Start: 2024-01-25 21:44:02 GMT [testing] Package: bio-tradis Version: 1.4.5+dfsg2-1 Installed-Size: 245 Maintainer: Debian Med Packaging Team Architecture: all Depends: perl:any, libbio-perl-perl, libexception-class-perl, libmoose-perl, libtext-csv-perl, libtry-tiny-perl, smalt, samtools, tabix, r-base-core, r-cran-getopt, r-cran-mass Suggests: artemis, r-bioc-edger Description: analyse the output from TraDIS analyses of genomic sequences Homepage: https://github.com/sanger-pathogens/Bio-Tradis Description-md5: ca2a4f3e521e51ca04cc5d201dc14492 Section: perl Priority: optional Filename: pool/main/b/bio-tradis/bio-tradis_1.4.5+dfsg2-1_all.deb Size: 86820 MD5sum: 104f03d7218a960d3fee874fee8bbfbd SHA256: 8dbf87181674572413a81020cfe1e90d08fdbff0f19dc39e5e54480e55bf8a2d [sid] Package: bio-tradis Version: 1.4.5+dfsg2-2 Installed-Size: 244 Maintainer: Debian Med Packaging Team Architecture: all Depends: perl:any, libbio-perl-perl, libexception-class-perl, libmoose-perl, libtext-csv-perl, libtry-tiny-perl, smalt, samtools, tabix, r-base-core, r-cran-getopt, r-cran-mass Recommends: artemis, r-bioc-edger Description: analyse the output from TraDIS analyses of genomic sequences Homepage: https://github.com/sanger-pathogens/Bio-Tradis Description-md5: ca2a4f3e521e51ca04cc5d201dc14492 Section: perl Priority: optional Filename: pool/main/b/bio-tradis/bio-tradis_1.4.5+dfsg2-2_all.deb Size: 80344 MD5sum: 0a68231f2b8c136a1ebcf01e3eac28f3 SHA256: c3e58470fcd4828ba9915419537ae78020822b5fe0180b599ab622ddf585e08b Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt bio-tradis=1.4.5+dfsg2-2 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 1.2 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz -d testing -d sid -B /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat --apt bio-tradis=1.4.5+dfsg2-2 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-27-amd64 #1 SMP Debian 5.10.205-2 (2023-12-31) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpnthwdq3l 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpnthwdq3l 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m1.4s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bookworm-merged-usr_amd64.tar.gz'] 0m1.4s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l/proc'] 0m1.4s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l/proc'] 0m1.4s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l/dev/pts'] 0m1.4s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l/dev/pts'] 0m1.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l/dev/ptmx'] 0m1.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l/dev/ptmx'] 0m1.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l/dev/console'] 0m1.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l/dev/console'] 0m1.4s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l/dev/shm'] 0m1.5s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l/dev/shm'] 0m1.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ bookworm main 0m1.5s DEBUG: Created policy-rc.d and chmodded it. 0m1.5s DEBUG: Created resolv.conf. 0m1.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpnthwdq3l/tmp/scripts/ 0m1.5s INFO: Running scripts post_chroot_unpack 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'apt-get', 'update'] 0m2.7s DUMP: Hit:1 http://deb.debian.org/debian bookworm InRelease Reading package lists... 0m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'apt-get', 'update'] 0m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'apt-get', '-yf', 'dist-upgrade'] 0m3.2s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'apt-get', '-yf', 'dist-upgrade'] 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.7s DUMP: c39ed9ca72afa1f69a1eea88b0965329 - 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.7s INFO: Running scripts post_setup 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/post_setup_dummy_users'] 0m4.4s DUMP: useradd warning: dummy1000's uid 1000 is greater than SYS_UID_MAX 999 useradd warning: dummy1001's uid 1001 is greater than SYS_UID_MAX 999 useradd warning: dummy1002's uid 1002 is greater than SYS_UID_MAX 999 useradd warning: dummy1003's uid 1003 is greater than SYS_UID_MAX 999 useradd warning: dummy1004's uid 1004 is greater than SYS_UID_MAX 999 useradd warning: dummy1005's uid 1005 is greater than SYS_UID_MAX 999 useradd warning: dummy1006's uid 1006 is greater than SYS_UID_MAX 999 useradd warning: dummy1007's uid 1007 is greater than SYS_UID_MAX 999 useradd warning: dummy1008's uid 1008 is greater than SYS_UID_MAX 999 useradd warning: dummy1009's uid 1009 is greater than SYS_UID_MAX 999 useradd warning: dummy1010's uid 1010 is greater than SYS_UID_MAX 999 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/post_setup_dummy_users'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/post_setup_forbid_home'] 0m4.4s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/post_setup_forbid_home'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.5s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' dpkg-divert: warning: diverting file '/bin/sync' from an Essential package with rename is dangerous, use --no-rename '/bin/sync' -> 'true' 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/post_setup_minimize'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/post_setup_minimize'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/post_setup_zz_backports'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/post_setup_zz_backports'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.5s DUMP: install ok installed adduser adduser 3.134 install ok installed apt apt 2.6.1 install ok installed base-files base-files 12.4+deb12u4 install ok installed base-passwd base-passwd 3.6.1 install ok installed bash bash 5.2.15-2+b2 install ok installed bsdutils bsdutils 1:2.38.1-5+b1 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+b1 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+deb12u3 install ok installed libc6:amd64 libc6 2.36-9+deb12u3 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+deb12u1 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+b1 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+b3 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+b1 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 252.19-1~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 libudev1:amd64 libudev1 252.19-1~deb12u1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libuuid1:amd64 libuuid1 2.38.1-5+b1 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+b1 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 install ok installed tzdata tzdata 2023c-5+deb12u1 install ok installed usr-is-merged usr-is-merged 35 install ok installed util-linux util-linux 2.38.1-5+b1 install ok installed util-linux-extra util-linux-extra 2.38.1-5+b1 install ok installed zlib1g:amd64 zlib1g 1:1.2.13.dfsg-1 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.5s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/testing2sid/reference-chroot-metadata.dat 0m4.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l'] 0m4.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l'] 0m4.9s INFO: Running scripts is_testable 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/is_testable_uninstallable'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/is_testable_uninstallable'] 0m4.9s INFO: Running scripts pre_test 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_test_exceptions'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_test_exceptions'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_test_root_password'] 0m4.9s DUMP: New password: Retype new password: passwd: password updated successfully 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_test_root_password'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'apt-cache', 'show', '--no-all-versions', 'bio-tradis'] 0m5.1s DUMP: Package: bio-tradis Version: 1.4.5+dfsg2-1 Installed-Size: 245 Maintainer: Debian Med Packaging Team Architecture: all Depends: perl:any, libbio-perl-perl, libexception-class-perl, libmoose-perl, libtext-csv-perl, libtry-tiny-perl, smalt, samtools, tabix, r-base-core, r-cran-getopt, r-cran-mass Suggests: artemis, r-bioc-edger Description-en: analyse the output from TraDIS analyses of genomic sequences Bio-Tradis contains a set of tools to analyse the output from TraDIS analyses. . The Bio-Tradis analysis pipeline is implemented as an extensible Perl library which can either be used as is, or as a basis for the development of more advanced analysis tools. . Please note: You need to manually install BioConductor Edger which can not be distributed by Debian in recent version since it is using non-distributable code locfit. Description-md5: ca2a4f3e521e51ca04cc5d201dc14492 Homepage: https://github.com/sanger-pathogens/Bio-Tradis Section: perl Priority: optional Filename: pool/main/b/bio-tradis/bio-tradis_1.4.5+dfsg2-1_all.deb Size: 86820 MD5sum: 104f03d7218a960d3fee874fee8bbfbd SHA256: 8dbf87181674572413a81020cfe1e90d08fdbff0f19dc39e5e54480e55bf8a2d 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'apt-cache', 'show', '--no-all-versions', 'bio-tradis'] 0m5.1s INFO: apt-cache knows about the following packages: bio-tradis 0m5.1s INFO: Running scripts pre_install 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_install_database-server'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_install_database-server'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_install_exceptions'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_install_exceptions'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_install_extras'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_install_extras'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'apt-cache', 'policy'] 0m5.2s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bookworm/main amd64 Packages release v=12.4,o=Debian,a=stable,n=bookworm,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'apt-cache', 'policy'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'apt-cache', 'policy', 'bio-tradis'] 0m5.2s DUMP: bio-tradis: Installed: (none) Candidate: 1.4.5+dfsg2-1 Version table: 1.4.5+dfsg2-1 500 500 http://deb.debian.org/debian bookworm/main amd64 Packages 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'apt-cache', 'policy', 'bio-tradis'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'apt-get', '-y', 'install', 'bio-tradis'] 0m20.0s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: ca-certificates fontconfig fontconfig-config fonts-dejavu-core libalgorithm-c3-perl libb-hooks-op-check-perl libbambamc0 libbio-perl-perl libblas3 libbrotli1 libbsd0 libcairo2 libclass-c3-perl libclass-data-inheritable-perl libclass-load-perl libclass-load-xs-perl libcurl3-gnutls libcurl4 libdata-optlist-perl libdata-stag-perl libdatrie1 libdeflate0 libdevel-callchecker-perl libdevel-globaldestruction-perl libdevel-overloadinfo-perl libdevel-stacktrace-perl libdist-checkconflicts-perl libdynaloader-functions-perl libeval-closure-perl libexception-class-perl libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgdbm-compat4 libgdbm6 libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts3 libhtscodecs2 libice6 libicu72 libio-string-perl libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 liblerc4 libmodule-implementation-perl libmodule-runtime-conflicts-perl libmodule-runtime-perl libmoose-perl libmro-compat-perl libncurses6 libnghttp2-14 libpackage-deprecationmanager-perl libpackage-stash-perl libpackage-stash-xs-perl libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libparams-classify-perl libparams-util-perl libperl5.36 libpixman-1-0 libpng16-16 libpsl5 libquadmath0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsm6 libssh2-1 libssl3 libsub-exporter-perl libsub-exporter-progressive-perl libsub-install-perl libtcl8.6 libtext-csv-perl libthai-data libthai0 libtiff6 libtirpc-common libtirpc3 libtk8.6 libtry-tiny-perl libwebp7 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxrender1 libxss1 libxt6 openssl perl perl-modules-5.36 r-base-core r-cran-getopt r-cran-mass readline-common samtools sensible-utils smalt tabix ucf unzip x11-common xdg-utils zip Suggested packages: artemis r-bioc-edger bioperl libxml-sax-expatxs-perl gdbm-l10n low-memory-monitor krb5-doc krb5-user libscalar-number-perl tcl8.6 tk8.6 libsub-name-perl perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html readline-doc cwltool Recommended packages: bioperl-run | libbio-perl-run-perl libace-perl libalgorithm-munkres-perl libarray-compare-perl libbio-asn1-entrezgene-perl libclone-perl libconvert-binary-c-perl libdbd-sqlite3-perl libdbd-mysql-perl libdbd-pg-perl libgd-perl libgraph-perl libgraphviz-perl libhtml-parser-perl libhtml-tableextract-perl liblist-moreutils-perl libpostscript-perl libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsvg-perl libsvg-graph-perl liburi-perl libxml-dom-xpath-perl libxml-parser-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl libxml-writer-perl libxml-libxml-perl libwww-perl libclass-c3-xs-perl perl-tk libgd-gd2-perl | libgd-gd2-noxpm-perl libxml-libxslt-perl libmldbm-perl libxml-perl libdevel-lexalias-perl libglib2.0-data shared-mime-info xdg-user-dirs krb5-locales libldap-common libdevel-partialdump-perl libgpm2 publicsuffix libsasl2-modules libtext-csv-xs-perl netbase r-recommended r-base-dev r-doc-html libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: bio-tradis ca-certificates fontconfig fontconfig-config fonts-dejavu-core libalgorithm-c3-perl libb-hooks-op-check-perl libbambamc0 libbio-perl-perl libblas3 libbrotli1 libbsd0 libcairo2 libclass-c3-perl libclass-data-inheritable-perl libclass-load-perl libclass-load-xs-perl libcurl3-gnutls libcurl4 libdata-optlist-perl libdata-stag-perl libdatrie1 libdeflate0 libdevel-callchecker-perl libdevel-globaldestruction-perl libdevel-overloadinfo-perl libdevel-stacktrace-perl libdist-checkconflicts-perl libdynaloader-functions-perl libeval-closure-perl libexception-class-perl libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgdbm-compat4 libgdbm6 libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts3 libhtscodecs2 libice6 libicu72 libio-string-perl libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 liblerc4 libmodule-implementation-perl libmodule-runtime-conflicts-perl libmodule-runtime-perl libmoose-perl libmro-compat-perl libncurses6 libnghttp2-14 libpackage-deprecationmanager-perl libpackage-stash-perl libpackage-stash-xs-perl libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libparams-classify-perl libparams-util-perl libperl5.36 libpixman-1-0 libpng16-16 libpsl5 libquadmath0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsm6 libssh2-1 libssl3 libsub-exporter-perl libsub-exporter-progressive-perl libsub-install-perl libtcl8.6 libtext-csv-perl libthai-data libthai0 libtiff6 libtirpc-common libtirpc3 libtk8.6 libtry-tiny-perl libwebp7 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxrender1 libxss1 libxt6 openssl perl perl-modules-5.36 r-base-core r-cran-getopt r-cran-mass readline-common samtools sensible-utils smalt tabix ucf unzip x11-common xdg-utils zip 0 upgraded, 127 newly installed, 0 to remove and 0 not upgraded. Need to get 73.8 MB of archives. After this operation, 211 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bookworm/main amd64 perl-modules-5.36 all 5.36.0-7+deb12u1 [2815 kB] Get:2 http://deb.debian.org/debian bookworm/main amd64 libgdbm6 amd64 1.23-3 [72.2 kB] Get:3 http://deb.debian.org/debian bookworm/main amd64 libgdbm-compat4 amd64 1.23-3 [48.2 kB] Get:4 http://deb.debian.org/debian bookworm/main amd64 libperl5.36 amd64 5.36.0-7+deb12u1 [4218 kB] Get:5 http://deb.debian.org/debian bookworm/main amd64 perl amd64 5.36.0-7+deb12u1 [239 kB] Get:6 http://deb.debian.org/debian bookworm/main amd64 readline-common all 8.2-1.3 [69.0 kB] Get:7 http://deb.debian.org/debian bookworm/main amd64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get:8 http://deb.debian.org/debian bookworm/main amd64 libssl3 amd64 3.0.11-1~deb12u2 [2019 kB] Get:9 http://deb.debian.org/debian bookworm/main amd64 openssl amd64 3.0.11-1~deb12u2 [1419 kB] Get:10 http://deb.debian.org/debian bookworm/main amd64 ca-certificates all 20230311 [153 kB] Get:11 http://deb.debian.org/debian bookworm/main amd64 ucf all 3.0043+nmu1 [55.2 kB] Get:12 http://deb.debian.org/debian bookworm/main amd64 libio-string-perl all 1.08-4 [12.1 kB] Get:13 http://deb.debian.org/debian bookworm/main amd64 libdata-stag-perl all 0.14-3 [448 kB] Get:14 http://deb.debian.org/debian bookworm/main amd64 libbio-perl-perl all 1.7.8-1 [2603 kB] Get:15 http://deb.debian.org/debian bookworm/main amd64 libclass-data-inheritable-perl all 0.08-3 [8588 B] Get:16 http://deb.debian.org/debian bookworm/main amd64 libdevel-stacktrace-perl all 2.0400-2 [26.8 kB] Get:17 http://deb.debian.org/debian bookworm/main amd64 libexception-class-perl all 1.45-1 [34.6 kB] Get:18 http://deb.debian.org/debian bookworm/main amd64 libparams-util-perl amd64 1.102-2+b1 [24.8 kB] Get:19 http://deb.debian.org/debian bookworm/main amd64 libsub-install-perl all 0.929-1 [10.5 kB] Get:20 http://deb.debian.org/debian bookworm/main amd64 libdata-optlist-perl all 0.113-1 [10.6 kB] Get:21 http://deb.debian.org/debian bookworm/main amd64 libb-hooks-op-check-perl amd64 0.22-2+b1 [10.5 kB] Get:22 http://deb.debian.org/debian bookworm/main amd64 libdynaloader-functions-perl all 0.003-3 [12.7 kB] Get:23 http://deb.debian.org/debian bookworm/main amd64 libdevel-callchecker-perl amd64 0.008-2 [15.8 kB] Get:24 http://deb.debian.org/debian bookworm/main amd64 libparams-classify-perl amd64 0.015-2+b1 [23.1 kB] Get:25 http://deb.debian.org/debian bookworm/main amd64 libmodule-runtime-perl all 0.016-2 [19.6 kB] Get:26 http://deb.debian.org/debian bookworm/main amd64 libtry-tiny-perl all 0.31-2 [22.6 kB] Get:27 http://deb.debian.org/debian bookworm/main amd64 libmodule-implementation-perl all 0.09-2 [12.6 kB] Get:28 http://deb.debian.org/debian bookworm/main amd64 libpackage-stash-perl all 0.40-1 [22.0 kB] Get:29 http://deb.debian.org/debian bookworm/main amd64 libclass-load-perl all 0.25-2 [15.3 kB] Get:30 http://deb.debian.org/debian bookworm/main amd64 libclass-load-xs-perl amd64 0.10-2+b1 [14.0 kB] Get:31 http://deb.debian.org/debian bookworm/main amd64 libsub-exporter-progressive-perl all 0.001013-3 [7496 B] Get:32 http://deb.debian.org/debian bookworm/main amd64 libdevel-globaldestruction-perl all 0.14-4 [7144 B] Get:33 http://deb.debian.org/debian bookworm/main amd64 libalgorithm-c3-perl all 0.11-2 [10.8 kB] Get:34 http://deb.debian.org/debian bookworm/main amd64 libclass-c3-perl all 0.35-2 [21.0 kB] Get:35 http://deb.debian.org/debian bookworm/main amd64 libmro-compat-perl all 0.15-2 [11.8 kB] Get:36 http://deb.debian.org/debian bookworm/main amd64 libdevel-overloadinfo-perl all 0.007-1 [7896 B] Get:37 http://deb.debian.org/debian bookworm/main amd64 libsub-exporter-perl all 0.989-1 [50.5 kB] Get:38 http://deb.debian.org/debian bookworm/main amd64 libeval-closure-perl all 0.14-3 [11.2 kB] Get:39 http://deb.debian.org/debian bookworm/main amd64 libdist-checkconflicts-perl all 0.11-2 [10.5 kB] Get:40 http://deb.debian.org/debian bookworm/main amd64 libmodule-runtime-conflicts-perl all 0.003-2 [7356 B] Get:41 http://deb.debian.org/debian bookworm/main amd64 libpackage-deprecationmanager-perl all 0.18-1 [17.6 kB] Get:42 http://deb.debian.org/debian bookworm/main amd64 libpackage-stash-xs-perl amd64 0.30-1+b1 [19.8 kB] Get:43 http://deb.debian.org/debian bookworm/main amd64 libmoose-perl amd64 2.2203-1 [794 kB] Get:44 http://deb.debian.org/debian bookworm/main amd64 libtext-csv-perl all 2.02-2 [110 kB] Get:45 http://deb.debian.org/debian bookworm/main amd64 libbambamc0 amd64 0.0.50-6+b1 [39.1 kB] Get:46 http://deb.debian.org/debian bookworm/main amd64 smalt amd64 0.7.6-12 [115 kB] Get:47 http://deb.debian.org/debian bookworm/main amd64 libbrotli1 amd64 1.0.9-2+b6 [275 kB] Get:48 http://deb.debian.org/debian bookworm/main amd64 libkrb5support0 amd64 1.20.1-2+deb12u1 [32.4 kB] Get:49 http://deb.debian.org/debian bookworm/main amd64 libk5crypto3 amd64 1.20.1-2+deb12u1 [78.9 kB] Get:50 http://deb.debian.org/debian bookworm/main amd64 libkeyutils1 amd64 1.6.3-2 [8808 B] Get:51 http://deb.debian.org/debian bookworm/main amd64 libkrb5-3 amd64 1.20.1-2+deb12u1 [332 kB] Get:52 http://deb.debian.org/debian bookworm/main amd64 libgssapi-krb5-2 amd64 1.20.1-2+deb12u1 [134 kB] Get:53 http://deb.debian.org/debian bookworm/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg-10 [20.3 kB] Get:54 http://deb.debian.org/debian bookworm/main amd64 libsasl2-2 amd64 2.1.28+dfsg-10 [59.7 kB] Get:55 http://deb.debian.org/debian bookworm/main amd64 libldap-2.5-0 amd64 2.5.13+dfsg-5 [183 kB] Get:56 http://deb.debian.org/debian bookworm/main amd64 libnghttp2-14 amd64 1.52.0-1+deb12u1 [72.4 kB] Get:57 http://deb.debian.org/debian bookworm/main amd64 libpsl5 amd64 0.21.2-1 [58.7 kB] Get:58 http://deb.debian.org/debian bookworm/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:59 http://deb.debian.org/debian bookworm/main amd64 libssh2-1 amd64 1.10.0-3+b1 [179 kB] Get:60 http://deb.debian.org/debian bookworm/main amd64 libcurl3-gnutls amd64 7.88.1-10+deb12u4 [385 kB] Get:61 http://deb.debian.org/debian bookworm/main amd64 libdeflate0 amd64 1.14-1 [61.4 kB] Get:62 http://deb.debian.org/debian bookworm/main amd64 libhtscodecs2 amd64 1.3.0-4 [87.5 kB] Get:63 http://deb.debian.org/debian bookworm/main amd64 libhts3 amd64 1.16+ds-3 [430 kB] Get:64 http://deb.debian.org/debian bookworm/main amd64 libncurses6 amd64 6.4-4 [103 kB] Get:65 http://deb.debian.org/debian bookworm/main amd64 samtools amd64 1.16.1-1 [607 kB] Get:66 http://deb.debian.org/debian bookworm/main amd64 tabix amd64 1.16+ds-3 [457 kB] Get:67 http://deb.debian.org/debian bookworm/main amd64 zip amd64 3.0-13 [230 kB] Get:68 http://deb.debian.org/debian bookworm/main amd64 unzip amd64 6.0-28 [166 kB] Get:69 http://deb.debian.org/debian bookworm/main amd64 libpaper1 amd64 1.1.29 [12.5 kB] Get:70 http://deb.debian.org/debian bookworm/main amd64 libpaper-utils amd64 1.1.29 [8868 B] Get:71 http://deb.debian.org/debian bookworm/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get:72 http://deb.debian.org/debian bookworm/main amd64 libblas3 amd64 3.11.0-2 [149 kB] Get:73 http://deb.debian.org/debian bookworm/main amd64 libexpat1 amd64 2.5.0-1 [99.3 kB] Get:74 http://deb.debian.org/debian bookworm/main amd64 libpng16-16 amd64 1.6.39-2 [276 kB] Get:75 http://deb.debian.org/debian bookworm/main amd64 libfreetype6 amd64 2.12.1+dfsg-5 [399 kB] Get:76 http://deb.debian.org/debian bookworm/main amd64 fonts-dejavu-core all 2.37-6 [1068 kB] Get:77 http://deb.debian.org/debian bookworm/main amd64 fontconfig-config amd64 2.14.1-4 [315 kB] Get:78 http://deb.debian.org/debian bookworm/main amd64 libfontconfig1 amd64 2.14.1-4 [386 kB] Get:79 http://deb.debian.org/debian bookworm/main amd64 libpixman-1-0 amd64 0.42.2-1 [546 kB] Get:80 http://deb.debian.org/debian bookworm/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get:81 http://deb.debian.org/debian bookworm/main amd64 libbsd0 amd64 0.11.7-2 [117 kB] Get:82 http://deb.debian.org/debian bookworm/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:83 http://deb.debian.org/debian bookworm/main amd64 libxcb1 amd64 1.15-1 [144 kB] Get:84 http://deb.debian.org/debian bookworm/main amd64 libx11-data all 2:1.8.4-2+deb12u2 [292 kB] Get:85 http://deb.debian.org/debian bookworm/main amd64 libx11-6 amd64 2:1.8.4-2+deb12u2 [760 kB] Get:86 http://deb.debian.org/debian bookworm/main amd64 libxcb-render0 amd64 1.15-1 [115 kB] Get:87 http://deb.debian.org/debian bookworm/main amd64 libxcb-shm0 amd64 1.15-1 [105 kB] Get:88 http://deb.debian.org/debian bookworm/main amd64 libxext6 amd64 2:1.3.4-1+b1 [52.9 kB] Get:89 http://deb.debian.org/debian bookworm/main amd64 libxrender1 amd64 1:0.9.10-1.1 [33.2 kB] Get:90 http://deb.debian.org/debian bookworm/main amd64 libcairo2 amd64 1.16.0-7 [575 kB] Get:91 http://deb.debian.org/debian bookworm/main amd64 libcurl4 amd64 7.88.1-10+deb12u4 [390 kB] Get:92 http://deb.debian.org/debian bookworm/main amd64 libglib2.0-0 amd64 2.74.6-2 [1398 kB] Get:93 http://deb.debian.org/debian bookworm/main amd64 libgomp1 amd64 12.2.0-14 [116 kB] Get:94 http://deb.debian.org/debian bookworm/main amd64 libicu72 amd64 72.1-3 [9376 kB] Get:95 http://deb.debian.org/debian bookworm/main amd64 libjpeg62-turbo amd64 1:2.1.5-2 [166 kB] Get:96 http://deb.debian.org/debian bookworm/main amd64 libquadmath0 amd64 12.2.0-14 [144 kB] Get:97 http://deb.debian.org/debian bookworm/main amd64 libgfortran5 amd64 12.2.0-14 [793 kB] Get:98 http://deb.debian.org/debian bookworm/main amd64 liblapack3 amd64 3.11.0-2 [2323 kB] Get:99 http://deb.debian.org/debian bookworm/main amd64 fontconfig amd64 2.14.1-4 [449 kB] Get:100 http://deb.debian.org/debian bookworm/main amd64 libfribidi0 amd64 1.0.8-2.1 [65.0 kB] Get:101 http://deb.debian.org/debian bookworm/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get:102 http://deb.debian.org/debian bookworm/main amd64 libharfbuzz0b amd64 6.0.0+dfsg-3 [1945 kB] Get:103 http://deb.debian.org/debian bookworm/main amd64 libthai-data all 0.1.29-1 [176 kB] Get:104 http://deb.debian.org/debian bookworm/main amd64 libdatrie1 amd64 0.2.13-2+b1 [43.3 kB] Get:105 http://deb.debian.org/debian bookworm/main amd64 libthai0 amd64 0.1.29-1 [57.5 kB] Get:106 http://deb.debian.org/debian bookworm/main amd64 libpango-1.0-0 amd64 1.50.12+ds-1 [212 kB] Get:107 http://deb.debian.org/debian bookworm/main amd64 libpangoft2-1.0-0 amd64 1.50.12+ds-1 [47.4 kB] Get:108 http://deb.debian.org/debian bookworm/main amd64 libpangocairo-1.0-0 amd64 1.50.12+ds-1 [34.2 kB] Get:109 http://deb.debian.org/debian bookworm/main amd64 libreadline8 amd64 8.2-1.3 [166 kB] Get:110 http://deb.debian.org/debian bookworm/main amd64 libtcl8.6 amd64 8.6.13+dfsg-2 [1035 kB] Get:111 http://deb.debian.org/debian bookworm/main amd64 libjbig0 amd64 2.1-6.1 [31.7 kB] Get:112 http://deb.debian.org/debian bookworm/main amd64 liblerc4 amd64 4.0.0+ds-2 [170 kB] Get:113 http://deb.debian.org/debian bookworm/main amd64 libwebp7 amd64 1.2.4-0.2+deb12u1 [286 kB] Get:114 http://deb.debian.org/debian bookworm/main amd64 libtiff6 amd64 4.5.0-6+deb12u1 [316 kB] Get:115 http://deb.debian.org/debian bookworm/main amd64 libtirpc-common all 1.3.3+ds-1 [14.0 kB] Get:116 http://deb.debian.org/debian bookworm/main amd64 libtirpc3 amd64 1.3.3+ds-1 [85.2 kB] Get:117 http://deb.debian.org/debian bookworm/main amd64 libxft2 amd64 2.3.6-1 [61.8 kB] Get:118 http://deb.debian.org/debian bookworm/main amd64 x11-common all 1:7.7+23 [252 kB] Get:119 http://deb.debian.org/debian bookworm/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get:120 http://deb.debian.org/debian bookworm/main amd64 libtk8.6 amd64 8.6.13-2 [781 kB] Get:121 http://deb.debian.org/debian bookworm/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB] Get:122 http://deb.debian.org/debian bookworm/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get:123 http://deb.debian.org/debian bookworm/main amd64 libxt6 amd64 1:1.2.1-1.1 [186 kB] Get:124 http://deb.debian.org/debian bookworm/main amd64 r-base-core amd64 4.2.2.20221110-2 [26.0 MB] Get:125 http://deb.debian.org/debian bookworm/main amd64 r-cran-getopt all 1.20.3-3 [35.8 kB] Get:126 http://deb.debian.org/debian bookworm/main amd64 r-cran-mass amd64 7.3-58.2-1 [1121 kB] Get:127 http://deb.debian.org/debian bookworm/main amd64 bio-tradis all 1.4.5+dfsg2-1 [86.8 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 73.8 MB in 0s (169 MB/s) Selecting previously unselected package perl-modules-5.36. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6100 files and directories currently installed.) Preparing to unpack .../000-perl-modules-5.36_5.36.0-7+deb12u1_all.deb ... Unpacking perl-modules-5.36 (5.36.0-7+deb12u1) ... Selecting previously unselected package libgdbm6:amd64. Preparing to unpack .../001-libgdbm6_1.23-3_amd64.deb ... Unpacking libgdbm6:amd64 (1.23-3) ... Selecting previously unselected package libgdbm-compat4:amd64. 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Unpacking libxt6:amd64 (1:1.2.1-1.1) ... Selecting previously unselected package r-base-core. Preparing to unpack .../123-r-base-core_4.2.2.20221110-2_amd64.deb ... Unpacking r-base-core (4.2.2.20221110-2) ... Selecting previously unselected package r-cran-getopt. Preparing to unpack .../124-r-cran-getopt_1.20.3-3_all.deb ... Unpacking r-cran-getopt (1.20.3-3) ... Selecting previously unselected package r-cran-mass. Preparing to unpack .../125-r-cran-mass_7.3-58.2-1_amd64.deb ... Unpacking r-cran-mass (7.3-58.2-1) ... Selecting previously unselected package bio-tradis. Preparing to unpack .../126-bio-tradis_1.4.5+dfsg2-1_all.deb ... Unpacking bio-tradis (1.4.5+dfsg2-1) ... Setting up libhtscodecs2:amd64 (1.3.0-4) ... Setting up libexpat1:amd64 (2.5.0-1) ... Setting up libgraphite2-3:amd64 (1.3.14-1) ... Setting up libpixman-1-0:amd64 (0.42.2-1) ... Setting up libxau6:amd64 (1:1.0.9-1) ... Setting up libkeyutils1:amd64 (1.6.3-2) ... Setting up libpsl5:amd64 (0.21.2-1) ... Setting up libicu72:amd64 (72.1-3) ... Setting up liblerc4:amd64 (4.0.0+ds-2) ... Setting up libdatrie1:amd64 (0.2.13-2+b1) ... Setting up libglib2.0-0:amd64 (2.74.6-2) ... No schema files found: doing nothing. Setting up libtirpc-common (1.3.3+ds-1) ... Setting up unzip (6.0-28) ... Setting up libbrotli1:amd64 (1.0.9-2+b6) ... Setting up libssl3:amd64 (3.0.11-1~deb12u2) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of restart. Setting up libnghttp2-14:amd64 (1.52.0-1+deb12u1) ... Setting up libdeflate0:amd64 (1.14-1) ... Setting up libgomp1:amd64 (12.2.0-14) ... Setting up libjbig0:amd64 (2.1-6.1) ... Setting up libkrb5support0:amd64 (1.20.1-2+deb12u1) ... Setting up libsasl2-modules-db:amd64 (2.1.28+dfsg-10) ... Setting up zip (3.0-13) ... Setting up perl-modules-5.36 (5.36.0-7+deb12u1) ... Setting up libblas3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libjpeg62-turbo:amd64 (1:2.1.5-2) ... Setting up libx11-data (2:1.8.4-2+deb12u2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncurses6:amd64 (6.4-4) ... Setting up libfribidi0:amd64 (1.0.8-2.1) ... Setting up libquadmath0:amd64 (12.2.0-14) ... Setting up libbambamc0:amd64 (0.0.50-6+b1) ... Setting up libpng16-16:amd64 (1.6.39-2) ... Setting up libtcl8.6:amd64 (8.6.13+dfsg-2) ... Setting up fonts-dejavu-core (2.37-6) ... Setting up libk5crypto3:amd64 (1.20.1-2+deb12u1) ... Setting up libsasl2-2:amd64 (2.1.28+dfsg-10) ... Setting up libgfortran5:amd64 (12.2.0-14) ... Setting up libwebp7:amd64 (1.2.4-0.2+deb12u1) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up libtiff6:amd64 (4.5.0-6+deb12u1) ... Setting up libthai-data (0.1.29-1) ... Setting up libssh2-1:amd64 (1.10.0-3+b1) ... Setting up libkrb5-3:amd64 (1.20.1-2+deb12u1) ... Setting up openssl (3.0.11-1~deb12u2) ... Setting up libbsd0:amd64 (0.11.7-2) ... Setting up tabix (1.16+ds-3) ... Setting up readline-common (8.2-1.3) ... Setting up xdg-utils (1.1.3-4.1) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up libgdbm6:amd64 (1.23-3) ... Setting up smalt (0.7.6-12) ... Setting up libice6:amd64 (2:1.0.10-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up liblapack3:amd64 (3.11.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxcb1:amd64 (1.15-1) ... Setting up libxcb-render0:amd64 (1.15-1) ... Setting up fontconfig-config (2.14.1-4) ... Setting up libreadline8:amd64 (8.2-1.3) ... Setting up libxcb-shm0:amd64 (1.15-1) ... Setting up libldap-2.5-0:amd64 (2.5.13+dfsg-5) ... Setting up libthai0:amd64 (0.1.29-1) ... Setting up ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 140 added, 0 removed; done. Setting up libfreetype6:amd64 (2.12.1+dfsg-5) ... Setting up libgssapi-krb5-2:amd64 (1.20.1-2+deb12u1) ... Setting up libgdbm-compat4:amd64 (1.23-3) ... Setting up ucf (3.0043+nmu1) ... Setting up libcurl4:amd64 (7.88.1-10+deb12u4) ... Setting up libx11-6:amd64 (2:1.8.4-2+deb12u2) ... Setting up libharfbuzz0b:amd64 (6.0.0+dfsg-3) ... Setting up libfontconfig1:amd64 (2.14.1-4) ... Setting up libsm6:amd64 (2:1.2.3-1) ... Setting up libperl5.36:amd64 (5.36.0-7+deb12u1) ... Setting up libtirpc3:amd64 (1.3.3+ds-1) ... Setting up libpaper1:amd64 (1.1.29) ... Creating config file /etc/papersize with new version Setting up fontconfig (2.14.1-4) ... Regenerating fonts cache... done. Setting up libxrender1:amd64 (1:0.9.10-1.1) ... Setting up libpango-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libxext6:amd64 (2:1.3.4-1+b1) ... Setting up libcurl3-gnutls:amd64 (7.88.1-10+deb12u4) ... Setting up libpaper-utils (1.1.29) ... Setting up libcairo2:amd64 (1.16.0-7) ... Setting up perl (5.36.0-7+deb12u1) ... Setting up libpackage-stash-xs-perl:amd64 (0.30-1+b1) ... Setting up libclass-data-inheritable-perl (0.08-3) ... Setting up libalgorithm-c3-perl (0.11-2) ... Setting up libb-hooks-op-check-perl:amd64 (0.22-2+b1) ... Setting up libxt6:amd64 (1:1.2.1-1.1) ... Setting up libparams-util-perl (1.102-2+b1) ... Setting up libsub-exporter-progressive-perl (0.001013-3) ... Setting up libdevel-globaldestruction-perl (0.14-4) ... Setting up libdevel-stacktrace-perl (2.0400-2) ... Setting up libxss1:amd64 (1:1.2.3-1) ... Setting up libpangoft2-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libpangocairo-1.0-0:amd64 (1.50.12+ds-1) ... Setting up libtext-csv-perl (2.02-2) ... Setting up libxft2:amd64 (2.3.6-1) ... Setting up libhts3:amd64 (1.16+ds-3) ... Setting up libdynaloader-functions-perl (0.003-3) ... Setting up libtk8.6:amd64 (8.6.13-2) ... Setting up libtry-tiny-perl (0.31-2) ... Setting up libexception-class-perl (1.45-1) ... Setting up libclass-c3-perl (0.35-2) ... Setting up libdevel-callchecker-perl:amd64 (0.008-2) ... Setting up libsub-install-perl (0.929-1) ... Setting up samtools (1.16.1-1) ... Setting up libio-string-perl (1.08-4) ... Setting up r-base-core (4.2.2.20221110-2) ... Creating config file /etc/R/Renviron with new version Setting up libdata-optlist-perl (0.113-1) ... Setting up libdata-stag-perl (0.14-3) ... Setting up libbio-perl-perl (1.7.8-1) ... Setting up libmro-compat-perl (0.15-2) ... Setting up libsub-exporter-perl (0.989-1) ... Setting up libeval-closure-perl (0.14-3) ... Setting up libparams-classify-perl:amd64 (0.015-2+b1) ... Setting up r-cran-mass (7.3-58.2-1) ... Setting up r-cran-getopt (1.20.3-3) ... Setting up libmodule-runtime-perl (0.016-2) ... Setting up libdist-checkconflicts-perl (0.11-2) ... Setting up libmodule-implementation-perl (0.09-2) ... Setting up libpackage-stash-perl (0.40-1) ... Setting up libmodule-runtime-conflicts-perl (0.003-2) ... Setting up libclass-load-perl (0.25-2) ... Setting up libpackage-deprecationmanager-perl (0.18-1) ... Setting up libdevel-overloadinfo-perl (0.007-1) ... Setting up libclass-load-xs-perl (0.10-2+b1) ... Setting up libmoose-perl:amd64 (2.2203-1) ... Setting up bio-tradis (1.4.5+dfsg2-1) ... Processing triggers for libc-bin (2.36-9+deb12u3) ... Processing triggers for ca-certificates (20230311) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 0m20.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'apt-get', '-y', 'install', 'bio-tradis'] 0m20.0s INFO: Running scripts post_install 0m20.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/post_install_exceptions'] 0m20.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/post_install_exceptions'] 0m20.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l'] 0m20.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l'] 0m20.8s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpnthwdq3l to sid 0m20.8s DEBUG: sources.list: deb http://deb.debian.org/debian/ sid main 0m20.8s INFO: Running scripts pre_distupgrade 0m20.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m20.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m20.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_distupgrade_exceptions'] 0m20.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_distupgrade_exceptions'] 0m20.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m20.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m20.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m20.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m20.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m20.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m20.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'apt-get', 'update'] 0m24.5s DUMP: Get:1 http://deb.debian.org/debian sid InRelease [198 kB] Get:2 http://deb.debian.org/debian sid/main amd64 Packages [9667 kB] Get:3 http://deb.debian.org/debian sid/main Translation-en [7107 kB] Fetched 17.0 MB in 2s (6992 kB/s) Reading package lists... 0m24.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'apt-get', 'update'] 0m24.