Start: 2024-08-23 11:48:24 GMT [bookworm] Package: python3-peptidebuilder Source: peptidebuilder Version: 1.1.0-3 Installed-Size: 104 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-biopython, python3:any Description: generate atomic oligopeptide 3D structure from sequence Homepage: https://github.com/clauswilke/PeptideBuilder/ Description-md5: 9d8dcf8e84f047bc502b102ffdbf4944 Section: science Priority: optional Filename: pool/main/p/peptidebuilder/python3-peptidebuilder_1.1.0-3_all.deb Size: 12780 MD5sum: c2277d261836aa5259d9e21bb7c5a2f3 SHA256: a85cba1037fbb6ee3a74267c5402047c23ffedd844fea3c714f62383e2bd4d5a [bookworm-next] Package: python3-peptidebuilder Source: peptidebuilder Version: 1.1.0-3 Installed-Size: 104 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-biopython, python3:any Description: generate atomic oligopeptide 3D structure from sequence Homepage: https://github.com/clauswilke/PeptideBuilder/ Description-md5: 9d8dcf8e84f047bc502b102ffdbf4944 Section: science Priority: optional Filename: pool/main/p/peptidebuilder/python3-peptidebuilder_1.1.0-3_all.deb Size: 12780 MD5sum: c2277d261836aa5259d9e21bb7c5a2f3 SHA256: a85cba1037fbb6ee3a74267c5402047c23ffedd844fea3c714f62383e2bd4d5a 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 python3-peptidebuilder=1.1.0-3 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 python3-peptidebuilder=1.1.0-3 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/tmpl5fpex_k 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpl5fpex_k 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', '--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/tmpl5fpex_k', '--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/tmpl5fpex_k/proc'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k/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/tmpl5fpex_k/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/tmpl5fpex_k/dev/pts'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k/dev/ptmx'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k/dev/ptmx'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/7', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k/dev/console'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/7', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k/dev/console'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k/dev/shm'] 0m0.4s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k/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/tmpl5fpex_k/tmp/scripts/ 0m0.4s INFO: Running scripts post_chroot_unpack 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'apt-get', 'update'] 0m1.2s DUMP: Hit:1 http://deb.debian.org/debian bookworm InRelease Reading package lists... 0m1.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'apt-get', 'update'] 0m1.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'apt-get', '-yf', 'dist-upgrade'] 0m1.7s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m1.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'apt-get', '-yf', 'dist-upgrade'] 0m1.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.0s DUMP: 913e17be84ed63a3110ce3137c1d003a - 0m2.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.0s INFO: Running scripts post_setup 0m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/post_setup_dummy_users'] 0m3.1s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/post_setup_dummy_users'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/post_setup_forbid_home'] 0m3.1s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/post_setup_forbid_home'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.1s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/post_setup_minimize'] 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/post_setup_minimize'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/post_setup_zz_backports'] 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/post_setup_zz_backports'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', '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/tmpl5fpex_k', '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 0m3.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k'] 0m3.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k'] 0m3.5s INFO: Running scripts is_testable 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/is_testable_uninstallable'] 0m3.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/is_testable_uninstallable'] 0m3.5s INFO: Running scripts pre_test 0m3.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_test_exceptions'] 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_test_exceptions'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', '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/tmpl5fpex_k', 'tmp/scripts/pre_test_root_password'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'apt-cache', 'show', '--no-all-versions', 'python3-peptidebuilder'] 0m3.8s DUMP: Package: python3-peptidebuilder Source: peptidebuilder Version: 1.1.0-3 Installed-Size: 104 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-biopython, python3:any Description-en: generate atomic oligopeptide 3D structure from sequence PeptideBuilder is a simple Python library to generate model peptides. Typically on daisychains a few residues in e.g. biopython, and so does PeptideBuilder, but it does it right. . Parameters like the backbone formation can be specified ab initio, rotamers/energy minimisation is left to respective specialist tools. Description-md5: 9d8dcf8e84f047bc502b102ffdbf4944 Homepage: https://github.com/clauswilke/PeptideBuilder/ Section: science Priority: optional Filename: pool/main/p/peptidebuilder/python3-peptidebuilder_1.1.0-3_all.deb Size: 12780 MD5sum: c2277d261836aa5259d9e21bb7c5a2f3 SHA256: a85cba1037fbb6ee3a74267c5402047c23ffedd844fea3c714f62383e2bd4d5a 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'apt-cache', 'show', '--no-all-versions', 'python3-peptidebuilder'] 0m3.8s