Start: 2023-08-19 00:21:33 GMT [buster] Package: cnvkit Version: 0.9.5-3 Installed-Size: 22874 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3-biopython, python3-future, python3-matplotlib, python3-numpy, python3-pandas, python3-pyfaidx, python3-pysam, python3-reportlab, python3-scipy, 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_0.9.5-3_amd64.deb Size: 22915844 MD5sum: 055256eecf461400edfe333538a31804 SHA256: 6d650f92a13692e568317ce139e359e533d5ba8d14be84c62eddfcdddb4315a5 [buster-next] Package: cnvkit Version: 0.9.5-3 Installed-Size: 22874 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3-biopython, python3-future, python3-matplotlib, python3-numpy, python3-pandas, python3-pyfaidx, python3-pysam, python3-reportlab, python3-scipy, 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_0.9.5-3_amd64.deb Size: 22915844 MD5sum: 055256eecf461400edfe333538a31804 SHA256: 6d650f92a13692e568317ce139e359e533d5ba8d14be84c62eddfcdddb4315a5 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --warn-on-debsums-errors --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/buster_amd64.tar.gz -d buster -d buster-next -B /srv/piuparts.debian.org/slave/refchroot/buster2next/reference-chroot-metadata.dat --apt cnvkit=0.9.5-3 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.1.8~202306121314~1.1.7-9-g57dfbde6 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --warn-on-debsums-errors --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/buster_amd64.tar.gz -d buster -d buster-next -B /srv/piuparts.debian.org/slave/refchroot/buster2next/reference-chroot-metadata.dat --apt cnvkit=0.9.5-3 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-25-amd64 #1 SMP Debian 5.10.191-1 (2023-08-16) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmp5ngcd_5a 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/buster_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp5ngcd_5a 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/buster_amd64.tar.gz'] 0m2.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/buster_amd64.tar.gz'] 0m2.2s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a/proc'] 0m2.3s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a/proc'] 0m2.3s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a/dev/pts'] 0m2.3s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a/dev/pts'] 0m2.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a/dev/ptmx'] 0m2.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a/dev/ptmx'] 0m2.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a/dev/console'] 0m2.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a/dev/console'] 0m2.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a/dev/shm'] 0m2.3s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a/dev/shm'] 0m2.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ buster main 0m2.3s DEBUG: Created policy-rc.d and chmodded it. 0m2.3s DEBUG: Created resolv.conf. 0m2.3s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp5ngcd_5a/tmp/scripts/ 0m2.3s INFO: Running scripts post_chroot_unpack 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'apt-get', 'update'] 0m3.6s DUMP: Hit:1 http://deb.debian.org/debian buster InRelease Reading package lists... 0m3.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'apt-get', 'update'] 0m3.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'apt-get', '-yf', 'dist-upgrade'] 0m4.0s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'apt-get', '-yf', 'dist-upgrade'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.5s DUMP: f6fc0f2636004ef589309651dfd778f4 - 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.5s INFO: Running scripts post_setup 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/post_setup_dummy_users'] 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/post_setup_dummy_users'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/post_setup_forbid_home'] 0m5.8s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/post_setup_forbid_home'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.8s 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' 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/post_setup_minimize'] 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/post_setup_minimize'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/post_setup_zz_backports'] 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/post_setup_zz_backports'] 0m5.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.8s DUMP: install ok installed adduser adduser 3.118 install ok installed apt apt 1.8.2.3 install ok installed base-files base-files 10.3+deb10u13 install ok installed base-passwd base-passwd 3.5.46 install ok installed bash bash 5.0-4 install ok installed bsdutils bsdutils 1:2.33.1-0.1 install ok installed coreutils coreutils 8.30-3 install ok installed dash dash 0.5.10.2-5 install ok installed debconf debconf 1.5.71+deb10u1 install ok installed debian-archive-keyring debian-archive-keyring 2019.1+deb10u1 install ok installed debianutils debianutils 4.8.6.1 install ok installed diffutils diffutils 1:3.7-3 install ok installed dpkg dpkg 1.19.8 install ok installed e2fsprogs e2fsprogs 1.44.5-1+deb10u3 install ok installed fdisk fdisk 2.33.1-0.1 install ok installed findutils findutils 4.6.0+git+20190209-2 install ok installed gcc-8-base:amd64 gcc-8-base 8.3.0-6 install ok installed gpgv gpgv 2.2.12-1+deb10u2 install ok installed grep grep 3.3-1 install ok installed gzip gzip 1.9-3+deb10u1 install ok installed hostname hostname 3.21 install ok installed init-system-helpers init-system-helpers 1.56+nmu1 install ok installed libacl1:amd64 libacl1 2.2.53-4 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.8.2.3 install ok installed libattr1:amd64 libattr1 1:2.4.48-4 install ok installed libaudit-common libaudit-common 1:2.8.4-3 install ok installed libaudit1:amd64 libaudit1 1:2.8.4-3 install ok installed libblkid1:amd64 libblkid1 2.33.1-0.1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-9.2~deb10u1 install ok installed libc-bin libc-bin 2.28-10+deb10u1 install ok installed libc6:amd64 libc6 2.28-10+deb10u1 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2 install ok installed libcom-err2:amd64 libcom-err2 1.44.5-1+deb10u3 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.5 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.249 install ok installed libext2fs2:amd64 libext2fs2 1.44.5-1+deb10u3 install ok installed libfdisk1:amd64 libfdisk1 2.33.1-0.1 install ok installed libffi6:amd64 libffi6 3.2.1-9 install ok installed libgcc1:amd64 libgcc1 1:8.3.0-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.4-5+deb10u1 install ok installed libgmp10:amd64 libgmp10 2:6.1.2+dfsg-4+deb10u1 install ok installed libgnutls30:amd64 libgnutls30 3.6.7-4+deb10u8 install ok installed libgpg-error0:amd64 libgpg-error0 1.35-1 install ok installed libhogweed4:amd64 libhogweed4 3.4.1-1+deb10u1 install ok installed libidn2-0:amd64 libidn2-0 2.0.5-1+deb10u1 install ok installed liblz4-1:amd64 liblz4-1 1.8.3-1+deb10u1 install ok installed liblzma5:amd64 liblzma5 5.2.4-1+deb10u1 install ok installed libmount1:amd64 libmount1 2.33.1-0.1 install ok installed libncursesw6:amd64 libncursesw6 6.1+20181013-2+deb10u2 install ok installed libnettle6:amd64 libnettle6 3.4.1-1+deb10u1 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.15-2+deb10u1 install ok installed libpam-modules:amd64 libpam-modules 1.3.1-5 install ok installed libpam-modules-bin libpam-modules-bin 1.3.1-5 install ok installed libpam-runtime libpam-runtime 1.3.1-5 install ok installed libpam0g:amd64 libpam0g 1.3.1-5 install ok installed libpcre3:amd64 libpcre3 2:8.39-12 install ok installed libseccomp2:amd64 libseccomp2 2.3.3-4 install ok installed libselinux1:amd64 libselinux1 2.8-1+b1 install ok installed libsemanage-common libsemanage-common 2.8-2 install ok installed libsemanage1:amd64 libsemanage1 2.8-2 install ok installed libsepol1:amd64 libsepol1 2.8-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.33.1-0.1 install ok installed libss2:amd64 libss2 1.44.5-1+deb10u3 install ok installed libstdc++6:amd64 libstdc++6 8.3.0-6 install ok installed libsystemd0:amd64 libsystemd0 241-7~deb10u8 install ok installed libtasn1-6:amd64 libtasn1-6 4.13-3 install ok installed libtinfo6:amd64 libtinfo6 6.1+20181013-2+deb10u2 install ok installed libudev1:amd64 libudev1 241-7~deb10u8 install ok installed libunistring2:amd64 libunistring2 0.9.10-1 install ok installed libuuid1:amd64 libuuid1 2.33.1-0.1 install ok installed libzstd1:amd64 libzstd1 1.3.8+dfsg-3+deb10u2 install ok installed login login 1:4.5-1.1 install ok installed mawk mawk 1.3.3-17+b3 install ok installed mount mount 2.33.1-0.1 install ok installed ncurses-base ncurses-base 6.1+20181013-2+deb10u2 install ok installed ncurses-bin ncurses-bin 6.1+20181013-2+deb10u2 install ok installed passwd passwd 1:4.5-1.1 install ok installed perl-base perl-base 5.28.1-6+deb10u1 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.93-8 install ok installed tar tar 1.30+dfsg-6 install ok installed tzdata tzdata 2021a-0+deb10u6 install ok installed util-linux util-linux 2.33.1-0.1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-1+deb10u1 0m5.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.8s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/buster2next/reference-chroot-metadata.dat 0m5.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a'] 0m6.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a'] 0m6.5s INFO: Running scripts is_testable 0m6.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/is_testable_uninstallable'] 0m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/is_testable_uninstallable'] 0m6.6s INFO: Running scripts pre_test 0m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_test_exceptions'] 0m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_test_exceptions'] 0m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_test_root_password'] 0m6.6s DUMP: New password: Retype new password: passwd: password updated successfully 0m6.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_test_root_password'] 0m6.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'apt-cache', 'show', '--no-all-versions', 'cnvkit'] 0m6.9s DUMP: Package: cnvkit Version: 0.9.5-3 Installed-Size: 22874 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3-biopython, python3-future, python3-matplotlib, python3-numpy, python3-pandas, python3-pyfaidx, python3-pysam, python3-reportlab, python3-scipy, python3:any, r-bioc-dnacopy Description-en: Copy number variant detection from targeted DNA sequencing A command-line toolkit and Python library for detecting copy number variants and alterations genome-wide from targeted DNA sequencing. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent. Description-md5: 0b8ab5ba6be9de3379277ab7a92a7b5d Homepage: http://cnvkit.readthedocs.org Section: science Priority: optional Filename: pool/main/c/cnvkit/cnvkit_0.9.5-3_amd64.deb Size: 22915844 MD5sum: 055256eecf461400edfe333538a31804 SHA256: 6d650f92a13692e568317ce139e359e533d5ba8d14be84c62eddfcdddb4315a5 0m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'apt-cache', 'show', '--no-all-versions', 'cnvkit'] 0m6.9s INFO: apt-cache knows about the following packages: cnvkit 0m6.9s INFO: Running scripts pre_install 0m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_install_database-server'] 0m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_install_database-server'] 0m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_install_exceptions'] 0m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_install_exceptions'] 0m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_install_extras'] 0m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_install_extras'] 0m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_install_foreign_architecture'] 0m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m6.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'apt-cache', 'policy'] 0m7.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian buster/main amd64 Packages release v=10.13,o=Debian,a=oldoldstable,n=buster,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'apt-cache', 'policy'] 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'apt-cache', 'policy', 'cnvkit'] 0m7.0s DUMP: cnvkit: Installed: (none) Candidate: 0.9.5-3 Version table: 0.9.5-3 500 500 http://deb.debian.org/debian buster/main amd64 Packages 0m7.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'apt-cache', 'policy', 'cnvkit'] 0m7.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'apt-get', '-y', 'install', 'cnvkit'] 0m46.6s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: ca-certificates fontconfig fontconfig-config fonts-lyx libblas3 libbsd0 libcairo2 libcurl3-gnutls libcurl4 libdatrie1 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts2 libice6 libicu63 libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 libldap-common libmpdec2 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libpng16-16 libpsl5 libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libquadmath0 libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsm6 libsqlite3-0 libssh2-1 libssl1.1 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 lsb-base mime-support openssl python-matplotlib-data python3 python3-biopython python3-cycler python3-dateutil python3-decorator python3-future python3-kiwisolver python3-lib2to3 python3-matplotlib python3-minimal python3-numpy python3-pandas python3-pandas-lib python3-pil python3-pkg-resources python3-pyfaidx python3-pyparsing python3-pysam python3-reportlab python3-reportlab-accel python3-scipy python3-six python3-tz python3.7 python3.7-minimal r-base-core r-bioc-dnacopy readline-common sensible-utils ttf-bitstream-vera ucf unzip x11-common xdg-utils zip Suggested packages: krb5-doc krb5-user libjs-jquery-ui-docs liblcms2-utils tcl8.6 tk8.6 python3-doc python3-tk python3-venv bwa clustalo clustalw dialign dssp emboss fasttree mafft muscle phylip phyml prank probcons python3-mysqldb python3-rdflib python3-renderpm python3-psycopg2 raxml samtools t-coffee wise w3-dtd-mathml python-cycler-doc python-future-doc dvipng ffmpeg gir1.2-gtk-3.0 ghostscript inkscape ipython3 librsvg2-common python-matplotlib-doc python3-cairocffi python3-gi python3-gi-cairo python3-gobject python3-nose python3-pyqt4 python3-sip python3-tornado texlive-extra-utils texlive-latex-extra ttf-staypuft gcc gfortran python-numpy-doc python3-dev python3-pytest python3-numpy-dbg python-pandas-doc python-pil-doc python3-pil-dbg python3-setuptools python-pyparsing-doc pdf-viewer python3-egenix-mxtexttools python-reportlab-doc python-scipy-doc python3.7-venv python3.7-doc binutils binfmt-support ess r-doc-info | r-doc-pdf r-mathlib r-base-html readline-doc Recommended packages: libglib2.0-data shared-mime-info xdg-user-dirs javascript-common krb5-locales publicsuffix libsasl2-modules bzip2 file xz-utils python-biopython-doc ncbi-blast+ python3-tk python3-numexpr python3-tables python3-bs4 python3-html5lib python3-lxml python3-olefile python3-renderpm g++ | c++-compiler r-recommended r-base-dev r-doc-html libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: ca-certificates cnvkit fontconfig fontconfig-config fonts-lyx libblas3 libbsd0 libcairo2 libcurl3-gnutls libcurl4 libdatrie1 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts2 libice6 libicu63 libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 libldap-common libmpdec2 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libpng16-16 libpsl5 libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libquadmath0 libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsm6 libsqlite3-0 libssh2-1 libssl1.1 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 lsb-base mime-support openssl python-matplotlib-data python3 python3-biopython python3-cycler python3-dateutil python3-decorator python3-future python3-kiwisolver python3-lib2to3 python3-matplotlib python3-minimal python3-numpy python3-pandas python3-pandas-lib python3-pil python3-pkg-resources python3-pyfaidx python3-pyparsing python3-pysam python3-reportlab python3-reportlab-accel python3-scipy python3-six python3-tz python3.7 python3.7-minimal r-base-core r-bioc-dnacopy readline-common sensible-utils ttf-bitstream-vera ucf unzip x11-common xdg-utils zip 0 upgraded, 119 newly installed, 0 to remove and 0 not upgraded. Need to get 114 MB of archives. After this operation, 309 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1n-0+deb10u3 [1551 kB] Get:2 http://deb.debian.org/debian buster/main amd64 libpython3.7-minimal amd64 3.7.3-2+deb10u3 [589 kB] Get:3 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u4 [108 kB] Get:4 http://deb.debian.org/debian buster/main amd64 python3.7-minimal amd64 3.7.3-2+deb10u3 [1737 kB] Get:5 http://deb.debian.org/debian buster/main amd64 python3-minimal amd64 3.7.3-1 [36.6 kB] Get:6 http://deb.debian.org/debian buster/main amd64 mime-support all 3.62 [37.2 kB] Get:7 http://deb.debian.org/debian buster/main amd64 libmpdec2 amd64 2.4.2-2 [87.2 kB] Get:8 http://deb.debian.org/debian buster/main amd64 readline-common all 7.0-5 [70.6 kB] Get:9 http://deb.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get:10 http://deb.debian.org/debian buster/main amd64 libsqlite3-0 amd64 3.27.2-3+deb10u1 [641 kB] Get:11 http://deb.debian.org/debian buster/main amd64 libpython3.7-stdlib amd64 3.7.3-2+deb10u3 [1734 kB] Get:12 http://deb.debian.org/debian buster/main amd64 python3.7 amd64 3.7.3-2+deb10u3 [330 kB] Get:13 http://deb.debian.org/debian buster/main amd64 libpython3-stdlib amd64 3.7.3-1 [20.0 kB] Get:14 http://deb.debian.org/debian buster/main amd64 python3 amd64 3.7.3-1 [61.5 kB] Get:15 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get:16 http://deb.debian.org/debian buster/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get:17 http://deb.debian.org/debian buster/main amd64 openssl amd64 1.1.1n-0+deb10u3 [855 kB] Get:18 http://deb.debian.org/debian buster/main amd64 ca-certificates all 20200601~deb10u2 [166 kB] Get:19 http://deb.debian.org/debian buster/main amd64 libquadmath0 amd64 8.3.0-6 [133 kB] Get:20 http://deb.debian.org/debian buster/main amd64 libgfortran5 amd64 8.3.0-6 [581 kB] Get:21 http://deb.debian.org/debian buster/main amd64 libblas3 amd64 3.8.0-2 [148 kB] Get:22 http://deb.debian.org/debian buster/main amd64 liblapack3 amd64 3.8.0-2 [2110 kB] Get:23 http://deb.debian.org/debian buster/main amd64 python3-pkg-resources all 40.8.0-1 [153 kB] Get:24 http://deb.debian.org/debian buster/main amd64 python3-numpy amd64 1:1.16.2-1 [2119 kB] Get:25 http://deb.debian.org/debian buster/main amd64 python3-reportlab-accel amd64 3.5.13-1+deb10u1 [35.3 kB] Get:26 http://deb.debian.org/debian buster/main amd64 libpng16-16 amd64 1.6.36-6 [292 kB] Get:27 http://deb.debian.org/debian buster/main amd64 libfreetype6 amd64 2.9.1-3+deb10u3 [380 kB] Get:28 http://deb.debian.org/debian buster/main amd64 libimagequant0 amd64 2.12.2-1.1 [32.5 kB] Get:29 http://deb.debian.org/debian buster/main amd64 libjpeg62-turbo amd64 1:1.5.2-2+deb10u1 [133 kB] Get:30 http://deb.debian.org/debian buster/main amd64 liblcms2-2 amd64 2.9-3 [145 kB] Get:31 http://deb.debian.org/debian buster/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get:32 http://deb.debian.org/debian buster/main amd64 libwebp6 amd64 0.6.1-2+deb10u1 [261 kB] Get:33 http://deb.debian.org/debian buster/main amd64 libtiff5 amd64 4.1.0+git191117-2~deb10u4 [271 kB] Get:34 http://deb.debian.org/debian buster/main amd64 libwebpdemux2 amd64 0.6.1-2+deb10u1 [87.6 kB] Get:35 http://deb.debian.org/debian buster/main amd64 libwebpmux3 amd64 0.6.1-2+deb10u1 [97.8 kB] Get:36 http://deb.debian.org/debian buster/main amd64 python3-pil amd64 5.4.1-2+deb10u3 [395 kB] Get:37 http://deb.debian.org/debian buster/main amd64 python3-reportlab all 3.5.13-1+deb10u1 [541 kB] Get:38 http://deb.debian.org/debian buster/main amd64 python3-biopython amd64 1.73+dfsg-1 [1287 kB] Get:39 http://deb.debian.org/debian buster/main amd64 python3-lib2to3 all 3.7.3-1 [76.7 kB] Get:40 http://deb.debian.org/debian buster/main amd64 python3-future all 0.16.0-1 [346 kB] Get:41 http://deb.debian.org/debian buster/main amd64 python3-six all 1.12.0-1 [15.7 kB] Get:42 http://deb.debian.org/debian buster/main amd64 python3-dateutil all 2.7.3-3 [64.5 kB] Get:43 http://deb.debian.org/debian buster/main amd64 fonts-lyx all 2.3.2-1 [199 kB] Get:44 http://deb.debian.org/debian buster/main amd64 ttf-bitstream-vera all 1.10-8 [352 kB] Get:45 http://deb.debian.org/debian buster/main amd64 python-matplotlib-data all 3.0.2-2 [4138 kB] Get:46 http://deb.debian.org/debian buster/main amd64 python3-pyparsing all 2.2.0+dfsg1-2 [89.6 kB] Get:47 http://deb.debian.org/debian buster/main amd64 libjs-jquery all 3.3.1~dfsg-3+deb10u1 [332 kB] Get:48 http://deb.debian.org/debian buster/main amd64 libjs-jquery-ui all 1.12.1+dfsg-5 [232 kB] Get:49 http://deb.debian.org/debian buster/main amd64 python3-cycler all 0.10.0-1 [7556 B] Get:50 http://deb.debian.org/debian buster/main amd64 python3-kiwisolver amd64 1.0.1-2+b1 [65.4 kB] Get:51 http://deb.debian.org/debian buster/main amd64 python3-matplotlib amd64 3.0.2-2 [5353 kB] Get:52 http://deb.debian.org/debian buster/main amd64 python3-tz all 2019.1-1 [27.1 kB] Get:53 http://deb.debian.org/debian buster/main amd64 python3-pandas-lib amd64 0.23.3+dfsg-3 [3475 kB] Get:54 http://deb.debian.org/debian buster/main amd64 python3-pandas all 0.23.3+dfsg-3 [1750 kB] Get:55 http://deb.debian.org/debian