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'apt-get', '-yf', 'dist-upgrade'] 0m45.6s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libperl5.36 libquadmath0 perl-modules-5.36 Use 'sudo apt autoremove' to remove them. The following NEW packages will be installed: fonts-dejavu-mono gcc-13-base libperl5.38 libsharpyuv0 libunistring5 perl-modules-5.38 The following packages will be upgraded: adduser apt base-files base-passwd bash bio-tradis bsdutils coreutils dash debconf debian-archive-keyring debianutils diffutils dpkg e2fsprogs findutils fontconfig fontconfig-config fonts-dejavu-core gcc-12-base gpgv grep hostname init-system-helpers libacl1 libapt-pkg6.0 libattr1 libaudit-common libaudit1 libb-hooks-op-check-perl libblkid1 libbrotli1 libbsd0 libbz2-1.0 libc-bin libc6 libcairo2 libcap-ng0 libcap2 libclass-load-xs-perl libcom-err2 libcrypt1 libcurl3-gnutls libcurl4 libdata-optlist-perl libdatrie1 libdb5.3 libdebconfclient0 libdeflate0 libdevel-callchecker-perl libdevel-stacktrace-perl libexpat1 libext2fs2 libffi8 libfontconfig1 libfreetype6 libfribidi0 libgcc-s1 libgcrypt20 libgdbm-compat4 libgdbm6 libgfortran5 libglib2.0-0 libgmp10 libgnutls30 libgomp1 libgpg-error0 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhogweed6 libhts3 libhtscodecs2 libicu72 libidn2-0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.5-0 liblerc4 liblz4-1 liblzma5 libmd0 libmoose-perl libmount1 libncurses6 libnettle8 libnghttp2-14 libp11-kit0 libpackage-stash-xs-perl libpam-modules libpam-modules-bin libpam-runtime libpam0g libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libparams-classify-perl libparams-util-perl libpcre2-8-0 libpng16-16 libpsl5 libquadmath0 libreadline8 libsasl2-2 libsasl2-modules-db libseccomp2 libselinux1 libsemanage-common libsemanage2 libsepol2 libsmartcols1 libss2 libssh2-1 libssl3 libstdc++6 libsub-exporter-perl libsystemd0 libtasn1-6 libtext-csv-perl libthai-data libthai0 libtiff6 libtinfo6 libtirpc-common libtirpc3 libudev1 libuuid1 libwebp7 libx11-6 libx11-data libxxhash0 libzstd1 login logsave mawk mount ncurses-base ncurses-bin openssl passwd perl perl-base r-base-core r-cran-getopt r-cran-mass readline-common samtools sed sensible-utils smalt sysvinit-utils tabix tar tzdata usr-is-merged util-linux util-linux-extra zlib1g 161 upgraded, 6 newly installed, 0 to remove and 0 not upgraded. Need to get 97.8 MB of archives. After this operation, 57.1 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian sid/main amd64 base-files amd64 13 [70.6 kB] Get:2 http://deb.debian.org/debian sid/main amd64 debianutils amd64 5.16 [88.9 kB] Get:3 http://deb.debian.org/debian sid/main amd64 bash amd64 5.2.21-2 [1492 kB] Get:4 http://deb.debian.org/debian sid/main amd64 bsdutils amd64 1:2.39.3-6 [96.9 kB] Get:5 http://deb.debian.org/debian sid/main amd64 libc6 amd64 2.37-14 [2756 kB] Get:6 http://deb.debian.org/debian sid/main amd64 libc-bin amd64 2.37-14 [602 kB] Get:7 http://deb.debian.org/debian sid/main amd64 gcc-13-base amd64 13.2.0-10 [42.1 kB] Get:8 http://deb.debian.org/debian sid/main amd64 libgcc-s1 amd64 13.2.0-10 [57.7 kB] Get:9 http://deb.debian.org/debian sid/main amd64 libgmp10 amd64 2:6.3.0+dfsg-2 [557 kB] Get:10 http://deb.debian.org/debian sid/main amd64 coreutils amd64 9.4-3+b1 [2950 kB] Get:11 http://deb.debian.org/debian sid/main amd64 libzstd1 amd64 1.5.5+dfsg2-2 [295 kB] Get:12 http://deb.debian.org/debian sid/main amd64 libstdc++6 amd64 13.2.0-10 [696 kB] Get:13 http://deb.debian.org/debian sid/main amd64 libbz2-1.0 amd64 1.0.8-5+b2 [38.2 kB] Get:14 http://deb.debian.org/debian sid/main amd64 libgpg-error0 amd64 1.47-3 [77.8 kB] Get:15 http://deb.debian.org/debian sid/main amd64 libgcrypt20 amd64 1.10.3-2 [708 kB] Get:16 http://deb.debian.org/debian sid/main amd64 liblz4-1 amd64 1.9.4-1+b2 [61.6 kB] Get:17 http://deb.debian.org/debian sid/main amd64 liblzma5 amd64 5.4.5-0.3 [240 kB] Get:18 http://deb.debian.org/debian sid/main amd64 libcap2 amd64 1:2.66-4+b2 [27.6 kB] Get:19 http://deb.debian.org/debian sid/main amd64 libsystemd0 amd64 255.3-1 [362 kB] Get:20 http://deb.debian.org/debian sid/main amd64 libudev1 amd64 255.3-1 [124 kB] Get:21 http://deb.debian.org/debian sid/main amd64 libxxhash0 amd64 0.8.2-2 [26.4 kB] Get:22 http://deb.debian.org/debian sid/main amd64 zlib1g amd64 1:1.3.dfsg-3+b1 [87.8 kB] Get:23 http://deb.debian.org/debian sid/main amd64 libapt-pkg6.0 amd64 2.7.10 [982 kB] Get:24 http://deb.debian.org/debian sid/main amd64 tar amd64 1.35+dfsg-3 [813 kB] Get:25 http://deb.debian.org/debian sid/main amd64 dpkg amd64 1.22.4 [1509 kB] Get:26 http://deb.debian.org/debian sid/main amd64 dash amd64 0.5.12-6 [92.1 kB] Get:27 http://deb.debian.org/debian sid/main amd64 diffutils amd64 1:3.10-1 [375 kB] Get:28 http://deb.debian.org/debian sid/main amd64 findutils amd64 4.9.0-5 [636 kB] Get:29 http://deb.debian.org/debian sid/main amd64 grep amd64 3.11-4 [431 kB] Get:30 http://deb.debian.org/debian sid/main amd64 hostname amd64 3.23+nmu2 [10.6 kB] Get:31 http://deb.debian.org/debian sid/main amd64 login amd64 1:4.13+dfsg1-3+b1 [616 kB] Get:32 http://deb.debian.org/debian sid/main amd64 libncurses6 amd64 6.4+20240113-1 [104 kB] Get:33 http://deb.debian.org/debian sid/main amd64 libtinfo6 amd64 6.4+20240113-1 [342 kB] Get:34 http://deb.debian.org/debian sid/main amd64 ncurses-bin amd64 6.4+20240113-1 [431 kB] Get:35 http://deb.debian.org/debian sid/main amd64 libparams-util-perl amd64 1.102-2+b2 [24.4 kB] Get:36 http://deb.debian.org/debian sid/main amd64 libparams-classify-perl amd64 0.015-2+b2 [22.4 kB] Get:37 http://deb.debian.org/debian sid/main amd64 libpackage-stash-xs-perl amd64 0.30-1+b2 [20.2 kB] Get:38 http://deb.debian.org/debian sid/main amd64 libmoose-perl amd64 2.2207-1 [765 kB] Get:39 http://deb.debian.org/debian sid/main amd64 libdevel-callchecker-perl amd64 0.008-2+b1 [15.1 kB] Get:40 http://deb.debian.org/debian sid/main amd64 libclass-load-xs-perl amd64 0.10-2+b2 [14.2 kB] Get:41 http://deb.debian.org/debian sid/main amd64 libb-hooks-op-check-perl amd64 0.22-2+b2 [10.7 kB] Get:42 http://deb.debian.org/debian sid/main amd64 perl-modules-5.38 all 5.38.2-3 [2899 kB] Get:43 http://deb.debian.org/debian sid/main amd64 libperl5.38 amd64 5.38.2-3 [4275 kB] Get:44 http://deb.debian.org/debian sid/main amd64 perl amd64 5.38.2-3 [236 kB] Get:45 http://deb.debian.org/debian sid/main amd64 perl-base amd64 5.38.2-3 [1643 kB] Get:46 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Setting up libcrypt1:amd64 (1:4.4.36-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 15530 files and directories currently installed.) Preparing to unpack .../libdb5.3_5.3.28+dfsg2-4+b1_amd64.deb ... Unpacking libdb5.3:amd64 (5.3.28+dfsg2-4+b1) over (5.3.28+dfsg2-1) ... Setting up libdb5.3:amd64 (5.3.28+dfsg2-4+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 15531 files and directories currently installed.) Preparing to unpack .../0-libgdbm6_1.23-5_amd64.deb ... Unpacking libgdbm6:amd64 (1.23-5) over (1.23-3) ... Preparing to unpack .../1-libgdbm-compat4_1.23-5_amd64.deb ... Unpacking libgdbm-compat4:amd64 (1.23-5) over (1.23-3) ... Preparing to unpack .../2-libdata-optlist-perl_0.114-1_all.deb ... Unpacking libdata-optlist-perl (0.114-1) over (0.113-1) ... 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Preparing to unpack .../libblkid1_2.39.3-6_amd64.deb ... Unpacking libblkid1:amd64 (2.39.3-6) over (2.38.1-5+b1) ... Setting up libblkid1:amd64 (2.39.3-6) ... (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 ... 15529 files and directories currently installed.) Preparing to unpack .../libpcre2-8-0_10.42-4_amd64.deb ... Unpacking libpcre2-8-0:amd64 (10.42-4) over (10.42-1) ... Setting up libpcre2-8-0:amd64 (10.42-4) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 15529 files and directories currently installed.) Preparing to unpack .../libmount1_2.39.3-6_amd64.deb ... Unpacking libmount1:amd64 (2.39.3-6) over (2.38.1-5+b1) ... Setting up libmount1:amd64 (2.39.3-6) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 15539 files and directories currently installed.) Preparing to unpack .../libsemanage-common_3.5-1_all.deb ... Unpacking libsemanage-common (3.5-1) over (3.4-1) ... Setting up libsemanage-common (3.5-1) ... (Reading database ... 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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 ... 15539 files and directories currently installed.) Preparing to unpack .../libpam-modules-bin_1.5.2-9.1+b1_amd64.deb ... Unpacking libpam-modules-bin (1.5.2-9.1+b1) over (1.5.2-6+deb12u1) ... Setting up libpam-modules-bin (1.5.2-9.1+b1) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 15539 files and directories currently installed.) Preparing to unpack .../passwd_1%3a4.13+dfsg1-3+b1_amd64.deb ... Unpacking passwd (1:4.13+dfsg1-3+b1) over (1:4.13+dfsg1-1+b1) ... Setting up passwd (1:4.13+dfsg1-3+b1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 15539 files and directories currently installed.) Preparing to unpack .../archives/adduser_3.137_all.deb ... Unpacking adduser (3.137) over (3.134) ... Setting up adduser (3.137) ... Installing new version of config file /etc/adduser.conf ... (Reading database ... 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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 ... 15534 files and directories currently installed.) Preparing to unpack .../libseccomp2_2.5.5-1_amd64.deb ... Unpacking libseccomp2:amd64 (2.5.5-1) over (2.5.4-1+b3) ... Setting up libseccomp2:amd64 (2.5.5-1) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 15533 files and directories currently installed.) Preparing to unpack .../archives/apt_2.7.10_amd64.deb ... Unpacking apt (2.7.10) over (2.6.1) ... Setting up apt (2.7.10) ... (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 ... 15529 files and directories currently installed.) Preparing to unpack .../usr-is-merged_39_all.deb ... Unpacking usr-is-merged (39) over (35) ... Setting up usr-is-merged (39) ... removed '/lib32' rmdir: removing directory, '/usr/lib32' removed '/libx32' rmdir: removing directory, '/usr/libx32' (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 ... 15529 files and directories currently installed.) Preparing to unpack .../init-system-helpers_1.66_all.deb ... Unpacking init-system-helpers (1.66) over (1.65.2) ... Setting up init-system-helpers (1.66) ... (Reading database ... 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(Reading database ... 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 ... 15527 files and directories currently installed.) Preparing to unpack .../sysvinit-utils_3.08-6_amd64.deb ... Unpacking sysvinit-utils (3.08-6) over (3.06-4) ... Setting up sysvinit-utils (3.08-6) ... (Reading database ... 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Setting up libpackage-stash-xs-perl:amd64 (0.30-1+b2) ... Setting up libb-hooks-op-check-perl:amd64 (0.22-2+b2) ... Setting up libparams-util-perl (1.102-2+b2) ... Setting up libclass-load-xs-perl (0.10-2+b2) ... Setting up libdevel-stacktrace-perl (2.0500-1) ... Setting up libpangoft2-1.0-0:amd64 (1.51.0+ds-4) ... Setting up libpangocairo-1.0-0:amd64 (1.51.0+ds-4) ... Setting up libtext-csv-perl (2.04-1) ... Setting up libhts3:amd64 (1.18+ds-1) ... Setting up libdevel-callchecker-perl:amd64 (0.008-2+b1) ... Setting up samtools (1.19-1) ... Setting up r-base-core (4.3.2-1) ... Installing new version of config file /etc/R/Makeconf ... Installing new version of config file /etc/R/repositories ... Setting up libdata-optlist-perl (0.114-1) ... Setting up libsub-exporter-perl (0.990-1) ... Setting up libmoose-perl:amd64 (2.2207-1) ... Setting up libparams-classify-perl:amd64 (0.015-2+b2) ... Setting up r-cran-mass (7.3-60.0.1-1) ... Setting up r-cran-getopt (1.20.4-1) ... Setting up bio-tradis (1.4.5+dfsg2-2) ... Processing triggers for libc-bin (2.37-14) ... Processing triggers for debianutils (5.16) ... 0m45.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'apt-get', '-yf', 'dist-upgrade'] 0m45.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m47.0s DUMP: b427540d916ad5d9f50f6b97c89e8e5f - 0m47.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m47.