Start: 2022-12-07 10:39:10 GMT [stretch] Package: nanopolish Source: nanopolish (0.5.0-1) Version: 0.5.0-1+b1 Installed-Size: 3519 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.23), libgcc1 (>= 1:3.0), libgomp1 (>= 4.9), libhdf5-100, libhts1 (>= 1.1), libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4) Suggests: python, perl, make Description: consensus caller for nanopore sequencing data Homepage: https://github.com/jts/nanopolish Description-md5: 9d79d36abbf48f8c897b51adbbf88535 Section: science Priority: optional Filename: pool/main/n/nanopolish/nanopolish_0.5.0-1+b1_amd64.deb Size: 1914528 MD5sum: 57f0e684ac2b4064df7bc14ba7c47e36 SHA256: cf497297cedc254051a6d915d411154b0a366e841e09cdcd71fdfb2aac0a7e80 [buster] Package: nanopolish Version: 0.11.0-2 Installed-Size: 9781 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.27), libgcc1 (>= 1:3.3.1), libgomp1 (>= 4.9), libhdf5-103, libhts2 (>= 1.4.1), libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4), python:any Recommends: python-biopython, python-pysam Suggests: perl, make Description: consensus caller for nanopore sequencing data Homepage: https://github.com/jts/nanopolish Description-md5: c65181cb6cafc3c3d9c0c69affe72640 Section: science Priority: optional Filename: pool/main/n/nanopolish/nanopolish_0.11.0-2_amd64.deb Size: 2214776 MD5sum: b72ff98f6e32ed73516e13727f75bbee SHA256: f8782c56f1b4ba784f8fb3a81c46c2d68beb5e3f434aa605bce2473789ab4a47 Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --install-recommends --upgrade-before-dist-upgrade --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz -d stretch -d buster -B /srv/piuparts.debian.org/slave/refchroot/stretch2Xbuster-rcmd/reference-chroot-metadata.dat --apt nanopolish=0.11.0-2 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.1.5 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --install-recommends --upgrade-before-dist-upgrade --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz -d stretch -d buster -B /srv/piuparts.debian.org/slave/refchroot/stretch2Xbuster-rcmd/reference-chroot-metadata.dat --apt nanopolish=0.11.0-2 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-19-amd64 #1 SMP Debian 5.10.149-2 (2022-10-21) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmphddufz4b 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmphddufz4b 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmphddufz4b', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m1.6s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmphddufz4b', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m1.6s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmphddufz4b/proc'] 0m1.6s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmphddufz4b/proc'] 0m1.6s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmphddufz4b/dev/pts'] 0m1.6s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmphddufz4b/dev/pts'] 0m1.6s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmphddufz4b/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmphddufz4b/dev/ptmx'] 0m1.6s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmphddufz4b/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmphddufz4b/dev/ptmx'] 0m1.6s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmphddufz4b/dev/console'] 0m1.6s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmphddufz4b/dev/console'] 0m1.6s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmphddufz4b/dev/shm'] 0m1.6s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmphddufz4b/dev/shm'] 0m1.6s DEBUG: sources.list: deb http://deb.debian.org/debian/ stretch main 0m1.7s DEBUG: Created policy-rc.d and chmodded it. 0m1.7s DEBUG: Created resolv.conf. 0m1.7s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmphddufz4b/tmp/scripts/ 0m1.7s INFO: Running scripts post_chroot_unpack 0m1.