Start: 2024-08-21 23:39:12 GMT [bookworm] Package: pyensembl Version: 2.2.4+ds-1 Installed-Size: 200 Maintainer: Debian Med Packaging Team Architecture: all Depends: pylint, python3-datacache, python3-gtfparse, python3-memoized-property, python3-nose, python3-serializable, python3-typechecks, python3:any Description: installs data from the Ensembl genome database Homepage: https://github.com/openvax/pyensembl Description-md5: 1970cd836ac9f39553376a6a1a7281ae Section: science Priority: optional Filename: pool/main/p/pyensembl/pyensembl_2.2.4+ds-1_all.deb Size: 34996 MD5sum: 3050ef621a2444044d2149b85c86d50c SHA256: 3a0859b867a8311760cb4d6bb0e1f6450cdbda3a9896a2b3e20b183cb6424286 [bookworm-next] Package: pyensembl Version: 2.2.4+ds-1 Installed-Size: 200 Maintainer: Debian Med Packaging Team Architecture: all Depends: pylint, python3-datacache, python3-gtfparse, python3-memoized-property, python3-nose, python3-serializable, python3-typechecks, python3:any Description: installs data from the Ensembl genome database Homepage: https://github.com/openvax/pyensembl Description-md5: 1970cd836ac9f39553376a6a1a7281ae Section: science Priority: optional Filename: pool/main/p/pyensembl/pyensembl_2.2.4+ds-1_all.deb Size: 34996 MD5sum: 3050ef621a2444044d2149b85c86d50c SHA256: 3a0859b867a8311760cb4d6bb0e1f6450cdbda3a9896a2b3e20b183cb6424286 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 pyensembl=2.2.4+ds-1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.4.4~202408201642~1.4.3-11-g36a88c35 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --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 pyensembl=2.2.4+ds-1 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-32-amd64 #1 SMP Debian 5.10.223-1 (2024-08-10) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpmrqj1ec0 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpmrqj1ec0 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', '--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/tmpmrqj1ec0', '--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/tmpmrqj1ec0/proc'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0/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/tmpmrqj1ec0/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/tmpmrqj1ec0/dev/pts'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0/dev/ptmx'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0/dev/ptmx'] 0m0.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0/dev/console'] 0m0.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/3', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0/dev/console'] 0m0.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0/dev/shm'] 0m0.3s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0/dev/shm'] 0m0.3s 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/tmpmrqj1ec0/tmp/scripts/ 0m0.4s INFO: Running scripts post_chroot_unpack 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m0.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'apt-get', 'update'] 0m1.1s DUMP: Hit:1 http://deb.debian.org/debian bookworm InRelease Reading package lists... 0m1.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'apt-get', 'update'] 0m1.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'apt-get', '-yf', 'dist-upgrade'] 0m1.4s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m1.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'apt-get', '-yf', 'dist-upgrade'] 0m1.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m1.7s DUMP: 913e17be84ed63a3110ce3137c1d003a - 0m1.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m1.7s INFO: Running scripts post_setup 0m1.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/post_setup_dummy_users'] 0m2.5s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/post_setup_dummy_users'] 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/post_setup_forbid_home'] 0m2.5s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/post_setup_forbid_home'] 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.5s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /usr/bin/sync to /usr/bin/sync.distrib' Adding 'local diversion of /bin/sync to /bin/sync.distrib.usr-is-merged' '/bin/sync' -> 'true' 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/post_setup_force-unsafe-io'] 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/post_setup_minimize'] 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/post_setup_minimize'] 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/post_setup_squeeze-backports'] 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/post_setup_zz_backports'] 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/post_setup_zz_backports'] 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m2.5s DUMP: install ok installed adduser adduser 3.134 install ok installed apt apt 2.6.1 install ok installed base-files base-files 12.4+deb12u6 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b7 install ok installed bsdutils bsdutils 1:2.38.1-5+deb12u1 install ok installed coreutils coreutils 9.1-1 install ok installed dash dash 0.5.12-2 install ok installed debconf debconf 1.5.82 install ok installed debian-archive-keyring debian-archive-keyring 2023.3+deb12u1 install ok installed debianutils debianutils 5.7-0.5~deb12u1 install ok installed diffutils diffutils 1:3.8-4 install ok installed dpkg dpkg 1.21.22 install ok installed e2fsprogs e2fsprogs 1.47.0-2 install ok installed findutils findutils 4.9.0-4 install ok installed gcc-12-base:amd64 gcc-12-base 12.2.0-14 install ok installed gpgv gpgv 2.2.40-1.1 install ok installed grep grep 3.8-5 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu1 install ok installed init-system-helpers init-system-helpers 1.65.2 install ok installed libacl1:amd64 libacl1 2.3.1-3 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.6.1 install ok installed libattr1:amd64 libattr1 1:2.5.1-4 install ok installed libaudit-common libaudit-common 1:3.0.9-1 install ok installed libaudit1:amd64 libaudit1 1:3.0.9-1 install ok installed libblkid1:amd64 libblkid1 2.38.1-5+deb12u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b1 install ok installed libc-bin libc-bin 2.36-9+deb12u7 install ok installed libc6:amd64 libc6 2.36-9+deb12u7 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.3-1+b3 install ok installed libcap2:amd64 libcap2 1:2.66-4 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.33-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.270 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2 install ok installed libffi8:amd64 libffi8 3.4.4-1 install ok installed libgcc-s1:amd64 libgcc-s1 12.2.0-14 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.1-3 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg1-1.1 install ok installed libgnutls30:amd64 libgnutls30 3.7.9-2+deb12u3 install ok installed libgpg-error0:amd64 libgpg-error0 1.46-1 install ok installed libhogweed6:amd64 libhogweed6 3.8.1-2 install ok installed libidn2-0:amd64 libidn2-0 2.3.3-1+b1 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1 install ok installed liblzma5:amd64 liblzma5 5.4.1-0.2 install ok installed libmd0:amd64 libmd0 1.0.4-2 install ok installed libmount1:amd64 libmount1 2.38.1-5+deb12u1 install ok installed libnettle8:amd64 libnettle8 3.8.1-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.24.1-2 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-6+deb12u1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-6+deb12u1 install ok installed libpam-runtime libpam-runtime 1.5.2-6+deb12u1 install ok installed libpam0g:amd64 libpam0g 1.5.2-6+deb12u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-1 install ok installed libseccomp2:amd64 libseccomp2 2.5.4-1+deb12u1 install ok installed libselinux1:amd64 libselinux1 3.4-1+b6 install ok installed libsemanage-common libsemanage-common 3.4-1 install ok installed libsemanage2:amd64 libsemanage2 3.4-1+b5 install