dpkg: warning: ignoring request to remove sphinx-rtd-theme-common which isn't installed 0m44.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'dpkg', '--purge', 'ca-certificates', 'fonts-font-awesome', 'fonts-lato', 'hmmer', 'libblas3:amd64', 'libdivsufsort3:amd64', 'libexpat1:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libjs-jquery', 'libjs-sphinxdoc', 'libjs-underscore', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblmdb0:amd64', 'libmbedcrypto7:amd64', 'libmbedtls14:amd64', 'libmbedx509-1:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libpcre3:amd64', 'libperl5.36:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libssl3:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libyaml-0-2:amd64', 'media-types', 'ncbi-blast+', 'ncbi-data', 'openssl', 'perl', 'perl-modules-5.36', 'python3', 'python3-certifi', 'python3-colorama', 'python3-colorlog', 'python3-dateutil', 'python3-minimal', 'python3-networkx', 'python3-numpy', 'python3-packaging', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-pkg-resources', 'python3-six', 'python3-tz', 'python3-yaml', 'python3.11', 'python3.11-minimal', 'readline-common', 'sphinx-rtd-theme-common'] 0m44.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'dpkg', '--purge', 'macsyfinder'] 0m44.5s DUMP: (Reading database ... 6094 files and directories currently installed.) Purging configuration files for macsyfinder (2.0-2+b1) ... 0m44.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'dpkg', '--purge', 'macsyfinder'] 0m44.5s INFO: Running scripts post_purge 0m44.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/post_purge_exceptions'] 0m44.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/post_purge_exceptions'] 0m44.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'dpkg', '--purge', '--pending'] 0m44.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'dpkg', '--purge', '--pending'] 0m44.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'dpkg', '--remove', '--pending'] 0m44.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'dpkg', '--remove', '--pending'] 0m44.6s INFO: Running scripts post_test 0m44.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/post_test_exceptions'] 0m44.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'tmp/scripts/post_test_exceptions'] 0m44.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpodzd5te6'] 0m44.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpodzd5te6'] 0m44.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'dpkg-divert', '--list'] 0m44.9s DUMP: local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib local diversion of /usr/bin/sync to /usr/bin/sync.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m44.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'dpkg-divert', '--list'] 0m44.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'apt-get', 'clean'] 0m45.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpodzd5te6', 'apt-get', 'clean'] 0m45.0s DEBUG: Recording chroot state 0m45.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpodzd5te6/dev/shm'] 0m45.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpodzd5te6/dev/shm'] 0m45.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpodzd5te6/dev/console'] 0m45.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpodzd5te6/dev/console'] 0m45.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpodzd5te6/dev/ptmx'] 0m45.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpodzd5te6/dev/ptmx'] 0m45.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpodzd5te6/dev/pts'] 0m46.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpodzd5te6/dev/pts'] 0m46.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpodzd5te6/proc'] 0m46.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpodzd5te6/proc'] 0m46.0s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpodzd5te6'] 0m46.1s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpodzd5te6'] 0m46.1s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpodzd5te6 0m46.1s INFO: PASS: Upgrading between Debian distributions. 0m46.1s INFO: PASS: All tests. 0m46.1s INFO: piuparts run ends. ret=0 End: 2024-08-23 02:06:25 GMT