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'apt-get', 'update'] 0m2.5s DUMP: Ign:1 http://deb.debian.org/debian stretch InRelease Hit:2 http://deb.debian.org/debian stretch Release Reading package lists... 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'apt-get', 'update'] 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'apt-get', '-yf', 'dist-upgrade'] 0m2.7s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'apt-get', '-yf', 'dist-upgrade'] 0m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.3s DUMP: 660e5103244a20b75ca08c3f8741e16e - 0m3.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.3s INFO: Running scripts post_setup 0m3.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/post_setup_dummy_users'] 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/post_setup_dummy_users'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/post_setup_forbid_home'] 0m3.9s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/post_setup_forbid_home'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.9s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' '/bin/sync' -> 'true' 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/post_setup_minimize'] 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/post_setup_minimize'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/post_setup_zz_backports'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/post_setup_zz_backports'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.0s DUMP: install ok installed adduser adduser 3.115 install ok installed apt apt 1.4.10 install ok installed base-files base-files 9.9+deb9u13 install ok installed base-passwd base-passwd 3.5.43 install ok installed bash bash 4.4-5 install ok installed bsdutils bsdutils 1:2.29.2-1+deb9u1 install ok installed coreutils coreutils 8.26-3 install ok installed dash dash 0.5.8-2.4 install ok installed debconf debconf 1.5.61 install ok installed debian-archive-keyring debian-archive-keyring 2017.5+deb9u1 install ok installed debianutils debianutils 4.8.1.1 install ok installed diffutils diffutils 1:3.5-3 install ok installed dpkg dpkg 1.18.25 install ok installed e2fslibs:amd64 e2fslibs 1.43.4-2+deb9u1 install ok installed e2fsprogs e2fsprogs 1.43.4-2+deb9u1 install ok installed findutils findutils 4.6.0+git+20161106-2 install ok installed gcc-6-base:amd64 gcc-6-base 6.3.0-18+deb9u1 install ok installed gpgv gpgv 2.1.18-8~deb9u4 install ok installed grep grep 2.27-2 install ok installed gzip gzip 1.6-5+b1 install ok installed hostname hostname 3.18+b1 install ok installed init-system-helpers init-system-helpers 1.48 install ok installed libacl1:amd64 libacl1 2.2.52-3+b1 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.4.10 install ok installed libattr1:amd64 libattr1 1:2.4.47-2+b2 install ok installed libaudit-common libaudit-common 1:2.6.7-2 install ok installed libaudit1:amd64 libaudit1 1:2.6.7-2 install ok installed libblkid1:amd64 libblkid1 2.29.2-1+deb9u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-8.1 install ok installed libc-bin libc-bin 2.24-11+deb9u4 install ok installed libc6:amd64 libc6 2.24-11+deb9u4 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.7-3+b1 install ok installed libcomerr2:amd64 libcomerr2 1.43.4-2+deb9u1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28-12+deb9u1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.227 install ok installed libfdisk1:amd64 libfdisk1 2.29.2-1+deb9u1 install ok installed libgcc1:amd64 libgcc1 1:6.3.0-18+deb9u1 install ok installed libgcrypt20:amd64 libgcrypt20 1.7.6-2+deb9u3 install ok installed libgpg-error0:amd64 libgpg-error0 