ok installed libsepol2:amd64 libsepol2 3.4-2.1 install ok installed libsmartcols1:amd64 libsmartcols1 2.38.1-5+deb12u1 install ok installed libss2:amd64 libss2 1.47.0-2 install ok installed libstdc++6:amd64 libstdc++6 12.2.0-14 install ok installed libsystemd0:amd64 libsystemd0 252.26-1~deb12u2 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-2 install ok installed libtinfo6:amd64 libtinfo6 6.4-4 install ok installed libudev1:amd64 libudev1 252.26-1~deb12u2 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+deb12u1 install ok installed libxxhash0:amd64 libxxhash0 0.8.1-1 install ok installed libzstd1:amd64 libzstd1 1.5.4+dfsg2-5 install ok installed login login 1:4.13+dfsg1-1+b1 install ok installed logsave logsave 1.47.0-2 install ok installed mawk mawk 1.3.4.20200120-3.1 install ok installed mount mount 2.38.1-5+deb12u1 install ok installed ncurses-base ncurses-base 6.4-4 install ok installed ncurses-bin ncurses-bin 6.4-4 install ok installed passwd passwd 1:4.13+dfsg1-1+b1 install ok installed perl-base perl-base 5.36.0-7+deb12u1 install ok installed sed sed 4.9-1 install ok installed sysvinit-utils sysvinit-utils 3.06-4 install ok installed tar tar 1.34+dfsg-1.2+deb12u1 install ok installed tzdata tzdata 2024a-0+deb12u1 install ok installed usr-is-merged usr-is-merged 37~deb12u1 install ok installed util-linux util-linux 2.38.1-5+deb12u1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+deb12u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m2.5s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/bookworm2next/reference-chroot-metadata.dat 0m2.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0'] 0m2.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0'] 0m2.8s INFO: Running scripts is_testable 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/is_testable_uninstallable'] 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/is_testable_uninstallable'] 0m2.8s INFO: Running scripts pre_test 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_test_exceptions'] 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_test_exceptions'] 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_test_root_password'] 0m2.9s DUMP: New password: Retype new password: passwd: password updated successfully 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_test_root_password'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'apt-cache', 'show', '--no-all-versions', 'pyensembl'] 0m3.0s DUMP: Package: pyensembl Version: 2.2.4+ds-1 Installed-Size: 200 Maintainer: Debian Med Packaging Team Architecture: all Depends: pylint, python3-datacache, python3-gtfparse, python3-memoized-property, python3-nose, python3-serializable, python3-typechecks, python3:any Description-en: installs data from the Ensembl genome database The Ensembl genome database is an established reference for genomic sequences and their automated annotation. To have this data local has advantages for bulk analyses, e.g. for the mapping of reads from RNA-seq against the latest golden path - or a previous one to compare analyses. . This package provides a reproducible way to insatll this data and thus simplify the automation of respective workflows. Description-md5: 1970cd836ac9f39553376a6a1a7281ae Homepage: https://github.com/openvax/pyensembl Section: science Priority: optional Filename: pool/main/p/pyensembl/pyensembl_2.2.4+ds-1_all.deb Size: 34996 MD5sum: 3050ef621a2444044d2149b85c86d50c SHA256: 3a0859b867a8311760cb4d6bb0e1f6450cdbda3a9896a2b3e20b183cb6424286 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'apt-cache', 'show', '--no-all-versions', 'pyensembl'] 0m3.0s INFO: apt-cache knows about the following packages: pyensembl 0m3.0s INFO: Running scripts pre_install 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_install_database-server'] 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_install_database-server'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_install_exceptions'] 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_install_exceptions'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_install_extras'] 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_install_extras'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_install_foreign_architecture'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'apt-cache', 'policy'] 0m3.1s 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: 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'apt-cache', 'policy'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'apt-cache', 'policy', 'pyensembl'] 0m3.1s DUMP: pyensembl: Installed: (none) Candidate: 2.2.4+ds-1 Version table: 2.2.4+ds-1 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m3.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'apt-cache', 'policy', 'pyensembl'] 0m3.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'apt-get', '-y', 'install', 'pyensembl'] 0m24.6s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: ca-certificates libblas3 libexpat1 libgfortran5 libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libncursesw6 libnsl2 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libquadmath0 libreadline8 libsqlite3-0 libssl3 libtirpc-common libtirpc3 media-types openssl pylint python3 python3-appdirs python3-astroid python3-certifi python3-chardet python3-charset-normalizer python3-datacache python3-dateutil python3-dill python3-distutils python3-gtfparse python3-idna python3-importlib-metadata python3-isort python3-lazy-object-proxy python3-lib2to3 python3-logilab-common python3-mccabe python3-memoized-property python3-minimal python3-mock python3-more-itertools python3-mypy-extensions python3-nose python3-numpy python3-pandas python3-pandas-lib python3-pbr python3-pkg-resources python3-platformdirs python3-requests python3-serializable python3-setuptools python3-simplejson python3-six python3-toml python3-tomlkit python3-typechecks python3-typing-extensions python3-tz python3-urllib3 python3-wrapt python3-zipp python3.11 python3.11-minimal readline-common Suggested packages: krb5-doc krb5-user pylint-doc python3-doc python3-tk python3-venv python3-objgraph python-mock-doc python-nose-doc gcc gfortran python3-dev python3-pytest python-pandas-doc python3-statsmodels python3-cryptography python3-openssl python3-socks python-requests-doc python-setuptools-doc python3-brotli python3.11-venv python3.11-doc binutils binfmt-support readline-doc Recommended packages: krb5-locales libgpm2 python3-tk python3-scipy python3-matplotlib 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 libblas3 libexpat1 libgfortran5 libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libncursesw6 libnsl2 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libquadmath0 libreadline8 libsqlite3-0 libssl3 libtirpc-common libtirpc3 media-types openssl pyensembl pylint python3 python3-appdirs python3-astroid python3-certifi python3-chardet python3-charset-normalizer python3-datacache python3-dateutil python3-dill python3-distutils python3-gtfparse python3-idna python3-importlib-metadata python3-isort python3-lazy-object-proxy python3-lib2to3 python3-logilab-common python3-mccabe python3-memoized-property python3-minimal python3-mock python3-more-itertools python3-mypy-extensions python3-nose python3-numpy python3-pandas python3-pandas-lib python3-pbr python3-pkg-resources python3-platformdirs python3-requests python3-serializable python3-setuptools python3-simplejson python3-six python3-toml python3-tomlkit python3-typechecks python3-typing-extensions python3-tz python3-urllib3 python3-wrapt python3-zipp python3.11 python3.11-minimal readline-common 0 upgraded, 71 newly installed, 0 to remove and 0 not upgraded. Need to get 29.4 MB of archives. After this operation, 134 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 libssl3 amd64 3.0.13-1~deb12u1 [2022 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-minimal