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'apt-cache', 'show', '--no-all-versions', 'bio-tradis'] 0m47.3s DUMP: Package: bio-tradis Version: 1.4.5+dfsg2-2 Installed-Size: 244 Maintainer: Debian Med Packaging Team Architecture: all Depends: perl:any, libbio-perl-perl, libexception-class-perl, libmoose-perl, libtext-csv-perl, libtry-tiny-perl, smalt, samtools, tabix, r-base-core, r-cran-getopt, r-cran-mass Recommends: artemis, r-bioc-edger Description-en: analyse the output from TraDIS analyses of genomic sequences Bio-Tradis contains a set of tools to analyse the output from TraDIS analyses. . The Bio-Tradis analysis pipeline is implemented as an extensible Perl library which can either be used as is, or as a basis for the development of more advanced analysis tools. . Please note: You need to manually install BioConductor Edger which can not be distributed by Debian in recent version since it is using non-distributable code locfit. Description-md5: ca2a4f3e521e51ca04cc5d201dc14492 Homepage: https://github.com/sanger-pathogens/Bio-Tradis Section: perl Priority: optional Filename: pool/main/b/bio-tradis/bio-tradis_1.4.5+dfsg2-2_all.deb Size: 80344 MD5sum: 0a68231f2b8c136a1ebcf01e3eac28f3 SHA256: c3e58470fcd4828ba9915419537ae78020822b5fe0180b599ab622ddf585e08b 0m47.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'apt-cache', 'show', '--no-all-versions', 'bio-tradis'] 0m47.3s INFO: apt-cache knows about the following packages: bio-tradis 0m47.3s INFO: Running scripts pre_install 0m47.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_install_database-server'] 0m47.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_install_database-server'] 0m47.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_install_exceptions'] 0m47.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_install_exceptions'] 0m47.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_install_extras'] 0m47.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_install_extras'] 0m47.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_install_foreign_architecture'] 0m47.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_install_foreign_architecture'] 0m47.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m47.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m47.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'apt-cache', 'policy'] 0m47.4s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m47.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'apt-cache', 'policy'] 0m47.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'apt-cache', 'policy', 'bio-tradis'] 0m47.4s DUMP: bio-tradis: Installed: 1.4.5+dfsg2-2 Candidate: 1.4.5+dfsg2-2 Version table: *** 1.4.5+dfsg2-2 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m47.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'apt-cache', 'policy', 'bio-tradis'] 0m47.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'apt-get', '-y', 'install', 'bio-tradis'] 0m47.9s DUMP: Reading package lists... Building dependency tree... Reading state information... bio-tradis is already the newest version (1.4.5+dfsg2-2). The following packages were automatically installed and are no longer required: libperl5.36 libquadmath0 perl-modules-5.36 Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m48.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'apt-get', '-y', 'install', 'bio-tradis'] 0m48.0s INFO: Running scripts post_install 0m48.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/post_install_exceptions'] 0m48.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/post_install_exceptions'] 0m48.0s INFO: Running scripts post_distupgrade 0m48.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m48.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m48.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/post_distupgrade_exceptions'] 0m48.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/post_distupgrade_exceptions'] 0m48.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m48.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m48.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m48.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m48.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/post_distupgrade_zz_backports'] 0m48.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/post_distupgrade_zz_backports'] 0m48.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l'] 0m49.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l'] 0m49.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l'] 0m49.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l'] 0m49.6s INFO: Running scripts pre_install 0m49.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_install_database-server'] 0m49.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_install_database-server'] 0m49.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_install_exceptions'] 0m49.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_install_exceptions'] 0m49.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_install_extras'] 0m49.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_install_extras'] 0m49.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_install_foreign_architecture'] 0m49.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_install_foreign_architecture'] 0m49.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m49.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m49.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'apt-cache', 'policy'] 0m49.7s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m49.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'apt-cache', 'policy'] 0m49.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'apt-cache', 'policy', 'bio-tradis'] 0m49.8s DUMP: bio-tradis: Installed: 1.4.5+dfsg2-2 Candidate: 1.4.5+dfsg2-2 Version table: *** 1.4.5+dfsg2-2 500 500 http://deb.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m49.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'apt-cache', 'policy', 'bio-tradis'] 0m49.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'apt-get', '-y', 'install', 'bio-tradis=1.4.5+dfsg2-2'] 0m50.3s DUMP: Reading package lists... Building dependency tree... Reading state information... bio-tradis is already the newest version (1.4.5+dfsg2-2). The following packages were automatically installed and are no longer required: libperl5.36 libquadmath0 perl-modules-5.36 Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m50.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'apt-get', '-y', 'install', 'bio-tradis=1.4.5+dfsg2-2'] 0m50.3s INFO: Running scripts post_install 0m50.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/post_install_exceptions'] 0m50.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/post_install_exceptions'] 0m50.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l'] 0m51.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l'] 0m51.0s INFO: /bin converted to /usr/bin by /usr merge 0m51.0s INFO: /lib converted to /usr/lib by /usr merge 0m51.0s INFO: /lib/init converted to /usr/lib/init by /usr merge 0m51.0s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 0m51.1s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 0m51.1s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 0m51.1s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 0m51.1s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 0m51.1s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 0m51.1s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 0m51.1s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 0m51.1s INFO: /lib64 converted to /usr/lib64 by /usr merge 0m51.1s INFO: /sbin converted to /usr/sbin by /usr merge 0m52.4s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', '-ac', '--ignore-obsolete'] 0m53.9s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', '-ac', '--ignore-obsolete'] 0m53.9s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m53.9s DUMP: 0.15.6 0m53.9s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m53.9s INFO: Running adequate version 0.15.6 now. 0m53.9s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'bio-tradis'] 0m54.2s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'bio-tradis'] 0m54.2s INFO: Running scripts pre_remove 0m54.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m54.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m54.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m54.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m54.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m56.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m56.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m56.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m56.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m56.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m56.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_remove_exceptions'] 0m57.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/pre_remove_exceptions'] 0m57.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m57.0s DUMP: install ok installed adduser adduser 3.137 install ok installed apt apt 2.7.10 install ok installed base-files base-files 13 install ok installed base-passwd base-passwd 3.6.3 install ok installed bash bash 5.2.21-2 install ok installed bio-tradis bio-tradis 1.4.5+dfsg2-2 install ok installed bsdutils bsdutils 1:2.39.3-6 install ok installed ca-certificates ca-certificates 20230311 install ok installed coreutils coreutils 9.4-3+b1 install ok installed dash dash 0.5.12-6 install ok installed debconf debconf 1.5.84 install ok installed debian-archive-keyring debian-archive-keyring 2023.4 install ok installed debianutils debianutils 5.16 install ok installed diffutils diffutils 1:3.10-1 install ok installed dpkg dpkg 1.22.4 install ok installed e2fsprogs e2fsprogs 1.47.0-2+b1 install ok installed findutils findutils 4.9.0-5 install ok installed fontconfig fontconfig 2.14.2-6+b1 install ok installed fontconfig-config fontconfig-config 2.14.2-6+b1 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-8 install ok installed fonts-dejavu-mono fonts-dejavu-mono 2.37-8 install ok installed gcc-12-base:amd64 gcc-12-base 12.3.0-14 install ok installed gcc-13-base:amd64 gcc-13-base 13.2.0-10 install ok installed gpgv gpgv 2.2.40-1.1+b1 install ok installed grep grep 3.11-4 install ok installed gzip gzip 1.12-1 install ok installed hostname hostname 3.23+nmu2 install ok installed init-system-helpers init-system-helpers 1.66 install ok installed libacl1:amd64 libacl1 2.3.2-1 install ok installed libalgorithm-c3-perl libalgorithm-c3-perl 0.11-2 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.7.10 install ok installed libattr1:amd64 libattr1 1:2.5.2-1 install ok installed libaudit-common libaudit-common 1:3.1.2-2 install ok installed libaudit1:amd64 libaudit1 1:3.1.2-2 install ok installed libb-hooks-op-check-perl:amd64 libb-hooks-op-check-perl 0.22-2+b2 install ok installed libbambamc0:amd64 libbambamc0 0.0.50-6+b1 install ok installed libbio-perl-perl libbio-perl-perl 1.7.8-1 install ok installed libblas3:amd64 libblas3 3.11.0-2 install ok installed libblkid1:amd64 libblkid1 2.39.3-6 install ok installed libbrotli1:amd64 libbrotli1 1.1.0-2+b3 install ok installed libbsd0:amd64 libbsd0 0.11.8-1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-5+b2 install ok installed libc-bin libc-bin 2.37-14 install ok installed libc6:amd64 libc6 2.37-14 install ok installed libcairo2:amd64 libcairo2 1.18.0-1+b1 install ok installed libcap-ng0:amd64 libcap-ng0 0.8.4-1 install ok installed libcap2:amd64 libcap2 1:2.66-4+b2 install ok installed libclass-c3-perl libclass-c3-perl 0.35-2 install ok installed libclass-data-inheritable-perl libclass-data-inheritable-perl 0.08-3 install ok installed libclass-load-perl libclass-load-perl 0.25-2 install ok installed libclass-load-xs-perl libclass-load-xs-perl 0.10-2+b2 install ok installed libcom-err2:amd64 libcom-err2 1.47.0-2+b1 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.36-4 install ok installed libcurl3-gnutls:amd64 libcurl3-gnutls 8.5.0-2 install ok installed libcurl4:amd64 libcurl4 8.5.0-2 install ok installed libdata-optlist-perl libdata-optlist-perl 0.114-1 install ok installed libdata-stag-perl libdata-stag-perl 0.14-3 install ok installed libdatrie1:amd64 libdatrie1 0.2.13-3 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg2-4+b1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.271 install ok installed libdeflate0:amd64 libdeflate0 1.18-1 install ok installed libdevel-callchecker-perl:amd64 libdevel-callchecker-perl 0.008-2+b1 install ok installed libdevel-globaldestruction-perl