1.26-2 install ok installed liblz4-1:amd64 liblz4-1 0.0~r131-2+b1 install ok installed liblzma5:amd64 liblzma5 5.2.2-1.2+b1 install ok installed libmount1:amd64 libmount1 2.29.2-1+deb9u1 install ok installed libncursesw5:amd64 libncursesw5 6.0+20161126-1+deb9u2 install ok installed libpam-modules:amd64 libpam-modules 1.1.8-3.6 install ok installed libpam-modules-bin libpam-modules-bin 1.1.8-3.6 install ok installed libpam-runtime libpam-runtime 1.1.8-3.6 install ok installed libpam0g:amd64 libpam0g 1.1.8-3.6 install ok installed libpcre3:amd64 libpcre3 2:8.39-3 install ok installed libselinux1:amd64 libselinux1 2.6-3+b3 install ok installed libsemanage-common libsemanage-common 2.6-2 install ok installed libsemanage1:amd64 libsemanage1 2.6-2 install ok installed libsepol1:amd64 libsepol1 2.6-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.29.2-1+deb9u1 install ok installed libss2:amd64 libss2 1.43.4-2+deb9u1 install ok installed libstdc++6:amd64 libstdc++6 6.3.0-18+deb9u1 install ok installed libsystemd0:amd64 libsystemd0 232-25+deb9u12 install ok installed libtinfo5:amd64 libtinfo5 6.0+20161126-1+deb9u2 install ok installed libudev1:amd64 libudev1 232-25+deb9u12 install ok installed libustr-1.0-1:amd64 libustr-1.0-1 1.0.4-6 install ok installed libuuid1:amd64 libuuid1 2.29.2-1+deb9u1 install ok installed login login 1:4.4-4.1 install ok installed mawk mawk 1.3.3-17+b3 install ok installed mount mount 2.29.2-1+deb9u1 install ok installed multiarch-support multiarch-support 2.24-11+deb9u4 install ok installed ncurses-base ncurses-base 6.0+20161126-1+deb9u2 install ok installed ncurses-bin ncurses-bin 6.0+20161126-1+deb9u2 install ok installed passwd passwd 1:4.4-4.1 install ok installed perl-base perl-base 5.24.1-3+deb9u7 install ok installed sed sed 4.4-1 install ok installed sensible-utils sensible-utils 0.0.9+deb9u1 install ok installed sysvinit-utils sysvinit-utils 2.88dsf-59.9 install ok installed tar tar 1.29b-1.1 install ok installed util-linux util-linux 2.29.2-1+deb9u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.8.dfsg-5 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.0s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/stretch2Xbuster-rcmd/reference-chroot-metadata.dat 0m4.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmphddufz4b'] 0m4.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmphddufz4b'] 0m4.4s INFO: Running scripts is_testable 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/is_testable_uninstallable'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/is_testable_uninstallable'] 0m4.5s INFO: Running scripts pre_test 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_test_exceptions'] 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_test_exceptions'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_test_root_password'] 0m4.5s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_test_root_password'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'apt-cache', 'show', '--no-all-versions', 'nanopolish'] 0m4.7s DUMP: Package: nanopolish Source: nanopolish (0.5.0-1) Version: 0.5.0-1+b1 Installed-Size: 3519 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.23), libgcc1 (>= 1:3.0), libgomp1 (>= 4.9), libhdf5-100, libhts1 (>= 1.1), libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4) Suggests: python, perl, make Description-en: consensus caller for nanopore sequencing data Nanopolish uses a signal-level hidden Markov model for consensus calling of nanopore genome sequencing data. Description-md5: 9d79d36abbf48f8c897b51adbbf88535 Homepage: https://github.com/jts/nanopolish Section: science Priority: optional Filename: pool/main/n/nanopolish/nanopolish_0.5.0-1+b1_amd64.deb