INFO: apt-cache knows about the following packages: python3-peptidebuilder 0m3.8s INFO: Running scripts pre_install 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_install_database-server'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_install_database-server'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_install_exceptions'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_install_exceptions'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_install_extras'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_install_extras'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'apt-cache', 'policy'] 0m3.9s 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: 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'apt-cache', 'policy'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'apt-cache', 'policy', 'python3-peptidebuilder'] 0m3.9s DUMP: python3-peptidebuilder: Installed: (none) Candidate: 1.1.0-3 Version table: 1.1.0-3 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'apt-cache', 'policy', 'python3-peptidebuilder'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'apt-get', '-y', 'install', 'python3-peptidebuilder'] 0m54.4s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: fonts-urw-base35 libblas3 libbrotli1 libbsd0 libdeflate0 libexpat1 libfontenc1 libfreetype6 libfribidi0 libgdbm-compat4 libgdbm6 libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libimagequant0 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 liblerc4 libncursesw6 libnsl2 libopenjp2-7 libperl5.36 libpng16-16 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libquadmath0 libraqm0 libreadline8 libsqlite3-0 libssl3 libtiff6 libtirpc-common libtirpc3 libwebp7 libwebpdemux2 libwebpmux3 libxau6 libxcb1 libxdmcp6 mailcap media-types mime-support perl perl-modules-5.36 python3 python3-biopython python3-minimal python3-numpy python3-pil python3-pkg-resources python3-renderpm python3-reportlab python3-reportlab-accel python3.11 python3.11-minimal readline-common sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core Suggested packages: fonts-freefont-otf | fonts-freefont-ttf fonts-texgyre gdbm-l10n low-memory-monitor krb5-doc krb5-user liblcms2-utils sensible-utils perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl python3-doc python3-tk python3-venv bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle3 phylip phyml prank probcons python3-mysqldb python3-matplotlib python3-mmtf python3-rdflib python3-psycopg2 python3-scipy raxml samtools t-coffee wise gcc gfortran python3-dev python3-pytest python-pil-doc python3-setuptools pdf-viewer python3-egenix-mxtexttools python-reportlab-doc python3.11-venv python3.11-doc binutils binfmt-support readline-doc sgml-base-doc debhelper Recommended packages: libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales libgpm2 bzip2 file xz-utils netbase python-biopython-doc ncbi-blast+ python3-olefile ca-certificates The following NEW packages will be installed: fonts-urw-base35 libblas3 libbrotli1 libbsd0 libdeflate0 libexpat1 libfontenc1 libfreetype6 libfribidi0 libgdbm-compat4 libgdbm6 libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libimagequant0 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 liblerc4 libncursesw6 libnsl2 libopenjp2-7 libperl5.36 libpng16-16 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libquadmath0 libraqm0 libreadline8 libsqlite3-0 libssl3 libtiff6 libtirpc-common libtirpc3 libwebp7 libwebpdemux2 libwebpmux3 libxau6 libxcb1 libxdmcp6 mailcap media-types mime-support perl perl-modules-5.36 python3 python3-biopython python3-minimal python3-numpy python3-peptidebuilder python3-pil python3-pkg-resources python3-renderpm python3-reportlab python3-reportlab-accel python3.11 python3.11-minimal readline-common sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 0 upgraded, 73 newly installed, 0 to remove and 0 not upgraded. Need to get 47.1 MB of archives. After this operation, 176 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 libssl3 amd64 3.0.13-1~deb12u1 [2022 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6+deb12u2 [814 kB] Get:8 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get:9 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6+deb12u2 [2067 kB] Get:10 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get:11 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get:12 http://deb.debian.org/debian bookworm/main amd64 mailcap all 3.70+nmu1 [32.0 kB] Get:13 http://deb.debian.org/debian bookworm/main amd64 mime-support all 3.66 [10.9 kB] Get:14 http://deb.debian.org/debian bookworm/main amd64 libncursesw6 amd64 6.4-4 [134 kB] Get:15 http://deb.debian.org/debian bookworm/main amd64 libkrb5support0 amd64 1.20.1-2+deb12u1 [32.4 kB] Get:16 http://deb.debian.org/debian bookworm/main amd64 libk5crypto3 amd64 1.20.1-2+deb12u1 [78.9 kB] Get:17 http://deb.debian.org/debian bookworm/main amd64 libkeyutils1 amd64 1.6.3-2 [8808 B] Get:18 http://deb.debian.org/debian bookworm/main amd64 libkrb5-3 amd64 1.20.1-2+deb12u1 [332 kB] Get:19 http://deb.debian.org/debian bookworm/main amd64 libgssapi-krb5-2 amd64 1.20.1-2+deb12u1 [134 kB] Get:20 http://deb.debian.org/debian bookworm/main amd64 libtirpc-common all 1.3.3+ds-1 [14.0 kB] Get:21 http://deb.debian.org/debian bookworm/main amd64 libtirpc3 amd64 1.3.3+ds-1 [85.2 kB] Get:22 http://deb.debian.org/debian bookworm/main amd64 libnsl2 amd64 1.3.0-2 [39.5 kB] Get:23 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get:24 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get:25 http://deb.debian.org/debian bookworm/main amd64 libsqlite3-0 amd64 3.40.1-2 [837 kB] Get:26 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6+deb12u2 [1799 kB] Get:27 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6+deb12u2 [573 kB] Get:28 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get:29 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get:30 http://deb.debian.org/debian