amd64 3.11.2-6+deb12u2 [814 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 python3.11-minimal amd64 3.11.2-6+deb12u2 [2067 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 python3-minimal amd64 3.11.2-1+b1 [26.3 kB] Get:6 http://deb.debian.org/debian bookworm/main amd64 media-types all 10.0.0 [26.1 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 libncursesw6 amd64 6.4-4 [134 kB] Get:8 http://deb.debian.org/debian bookworm/main amd64 libkrb5support0 amd64 1.20.1-2+deb12u1 [32.4 kB] Get:9 http://deb.debian.org/debian bookworm/main amd64 libk5crypto3 amd64 1.20.1-2+deb12u1 [78.9 kB] Get:10 http://deb.debian.org/debian bookworm/main amd64 libkeyutils1 amd64 1.6.3-2 [8808 B] Get:11 http://deb.debian.org/debian bookworm/main amd64 libkrb5-3 amd64 1.20.1-2+deb12u1 [332 kB] Get:12 http://deb.debian.org/debian bookworm/main amd64 libgssapi-krb5-2 amd64 1.20.1-2+deb12u1 [134 kB] Get:13 http://deb.debian.org/debian bookworm/main amd64 libtirpc-common all 1.3.3+ds-1 [14.0 kB] Get:14 http://deb.debian.org/debian bookworm/main amd64 libtirpc3 amd64 1.3.3+ds-1 [85.2 kB] Get:15 http://deb.debian.org/debian bookworm/main amd64 libnsl2 amd64 1.3.0-2 [39.5 kB] Get:16 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get:17 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get:18 http://deb.debian.org/debian bookworm/main amd64 libsqlite3-0 amd64 3.40.1-2 [837 kB] Get:19 http://deb.debian.org/debian bookworm/main amd64 libpython3.11-stdlib amd64 3.11.2-6+deb12u2 [1799 kB] Get:20 http://deb.debian.org/debian bookworm/main amd64 python3.11 amd64 3.11.2-6+deb12u2 [573 kB] Get:21 http://deb.debian.org/debian bookworm/main amd64 libpython3-stdlib amd64 3.11.2-1+b1 [9312 B] Get:22 http://deb.debian.org/debian bookworm/main amd64 python3 amd64 3.11.2-1+b1 [26.3 kB] Get:23 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.13-1~deb12u1 [1418 kB] Get:24 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB] Get:25 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB] Get:26 http://deb.debian.org/debian bookworm/main amd64 libquadmath0 amd64 12.2.0-14 [144 kB] Get:27 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get:28 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get:29 http://deb.debian.org/debian bookworm/main amd64 python3-pkg-resources all 66.1.1-1 [296 kB] Get:30 http://deb.debian.org/debian bookworm/main amd64 python3-lib2to3 all 3.11.2-3 [76.3 kB] Get:31 http://deb.debian.org/debian bookworm/main amd64 python3-distutils all 3.11.2-3 [131 kB] Get:32 http://deb.debian.org/debian bookworm/main amd64 python3-setuptools all 66.1.1-1 [521 kB] Get:33 http://deb.debian.org/debian bookworm/main amd64 python3-six all 1.16.0-4 [17.5 kB] Get:34 http://deb.debian.org/debian bookworm/main amd64 python3-typing-extensions all 4.4.0-1 [45.2 kB] Get:35 http://deb.debian.org/debian bookworm/main amd64 python3-lazy-object-proxy amd64 1.9.0-1+b1 [21.5 kB] Get:36 http://deb.debian.org/debian bookworm/main amd64 python3-wrapt amd64 1.14.1-2+b2 [42.1 kB] Get:37 http://deb.debian.org/debian bookworm/main amd64 python3-astroid all 2.14.2-1 [209 kB] Get:38 http://deb.debian.org/debian bookworm/main amd64 python3-toml all 0.10.2-1 [16.2 kB] Get:39 http://deb.debian.org/debian bookworm/main amd64 python3-isort all 5.6.4-1 [63.2 kB] Get:40 http://deb.debian.org/debian bookworm/main amd64 python3-more-itertools all 8.10.0-2 [53.0 kB] Get:41 http://deb.debian.org/debian bookworm/main amd64 python3-zipp all 1.0.0-6 [6696 B] Get:42 http://deb.debian.org/debian bookworm/main amd64 python3-importlib-metadata all 4.12.0-1 [24.9 kB] Get:43 http://deb.debian.org/debian bookworm/main amd64 python3-mypy-extensions all 0.4.3-4 [5788 B] Get:44 http://deb.debian.org/debian bookworm/main amd64 python3-logilab-common all 1.9.8-1 [380 kB] Get:45 http://deb.debian.org/debian bookworm/main amd64 python3-dill all 0.3.6-1 [79.5 kB] Get:46 http://deb.debian.org/debian bookworm/main amd64 python3-mccabe all 0.7.0-1 [10.5 kB] Get:47 http://deb.debian.org/debian bookworm/main amd64 python3-platformdirs all 2.6.0-1 [16.3 kB] Get:48 http://deb.debian.org/debian bookworm/main amd64 python3-tomlkit all 0.11.7-1 [40.5 kB] Get:49 http://deb.debian.org/debian bookworm/main amd64 pylint all 2.16.2-2 [339 kB] Get:50 http://deb.debian.org/debian bookworm/main amd64 python3-appdirs all 1.4.4-3 [13.0 kB] Get:51 http://deb.debian.org/debian bookworm/main amd64 python3-pbr all 5.10.0-2 [61.4 kB] Get:52 http://deb.debian.org/debian bookworm/main amd64 python3-mock all 4.0.3-4 [64.0 kB] Get:53 http://deb.debian.org/debian bookworm/main amd64 python3-dateutil all 2.8.2-2 [78.3 kB] Get:54 http://deb.debian.org/debian bookworm/main amd64 python3-numpy amd64 1:1.24.2-1 [5209 kB] Get:55 http://deb.debian.org/debian bookworm/main amd64 python3-tz all 2022.7.1-4 [30.1 kB] Get:56 http://deb.debian.org/debian bookworm/main amd64 python3-pandas-lib amd64 1.5.3+dfsg-2 [3499 kB] Get:57 http://deb.debian.org/debian bookworm/main amd64 python3-pandas all 1.5.3+dfsg-2 [2885 kB] Get:58 http://deb.debian.org/debian bookworm/main amd64 python3-certifi all 2022.9.24-1 [153 kB] Get:59 http://deb.debian.org/debian bookworm/main amd64 python3-charset-normalizer all 3.0.1-2 [49.3 kB] Get:60 http://deb.debian.org/debian bookworm/main amd64 python3-idna all 3.3-1+deb12u1 [41.0 kB] Get:61 http://deb.debian.org/debian bookworm/main amd64 python3-urllib3 all 1.26.12-1 [117 kB] Get:62 http://deb.debian.org/debian bookworm/main amd64 python3-chardet all 5.1.0+dfsg-2 [110 kB] Get:63 http://deb.debian.org/debian bookworm/main amd64 python3-requests all 2.28.1+dfsg-1 [67.9 kB] Get:64 http://deb.debian.org/debian bookworm/main amd64 python3-typechecks all 0.1.0+ds-3 [4484 B] Get:65 http://deb.debian.org/debian bookworm/main amd64 python3-datacache all 1.2.1-1 [12.6 kB] Get:66 http://deb.debian.org/debian bookworm/main amd64 python3-gtfparse all 1.3.0+ds-1 [10.1 kB] Get:67 http://deb.debian.org/debian bookworm/main amd64 python3-memoized-property all 1.0.3-2 [5552 B] Get:68 http://deb.debian.org/debian bookworm/main amd64 python3-nose all 1.3.7-9 [130 kB] Get:69 http://deb.debian.org/debian bookworm/main amd64 python3-simplejson amd64 3.18.3-1 [59.8 kB] Get:70 http://deb.debian.org/debian bookworm/main amd64 python3-serializable all 0.2.1+ds-2 [8176 B] Get:71 http://deb.debian.org/debian bookworm/main amd64 pyensembl all 2.2.4+ds-1 [35.0 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 29.4 MB in 0s (129 MB/s) Selecting previously unselected package libssl3:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6093 files and directories currently installed.) Preparing to unpack .../libssl3_3.0.13-1~deb12u1_amd64.deb ... Unpacking libssl3:amd64 (3.0.13-1~deb12u1) ... Selecting previously unselected package libpython3.11-minimal:amd64. Preparing to unpack .../libpython3.11-minimal_3.11.2-6+deb12u2_amd64.deb ... Unpacking libpython3.11-minimal:amd64 (3.11.2-6+deb12u2) ... Selecting previously unselected package libexpat1:amd64. 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Unpacking ca-certificates (20230311) ... Selecting previously unselected package libblas3:amd64. Preparing to unpack .../03-libblas3_3.11.0-2_amd64.deb ... Unpacking libblas3:amd64 (3.11.0-2) ... Selecting previously unselected package libquadmath0:amd64. Preparing to unpack .../04-libquadmath0_12.2.0-14_amd64.deb ... Unpacking libquadmath0:amd64 (12.2.0-14) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../05-libgfortran5_12.2.0-14_amd64.deb ... Unpacking libgfortran5:amd64 (12.2.0-14) ... Selecting previously unselected package liblapack3:amd64. Preparing to unpack .../06-liblapack3_3.11.0-2_amd64.deb ... Unpacking liblapack3:amd64 (3.11.0-2) ... Selecting previously unselected package python3-pkg-resources. Preparing to unpack .../07-python3-pkg-resources_66.1.1-1_all.deb ... Unpacking python3-pkg-resources (66.1.1-1) ... Selecting previously unselected package python3-lib2to3. Preparing to unpack .../08-python3-lib2to3_3.11.2-3_all.deb ... 