libdevel-globaldestruction-perl 0.14-4 install ok installed libdevel-overloadinfo-perl libdevel-overloadinfo-perl 0.007-1 install ok installed libdevel-stacktrace-perl libdevel-stacktrace-perl 2.0500-1 install ok installed libdist-checkconflicts-perl libdist-checkconflicts-perl 0.11-2 install ok installed libdynaloader-functions-perl libdynaloader-functions-perl 0.003-3 install ok installed libeval-closure-perl libeval-closure-perl 0.14-3 install ok installed libexception-class-perl libexception-class-perl 1.45-1 install ok installed libexpat1:amd64 libexpat1 2.5.0-2+b2 install ok installed libext2fs2:amd64 libext2fs2 1.47.0-2+b1 install ok installed libffi8:amd64 libffi8 3.4.4-2 install ok installed libfontconfig1:amd64 libfontconfig1 2.14.2-6+b1 install ok installed libfreetype6:amd64 libfreetype6 2.13.2+dfsg-1+b1 install ok installed libfribidi0:amd64 libfribidi0 1.0.13-3+b1 install ok installed libgcc-s1:amd64 libgcc-s1 13.2.0-10 install ok installed libgcrypt20:amd64 libgcrypt20 1.10.3-2 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.23-5 install ok installed libgdbm6:amd64 libgdbm6 1.23-5 install ok installed libgfortran5:amd64 libgfortran5 13.2.0-10 install ok installed libglib2.0-0:amd64 libglib2.0-0 2.78.3-2 install ok installed libgmp10:amd64 libgmp10 2:6.3.0+dfsg-2 install ok installed libgnutls30:amd64 libgnutls30 3.8.3-1 install ok installed libgomp1:amd64 libgomp1 13.2.0-10 install ok installed libgpg-error0:amd64 libgpg-error0 1.47-3 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.20.1-5 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 8.3.0-2 install ok installed libhogweed6:amd64 libhogweed6 3.9.1-2 install ok installed libhts3:amd64 libhts3 1.18+ds-1 install ok installed libhtscodecs2:amd64 libhtscodecs2 1.6.0-1 install ok installed libice6:amd64 libice6 2:1.0.10-1 install ok installed libicu72:amd64 libicu72 72.1-4 install ok installed libidn2-0:amd64 libidn2-0 2.3.4-1+b2 install ok installed libio-string-perl libio-string-perl 1.08-4 install ok installed libjbig0:amd64 libjbig0 2.1-6.1 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.1.5-2+b2 install ok installed libk5crypto3:amd64 libk5crypto3 1.20.1-5 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.3-2+b2 install ok installed libkrb5-3:amd64 libkrb5-3 1.20.1-5 install ok installed libkrb5support0:amd64 libkrb5support0 1.20.1-5 install ok installed liblapack3:amd64 liblapack3 3.11.0-2 install ok installed libldap-2.5-0:amd64 libldap-2.5-0 2.5.13+dfsg-5+b3 install ok installed liblerc4:amd64 liblerc4 4.0.0+ds-4 install ok installed liblz4-1:amd64 liblz4-1 1.9.4-1+b2 install ok installed liblzma5:amd64 liblzma5 5.4.5-0.3 install ok installed libmd0:amd64 libmd0 1.1.0-2 install ok installed libmodule-implementation-perl libmodule-implementation-perl 0.09-2 install ok installed libmodule-runtime-conflicts-perl libmodule-runtime-conflicts-perl 0.003-2 install ok installed libmodule-runtime-perl libmodule-runtime-perl 0.016-2 install ok installed libmoose-perl:amd64 libmoose-perl 2.2207-1 install ok installed libmount1:amd64 libmount1 2.39.3-6 install ok installed libmro-compat-perl libmro-compat-perl 0.15-2 install ok installed libncurses6:amd64 libncurses6 6.4+20240113-1 install ok installed libnettle8:amd64 libnettle8 3.9.1-2 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.58.0-1 install ok installed libp11-kit0:amd64 libp11-kit0 0.25.3-4 install ok installed libpackage-deprecationmanager-perl libpackage-deprecationmanager-perl 0.18-1 install ok installed libpackage-stash-perl libpackage-stash-perl 0.40-1 install ok installed libpackage-stash-xs-perl:amd64 libpackage-stash-xs-perl 0.30-1+b2 install ok installed libpam-modules:amd64 libpam-modules 1.5.2-9.1+b1 install ok installed libpam-modules-bin libpam-modules-bin 1.5.2-9.1+b1 install ok installed libpam-runtime libpam-runtime 1.5.2-9.1 install ok installed libpam0g:amd64 libpam0g 1.5.2-9.1+b1 install ok installed libpango-1.0-0:amd64 libpango-1.0-0 1.51.0+ds-4 install ok installed libpangocairo-1.0-0:amd64 libpangocairo-1.0-0 1.51.0+ds-4 install ok installed libpangoft2-1.0-0:amd64 libpangoft2-1.0-0 1.51.0+ds-4 install ok installed libpaper-utils libpaper-utils 1.1.29 install ok installed libpaper1:amd64 libpaper1 1.1.29 install ok installed libparams-classify-perl:amd64 libparams-classify-perl 0.015-2+b2 install ok installed libparams-util-perl libparams-util-perl 1.102-2+b2 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.42-4 install ok installed libperl5.36:amd64 libperl5.36 5.36.0-7+deb12u1 install ok installed libperl5.38:amd64 libperl5.38 5.38.2-3 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.42.2-1 install ok installed libpng16-16:amd64 libpng16-16 1.6.40-3 install ok installed libpsl5:amd64 libpsl5 0.21.2-1+b1 install ok installed libquadmath0:amd64 libquadmath0 13.2.0-10 install ok installed libreadline8:amd64 libreadline8 8.2-3 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b2 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.28+dfsg1-4+b1 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.28+dfsg1-4+b1 install ok installed libseccomp2:amd64 libseccomp2 2.5.5-1 install ok installed libselinux1:amd64 libselinux1 3.5-2 install ok installed libsemanage-common libsemanage-common 3.5-1 install ok installed libsemanage2:amd64 libsemanage2 3.5-1+b2 install ok installed libsepol2:amd64 libsepol2 3.5-2 install ok installed libsharpyuv0:amd64 libsharpyuv0 1.3.2-0.3 install ok installed libsm6:amd64 libsm6 2:1.2.3-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.39.3-6 install ok installed libss2:amd64 libss2 1.47.0-2+b1 install ok installed libssh2-1:amd64 libssh2-1 1.11.0-4 install ok installed libssl3:amd64 libssl3 3.1.4-2 install ok installed libstdc++6:amd64 libstdc++6 13.2.0-10 install ok installed libsub-exporter-perl libsub-exporter-perl 0.990-1 install ok installed libsub-exporter-progressive-perl libsub-exporter-progressive-perl 0.001013-3 install ok installed libsub-install-perl libsub-install-perl 0.929-1 install ok installed libsystemd0:amd64 libsystemd0 255.3-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.19.0-3+b2 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.13+dfsg-2 install ok installed libtext-csv-perl libtext-csv-perl 2.04-1 install ok installed libthai-data libthai-data 0.1.29-2 install ok installed libthai0:amd64 libthai0 0.1.29-2 install ok installed libtiff6:amd64 libtiff6 4.5.1+git230720-3 install ok installed libtinfo6:amd64 libtinfo6 6.4+20240113-1 install ok installed libtirpc-common libtirpc-common 1.3.4+ds-1 install ok installed libtirpc3:amd64 libtirpc3 1.3.4+ds-1 install ok installed libtk8.6:amd64 libtk8.6 8.6.13-2 install ok installed libtry-tiny-perl libtry-tiny-perl 0.31-2 install ok installed libudev1:amd64 libudev1 255.3-1 install ok installed libunistring2:amd64 libunistring2 1.0-2 install ok installed libunistring5:amd64 libunistring5 1.1-2 install ok installed libuuid1:amd64 libuuid1 2.39.3-6 install ok installed libwebp7:amd64 libwebp7 1.3.2-0.3 install ok installed libx11-6:amd64 libx11-6 2:1.8.7-1 install ok installed libx11-data libx11-data 2:1.8.7-1 install ok installed libxau6:amd64 libxau6 1:1.0.9-1 install ok installed libxcb-render0:amd64 libxcb-render0 1.15-1 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.15-1 install ok installed libxcb1:amd64 libxcb1 1.15-1 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3 install ok installed libxext6:amd64 libxext6 2:1.3.4-1+b1 install ok installed libxft2:amd64 libxft2 2.3.6-1 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1.1 install ok installed libxss1:amd64 libxss1 1:1.2.3-1 install ok installed libxt6:amd64 libxt6 1:1.2.1-1.1 install ok installed libxxhash0:amd64 libxxhash0 0.8.2-2 install ok installed libzstd1:amd64 libzstd1 1.5.5+dfsg2-2 install ok installed login login 1:4.13+dfsg1-3+b1 install ok installed logsave logsave 1.47.0-2+b1 install ok installed mawk mawk 1.3.4.20231126-1 install ok installed mount mount 2.39.3-6 install ok installed ncurses-base ncurses-base 6.4+20240113-1 install ok installed ncurses-bin ncurses-bin 6.4+20240113-1 install ok installed openssl openssl 3.1.4-2 install ok installed passwd passwd 1:4.13+dfsg1-3+b1 install ok installed perl perl 5.38.2-3 install ok installed perl-base perl-base 5.38.2-3 install ok installed perl-modules-5.36 perl-modules-5.36 5.36.0-7+deb12u1 install ok installed perl-modules-5.38 perl-modules-5.38 5.38.2-3 install ok installed r-base-core r-base-core 4.3.2-1 install ok installed r-cran-getopt r-cran-getopt 1.20.4-1 install ok installed r-cran-mass r-cran-mass 7.3-60.0.1-1 install ok installed readline-common readline-common 8.2-3 install ok installed samtools samtools 1.19-1 install ok installed sed sed 4.9-2 install ok installed sensible-utils sensible-utils 0.0.20 install ok installed smalt smalt 0.7.6-13 install ok installed sysvinit-utils sysvinit-utils 3.08-6 install ok installed tabix tabix 1.18+ds-1 install ok installed tar tar 1.35+dfsg-3 install ok installed tzdata tzdata 2023d-1 install ok installed ucf ucf 3.0043+nmu1 install ok installed unzip unzip 6.0-28 install ok installed usr-is-merged usr-is-merged 39 install ok installed util-linux util-linux 2.39.3-6 install ok installed util-linux-extra util-linux-extra 2.39.3-6 install ok installed x11-common x11-common 1:7.7+23 install ok installed xdg-utils xdg-utils 1.1.3-4.1 install ok installed zip zip 3.0-13 install ok installed zlib1g:amd64 zlib1g 1:1.3.dfsg-3+b1 0m57.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m57.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'apt-get', 'remove', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'libalgorithm-c3-perl', 'libb-hooks-op-check-perl:amd64', 'libbambamc0:amd64', 'libbio-perl-perl', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libclass-c3-perl', 'libclass-data-inheritable-perl', 'libclass-load-perl', 'libclass-load-xs-perl', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdata-optlist-perl', 'libdata-stag-perl', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libdevel-callchecker-perl:amd64', 'libdevel-globaldestruction-perl', 'libdevel-overloadinfo-perl', 'libdevel-stacktrace-perl', 'libdist-checkconflicts-perl', 'libdynaloader-functions-perl', 'libeval-closure-perl', 'libexception-class-perl', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libice6:amd64', 'libicu72:amd64', 'libio-string-perl', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libmodule-implementation-perl', 'libmodule-runtime-conflicts-perl', 'libmodule-runtime-perl', 'libmoose-perl:amd64', 'libmro-compat-perl', 'libncurses6:amd64', 'libnghttp2-14:amd64', 'libpackage-deprecationmanager-perl', 'libpackage-stash-perl', 'libpackage-stash-xs-perl:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libparams-classify-perl:amd64', 'libparams-util-perl', 'libperl5.36:amd64', 'libperl5.38:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libssh2-1:amd64', 'libsub-exporter-perl', 'libsub-exporter-progressive-perl', 'libsub-install-perl', 'libtcl8.6:amd64', 'libtext-csv-perl', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libtk8.6:amd64', 'libtry-tiny-perl', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6:amd64', 'openssl', 'perl', 'perl-modules-5.36', 'perl-modules-5.38', 'r-base-core', 'r-cran-getopt', 'r-cran-mass', 'readline-common', 'samtools', 'sensible-utils', 'smalt', 'tabix', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'bio-tradis'] 0m59.1s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: bio-tradis ca-certificates fontconfig fontconfig-config fonts-dejavu-core fonts-dejavu-mono libalgorithm-c3-perl libb-hooks-op-check-perl libbambamc0 libbio-perl-perl libblas3 libbrotli1 libbsd0 libcairo2 libclass-c3-perl libclass-data-inheritable-perl libclass-load-perl libclass-load-xs-perl libcurl3-gnutls libcurl4 libdata-optlist-perl libdata-stag-perl libdatrie1 libdeflate0 libdevel-callchecker-perl libdevel-globaldestruction-perl libdevel-overloadinfo-perl libdevel-stacktrace-perl libdist-checkconflicts-perl libdynaloader-functions-perl libeval-closure-perl libexception-class-perl libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgdbm-compat4 libgdbm6 libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts3 libhtscodecs2 libice6 libicu72 libio-string-perl libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 libldap-2.5-0 liblerc4 libmodule-implementation-perl libmodule-runtime-conflicts-perl libmodule-runtime-perl libmoose-perl libmro-compat-perl libncurses6 libnghttp2-14 libpackage-deprecationmanager-perl libpackage-stash-perl libpackage-stash-xs-perl libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libparams-classify-perl libparams-util-perl libperl5.36 libperl5.38 libpixman-1-0 libpng16-16 libpsl5 libquadmath0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsharpyuv0 libsm6 libssh2-1 libsub-exporter-perl libsub-exporter-progressive-perl libsub-install-perl libtcl8.6 libtext-csv-perl libthai-data libthai0 libtiff6 libtirpc-common libtirpc3 libtk8.6 libtry-tiny-perl libwebp7 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxrender1 libxss1 libxt6 openssl perl perl-modules-5.36 perl-modules-5.38 r-base-core r-cran-getopt r-cran-mass readline-common samtools sensible-utils smalt tabix ucf unzip x11-common xdg-utils zip 0 upgraded, 0 newly installed, 130 to remove and 0 not upgraded. After this operation, 258 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 ... 