bookworm/main amd64 sgml-base all 1.31 [15.4 kB] Get:31 http://deb.debian.org/debian bookworm/main amd64 libfontenc1 amd64 1:1.1.4-1 [24.3 kB] Get:32 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get:33 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB] Get:34 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-5+deb12u3 [398 kB] Get:35 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB] Get:36 http://deb.debian.org/debian bookworm/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get:37 http://deb.debian.org/debian bookworm/main amd64 xfonts-utils amd64 1:7.7+6 [93.0 kB] Get:38 http://deb.debian.org/debian bookworm/main amd64 fonts-urw-base35 all 20200910-7 [10.8 MB] Get:39 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB] Get:40 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get:41 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get:42 http://deb.debian.org/debian bookworm/main amd64 libfribidi0 amd64 1.0.8-2.1 [65.0 kB] Get:43 http://deb.debian.org/debian bookworm/main amd64 libquadmath0 amd64 12.2.0-14 [144 kB] Get:44 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get:45 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2+deb12u3 [1400 kB] Get:46 http://deb.debian.org/debian bookworm/main amd64 libgomp1 amd64 12.2.0-14 [116 kB] Get:47 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get:48 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB] Get:49 http://deb.debian.org/debian bookworm/main amd64 libimagequant0 amd64 2.17.0-1 [32.5 kB] Get:50 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB] Get:51 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB] Get:52 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get:53 http://deb.debian.org/debian bookworm/main amd64 liblcms2-2 amd64 2.14-2 [154 kB] Get:54 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB] Get:55 http://deb.debian.org/debian bookworm/main amd64 libopenjp2-7 amd64 2.5.0-2 [189 kB] Get:56 http://deb.debian.org/debian bookworm/main amd64 libraqm0 amd64 0.7.0-4.1 [10.6 kB] Get:57 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.2+deb12u1 [286 kB] Get:58 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-6+deb12u1 [316 kB] Get:59 http://deb.debian.org/debian bookworm/main amd64 libwebpdemux2 amd64 1.2.4-0.2+deb12u1 [99.4 kB] Get:60 http://deb.debian.org/debian bookworm/main amd64 libwebpmux3 amd64 1.2.4-0.2+deb12u1 [109 kB] Get:61 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get:62 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:63 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get:64 http://deb.debian.org/debian bookworm/main amd64 python3-pkg-resources all 66.1.1-1 [296 kB] Get:65 http://deb.debian.org/debian bookworm/main amd64 python3-numpy amd64 1:1.24.2-1 [5209 kB] Get:66 http://deb.debian.org/debian bookworm/main amd64 python3-renderpm amd64 3.6.12-1+b1 [79.2 kB] Get:67 http://deb.debian.org/debian bookworm/main amd64 python3-reportlab-accel amd64 3.6.12-1+b1 [38.6 kB] Get:68 http://deb.debian.org/debian bookworm/main amd64 python3-pil amd64 9.4.0-1.1+deb12u1 [472 kB] Get:69 http://deb.debian.org/debian bookworm/main amd64 python3-reportlab all 3.6.12-1 [564 kB] Get:70 http://deb.debian.org/debian bookworm/main amd64 xml-core all 0.18+nmu1 [23.8 kB] Get:71 http://deb.debian.org/debian bookworm/main amd64 w3c-sgml-lib all 1.3-3 [273 kB] Get:72 http://deb.debian.org/debian bookworm/main amd64 python3-biopython amd64 1.80+dfsg-4+b1 [1593 kB] Get:73 http://deb.debian.org/debian bookworm/main amd64 python3-peptidebuilder all 1.1.0-3 [12.8 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 47.1 MB in 1s (78.9 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 python3-biopython (1.80+dfsg-4+b1) ... Selecting previously unselected package python3-peptidebuilder. Preparing to unpack .../44-python3-peptidebuilder_1.1.0-3_all.deb ... Unpacking python3-peptidebuilder (1.1.0-3) ... Setting up media-types (10.0.0) ... Setting up libgraphite2-3:amd64 (1.3.14-1) ... Setting up liblcms2-2:amd64 (2.14-2) ... Setting up libxau6:amd64 (1:1.0.9-1) ... Setting up libkeyutils1:amd64 (1.6.3-2) ... Setting up liblerc4:amd64 (4.0.0+ds-2) ... Setting up libglib2.0-0:amd64 (2.74.6-2+deb12u3) ... No schema files found: doing nothing. Setting up libtirpc-common (1.3.3+ds-1) ... Setting up libbrotli1:amd64 (1.0.9-2+b6) ... Setting up libsqlite3-0:amd64 (3.40.1-2) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of restart. Setting up libdeflate0:amd64 (1.14-1) ... Setting up libgomp1:amd64 (12.2.0-14) ... Setting up libjbig0:amd64 (2.1-6.1) ... Setting up libkrb5support0:amd64 (1.20.1-2+deb12u1) ... Setting up libfontenc1:amd64 (1:1.1.4-1) ... 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 libjpeg62-turbo:amd64 (1:2.1.5-2) ... Setting up xfonts-encodings (1:1.0.4-2.2) ... Setting up libfribidi0:amd64 (1.0.8-2.1) ... Setting up libquadmath0:amd64 (12.2.0-14) ... Setting up libimagequant0:amd64 (2.17.0-1) ... Setting up libpng16-16:amd64 (1.6.39-2) ... 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 libwebp7:amd64 (1.2.4-0.2+deb12u1) ... Setting up libtiff6:amd64 (4.5.0-6+deb12u1) ... Setting up libopenjp2-7:amd64 (2.5.0-2) ... Setting up sgml-base (1.31) ... Setting up libkrb5-3:amd64 (1.20.1-2+deb12u1) ... Setting up libwebpmux3:amd64 (1.2.4-0.2+deb12u1) ... Setting up libbsd0:amd64 (0.11.7-2) ... Setting up readline-common (8.2-1.3) ... Setting up libgdbm6:amd64 (1.23-3) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up liblapack3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxcb1:amd64 (1.15-1) ... Setting up libwebpdemux2:amd64 (1.2.4-0.2+deb12u1) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up libfreetype6:amd64 (2.12.1+dfsg-5+deb12u3) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-2+deb12u1) ... Setting up libgdbm-compat4:amd64 (1.23-3) ... Setting up xml-core (0.18+nmu1) ... Setting up libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Setting up libperl5.36:amd64 (5.36.0-7+deb12u1) ... Setting up libtirpc3:amd64 (1.3.3+ds-1) ... Setting up xfonts-utils (1:7.7+6) ... Setting up perl (5.36.0-7+deb12u1) ... Setting up libraqm0:amd64 (0.7.0-4.1) ... Setting up libnsl2:amd64 (1.3.0-2) ... Setting up mailcap (3.70+nmu1) ... Setting up mime-support (3.66) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6+deb12u2) ... Setting up fonts-urw-base35 (20200910-7) ... 