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Preparing to unpack .../14-python3-wrapt_1.14.1-2+b2_amd64.deb ... Unpacking python3-wrapt (1.14.1-2+b2) ... Selecting previously unselected package python3-astroid. Preparing to unpack .../15-python3-astroid_2.14.2-1_all.deb ... Unpacking python3-astroid (2.14.2-1) ... Selecting previously unselected package python3-toml. Preparing to unpack .../16-python3-toml_0.10.2-1_all.deb ... Unpacking python3-toml (0.10.2-1) ... Selecting previously unselected package python3-isort. Preparing to unpack .../17-python3-isort_5.6.4-1_all.deb ... Unpacking python3-isort (5.6.4-1) ... Selecting previously unselected package python3-more-itertools. Preparing to unpack .../18-python3-more-itertools_8.10.0-2_all.deb ... Unpacking python3-more-itertools (8.10.0-2) ... Selecting previously unselected package python3-zipp. Preparing to unpack .../19-python3-zipp_1.0.0-6_all.deb ... Unpacking python3-zipp (1.0.0-6) ... Selecting previously unselected package python3-importlib-metadata. 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Selecting previously unselected package python3-tomlkit. Preparing to unpack .../26-python3-tomlkit_0.11.7-1_all.deb ... Unpacking python3-tomlkit (0.11.7-1) ... Selecting previously unselected package pylint. Preparing to unpack .../27-pylint_2.16.2-2_all.deb ... Unpacking pylint (2.16.2-2) ... Selecting previously unselected package python3-appdirs. Preparing to unpack .../28-python3-appdirs_1.4.4-3_all.deb ... Unpacking python3-appdirs (1.4.4-3) ... Selecting previously unselected package python3-pbr. Preparing to unpack .../29-python3-pbr_5.10.0-2_all.deb ... Unpacking python3-pbr (5.10.0-2) ... Selecting previously unselected package python3-mock. Preparing to unpack .../30-python3-mock_4.0.3-4_all.deb ... Unpacking python3-mock (4.0.3-4) ... Selecting previously unselected package python3-dateutil. Preparing to unpack .../31-python3-dateutil_2.8.2-2_all.deb ... Unpacking python3-dateutil (2.8.2-2) ... Selecting previously unselected package python3-numpy. Preparing to unpack .../32-python3-numpy_1%3a1.24.2-1_amd64.deb ... Unpacking python3-numpy (1:1.24.2-1) ... Selecting previously unselected package python3-tz. Preparing to unpack .../33-python3-tz_2022.7.1-4_all.deb ... Unpacking python3-tz (2022.7.1-4) ... Selecting previously unselected package python3-pandas-lib:amd64. Preparing to unpack .../34-python3-pandas-lib_1.5.3+dfsg-2_amd64.deb ... Unpacking python3-pandas-lib:amd64 (1.5.3+dfsg-2) ... Selecting previously unselected package python3-pandas. Preparing to unpack .../35-python3-pandas_1.5.3+dfsg-2_all.deb ... Unpacking python3-pandas (1.5.3+dfsg-2) ... Selecting previously unselected package python3-certifi. Preparing to unpack .../36-python3-certifi_2022.9.24-1_all.deb ... Unpacking python3-certifi (2022.9.24-1) ... Selecting previously unselected package python3-charset-normalizer. Preparing to unpack .../37-python3-charset-normalizer_3.0.1-2_all.deb ... Unpacking python3-charset-normalizer (3.0.1-2) ... 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Unpacking python3-datacache (1.2.1-1) ... Selecting previously unselected package python3-gtfparse. Preparing to unpack .../44-python3-gtfparse_1.3.0+ds-1_all.deb ... Unpacking python3-gtfparse (1.3.0+ds-1) ... Selecting previously unselected package python3-memoized-property. Preparing to unpack .../45-python3-memoized-property_1.0.3-2_all.deb ... Unpacking python3-memoized-property (1.0.3-2) ... Selecting previously unselected package python3-nose. Preparing to unpack .../46-python3-nose_1.3.7-9_all.deb ... Unpacking python3-nose (1.3.7-9) ... Selecting previously unselected package python3-simplejson. Preparing to unpack .../47-python3-simplejson_3.18.3-1_amd64.deb ... Unpacking python3-simplejson (3.18.3-1) ... Selecting previously unselected package python3-serializable. Preparing to unpack .../48-python3-serializable_0.2.1+ds-2_all.deb ... Unpacking python3-serializable (0.2.1+ds-2) ... Selecting previously unselected package pyensembl. Preparing to unpack .../49-pyensembl_2.2.4+ds-1_all.deb ... Unpacking pyensembl (2.2.4+ds-1) ... Setting up media-types (10.0.0) ... Setting up libkeyutils1:amd64 (1.6.3-2) ... Setting up libtirpc-common (1.3.3+ds-1) ... Setting up libsqlite3-0:amd64 (3.40.1-2) ... Setting up libkrb5support0:amd64 (1.20.1-2+deb12u1) ... Setting up libblas3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libquadmath0:amd64 (12.2.0-14) ... Setting up libncursesw6:amd64 (6.4-4) ... Setting up libk5crypto3:amd64 (1.20.1-2+deb12u1) ... Setting up libgfortran5:amd64 (12.2.0-14) ... Setting up libkrb5-3:amd64 (1.20.1-2+deb12u1) ... Setting up openssl (3.0.13-1~deb12u1) ... Setting up readline-common (8.2-1.3) ... Setting up liblapack3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libreadline8:amd64 (8.2-1.3) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libgssapi-krb5-2:amd64 (1.20.1-2+deb12u1) ... Setting up libtirpc3:amd64 (1.3.3+ds-1) ... Setting up libnsl2:amd64 (1.3.0-2) ... Setting up libpython3.11-stdlib:amd64 (3.11.2-6+deb12u2) ... Setting up libpython3-stdlib:amd64 (3.11.2-1+b1) ... Setting up python3.11 (3.11.2-6+deb12u2) ... Setting up python3 (3.11.2-1+b1) ... Setting up python3-platformdirs (2.6.0-1) ... Setting up python3-tz (2022.7.1-4) ... Setting up python3-six (1.16.0-4) ... Setting up python3-simplejson (3.18.3-1) ... Setting up python3-certifi (2022.9.24-1) ... Setting up python3-dill (0.3.6-1) ... Setting up python3-idna (3.3-1+deb12u1) ... Setting up python3-wrapt (1.14.1-2+b2) ... Setting up python3-typing-extensions (4.4.0-1) ... Setting up python3-toml (0.10.2-1) ... Setting up python3-isort (5.6.4-1) ... Setting up python3-urllib3 (1.26.12-1) ... Setting up python3-dateutil (2.8.2-2) ... Setting up python3-mccabe (0.7.0-1) ... Setting up python3-lazy-object-proxy (1.9.0-1+b1) ... Setting up python3-tomlkit (0.11.7-1) ... Setting up python3-lib2to3 (3.11.2-3) ... Setting up python3-appdirs (1.4.4-3) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-distutils (3.11.2-3) ... Setting up python3-more-itertools (8.10.0-2) ... Setting up python3-setuptools (66.1.1-1) ... Setting up python3-typechecks (0.1.0+ds-3) ... Setting up python3-memoized-property (1.0.3-2) ... Setting up python3-pbr (5.10.0-2) ... Setting up python3-charset-normalizer (3.0.1-2) ... Setting up python3-mypy-extensions (0.4.3-4) ... Setting up python3-serializable (0.2.1+ds-2) ... Setting up python3-zipp (1.0.0-6) ... Setting up python3-nose (1.3.7-9) ... Setting up python3-mock (4.0.3-4) ... Setting up python3-chardet (5.1.0+dfsg-2) ... Setting up python3-requests (2.28.1+dfsg-1) ... Setting up python3-numpy (1:1.24.2-1) ... Setting up python3-astroid (2.14.2-1) ... Setting up python3-importlib-metadata (4.12.0-1) ... Setting up python3-logilab-common (1.9.8-1) ... Setting up python3-pandas-lib:amd64 (1.5.3+dfsg-2) ... Setting up python3-pandas (1.5.3+dfsg-2) ... Setting up pylint (2.16.2-2) ... Setting up python3-datacache (1.2.1-1) ... Setting up python3-gtfparse (1.3.0+ds-1) ... Setting up pyensembl (2.2.4+ds-1) ... 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. 0m24.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'apt-get', '-y', 'install', 'pyensembl'] 0m24.6s INFO: Running scripts post_install 0m24.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/post_install_exceptions'] 0m24.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/post_install_exceptions'] 0m24.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0'] 0m25.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0'] 0m25.2s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpmrqj1ec0 to bookworm-next 0m25.2s 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 0m25.2s INFO: Running scripts pre_distupgrade 0m25.