Start: 2023-12-28 16:20:25 GMT Package: cnvkit Version: 0.9.8-1 Installed-Size: 69059 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3-biopython, python3-matplotlib, python3-numpy, python3-pandas, python3-pomegranate, python3-pyfaidx, python3-pysam, python3-reportlab, python3-scipy, python3-sklearn, python3:any, r-bioc-dnacopy Description: Copy number variant detection from targeted DNA sequencing Homepage: http://cnvkit.readthedocs.org Description-md5: 0b8ab5ba6be9de3379277ab7a92a7b5d Section: science Priority: optional Filename: pool/main/c/cnvkit/cnvkit_0.9.8-1_amd64.deb Size: 15426740 MD5sum: 6647858ecca063375d0e870f2169eb9b SHA256: b015c3352c86bffb17381dea0be72d3284ad785d74a7e4c3e3ac4684e99ee493 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-log-alternatives --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --warn-on-usr-move fail --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz -d bullseye --no-upgrade-test --apt cnvkit=0.9.8-1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.2 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts-log-alternatives --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --warn-on-usr-move fail --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz -d bullseye --no-upgrade-test --apt cnvkit=0.9.8-1 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-26-amd64 #1 SMP Debian 5.10.197-1 (2023-09-29) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpd2v957bx 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpd2v957bx 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m1.5s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/bullseye-merged-usr_amd64.tar.gz'] 0m1.5s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpd2v957bx/proc'] 0m1.5s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpd2v957bx/proc'] 0m1.5s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpd2v957bx/dev/pts'] 0m1.5s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpd2v957bx/dev/pts'] 0m1.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpd2v957bx/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpd2v957bx/dev/ptmx'] 0m1.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpd2v957bx/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpd2v957bx/dev/ptmx'] 0m1.5s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpd2v957bx/dev/console'] 0m1.5s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmpd2v957bx/dev/console'] 0m1.5s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpd2v957bx/dev/shm'] 0m1.5s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpd2v957bx/dev/shm'] 0m1.5s DEBUG: sources.list: deb http://deb.debian.org/debian/ bullseye 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-log-alternatives to /srv/piuparts.debian.org/tmp/tmpd2v957bx/tmp/scripts/ 0m1.5s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpd2v957bx/tmp/scripts/ 0m1.5s INFO: Running scripts post_chroot_unpack 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'apt-get', 'update'] 0m2.1s DUMP: Hit:1 http://deb.debian.org/debian bullseye InRelease Reading package lists... 0m2.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'apt-get', 'update'] 0m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'apt-get', '-yf', 'dist-upgrade'] 0m2.4s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'apt-get', '-yf', 'dist-upgrade'] 0m2.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.7s DUMP: cd994be14815166bf41ad7cebd6f56fc - 0m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.7s INFO: Running scripts post_setup 0m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/post_setup_dummy_users'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/post_setup_dummy_users'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/post_setup_forbid_home'] 0m3.7s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/post_setup_forbid_home'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.7s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' dpkg-divert: warning: diverting file '/bin/sync' from an Essential package with rename is dangerous, use --no-rename '/bin/sync' -> 'true' 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/post_setup_minimize'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/post_setup_minimize'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/post_setup_zz_backports'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/post_setup_zz_backports'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'apt-get', 'clean'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'apt-get', 'clean'] 0m3.8s DEBUG: Recording chroot state 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.2s DUMP: install ok installed adduser adduser 3.118+deb11u1 install ok installed apt apt 2.2.4 install ok installed base-files base-files 11.1+deb11u8 install ok installed base-passwd base-passwd 3.5.51 install ok installed bash bash 5.1-2+deb11u1 install ok installed bsdutils bsdutils 1:2.36.1-8+deb11u1 install ok installed coreutils coreutils 8.32-4+b1 install ok installed dash dash 0.5.11+git20200708+dd9ef66-5 install ok installed debconf debconf 1.5.77 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1+deb11u1 install ok installed debianutils debianutils 4.11.2 install ok installed diffutils diffutils 1:3.7-5 install ok installed dpkg dpkg 1.20.13 install ok installed e2fsprogs e2fsprogs 1.46.2-2 install ok installed findutils findutils 4.8.0-1 install ok installed gcc-10-base:amd64 gcc-10-base 10.2.1-6 install ok installed gcc-9-base:amd64 gcc-9-base 9.3.0-22 install ok installed gpgv gpgv 2.2.27-2+deb11u2 install ok installed grep grep 3.6-1+deb11u1 install ok installed gzip gzip 1.10-4+deb11u1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.60 install ok installed libacl1:amd64 libacl1 2.2.53-10 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.2.4 install ok installed libattr1:amd64 libattr1 1:2.4.48-6 install ok installed libaudit-common libaudit-common 1:3.0-2 install ok installed libaudit1:amd64 libaudit1 1:3.0-2 install ok installed libblkid1:amd64 libblkid1 2.36.1-8+deb11u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4 install ok installed libc-bin libc-bin 2.31-13+deb11u6 install ok installed libc6:amd64 libc6 2.31-13+deb11u6 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2+b1 install ok installed libcom-err2:amd64 libcom-err2 1.46.2-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.18-4 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.8 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.260 install ok installed libext2fs2:amd64 libext2fs2 1.46.2-2 install ok installed libffi7:amd64 libffi7 3.3-6 install ok installed libgcc-s1:amd64 libgcc-s1 10.2.1-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.7-6 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg-1+deb11u1 install ok installed libgnutls30:amd64 libgnutls30 3.7.1-5+deb11u3 install ok installed libgpg-error0:amd64 libgpg-error0 1.38-2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.18.3-6+deb11u4 install ok installed libhogweed6:amd64 libhogweed6 3.7.3-1 install ok installed libidn2-0:amd64 libidn2-0 2.3.0-5 install ok installed libk5crypto3:amd64 libk5crypto3 1.18.3-6+deb11u4 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.18.3-6+deb11u4 install ok installed libkrb5support0:amd64 libkrb5support0 1.18.3-6+deb11u4 install ok installed liblz4-1:amd64 liblz4-1 1.9.3-2 install ok installed liblzma5:amd64 liblzma5 5.2.5-2.1~deb11u1 install ok installed libmount1:amd64 libmount1 2.36.1-8+deb11u1 install ok installed libnettle8:amd64 libnettle8 3.7.3-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.22-1 install ok installed libpam-modules:amd64 libpam-modules 1.4.0-9+deb11u1 install ok installed libpam-modules-bin libpam-modules-bin 1.4.0-9+deb11u1 install ok installed libpam-runtime libpam-runtime 1.4.0-9+deb11u1 install ok installed libpam0g:amd64 libpam0g 1.4.0-9+deb11u1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.36-2+deb11u1 install ok installed libpcre3:amd64 libpcre3 2:8.39-13 install ok installed libseccomp2:amd64 libseccomp2 2.5.1-1+deb11u1 install ok installed libselinux1:amd64 libselinux1 3.1-3 install ok installed libsemanage-common libsemanage-common 3.1-1 install ok installed libsemanage1:amd64 libsemanage1 3.1-1+b2 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.36.1-8+deb11u1 install ok installed libss2:amd64 libss2 1.46.2-2 install ok installed libssl1.1:amd64 libssl1.1 1.1.1w-0+deb11u1 install ok installed libstdc++6:amd64 libstdc++6 10.2.1-6 install ok installed libsystemd0:amd64 libsystemd0 247.3-7+deb11u4 install ok installed libtasn1-6:amd64 libtasn1-6 4.16.0-2+deb11u1 install ok installed libtinfo6:amd64 libtinfo6 6.2+20201114-2+deb11u2 install ok installed libtirpc-common libtirpc-common 1.3.1-1+deb11u1 install ok installed libtirpc3:amd64 libtirpc3 1.3.1-1+deb11u1 install ok installed libudev1:amd64 libudev1 247.3-7+deb11u4 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed libuuid1:amd64 libuuid1 2.36.1-8+deb11u1 install ok installed libxxhash0:amd64 libxxhash0 0.8.0-2 install ok installed libzstd1:amd64 libzstd1 1.4.8+dfsg-2.1 install ok installed login login 1:4.8.1-1 install ok installed logsave logsave 1.46.2-2 install ok installed lsb-base lsb-base 11.1.0 install ok installed mawk mawk 1.3.4.20200120-2 install ok installed mount mount 2.36.1-8+deb11u1 install ok installed ncurses-base ncurses-base 6.2+20201114-2+deb11u2 install ok installed ncurses-bin ncurses-bin 6.2+20201114-2+deb11u2 install ok installed passwd passwd 1:4.8.1-1 install ok installed perl-base perl-base 5.32.1-4+deb11u2 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.96-7+deb11u1 install ok installed tar tar 1.34+dfsg-1 install ok installed tzdata tzdata 2021a-1+deb11u10 install ok installed util-linux util-linux 2.36.1-8+deb11u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2+deb11u2 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'dpkg-divert', '--list'] 0m4.2s DUMP: local diversion of /bin/sync to /bin/sync.distrib diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'dpkg-divert', '--list'] 0m4.2s INFO: Running scripts is_testable 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/is_testable_uninstallable'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/is_testable_uninstallable'] 0m4.2s INFO: apt-cache does not know about any of the requested packages 0m4.2s INFO: Running scripts pre_test 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/pre_test_exceptions'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/pre_test_exceptions'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/pre_test_root_password'] 0m4.3s DUMP: New password: Retype new password: passwd: password updated successfully 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/pre_test_root_password'] 0m4.