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-pil:amd64 (9.4.0-1.1+deb12u1) ... Setting up python3-reportlab-accel:amd64 (3.6.12-1+b1) ... Setting up python3-reportlab (3.6.12-1) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-renderpm:amd64 (3.6.12-1+b1) ... Setting up python3-numpy (1:1.24.2-1) ... Processing triggers for libc-bin (2.36-9+deb12u7) ... Processing triggers for sgml-base (1.31) ... Setting up w3c-sgml-lib (1.3-3) ... Setting up python3-biopython (1.80+dfsg-4+b1) ... Setting up python3-peptidebuilder (1.1.0-3) ... 0m54.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'apt-get', '-y', 'install', 'python3-peptidebuilder'] 0m54.4s INFO: Running scripts post_install 0m54.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/post_install_exceptions'] 0m54.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/post_install_exceptions'] 0m54.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k'] 0m55.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k'] 0m55.2s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpl5fpex_k to bookworm-next 0m55.2s 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 0m55.2s INFO: Running scripts pre_distupgrade 0m55.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m55.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m55.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_distupgrade_exceptions'] 0m55.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_distupgrade_exceptions'] 0m55.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m55.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m55.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m55.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m55.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m55.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m55.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'apt-get', 'update'] 0m56.4s 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 [64.5 kB] Fetched 650 kB in 1s (1109 kB/s) Reading package lists... 0m56.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'apt-get', 'update'] 0m56.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'apt-get', '-yf', 'dist-upgrade'] 1m0.2s 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 python3-numpy 10 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 11.4 MB of archives. After this operation, 1628 kB disk space will be freed. Get:1 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 libc6 amd64 2.36-9+deb12u8 [2754 kB] Get:2 http://security.debian.org bookworm-security/main amd64 libgssapi-krb5-2 amd64 1.20.1-2+deb12u2 [135 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 python3-numpy amd64 1:1.24.2-1+deb12u1 [4960 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 11.4 MB in 0s (100 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 ... 12024 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 ... 12024 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 ... 12024 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-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 libgssapi-krb5-2:amd64 (1.20.1-2+deb12u2) ... Processing triggers for libc-bin (2.36-9+deb12u8) ... 1m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'apt-get', '-yf', 'dist-upgrade'] 1m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m0.6s DUMP: a7383adc5fdea12f93db4552c396e73a - 1m0.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 1m0.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'apt-cache', 'show', '--no-all-versions', 'python3-peptidebuilder'] 1m0.7s DUMP: Package: python3-peptidebuilder Source: peptidebuilder Version: 1.1.0-3 Installed-Size: 104 Maintainer: Debian Med Packaging Team Architecture: all Depends: python3-biopython, python3:any Description-en: generate atomic oligopeptide 3D structure from sequence PeptideBuilder is a simple Python library to generate model peptides. Typically on daisychains a few residues in e.g. biopython, and so does PeptideBuilder, but it does it right. . Parameters like the backbone formation can be specified ab initio, rotamers/energy minimisation is left to respective specialist tools. Description-md5: 9d8dcf8e84f047bc502b102ffdbf4944 Homepage: https://github.com/clauswilke/PeptideBuilder/ Section: science Priority: optional Filename: pool/main/p/peptidebuilder/python3-peptidebuilder_1.1.0-3_all.deb Size: 12780 MD5sum: c2277d261836aa5259d9e21bb7c5a2f3 SHA256: a85cba1037fbb6ee3a74267c5402047c23ffedd844fea3c714f62383e2bd4d5a 1m0.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'apt-cache', 'show', '--no-all-versions', 'python3-peptidebuilder'] 1m0.7s INFO: apt-cache knows about the following packages: python3-peptidebuilder 1m0.7s INFO: Running scripts pre_install 1m0.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_install_database-server'] 1m0.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_install_database-server'] 1m0.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_install_exceptions'] 1m0.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_install_exceptions'] 1m0.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_install_extras'] 1m0.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_install_extras'] 1m0.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_install_foreign_architecture'] 1m0.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_install_foreign_architecture'] 1m0.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m0.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m0.