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m25.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m25.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_distupgrade_exceptions'] 0m25.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_distupgrade_exceptions'] 0m25.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m25.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m25.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m25.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m25.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m25.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m25.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'apt-get', 'update'] 0m26.8s 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 [90.8 kB] Get:10 http://deb.debian.org/debian bookworm-proposed-updates/main Translation-en [51.3 kB] Fetched 616 kB in 1s (677 kB/s) Reading package lists... 0m26.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'apt-get', 'update'] 0m26.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'apt-get', '-yf', 'dist-upgrade'] 0m31.8s 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, 1641 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 3.0.13-1~deb12u2 [2023 kB] Get:10 http://deb.debian.org/debian bookworm-proposed-updates/main amd64 openssl amd64 3.0.13-1~deb12u2 [1421 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 (135 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 ... 11887 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_3.0.13-1~deb12u2_amd64.deb ... Unpacking libssl3:amd64 (3.0.13-1~deb12u2) over (3.0.13-1~deb12u1) ... Preparing to unpack .../5-openssl_3.0.13-1~deb12u2_amd64.deb ... Unpacking openssl (3.0.13-1~deb12u2) 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 (3.0.13-1~deb12u2) ... 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 (3.0.13-1~deb12u2) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-2+deb12u2) ... Processing triggers for libc-bin (2.36-9+deb12u8) ... 0m31.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'apt-get', '-yf', 'dist-upgrade'] 0m31.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m32.1s DUMP: d8d332c94c6ed6182814c5286ffa0dd5 - 0m32.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m32.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'apt-cache', 'show', '--no-all-versions', 'pyensembl'] 0m32.5s DUMP: Package: pyensembl Version: 2.2.4+ds-1 Installed-Size: 200 Maintainer: Debian Med Packaging Team Architecture: all Depends: pylint, python3-datacache, python3-gtfparse, python3-memoized-property, python3-nose, python3-serializable, python3-typechecks, python3:any Description-en: installs data from the Ensembl genome database The Ensembl genome database is an established reference for genomic sequences and their automated annotation. To have this data local has advantages for bulk analyses, e.g. for the mapping of reads from RNA-seq against the latest golden path - or a previous one to compare analyses. . This package provides a reproducible way to insatll this data and thus simplify the automation of respective workflows. Description-md5: 1970cd836ac9f39553376a6a1a7281ae Homepage: https://github.com/openvax/pyensembl Section: science Priority: optional Filename: pool/main/p/pyensembl/pyensembl_2.2.4+ds-1_all.deb Size: 34996 MD5sum: 3050ef621a2444044d2149b85c86d50c SHA256: 3a0859b867a8311760cb4d6bb0e1f6450cdbda3a9896a2b3e20b183cb6424286 0m32.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'apt-cache', 'show', '--no-all-versions', 'pyensembl'] 0m32.5s INFO: apt-cache knows about the following packages: pyensembl 0m32.5s INFO: Running scripts pre_install 0m32.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_install_database-server'] 0m32.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_install_database-server'] 0m32.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_install_exceptions'] 0m32.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_install_exceptions'] 0m32.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_install_extras'] 0m32.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_install_extras'] 0m32.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_install_foreign_architecture'] 0m32.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_install_foreign_architecture'] 0m32.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m32.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m32.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'apt-cache', 'policy'] 0m32.7s 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: 0m32.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'apt-cache', 'policy'] 0m32.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'apt-cache', 'policy', 'pyensembl'] 0m32.8s DUMP: pyensembl: Installed: 2.2.4+ds-1 Candidate: 2.2.4+ds-1 Version table: *** 2.2.4+ds-1 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 100 /var/lib/dpkg/status 0m32.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'apt-cache', 'policy', 'pyensembl'] 0m32.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'apt-get', '-y', 'install', 'pyensembl'] 0m33.1s DUMP: Reading package lists... Building dependency tree... Reading state information... pyensembl is already the newest version (2.2.4+ds-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m33.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'apt-get', '-y', 'install', 'pyensembl'] 0m33.1s INFO: Running scripts post_install 0m33.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/post_install_exceptions'] 0m33.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/post_install_exceptions'] 0m33.1s INFO: Running scripts post_distupgrade 0m33.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m33.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m33.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/post_distupgrade_exceptions'] 0m33.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/post_distupgrade_exceptions'] 0m33.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m33.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m33.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m33.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m33.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/post_distupgrade_zz_backports'] 0m33.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/post_distupgrade_zz_backports'] 0m33.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0'] 0m33.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0'] 0m33.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0'] 0m35.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0'] 0m35.3s INFO: Running scripts pre_install 0m35.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_install_database-server'] 0m35.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_install_database-server'] 0m35.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_install_exceptions'] 0m35.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_install_exceptions'] 0m35.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_install_extras'] 0m35.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_install_extras'] 0m35.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_install_foreign_architecture'] 0m35.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_install_foreign_architecture'] 0m35.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m35.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m35.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'apt-cache', 'policy'] 0m35.4s 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: 0m35.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'apt-cache', 'policy'] 0m35.