Size: 1914528 MD5sum: 57f0e684ac2b4064df7bc14ba7c47e36 SHA256: cf497297cedc254051a6d915d411154b0a366e841e09cdcd71fdfb2aac0a7e80 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'apt-cache', 'show', '--no-all-versions', 'nanopolish'] 0m4.7s INFO: apt-cache knows about the following packages: nanopolish 0m4.7s INFO: Running scripts pre_install 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_install_database-server'] 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_install_database-server'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_install_exceptions'] 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_install_exceptions'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_install_extras'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_install_extras'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'apt-cache', 'policy'] 0m4.9s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian stretch/main amd64 Packages release v=9.13,o=Debian,a=oldoldstable,n=stretch,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'apt-cache', 'policy'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'apt-cache', 'policy', 'nanopolish'] 0m4.9s DUMP: nanopolish: Installed: (none) Candidate: 0.5.0-1+b1 Version table: 0.5.0-1+b1 500 500 http://deb.debian.org/debian stretch/main amd64 Packages 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'apt-cache', 'policy', 'nanopolish'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'apt-get', '-y', 'install', 'nanopolish'] 0m10.9s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: ca-certificates krb5-locales libaec0 libcurl3-gnutls libffi6 libgfortran3 libgmp10 libgnutls30 libgomp1 libgssapi-krb5-2 libhdf5-100 libhogweed4 libhts1 libidn11 libidn2-0 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libnettle6 libnghttp2-14 libp11-kit0 libpsl5 libquadmath0 librtmp1 libsasl2-2 libsasl2-modules libsasl2-modules-db libssh2-1 libssl1.1 libsz2 libtasn1-6 libunistring0 openssl publicsuffix Suggested packages: gnutls-bin krb5-doc krb5-user libsasl2-modules-gssapi-mit | libsasl2-modules-gssapi-heimdal libsasl2-modules-ldap libsasl2-modules-otp libsasl2-modules-sql python perl make The following NEW packages will be installed: ca-certificates krb5-locales libaec0 libcurl3-gnutls libffi6 libgfortran3 libgmp10 libgnutls30 libgomp1 libgssapi-krb5-2 libhdf5-100 libhogweed4 libhts1 libidn11 libidn2-0 libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libldap-2.4-2 libldap-common libnettle6 libnghttp2-14 libp11-kit0 libpsl5 libquadmath0 librtmp1 libsasl2-2 libsasl2-modules libsasl2-modules-db libssh2-1 libssl1.1 libsz2 libtasn1-6 libunistring0 nanopolish openssl publicsuffix 0 upgraded, 38 newly installed, 0 to remove and 0 not upgraded. Need to get 10.4 MB of archives. After this operation, 27.0 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian stretch/main amd64 libssl1.1 amd64 1.1.0l-1~deb9u1 [1358 kB] Get:2 http://deb.debian.org/debian stretch/main amd64 krb5-locales all 1.15-1+deb9u1 [93.8 kB] Get:3 http://deb.debian.org/debian stretch/main amd64 libgmp10 amd64 2:6.1.2+dfsg-1 [253 kB] Get:4 http://deb.debian.org/debian stretch/main amd64 libnettle6 amd64 3.3-1+b2 [192 kB] Get:5 http://deb.debian.org/debian stretch/main amd64 libhogweed4 amd64 3.3-1+b2 [136 kB] Get:6 http://deb.debian.org/debian stretch/main amd64 libidn11 amd64 1.33-1+deb9u1 [115 kB] Get:7 http://deb.debian.org/debian stretch/main amd64 libffi6 amd64 3.2.1-6 [20.4 kB] Get:8 http://deb.debian.org/debian stretch/main amd64 libp11-kit0 amd64 0.23.3-2 [111 kB] Get:9 http://deb.debian.org/debian stretch/main amd64 libtasn1-6 amd64 4.10-1.1+deb9u1 [50.6 kB] Get:10 http://deb.debian.org/debian stretch/main