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'apt-cache', 'policy'] 1m0.8s 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: 1m0.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'apt-cache', 'policy'] 1m0.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'apt-cache', 'policy', 'python3-peptidebuilder'] 1m0.9s DUMP: python3-peptidebuilder: Installed: 1.1.0-3 Candidate: 1.1.0-3 Version table: *** 1.1.0-3 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 100 /var/lib/dpkg/status 1m0.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'apt-cache', 'policy', 'python3-peptidebuilder'] 1m0.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'apt-get', '-y', 'install', 'python3-peptidebuilder'] 1m1.2s DUMP: Reading package lists... Building dependency tree... Reading state information... python3-peptidebuilder is already the newest version (1.1.0-3). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m1.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'apt-get', '-y', 'install', 'python3-peptidebuilder'] 1m1.2s INFO: Running scripts post_install 1m1.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/post_install_exceptions'] 1m1.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/post_install_exceptions'] 1m1.2s INFO: Running scripts post_distupgrade 1m1.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m1.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m1.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/post_distupgrade_exceptions'] 1m1.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/post_distupgrade_exceptions'] 1m1.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m1.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m1.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m1.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m1.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/post_distupgrade_zz_backports'] 1m1.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/post_distupgrade_zz_backports'] 1m1.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k'] 1m2.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k'] 1m2.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k'] 1m2.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k'] 1m2.9s INFO: Running scripts pre_install 1m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_install_database-server'] 1m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_install_database-server'] 1m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_install_exceptions'] 1m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_install_exceptions'] 1m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_install_extras'] 1m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_install_extras'] 1m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_install_foreign_architecture'] 1m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_install_foreign_architecture'] 1m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'apt-cache', 'policy'] 1m3.0s 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: 1m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'apt-cache', 'policy'] 1m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'apt-cache', 'policy', 'python3-peptidebuilder'] 1m3.1s DUMP: python3-peptidebuilder: Installed: 1.1.0-3 Candidate: 1.1.0-3 Version table: *** 1.1.0-3 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 100 /var/lib/dpkg/status 1m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'apt-cache', 'policy', 'python3-peptidebuilder'] 1m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'apt-get', '-y', 'install', 'python3-peptidebuilder=1.1.0-3'] 1m3.4s DUMP: Reading package lists... Building dependency tree... Reading state information... python3-peptidebuilder is already the newest version (1.1.0-3). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'apt-get', '-y', 'install', 'python3-peptidebuilder=1.1.0-3'] 1m3.4s INFO: Running scripts post_install 1m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/post_install_exceptions'] 1m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/post_install_exceptions'] 1m3.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k'] 1m4.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k'] 1m4.2s DEBUG: No file moved between /{bin|sbin|lib*} and /usr/{bin|sbin|lib*}. 1m4.2s INFO: /bin converted to /usr/bin by /usr merge 1m4.2s INFO: /lib converted to /usr/lib by /usr merge 1m4.2s INFO: /lib/init converted to /usr/lib/init by /usr merge 1m4.2s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 1m4.2s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 1m4.2s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 1m4.2s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 1m4.2s INFO: /lib/terminfo converted to /usr/lib/terminfo by /usr merge 1m4.2s INFO: /lib/terminfo/E converted to /usr/lib/terminfo/E by /usr merge 1m4.2s INFO: /lib/terminfo/a converted to /usr/lib/terminfo/a by /usr merge 1m4.2s INFO: /lib/terminfo/c converted to /usr/lib/terminfo/c by /usr merge 1m4.2s INFO: /lib/terminfo/d converted to /usr/lib/terminfo/d by /usr merge 1m4.2s INFO: /lib/terminfo/h converted to /usr/lib/terminfo/h by /usr merge 1m4.2s INFO: /lib/terminfo/l converted to /usr/lib/terminfo/l by /usr merge 1m4.2s INFO: /lib/terminfo/m converted to /usr/lib/terminfo/m by /usr merge 1m4.2s INFO: /lib/terminfo/p converted to /usr/lib/terminfo/p by /usr merge 1m4.2s INFO: /lib/terminfo/r converted to /usr/lib/terminfo/r by /usr merge 1m4.2s INFO: /lib/terminfo/s converted to /usr/lib/terminfo/s by /usr merge 1m4.2s INFO: /lib/terminfo/t converted to /usr/lib/terminfo/t by /usr merge 1m4.2s INFO: /lib/terminfo/v converted to /usr/lib/terminfo/v by /usr merge 1m4.2s INFO: /lib/terminfo/w converted to /usr/lib/terminfo/w by /usr merge 1m4.2s INFO: /lib/terminfo/x converted to /usr/lib/terminfo/x by /usr merge 1m4.2s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 