buster/main amd64 python3-pyfaidx all 0.5.5.2-1 [25.3 kB] Get:56 http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get:57 http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u4 [65.9 kB] Get:58 http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u4 [122 kB] Get:59 http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u4 [369 kB] Get:60 http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u4 [158 kB] Get:61 http://deb.debian.org/debian buster/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-1+deb10u2 [69.2 kB] Get:62 http://deb.debian.org/debian buster/main amd64 libsasl2-2 amd64 2.1.27+dfsg-1+deb10u2 [106 kB] Get:63 http://deb.debian.org/debian buster/main amd64 libldap-common all 2.4.47+dfsg-3+deb10u7 [90.1 kB] Get:64 http://deb.debian.org/debian buster/main amd64 libldap-2.4-2 amd64 2.4.47+dfsg-3+deb10u7 [224 kB] Get:65 http://deb.debian.org/debian buster/main amd64 libnghttp2-14 amd64 1.36.0-2+deb10u1 [85.0 kB] Get:66 http://deb.debian.org/debian buster/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get:67 http://deb.debian.org/debian buster/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [60.5 kB] Get:68 http://deb.debian.org/debian buster/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get:69 http://deb.debian.org/debian buster/main amd64 libcurl3-gnutls amd64 7.64.0-4+deb10u2 [330 kB] Get:70 http://deb.debian.org/debian buster/main amd64 libdeflate0 amd64 1.2-1 [55.4 kB] Get:71 http://deb.debian.org/debian buster/main amd64 libhts2 amd64 1.9-12~deb10u1 [305 kB] Get:72 http://deb.debian.org/debian buster/main amd64 python3-pysam amd64 0.15.2+ds-2 [1661 kB] Get:73 http://deb.debian.org/debian buster/main amd64 python3-decorator all 4.3.0-1.1 [14.5 kB] Get:74 http://deb.debian.org/debian buster/main amd64 python3-scipy amd64 1.1.0-7 [10.0 MB] Get:75 http://deb.debian.org/debian buster/main amd64 zip amd64 3.0-11+b1 [234 kB] Get:76 http://deb.debian.org/debian buster/main amd64 unzip amd64 6.0-23+deb10u2 [172 kB] Get:77 http://deb.debian.org/debian buster/main amd64 libpaper1 amd64 1.1.28 [21.3 kB] Get:78 http://deb.debian.org/debian buster/main amd64 libpaper-utils amd64 1.1.28 [18.0 kB] Get:79 http://deb.debian.org/debian buster/main amd64 xdg-utils all 1.1.3-1+deb10u1 [73.7 kB] Get:80 http://deb.debian.org/debian buster/main amd64 fontconfig-config all 2.13.1-2 [280 kB] Get:81 http://deb.debian.org/debian buster/main amd64 libfontconfig1 amd64 2.13.1-2 [346 kB] Get:82 http://deb.debian.org/debian buster/main amd64 libpixman-1-0 amd64 0.36.0-1 [537 kB] Get:83 http://deb.debian.org/debian buster/main amd64 libxau6 amd64 1:1.0.8-1+b2 [19.9 kB] Get:84 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2+deb10u1 [99.5 kB] Get:85 http://deb.debian.org/debian buster/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:86 http://deb.debian.org/debian buster/main amd64 libxcb1 amd64 1.13.1-2 [137 kB] Get:87 http://deb.debian.org/debian buster/main amd64 libx11-data all 2:1.6.7-1+deb10u2 [299 kB] Get:88 http://deb.debian.org/debian buster/main amd64 libx11-6 amd64 2:1.6.7-1+deb10u2 [757 kB] Get:89 http://deb.debian.org/debian buster/main amd64 libxcb-render0 amd64 1.13.1-2 [109 kB] Get:90 http://deb.debian.org/debian buster/main amd64 libxcb-shm0 amd64 1.13.1-2 [99.2 kB] Get:91 http://deb.debian.org/debian buster/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get:92 http://deb.debian.org/debian buster/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get:93 http://deb.debian.org/debian buster/main amd64 libcairo2 amd64 1.16.0-4+deb10u1 [688 kB] Get:94 http://deb.debian.org/debian buster/main amd64 libcurl4 amd64 7.64.0-4+deb10u2 [332 kB] Get:95 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u3 [1259 kB] Get:96 http://deb.debian.org/debian buster/main amd64 libgomp1 amd64 8.3.0-6 [75.8 kB] Get:97 http://deb.debian.org/debian buster/main amd64 lsb-base all 10.2019051400 [28.4 kB] Get:98 http://deb.debian.org/debian buster/main amd64 x11-common all 1:7.7+19 [251 kB] Get:99 http://deb.debian.org/debian buster/main amd64 libice6 amd64 2:1.0.9-2 [58.7 kB] Get:100 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u3 [8293 kB] Get:101 http://deb.debian.org/debian buster/main amd64 fontconfig amd64 2.13.1-2 [405 kB] Get:102 http://deb.debian.org/debian buster/main amd64 libfribidi0 amd64 1.0.5-3.1+deb10u2 [63.9 kB] Get:103 http://deb.debian.org/debian buster/main amd64 libthai-data all 0.1.28-2 [170 kB] Get:104 http://deb.debian.org/debian buster/main amd64 libdatrie1 amd64 0.2.12-2 [39.3 kB] Get:105 http://deb.debian.org/debian buster/main amd64 libthai0 amd64 0.1.28-2 [54.1 kB] Get:106 http://deb.debian.org/debian buster/main amd64 libpango-1.0-0 amd64 1.42.4-8~deb10u1 [186 kB] Get:107 http://deb.debian.org/debian buster/main amd64 libgraphite2-3 amd64 1.3.13-7 [80.7 kB] Get:108 http://deb.debian.org/debian buster/main amd64 libharfbuzz0b amd64 2.3.1-1 [1187 kB] Get:109 http://deb.debian.org/debian buster/main amd64 libpangoft2-1.0-0 amd64 1.42.4-8~deb10u1 [68.3 kB] Get:110 http://deb.debian.org/debian buster/main amd64 libpangocairo-1.0-0 amd64 1.42.4-8~deb10u1 [55.7 kB] Get:111 http://deb.debian.org/debian buster/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get:112 http://deb.debian.org/debian buster/main amd64 libtcl8.6 amd64 8.6.9+dfsg-2 [1005 kB] Get:113 http://deb.debian.org/debian buster/main amd64 libxft2 amd64 2.3.2-2 [57.2 kB] Get:114 http://deb.debian.org/debian buster/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get:115 http://deb.debian.org/debian buster/main amd64 libtk8.6 amd64 8.6.9-2 [768 kB] Get:116 http://deb.debian.org/debian buster/main amd64 libxt6 amd64 1:1.1.5-1+b3 [190 kB] Get:117 http://deb.debian.org/debian buster/main amd64 r-base-core amd64 3.5.2-1 [23.9 MB] Get:118 http://deb.debian.org/debian buster/main amd64 r-bioc-dnacopy amd64 1.56.0-1 [419 kB] Get:119 http://deb.debian.org/debian buster/main amd64 cnvkit amd64 0.9.5-3 [22.9 MB] debconf: delaying package configuration, since apt-utils is not installed Fetched 114 MB in 2s (47.2 MB/s) Selecting previously unselected package libssl1.1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6462 files and directories currently installed.) Preparing to unpack .../libssl1.1_1.1.1n-0+deb10u3_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.1n-0+deb10u3) ... Selecting previously unselected package libpython3.7-minimal:amd64. Preparing to unpack .../libpython3.7-minimal_3.7.3-2+deb10u3_amd64.deb ... Unpacking libpython3.7-minimal:amd64 (3.7.3-2+deb10u3) ... Selecting previously unselected package libexpat1:amd64. 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Selecting previously unselected package libgraphite2-3:amd64. Preparing to unpack .../093-libgraphite2-3_1.3.13-7_amd64.deb ... Unpacking libgraphite2-3:amd64 (1.3.13-7) ... Selecting previously unselected package libharfbuzz0b:amd64. Preparing to unpack .../094-libharfbuzz0b_2.3.1-1_amd64.deb ... Unpacking libharfbuzz0b:amd64 (2.3.1-1) ... Selecting previously unselected package libpangoft2-1.0-0:amd64. Preparing to unpack .../095-libpangoft2-1.0-0_1.42.4-8~deb10u1_amd64.deb ... Unpacking libpangoft2-1.0-0:amd64 (1.42.4-8~deb10u1) ... Selecting previously unselected package libpangocairo-1.0-0:amd64. Preparing to unpack .../096-libpangocairo-1.0-0_1.42.4-8~deb10u1_amd64.deb ... Unpacking libpangocairo-1.0-0:amd64 (1.42.4-8~deb10u1) ... Selecting previously unselected package libsm6:amd64. Preparing to unpack .../097-libsm6_2%3a1.2.3-1_amd64.deb ... Unpacking libsm6:amd64 (2:1.2.3-1) ... Selecting previously unselected package libtcl8.6:amd64. Preparing to unpack .../098-libtcl8.6_8.6.9+dfsg-2_amd64.deb ... Unpacking libtcl8.6:amd64 (8.6.9+dfsg-2) ... Selecting previously unselected package libxft2:amd64. Preparing to unpack .../099-libxft2_2.3.2-2_amd64.deb ... Unpacking libxft2:amd64 (2.3.2-2) ... Selecting previously unselected package libxss1:amd64. Preparing to unpack .../100-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 .../101-libtk8.6_8.6.9-2_amd64.deb ... Unpacking libtk8.6:amd64 (8.6.9-2) ... Selecting previously unselected package libxt6:amd64. Preparing to unpack .../102-libxt6_1%3a1.1.5-1+b3_amd64.deb ... Unpacking libxt6:amd64 (1:1.1.5-1+b3) ... Selecting previously unselected package r-base-core. Preparing to unpack .../103-r-base-core_3.5.2-1_amd64.deb ... Unpacking r-base-core (3.5.2-1) ... Selecting previously unselected package r-bioc-dnacopy. Preparing to unpack .../104-r-bioc-dnacopy_1.56.0-1_amd64.deb ... Unpacking r-bioc-dnacopy (1.56.0-1) ... Selecting previously unselected package cnvkit. Preparing to unpack .../105-cnvkit_0.9.5-3_amd64.deb ... Unpacking cnvkit (0.9.5-3) ... Setting up libgraphite2-3:amd64 (1.3.13-7) ... Setting up liblcms2-2:amd64 (2.9-3) ... Setting up libpixman-1-0:amd64 (0.36.0-1) ... Setting up lsb-base (10.2019051400) ... Setting up libxau6:amd64 (1:1.0.8-1+b2) ... Setting up libkeyutils1:amd64 (1.6-6) ... Setting up libpsl5:amd64 (0.20.2-2) ... Setting up ttf-bitstream-vera (1.10-8) ... Setting up mime-support (3.62) ... Setting up libdatrie1:amd64 (0.2.12-2) ... Setting up libglib2.0-0:amd64 (2.58.3-2+deb10u3) ... No schema files found: doing nothing. Setting up fonts-lyx (2.3.2-1) ... Setting up unzip (6.0-23+deb10u2) ... Setting up libsqlite3-0:amd64 (3.27.2-3+deb10u1) ... Setting up x11-common (1:7.7+19) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up libnghttp2-14:amd64 (1.36.0-2+deb10u1) ... Setting up libdeflate0:amd64 (1.2-1) ... Setting up libgomp1:amd64 (8.3.0-6) ... Setting up libldap-common (2.4.47+dfsg-3+deb10u7) ... Setting up libjbig0:amd64 (2.1-3.1+b2) ... Setting up libicu63:amd64 (63.1-6+deb10u3) ... Setting up libkrb5support0:amd64 (1.17-3+deb10u4) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-1+deb10u2) ... Setting up zip (3.0-11+b1) ... Setting up libjpeg62-turbo:amd64 (1:1.5.2-2+deb10u1) ... Setting up libx11-data (2:1.6.7-1+deb10u2) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Setting up libfribidi0:amd64 (1.0.5-3.1+deb10u2) ... Setting up libquadmath0:amd64 (8.3.0-6) ... Setting up libimagequant0:amd64 (2.12.2-1.1) ... Setting up libpng16-16:amd64 (1.6.36-6) ... Setting up libtcl8.6:amd64 (8.6.9+dfsg-2) ... Setting up libwebp6:amd64 (0.6.1-2+deb10u1) ... Setting up libk5crypto3:amd64 (1.17-3+deb10u4) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-1+deb10u2) ... Setting up libgfortran5:amd64 (8.3.0-6) ... Setting up sensible-utils (0.0.12) ... Setting up libthai-data (0.1.28-2) ... Setting up libssh2-1:amd64 (1.8.0-2.1) ... Setting up libkrb5-3:amd64 (1.17-3+deb10u4) ... Setting up libtiff5:amd64 (4.1.0+git191117-2~deb10u4) ... Setting up libmpdec2:amd64 (2.4.2-2) ... Setting up libjs-jquery (3.3.1~dfsg-3+deb10u1) ... Setting up python-matplotlib-data (3.0.2-2) ... Setting up openssl (1.1.1n-0+deb10u3) ... Setting up libwebpmux3:amd64 (0.6.1-2+deb10u1) ... Setting up libbsd0:amd64 (0.9.1-2+deb10u1) ... Setting up readline-common (7.0-5) ... Setting up xdg-utils (1.1.3-1+deb10u1) ... Setting up libreadline7:amd64 (7.0-5) ... Setting up libice6:amd64 (2:1.0.9-2) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libpython3.7-stdlib:amd64 (3.7.3-2+deb10u3) ... Setting up libxcb1:amd64 (1.13.1-2) ... Setting up libxcb-render0:amd64 (1.13.1-2) ... Setting up libwebpdemux2:amd64 (0.6.1-2+deb10u1) ... Setting up libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u7) ... Setting up libxcb-shm0:amd64 (1.13.1-2) ... Setting up libthai0:amd64 (0.1.28-2) ... Setting up ca-certificates (20200601~deb10u2) ... Updating certificates in /etc/ssl/certs... 