amd64 libgnutls30 amd64 3.5.8-5+deb9u5 [896 kB] Get:11 http://deb.debian.org/debian stretch/main amd64 libkeyutils1 amd64 1.5.9-9 [12.4 kB] Get:12 http://deb.debian.org/debian stretch/main amd64 libkrb5support0 amd64 1.15-1+deb9u1 [61.9 kB] Get:13 http://deb.debian.org/debian stretch/main amd64 libk5crypto3 amd64 1.15-1+deb9u1 [119 kB] Get:14 http://deb.debian.org/debian stretch/main amd64 libkrb5-3 amd64 1.15-1+deb9u1 [311 kB] Get:15 http://deb.debian.org/debian stretch/main amd64 libgssapi-krb5-2 amd64 1.15-1+deb9u1 [155 kB] Get:16 http://deb.debian.org/debian stretch/main amd64 libsasl2-modules-db amd64 2.1.27~101-g0780600+dfsg-3+deb9u1 [68.4 kB] Get:17 http://deb.debian.org/debian stretch/main amd64 libsasl2-2 amd64 2.1.27~101-g0780600+dfsg-3+deb9u1 [105 kB] Get:18 http://deb.debian.org/debian stretch/main amd64 libldap-common all 2.4.44+dfsg-5+deb9u4 [85.7 kB] Get:19 http://deb.debian.org/debian stretch/main amd64 libldap-2.4-2 amd64 2.4.44+dfsg-5+deb9u4 [219 kB] Get:20 http://deb.debian.org/debian stretch/main amd64 openssl amd64 1.1.0l-1~deb9u1 [749 kB] Get:21 http://deb.debian.org/debian stretch/main amd64 ca-certificates all 20200601~deb9u1 [160 kB] Get:22 http://deb.debian.org/debian stretch/main amd64 libaec0 amd64 0.3.2-1 [18.5 kB] Get:23 http://deb.debian.org/debian stretch/main amd64 libunistring0 amd64 0.9.6+really0.9.3-0.1 [279 kB] Get:24 http://deb.debian.org/debian stretch/main amd64 libidn2-0 amd64 0.16-1+deb9u1 [60.7 kB] Get:25 http://deb.debian.org/debian stretch/main amd64 libnghttp2-14 amd64 1.18.1-1+deb9u1 [79.2 kB] Get:26 http://deb.debian.org/debian stretch/main amd64 libpsl5 amd64 0.17.0-3 [41.8 kB] Get:27 http://deb.debian.org/debian stretch/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-1+b1 [60.4 kB] Get:28 http://deb.debian.org/debian stretch/main amd64 libssh2-1 amd64 1.7.0-1+deb9u1 [139 kB] Get:29 http://deb.debian.org/debian stretch/main amd64 libcurl3-gnutls amd64 7.52.1-5+deb9u10 [290 kB] Get:30 http://deb.debian.org/debian stretch/main amd64 libquadmath0 amd64 6.3.0-18+deb9u1 [131 kB] Get:31 http://deb.debian.org/debian stretch/main amd64 libgfortran3 amd64 6.3.0-18+deb9u1 [265 kB] Get:32 http://deb.debian.org/debian stretch/main amd64 libgomp1 amd64 6.3.0-18+deb9u1 [73.3 kB] Get:33 http://deb.debian.org/debian stretch/main amd64 libsz2 amd64 0.3.2-1 [5730 B] Get:34 http://deb.debian.org/debian stretch/main amd64 libhdf5-100 amd64 1.10.0-patch1+docs-3+deb9u1 [1282 kB] Get:35 http://deb.debian.org/debian stretch/main amd64 libhts1 amd64 1.3.2-2 [257 kB] Get:36 http://deb.debian.org/debian stretch/main amd64 libsasl2-modules amd64 2.1.27~101-g0780600+dfsg-3+deb9u1 [102 kB] Get:37 http://deb.debian.org/debian stretch/main amd64 nanopolish amd64 0.5.0-1+b1 [1915 kB] Get:38 http://deb.debian.org/debian stretch/main amd64 publicsuffix all 20190415.1030-0+deb9u1 [108 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 10.4 MB in 0s (12.9 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 ... 4411 files and directories currently installed.) Preparing to unpack .../00-libssl1.1_1.1.0l-1~deb9u1_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.0l-1~deb9u1) ... Selecting previously unselected package krb5-locales. Preparing to unpack .../01-krb5-locales_1.15-1+deb9u1_all.deb ... Unpacking krb5-locales (1.15-1+deb9u1) ... Selecting previously unselected package libgmp10:amd64. Preparing to unpack .../02-libgmp10_2%3a6.1.2+dfsg-1_amd64.deb ... Unpacking libgmp10:amd64 (2:6.1.2+dfsg-1) ... Selecting previously unselected package libnettle6:amd64. Preparing to unpack .../03-libnettle6_3.3-1+b2_amd64.deb ... Unpacking libnettle6:amd64 (3.3-1+b2) ... Selecting previously unselected package