1m4.2s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 1m4.2s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 1m4.2s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 1m4.2s INFO: /lib64 converted to /usr/lib64 by /usr merge 1m4.2s INFO: /sbin converted to /usr/sbin by /usr merge 1m5.0s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', '-ac', '--ignore-obsolete'] 1m6.1s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', '-ac', '--ignore-obsolete'] 1m6.1s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m6.1s DUMP: 0.15.6 1m6.1s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m6.1s INFO: Running adequate version 0.15.6 now. 1m6.1s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'python3-peptidebuilder'] 1m6.2s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'python3-peptidebuilder'] 1m6.2s INFO: Running scripts pre_remove 1m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m6.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m6.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m8.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m8.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_remove_exceptions'] 1m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/pre_remove_exceptions'] 1m8.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m8.4s 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 fonts-urw-base35 fonts-urw-base35 20200910-7 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 libblas3:amd64 libblas3 3.11.0-2 install ok installed libblkid1:amd64 libblkid1 2.38.1-5+deb12u1 install ok installed libbrotli1:amd64 libbrotli1 1.0.9-2+b6 install ok installed libbsd0:amd64 libbsd0 0.11.7-2 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 libdeflate0:amd64 libdeflate0 1.14-1 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 libfontenc1:amd64 libfontenc1 1:1.1.4-1 install ok installed libfreetype6:amd64 libfreetype6 2.12.1+dfsg-5+deb12u3 install ok installed libfribidi0:amd64 libfribidi0 1.0.8-2.1 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 libglib2.0-0:amd64 libglib2.0-0 2.74.6-2+deb12u3 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 libgraphite2-3:amd64 libgraphite2-3 1.3.14-1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.20.1-2+deb12u2 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 6.0.0+dfsg-3 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 libimagequant0:amd64 libimagequant0 2.17.0-1 install ok installed libjbig0:amd64 libjbig0 2.1-6.1 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-2 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 liblcms2-2:amd64 liblcms2-2 2.14-2 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-2 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 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 libopenjp2-7:amd64 libopenjp2-7 2.5.0-2 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 libperl5.36:amd64 libperl5.36 5.36.0-7+deb12u1 install ok installed libpng16-16:amd64 libpng16-16 1.6.39-2 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 libraqm0:amd64 libraqm0 0.7.0-4.1 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 libtiff6:amd64 libtiff6 4.5.0-6+deb12u1 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 libwebp7:amd64 libwebp7 1.2.4-0.2+deb12u1 install ok installed libwebpdemux2:amd64 libwebpdemux2 1.2.4-0.2+deb12u1 install ok installed libwebpmux3:amd64 libwebpmux3 1.2.4-0.2+deb12u1 install ok installed libxau6:amd64 libxau6 1:1.0.9-1 install ok installed libxcb1:amd64 libxcb1 1.15-1 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3 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 mailcap mailcap 3.70+nmu1 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed media-types media-types 10.0.0 install ok installed mime-support mime-support 3.66 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 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-biopython python3-biopython 1.80+dfsg-4+b1 install ok installed python3-minimal python3-minimal 3.11.2-1+b1 install ok installed python3-numpy python3-numpy 1:1.24.2-1+deb12u1 install ok installed python3-peptidebuilder python3-peptidebuilder 1.1.0-3 install ok installed python3-pil:amd64 python3-pil 9.4.0-1.1+deb12u1 install ok installed python3-pkg-resources python3-pkg-resources 66.1.1-1 install ok installed python3-renderpm:amd64 python3-renderpm 3.6.12-1+b1 install ok installed python3-reportlab python3-reportlab 3.6.12-1 install ok installed python3-reportlab-accel:amd64 python3-reportlab-accel 3.6.12-1+b1 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 sgml-base sgml-base 1.31 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 w3c-sgml-lib w3c-sgml-lib 1.3-3 install ok installed x11-common x11-common 1:7.7+23 install ok installed xfonts-encodings xfonts-encodings 1:1.0.4-2.2 install ok installed xfonts-utils xfonts-utils 1:7.7+6 install ok installed xml-core xml-core 0.18+nmu1 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 1m8.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m8.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'apt-get', 'remove', 'fonts-urw-base35', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libperl5.36:amd64', 'libpng16-16:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libssl3:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'mailcap', 'media-types', 'mime-support', 'perl', 'perl-modules-5.36', 'python3', 'python3-biopython', 'python3-minimal', 'python3-numpy', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-renderpm:amd64', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3.11', 'python3.11-minimal', 'readline-common', 'sgml-base', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'python3-peptidebuilder'] 1m44.8s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: fonts-urw-base35 libblas3 libbrotli1 libbsd0 libdeflate0 libexpat1 libfontenc1 libfreetype6 libfribidi0 libgdbm-compat4 libgdbm6 libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libimagequant0 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 liblerc4 libncursesw6 libnsl2 libopenjp2-7 libperl5.36 libpng16-16 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libquadmath0 libraqm0 libreadline8 libsqlite3-0 libssl3 libtiff6 libtirpc-common libtirpc3 libwebp7 libwebpdemux2 libwebpmux3 libxau6 libxcb1 libxdmcp6 mailcap media-types mime-support perl perl-modules-5.36 python3 python3-biopython python3-minimal python3-numpy python3-peptidebuilder python3-pil python3-pkg-resources python3-renderpm python3-reportlab python3-reportlab-accel python3.11 python3.11-minimal readline-common sgml-base w3c-sgml-lib x11-common xfonts-encodings xfonts-utils xml-core 0 upgraded, 0 newly installed, 73 to remove and 0 not upgraded. After this operation, 174 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 ... 