137 added, 0 removed; done. Setting up libblas3:amd64 (3.8.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libjs-jquery-ui (1.12.1+dfsg-5) ... Setting up libfreetype6:amd64 (2.9.1-3+deb10u3) ... Setting up libgssapi-krb5-2:amd64 (1.17-3+deb10u4) ... Setting up ucf (3.0038+nmu1) ... Setting up libcurl4:amd64 (7.64.0-4+deb10u2) ... Setting up libx11-6:amd64 (2:1.6.7-1+deb10u2) ... Setting up libharfbuzz0b:amd64 (2.3.1-1) ... Setting up libsm6:amd64 (2:1.2.3-1) ... Setting up libpython3-stdlib:amd64 (3.7.3-1) ... Setting up libpaper1:amd64 (1.1.28) ... Creating config file /etc/papersize with new version Setting up python3.7 (3.7.3-2+deb10u3) ... Setting up liblapack3:amd64 (3.8.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up fontconfig-config (2.13.1-2) ... Setting up libxext6:amd64 (2:1.3.3-1+b2) ... Setting up libcurl3-gnutls:amd64 (7.64.0-4+deb10u2) ... Setting up python3 (3.7.3-1) ... Setting up libpaper-utils (1.1.28) ... Setting up python3-tz (2019.1-1) ... Setting up python3-six (1.12.0-1) ... Setting up python3-pil:amd64 (5.4.1-2+deb10u3) ... Setting up python3-decorator (4.3.0-1.1) ... Setting up python3-pyparsing (2.2.0+dfsg1-2) ... Setting up python3-cycler (0.10.0-1) ... Setting up python3-reportlab-accel:amd64 (3.5.13-1+deb10u1) ... Setting up libxt6:amd64 (1:1.1.5-1+b3) ... Setting up python3-reportlab (3.5.13-1+deb10u1) ... Setting up python3-dateutil (2.7.3-3) ... Setting up libxss1:amd64 (1:1.2.3-1) ... Setting up libfontconfig1:amd64 (2.13.1-2) ... Setting up python3-lib2to3 (3.7.3-1) ... Setting up python3-pkg-resources (40.8.0-1) ... Setting up python3-pyfaidx (0.5.5.2-1) ... Setting up fontconfig (2.13.1-2) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.2-2) ... Setting up libhts2:amd64 (1.9-12~deb10u1) ... Setting up libtk8.6:amd64 (8.6.9-2) ... Setting up libpango-1.0-0:amd64 (1.42.4-8~deb10u1) ... Setting up libcairo2:amd64 (1.16.0-4+deb10u1) ... Setting up python3-kiwisolver (1.0.1-2+b1) ... Setting up python3-numpy (1:1.16.2-1) ... Setting up libpangoft2-1.0-0:amd64 (1.42.4-8~deb10u1) ... Setting up python3-future (0.16.0-1) ... update-alternatives: using /usr/bin/python3-futurize to provide /usr/bin/futurize (futurize) in auto mode update-alternatives: using /usr/bin/python3-pasteurize to provide /usr/bin/pasteurize (pasteurize) in auto mode Setting up python3-biopython (1.73+dfsg-1) ... Setting up libpangocairo-1.0-0:amd64 (1.42.4-8~deb10u1) ... Setting up python3-matplotlib (3.0.2-2) ... Setting up python3-pysam (0.15.2+ds-2) ... Setting up python3-scipy (1.1.0-7) ... Setting up python3-pandas-lib (0.23.3+dfsg-3) ... Setting up python3-pandas (0.23.3+dfsg-3) ... Setting up r-base-core (3.5.2-1) ... Creating config file /etc/R/Renviron with new version Setting up r-bioc-dnacopy (1.56.0-1) ... Setting up cnvkit (0.9.5-3) ... Processing triggers for libc-bin (2.28-10+deb10u1) ... Processing triggers for ca-certificates (20200601~deb10u2) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 0m46.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'apt-get', '-y', 'install', 'cnvkit'] 0m46.6s INFO: Running scripts post_install 0m46.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/post_install_exceptions'] 0m46.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/post_install_exceptions'] 0m46.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a'] 0m48.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a'] 0m48.0s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmp5ngcd_5a to buster-next 0m48.0s DEBUG: sources.list: deb http://deb.debian.org/debian/ buster main deb http://security.debian.org buster/updates main deb http://deb.debian.org/debian/ buster-updates main deb http://deb.debian.org/debian/ buster-proposed-updates main 0m48.0s INFO: Running scripts pre_distupgrade 0m48.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m48.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m48.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_distupgrade_exceptions'] 0m48.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_distupgrade_exceptions'] 0m48.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m48.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m48.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m48.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m48.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m48.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m48.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'apt-get', 'update'] 0m50.1s DUMP: Get:1 http://security.debian.org buster/updates InRelease [34.8 kB] Hit:2 http://deb.debian.org/debian buster InRelease Get:3 http://deb.debian.org/debian buster-updates InRelease [56.6 kB] Get:4 http://deb.debian.org/debian buster-proposed-updates InRelease [59.2 kB] Get:5 http://deb.debian.org/debian buster-updates/main amd64 Packages [8788 B] Get:6 http://deb.debian.org/debian buster-updates/main Translation-en [6915 B] Get:7 http://security.debian.org buster/updates/main amd64 Packages [546 kB] Get:8 http://security.debian.org buster/updates/main Translation-en [295 kB] Get:9 http://deb.debian.org/debian buster-proposed-updates/main amd64 Packages [728 B] Get:10 http://deb.debian.org/debian buster-proposed-updates/main Translation-en [859 B] Fetched 1008 kB in 1s (1151 kB/s) Reading package lists... 0m50.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'apt-get', 'update'] 0m50.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'apt-get', '-yf', 'dist-upgrade'] 0m58.8s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: debian-archive-keyring libbz2-1.0 libc-bin libc6 libcurl3-gnutls libcurl4 libexpat1 libglib2.0-0 libgnutls30 libgssapi-krb5-2 libjs-jquery-ui libk5crypto3 libkrb5-3 libkrb5support0 libncursesw6 libpixman-1-0 libpython3.7-minimal libpython3.7-stdlib libsqlite3-0 libssl1.1 libsystemd0 libtasn1-6 libtiff5 libtinfo6 libudev1 libwebp6 libwebpdemux2 libwebpmux3 libx11-6 libx11-data ncurses-base ncurses-bin openssl python3.7 python3.7-minimal tzdata unzip zlib1g 38 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 19.6 MB of archives. After this operation, 274 kB disk space will be freed. Get:1 http://security.debian.org buster/updates/main amd64 ncurses-bin amd64 6.1+20181013-2+deb10u3 [407 kB] Get:2 http://security.debian.org buster/updates/main amd64 libc6 amd64 2.28-10+deb10u2 [2869 kB] Get:3 http://security.debian.org buster/updates/main amd64 libc-bin amd64 2.28-10+deb10u2 [793 kB] Get:4 http://security.debian.org buster/updates/main amd64 ncurses-base all 6.1+20181013-2+deb10u3 [259 kB] Get:5 http://security.debian.org buster/updates/main amd64 libsystemd0 amd64 241-7~deb10u10 [332 kB] Get:6 http://security.debian.org buster/updates/main amd64 libssl1.1 amd64 1.1.1n-0+deb10u6 [1552 kB] Get:7 http://security.debian.org buster/updates/main amd64 python3.7 amd64 3.7.3-2+deb10u5 [330 kB] Get:8 http://security.debian.org buster/updates/main amd64 libpython3.7-stdlib amd64 3.7.3-2+deb10u5 [1734 kB] Get:9 http://security.debian.org buster/updates/main amd64 python3.7-minimal amd64 3.7.3-2+deb10u5 [1728 kB] Get:10 http://security.debian.org buster/updates/main amd64 libpython3.7-minimal amd64 3.7.3-2+deb10u5 [589 kB] Get:11 http://security.debian.org buster/updates/main amd64 libbz2-1.0 amd64 1.0.6-9.2~deb10u2 [45.4 kB] Get:12 http://security.debian.org buster/updates/main amd64 libtinfo6 amd64 6.1+20181013-2+deb10u3 [326 kB] Get:13 http://security.debian.org buster/updates/main amd64 libncursesw6 amd64 6.1+20181013-2+deb10u3 [132 kB] Get:14 http://security.debian.org buster/updates/main amd64 libsqlite3-0 amd64 3.27.2-3+deb10u2 [641 kB] Get:15 http://security.debian.org buster/updates/main amd64 libexpat1 amd64 2.2.6-2+deb10u6 [108 kB] Get:16 http://security.debian.org buster/updates/main amd64 zlib1g amd64 1:1.2.11.dfsg-1+deb10u2 [90.9 kB] Get:17 http://security.debian.org buster/updates/main amd64 debian-archive-keyring all 2019.1+deb10u2 [110 kB] Get:18 http://security.debian.org buster/updates/main amd64 libudev1 amd64 241-7~deb10u10 [151 kB] Get:19 http://security.debian.org buster/updates/main amd64 libtasn1-6 amd64 4.13-3+deb10u1 [52.0 kB] Get:20 http://security.debian.org buster/updates/main amd64 libgnutls30 amd64 3.6.7-4+deb10u10 [1126 kB] Get:21 http://security.debian.org buster/updates/main amd64 tzdata all 2021a-0+deb10u11 [267 kB] Get:22 http://security.debian.org buster/updates/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u5 [159 kB] Get:23 http://security.debian.org buster/updates/main amd64 libkrb5-3 amd64 1.17-3+deb10u5 [369 kB] Get:24 http://security.debian.org buster/updates/main amd64 libkrb5support0 amd64 1.17-3+deb10u5 [66.0 kB] Get:25 http://security.debian.org buster/updates/main amd64 libk5crypto3 amd64 1.17-3+deb10u5 [122 kB] Get:26 http://security.debian.org buster/updates/main amd64 libcurl3-gnutls amd64 7.64.0-4+deb10u6 [333 kB] Get:27 http://security.debian.org buster/updates/main amd64 libcurl4 amd64 7.64.0-4+deb10u6 [335 kB] Get:28 http://security.debian.org buster/updates/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u4 [1259 kB] Get:29 http://security.debian.org buster/updates/main amd64 libjs-jquery-ui all 1.12.1+dfsg-5+deb10u1 [232 kB] Get:30 http://security.debian.org buster/updates/main amd64 libpixman-1-0 amd64 0.36.0-1+deb10u1 [234 kB] Get:31 http://security.debian.org buster/updates/main amd64 libwebp6 amd64 0.6.1-2+deb10u2 [262 kB] Get:32 http://security.debian.org buster/updates/main amd64 libtiff5 amd64 4.1.0+git191117-2~deb10u8 [273 kB] Get:33 http://security.debian.org buster/updates/main amd64 libwebpdemux2 amd64 0.6.1-2+deb10u2 [87.7 kB] Get:34 http://security.debian.org buster/updates/main amd64 libwebpmux3 amd64 0.6.1-2+deb10u2 [97.9 kB] Get:35 http://security.debian.org buster/updates/main amd64 libx11-data all 2:1.6.7-1+deb10u3 [299 kB] Get:36 http://security.debian.org buster/updates/main amd64 libx11-6 amd64 2:1.6.7-1+deb10u3 [757 kB] Get:37 http://security.debian.org buster/updates/main amd64 openssl amd64 1.1.1n-0+deb10u6 [855 kB] Get:38 http://security.debian.org buster/updates/main amd64 unzip amd64 6.0-23+deb10u3 [172 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 19.6 MB in 0s (64.1 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 14993 files and directories currently installed.) Preparing to unpack .../ncurses-bin_6.1+20181013-2+deb10u3_amd64.deb ... Unpacking ncurses-bin (6.1+20181013-2+deb10u3) over (6.1+20181013-2+deb10u2) ... Setting up ncurses-bin (6.1+20181013-2+deb10u3) ... (Reading database ... 