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpd2v957bx'] 0m4.7s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpd2v957bx'] 0m5.1s DEBUG: No broken symlinks as far as we can find. 0m5.1s INFO: Running scripts pre_install 0m5.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/pre_install_database-server'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/pre_install_database-server'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/pre_install_exceptions'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/pre_install_exceptions'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/pre_install_extras'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/pre_install_extras'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/pre_install_log_alternatives'] 0m5.2s DUMP: Adding 'local diversion of /usr/bin/update-alternatives to /usr/bin/update-alternatives.orig' dpkg-divert: warning: diverting file '/usr/bin/update-alternatives' from an Essential package with rename is dangerous, use --no-rename 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/pre_install_log_alternatives'] 0m5.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpd2v957bx'] 0m5.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpd2v957bx'] 0m6.0s DEBUG: No broken symlinks as far as we can find. 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'apt-cache', 'policy'] 0m6.5s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian bullseye/main amd64 Packages release v=11.8,o=Debian,a=oldstable,n=bullseye,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m6.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'apt-cache', 'policy'] 0m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'apt-cache', 'policy', 'cnvkit'] 0m6.6s DUMP: cnvkit: Installed: (none) Candidate: 0.9.8-1 Version table: 0.9.8-1 500 500 http://deb.debian.org/debian bullseye/main amd64 Packages 0m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'apt-cache', 'policy', 'cnvkit'] 0m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'apt-get', '-y', 'install', 'cnvkit=0.9.8-1'] 0m39.1s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: ca-certificates fontconfig fontconfig-config fonts-lyx libblas3 libbrotli1 libbsd0 libcairo2 libcurl3-gnutls libcurl4 libdatrie1 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgdbm-compat4 libgdbm6 libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libharfbuzz0b libhts3 libice6 libicu67 libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 libldap-2.4-2 libmd0 libmpdec3 libncurses6 libncursesw6 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libperl5.32 libpixman-1-0 libpng16-16 libprocps8 libpsl5 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libquadmath0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsm6 libsqlite3-0 libssh2-1 libtcl8.6 libthai-data libthai0 libtiff5 libtk8.6 libwebp6 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxrender1 libxss1 libxt6 libyaml-0-2 mailcap media-types mime-support openssl perl perl-modules-5.32 procps python-matplotlib-data python3 python3-biopython python3-cycler python3-dateutil python3-decorator python3-joblib python3-kiwisolver python3-matplotlib python3-minimal python3-networkx python3-numpy python3-pandas python3-pandas-lib python3-pil python3-pkg-resources python3-pomegranate python3-pyfaidx python3-pyparsing python3-pysam python3-reportlab python3-reportlab-accel python3-scipy python3-six python3-sklearn python3-sklearn-lib python3-threadpoolctl python3-tz python3-yaml python3.9 python3.9-minimal r-base-core r-bioc-biocgenerics r-bioc-dnacopy readline-common sensible-utils ttf-bitstream-vera ucf unzip x11-common xdg-utils zip Suggested packages: gdbm-l10n libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libtap-harness-archive-perl python3-doc python3-tk python3-venv bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle phylip phyml prank probcons python3-mysqldb python3-mmtf python3-rdflib python3-renderpm python3-psycopg2 raxml samtools t-coffee wise w3-dtd-mathml python-cycler-doc dvipng ffmpeg ghostscript gir1.2-gtk-3.0 inkscape ipython3 librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi python3-gi-cairo python3-gobject python3-nose python3-pyqt5 python3-sip python3-tornado texlive-extra-utils texlive-latex-extra ttf-staypuft python-networkx-doc gcc gfortran python-numpy-doc python3-dev python3-numpy-dbg python3-pytest python-pandas-doc python3-statsmodels python-pil-doc python3-pil-dbg python3-setuptools python-pomegranate-doc python-pyparsing-doc pdf-viewer python3-egenix-mxtexttools python-reportlab-doc python-scipy-doc python3-dap python-sklearn-doc python3.9-venv python3.9-doc binutils binfmt-support elpa-ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-bioc-biobase r-bioc-s4vectors r-bioc-iranges r-bioc-genomicranges r-bioc-delayedarray r-bioc-biostrings r-bioc-rsamtools r-bioc-annotationdbi r-bioc-affy r-bioc-deseq2 r-bioc-annotate readline-doc Recommended packages: libglib2.0-data shared-mime-info xdg-user-dirs javascript-common libldap-common libgpm2 publicsuffix libsasl2-modules bzip2 file xz-utils netbase psmisc python-biopython-doc ncbi-blast+ python3-pytest python3-simplejson python3-psutil python3-tk python3-gdal python3-pydot python3-pygraphviz python3-bottleneck python3-numexpr python3-odf python3-openpyxl python3-xlwt python3-bs4 python3-html5lib python3-lxml python3-tables python3-jinja2 python3-numba python3-olefile python3-renderpm g++ | c++-compiler python3-nose r-recommended r-base-dev r-doc-html r-cran-runit libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: ca-certificates cnvkit fontconfig fontconfig-config fonts-lyx libblas3 libbrotli1 libbsd0 libcairo2 libcurl3-gnutls libcurl4 libdatrie1 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgdbm-compat4 libgdbm6 libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libharfbuzz0b libhts3 libice6 libicu67 libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 libldap-2.4-2 libmd0 libmpdec3 libncurses6 libncursesw6 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libperl5.32 libpixman-1-0 libpng16-16 libprocps8 libpsl5 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libquadmath0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsm6 libsqlite3-0 libssh2-1 libtcl8.6 libthai-data libthai0 libtiff5 libtk8.6 libwebp6 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxrender1 libxss1 libxt6 libyaml-0-2 mailcap media-types mime-support openssl perl perl-modules-5.32 procps python-matplotlib-data python3 python3-biopython python3-cycler python3-dateutil python3-decorator python3-joblib python3-kiwisolver python3-matplotlib python3-minimal python3-networkx python3-numpy python3-pandas python3-pandas-lib python3-pil python3-pkg-resources python3-pomegranate python3-pyfaidx python3-pyparsing python3-pysam python3-reportlab python3-reportlab-accel python3-scipy python3-six python3-sklearn python3-sklearn-lib python3-threadpoolctl python3-tz python3-yaml python3.9 python3.9-minimal r-base-core r-bioc-biocgenerics r-bioc-dnacopy readline-common sensible-utils ttf-bitstream-vera ucf unzip x11-common xdg-utils zip 0 upgraded, 132 newly installed, 0 to remove and 0 not upgraded. Need to get 125 MB of archives. After this operation, 481 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian bullseye/main amd64 perl-modules-5.32 all 5.32.1-4+deb11u2 [2823 kB] Get:2 http://deb.debian.org/debian bullseye/main amd64 libgdbm6 amd64 1.19-2 [64.9 kB] Get:3 http://deb.debian.org/debian bullseye/main amd64 libgdbm-compat4 amd64 1.19-2 [44.7 kB] Get:4 http://deb.debian.org/debian bullseye/main amd64 libperl5.32 amd64 5.32.1-4+deb11u2 [4106 kB] Get:5 http://deb.debian.org/debian bullseye/main amd64 perl amd64 5.32.1-4+deb11u2 [293 kB] Get:6 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-minimal amd64 3.9.2-1 [801 kB] Get:7 http://deb.debian.org/debian bullseye/main amd64 libexpat1 amd64 2.2.10-2+deb11u5 [98.2 kB] Get:8 http://deb.debian.org/debian bullseye/main amd64 python3.9-minimal amd64 3.9.2-1 [1955 kB] Get:9 http://deb.debian.org/debian bullseye/main amd64 python3-minimal amd64 3.9.2-3 [38.2 kB] Get:10 http://deb.debian.org/debian bullseye/main amd64 media-types all 4.0.0 [30.3 kB] Get:11 http://deb.debian.org/debian bullseye/main amd64 mailcap all 3.69 [31.7 kB] Get:12 http://deb.debian.org/debian bullseye/main amd64 mime-support all 3.66 [10.9 kB] Get:13 http://deb.debian.org/debian bullseye/main amd64 libmpdec3 amd64 2.5.1-1 [87.7 kB] Get:14 http://deb.debian.org/debian bullseye/main amd64 libncursesw6 amd64 6.2+20201114-2+deb11u2 [132 kB] Get:15 http://deb.debian.org/debian bullseye/main amd64 readline-common all 8.1-1 [73.7 kB] Get:16 http://deb.debian.org/debian bullseye/main amd64 libreadline8 amd64 8.1-1 [169 kB] Get:17 http://deb.debian.org/debian bullseye/main amd64 libsqlite3-0 amd64 3.34.1-3 [797 kB] Get:18 http://deb.debian.org/debian bullseye/main amd64 libpython3.9-stdlib amd64 3.9.2-1 [1684 kB] Get:19 http://deb.debian.org/debian bullseye/main amd64 python3.9 amd64 3.9.2-1 [466 kB] Get:20 http://deb.debian.org/debian bullseye/main amd64 libpython3-stdlib amd64 3.9.2-3 [21.4 kB] Get:21 http://deb.debian.org/debian bullseye/main amd64 python3 amd64 3.9.2-3 [37.9 kB] Get:22 http://deb.debian.org/debian bullseye/main amd64 libncurses6 amd64 6.2+20201114-2+deb11u2 [102 kB] Get:23 http://deb.debian.org/debian bullseye/main amd64 libprocps8 amd64 2:3.3.17-5 [63.9 kB] Get:24 http://deb.debian.org/debian bullseye/main amd64 procps amd64 2:3.3.17-5 [502 kB] Get:25 http://deb.debian.org/debian bullseye/main amd64 sensible-utils all 0.0.14 [14.8 kB] Get:26 http://deb.debian.org/debian bullseye/main amd64 openssl amd64 1.1.1w-0+deb11u1 [859 kB] Get:27 http://deb.debian.org/debian bullseye/main amd64 ca-certificates all 20210119 [158 kB] Get:28 http://deb.debian.org/debian bullseye/main amd64 ucf all 3.0043 [74.0 kB] Get:29 http://deb.debian.org/debian bullseye/main amd64 python3-pkg-resources all 52.0.0-4 [190 kB] Get:30 http://deb.debian.org/debian bullseye/main amd64 libblas3 amd64 3.9.0-3+deb11u1 [153 kB] Get:31 http://deb.debian.org/debian bullseye/main amd64 libquadmath0 amd64 10.2.1-6 [145 kB] Get:32 http://deb.debian.org/debian bullseye/main amd64 libgfortran5 amd64 10.2.1-6 [727 kB] Get:33 http://deb.debian.org/debian bullseye/main amd64 liblapack3 amd64 3.9.0-3+deb11u1 [2166 kB] Get:34 http://deb.debian.org/debian bullseye/main amd64 python3-numpy