14794 files and directories currently installed.) Removing bio-tradis (1.4.5+dfsg2-2) ... Removing r-cran-mass (7.3-60.0.1-1) ... Removing r-cran-getopt (1.20.4-1) ... Removing r-base-core (4.3.2-1) ... Removing ca-certificates (20230311) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing libpangocairo-1.0-0:amd64 (1.51.0+ds-4) ... Removing libpangoft2-1.0-0:amd64 (1.51.0+ds-4) ... Removing libpango-1.0-0:amd64 (1.51.0+ds-4) ... Removing fontconfig (2.14.2-6+b1) ... Removing libtk8.6:amd64 (8.6.13-2) ... Removing libxft2:amd64 (2.3.6-1) ... Removing libcairo2:amd64 (1.18.0-1+b1) ... Removing libfontconfig1:amd64 (2.14.2-6+b1) ... Removing fontconfig-config (2.14.2-6+b1) ... Removing fonts-dejavu-core (2.37-8) ... Removing fonts-dejavu-mono (2.37-8) ... Removing libmoose-perl:amd64 (2.2207-1) ... Removing libdevel-overloadinfo-perl (0.007-1) ... Removing libmro-compat-perl (0.15-2) ... Removing libclass-c3-perl (0.35-2) ... Removing libalgorithm-c3-perl (0.11-2) ... Removing libmodule-runtime-conflicts-perl (0.003-2) ... Removing libpackage-deprecationmanager-perl (0.18-1) ... Removing smalt (0.7.6-13) ... Removing libbambamc0:amd64 (0.0.50-6+b1) ... Removing libbio-perl-perl (1.7.8-1) ... Removing liblapack3:amd64 (3.11.0-2) ... Removing libblas3:amd64 (3.11.0-2) ... Removing libharfbuzz0b:amd64 (8.3.0-2) ... Removing libfreetype6:amd64 (2.13.2+dfsg-1+b1) ... Removing libcurl4:amd64 (8.5.0-2) ... Removing libxt6:amd64 (1:1.2.1-1.1) ... Removing libxss1:amd64 (1:1.2.3-1) ... Removing libxcb-shm0:amd64 (1.15-1) ... Removing libsm6:amd64 (2:1.2.3-1) ... Removing libice6:amd64 (2:1.0.10-1) ... Removing libexception-class-perl (1.45-1) ... Removing libclass-data-inheritable-perl (0.08-3) ... Removing libclass-load-xs-perl (0.10-2+b2) ... Removing libclass-load-perl (0.25-2) ... Removing samtools (1.19-1) ... Removing libhts3:amd64 (1.18+ds-1) ... Removing libcurl3-gnutls:amd64 (8.5.0-2) ... Removing libeval-closure-perl (0.14-3) ... Removing libsub-exporter-perl (0.990-1) ... Removing libdata-optlist-perl (0.114-1) ... Removing libdata-stag-perl (0.14-3) ... Removing libthai0:amd64 (0.1.29-2) ... Removing libdatrie1:amd64 (0.2.13-3) ... Removing libtiff6:amd64 (4.5.1+git230720-3) ... Removing tabix (1.18+ds-1) ... Removing libdeflate0:amd64 (1.18-1) ... Removing libdevel-globaldestruction-perl (0.14-4) ... Removing libdevel-stacktrace-perl (2.0500-1) ... Removing libdist-checkconflicts-perl (0.11-2) ... Removing libexpat1:amd64 (2.5.0-2+b2) ... Removing libfribidi0:amd64 (1.0.13-3+b1) ... Removing libperl5.36:amd64 (5.36.0-7+deb12u1) ... Removing libparams-util-perl (1.102-2+b2) ... Removing libgfortran5:amd64 (13.2.0-10) ... Removing libglib2.0-0:amd64 (2.78.3-2) ... Removing libgomp1:amd64 (13.2.0-10) ... Removing libgraphite2-3:amd64 (1.3.14-2) ... Removing libtirpc3:amd64 (1.3.4+ds-1) ... Removing libgssapi-krb5-2:amd64 (1.20.1-5) ... Removing libhtscodecs2:amd64 (1.6.0-1) ... Removing libicu72:amd64 (72.1-4) ... Removing libio-string-perl (1.08-4) ... Removing libjbig0:amd64 (2.1-6.1) ... Removing libjpeg62-turbo:amd64 (1:2.1.5-2+b2) ... Removing libkrb5-3:amd64 (1.20.1-5) ... Removing libk5crypto3:amd64 (1.20.1-5) ... Removing libkeyutils1:amd64 (1.6.3-2+b2) ... Removing libkrb5support0:amd64 (1.20.1-5) ... Removing libldap-2.5-0:amd64 (2.5.13+dfsg-5+b3) ... Removing liblerc4:amd64 (4.0.0+ds-4) ... Removing libncurses6:amd64 (6.4+20240113-1) ... Removing libnghttp2-14:amd64 (1.58.0-1) ... Removing libpackage-stash-xs-perl:amd64 (0.30-1+b2) ... Removing libpaper-utils (1.1.29) ... Removing libpaper1:amd64 (1.1.29) ... Removing libpixman-1-0:amd64 (0.42.2-1) ... Removing libpng16-16:amd64 (1.6.40-3) ... Removing libpsl5:amd64 (0.21.2-1+b1) ... Removing libquadmath0:amd64 (13.2.0-10) ... Removing libreadline8:amd64 (8.2-3) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Removing libsasl2-2:amd64 (2.1.28+dfsg1-4+b1) ... Removing libsasl2-modules-db:amd64 (2.1.28+dfsg1-4+b1) ... Removing libwebp7:amd64 (1.3.2-0.3) ... Removing libsharpyuv0:amd64 (1.3.2-0.3) ... Removing libssh2-1:amd64 (1.11.0-4) ... Removing libsub-exporter-progressive-perl (0.001013-3) ... Removing libsub-install-perl (0.929-1) ... Removing libtcl8.6:amd64 (8.6.13+dfsg-2) ... Removing libtext-csv-perl (2.04-1) ... Removing libthai-data (0.1.29-2) ... Removing libtirpc-common (1.3.4+ds-1) ... Removing libxcb-render0:amd64 (1.15-1) ... Removing libxext6:amd64 (2:1.3.4-1+b1) ... Removing libxrender1:amd64 (1:0.9.10-1.1) ... Removing openssl (3.1.4-2) ... Removing perl-modules-5.36 (5.36.0-7+deb12u1) ... Removing readline-common (8.2-3) ... Removing ucf (3.0043+nmu1) ... Removing sensible-utils (0.0.20) ... Removing unzip (6.0-28) ... Removing x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing xdg-utils (1.1.3-4.1) ... Removing zip (3.0-13) ... Removing libpackage-stash-perl (0.40-1) ... Removing libmodule-implementation-perl (0.09-2) ... Removing libmodule-runtime-perl (0.016-2) ... Removing libparams-classify-perl:amd64 (0.015-2+b2) ... Removing libdevel-callchecker-perl:amd64 (0.008-2+b1) ... Removing libb-hooks-op-check-perl:amd64 (0.22-2+b2) ... Removing libbrotli1:amd64 (1.1.0-2+b3) ... Removing libx11-6:amd64 (2:1.8.7-1) ... Removing libxcb1:amd64 (1.15-1) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libbsd0:amd64 (0.11.8-1) ... Removing libdynaloader-functions-perl (0.003-3) ... Removing libtry-tiny-perl (0.31-2) ... Removing perl (5.38.2-3) ... Removing libperl5.38:amd64 (5.38.2-3) ... Removing libgdbm-compat4:amd64 (1.23-5) ... Removing libgdbm6:amd64 (1.23-5) ... Removing libx11-data (2:1.8.7-1) ... Removing libxau6:amd64 (1:1.0.9-1) ... Removing perl-modules-5.38 (5.38.2-3) ... Processing triggers for libc-bin (2.37-14) ... 0m59.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'apt-get', 'remove', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'libalgorithm-c3-perl', 'libb-hooks-op-check-perl:amd64', 'libbambamc0:amd64', 'libbio-perl-perl', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libclass-c3-perl', 'libclass-data-inheritable-perl', 'libclass-load-perl', 'libclass-load-xs-perl', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdata-optlist-perl', 'libdata-stag-perl', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libdevel-callchecker-perl:amd64', 'libdevel-globaldestruction-perl', 'libdevel-overloadinfo-perl', 'libdevel-stacktrace-perl', 'libdist-checkconflicts-perl', 'libdynaloader-functions-perl', 'libeval-closure-perl', 'libexception-class-perl', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libice6:amd64', 'libicu72:amd64', 'libio-string-perl', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libmodule-implementation-perl', 'libmodule-runtime-conflicts-perl', 'libmodule-runtime-perl', 'libmoose-perl:amd64', 'libmro-compat-perl', 'libncurses6:amd64', 'libnghttp2-14:amd64', 'libpackage-deprecationmanager-perl', 'libpackage-stash-perl', 'libpackage-stash-xs-perl:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libparams-classify-perl:amd64', 'libparams-util-perl', 'libperl5.36:amd64', 'libperl5.38:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libssh2-1:amd64', 'libsub-exporter-perl', 'libsub-exporter-progressive-perl', 'libsub-install-perl', 'libtcl8.6:amd64', 'libtext-csv-perl', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libtk8.6:amd64', 'libtry-tiny-perl', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6:amd64', 'openssl', 'perl', 'perl-modules-5.36', 'perl-modules-5.38', 'r-base-core', 'r-cran-getopt', 'r-cran-mass', 'readline-common', 'samtools', 'sensible-utils', 'smalt', 'tabix', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'bio-tradis'] 0m59.1s INFO: Running scripts post_remove 0m59.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/post_remove_exceptions'] 0m59.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/post_remove_exceptions'] 0m59.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'dpkg', '--purge', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'libalgorithm-c3-perl', 'libb-hooks-op-check-perl:amd64', 'libbambamc0:amd64', 'libbio-perl-perl', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libclass-c3-perl', 'libclass-data-inheritable-perl', 'libclass-load-perl', 'libclass-load-xs-perl', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdata-optlist-perl', 'libdata-stag-perl', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libdevel-callchecker-perl:amd64', 'libdevel-globaldestruction-perl', 'libdevel-overloadinfo-perl', 'libdevel-stacktrace-perl', 'libdist-checkconflicts-perl', 'libdynaloader-functions-perl', 'libeval-closure-perl', 'libexception-class-perl', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libice6:amd64', 'libicu72:amd64', 'libio-string-perl', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libmodule-implementation-perl', 'libmodule-runtime-conflicts-perl', 'libmodule-runtime-perl', 'libmoose-perl:amd64', 'libmro-compat-perl', 'libncurses6:amd64', 'libnghttp2-14:amd64', 'libpackage-deprecationmanager-perl', 'libpackage-stash-perl', 'libpackage-stash-xs-perl:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libparams-classify-perl:amd64', 'libparams-util-perl', 'libperl5.36:amd64', 'libperl5.38:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libssh2-1:amd64', 'libsub-exporter-perl', 'libsub-exporter-progressive-perl', 'libsub-install-perl', 'libtcl8.6:amd64', 'libtext-csv-perl', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libtk8.6:amd64', 'libtry-tiny-perl', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6:amd64', 'openssl', 'perl', 'perl-modules-5.36', 'perl-modules-5.38', 'r-base-core', 'r-cran-getopt', 'r-cran-mass', 'readline-common', 'samtools', 'sensible-utils', 'smalt', 'tabix', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip'] 0m59.7s DUMP: (Reading database ... 