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Preparing to unpack .../09-libpixman-1-0_0.36.0-1+deb10u1_amd64.deb ... Unpacking libpixman-1-0:amd64 (0.36.0-1+deb10u1) over (0.36.0-1) ... Preparing to unpack .../10-libwebp6_0.6.1-2+deb10u2_amd64.deb ... Unpacking libwebp6:amd64 (0.6.1-2+deb10u2) over (0.6.1-2+deb10u1) ... Preparing to unpack .../11-libtiff5_4.1.0+git191117-2~deb10u8_amd64.deb ... Unpacking libtiff5:amd64 (4.1.0+git191117-2~deb10u8) over (4.1.0+git191117-2~deb10u4) ... Preparing to unpack .../12-libwebpdemux2_0.6.1-2+deb10u2_amd64.deb ... Unpacking libwebpdemux2:amd64 (0.6.1-2+deb10u2) over (0.6.1-2+deb10u1) ... Preparing to unpack .../13-libwebpmux3_0.6.1-2+deb10u2_amd64.deb ... Unpacking libwebpmux3:amd64 (0.6.1-2+deb10u2) over (0.6.1-2+deb10u1) ... Preparing to unpack .../14-libx11-data_2%3a1.6.7-1+deb10u3_all.deb ... Unpacking libx11-data (2:1.6.7-1+deb10u3) over (2:1.6.7-1+deb10u2) ... Preparing to unpack .../15-libx11-6_2%3a1.6.7-1+deb10u3_amd64.deb ... Unpacking libx11-6:amd64 (2:1.6.7-1+deb10u3) over (2:1.6.7-1+deb10u2) ... Preparing to unpack .../16-openssl_1.1.1n-0+deb10u6_amd64.deb ... Unpacking openssl (1.1.1n-0+deb10u6) over (1.1.1n-0+deb10u3) ... Preparing to unpack .../17-unzip_6.0-23+deb10u3_amd64.deb ... Unpacking unzip (6.0-23+deb10u3) over (6.0-23+deb10u2) ... Setting up libexpat1:amd64 (2.2.6-2+deb10u6) ... Setting up libpixman-1-0:amd64 (0.36.0-1+deb10u1) ... Setting up libglib2.0-0:amd64 (2.58.3-2+deb10u4) ... No schema files found: doing nothing. Setting up libssl1.1:amd64 (1.1.1n-0+deb10u6) ... Setting up unzip (6.0-23+deb10u3) ... Setting up libsqlite3-0:amd64 (3.27.2-3+deb10u2) ... Setting up libpython3.7-minimal:amd64 (3.7.3-2+deb10u5) ... Setting up libkrb5support0:amd64 (1.17-3+deb10u5) ... Setting up tzdata (2021a-0+deb10u11) ... Current default time zone: 'Etc/UTC' Local time is now: Sat Aug 19 00:22:31 UTC 2023. Universal Time is now: Sat Aug 19 00:22:31 UTC 2023. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libjs-jquery-ui (1.12.1+dfsg-5+deb10u1) ... Setting up libx11-data (2:1.6.7-1+deb10u3) ... Setting up libwebp6:amd64 (0.6.1-2+deb10u2) ... Setting up libk5crypto3:amd64 (1.17-3+deb10u5) ... Setting up python3.7-minimal (3.7.3-2+deb10u5) ... Setting up libx11-6:amd64 (2:1.6.7-1+deb10u3) ... Setting up libkrb5-3:amd64 (1.17-3+deb10u5) ... Setting up libtiff5:amd64 (4.1.0+git191117-2~deb10u8) ... Setting up openssl (1.1.1n-0+deb10u6) ... Setting up libwebpmux3:amd64 (0.6.1-2+deb10u2) ... Setting up libpython3.7-stdlib:amd64 (3.7.3-2+deb10u5) ... Setting up libwebpdemux2:amd64 (0.6.1-2+deb10u2) ... Setting up libgssapi-krb5-2:amd64 (1.17-3+deb10u5) ... Setting up libcurl4:amd64 (7.64.0-4+deb10u6) ... Setting up python3.7 (3.7.3-2+deb10u5) ... Setting up libcurl3-gnutls:amd64 (7.64.0-4+deb10u6) ... Processing triggers for libc-bin (2.28-10+deb10u2) ... Processing triggers for mime-support (3.62) ... 0m58.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'apt-get', '-yf', 'dist-upgrade'] 0m58.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m59.3s DUMP: 69ab5fceead76a7ef0592607ac7084bd - 0m59.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m59.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'apt-cache', 'show', '--no-all-versions', 'cnvkit'] 0m59.5s DUMP: Package: cnvkit Version: 0.9.5-3 Installed-Size: 22874 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: python3-biopython, python3-future, python3-matplotlib, python3-numpy, python3-pandas, python3-pyfaidx, python3-pysam, python3-reportlab, python3-scipy, python3:any, r-bioc-dnacopy Description-en: Copy number variant detection from targeted DNA sequencing A command-line toolkit and Python library for detecting copy number variants and alterations genome-wide from targeted DNA sequencing. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent. Description-md5: 0b8ab5ba6be9de3379277ab7a92a7b5d Homepage: http://cnvkit.readthedocs.org Section: science Priority: optional Filename: pool/main/c/cnvkit/cnvkit_0.9.5-3_amd64.deb Size: 22915844 MD5sum: 055256eecf461400edfe333538a31804 SHA256: 6d650f92a13692e568317ce139e359e533d5ba8d14be84c62eddfcdddb4315a5 0m59.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'apt-cache', 'show', '--no-all-versions', 'cnvkit'] 0m59.5s INFO: apt-cache knows about the following packages: cnvkit 0m59.5s INFO: Running scripts pre_install 0m59.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_install_database-server'] 0m59.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_install_database-server'] 0m59.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_install_exceptions'] 0m59.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_install_exceptions'] 0m59.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_install_extras'] 0m59.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_install_extras'] 0m59.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_install_foreign_architecture'] 0m59.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_install_foreign_architecture'] 0m59.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m59.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m59.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'apt-cache', 'policy'] 0m59.7s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian buster-proposed-updates/main amd64 Packages release v=10-updates,o=Debian,a=oldoldstable-proposed-updates,n=buster-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian buster-updates/main amd64 Packages release o=Debian,a=oldoldstable-updates,n=buster-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org buster/updates/main amd64 Packages release v=10,o=Debian,a=oldoldstable,n=buster,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian buster/main amd64 Packages release v=10.13,o=Debian,a=oldoldstable,n=buster,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m59.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'apt-cache', 'policy'] 0m59.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'apt-cache', 'policy', 'cnvkit'] 0m59.7s DUMP: cnvkit: Installed: 0.9.5-3 Candidate: 0.9.5-3 Version table: *** 0.9.5-3 500 500 http://deb.debian.org/debian buster/main amd64 Packages 100 /var/lib/dpkg/status 0m59.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'apt-cache', 'policy', 'cnvkit'] 0m59.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'apt-get', '-y', 'install', 'cnvkit'] 1m0.2s DUMP: Reading package lists... Building dependency tree... Reading state information... cnvkit is already the newest version (0.9.5-3). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'apt-get', '-y', 'install', 'cnvkit'] 1m0.2s INFO: Running scripts post_install 1m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/post_install_exceptions'] 1m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/post_install_exceptions'] 1m0.2s INFO: Running scripts post_distupgrade 1m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/post_distupgrade_base_cleanup'] 1m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/post_distupgrade_exceptions'] 1m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/post_distupgrade_exceptions'] 1m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 1m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/post_distupgrade_squeeze-backports'] 1m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/post_distupgrade_zz_backports'] 1m0.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/post_distupgrade_zz_backports'] 1m0.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a'] 1m1.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a'] 1m1.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a'] 1m2.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a'] 1m2.5s INFO: Running scripts pre_install 1m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_install_database-server'] 1m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_install_database-server'] 1m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_install_exceptions'] 1m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_install_exceptions'] 1m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_install_extras'] 1m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_install_extras'] 1m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_install_foreign_architecture'] 1m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_install_foreign_architecture'] 1m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m2.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_install_foreign_architecture_i386'] 1m2.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'apt-cache', 'policy'] 1m2.7s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian buster-proposed-updates/main amd64 Packages release v=10-updates,o=Debian,a=oldoldstable-proposed-updates,n=buster-proposed-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://deb.debian.org/debian buster-updates/main amd64 Packages release o=Debian,a=oldoldstable-updates,n=buster-updates,l=Debian,c=main,b=amd64 origin deb.debian.org 500 http://security.debian.org buster/updates/main amd64 Packages release v=10,o=Debian,a=oldoldstable,n=buster,l=Debian-Security,c=main,b=amd64 origin security.debian.org 500 http://deb.debian.org/debian buster/main amd64 Packages release v=10.13,o=Debian,a=oldoldstable,n=buster,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 1m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'apt-cache', 'policy'] 1m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'apt-cache', 'policy', 'cnvkit'] 1m2.8s DUMP: cnvkit: Installed: 0.9.5-3 Candidate: 0.9.5-3 Version table: *** 0.9.5-3 500 500 http://deb.debian.org/debian buster/main amd64 Packages 100 /var/lib/dpkg/status 1m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'apt-cache', 'policy', 'cnvkit'] 1m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'apt-get', '-y', 'install', 'cnvkit=0.9.5-3'] 1m3.2s DUMP: Reading package lists... Building dependency tree... Reading state information... cnvkit is already the newest version (0.9.5-3). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 1m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'apt-get', '-y', 'install', 'cnvkit=0.9.5-3'] 1m3.2s INFO: Running scripts post_install 1m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/post_install_exceptions'] 1m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/post_install_exceptions'] 1m3.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a'] 1m4.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a'] 1m6.0s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', '-ac', '--ignore-obsolete'] 1m8.8s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', '-ac', '--ignore-obsolete'] 1m8.8s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m8.8s DUMP: 0.15.6 1m8.8s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m8.8s INFO: Running adequate version 0.15.6 now. 1m8.8s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'cnvkit'] 1m9.0s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'cnvkit'] 1m9.0s INFO: Running scripts pre_remove 1m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m12.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m12.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m12.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m12.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m12.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_remove_exceptions'] 1m13.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/pre_remove_exceptions'] 1m13.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m13.0s DUMP: install ok installed adduser adduser 3.118 install ok installed apt apt 1.8.2.3 install ok installed base-files base-files 10.3+deb10u13 install ok installed base-passwd base-passwd 3.5.46 install ok installed bash bash 5.0-4 install ok installed bsdutils bsdutils 1:2.33.1-0.1 install ok installed ca-certificates ca-certificates 20200601~deb10u2 install ok installed cnvkit cnvkit 0.9.5-3 install ok installed coreutils coreutils 8.30-3 install ok installed dash dash 0.5.10.2-5 install ok installed debconf debconf 1.5.71+deb10u1 install ok installed debian-archive-keyring debian-archive-keyring 2019.1+deb10u2 install ok installed debianutils debianutils 4.8.6.1 install ok installed diffutils diffutils 1:3.7-3 install ok installed dpkg dpkg 1.19.8 install ok installed e2fsprogs e2fsprogs 1.44.5-1+deb10u3 install ok installed fdisk fdisk 2.33.1-0.1 install ok installed findutils findutils 4.6.0+git+20190209-2 install ok installed fontconfig fontconfig 2.13.1-2 install ok installed fontconfig-config fontconfig-config 2.13.1-2 install ok installed fonts-lyx fonts-lyx 2.3.2-1 install ok installed gcc-8-base:amd64 gcc-8-base 8.3.0-6 install ok installed gpgv gpgv 2.2.12-1+deb10u2 install ok installed grep grep 3.3-1 install ok installed gzip gzip 1.9-3+deb10u1 install ok installed hostname hostname 3.21 install ok installed init-system-helpers init-system-helpers 1.56+nmu1 install ok installed libacl1:amd64 libacl1 2.2.53-4 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.8.2.3 install ok installed libattr1:amd64 libattr1 1:2.4.48-4 install ok installed libaudit-common libaudit-common 1:2.8.4-3 install ok installed libaudit1:amd64 libaudit1 1:2.8.4-3 install ok installed libblas3:amd64 libblas3 3.8.0-2 install ok installed libblkid1:amd64 libblkid1 2.33.1-0.1 install ok installed libbsd0:amd64 libbsd0 0.9.1-2+deb10u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-9.2~deb10u2 install ok installed libc-bin libc-bin 2.28-10+deb10u2 install ok installed libc6:amd64 libc6 2.28-10+deb10u2 install ok installed libcairo2:amd64 libcairo2 1.16.0-4+deb10u1 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2 install ok installed libcom-err2:amd64 libcom-err2 1.44.5-1+deb10u3 install ok installed libcurl3-gnutls:amd64 libcurl3-gnutls 7.64.0-4+deb10u6 install ok installed libcurl4:amd64 libcurl4 7.64.0-4+deb10u6 install ok installed libdatrie1:amd64 libdatrie1 0.2.12-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.5 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.249 install ok installed libdeflate0:amd64 libdeflate0 1.2-1 install ok installed libexpat1:amd64 libexpat1 2.2.6-2+deb10u6 install ok installed libext2fs2:amd64 libext2fs2 1.44.5-1+deb10u3 install ok installed libfdisk1:amd64 libfdisk1 2.33.1-0.1 install ok installed libffi6:amd64 libffi6 3.2.1-9 install ok installed libfontconfig1:amd64 libfontconfig1 2.13.1-2 install ok installed libfreetype6:amd64 libfreetype6 2.9.1-3+deb10u3 install ok installed libfribidi0:amd64 libfribidi0 1.0.5-3.1+deb10u2 install ok installed libgcc1:amd64 libgcc1 1:8.3.0-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.4-5+deb10u1 install ok installed libgfortran5:amd64 libgfortran5 8.3.0-6 install ok installed libglib2.0-0:amd64 libglib2.0-0 2.58.3-2+deb10u4 install ok installed libgmp10:amd64 libgmp10 2:6.1.2+dfsg-4+deb10u1 install ok installed libgnutls30:amd64 libgnutls30 3.6.7-4+deb10u10 install ok installed libgomp1:amd64 libgomp1 8.3.0-6 install ok installed libgpg-error0:amd64 libgpg-error0 1.35-1 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.13-7 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.17-3+deb10u5 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 2.3.1-1 install ok installed libhogweed4:amd64 libhogweed4 3.4.1-1+deb10u1 install ok installed libhts2:amd64 libhts2 1.9-12~deb10u1 install ok installed libice6:amd64 libice6 2:1.0.9-2 install ok installed libicu63:amd64 libicu63 63.1-6+deb10u3 install ok installed libidn2-0:amd64 libidn2-0 2.0.5-1+deb10u1 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 1:1.5.2-2+deb10u1 install ok installed libjs-jquery libjs-jquery 3.3.1~dfsg-3+deb10u1 install ok installed libjs-jquery-ui libjs-jquery-ui 1.12.1+dfsg-5+deb10u1 install ok installed libk5crypto3:amd64 libk5crypto3 1.17-3+deb10u5 install ok installed libkeyutils1:amd64 libkeyutils1 1.6-6 install ok installed libkrb5-3:amd64 libkrb5-3 1.17-3+deb10u5 install ok installed libkrb5support0:amd64 libkrb5support0 1.17-3+deb10u5 install ok installed liblapack3:amd64 liblapack3 3.8.0-2 install ok installed liblcms2-2:amd64 liblcms2-2 2.9-3 install ok installed libldap-2.4-2:amd64 libldap-2.4-2 2.4.47+dfsg-3+deb10u7 install ok installed libldap-common libldap-common 2.4.47+dfsg-3+deb10u7 install ok installed liblz4-1:amd64 liblz4-1 1.8.3-1+deb10u1 install ok installed liblzma5:amd64 liblzma5 5.2.4-1+deb10u1 install ok installed libmount1:amd64 libmount1 2.33.1-0.1 install ok installed libmpdec2:amd64 libmpdec2 2.4.2-2 install ok installed libncursesw6:amd64 libncursesw6 6.1+20181013-2+deb10u3 install ok installed libnettle6:amd64 libnettle6 3.4.1-1+deb10u1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.36.0-2+deb10u1 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.15-2+deb10u1 install ok installed libpam-modules:amd64 libpam-modules 1.3.1-5 install ok installed libpam-modules-bin libpam-modules-bin 1.3.1-5 install ok installed libpam-runtime libpam-runtime 1.3.1-5 install ok installed libpam0g:amd64 libpam0g 1.3.1-5 install ok installed libpango-1.0-0:amd64 libpango-1.0-0 1.42.4-8~deb10u1 install ok installed libpangocairo-1.0-0:amd64 libpangocairo-1.0-0 1.42.4-8~deb10u1 install ok installed libpangoft2-1.0-0:amd64 libpangoft2-1.0-0 1.42.4-8~deb10u1 install ok installed libpaper-utils libpaper-utils 1.1.28 install ok installed libpaper1:amd64 libpaper1 1.1.28 install ok installed libpcre3:amd64 libpcre3 2:8.39-12 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.36.0-1+deb10u1 install ok installed libpng16-16:amd64 libpng16-16 1.6.36-6 install ok installed libpsl5:amd64 libpsl5 0.20.2-2 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.7.3-1 install ok installed libpython3.7-minimal:amd64 libpython3.7-minimal 3.7.3-2+deb10u5 install ok installed libpython3.7-stdlib:amd64 libpython3.7-stdlib 3.7.3-2+deb10u5 install ok installed libquadmath0:amd64 libquadmath0 8.3.0-6 install ok installed libreadline7:amd64 libreadline7 7.0-5 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.27+dfsg-1+deb10u2 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.27+dfsg-1+deb10u2 install ok installed libseccomp2:amd64 libseccomp2 2.3.3-4 install ok installed libselinux1:amd64 libselinux1 2.8-1+b1 install ok installed libsemanage-common libsemanage-common 2.8-2 install ok installed libsemanage1:amd64 libsemanage1 2.8-2 install ok installed libsepol1:amd64 libsepol1 2.8-1 install ok installed libsm6:amd64 libsm6 2:1.2.3-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.33.1-0.1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.27.2-3+deb10u2 install ok installed libss2:amd64 libss2 1.44.5-1+deb10u3 install ok installed libssh2-1:amd64 libssh2-1 1.8.0-2.1 install ok installed libssl1.1:amd64 libssl1.1 1.1.1n-0+deb10u6 install ok installed libstdc++6:amd64 libstdc++6 8.3.0-6 install ok installed libsystemd0:amd64 libsystemd0 241-7~deb10u10 install ok installed libtasn1-6:amd64 libtasn1-6 4.13-3+deb10u1 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.9+dfsg-2 install ok installed libthai-data libthai-data 0.1.28-2 install ok installed libthai0:amd64 libthai0 0.1.28-2 install ok installed libtiff5:amd64 libtiff5 4.1.0+git191117-2~deb10u8 install ok installed libtinfo6:amd64 libtinfo6 6.1+20181013-2+deb10u3 install ok installed libtk8.6:amd64 libtk8.6 8.6.9-2 install ok installed libudev1:amd64 libudev1 241-7~deb10u10 install ok installed libunistring2:amd64 libunistring2 0.9.10-1 install ok installed libuuid1:amd64 libuuid1 2.33.1-0.1 install ok installed libwebp6:amd64 libwebp6 0.6.1-2+deb10u2 install ok installed libwebpdemux2:amd64 libwebpdemux2 0.6.1-2+deb10u2 install ok installed libwebpmux3:amd64 libwebpmux3 0.6.1-2+deb10u2 install ok installed libx11-6:amd64 libx11-6 2:1.6.7-1+deb10u3 install ok installed libx11-data libx11-data 2:1.6.7-1+deb10u3 install ok installed libxau6:amd64 libxau6 1:1.0.8-1+b2 install ok installed libxcb-render0:amd64 libxcb-render0 1.13.1-2 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.13.1-2 install ok installed libxcb1:amd64 libxcb1 1.13.1-2 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3 install ok installed libxext6:amd64 libxext6 2:1.3.3-1+b2 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 1:1.1.5-1+b3 install ok installed libzstd1:amd64 libzstd1 1.3.8+dfsg-3+deb10u2 install ok installed login login 1:4.5-1.1 install ok installed lsb-base lsb-base 10.2019051400 install ok installed mawk mawk 1.3.3-17+b3 install ok installed mime-support mime-support 3.62 install ok installed mount mount 2.33.1-0.1 install ok installed ncurses-base ncurses-base 6.1+20181013-2+deb10u3 install ok installed ncurses-bin ncurses-bin 6.1+20181013-2+deb10u3 install ok installed openssl openssl 1.1.1n-0+deb10u6 install ok installed passwd passwd 1:4.5-1.1 install ok installed perl-base perl-base 5.28.1-6+deb10u1 install ok installed python-matplotlib-data python-matplotlib-data 3.0.2-2 install ok installed python3 