libhogweed4:amd64. Preparing to unpack .../04-libhogweed4_3.3-1+b2_amd64.deb ... Unpacking libhogweed4:amd64 (3.3-1+b2) ... Selecting previously unselected package libidn11:amd64. Preparing to unpack .../05-libidn11_1.33-1+deb9u1_amd64.deb ... Unpacking libidn11:amd64 (1.33-1+deb9u1) ... Selecting previously unselected package libffi6:amd64. Preparing to unpack .../06-libffi6_3.2.1-6_amd64.deb ... Unpacking libffi6:amd64 (3.2.1-6) ... Selecting previously unselected package libp11-kit0:amd64. Preparing to unpack .../07-libp11-kit0_0.23.3-2_amd64.deb ... Unpacking libp11-kit0:amd64 (0.23.3-2) ... Selecting previously unselected package libtasn1-6:amd64. Preparing to unpack .../08-libtasn1-6_4.10-1.1+deb9u1_amd64.deb ... Unpacking libtasn1-6:amd64 (4.10-1.1+deb9u1) ... Selecting previously unselected package libgnutls30:amd64. Preparing to unpack .../09-libgnutls30_3.5.8-5+deb9u5_amd64.deb ... Unpacking libgnutls30:amd64 (3.5.8-5+deb9u5) ... Selecting previously unselected package libkeyutils1:amd64. Preparing to unpack .../10-libkeyutils1_1.5.9-9_amd64.deb ... Unpacking libkeyutils1:amd64 (1.5.9-9) ... Selecting previously unselected package libkrb5support0:amd64. Preparing to unpack .../11-libkrb5support0_1.15-1+deb9u1_amd64.deb ... Unpacking libkrb5support0:amd64 (1.15-1+deb9u1) ... Selecting previously unselected package libk5crypto3:amd64. Preparing to unpack .../12-libk5crypto3_1.15-1+deb9u1_amd64.deb ... Unpacking libk5crypto3:amd64 (1.15-1+deb9u1) ... Selecting previously unselected package libkrb5-3:amd64. Preparing to unpack .../13-libkrb5-3_1.15-1+deb9u1_amd64.deb ... Unpacking libkrb5-3:amd64 (1.15-1+deb9u1) ... Selecting previously unselected package libgssapi-krb5-2:amd64. Preparing to unpack .../14-libgssapi-krb5-2_1.15-1+deb9u1_amd64.deb ... Unpacking libgssapi-krb5-2:amd64 (1.15-1+deb9u1) ... Selecting previously unselected package libsasl2-modules-db:amd64. Preparing to unpack .../15-libsasl2-modules-db_2.1.27~101-g0780600+dfsg-3+deb9u1_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Selecting previously unselected package libsasl2-2:amd64. Preparing to unpack .../16-libsasl2-2_2.1.27~101-g0780600+dfsg-3+deb9u1_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Selecting previously unselected package libldap-common. Preparing to unpack .../17-libldap-common_2.4.44+dfsg-5+deb9u4_all.deb ... Unpacking libldap-common (2.4.44+dfsg-5+deb9u4) ... Selecting previously unselected package libldap-2.4-2:amd64. Preparing to unpack .../18-libldap-2.4-2_2.4.44+dfsg-5+deb9u4_amd64.deb ... Unpacking libldap-2.4-2:amd64 (2.4.44+dfsg-5+deb9u4) ... Selecting previously unselected package openssl. Preparing to unpack .../19-openssl_1.1.0l-1~deb9u1_amd64.deb ... Unpacking openssl (1.1.0l-1~deb9u1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../20-ca-certificates_20200601~deb9u1_all.deb ... Unpacking ca-certificates (20200601~deb9u1) ... Selecting previously unselected package libaec0:amd64. Preparing to unpack .../21-libaec0_0.3.2-1_amd64.deb ... Unpacking libaec0:amd64 (0.3.2-1) ... Selecting previously unselected package libunistring0:amd64. Preparing to unpack .../22-libunistring0_0.9.6+really0.9.3-0.1_amd64.deb ... Unpacking libunistring0:amd64 (0.9.6+really0.9.3-0.1) ... Selecting previously unselected package libidn2-0:amd64. Preparing to unpack .../23-libidn2-0_0.16-1+deb9u1_amd64.deb ... Unpacking libidn2-0:amd64 (0.16-1+deb9u1) ... Selecting previously unselected package libnghttp2-14:amd64. Preparing to unpack .../24-libnghttp2-14_1.18.1-1+deb9u1_amd64.deb ... Unpacking libnghttp2-14:amd64 (1.18.1-1+deb9u1) ... Selecting previously unselected package libpsl5:amd64. Preparing to unpack .../25-libpsl5_0.17.0-3_amd64.deb ... Unpacking