amd64 1:1.19.5-1 [2693 kB] Get:35 http://deb.debian.org/debian bullseye/main amd64 python3-reportlab-accel amd64 3.5.59-2 [39.1 kB] Get:36 http://deb.debian.org/debian bullseye/main amd64 libbrotli1 amd64 1.0.9-2+b2 [279 kB] Get:37 http://deb.debian.org/debian bullseye/main amd64 libpng16-16 amd64 1.6.37-3 [294 kB] Get:38 http://deb.debian.org/debian bullseye/main amd64 libfreetype6 amd64 2.10.4+dfsg-1+deb11u1 [418 kB] Get:39 http://deb.debian.org/debian bullseye/main amd64 libimagequant0 amd64 2.12.2-1.1 [32.5 kB] Get:40 http://deb.debian.org/debian bullseye/main amd64 libjpeg62-turbo amd64 1:2.0.6-4 [151 kB] Get:41 http://deb.debian.org/debian bullseye/main amd64 liblcms2-2 amd64 2.12~rc1-2 [150 kB] Get:42 http://deb.debian.org/debian bullseye/main amd64 libdeflate0 amd64 1.7-1 [53.1 kB] Get:43 http://deb.debian.org/debian bullseye/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get:44 http://deb.debian.org/debian bullseye/main amd64 libwebp6 amd64 0.6.1-2.1+deb11u2 [259 kB] Get:45 http://deb.debian.org/debian bullseye/main amd64 libtiff5 amd64 4.2.0-1+deb11u4 [290 kB] Get:46 http://deb.debian.org/debian bullseye/main amd64 libwebpdemux2 amd64 0.6.1-2.1+deb11u2 [87.8 kB] Get:47 http://deb.debian.org/debian bullseye/main amd64 libwebpmux3 amd64 0.6.1-2.1+deb11u2 [97.7 kB] Get:48 http://deb.debian.org/debian bullseye/main amd64 libxau6 amd64 1:1.0.9-1 [19.7 kB] Get:49 http://deb.debian.org/debian bullseye/main amd64 libmd0 amd64 1.0.3-3 [28.0 kB] Get:50 http://deb.debian.org/debian bullseye/main amd64 libbsd0 amd64 0.11.3-1+deb11u1 [108 kB] Get:51 http://deb.debian.org/debian bullseye/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:52 http://deb.debian.org/debian bullseye/main amd64 libxcb1 amd64 1.14-3 [140 kB] Get:53 http://deb.debian.org/debian bullseye/main amd64 python3-pil amd64 8.1.2+dfsg-0.3+deb11u1 [445 kB] Get:54 http://deb.debian.org/debian bullseye/main amd64 python3-reportlab all 3.5.59-2 [575 kB] Get:55 http://deb.debian.org/debian bullseye/main amd64 python3-biopython amd64 1.78+dfsg-4 [1402 kB] Get:56 http://deb.debian.org/debian bullseye/main amd64 libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB] Get:57 http://deb.debian.org/debian bullseye/main amd64 libjs-jquery-ui all 1.12.1+dfsg-8+deb11u1 [232 kB] Get:58 http://deb.debian.org/debian bullseye/main amd64 fonts-lyx all 2.3.6-1 [205 kB] Get:59 http://deb.debian.org/debian bullseye/main amd64 ttf-bitstream-vera all 1.10-8.1 [223 kB] Get:60 http://deb.debian.org/debian bullseye/main amd64 python-matplotlib-data all 3.3.4-1 [4153 kB] Get:61 http://deb.debian.org/debian bullseye/main amd64 python3-six all 1.16.0-2 [17.5 kB] Get:62 http://deb.debian.org/debian bullseye/main amd64 python3-dateutil all 2.8.1-6 [79.2 kB] Get:63 http://deb.debian.org/debian bullseye/main amd64 python3-pyparsing all 2.4.7-1 [109 kB] Get:64 http://deb.debian.org/debian bullseye/main amd64 python3-cycler all 0.10.0-3 [8084 B] Get:65 http://deb.debian.org/debian bullseye/main amd64 python3-kiwisolver amd64 1.3.1-1+b1 [55.7 kB] Get:66 http://deb.debian.org/debian bullseye/main amd64 python3-matplotlib amd64 3.3.4-1 [4163 kB] Get:67 http://deb.debian.org/debian bullseye/main amd64 python3-tz all 2021.1-1 [34.8 kB] Get:68 http://deb.debian.org/debian bullseye/main amd64 python3-pandas-lib amd64 1.1.5+dfsg-2 [3287 kB] Get:69 http://deb.debian.org/debian bullseye/main amd64 python3-pandas all 1.1.5+dfsg-2 [2096 kB] Get:70 http://deb.debian.org/debian bullseye/main amd64 python3-joblib all 0.17.0-4+deb11u1 [214 kB] Get:71 http://deb.debian.org/debian bullseye/main amd64 python3-decorator all 4.4.2-2 [15.8 kB] Get:72 http://deb.debian.org/debian bullseye/main amd64 python3-networkx all 2.5+ds-2 [900 kB] Get:73 http://deb.debian.org/debian bullseye/main amd64 liblbfgsb0 amd64 3.0+dfsg.3-9 [28.5 kB] Get:74 http://deb.debian.org/debian bullseye/main amd64 python3-scipy amd64 1.6.0-2 [12.3 MB] Get:75 http://deb.debian.org/debian bullseye/main amd64 libyaml-0-2 amd64 0.2.2-1 [49.6 kB] Get:76 http://deb.debian.org/debian bullseye/main amd64 python3-yaml amd64 5.3.1-5 [138 kB] Get:77 http://deb.debian.org/debian bullseye/main amd64 python3-pomegranate amd64 0.13.5-1 [2482 kB] Get:78 http://deb.debian.org/debian bullseye/main amd64 python3-pyfaidx all 0.5.9.2-1 [26.4 kB] Get:79 http://deb.debian.org/debian bullseye/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-2.1+deb11u1 [69.1 kB] Get:80 http://deb.debian.org/debian bullseye/main amd64 libsasl2-2 amd64 2.1.27+dfsg-2.1+deb11u1 [106 kB] Get:81 http://deb.debian.org/debian bullseye/main amd64 libldap-2.4-2 amd64 2.4.57+dfsg-3+deb11u1 [232 kB] Get:82 http://deb.debian.org/debian bullseye/main amd64 libnghttp2-14 amd64 1.43.0-1 [77.1 kB] Get:83 http://deb.debian.org/debian bullseye/main amd64 libpsl5 amd64 0.21.0-1.2 [57.3 kB] Get:84 http://deb.debian.org/debian bullseye/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b2 [60.8 kB] Get:85 http://deb.debian.org/debian bullseye/main amd64 libssh2-1 amd64 1.9.0-2 [156 kB] Get:86 http://deb.debian.org/debian bullseye/main amd64 libcurl3-gnutls amd64 7.74.0-1.3+deb11u9 [344 kB] Get:87 http://deb.debian.org/debian bullseye/main amd64 libhts3 amd64 1.11-4 [378 kB] Get:88 http://deb.debian.org/debian bullseye/main amd64 python3-pysam amd64 0.15.4+ds-3+b2 [1536 kB] Get:89 http://deb.debian.org/debian bullseye/main amd64 libgomp1 amd64 10.2.1-6 [99.9 kB] Get:90 http://deb.debian.org/debian bullseye/main amd64 python3-sklearn-lib amd64 0.23.2-5 [1884 kB] Get:91 http://deb.debian.org/debian bullseye/main amd64 python3-threadpoolctl all 2.1.0-1 [15.3 kB] Get:92 http://deb.debian.org/debian bullseye/main amd64 python3-sklearn all 0.23.2-5 [1818 kB] Get:93 http://deb.debian.org/debian bullseye/main amd64 zip amd64 3.0-12 [232 kB] Get:94 http://deb.debian.org/debian bullseye/main amd64 unzip amd64 6.0-26+deb11u1 [172 kB] Get:95 http://deb.debian.org/debian bullseye/main amd64 libpaper1 amd64 1.1.28+b1 [21.6 kB] Get:96 http://deb.debian.org/debian bullseye/main amd64 libpaper-utils amd64 1.1.28+b1 [18.3 kB] Get:97 http://deb.debian.org/debian bullseye/main amd64 xdg-utils all 1.1.3-4.1 [75.5 kB] Get:98 http://deb.debian.org/debian bullseye/main amd64 fontconfig-config all 2.13.1-4.2 [281 kB] Get:99 http://deb.debian.org/debian bullseye/main amd64 libfontconfig1 amd64 2.13.1-4.2 [347 kB] Get:100 http://deb.debian.org/debian bullseye/main amd64 libpixman-1-0 amd64 0.40.0-1.1~deb11u1 [543 kB] Get:101 http://deb.debian.org/debian bullseye/main amd64 libx11-data all 2:1.7.2-1+deb11u1 [311 kB] Get:102 http://deb.debian.org/debian bullseye/main amd64 libx11-6 amd64 2:1.7.2-1+deb11u1 [772 kB] Get:103 http://deb.debian.org/debian bullseye/main amd64 libxcb-render0 amd64 1.14-3 [111 kB] Get:104 http://deb.debian.org/debian bullseye/main amd64 libxcb-shm0 amd64 1.14-3 [101 kB] Get:105 http://deb.debian.org/debian bullseye/main amd64 libxext6 amd64 2:1.3.3-1.1 [52.7 kB] Get:106 http://deb.debian.org/debian bullseye/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get:107 http://deb.debian.org/debian bullseye/main amd64 libcairo2 amd64 1.16.0-5 [694 kB] Get:108 http://deb.debian.org/debian bullseye/main amd64 libcurl4 amd64 7.74.0-1.3+deb11u9 [347 kB] Get:109 http://deb.debian.org/debian bullseye/main amd64 libglib2.0-0 amd64 2.66.8-1 [1370 kB] Get:110 http://deb.debian.org/debian bullseye/main amd64 libicu67 amd64 67.1-7 [8622 kB] Get:111 http://deb.debian.org/debian bullseye/main amd64 fontconfig amd64 2.13.1-4.2 [417 kB] Get:112 http://deb.debian.org/debian bullseye/main amd64 libfribidi0 amd64 1.0.8-2+deb11u1 [64.9 kB] Get:113 http://deb.debian.org/debian bullseye/main amd64 libgraphite2-3 amd64 1.3.14-1 [81.2 kB] Get:114 http://deb.debian.org/debian bullseye/main amd64 libharfbuzz0b amd64 2.7.4-1 [1471 kB] Get:115 http://deb.debian.org/debian bullseye/main amd64 libthai-data all 0.1.28-3 [170 kB] Get:116 http://deb.debian.org/debian bullseye/main amd64 libdatrie1 amd64 0.2.13-1 [42.7 kB] Get:117 http://deb.debian.org/debian bullseye/main amd64 libthai0 amd64 0.1.28-3 [54.2 kB] Get:118 http://deb.debian.org/debian bullseye/main amd64 libpango-1.0-0 amd64 1.46.2-3 [191 kB] Get:119 http://deb.debian.org/debian bullseye/main amd64 libpangoft2-1.0-0 amd64 1.46.2-3 [62.2 kB] Get:120 http://deb.debian.org/debian bullseye/main amd64 libpangocairo-1.0-0 amd64 1.46.2-3 [50.6 kB] Get:121 http://deb.debian.org/debian bullseye/main amd64 libtcl8.6 amd64 8.6.11+dfsg-1 [1018 kB] Get:122 http://deb.debian.org/debian bullseye/main amd64 libxft2 amd64 2.3.2-2 [57.2 kB] Get:123 http://deb.debian.org/debian bullseye/main amd64 x11-common all 1:7.7+22 [252 kB] Get:124 http://deb.debian.org/debian bullseye/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get:125 http://deb.debian.org/debian bullseye/main amd64 libtk8.6 amd64 8.6.11-2 [780 kB] Get:126 http://deb.debian.org/debian bullseye/main amd64 libice6 amd64 2:1.0.10-1 [58.5 kB] Get:127 http://deb.debian.org/debian bullseye/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get:128 http://deb.debian.org/debian bullseye/main amd64 libxt6 amd64 1:1.2.0-1 [189 kB] Get:129 http://deb.debian.org/debian bullseye/main amd64 r-base-core amd64 4.0.4-1 [25.1 MB] Get:130 http://deb.debian.org/debian bullseye/main amd64 r-bioc-biocgenerics all 0.36.0-1 [648 kB] Get:131 http://deb.debian.org/debian bullseye/main amd64 r-bioc-dnacopy amd64 1.64.0-1 [420 kB] Get:132 http://deb.debian.org/debian bullseye/main amd64 cnvkit amd64 0.9.8-1 [15.4 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 125 MB in 1s (116 MB/s) Selecting previously unselected package perl-modules-5.32. (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 ... 6667 files and directories currently installed.) Preparing to unpack .../0-perl-modules-5.32_5.32.1-4+deb11u2_all.deb ... Unpacking perl-modules-5.32 (5.32.1-4+deb11u2) ... Selecting previously unselected package libgdbm6:amd64. Preparing to unpack .../1-libgdbm6_1.19-2_amd64.deb ... Unpacking libgdbm6:amd64 (1.19-2) ... Selecting previously unselected package libgdbm-compat4:amd64. 