python3 3.7.3-1 install ok installed python3-biopython python3-biopython 1.73+dfsg-1 install ok installed python3-cycler python3-cycler 0.10.0-1 install ok installed python3-dateutil python3-dateutil 2.7.3-3 install ok installed python3-decorator python3-decorator 4.3.0-1.1 install ok installed python3-future python3-future 0.16.0-1 install ok installed python3-kiwisolver python3-kiwisolver 1.0.1-2+b1 install ok installed python3-lib2to3 python3-lib2to3 3.7.3-1 install ok installed python3-matplotlib python3-matplotlib 3.0.2-2 install ok installed python3-minimal python3-minimal 3.7.3-1 install ok installed python3-numpy python3-numpy 1:1.16.2-1 install ok installed python3-pandas python3-pandas 0.23.3+dfsg-3 install ok installed python3-pandas-lib python3-pandas-lib 0.23.3+dfsg-3 install ok installed python3-pil:amd64 python3-pil 5.4.1-2+deb10u3 install ok installed python3-pkg-resources python3-pkg-resources 40.8.0-1 install ok installed python3-pyfaidx python3-pyfaidx 0.5.5.2-1 install ok installed python3-pyparsing python3-pyparsing 2.2.0+dfsg1-2 install ok installed python3-pysam python3-pysam 0.15.2+ds-2 install ok installed python3-reportlab python3-reportlab 3.5.13-1+deb10u1 install ok installed python3-reportlab-accel:amd64 python3-reportlab-accel 3.5.13-1+deb10u1 install ok installed python3-scipy python3-scipy 1.1.0-7 install ok installed python3-six python3-six 1.12.0-1 install ok installed python3-tz python3-tz 2019.1-1 install ok installed python3.7 python3.7 3.7.3-2+deb10u5 install ok installed python3.7-minimal python3.7-minimal 3.7.3-2+deb10u5 install ok installed r-base-core r-base-core 3.5.2-1 install ok installed r-bioc-dnacopy r-bioc-dnacopy 1.56.0-1 install ok installed readline-common readline-common 7.0-5 install ok installed sed sed 4.7-1 install ok installed sensible-utils sensible-utils 0.0.12 install ok installed sysvinit-utils sysvinit-utils 2.93-8 install ok installed tar tar 1.30+dfsg-6 install ok installed ttf-bitstream-vera ttf-bitstream-vera 1.10-8 install ok installed tzdata tzdata 2021a-0+deb10u11 install ok installed ucf ucf 3.0038+nmu1 install ok installed unzip unzip 6.0-23+deb10u3 install ok installed util-linux util-linux 2.33.1-0.1 install ok installed x11-common x11-common 1:7.7+19 install ok installed xdg-utils xdg-utils 1.1.3-1+deb10u1 install ok installed zip zip 3.0-11+b1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-1+deb10u2 1m13.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m13.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'apt-get', 'remove', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-lyx', 'libblas3:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts2:amd64', 'libice6:amd64', 'libicu63:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libmpdec2:amd64', 'libnghttp2-14:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.7-minimal:amd64', 'libpython3.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsm6:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1: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', 'lsb-base', 'mime-support', 'openssl', 'python-matplotlib-data', 'python3', 'python3-biopython', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-future', 'python3-kiwisolver', 'python3-lib2to3', 'python3-matplotlib', 'python3-minimal', 'python3-numpy', 'python3-pandas', 'python3-pandas-lib', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-pyfaidx', 'python3-pyparsing', 'python3-pysam', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3-scipy', 'python3-six', 'python3-tz', 'python3.7', 'python3.7-minimal', 'r-base-core', 'r-bioc-dnacopy', 'readline-common', 'sensible-utils', 'ttf-bitstream-vera', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'cnvkit'] 1m18.9s 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 libbsd0 libcairo2 libcurl3-gnutls libcurl4 libdatrie1 libdeflate0 libexpat1 libfontconfig1 libfreetype6 libfribidi0 libgfortran5 libglib2.0-0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhts2 libice6 libicu63 libimagequant0 libjbig0 libjpeg62-turbo libjs-jquery libjs-jquery-ui libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 libldap-common libmpdec2 libnghttp2-14 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpixman-1-0 libpng16-16 libpsl5 libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libquadmath0 libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsm6 libsqlite3-0 libssh2-1 libssl1.1 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 lsb-base mime-support openssl python-matplotlib-data python3 python3-biopython python3-cycler python3-dateutil python3-decorator python3-future python3-kiwisolver python3-lib2to3 python3-matplotlib python3-minimal python3-numpy python3-pandas python3-pandas-lib python3-pil python3-pkg-resources python3-pyfaidx python3-pyparsing python3-pysam python3-reportlab python3-reportlab-accel python3-scipy python3-six python3-tz python3.7 python3.7-minimal r-base-core r-bioc-dnacopy readline-common sensible-utils ttf-bitstream-vera ucf unzip x11-common xdg-utils zip 0 upgraded, 0 newly installed, 119 to remove and 0 not upgraded. After this operation, 309 MB disk space will be freed. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 15001 files and directories currently installed.) Removing cnvkit (0.9.5-3) ... Removing r-bioc-dnacopy (1.56.0-1) ... Removing r-base-core (3.5.2-1) ... Removing ca-certificates (20200601~deb10u2) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing libpangocairo-1.0-0:amd64 (1.42.4-8~deb10u1) ... Removing libpangoft2-1.0-0:amd64 (1.42.4-8~deb10u1) ... Removing libpango-1.0-0:amd64 (1.42.4-8~deb10u1) ... Removing fontconfig (2.13.1-2) ... Removing libtk8.6:amd64 (8.6.9-2) ... Removing libxft2:amd64 (2.3.2-2) ... Removing libcairo2:amd64 (1.16.0-4+deb10u1) ... Removing libfontconfig1:amd64 (2.13.1-2) ... Removing fontconfig-config (2.13.1-2) ... Removing python3-matplotlib (3.0.2-2) ... Removing python-matplotlib-data (3.0.2-2) ... Removing fonts-lyx (2.3.2-1) ... dpkg: warning: while removing fonts-lyx, directory '/usr/share/fonts/truetype/lyx' not empty so not removed Removing python3-scipy (1.1.0-7) ... Removing python3-biopython (1.73+dfsg-1) ... Removing python3-pandas (0.23.3+dfsg-3) ... Removing python3-pandas-lib (0.23.3+dfsg-3) ... Removing python3-numpy (1:1.16.2-1) ... Removing liblapack3:amd64 (3.8.0-2) ... Removing libblas3:amd64 (3.8.0-2) ... Removing libxt6:amd64 (1:1.1.5-1+b3) ... Removing libxss1:amd64 (1:1.2.3-1) ... Removing libxcb-shm0:amd64 (1.13.1-2) ... Removing libsm6:amd64 (2:1.2.3-1) ... Removing libice6:amd64 (2:1.0.9-2) ... Removing python3-pysam (0.15.2+ds-2) ... Removing libhts2:amd64 (1.9-12~deb10u1) ... Removing libcurl3-gnutls:amd64 (7.64.0-4+deb10u6) ... Removing libcurl4:amd64 (7.64.0-4+deb10u6) ... Removing libthai0:amd64 (0.1.28-2) ... Removing libdatrie1:amd64 (0.2.12-2) ... Removing libdeflate0:amd64 (1.2-1) ... Removing python3-future (0.16.0-1) ... Removing python3-lib2to3 (3.7.3-1) ... Removing python3-pyfaidx (0.5.5.2-1) ... Removing python3-dateutil (2.7.3-3) ... Removing python3-reportlab (3.5.13-1+deb10u1) ... Removing python3-reportlab-accel:amd64 (3.5.13-1+deb10u1) ... Removing python3-tz (2019.1-1) ... Removing python3-pil:amd64 (5.4.1-2+deb10u3) ... Removing libharfbuzz0b:amd64 (2.3.1-1) ... Removing libfreetype6:amd64 (2.9.1-3+deb10u3) ... Removing libfribidi0:amd64 (1.0.5-3.1+deb10u2) ... Removing libgfortran5:amd64 (8.3.0-6) ... Removing libglib2.0-0:amd64 (2.58.3-2+deb10u4) ... Removing libgomp1:amd64 (8.3.0-6) ... Removing libgraphite2-3:amd64 (1.3.13-7) ... Removing libgssapi-krb5-2:amd64 (1.17-3+deb10u5) ... Removing libicu63:amd64 (63.1-6+deb10u3) ... Removing libimagequant0:amd64 (2.12.2-1.1) ... Removing libtiff5:amd64 (4.1.0+git191117-2~deb10u8) ... Removing libjbig0:amd64 (2.1-3.1+b2) ... Removing libjpeg62-turbo:amd64 (1:1.5.2-2+deb10u1) ... Removing libjs-jquery-ui (1.12.1+dfsg-5+deb10u1) ... Removing libjs-jquery (3.3.1~dfsg-3+deb10u1) ... Removing libkrb5-3:amd64 (1.17-3+deb10u5) ... Removing libk5crypto3:amd64 (1.17-3+deb10u5) ... Removing libkrb5support0:amd64 (1.17-3+deb10u5) ... Removing libkeyutils1:amd64 (1.6-6) ... Removing liblcms2-2:amd64 (2.9-3) ... Removing libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u7) ... Removing libldap-common (2.4.47+dfsg-3+deb10u7) ... Removing libnghttp2-14:amd64 (1.36.0-2+deb10u1) ... Removing libpaper-utils (1.1.28) ... Removing libpaper1:amd64 (1.1.28) ... Removing libpixman-1-0:amd64 (0.36.0-1+deb10u1) ... Removing libpng16-16:amd64 (1.6.36-6) ... Removing libpsl5:amd64 (0.20.2-2) ... Removing libquadmath0:amd64 (8.3.0-6) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Removing libsasl2-2:amd64 (2.1.27+dfsg-1+deb10u2) ... Removing libsasl2-modules-db:amd64 (2.1.27+dfsg-1+deb10u2) ... Removing libssh2-1:amd64 (1.8.0-2.1) ... Removing openssl (1.1.1n-0+deb10u6) ... Removing libtcl8.6:amd64 (8.6.9+dfsg-2) ... Removing libthai-data (0.1.28-2) ... Removing libwebpmux3:amd64 (0.6.1-2+deb10u2) ... Removing libwebpdemux2:amd64 (0.6.1-2+deb10u2) ... Removing libwebp6:amd64 (0.6.1-2+deb10u2) ... Removing libxcb-render0:amd64 (1.13.1-2) ... Removing libxext6:amd64 (2:1.3.3-1+b2) ... Removing libxrender1:amd64 (1:0.9.10-1) ... Removing x11-common (1:7.7+19) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing lsb-base (10.2019051400) ... Removing python3-cycler (0.10.0-1) ... Removing python3-decorator (4.3.0-1.1) ... Removing python3-kiwisolver (1.0.1-2+b1) ... Removing python3-pkg-resources (40.8.0-1) ... Removing python3-pyparsing (2.2.0+dfsg1-2) ... Removing ucf (3.0038+nmu1) ... Removing sensible-utils (0.0.12) ... Removing ttf-bitstream-vera (1.10-8) ... dpkg: warning: while removing ttf-bitstream-vera, directory '/usr/share/fonts/truetype/ttf-bitstream-vera' not empty so not removed Removing unzip (6.0-23+deb10u3) ... Removing xdg-utils (1.1.3-1+deb10u1) ... Removing zip (3.0-11+b1) ... Removing libx11-6:amd64 (2:1.6.7-1+deb10u3) ... Removing libxcb1:amd64 (1.13.1-2) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libbsd0:amd64 (0.9.1-2+deb10u1) ... Removing python3-six (1.12.0-1) ... Removing python3 (3.7.3-1) ... Removing python3.7 (3.7.3-2+deb10u5) ... Removing python3-minimal (3.7.3-1) ... Removing python3.7-minimal (3.7.3-2+deb10u5) ... Removing libexpat1:amd64 (2.2.6-2+deb10u6) ... Removing libpython3-stdlib:amd64 (3.7.3-1) ... Removing libpython3.7-stdlib:amd64 (3.7.3-2+deb10u5) ... find: '/usr/lib/python3': No such file or directory Removing libmpdec2:amd64 (2.4.2-2) ... Removing libpython3.7-minimal:amd64 (3.7.3-2+deb10u5) ... find: '/usr/lib/python3': No such file or directory Removing libreadline7:amd64 (7.0-5) ... Removing libsqlite3-0:amd64 (3.27.2-3+deb10u2) ... Removing libssl1.1:amd64 (1.1.1n-0+deb10u6) ... Removing libx11-data (2:1.6.7-1+deb10u3) ... Removing libxau6:amd64 (1:1.0.8-1+b2) ... Removing mime-support (3.62) ... Removing readline-common (7.0-5) ... Processing triggers for libc-bin (2.28-10+deb10u2) ... 