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'apt-cache', 'policy', 'pyensembl'] 0m35.4s DUMP: pyensembl: Installed: 2.2.4+ds-1 Candidate: 2.2.4+ds-1 Version table: *** 2.2.4+ds-1 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 100 /var/lib/dpkg/status 0m35.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'apt-cache', 'policy', 'pyensembl'] 0m35.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'apt-get', '-y', 'install', 'pyensembl=2.2.4+ds-1'] 0m36.0s DUMP: Reading package lists... Building dependency tree... Reading state information... pyensembl is already the newest version (2.2.4+ds-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m36.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'apt-get', '-y', 'install', 'pyensembl=2.2.4+ds-1'] 0m36.0s INFO: Running scripts post_install 0m36.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/post_install_exceptions'] 0m36.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/post_install_exceptions'] 0m36.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0'] 0m36.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0'] 0m36.9s DEBUG: No file moved between /{bin|sbin|lib*} and /usr/{bin|sbin|lib*}. 0m36.9s INFO: /bin converted to /usr/bin by /usr merge 0m36.9s INFO: /lib converted to /usr/lib by /usr merge 0m36.9s INFO: /lib/init converted to /usr/lib/init by /usr merge 0m36.9s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 0m36.9s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 0m36.9s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 0m36.9s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 0m36.9s INFO: /lib/terminfo converted to /usr/lib/terminfo by /usr merge 0m36.9s INFO: /lib/terminfo/E converted to /usr/lib/terminfo/E by /usr merge 0m36.9s INFO: /lib/terminfo/a converted to /usr/lib/terminfo/a by /usr merge 0m36.9s INFO: /lib/terminfo/c converted to /usr/lib/terminfo/c by /usr merge 0m36.9s INFO: /lib/terminfo/d converted to /usr/lib/terminfo/d by /usr merge 0m36.9s INFO: /lib/terminfo/h converted to /usr/lib/terminfo/h by /usr merge 0m36.9s INFO: /lib/terminfo/l converted to /usr/lib/terminfo/l by /usr merge 0m36.9s INFO: /lib/terminfo/m converted to /usr/lib/terminfo/m by /usr merge 0m36.9s INFO: /lib/terminfo/p converted to /usr/lib/terminfo/p by /usr merge 0m36.9s INFO: /lib/terminfo/r converted to /usr/lib/terminfo/r by /usr merge 0m36.9s INFO: /lib/terminfo/s converted to /usr/lib/terminfo/s by /usr merge 0m36.9s INFO: /lib/terminfo/t converted to /usr/lib/terminfo/t by /usr merge 0m36.9s INFO: /lib/terminfo/v converted to /usr/lib/terminfo/v by /usr merge 0m36.9s INFO: /lib/terminfo/w converted to /usr/lib/terminfo/w by /usr merge 0m36.9s INFO: /lib/terminfo/x converted to /usr/lib/terminfo/x by /usr merge 0m36.9s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 0m36.9s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 0m36.9s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 0m37.0s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 0m37.0s INFO: /lib64 converted to /usr/lib64 by /usr merge 0m37.0s INFO: /sbin converted to /usr/sbin by /usr merge 0m37.6s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', '-ac', '--ignore-obsolete'] 0m38.6s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', '-ac', '--ignore-obsolete'] 0m38.6s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m38.7s DUMP: 0.15.6 0m38.7s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m38.7s INFO: Running adequate version 0.15.6 now. 0m38.7s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'pyensembl'] 0m38.8s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'pyensembl'] 0m38.8s INFO: Running scripts pre_remove 0m38.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m38.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m38.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m38.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m38.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m39.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m39.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m40.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m40.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m40.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m40.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_remove_exceptions'] 0m40.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/pre_remove_exceptions'] 0m40.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m40.1s 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 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 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 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 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 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 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 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 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 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 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 3.0.13-1~deb12u2 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 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 media-types media-types 10.0.0 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 openssl openssl 3.0.13-1~deb12u2 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 pyensembl pyensembl 2.2.4+ds-1 install ok installed pylint pylint 2.16.2-2 install ok installed python3 python3 3.11.2-1+b1 install ok installed python3-appdirs python3-appdirs 1.4.4-3 install ok installed python3-astroid python3-astroid 2.14.2-1 install ok installed python3-certifi python3-certifi 2022.9.24-1 install ok installed python3-chardet python3-chardet 5.1.0+dfsg-2 install ok installed python3-charset-normalizer python3-charset-normalizer 3.0.1-2 install ok installed python3-datacache python3-datacache 1.2.1-1 install ok installed python3-dateutil python3-dateutil 2.8.2-2 install ok installed python3-dill python3-dill 0.3.6-1 install ok installed python3-distutils python3-distutils 3.11.2-3 install ok installed python3-gtfparse python3-gtfparse 1.3.0+ds-1 install ok installed python3-idna python3-idna 3.3-1+deb12u1 install ok installed python3-importlib-metadata python3-importlib-metadata 4.12.0-1 install ok installed python3-isort python3-isort 5.6.4-1 install ok installed python3-lazy-object-proxy python3-lazy-object-proxy 1.9.0-1+b1 install ok installed python3-lib2to3 python3-lib2to3 3.11.2-3 install ok installed python3-logilab-common python3-logilab-common 1.9.8-1 install ok installed python3-mccabe python3-mccabe 0.7.0-1 install ok installed python3-memoized-property python3-memoized-property 1.0.3-2 install ok installed python3-minimal python3-minimal 3.11.2-1+b1 install ok installed python3-mock python3-mock 4.0.3-4 install ok installed python3-more-itertools python3-more-itertools 8.10.0-2 install ok installed python3-mypy-extensions python3-mypy-extensions 0.4.3-4 install ok installed python3-nose python3-nose 1.3.7-9 install ok installed python3-numpy python3-numpy 1:1.24.2-1+deb12u1 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-pbr python3-pbr 5.10.0-2 install ok installed python3-pkg-resources python3-pkg-resources 66.1.1-1 install ok installed python3-platformdirs python3-platformdirs 2.6.0-1 install ok installed python3-requests python3-requests 2.28.1+dfsg-1 install ok installed python3-serializable python3-serializable 0.2.1+ds-2 install ok installed python3-setuptools python3-setuptools 66.1.1-1 install ok installed python3-simplejson python3-simplejson 3.18.3-1 install ok installed python3-six python3-six 1.16.0-4 install ok installed python3-toml python3-toml 0.10.2-1 install ok installed python3-tomlkit python3-tomlkit 0.11.7-1 install ok installed python3-typechecks python3-typechecks 0.1.0+ds-3 install ok installed python3-typing-extensions python3-typing-extensions 4.4.0-1 install ok installed python3-tz python3-tz 2022.7.1-4 install ok installed python3-urllib3 python3-urllib3 1.26.12-1 install ok installed python3-wrapt python3-wrapt 1.14.1-2+b2 install ok installed python3-zipp python3-zipp 1.0.0-6 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 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 0m40.