12024 files and directories currently installed.) Removing python3-peptidebuilder (1.1.0-3) ... Removing python3-biopython (1.80+dfsg-4+b1) ... Removing python3-renderpm:amd64 (3.6.12-1+b1) ... Removing fonts-urw-base35 (20200910-7) ... Removing python3-numpy (1:1.24.2-1+deb12u1) ... Removing liblapack3:amd64 (3.11.0-2) ... Removing libblas3:amd64 (3.11.0-2) ... Removing xfonts-utils (1:7.7+6) ... Removing python3-reportlab (3.6.12-1) ... Removing python3-pil:amd64 (9.4.0-1.1+deb12u1) ... Removing libraqm0:amd64 (0.7.0-4.1) ... Removing libxcb1:amd64 (1.15-1) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libbsd0:amd64 (0.11.7-2) ... Removing libtiff6:amd64 (4.5.0-6+deb12u1) ... Removing libdeflate0:amd64 (1.14-1) ... Removing python3-reportlab-accel:amd64 (3.6.12-1+b1) ... Removing python3-pkg-resources (66.1.1-1) ... 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 libfontenc1:amd64 (1:1.1.4-1) ... Removing libfribidi0:amd64 (1.0.8-2.1) ... 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 mime-support (3.66) ... Removing mailcap (3.70+nmu1) ... 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 libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Removing libglib2.0-0:amd64 (2.74.6-2+deb12u3) ... Removing libimagequant0:amd64 (2.17.0-1) ... Removing libgomp1:amd64 (12.2.0-14) ... Removing libgraphite2-3:amd64 (1.3.14-1) ... 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 libjbig0:amd64 (2.1-6.1) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-2) ... 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 liblcms2-2:amd64 (2.14-2) ... Removing liblerc4:amd64 (4.0.0+ds-2) ... Removing libncursesw6:amd64 (6.4-4) ... Removing libopenjp2-7:amd64 (2.5.0-2) ... Removing libpython3.11-minimal:amd64 (3.11.2-6+deb12u2) ... find: '/usr/lib/python3': No such file or directory Removing libquadmath0:amd64 (12.2.0-14) ... 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 libwebpmux3:amd64 (1.2.4-0.2+deb12u1) ... Removing libwebpdemux2:amd64 (1.2.4-0.2+deb12u1) ... Removing libwebp7:amd64 (1.2.4-0.2+deb12u1) ... Removing libxau6:amd64 (1:1.0.9-1) ... Removing media-types (10.0.0) ... Removing perl-modules-5.36 (5.36.0-7+deb12u1) ... Removing readline-common (8.2-1.3) ... Removing w3c-sgml-lib (1.3-3) ... Removing xml-core (0.18+nmu1) ... Removing sgml-base (1.31) ... Removing xfonts-encodings (1:1.0.4-2.2) ... Removing x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing libfreetype6:amd64 (2.12.1+dfsg-5+deb12u3) ... Removing libbrotli1:amd64 (1.0.9-2+b6) ... Removing libpng16-16:amd64 (1.6.39-2) ... Processing triggers for libc-bin (2.36-9+deb12u8) ... 1m44.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'apt-get', 'remove', 'fonts-urw-base35', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libperl5.36:amd64', 'libpng16-16:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libssl3:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'mailcap', 'media-types', 'mime-support', 'perl', 'perl-modules-5.36', 'python3', 'python3-biopython', 'python3-minimal', 'python3-numpy', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-renderpm:amd64', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3.11', 'python3.11-minimal', 'readline-common', 'sgml-base', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core', 'python3-peptidebuilder'] 1m44.8s INFO: Running scripts post_remove 1m44.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/post_remove_exceptions'] 1m44.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/post_remove_exceptions'] 1m44.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'dpkg', '--purge', 'fonts-urw-base35', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libperl5.36:amd64', 'libpng16-16:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libssl3:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'mailcap', 'media-types', 'mime-support', 'perl', 'perl-modules-5.36', 'python3', 'python3-biopython', 'python3-minimal', 'python3-numpy', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-renderpm:amd64', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3.11', 'python3.11-minimal', 'readline-common', 'sgml-base', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core'] 1m45.0s DUMP: (Reading database ... 