libpsl5:amd64 (0.17.0-3) ... Selecting previously unselected package librtmp1:amd64. Preparing to unpack .../26-librtmp1_2.4+20151223.gitfa8646d.1-1+b1_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-1+b1) ... Selecting previously unselected package libssh2-1:amd64. Preparing to unpack .../27-libssh2-1_1.7.0-1+deb9u1_amd64.deb ... Unpacking libssh2-1:amd64 (1.7.0-1+deb9u1) ... Selecting previously unselected package libcurl3-gnutls:amd64. Preparing to unpack .../28-libcurl3-gnutls_7.52.1-5+deb9u10_amd64.deb ... Unpacking libcurl3-gnutls:amd64 (7.52.1-5+deb9u10) ... Selecting previously unselected package libquadmath0:amd64. Preparing to unpack .../29-libquadmath0_6.3.0-18+deb9u1_amd64.deb ... Unpacking libquadmath0:amd64 (6.3.0-18+deb9u1) ... Selecting previously unselected package libgfortran3:amd64. Preparing to unpack .../30-libgfortran3_6.3.0-18+deb9u1_amd64.deb ... Unpacking libgfortran3:amd64 (6.3.0-18+deb9u1) ... Selecting previously unselected package libgomp1:amd64. Preparing to unpack .../31-libgomp1_6.3.0-18+deb9u1_amd64.deb ... Unpacking libgomp1:amd64 (6.3.0-18+deb9u1) ... Selecting previously unselected package libsz2:amd64. Preparing to unpack .../32-libsz2_0.3.2-1_amd64.deb ... Unpacking libsz2:amd64 (0.3.2-1) ... Selecting previously unselected package libhdf5-100:amd64. Preparing to unpack .../33-libhdf5-100_1.10.0-patch1+docs-3+deb9u1_amd64.deb ... Unpacking libhdf5-100:amd64 (1.10.0-patch1+docs-3+deb9u1) ... Selecting previously unselected package libhts1:amd64. Preparing to unpack .../34-libhts1_1.3.2-2_amd64.deb ... Unpacking libhts1:amd64 (1.3.2-2) ... Selecting previously unselected package libsasl2-modules:amd64. Preparing to unpack .../35-libsasl2-modules_2.1.27~101-g0780600+dfsg-3+deb9u1_amd64.deb ... Unpacking libsasl2-modules:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Selecting previously unselected package nanopolish. Preparing to unpack .../36-nanopolish_0.5.0-1+b1_amd64.deb ... Unpacking nanopolish (0.5.0-1+b1) ... Selecting previously unselected package publicsuffix. Preparing to unpack .../37-publicsuffix_20190415.1030-0+deb9u1_all.deb ... Unpacking publicsuffix (20190415.1030-0+deb9u1) ... Setting up libquadmath0:amd64 (6.3.0-18+deb9u1) ... Setting up libgomp1:amd64 (6.3.0-18+deb9u1) ... Setting up libnettle6:amd64 (3.3-1+b2) ... Setting up libaec0:amd64 (0.3.2-1) ... Setting up libnghttp2-14:amd64 (1.18.1-1+deb9u1) ... Setting up libldap-common (2.4.44+dfsg-5+deb9u4) ... Setting up libgfortran3:amd64 (6.3.0-18+deb9u1) ... Setting up libsasl2-modules-db:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Setting up libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Setting up libtasn1-6:amd64 (4.10-1.1+deb9u1) ... Setting up libgmp10:amd64 (2:6.1.2+dfsg-1) ... Setting up libssh2-1:amd64 (1.7.0-1+deb9u1) ... Setting up krb5-locales (1.15-1+deb9u1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up publicsuffix (20190415.1030-0+deb9u1) ... Setting up libunistring0:amd64 (0.9.6+really0.9.3-0.1) ... Setting up libssl1.1:amd64 (1.1.0l-1~deb9u1) ... Setting up openssl (1.1.0l-1~deb9u1) ... Setting up libffi6:amd64 (3.2.1-6) ... Setting up libkeyutils1:amd64 (1.5.9-9) ... Setting up libsasl2-modules:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Setting up ca-certificates (20200601~deb9u1) ... Updating certificates in /etc/ssl/certs... 