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m40.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'apt-get', 'remove', 'ca-certificates', 'libblas3:amd64', 'libexpat1:amd64', 'libgfortran5:amd64', 'libgssapi-krb5-2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libssl3:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'media-types', 'openssl', 'pylint', 'python3', 'python3-appdirs', 'python3-astroid', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-datacache', 'python3-dateutil', 'python3-dill', 'python3-distutils', 'python3-gtfparse', 'python3-idna', 'python3-importlib-metadata', 'python3-isort', 'python3-lazy-object-proxy', 'python3-lib2to3', 'python3-logilab-common', 'python3-mccabe', 'python3-memoized-property', 'python3-minimal', 'python3-mock', 'python3-more-itertools', 'python3-mypy-extensions', 'python3-nose', 'python3-numpy', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-pbr', 'python3-pkg-resources', 'python3-platformdirs', 'python3-requests', 'python3-serializable', 'python3-setuptools', 'python3-simplejson', 'python3-six', 'python3-toml', 'python3-tomlkit', 'python3-typechecks', 'python3-typing-extensions', 'python3-tz', 'python3-urllib3', 'python3-wrapt', 'python3-zipp', 'python3.11', 'python3.11-minimal', 'readline-common', 'pyensembl'] 0m45.0s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: ca-certificates libblas3 libexpat1 libgfortran5 libgssapi-krb5-2 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libncursesw6 libnsl2 libpython3-stdlib libpython3.11-minimal libpython3.11-stdlib libquadmath0 libreadline8 libsqlite3-0 libssl3 libtirpc-common libtirpc3 media-types openssl pyensembl pylint python3 python3-appdirs python3-astroid python3-certifi python3-chardet python3-charset-normalizer python3-datacache python3-dateutil python3-dill python3-distutils python3-gtfparse python3-idna python3-importlib-metadata python3-isort python3-lazy-object-proxy python3-lib2to3 python3-logilab-common python3-mccabe python3-memoized-property python3-minimal python3-mock python3-more-itertools python3-mypy-extensions python3-nose python3-numpy python3-pandas python3-pandas-lib python3-pbr python3-pkg-resources python3-platformdirs python3-requests python3-serializable python3-setuptools python3-simplejson python3-six python3-toml python3-tomlkit python3-typechecks python3-typing-extensions python3-tz python3-urllib3 python3-wrapt python3-zipp python3.11 python3.11-minimal readline-common 0 upgraded, 0 newly installed, 71 to remove and 0 not upgraded. After this operation, 133 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 ... 11887 files and directories currently installed.) Removing pyensembl (2.2.4+ds-1) ... Removing python3-datacache (1.2.1-1) ... Removing python3-requests (2.28.1+dfsg-1) ... Removing python3-certifi (2022.9.24-1) ... Removing ca-certificates (20230311) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing python3-gtfparse (1.3.0+ds-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 python3-serializable (0.2.1+ds-2) ... Removing python3-simplejson (3.18.3-1) ... Removing python3-mock (4.0.3-4) ... Removing python3-pbr (5.10.0-2) ... Removing pylint (2.16.2-2) ... Removing python3-astroid (2.14.2-1) ... Removing python3-wrapt (1.14.1-2+b2) ... Removing python3-urllib3 (1.26.12-1) ... Removing libgfortran5:amd64 (12.2.0-14) ... Removing libquadmath0:amd64 (12.2.0-14) ... Removing openssl (3.0.13-1~deb12u2) ... Removing python3-appdirs (1.4.4-3) ... Removing python3-chardet (5.1.0+dfsg-2) ... Removing python3-charset-normalizer (3.0.1-2) ... Removing python3-dateutil (2.8.2-2) ... Removing python3-dill (0.3.6-1) ... Removing python3-idna (3.3-1+deb12u1) ... Removing python3-logilab-common (1.9.8-1) ... Removing python3-importlib-metadata (4.12.0-1) ... Removing python3-isort (5.6.4-1) ... Removing python3-lazy-object-proxy (1.9.0-1+b1) ... Removing python3-mccabe (0.7.0-1) ... Removing python3-memoized-property (1.0.3-2) ... Removing python3-zipp (1.0.0-6) ... Removing python3-more-itertools (8.10.0-2) ... Removing python3-mypy-extensions (0.4.3-4) ... Removing python3-nose (1.3.7-9) ... Removing python3-platformdirs (2.6.0-1) ... Removing python3-toml (0.10.2-1) ... Removing python3-tomlkit (0.11.7-1) ... Removing python3-typechecks (0.1.0+ds-3) ... Removing python3-typing-extensions (4.4.0-1) ... Removing python3-tz (2022.7.1-4) ... Removing python3-setuptools (66.1.1-1) ... Removing python3-distutils (3.11.2-3) ... Removing python3-six (1.16.0-4) ... Removing python3-lib2to3 (3.11.2-3) ... 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 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 (3.0.13-1~deb12u2) ... 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) ... 0m45.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'apt-get', 'remove', 'ca-certificates', 'libblas3:amd64', 'libexpat1:amd64', 'libgfortran5:amd64', 'libgssapi-krb5-2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libssl3:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'media-types', 'openssl', 'pylint', 'python3', 'python3-appdirs', 'python3-astroid', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-datacache', 'python3-dateutil', 'python3-dill', 'python3-distutils', 'python3-gtfparse', 'python3-idna', 'python3-importlib-metadata', 'python3-isort', 'python3-lazy-object-proxy', 'python3-lib2to3', 'python3-logilab-common', 'python3-mccabe', 'python3-memoized-property', 'python3-minimal', 'python3-mock', 'python3-more-itertools', 'python3-mypy-extensions', 'python3-nose', 'python3-numpy', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-pbr', 'python3-pkg-resources', 'python3-platformdirs', 'python3-requests', 'python3-serializable', 'python3-setuptools', 'python3-simplejson', 'python3-six', 'python3-toml', 'python3-tomlkit', 'python3-typechecks', 'python3-typing-extensions', 'python3-tz', 'python3-urllib3', 'python3-wrapt', 'python3-zipp', 'python3.11', 'python3.11-minimal', 'readline-common', 'pyensembl'] 0m45.0s INFO: Running scripts post_remove 0m45.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/post_remove_exceptions'] 0m45.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/post_remove_exceptions'] 0m45.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'dpkg', '--purge', 'ca-certificates', 'libblas3:amd64', 'libexpat1:amd64', 'libgfortran5:amd64', 'libgssapi-krb5-2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libssl3:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'media-types', 'openssl', 'pylint', 'python3', 'python3-appdirs', 'python3-astroid', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-datacache', 'python3-dateutil', 'python3-dill', 'python3-distutils', 'python3-gtfparse', 'python3-idna', 'python3-importlib-metadata', 'python3-isort', 'python3-lazy-object-proxy', 'python3-lib2to3', 'python3-logilab-common', 'python3-mccabe', 'python3-memoized-property', 'python3-minimal', 'python3-mock', 'python3-more-itertools', 'python3-mypy-extensions', 'python3-nose', 'python3-numpy', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-pbr', 'python3-pkg-resources', 'python3-platformdirs', 'python3-requests', 'python3-serializable', 'python3-setuptools', 'python3-simplejson', 'python3-six', 'python3-toml', 'python3-tomlkit', 'python3-typechecks', 'python3-typing-extensions', 'python3-tz', 'python3-urllib3', 'python3-wrapt', 'python3-zipp', 'python3.11', 'python3.11-minimal', 'readline-common'] 0m45.1s DUMP: (Reading database ... 