5386 files and directories currently installed.) Purging configuration files for ca-certificates (20230311) ... Removing dangling symlinks from /etc/ssl/certs... done. Purging configuration files for fontconfig (2.14.2-6+b1) ... Purging configuration files for fontconfig-config (2.14.2-6+b1) ... Purging configuration files for fonts-dejavu-core (2.37-8) ... Purging configuration files for fonts-dejavu-mono (2.37-8) ... dpkg: warning: ignoring request to remove libalgorithm-c3-perl which isn't installed dpkg: warning: ignoring request to remove libb-hooks-op-check-perl which isn't installed dpkg: warning: ignoring request to remove libbambamc0 which isn't installed dpkg: warning: ignoring request to remove libbio-perl-perl which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libbrotli1 which isn't installed dpkg: warning: ignoring request to remove libbsd0 which isn't installed dpkg: warning: ignoring request to remove libcairo2 which isn't installed dpkg: warning: ignoring request to remove libclass-c3-perl which isn't installed dpkg: warning: ignoring request to remove libclass-data-inheritable-perl which isn't installed dpkg: warning: ignoring request to remove libclass-load-perl which isn't installed dpkg: warning: ignoring request to remove libclass-load-xs-perl which isn't installed dpkg: warning: ignoring request to remove libcurl3-gnutls which isn't installed dpkg: warning: ignoring request to remove libcurl4 which isn't installed dpkg: warning: ignoring request to remove libdata-optlist-perl which isn't installed dpkg: warning: ignoring request to remove libdata-stag-perl which isn't installed dpkg: warning: ignoring request to remove libdatrie1 which isn't installed dpkg: warning: ignoring request to remove libdeflate0 which isn't installed dpkg: warning: ignoring request to remove libdevel-callchecker-perl which isn't installed dpkg: warning: ignoring request to remove libdevel-globaldestruction-perl which isn't installed dpkg: warning: ignoring request to remove libdevel-overloadinfo-perl which isn't installed dpkg: warning: ignoring request to remove libdevel-stacktrace-perl which isn't installed dpkg: warning: ignoring request to remove libdist-checkconflicts-perl which isn't installed dpkg: warning: ignoring request to remove libdynaloader-functions-perl which isn't installed dpkg: warning: ignoring request to remove libeval-closure-perl which isn't installed dpkg: warning: ignoring request to remove libexception-class-perl which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libfontconfig1 which isn't installed dpkg: warning: ignoring request to remove libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libfribidi0 which isn't installed dpkg: warning: ignoring request to remove libgdbm-compat4 which isn't installed dpkg: warning: ignoring request to remove libgdbm6 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed Purging configuration files for libglib2.0-0:amd64 (2.78.3-2) ... dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.20.1-5) ... dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed dpkg: warning: ignoring request to remove libhts3 which isn't installed dpkg: warning: ignoring request to remove libhtscodecs2 which isn't installed dpkg: warning: ignoring request to remove libice6 which isn't installed dpkg: warning: ignoring request to remove libicu72 which isn't installed dpkg: warning: ignoring request to remove libio-string-perl which isn't installed dpkg: warning: ignoring request to remove libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove libldap-2.5-0 which isn't installed dpkg: warning: ignoring request to remove liblerc4 which isn't installed dpkg: warning: ignoring request to remove libmodule-implementation-perl which isn't installed dpkg: warning: ignoring request to remove libmodule-runtime-conflicts-perl which isn't installed dpkg: warning: ignoring request to remove libmodule-runtime-perl which isn't installed dpkg: warning: ignoring request to remove libmoose-perl which isn't installed dpkg: warning: ignoring request to remove libmro-compat-perl which isn't installed dpkg: warning: ignoring request to remove libncurses6 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libpackage-deprecationmanager-perl which isn't installed dpkg: warning: ignoring request to remove libpackage-stash-perl which isn't installed dpkg: warning: ignoring request to remove libpackage-stash-xs-perl which isn't installed dpkg: warning: ignoring request to remove libpango-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpangocairo-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpangoft2-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpaper-utils which isn't installed Purging configuration files for libpaper1:amd64 (1.1.29) ... dpkg: warning: ignoring request to remove libparams-classify-perl which isn't installed dpkg: warning: ignoring request to remove libparams-util-perl which isn't installed dpkg: warning: ignoring request to remove libperl5.36 which isn't installed dpkg: warning: ignoring request to remove libperl5.38 which isn't installed dpkg: warning: ignoring request to remove libpixman-1-0 which isn't installed dpkg: warning: ignoring request to remove libpng16-16 which isn't installed dpkg: warning: ignoring request to remove libpsl5 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 librtmp1 which isn't installed dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed dpkg: warning: ignoring request to remove libsasl2-modules-db which isn't installed dpkg: warning: ignoring request to remove libsharpyuv0 which isn't installed dpkg: warning: ignoring request to remove libsm6 which isn't installed dpkg: warning: ignoring request to remove libssh2-1 which isn't installed dpkg: warning: ignoring request to remove libsub-exporter-perl which isn't installed dpkg: warning: ignoring request to remove libsub-exporter-progressive-perl which isn't installed dpkg: warning: ignoring request to remove libsub-install-perl which isn't installed dpkg: warning: ignoring request to remove libtcl8.6 which isn't installed dpkg: warning: ignoring request to remove libtext-csv-perl which isn't installed dpkg: warning: ignoring request to remove libthai-data which isn't installed dpkg: warning: ignoring request to remove libthai0 which isn't installed dpkg: warning: ignoring request to remove libtiff6 which isn't installed Purging configuration files for libtirpc-common (1.3.4+ds-1) ... dpkg: warning: ignoring request to remove libtirpc3 which isn't installed dpkg: warning: ignoring request to remove libtk8.6 which isn't installed dpkg: warning: ignoring request to remove libtry-tiny-perl which isn't installed dpkg: warning: ignoring request to remove libwebp7 which isn't installed dpkg: warning: ignoring request to remove libx11-6 which isn't installed dpkg: warning: ignoring request to remove libx11-data which isn't installed dpkg: warning: ignoring request to remove libxau6 which isn't installed dpkg: warning: ignoring request to remove libxcb-render0 which isn't installed dpkg: warning: ignoring request to remove libxcb-shm0 which isn't installed dpkg: warning: ignoring request to remove libxcb1 which isn't installed dpkg: warning: ignoring request to remove libxdmcp6 which isn't installed dpkg: warning: ignoring request to remove libxext6 which isn't installed dpkg: warning: ignoring request to remove libxft2 which isn't installed dpkg: warning: ignoring request to remove libxrender1 which isn't installed dpkg: warning: ignoring request to remove libxss1 which isn't installed dpkg: warning: ignoring request to remove libxt6 which isn't installed Purging configuration files for openssl (3.1.4-2) ... Purging configuration files for perl (5.38.2-3) ... dpkg: warning: ignoring request to remove perl-modules-5.36 which isn't installed dpkg: warning: ignoring request to remove perl-modules-5.38 which isn't installed Purging configuration files for r-base-core (4.3.2-1) ... dpkg: warning: ignoring request to remove r-cran-getopt which isn't installed dpkg: warning: ignoring request to remove r-cran-mass which isn't installed Purging configuration files for readline-common (8.2-3) ... dpkg: warning: ignoring request to remove samtools which isn't installed dpkg: warning: ignoring request to remove sensible-utils which isn't installed dpkg: warning: ignoring request to remove smalt which isn't installed dpkg: warning: ignoring request to remove tabix which isn't installed Purging configuration files for ucf (3.0043+nmu1) ... Purging configuration files for unzip (6.0-28) ... Purging configuration files for x11-common (1:7.7+23) ... dpkg: warning: while removing x11-common, directory '/etc/init.d' not empty so not removed dpkg: warning: ignoring request to remove xdg-utils which isn't installed dpkg: warning: ignoring request to remove zip which isn't installed 0m59.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'dpkg', '--purge', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-dejavu-mono', 'libalgorithm-c3-perl', 'libb-hooks-op-check-perl:amd64', 'libbambamc0:amd64', 'libbio-perl-perl', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libclass-c3-perl', 'libclass-data-inheritable-perl', 'libclass-load-perl', 'libclass-load-xs-perl', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdata-optlist-perl', 'libdata-stag-perl', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libdevel-callchecker-perl:amd64', 'libdevel-globaldestruction-perl', 'libdevel-overloadinfo-perl', 'libdevel-stacktrace-perl', 'libdist-checkconflicts-perl', 'libdynaloader-functions-perl', 'libeval-closure-perl', 'libexception-class-perl', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libhtscodecs2:amd64', 'libice6:amd64', 'libicu72:amd64', 'libio-string-perl', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'libldap-2.5-0:amd64', 'liblerc4:amd64', 'libmodule-implementation-perl', 'libmodule-runtime-conflicts-perl', 'libmodule-runtime-perl', 'libmoose-perl:amd64', 'libmro-compat-perl', 'libncurses6:amd64', 'libnghttp2-14:amd64', 'libpackage-deprecationmanager-perl', 'libpackage-stash-perl', 'libpackage-stash-xs-perl:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libparams-classify-perl:amd64', 'libparams-util-perl', 'libperl5.36:amd64', 'libperl5.38:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsharpyuv0:amd64', 'libsm6:amd64', 'libssh2-1:amd64', 'libsub-exporter-perl', 'libsub-exporter-progressive-perl', 'libsub-install-perl', 'libtcl8.6:amd64', 'libtext-csv-perl', 'libthai-data', 'libthai0:amd64', 'libtiff6:amd64', 'libtirpc-common', 'libtirpc3:amd64', 'libtk8.6:amd64', 'libtry-tiny-perl', 'libwebp7:amd64', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxft2:amd64', 'libxrender1:amd64', 'libxss1:amd64', 'libxt6:amd64', 'openssl', 'perl', 'perl-modules-5.36', 'perl-modules-5.38', 'r-base-core', 'r-cran-getopt', 'r-cran-mass', 'readline-common', 'samtools', 'sensible-utils', 'smalt', 'tabix', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip'] 0m59.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'dpkg', '--purge', 'bio-tradis'] 0m59.7s DUMP: dpkg: warning: ignoring request to remove bio-tradis which isn't installed 0m59.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'dpkg', '--purge', 'bio-tradis'] 0m59.7s INFO: Running scripts post_purge 0m59.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/post_purge_exceptions'] 0m59.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/post_purge_exceptions'] 0m59.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'dpkg', '--purge', '--pending'] 0m59.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'dpkg', '--purge', '--pending'] 0m59.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'dpkg', '--remove', '--pending'] 0m59.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'dpkg', '--remove', '--pending'] 0m59.7s INFO: Running scripts post_test 0m59.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/post_test_exceptions'] 0m59.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'tmp/scripts/post_test_exceptions'] 0m59.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l'] 1m0.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l'] 1m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'dpkg-divert', '--list'] 1m0.2s DUMP: local diversion of /bin/sync to /bin/sync.distrib local diversion of /home to /home.distrib 1m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'dpkg-divert', '--list'] 1m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'apt-get', 'clean'] 1m0.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l', 'apt-get', 'clean'] 1m0.3s DEBUG: Recording chroot state 1m1.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l/dev/shm'] 1m1.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l/dev/shm'] 1m1.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l/dev/console'] 1m1.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l/dev/console'] 1m1.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l/dev/ptmx'] 1m1.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l/dev/ptmx'] 1m1.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l/dev/pts'] 1m1.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l/dev/pts'] 1m1.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l/proc'] 1m1.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l/proc'] 1m1.6s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l'] 1m1.7s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpnthwdq3l'] 1m1.7s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpnthwdq3l 1m1.7s INFO: PASS: Upgrading between Debian distributions. 1m1.7s INFO: PASS: All tests. 1m1.7s INFO: piuparts run ends. ret=0 End: 2024-01-25 21:45:04 GMT