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Preparing to unpack .../089-libicu67_67.1-7_amd64.deb ... Unpacking libicu67:amd64 (67.1-7) ... Selecting previously unselected package fontconfig. Preparing to unpack .../090-fontconfig_2.13.1-4.2_amd64.deb ... Unpacking fontconfig (2.13.1-4.2) ... Selecting previously unselected package libfribidi0:amd64. Preparing to unpack .../091-libfribidi0_1.0.8-2+deb11u1_amd64.deb ... Unpacking libfribidi0:amd64 (1.0.8-2+deb11u1) ... Selecting previously unselected package libgraphite2-3:amd64. Preparing to unpack .../092-libgraphite2-3_1.3.14-1_amd64.deb ... Unpacking libgraphite2-3:amd64 (1.3.14-1) ... Selecting previously unselected package libharfbuzz0b:amd64. Preparing to unpack .../093-libharfbuzz0b_2.7.4-1_amd64.deb ... Unpacking libharfbuzz0b:amd64 (2.7.4-1) ... Selecting previously unselected package libthai-data. Preparing to unpack .../094-libthai-data_0.1.28-3_all.deb ... Unpacking libthai-data (0.1.28-3) ... Selecting previously unselected package libdatrie1:amd64. Preparing to unpack .../095-libdatrie1_0.2.13-1_amd64.deb ... Unpacking libdatrie1:amd64 (0.2.13-1) ... Selecting previously unselected package libthai0:amd64. Preparing to unpack .../096-libthai0_0.1.28-3_amd64.deb ... Unpacking libthai0:amd64 (0.1.28-3) ... Selecting previously unselected package libpango-1.0-0:amd64. Preparing to unpack .../097-libpango-1.0-0_1.46.2-3_amd64.deb ... Unpacking libpango-1.0-0:amd64 (1.46.2-3) ... Selecting previously unselected package libpangoft2-1.0-0:amd64. Preparing to unpack .../098-libpangoft2-1.0-0_1.46.2-3_amd64.deb ... Unpacking libpangoft2-1.0-0:amd64 (1.46.2-3) ... Selecting previously unselected package libpangocairo-1.0-0:amd64. Preparing to unpack .../099-libpangocairo-1.0-0_1.46.2-3_amd64.deb ... Unpacking libpangocairo-1.0-0:amd64 (1.46.2-3) ... Selecting previously unselected package libtcl8.6:amd64. Preparing to unpack .../100-libtcl8.6_8.6.11+dfsg-1_amd64.deb ... Unpacking libtcl8.6:amd64 (8.6.11+dfsg-1) ... Selecting previously unselected package libxft2:amd64. Preparing to unpack .../101-libxft2_2.3.2-2_amd64.deb ... Unpacking libxft2:amd64 (2.3.2-2) ... Selecting previously unselected package x11-common. Preparing to unpack .../102-x11-common_1%3a7.7+22_all.deb ... Unpacking x11-common (1:7.7+22) ... Selecting previously unselected package libxss1:amd64. Preparing to unpack .../103-libxss1_1%3a1.2.3-1_amd64.deb ... Unpacking libxss1:amd64 (1:1.2.3-1) ... Selecting previously unselected package libtk8.6:amd64. Preparing to unpack .../104-libtk8.6_8.6.11-2_amd64.deb ... Unpacking libtk8.6:amd64 (8.6.11-2) ... Selecting previously unselected package libice6:amd64. Preparing to unpack .../105-libice6_2%3a1.0.10-1_amd64.deb ... Unpacking libice6:amd64 (2:1.0.10-1) ... Selecting previously unselected package libsm6:amd64. Preparing to unpack .../106-libsm6_2%3a1.2.3-1_amd64.deb ... Unpacking libsm6:amd64 (2:1.2.3-1) ... Selecting previously unselected package libxt6:amd64. Preparing to unpack .../107-libxt6_1%3a1.2.0-1_amd64.deb ... Unpacking libxt6:amd64 (1:1.2.0-1) ... Selecting previously unselected package r-base-core. Preparing to unpack .../108-r-base-core_4.0.4-1_amd64.deb ... Unpacking r-base-core (4.0.4-1) ... Selecting previously unselected package r-bioc-biocgenerics. Preparing to unpack .../109-r-bioc-biocgenerics_0.36.0-1_all.deb ... Unpacking r-bioc-biocgenerics (0.36.0-1) ... Selecting previously unselected package r-bioc-dnacopy. Preparing to unpack .../110-r-bioc-dnacopy_1.64.0-1_amd64.deb ... Unpacking r-bioc-dnacopy (1.64.0-1) ... Selecting previously unselected package cnvkit. Preparing to unpack .../111-cnvkit_0.9.8-1_amd64.deb ... Unpacking cnvkit (0.9.8-1) ... Setting up media-types (4.0.0) ... Setting up libgraphite2-3:amd64 (1.3.14-1) ... Setting up liblcms2-2:amd64 (2.12~rc1-2) ... Setting up libpixman-1-0:amd64 (0.40.0-1.1~deb11u1) ... Setting up libxau6:amd64 (1:1.0.9-1) ... Setting up libpsl5:amd64 (0.21.0-1.2) ... Setting up ttf-bitstream-vera (1.10-8.1) ... Setting up libicu67:amd64 (67.1-7) ... Setting up libdatrie1:amd64 (0.2.13-1) ... Setting up libyaml-0-2:amd64 (0.2.2-1) ... Setting up libglib2.0-0:amd64 (2.66.8-1) ... No schema files found: doing nothing. Setting up fonts-lyx (2.3.6-1) ... Setting up unzip (6.0-26+deb11u1) ... Setting up perl-modules-5.32 (5.32.1-4+deb11u2) ... Setting up libbrotli1:amd64 (1.0.9-2+b2) ... Setting up libsqlite3-0:amd64 (3.34.1-3) ... Setting up x11-common (1:7.7+22) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up libnghttp2-14:amd64 (1.43.0-1) ... Setting up libdeflate0:amd64 (1.7-1) ... Setting up libgomp1:amd64 (10.2.1-6) ... Setting up libjbig0:amd64 (2.1-3.1+b2) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Setting up zip (3.0-12) ... Setting up libblas3:amd64 (3.9.0-3+deb11u1) ... 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 (1:2.0.6-4) ... Setting up libx11-data (2:1.7.2-1+deb11u1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libncurses6:amd64 (6.2+20201114-2+deb11u2) ... Setting up libfribidi0:amd64 (1.0.8-2+deb11u1) ... Setting up libquadmath0:amd64 (10.2.1-6) ... Setting up libimagequant0:amd64 (2.12.2-1.1) ... Setting up libpng16-16:amd64 (1.6.37-3) ... Setting up libtcl8.6:amd64 (8.6.11+dfsg-1) ... Setting up libwebp6:amd64 (0.6.1-2.1+deb11u2) ... Setting up libncursesw6:amd64 (6.2+20201114-2+deb11u2) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Setting up libgfortran5:amd64 (10.2.1-6) ... Setting up libmd0:amd64 (1.0.3-3) ... Setting up sensible-utils (0.0.14) ... Setting up libmpdec3:amd64 (2.5.1-1) ... Setting up libthai-data (0.1.28-3) ... Setting up libssh2-1:amd64 (1.9.0-2) ... Setting up libtiff5:amd64 (4.2.0-1+deb11u4) ... Setting up libjs-jquery (3.5.1+dfsg+~3.5.5-7) ... Setting up python-matplotlib-data (3.3.4-1) ... Setting up openssl (1.1.1w-0+deb11u1) ... Setting up libwebpmux3:amd64 (0.6.1-2.1+deb11u2) ... Setting up libbsd0:amd64 (0.11.3-1+deb11u1) ... Setting up readline-common (8.1-1) ... 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 libprocps8:amd64 (2:3.3.17-5) ... Setting up libgdbm6:amd64 (1.19-2) ... Setting up libice6:amd64 (2:1.0.10-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up liblapack3:amd64 (3.9.0-3+deb11u1) ... 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 (1.14-3) ... Setting up libxcb-render0:amd64 (1.14-3) ... Setting up libwebpdemux2:amd64 (0.6.1-2.1+deb11u2) ... Setting up libreadline8:amd64 (8.1-1) ... Setting up libldap-2.4-2:amd64 (2.4.57+dfsg-3+deb11u1) ... Setting up libcurl3-gnutls:amd64 (7.74.0-1.3+deb11u9) ... Setting up libxcb-shm0:amd64 (1.14-3) ... Setting up libthai0:amd64 (0.1.28-3) ... Setting up ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 129 added, 0 removed; done. Setting up libjs-jquery-ui (1.12.1+dfsg-8+deb11u1) ... Setting up libfreetype6:amd64 (2.10.4+dfsg-1+deb11u1) ... Setting up libgdbm-compat4:amd64 (1.19-2) ... Setting up ucf (3.0043) ... Setting up libperl5.32:amd64 (5.32.1-4+deb11u2) ... Setting up procps (2:3.3.17-5) ... Setting up libcurl4:amd64 (7.74.0-1.3+deb11u9) ... Setting up libx11-6:amd64 (2:1.7.2-1+deb11u1) ... Setting up libharfbuzz0b:amd64 (2.7.4-1) ... Setting up libsm6:amd64 (2:1.2.3-1) ... Setting up libpython3.9-stdlib:amd64 (3.9.2-1) ... Setting up libpython3-stdlib:amd64 (3.9.2-3) ... Setting up liblbfgsb0:amd64 (3.0+dfsg.3-9) ... Setting up libpaper1:amd64 (1.1.28+b1) ... Creating config file /etc/papersize with new version Setting up libhts3:amd64 (1.11-4) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up fontconfig-config (2.13.1-4.2) ... Setting up libxext6:amd64 (2:1.3.3-1.1) ... Setting up libpaper-utils (1.1.28+b1) ... Setting up perl (5.32.1-4+deb11u2) ... Setting up libxt6:amd64 (1:1.2.0-1) ... Setting up libxss1:amd64 (1:1.2.3-1) ... Setting up libfontconfig1:amd64 (2.13.1-4.2) ... Setting up mailcap (3.69) ... Setting up python3.9 (3.9.2-1) ... Setting up fontconfig (2.13.1-4.2) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.2-2) ... Setting up mime-support (3.66) ... Setting up libtk8.6:amd64 (8.6.11-2) ... Setting up libpango-1.0-0:amd64 (1.46.2-3) ... Setting up python3 (3.9.2-3) ... Setting up libcairo2:amd64 (1.16.0-5) ... Setting up python3-tz (2021.1-1) ... Setting up python3-six (1.16.0-2) ... Setting up python3-pil:amd64 (8.1.2+dfsg-0.3+deb11u1) ... Setting up python3-decorator (4.4.2-2) ... Setting up python3-pyparsing (2.4.7-1) ... Setting up python3-cycler (0.10.0-3) ... Setting up python3-reportlab-accel:amd64 (3.5.59-2) ... Setting up python3-kiwisolver (1.3.1-1+b1) ... Setting up python3-reportlab (3.5.59-2) ... Setting up python3-dateutil (2.8.1-6) ... Setting up libpangoft2-1.0-0:amd64 (1.46.2-3) ... Setting up libpangocairo-1.0-0:amd64 (1.46.2-3) ... Setting up python3-pkg-resources (52.0.0-4) ... Setting up python3-pyfaidx (0.5.9.2-1) ... Setting up python3-pysam (0.15.4+ds-3+b2) ... Setting up python3-joblib (0.17.0-4+deb11u1) ... Setting up python3-threadpoolctl (2.1.0-1) ... Setting up python3-yaml (5.3.1-5) ... Setting up python3-networkx (2.5+ds-2) ... Setting up r-base-core (4.0.4-1) ... Creating config file /etc/R/Renviron with new version Setting up python3-numpy (1:1.19.5-1) ... Setting up python3-biopython (1.78+dfsg-4) ... Setting up python3-matplotlib (3.3.4-1) ... Setting up r-bioc-biocgenerics (0.36.0-1) ... Setting up python3-scipy (1.6.0-2) ... Setting up python3-pomegranate (0.13.5-1) ... Setting up python3-pandas-lib:amd64 (1.1.5+dfsg-2) ... Setting up python3-sklearn-lib:amd64 (0.23.2-5) ... Setting up python3-pandas (1.1.5+dfsg-2) ... Setting up python3-sklearn (0.23.2-5) ... Setting up r-bioc-dnacopy (1.64.0-1) ... Setting up cnvkit (0.9.8-1) ... Processing triggers for libc-bin (2.31-13+deb11u6) ... Processing triggers for ca-certificates (20210119) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 0m39.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'apt-get', '-y', 'install', 'cnvkit=0.9.8-1'] 0m39.1s INFO: Running scripts post_install 0m39.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/post_install_exceptions'] 0m39.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/post_install_exceptions'] 0m39.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/post_install_log_alternatives'] 0m39.1s DUMP: Removing 'local diversion of /usr/bin/update-alternatives to /usr/bin/update-alternatives.orig' LOG-ALTERNATIVES: dpkg=python3: piuparts=cnvkit=0.9.8-1: /usr/bin/update-alternatives --auto /usr/bin/python3 LOG-ALTERNATIVES: dpkg=libblas3: piuparts=cnvkit=0.9.8-1: /usr/bin/update-alternatives --install /usr/lib/x86_64-linux-gnu/libblas.so.3 libblas.so.3-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 10 LOG-ALTERNATIVES: dpkg=xdg-utils: piuparts=cnvkit=0.9.8-1: /usr/bin/update-alternatives --install /usr/bin/open open /usr/bin/xdg-open 50 --slave /usr/share/man/man1/open.1.gz open.1.gz /usr/share/man/man1/xdg-open.1.gz LOG-ALTERNATIVES: dpkg=liblapack3: piuparts=cnvkit=0.9.8-1: /usr/bin/update-alternatives --install /usr/lib/x86_64-linux-gnu/liblapack.so.3 liblapack.so.3-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 10 LOG-ALTERNATIVES: dpkg=procps: piuparts=cnvkit=0.9.8-1: /usr/bin/update-alternatives --remove w /usr/bin/w.procps LOG-ALTERNATIVES: dpkg=perl: piuparts=cnvkit=0.9.8-1: /usr/bin/update-alternatives --remove rename /usr/bin/prename LOG-ALTERNATIVES: dpkg=mailcap: piuparts=cnvkit=0.9.8-1: /usr/bin/update-alternatives --quiet --install /usr/bin/open open /usr/bin/run-mailcap 30 --slave /usr/share/man/man1/open.1.gz open.1.gz /usr/share/man/man1/run-mailcap.1.gz 0m39.