6100 files and directories currently installed.) Purging configuration files for ca-certificates (20230311) ... Removing dangling symlinks from /etc/ssl/certs... done. dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.20.1-2+deb12u2) ... dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libnsl2 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.11-minimal:amd64 (3.11.2-6+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 Purging configuration files for media-types (10.0.0) ... Purging configuration files for openssl (3.0.13-1~deb12u2) ... dpkg: warning: ignoring request to remove pylint which isn't installed Purging configuration files for python3 (3.11.2-1+b1) ... dpkg: warning: ignoring request to remove python3-appdirs which isn't installed dpkg: warning: ignoring request to remove python3-astroid which isn't installed dpkg: warning: ignoring request to remove python3-certifi which isn't installed dpkg: warning: ignoring request to remove python3-chardet which isn't installed dpkg: warning: ignoring request to remove python3-charset-normalizer which isn't installed dpkg: warning: ignoring request to remove python3-datacache which isn't installed dpkg: warning: ignoring request to remove python3-dateutil which isn't installed dpkg: warning: ignoring request to remove python3-dill which isn't installed dpkg: warning: ignoring request to remove python3-distutils which isn't installed dpkg: warning: ignoring request to remove python3-gtfparse which isn't installed dpkg: warning: ignoring request to remove python3-idna which isn't installed dpkg: warning: ignoring request to remove python3-importlib-metadata which isn't installed dpkg: warning: ignoring request to remove python3-isort which isn't installed dpkg: warning: ignoring request to remove python3-lazy-object-proxy which isn't installed dpkg: warning: ignoring request to remove python3-lib2to3 which isn't installed dpkg: warning: ignoring request to remove python3-logilab-common which isn't installed dpkg: warning: ignoring request to remove python3-mccabe which isn't installed dpkg: warning: ignoring request to remove python3-memoized-property which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-mock which isn't installed dpkg: warning: ignoring request to remove python3-more-itertools which isn't installed dpkg: warning: ignoring request to remove python3-mypy-extensions which isn't installed dpkg: warning: ignoring request to remove python3-nose which isn't installed dpkg: warning: ignoring request to remove python3-numpy 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 Purging configuration files for python3-pbr (5.10.0-2) ... dpkg: warning: ignoring request to remove python3-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python3-platformdirs which isn't installed dpkg: warning: ignoring request to remove python3-requests which isn't installed dpkg: warning: ignoring request to remove python3-serializable which isn't installed dpkg: warning: ignoring request to remove python3-setuptools which isn't installed dpkg: warning: ignoring request to remove python3-simplejson which isn't installed dpkg: warning: ignoring request to remove python3-six which isn't installed dpkg: warning: ignoring request to remove python3-toml which isn't installed dpkg: warning: ignoring request to remove python3-tomlkit which isn't installed dpkg: warning: ignoring request to remove python3-typechecks which isn't installed dpkg: warning: ignoring request to remove python3-typing-extensions which isn't installed dpkg: warning: ignoring request to remove python3-tz which isn't installed dpkg: warning: ignoring request to remove python3-urllib3 which isn't installed dpkg: warning: ignoring request to remove python3-wrapt which isn't installed dpkg: warning: ignoring request to remove python3-zipp 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) ... 0m45.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'dpkg', '--purge', 'ca-certificates', 'libblas3:amd64', 'libexpat1:amd64', 'libgfortran5:amd64', 'libgssapi-krb5-2:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libncursesw6:amd64', 'libnsl2:amd64', 'libpython3-stdlib:amd64', 'libpython3.11-minimal:amd64', 'libpython3.11-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'libsqlite3-0:amd64', 'libssl3:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'media-types', 'openssl', 'pylint', 'python3', 'python3-appdirs', 'python3-astroid', 'python3-certifi', 'python3-chardet', 'python3-charset-normalizer', 'python3-datacache', 'python3-dateutil', 'python3-dill', 'python3-distutils', 'python3-gtfparse', 'python3-idna', 'python3-importlib-metadata', 'python3-isort', 'python3-lazy-object-proxy', 'python3-lib2to3', 'python3-logilab-common', 'python3-mccabe', 'python3-memoized-property', 'python3-minimal', 'python3-mock', 'python3-more-itertools', 'python3-mypy-extensions', 'python3-nose', 'python3-numpy', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-pbr', 'python3-pkg-resources', 'python3-platformdirs', 'python3-requests', 'python3-serializable', 'python3-setuptools', 'python3-simplejson', 'python3-six', 'python3-toml', 'python3-tomlkit', 'python3-typechecks', 'python3-typing-extensions', 'python3-tz', 'python3-urllib3', 'python3-wrapt', 'python3-zipp', 'python3.11', 'python3.11-minimal', 'readline-common'] 0m45.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'dpkg', '--purge', 'pyensembl'] 0m45.1s DUMP: dpkg: warning: ignoring request to remove pyensembl which isn't installed 0m45.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'dpkg', '--purge', 'pyensembl'] 0m45.1s INFO: Running scripts post_purge 0m45.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/post_purge_exceptions'] 0m45.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/post_purge_exceptions'] 0m45.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'dpkg', '--purge', '--pending'] 0m45.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'dpkg', '--purge', '--pending'] 0m45.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'dpkg', '--remove', '--pending'] 0m45.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'dpkg', '--remove', '--pending'] 0m45.2s INFO: Running scripts post_test 0m45.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/post_test_exceptions'] 0m45.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'tmp/scripts/post_test_exceptions'] 0m45.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0'] 0m45.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0'] 0m45.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'dpkg-divert', '--list'] 0m45.5s 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 0m45.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'dpkg-divert', '--list'] 0m45.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'apt-get', 'clean'] 0m45.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0', 'apt-get', 'clean'] 0m45.5s DEBUG: Recording chroot state 0m46.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0/dev/shm'] 0m46.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0/dev/shm'] 0m46.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0/dev/console'] 0m46.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0/dev/console'] 0m46.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0/dev/ptmx'] 0m46.4s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0/dev/ptmx'] 0m46.4s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0/dev/pts'] 0m46.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0/dev/pts'] 0m46.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0/proc'] 0m46.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0/proc'] 0m46.5s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0'] 0m46.6s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpmrqj1ec0'] 0m46.6s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpmrqj1ec0 0m46.6s INFO: PASS: Upgrading between Debian distributions. 0m46.6s INFO: PASS: All tests. 0m46.6s INFO: piuparts run ends. ret=0 End: 2024-08-21 23:39:59 GMT