1m18.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'apt-get', 'remove', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-lyx', 'libblas3:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts2:amd64', 'libice6:amd64', 'libicu63:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libmpdec2:amd64', 'libnghttp2-14:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.7-minimal:amd64', 'libpython3.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsm6:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1: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', 'lsb-base', 'mime-support', 'openssl', 'python-matplotlib-data', 'python3', 'python3-biopython', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-future', 'python3-kiwisolver', 'python3-lib2to3', 'python3-matplotlib', 'python3-minimal', 'python3-numpy', 'python3-pandas', 'python3-pandas-lib', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-pyfaidx', 'python3-pyparsing', 'python3-pysam', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3-scipy', 'python3-six', 'python3-tz', 'python3.7', 'python3.7-minimal', 'r-base-core', 'r-bioc-dnacopy', 'readline-common', 'sensible-utils', 'ttf-bitstream-vera', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'cnvkit'] 1m18.9s INFO: Running scripts post_remove 1m18.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/post_remove_exceptions'] 1m18.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/post_remove_exceptions'] 1m18.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'dpkg', '--purge', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-lyx', 'libblas3:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts2:amd64', 'libice6:amd64', 'libicu63:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libmpdec2:amd64', 'libnghttp2-14:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.7-minimal:amd64', 'libpython3.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsm6:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1: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', 'lsb-base', 'mime-support', 'openssl', 'python-matplotlib-data', 'python3', 'python3-biopython', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-future', 'python3-kiwisolver', 'python3-lib2to3', 'python3-matplotlib', 'python3-minimal', 'python3-numpy', 'python3-pandas', 'python3-pandas-lib', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-pyfaidx', 'python3-pyparsing', 'python3-pysam', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3-scipy', 'python3-six', 'python3-tz', 'python3.7', 'python3.7-minimal', 'r-base-core', 'r-bioc-dnacopy', 'readline-common', 'sensible-utils', 'ttf-bitstream-vera', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip'] 1m20.0s DUMP: (Reading database ... 6511 files and directories currently installed.) Purging configuration files for ca-certificates (20200601~deb10u2) ... Removing dangling symlinks from /etc/ssl/certs... done. Purging configuration files for fontconfig (2.13.1-2) ... Purging configuration files for fontconfig-config (2.13.1-2) ... 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 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 libgfortran5 which isn't installed Purging configuration files for libglib2.0-0:amd64 (2.58.3-2+deb10u4) ... dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.17-3+deb10u5) ... dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed dpkg: warning: ignoring request to remove libhts2 which isn't installed dpkg: warning: ignoring request to remove libice6 which isn't installed dpkg: warning: ignoring request to remove libicu63 which isn't installed dpkg: warning: ignoring request to remove libimagequant0 which isn't installed dpkg: warning: ignoring request to remove libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed dpkg: warning: ignoring request to remove libjs-jquery which isn't installed Purging configuration files for libjs-jquery-ui (1.12.1+dfsg-5+deb10u1) ... dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove liblcms2-2 which isn't installed dpkg: warning: ignoring request to remove libldap-2.4-2 which isn't installed Purging configuration files for libldap-common (2.4.47+dfsg-3+deb10u7) ... dpkg: warning: ignoring request to remove libmpdec2 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) ... dpkg: warning: ignoring request to remove libpixman-1-0 which isn't installed dpkg: warning: ignoring request to remove libpng16-16 which isn't installed dpkg: warning: ignoring request to remove libpsl5 which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.7-minimal:amd64 (3.7.3-2+deb10u5) ... dpkg: warning: ignoring request to remove libpython3.7-stdlib which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed dpkg: warning: ignoring request to remove libreadline7 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 Purging configuration files for libssl1.1:amd64 (1.1.1n-0+deb10u6) ... 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 lsb-base which isn't installed Purging configuration files for mime-support (3.62) ... Purging configuration files for openssl (1.1.1n-0+deb10u6) ... Purging configuration files for python-matplotlib-data (3.0.2-2) ... Purging configuration files for python3 (3.7.3-1) ... 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-future which isn't installed dpkg: warning: ignoring request to remove python3-kiwisolver which isn't installed dpkg: warning: ignoring request to remove python3-lib2to3 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-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-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-tz which isn't installed dpkg: warning: ignoring request to remove python3.7 which isn't installed Purging configuration files for python3.7-minimal (3.7.3-2+deb10u5) ... Purging configuration files for r-base-core (3.5.2-1) ... dpkg: warning: ignoring request to remove r-bioc-dnacopy which isn't installed Purging configuration files for readline-common (7.0-5) ... 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 (3.0038+nmu1) ... Purging configuration files for unzip (6.0-23+deb10u3) ... Purging configuration files for x11-common (1:7.7+19) ... dpkg: warning: ignoring request to remove xdg-utils which isn't installed dpkg: warning: ignoring request to remove zip which isn't installed 1m20.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'dpkg', '--purge', 'ca-certificates', 'fontconfig', 'fontconfig-config', 'fonts-lyx', 'libblas3:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdatrie1:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgfortran5:amd64', 'libglib2.0-0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhts2:amd64', 'libice6:amd64', 'libicu63:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-jquery-ui', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libmpdec2:amd64', 'libnghttp2-14:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython3-stdlib:amd64', 'libpython3.7-minimal:amd64', 'libpython3.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsm6:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1: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', 'lsb-base', 'mime-support', 'openssl', 'python-matplotlib-data', 'python3', 'python3-biopython', 'python3-cycler', 'python3-dateutil', 'python3-decorator', 'python3-future', 'python3-kiwisolver', 'python3-lib2to3', 'python3-matplotlib', 'python3-minimal', 'python3-numpy', 'python3-pandas', 'python3-pandas-lib', 'python3-pil:amd64', 'python3-pkg-resources', 'python3-pyfaidx', 'python3-pyparsing', 'python3-pysam', 'python3-reportlab', 'python3-reportlab-accel:amd64', 'python3-scipy', 'python3-six', 'python3-tz', 'python3.7', 'python3.7-minimal', 'r-base-core', 'r-bioc-dnacopy', 'readline-common', 'sensible-utils', 'ttf-bitstream-vera', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip'] 1m20.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'dpkg', '--purge', 'cnvkit'] 1m20.0s DUMP: dpkg: warning: ignoring request to remove cnvkit which isn't installed 1m20.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'dpkg', '--purge', 'cnvkit'] 1m20.0s INFO: Running scripts post_purge 1m20.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/post_purge_exceptions'] 1m20.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/post_purge_exceptions'] 1m20.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'dpkg', '--purge', '--pending'] 1m20.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'dpkg', '--purge', '--pending'] 1m20.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'dpkg', '--remove', '--pending'] 1m20.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'dpkg', '--remove', '--pending'] 1m20.1s INFO: Running scripts post_test 1m20.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/post_test_exceptions'] 1m20.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'tmp/scripts/post_test_exceptions'] 1m20.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a'] 1m20.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a'] 1m20.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'dpkg-divert', '--list'] 1m20.8s 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 1m20.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'dpkg-divert', '--list'] 1m20.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'apt-get', 'clean'] 1m20.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a', 'apt-get', 'clean'] 1m20.9s DEBUG: Recording chroot state 1m21.9s 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 1m22.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a/dev/shm'] 1m22.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a/dev/shm'] 1m22.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a/dev/console'] 1m22.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a/dev/console'] 1m22.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a/dev/ptmx'] 1m22.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a/dev/ptmx'] 1m22.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a/dev/pts'] 1m22.5s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a/dev/pts'] 1m22.5s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a/proc'] 1m22.6s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a/proc'] 1m22.6s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a'] 1m22.8s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp5ngcd_5a'] 1m22.8s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp5ngcd_5a 1m22.9s INFO: PASS: Upgrading between Debian distributions. 1m22.9s INFO: PASS: All tests. 1m22.9s INFO: piuparts run ends. ret=0 End: 2023-08-19 00:22:57 GMT