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/post_install_log_alternatives'] 0m39.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpd2v957bx'] 0m40.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpd2v957bx'] 0m42.1s ERROR: WARN: Broken symlinks: /usr/lib/python3/dist-packages/Bio/Entrez/DTDs/mathml2.dtd -> ../../../../../../share/xml/schema/w3c/mathml/dtd/mathml2.dtd (python3-biopython) 0m42.1s INFO: /bin converted to /usr/bin by /usr merge 0m42.1s INFO: /lib converted to /usr/lib by /usr merge 0m42.1s INFO: /lib/init converted to /usr/lib/init by /usr merge 0m42.1s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 0m42.1s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 0m42.1s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 0m42.1s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 0m42.1s INFO: /lib/terminfo converted to /usr/lib/terminfo by /usr merge 0m42.1s INFO: /lib/terminfo/E converted to /usr/lib/terminfo/E by /usr merge 0m42.1s INFO: /lib/terminfo/a converted to /usr/lib/terminfo/a by /usr merge 0m42.1s INFO: /lib/terminfo/c converted to /usr/lib/terminfo/c by /usr merge 0m42.1s INFO: /lib/terminfo/d converted to /usr/lib/terminfo/d by /usr merge 0m42.1s INFO: /lib/terminfo/h converted to /usr/lib/terminfo/h by /usr merge 0m42.1s INFO: /lib/terminfo/l converted to /usr/lib/terminfo/l by /usr merge 0m42.1s INFO: /lib/terminfo/m converted to /usr/lib/terminfo/m by /usr merge 0m42.1s INFO: /lib/terminfo/p converted to /usr/lib/terminfo/p by /usr merge 0m42.1s INFO: /lib/terminfo/r converted to /usr/lib/terminfo/r by /usr merge 0m42.1s INFO: /lib/terminfo/s converted to /usr/lib/terminfo/s by /usr merge 0m42.1s INFO: /lib/terminfo/t converted to /usr/lib/terminfo/t by /usr merge 0m42.1s INFO: /lib/terminfo/v converted to /usr/lib/terminfo/v by /usr merge 0m42.1s INFO: /lib/terminfo/w converted to /usr/lib/terminfo/w by /usr merge 0m42.1s INFO: /lib/terminfo/x converted to /usr/lib/terminfo/x by /usr merge 0m42.1s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 0m42.1s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 0m42.1s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 0m42.1s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 0m42.1s INFO: /lib64 converted to /usr/lib64 by /usr merge 0m42.1s INFO: /sbin converted to /usr/sbin by /usr merge 0m43.2s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', '-ac', '--ignore-obsolete'] 0m45.3s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', '-ac', '--ignore-obsolete'] 0m45.3s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m45.3s DUMP: 0.15.6 0m45.3s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m45.3s INFO: Running adequate version 0.15.6 now. 0m45.3s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'cnvkit'] 0m45.4s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'cnvkit'] 0m45.4s INFO: Running scripts pre_remove 0m45.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m45.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m45.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m45.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m45.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m49.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m49.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m49.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m49.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m49.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m49.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/pre_remove_exceptions'] 0m49.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/pre_remove_exceptions'] 0m49.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m49.3s DUMP: install ok installed adduser adduser 3.118+deb11u1 install ok installed apt apt 2.2.4 install ok installed base-files base-files 11.1+deb11u8 install ok installed base-passwd base-passwd 3.5.51 install ok installed bash bash 5.1-2+deb11u1 install ok installed bsdutils bsdutils 1:2.36.1-8+deb11u1 install ok installed ca-certificates ca-certificates 20210119 install ok installed cnvkit cnvkit 0.9.8-1 install ok installed coreutils coreutils 8.32-4+b1 install ok installed dash dash 0.5.11+git20200708+dd9ef66-5 install ok installed debconf debconf 1.5.77 install ok installed debian-archive-keyring debian-archive-keyring 2021.1.1+deb11u1 install ok installed debianutils debianutils 4.11.2 install ok installed diffutils diffutils 1:3.7-5 install ok installed dpkg dpkg 1.20.13 install ok installed e2fsprogs e2fsprogs 1.46.2-2 install ok installed findutils findutils 4.8.0-1 install ok installed fontconfig fontconfig 2.13.1-4.2 install ok installed fontconfig-config fontconfig-config 2.13.1-4.2 install ok installed fonts-lyx fonts-lyx 2.3.6-1 install ok installed gcc-10-base:amd64 gcc-10-base 10.2.1-6 install ok installed gcc-9-base:amd64 gcc-9-base 9.3.0-22 install ok installed gpgv gpgv 2.2.27-2+deb11u2 install ok installed grep grep 3.6-1+deb11u1 install ok installed gzip gzip 1.10-4+deb11u1 install ok installed hostname hostname 3.23 install ok installed init-system-helpers init-system-helpers 1.60 install ok installed libacl1:amd64 libacl1 2.2.53-10 install ok installed libapt-pkg6.0:amd64 libapt-pkg6.0 2.2.4 install ok installed libattr1:amd64 libattr1 1:2.4.48-6 install ok installed libaudit-common libaudit-common 1:3.0-2 install ok installed libaudit1:amd64 libaudit1 1:3.0-2 install ok installed libblas3:amd64 libblas3 3.9.0-3+deb11u1 install ok installed libblkid1:amd64 libblkid1 2.36.1-8+deb11u1 install ok installed libbrotli1:amd64 libbrotli1 1.0.9-2+b2 install ok installed libbsd0:amd64 libbsd0 0.11.3-1+deb11u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.8-4 install ok installed libc-bin libc-bin 2.31-13+deb11u6 install ok installed libc6:amd64 libc6 2.31-13+deb11u6 install ok installed libcairo2:amd64 libcairo2 1.16.0-5 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2.2+b1 install ok installed libcom-err2:amd64 libcom-err2 1.46.2-2 install ok installed libcrypt1:amd64 libcrypt1 1:4.4.18-4 install ok installed libcurl3-gnutls:amd64 libcurl3-gnutls 7.74.0-1.3+deb11u9 install ok installed libcurl4:amd64 libcurl4 7.74.0-1.3+deb11u9 install ok installed libdatrie1:amd64 libdatrie1 0.2.13-1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.8 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.260 install ok installed libdeflate0:amd64 libdeflate0 1.7-1 install ok installed libexpat1:amd64 libexpat1 2.2.10-2+deb11u5 install ok installed libext2fs2:amd64 libext2fs2 1.46.2-2 install ok installed libffi7:amd64 libffi7 3.3-6 install ok installed libfontconfig1:amd64 libfontconfig1 2.13.1-4.2 install ok installed libfreetype6:amd64 libfreetype6 2.10.4+dfsg-1+deb11u1 install ok installed libfribidi0:amd64 libfribidi0 1.0.8-2+deb11u1 install ok installed libgcc-s1:amd64 libgcc-s1 10.2.1-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.7-6 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.19-2 install ok installed libgdbm6:amd64 libgdbm6 1.19-2 install ok installed libgfortran5:amd64 libgfortran5 10.2.1-6 install ok installed libglib2.0-0:amd64 libglib2.0-0 2.66.8-1 install ok installed libgmp10:amd64 libgmp10 2:6.2.1+dfsg-1+deb11u1 install ok installed libgnutls30:amd64 libgnutls30 3.7.1-5+deb11u3 install ok installed libgomp1:amd64 libgomp1 10.2.1-6 install ok installed libgpg-error0:amd64 libgpg-error0 1.38-2 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.14-1 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.18.3-6+deb11u4 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 2.7.4-1 install ok installed libhogweed6:amd64 libhogweed6 3.7.3-1 install ok installed libhts3:amd64 libhts3 1.11-4 install ok installed libice6:amd64 libice6 2:1.0.10-1 install ok installed libicu67:amd64 libicu67 67.1-7 install ok installed libidn2-0:amd64 libidn2-0 2.3.0-5 install ok installed libimagequant0:amd64 libimagequant0 2.12.2-1.1 install ok installed libjbig0:amd64 libjbig0 2.1-3.1+b2 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:2.0.6-4 install ok installed libjs-jquery libjs-jquery 3.5.1+dfsg+~3.5.5-7 install ok installed libjs-jquery-ui libjs-jquery-ui 1.12.1+dfsg-8+deb11u1 install ok installed libk5crypto3:amd64 libk5crypto3 1.18.3-6+deb11u4 install ok installed libkeyutils1:amd64 libkeyutils1 1.6.1-2 install ok installed libkrb5-3:amd64 libkrb5-3 1.18.3-6+deb11u4 install ok installed libkrb5support0:amd64 libkrb5support0 1.18.3-6+deb11u4 install ok installed liblapack3:amd64 liblapack3 3.9.0-3+deb11u1 install ok installed liblbfgsb0:amd64 liblbfgsb0 3.0+dfsg.3-9 install ok installed liblcms2-2:amd64 liblcms2-2 2.12~rc1-2 install ok installed libldap-2.4-2:amd64 libldap-2.4-2 2.4.57+dfsg-3+deb11u1 install ok installed liblz4-1:amd64 liblz4-1 1.9.3-2 install ok installed liblzma5:amd64 liblzma5 5.2.5-2.1~deb11u1 install ok installed libmd0:amd64 libmd0 1.0.3-3 install ok installed libmount1:amd64 libmount1 2.36.1-8+deb11u1 install ok installed libmpdec3:amd64 libmpdec3 2.5.1-1 install ok installed libncurses6:amd64 libncurses6 6.2+20201114-2+deb11u2 install ok installed libncursesw6:amd64 libncursesw6 6.2+20201114-2+deb11u2 install ok installed libnettle8:amd64 libnettle8 3.7.3-1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.43.0-1 install ok installed libnsl2:amd64 libnsl2 1.3.0-2 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.22-1 install ok installed libpam-modules:amd64 libpam-modules 1.4.0-9+deb11u1 install ok installed libpam-modules-bin libpam-modules-bin 1.4.0-9+deb11u1 install ok installed libpam-runtime libpam-runtime 1.4.0-9+deb11u1 install ok installed libpam0g:amd64 libpam0g 1.4.0-9+deb11u1 install ok installed libpango-1.0-0:amd64 libpango-1.0-0 1.46.2-3 install ok installed libpangocairo-1.0-0:amd64 libpangocairo-1.0-0 1.46.2-3 install ok installed libpangoft2-1.0-0:amd64 libpangoft2-1.0-0 1.46.2-3 install ok installed libpaper-utils libpaper-utils 1.1.28+b1 install ok installed libpaper1:amd64 libpaper1 1.1.28+b1 install ok installed libpcre2-8-0:amd64 libpcre2-8-0 10.36-2+deb11u1 install ok installed libpcre3:amd64 libpcre3 2:8.39-13 install ok installed libperl5.32:amd64 libperl5.32 5.32.1-4+deb11u2 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.40.0-1.1~deb11u1 