6133 files and directories currently installed.) Purging configuration files for fonts-urw-base35 (20200910-7) ... dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libbsd0 which isn't installed dpkg: warning: ignoring request to remove libdeflate0 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libfontenc1 which isn't installed dpkg: warning: ignoring request to remove libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libfribidi0 which isn't installed dpkg: warning: ignoring request to remove 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 Purging configuration files for libglib2.0-0:amd64 (2.74.6-2+deb12u3) ... dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.20.1-2+deb12u2) ... dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed dpkg: warning: ignoring request to remove libimagequant0 which isn't installed dpkg: warning: ignoring request to remove libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed 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 liblcms2-2 which isn't installed dpkg: warning: ignoring request to remove liblerc4 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 libopenjp2-7 which isn't installed dpkg: warning: ignoring request to remove libperl5.36 which isn't installed dpkg: warning: ignoring request to remove libpng16-16 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 libraqm0 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 dpkg: warning: ignoring request to remove libtiff6 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 libwebp7 which isn't installed dpkg: warning: ignoring request to remove libwebpdemux2 which isn't installed dpkg: warning: ignoring request to remove libwebpmux3 which isn't installed dpkg: warning: ignoring request to remove libxau6 which isn't installed dpkg: warning: ignoring request to remove libxcb1 which isn't installed dpkg: warning: ignoring request to remove libxdmcp6 which isn't installed Purging configuration files for mailcap (3.70+nmu1) ... Purging configuration files for media-types (10.0.0) ... dpkg: warning: ignoring request to remove mime-support which isn't installed 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-biopython which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-numpy which isn't installed dpkg: warning: ignoring request to remove python3-pil which isn't installed dpkg: warning: ignoring request to remove python3-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python3-renderpm which isn't installed dpkg: warning: ignoring request to remove python3-reportlab which isn't installed dpkg: warning: ignoring request to remove python3-reportlab-accel 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) ... Purging configuration files for sgml-base (1.31) ... Purging configuration files for w3c-sgml-lib (1.3-3) ... Purging configuration files for x11-common (1:7.7+23) ... dpkg: warning: ignoring request to remove xfonts-encodings which isn't installed Purging configuration files for xfonts-utils (1:7.7+6) ... Purging configuration files for xml-core (0.18+nmu1) ... 1m45.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'dpkg', '--purge', 'fonts-urw-base35', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'liblerc4:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libopenjp2-7:amd64', 'libperl5.36:amd64', 'libpng16-16:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libquadmath0:amd64', 'libraqm0:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libssl3:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libwebp7:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'libxau6:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'mailcap', 'media-types', 'mime-support', 'perl', 'perl-modules-5.36', 'python3', 'python3-biopython', 'python3-minimal', 'python3-numpy', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-renderpm:amd64', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3.11', 'python3.11-minimal', 'readline-common', 'sgml-base', 'w3c-sgml-lib', 'x11-common', 'xfonts-encodings', 'xfonts-utils', 'xml-core'] 1m45.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'dpkg', '--purge', 'python3-peptidebuilder'] 1m45.0s DUMP: dpkg: warning: ignoring request to remove python3-peptidebuilder which isn't installed 1m45.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'dpkg', '--purge', 'python3-peptidebuilder'] 1m45.0s INFO: Running scripts post_purge 1m45.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/post_purge_exceptions'] 1m45.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/post_purge_exceptions'] 1m45.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'dpkg', '--purge', '--pending'] 1m45.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'dpkg', '--purge', '--pending'] 1m45.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'dpkg', '--remove', '--pending'] 1m45.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'dpkg', '--remove', '--pending'] 1m45.0s INFO: Running scripts post_test 1m45.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/post_test_exceptions'] 1m45.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'tmp/scripts/post_test_exceptions'] 1m45.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k'] 1m45.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k'] 1m45.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'dpkg-divert', '--list'] 1m45.4s 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 1m45.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'dpkg-divert', '--list'] 1m45.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'apt-get', 'clean'] 1m45.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k', 'apt-get', 'clean'] 1m45.4s DEBUG: Recording chroot state 1m46.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k/dev/shm'] 1m46.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k/dev/shm'] 1m46.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k/dev/console'] 1m46.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k/dev/console'] 1m46.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k/dev/ptmx'] 1m46.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k/dev/ptmx'] 1m46.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k/dev/pts'] 1m46.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k/dev/pts'] 1m46.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k/proc'] 1m46.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k/proc'] 1m46.5s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k'] 1m46.6s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpl5fpex_k'] 1m46.6s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpl5fpex_k 1m46.7s INFO: PASS: Upgrading between Debian distributions. 1m46.7s INFO: PASS: All tests. 1m46.7s INFO: piuparts run ends. ret=0 End: 2024-08-23 11:50:11 GMT