install ok installed libpng16-16:amd64 libpng16-16 1.6.37-3 install ok installed libprocps8:amd64 libprocps8 2:3.3.17-5 install ok installed libpsl5:amd64 libpsl5 0.21.0-1.2 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.9.2-3 install ok installed libpython3.9-minimal:amd64 libpython3.9-minimal 3.9.2-1 install ok installed libpython3.9-stdlib:amd64 libpython3.9-stdlib 3.9.2-1 install ok installed libquadmath0:amd64 libquadmath0 10.2.1-6 install ok installed libreadline8:amd64 libreadline8 8.1-1 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2+b2 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.27+dfsg-2.1+deb11u1 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.27+dfsg-2.1+deb11u1 install ok installed libseccomp2:amd64 libseccomp2 2.5.1-1+deb11u1 install ok installed libselinux1:amd64 libselinux1 3.1-3 install ok installed libsemanage-common libsemanage-common 3.1-1 install ok installed libsemanage1:amd64 libsemanage1 3.1-1+b2 install ok installed libsepol1:amd64 libsepol1 3.1-1 install ok installed libsm6:amd64 libsm6 2:1.2.3-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.36.1-8+deb11u1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.34.1-3 install ok installed libss2:amd64 libss2 1.46.2-2 install ok installed libssh2-1:amd64 libssh2-1 1.9.0-2 install ok installed libssl1.1:amd64 libssl1.1 1.1.1w-0+deb11u1 install ok installed libstdc++6:amd64 libstdc++6 10.2.1-6 install ok installed libsystemd0:amd64 libsystemd0 247.3-7+deb11u4 install ok installed libtasn1-6:amd64 libtasn1-6 4.16.0-2+deb11u1 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.11+dfsg-1 install ok installed libthai-data libthai-data 0.1.28-3 install ok installed libthai0:amd64 libthai0 0.1.28-3 install ok installed libtiff5:amd64 libtiff5 4.2.0-1+deb11u4 install ok installed libtinfo6:amd64 libtinfo6 6.2+20201114-2+deb11u2 install ok installed libtirpc-common libtirpc-common 1.3.1-1+deb11u1 install ok installed libtirpc3:amd64 libtirpc3 1.3.1-1+deb11u1 install ok installed libtk8.6:amd64 libtk8.6 8.6.11-2 install ok installed libudev1:amd64 libudev1 247.3-7+deb11u4 install ok installed libunistring2:amd64 libunistring2 0.9.10-4 install ok installed libuuid1:amd64 libuuid1 2.36.1-8+deb11u1 install ok installed libwebp6:amd64 libwebp6 0.6.1-2.1+deb11u2 install ok installed libwebpdemux2:amd64 libwebpdemux2 0.6.1-2.1+deb11u2 install ok installed libwebpmux3:amd64 libwebpmux3 0.6.1-2.1+deb11u2 install ok installed libx11-6:amd64 libx11-6 2:1.7.2-1+deb11u1 install ok installed libx11-data libx11-data 2:1.7.2-1+deb11u1 install ok installed libxau6:amd64 libxau6 1:1.0.9-1 install ok installed libxcb-render0:amd64 libxcb-render0 1.14-3 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.14-3 install ok installed libxcb1:amd64 libxcb1 1.14-3 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3 install ok installed libxext6:amd64 libxext6 2:1.3.3-1.1 install ok installed libxft2:amd64 libxft2 2.3.2-2 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1 install ok installed libxss1:amd64 libxss1 1:1.2.3-1 install ok installed libxt6:amd64 libxt6 1:1.2.0-1 install ok installed libxxhash0:amd64 libxxhash0 0.8.0-2 install ok installed libyaml-0-2:amd64 libyaml-0-2 0.2.2-1 install ok installed libzstd1:amd64 libzstd1 1.4.8+dfsg-2.1 install ok installed login login 1:4.8.1-1 install ok installed logsave logsave 1.46.2-2 install ok installed lsb-base lsb-base 11.1.0 install ok installed mailcap mailcap 3.69 install ok installed mawk mawk 1.3.4.20200120-2 install ok installed media-types media-types 4.0.0 install ok installed mime-support mime-support 3.66 install ok installed mount mount 2.36.1-8+deb11u1 install ok installed ncurses-base ncurses-base 6.2+20201114-2+deb11u2 install ok installed ncurses-bin ncurses-bin 6.2+20201114-2+deb11u2 install ok installed openssl openssl 1.1.1w-0+deb11u1 install ok installed passwd passwd 1:4.8.1-1 install ok installed perl perl 5.32.1-4+deb11u2 install ok installed perl-base perl-base 5.32.1-4+deb11u2 install ok installed perl-modules-5.32 perl-modules-5.32 5.32.1-4+deb11u2 install ok installed procps procps 2:3.3.17-5 install ok installed python-matplotlib-data python-matplotlib-data 3.3.4-1 install ok installed python3 python3 3.9.2-3 install ok installed python3-biopython python3-biopython 1.78+dfsg-4 install ok installed python3-cycler python3-cycler 0.10.0-3 install ok installed python3-dateutil python3-dateutil 2.8.1-6 install ok installed python3-decorator python3-decorator 4.4.2-2 install ok installed python3-joblib python3-joblib 0.17.0-4+deb11u1 install ok installed python3-kiwisolver python3-kiwisolver 1.3.1-1+b1 install ok installed python3-matplotlib python3-matplotlib 3.3.4-1 install ok installed python3-minimal python3-minimal 3.9.2-3 install ok installed python3-networkx python3-networkx 2.5+ds-2 install ok installed python3-numpy python3-numpy 1:1.19.5-1 install ok installed python3-pandas python3-pandas 1.1.5+dfsg-2 install ok installed python3-pandas-lib:amd64 python3-pandas-lib 1.1.5+dfsg-2 install ok installed python3-pil:amd64 python3-pil 8.1.2+dfsg-0.3+deb11u1 install ok installed python3-pkg-resources python3-pkg-resources 52.0.0-4 install ok installed python3-pomegranate python3-pomegranate 0.13.5-1 install ok installed python3-pyfaidx python3-pyfaidx 0.5.9.2-1 install ok installed python3-pyparsing python3-pyparsing 2.4.7-1 install ok installed python3-pysam python3-pysam 0.15.4+ds-3+b2 install ok installed python3-reportlab python3-reportlab 3.5.59-2 install ok installed python3-reportlab-accel:amd64 python3-reportlab-accel 3.5.59-2 install ok installed python3-scipy python3-scipy 1.6.0-2 install ok installed python3-six python3-six 1.16.0-2 install ok installed python3-sklearn python3-sklearn 0.23.2-5 install ok installed python3-sklearn-lib:amd64 python3-sklearn-lib 0.23.2-5 install ok installed python3-threadpoolctl python3-threadpoolctl 2.1.0-1 install ok installed python3-tz python3-tz 2021.1-1 install ok installed python3-yaml python3-yaml 5.3.1-5 install ok installed python3.9 python3.9 3.9.2-1 install ok installed python3.9-minimal python3.9-minimal 3.9.2-1 install ok installed r-base-core r-base-core 4.0.4-1 install ok installed r-bioc-biocgenerics r-bioc-biocgenerics 0.36.0-1 install ok installed r-bioc-dnacopy r-bioc-dnacopy 1.64.0-1 install ok installed readline-common readline-common 8.1-1 install ok installed sed sed 4.7-1 install ok installed sensible-utils sensible-utils 0.0.14 install ok installed sysvinit-utils sysvinit-utils 2.96-7+deb11u1 install ok installed tar tar 1.34+dfsg-1 install ok installed ttf-bitstream-vera ttf-bitstream-vera 1.10-8.1 install ok installed tzdata tzdata 2021a-1+deb11u10 install ok installed ucf ucf 3.0043 install ok installed unzip unzip 6.0-26+deb11u1 install ok installed util-linux util-linux 2.36.1-8+deb11u1 install ok installed x11-common x11-common 1:7.7+22 install ok installed xdg-utils xdg-utils 1.1.3-4.1 install ok installed zip zip 3.0-12 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-2+deb11u2 0m49.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m49.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'apt-get', 'remove', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-lyx', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libice6:amd64', 'libicu67:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libmd0:amd64', 'libmpdec3:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libperl5.32:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libprocps8:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsm6:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtk8.6:amd64', 'libwebp6:amd64', 'libwebpdemux2:amd64', 'libwebpmux3: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', 'libyaml-0-2:amd64', 'mailcap', 'media-types', 'mime-support', 'openssl', 'perl', 'perl-modules-5.32', 'procps', 'python-matplotlib-data', 'python3', 'python3-biopython', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-joblib', 'python3-kiwisolver', 'python3-matplotlib', 'python3-minimal', 'python3-networkx', 'python3-numpy', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-pomegranate', 'python3-pyfaidx', 'python3-pyparsing', 'python3-pysam', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3-scipy', 'python3-six', 'python3-sklearn', 'python3-sklearn-lib:amd64', 'python3-threadpoolctl', 'python3-tz', 'python3-yaml', 'python3.9', 'python3.9-minimal', 'r-base-core', 'r-bioc-biocgenerics', 'r-bioc-dnacopy', 'readline-common', 'sensible-utils', 'ttf-bitstream-vera', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'cnvkit'] 0m53.2s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: ca-certificates cnvkit fontconfig fontconfig-config fonts-lyx libblas3 libbrotli1 libbsd0 libcairo2 libcurl3-gnutls libcurl4 libdatrie1 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgdbm-compat4 libgdbm6 libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libharfbuzz0b libhts3 libice6 libicu67 libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui liblapack3 liblbfgsb0 liblcms2-2 libldap-2.4-2 libmd0 libmpdec3 libncurses6 libncursesw6 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libperl5.32 libpixman-1-0 libpng16-16 libprocps8 libpsl5 libpython3-stdlib libpython3.9-minimal libpython3.9-stdlib libquadmath0 libreadline8 librtmp1 libsasl2-2 libsasl2-modules-db libsm6 libsqlite3-0 libssh2-1 libtcl8.6 libthai-data libthai0 libtiff5 libtk8.6 libwebp6 libwebpdemux2 libwebpmux3 libx11-6 libx11-data libxau6 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxext6 libxft2 libxrender1 libxss1 libxt6 libyaml-0-2 mailcap media-types mime-support openssl perl perl-modules-5.32 procps python-matplotlib-data python3 python3-biopython python3-cycler python3-dateutil python3-decorator python3-joblib python3-kiwisolver python3-matplotlib python3-minimal python3-networkx python3-numpy python3-pandas python3-pandas-lib python3-pil python3-pkg-resources python3-pomegranate python3-pyfaidx python3-pyparsing python3-pysam python3-reportlab python3-reportlab-accel python3-scipy python3-six python3-sklearn python3-sklearn-lib python3-threadpoolctl python3-tz python3-yaml python3.9 python3.9-minimal r-base-core r-bioc-biocgenerics r-bioc-dnacopy readline-common sensible-utils ttf-bitstream-vera ucf unzip x11-common xdg-utils zip 0 upgraded, 0 newly installed, 132 to remove and 0 not upgraded. After this operation, 481 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 ... 19457 files and directories currently installed.) Removing cnvkit (0.9.8-1) ... Removing r-bioc-dnacopy (1.64.0-1) ... Removing r-bioc-biocgenerics (0.36.0-1) ... Removing r-base-core (4.0.4-1) ... Removing ca-certificates (20210119) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing libpangocairo-1.0-0:amd64 (1.46.2-3) ... Removing libpangoft2-1.0-0:amd64 (1.46.2-3) ... Removing libpango-1.0-0:amd64 (1.46.2-3) ... Removing fontconfig (2.13.1-4.2) ... Removing libtk8.6:amd64 (8.6.11-2) ... Removing libxft2:amd64 (2.3.2-2) ... Removing libcairo2:amd64 (1.16.0-5) ... Removing libfontconfig1:amd64 (2.13.1-4.2) ... Removing fontconfig-config (2.13.1-4.2) ... Removing python3-matplotlib (3.3.4-1) ... Removing python-matplotlib-data (3.3.4-1) ... Removing fonts-lyx (2.3.6-1) ... dpkg: warning: while removing fonts-lyx, directory '/usr/share/fonts/truetype/lyx' not empty so not removed Removing python3-sklearn (0.23.2-5) ... Removing python3-pomegranate (0.13.5-1) ... Removing python3-scipy (1.6.0-2) ... Removing python3-sklearn-lib:amd64 (0.23.2-5) ... Removing python3-biopython (1.78+dfsg-4) ... Removing python3-pandas (1.1.5+dfsg-2) ... Removing python3-pandas-lib:amd64 (1.1.5+dfsg-2) ... Removing python3-numpy (1:1.19.5-1) ... Removing liblbfgsb0:amd64 (3.0+dfsg.3-9) ... Removing liblapack3:amd64 (3.9.0-3+deb11u1) ... Removing libblas3:amd64 (3.9.0-3+deb11u1) ... Removing python3-reportlab (3.5.59-2) ... Removing python3-pil:amd64 (8.1.2+dfsg-0.3+deb11u1) ... Removing libharfbuzz0b:amd64 (2.7.4-1) ... Removing libfreetype6:amd64 (2.10.4+dfsg-1+deb11u1) ... Removing libcurl4:amd64 (7.74.0-1.3+deb11u9) ... Removing libxt6:amd64 (1:1.2.0-1) ... Removing libxss1:amd64 (1:1.2.3-1) ... Removing libxcb-shm0:amd64 (1.14-3) ... Removing libsm6:amd64 (2:1.2.3-1) ... Removing libice6:amd64 (2:1.0.10-1) ... Removing python3-pysam (0.15.4+ds-3+b2) ... Removing libhts3:amd64 (1.11-4) ... Removing libcurl3-gnutls:amd64 (7.74.0-1.3+deb11u9) ... Removing libthai0:amd64 (0.1.28-3) ... Removing libdatrie1:amd64 (0.2.13-1) ... Removing libtiff5:amd64 (4.2.0-1+deb11u4) ... Removing libdeflate0:amd64 (1.7-1) ... Removing python3-yaml (5.3.1-5) ... Removing python3-pyfaidx (0.5.9.2-1) ... Removing python3-dateutil (2.8.1-6) ... Removing python3-reportlab-accel:amd64 (3.5.59-2) ... Removing python3-networkx (2.5+ds-2) ... Removing libfribidi0:amd64 (1.0.8-2+deb11u1) ... Removing mime-support (3.66) ... Removing mailcap (3.69) ... Removing perl (5.32.1-4+deb11u2) ... Removing libperl5.32:amd64 (5.32.1-4+deb11u2) ... Removing libgdbm-compat4:amd64 (1.19-2) ... Removing libgdbm6:amd64 (1.19-2) ... Removing libgfortran5:amd64 (10.2.1-6) ... Removing libglib2.0-0:amd64 (2.66.8-1) ... Removing libgomp1:amd64 (10.2.1-6) ... Removing libgraphite2-3:amd64 (1.3.14-1) ... Removing libicu67:amd64 (67.1-7) ... Removing libimagequant0:amd64 (2.12.2-1.1) ... Removing libjbig0:amd64 (2.1-3.1+b2) ... Removing libjpeg62-turbo:amd64 (1:2.0.6-4) ... Removing libjs-jquery-ui (1.12.1+dfsg-8+deb11u1) ... Removing libjs-jquery (3.5.1+dfsg+~3.5.5-7) ... Removing liblcms2-2:amd64 (2.12~rc1-2) ... Removing libldap-2.4-2:amd64 (2.4.57+dfsg-3+deb11u1) ... Removing python3-joblib (0.17.0-4+deb11u1) ... Removing procps (2:3.3.17-5) ... Removing libncurses6:amd64 (6.2+20201114-2+deb11u2) ... Removing libnghttp2-14:amd64 (1.43.0-1) ... Removing libpaper-utils (1.1.28+b1) ... Removing libpaper1:amd64 (1.1.28+b1) ... Removing libpixman-1-0:amd64 (0.40.0-1.1~deb11u1) ... Removing libpng16-16:amd64 (1.6.37-3) ... Removing libprocps8:amd64 (2:3.3.17-5) ... Removing libpsl5:amd64 (0.21.0-1.2) ... Removing libquadmath0:amd64 (10.2.1-6) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2+b2) ... Removing libsasl2-2:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Removing libsasl2-modules-db:amd64 (2.1.27+dfsg-2.1+deb11u1) ... Removing libssh2-1:amd64 (1.9.0-2) ... Removing libtcl8.6:amd64 (8.6.11+dfsg-1) ... Removing libthai-data (0.1.28-3) ... Removing libwebpmux3:amd64 (0.6.1-2.1+deb11u2) ... Removing libwebpdemux2:amd64 (0.6.1-2.1+deb11u2) ... Removing libwebp6:amd64 (0.6.1-2.1+deb11u2) ... Removing libxcb-render0:amd64 (1.14-3) ... Removing libxext6:amd64 (2:1.3.3-1.1) ... Removing libxrender1:amd64 (1:0.9.10-1) ... Removing libyaml-0-2:amd64 (0.2.2-1) ... Removing openssl (1.1.1w-0+deb11u1) ... Removing perl-modules-5.32 (5.32.1-4+deb11u2) ... Removing python3-cycler (0.10.0-3) ... Removing python3-decorator (4.4.2-2) ... Removing python3-kiwisolver (1.3.1-1+b1) ... Removing python3-pyparsing (2.4.7-1) ... Removing python3-threadpoolctl (2.1.0-1) ... Removing python3-tz (2021.1-1) ... Removing ucf (3.0043) ... Removing sensible-utils (0.0.14) ... Removing ttf-bitstream-vera (1.10-8.1) ... dpkg: warning: while removing ttf-bitstream-vera, directory '/usr/share/fonts/truetype/ttf-bitstream-vera' not empty so not removed Removing unzip (6.0-26+deb11u1) ... Removing x11-common (1:7.7+22) ... 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 (3.0-12) ... Removing libbrotli1:amd64 (1.0.9-2+b2) ... Removing libx11-6:amd64 (2:1.7.2-1+deb11u1) ... Removing libxcb1:amd64 (1.14-3) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libbsd0:amd64 (0.11.3-1+deb11u1) ... Removing python3-six (1.16.0-2) ... Removing python3-pkg-resources (52.0.0-4) ... Removing python3 (3.9.2-3) ... Removing python3-minimal (3.9.2-3) ... Removing python3.9 (3.9.2-1) ... Removing python3.9-minimal (3.9.2-1) ... Removing libexpat1:amd64 (2.2.10-2+deb11u5) ... Removing libpython3-stdlib:amd64 (3.9.2-3) ... Removing libpython3.9-stdlib:amd64 (3.9.2-1) ... find: '/usr/lib/python3': No such file or directory Removing libmd0:amd64 (1.0.3-3) ... Removing libmpdec3:amd64 (2.5.1-1) ... Removing libncursesw6:amd64 (6.2+20201114-2+deb11u2) ... Removing libpython3.9-minimal:amd64 (3.9.2-1) ... find: '/usr/lib/python3': No such file or directory Removing libreadline8:amd64 (8.1-1) ... Removing libsqlite3-0:amd64 (3.34.1-3) ... Removing libx11-data (2:1.7.2-1+deb11u1) ... Removing libxau6:amd64 (1:1.0.9-1) ... Removing media-types (4.0.0) ... Removing readline-common (8.1-1) ... Processing triggers for libc-bin (2.31-13+deb11u6) ... 0m53.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'apt-get', 'remove', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-lyx', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libice6:amd64', 'libicu67:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libmd0:amd64', 'libmpdec3:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libperl5.32:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libprocps8:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsm6:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtk8.6:amd64', 'libwebp6:amd64', 'libwebpdemux2:amd64', 'libwebpmux3: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', 'libyaml-0-2:amd64', 'mailcap', 'media-types', 'mime-support', 'openssl', 'perl', 'perl-modules-5.32', 'procps', 'python-matplotlib-data', 'python3', 'python3-biopython', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-joblib', 'python3-kiwisolver', 'python3-matplotlib', 'python3-minimal', 'python3-networkx', 'python3-numpy', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-pomegranate', 'python3-pyfaidx', 'python3-pyparsing', 'python3-pysam', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3-scipy', 'python3-six', 'python3-sklearn', 'python3-sklearn-lib:amd64', 'python3-threadpoolctl', 'python3-tz', 'python3-yaml', 'python3.9', 'python3.9-minimal', 'r-base-core', 'r-bioc-biocgenerics', 'r-bioc-dnacopy', 'readline-common', 'sensible-utils', 'ttf-bitstream-vera', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'cnvkit'] 0m53.2s INFO: Running scripts post_remove 0m53.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/post_remove_exceptions'] 0m53.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/post_remove_exceptions'] 0m53.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'dpkg', '--purge', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-lyx', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libice6:amd64', 'libicu67:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libmd0:amd64', 'libmpdec3:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libperl5.32:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libprocps8:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsm6:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtk8.6:amd64', 'libwebp6:amd64', 'libwebpdemux2:amd64', 'libwebpmux3: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', 'libyaml-0-2:amd64', 'mailcap', 'media-types', 'mime-support', 'openssl', 'perl', 'perl-modules-5.32', 'procps', 'python-matplotlib-data', 'python3', 'python3-biopython', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-joblib', 'python3-kiwisolver', 'python3-matplotlib', 'python3-minimal', 'python3-networkx', 'python3-numpy', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-pomegranate', 'python3-pyfaidx', 'python3-pyparsing', 'python3-pysam', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3-scipy', 'python3-six', 'python3-sklearn', 'python3-sklearn-lib:amd64', 'python3-threadpoolctl', 'python3-tz', 'python3-yaml', 'python3.9', 'python3.9-minimal', 'r-base-core', 'r-bioc-biocgenerics', 'r-bioc-dnacopy', 'readline-common', 'sensible-utils', 'ttf-bitstream-vera', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip'] 0m53.8s DUMP: (Reading database ... 6711 files and directories currently installed.) Purging configuration files for ca-certificates (20210119) ... Removing dangling symlinks from /etc/ssl/certs... done. Purging configuration files for fontconfig (2.13.1-4.2) ... Purging configuration files for fontconfig-config (2.13.1-4.2) ... dpkg: warning: ignoring request to remove fonts-lyx 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 libcurl3-gnutls which isn't installed dpkg: warning: ignoring request to remove libcurl4 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 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 (2.66.8-1) ... dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed 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 libice6 which isn't installed dpkg: warning: ignoring request to remove libicu67 which isn't installed dpkg: warning: ignoring request to remove libimagequant0 which isn't installed dpkg: warning: ignoring request to remove libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed Purging configuration files for libjs-jquery (3.5.1+dfsg+~3.5.5-7) ... Purging configuration files for libjs-jquery-ui (1.12.1+dfsg-8+deb11u1) ... dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove liblbfgsb0 which isn't installed dpkg: warning: ignoring request to remove liblcms2-2 which isn't installed dpkg: warning: ignoring request to remove libldap-2.4-2 which isn't installed dpkg: warning: ignoring request to remove libmd0 which isn't installed dpkg: warning: ignoring request to remove libmpdec3 which isn't installed dpkg: warning: ignoring request to remove libncurses6 which isn't installed dpkg: warning: ignoring request to remove libncursesw6 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 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 (1.1.28+b1) ... dpkg: warning: ignoring request to remove libperl5.32 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 libprocps8 which isn't installed dpkg: warning: ignoring request to remove libpsl5 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.9-minimal:amd64 (3.9.2-1) ... dpkg: warning: ignoring request to remove libpython3.9-stdlib which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed dpkg: warning: ignoring request to remove libreadline8 which isn't installed dpkg: warning: ignoring request to remove 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 libsm6 which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libssh2-1 which isn't installed dpkg: warning: ignoring request to remove libtcl8.6 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 libtiff5 which isn't installed dpkg: warning: ignoring request to remove libtk8.6 which isn't installed dpkg: warning: ignoring request to remove libwebp6 which isn't installed dpkg: warning: ignoring request to remove libwebpdemux2 which isn't installed dpkg: warning: ignoring request to remove libwebpmux3 which isn't installed dpkg: warning: ignoring request to remove 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 dpkg: warning: ignoring request to remove libyaml-0-2 which isn't installed Purging configuration files for mailcap (3.69) ... Purging configuration files for media-types (4.0.0) ... dpkg: warning: ignoring request to remove mime-support which isn't installed Purging configuration files for openssl (1.1.1w-0+deb11u1) ... Purging configuration files for perl (5.32.1-4+deb11u2) ... dpkg: warning: ignoring request to remove perl-modules-5.32 which isn't installed Purging configuration files for procps (2:3.3.17-5) ... Purging configuration files for python-matplotlib-data (3.3.4-1) ... Purging configuration files for python3 (3.9.2-3) ... dpkg: warning: ignoring request to remove python3-biopython which isn't installed dpkg: warning: ignoring request to remove python3-cycler which isn't installed dpkg: warning: ignoring request to remove python3-dateutil which isn't installed dpkg: warning: ignoring request to remove python3-decorator which isn't installed dpkg: warning: ignoring request to remove python3-joblib which isn't installed dpkg: warning: ignoring request to remove python3-kiwisolver which isn't installed dpkg: warning: ignoring request to remove python3-matplotlib which isn't installed dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-networkx which isn't installed dpkg: warning: ignoring request to remove python3-numpy which isn't installed dpkg: warning: ignoring request to remove python3-pandas which isn't installed dpkg: warning: ignoring request to remove python3-pandas-lib which isn't installed dpkg: warning: ignoring request to remove python3-pil which isn't installed dpkg: warning: ignoring request to remove python3-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python3-pomegranate which isn't installed dpkg: warning: ignoring request to remove python3-pyfaidx which isn't installed dpkg: warning: ignoring request to remove python3-pyparsing which isn't installed dpkg: warning: ignoring request to remove python3-pysam which isn't installed dpkg: warning: ignoring request to remove python3-reportlab which isn't installed dpkg: warning: ignoring request to remove python3-reportlab-accel which isn't installed dpkg: warning: ignoring request to remove python3-scipy which isn't installed dpkg: warning: ignoring request to remove python3-six which isn't installed dpkg: warning: ignoring request to remove python3-sklearn which isn't installed dpkg: warning: ignoring request to remove python3-sklearn-lib which isn't installed dpkg: warning: ignoring request to remove python3-threadpoolctl which isn't installed dpkg: warning: ignoring request to remove python3-tz which isn't installed dpkg: warning: ignoring request to remove python3-yaml which isn't installed dpkg: warning: ignoring request to remove python3.9 which isn't installed Purging configuration files for python3.9-minimal (3.9.2-1) ... Purging configuration files for r-base-core (4.0.4-1) ... dpkg: warning: ignoring request to remove r-bioc-biocgenerics which isn't installed dpkg: warning: ignoring request to remove r-bioc-dnacopy which isn't installed Purging configuration files for readline-common (8.1-1) ... dpkg: warning: ignoring request to remove sensible-utils which isn't installed dpkg: warning: ignoring request to remove ttf-bitstream-vera which isn't installed Purging configuration files for ucf (3.0043) ... Purging configuration files for unzip (6.0-26+deb11u1) ... Purging configuration files for x11-common (1:7.7+22) ... dpkg: warning: ignoring request to remove xdg-utils which isn't installed dpkg: warning: ignoring request to remove zip which isn't installed 0m53.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'dpkg', '--purge', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-lyx', 'libblas3:amd64', 'libbrotli1:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libharfbuzz0b:amd64', 'libhts3:amd64', 'libice6:amd64', 'libicu67:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'liblapack3:amd64', 'liblbfgsb0:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libmd0:amd64', 'libmpdec3:amd64', 'libncurses6:amd64', 'libncursesw6:amd64', 'libnghttp2-14:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libperl5.32:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libprocps8:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.9-minimal:amd64', 'libpython3.9-stdlib:amd64', 'libquadmath0:amd64', 'libreadline8:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsm6:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtk8.6:amd64', 'libwebp6:amd64', 'libwebpdemux2:amd64', 'libwebpmux3: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', 'libyaml-0-2:amd64', 'mailcap', 'media-types', 'mime-support', 'openssl', 'perl', 'perl-modules-5.32', 'procps', 'python-matplotlib-data', 'python3', 'python3-biopython', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-joblib', 'python3-kiwisolver', 'python3-matplotlib', 'python3-minimal', 'python3-networkx', 'python3-numpy', 'python3-pandas', 'python3-pandas-lib:amd64', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-pomegranate', 'python3-pyfaidx', 'python3-pyparsing', 'python3-pysam', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3-scipy', 'python3-six', 'python3-sklearn', 'python3-sklearn-lib:amd64', 'python3-threadpoolctl', 'python3-tz', 'python3-yaml', 'python3.9', 'python3.9-minimal', 'r-base-core', 'r-bioc-biocgenerics', 'r-bioc-dnacopy', 'readline-common', 'sensible-utils', 'ttf-bitstream-vera', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip'] 0m53.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'dpkg', '--purge', 'cnvkit'] 0m53.8s DUMP: dpkg: warning: ignoring request to remove cnvkit which isn't installed 0m53.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'dpkg', '--purge', 'cnvkit'] 0m53.8s INFO: Running scripts post_purge 0m53.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/post_purge_exceptions'] 0m53.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/post_purge_exceptions'] 0m53.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'dpkg', '--purge', '--pending'] 0m53.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'dpkg', '--purge', '--pending'] 0m53.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'dpkg', '--remove', '--pending'] 0m53.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'dpkg', '--remove', '--pending'] 0m53.8s INFO: Running scripts post_test 0m53.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/post_test_exceptions'] 0m53.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'tmp/scripts/post_test_exceptions'] 0m53.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpd2v957bx'] 0m54.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpd2v957bx'] 0m54.7s DEBUG: No broken symlinks as far as we can find. 0m54.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'dpkg-divert', '--list'] 0m54.7s DUMP: local diversion of /bin/sync to /bin/sync.distrib diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m54.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'dpkg-divert', '--list'] 0m54.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'apt-get', 'clean'] 0m54.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpd2v957bx', 'apt-get', 'clean'] 0m54.7s DEBUG: Recording chroot state 0m55.2s INFO: Warning: Package purging left files on system: /usr/local/share/fonts/ not owned /usr/local/share/fonts/.uuid not owned /usr/share/fonts/ owned by: ttf-bitstream-vera, fonts-lyx /usr/share/fonts/.uuid not owned /usr/share/fonts/truetype/ owned by: ttf-bitstream-vera, fonts-lyx /usr/share/fonts/truetype/.uuid not owned /usr/share/fonts/truetype/lyx/ owned by: fonts-lyx /usr/share/fonts/truetype/lyx/.uuid not owned /usr/share/fonts/truetype/ttf-bitstream-vera/ owned by: ttf-bitstream-vera /usr/share/fonts/truetype/ttf-bitstream-vera/.uuid not owned 0m55.2s INFO: PASS: Installation and purging test. 0m55.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpd2v957bx/dev/shm'] 0m55.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpd2v957bx/dev/shm'] 0m55.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpd2v957bx/dev/console'] 0m55.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpd2v957bx/dev/console'] 0m55.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpd2v957bx/dev/ptmx'] 0m55.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpd2v957bx/dev/ptmx'] 0m55.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpd2v957bx/dev/pts'] 0m55.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpd2v957bx/dev/pts'] 0m55.6s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpd2v957bx/proc'] 0m55.7s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpd2v957bx/proc'] 0m55.7s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpd2v957bx'] 0m55.8s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpd2v957bx'] 0m55.8s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpd2v957bx 0m55.8s INFO: PASS: All tests. 0m55.8s INFO: piuparts run ends. ret=0 End: 2023-12-28 16:21:21 GMT