126 added, 0 removed; done. Setting up libidn11:amd64 (1.33-1+deb9u1) ... Setting up libsz2:amd64 (0.3.2-1) ... Setting up libidn2-0:amd64 (0.16-1+deb9u1) ... Setting up libhdf5-100:amd64 (1.10.0-patch1+docs-3+deb9u1) ... Setting up libpsl5:amd64 (0.17.0-3) ... Setting up libkrb5support0:amd64 (1.15-1+deb9u1) ... Setting up libhogweed4:amd64 (3.3-1+b2) ... Setting up libp11-kit0:amd64 (0.23.3-2) ... Setting up libk5crypto3:amd64 (1.15-1+deb9u1) ... Setting up libgnutls30:amd64 (3.5.8-5+deb9u5) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-1+b1) ... Setting up libldap-2.4-2:amd64 (2.4.44+dfsg-5+deb9u4) ... Setting up libkrb5-3:amd64 (1.15-1+deb9u1) ... Setting up libgssapi-krb5-2:amd64 (1.15-1+deb9u1) ... Setting up libcurl3-gnutls:amd64 (7.52.1-5+deb9u10) ... Setting up libhts1:amd64 (1.3.2-2) ... Setting up nanopolish (0.5.0-1+b1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Processing triggers for ca-certificates (20200601~deb9u1) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 0m10.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'apt-get', '-y', 'install', 'nanopolish'] 0m10.9s INFO: Running scripts post_install 0m10.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/post_install_exceptions'] 0m10.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/post_install_exceptions'] 0m10.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmphddufz4b'] 0m11.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmphddufz4b'] 0m11.3s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmphddufz4b to buster 0m11.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ buster main 0m11.3s INFO: Running scripts pre_distupgrade 0m11.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m11.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m11.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_distupgrade_exceptions'] 0m11.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_distupgrade_exceptions'] 0m11.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'apt-get', 'update'] 0m14.7s DUMP: Get:1 http://deb.debian.org/debian buster InRelease [122 kB] Get:2 http://deb.debian.org/debian buster/main amd64 Packages [7909 kB] Get:3 http://deb.debian.org/debian buster/main Translation-en [5969 kB] Fetched 14.0 MB in 2s (5338 kB/s) Reading package lists... 0m14.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'apt-get', 'update'] 0m14.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'apt-get', '-y', 'upgrade'] 0m19.3s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages have been kept back: apt bash ca-certificates coreutils dash dpkg e2fslibs e2fsprogs gpgv libapt-pkg5.0 libblkid1 libc-bin libc6 libcomerr2 libcurl3-gnutls libfdisk1 libgcc1 libgnutls30 libgomp1 libgpg-error0 libgssapi-krb5-2 libidn2-0 libk5crypto3 libkrb5-3 libkrb5support0 libldap-2.4-2 libmount1 libncursesw5 libp11-kit0 libpam-modules libpam-modules-bin libpsl5 libquadmath0 libsmartcols1 libss2 libssl1.1 libstdc++6 libsystemd0 libtinfo5 libudev1 libuuid1 login mount nanopolish ncurses-base ncurses-bin openssl perl-base util-linux The following packages will be upgraded: adduser base-files base-passwd bsdutils debconf debian-archive-keyring debianutils diffutils findutils grep gzip hostname init-system-helpers krb5-locales libacl1 libaec0 libattr1 libaudit-common libaudit1 libbz2-1.0 libcap-ng0 libdb5.3 libdebconfclient0 libffi6 libgcrypt20 libgmp10 libhogweed4 libidn11 libkeyutils1 libldap-common liblz4-1 liblzma5 libnettle6 libnghttp2-14 libpam-runtime libpam0g libpcre3 librtmp1 libsasl2-2 libsasl2-modules libsasl2-modules-db libselinux1 libsemanage-common libsemanage1 libsepol1 libssh2-1 libsz2 libtasn1-6 multiarch-support passwd publicsuffix sed sensible-utils sysvinit-utils tar zlib1g 56 upgraded, 0 newly installed, 0 to remove and 49 not upgraded. Need to get 9482 kB of archives. After this operation, 1091 kB of additional disk space will be used. Get:1 http://deb.debian.org/debian buster/main amd64 base-files amd64 10.3+deb10u13 [69.9 kB] Get:2 http://deb.debian.org/debian buster/main amd64 bsdutils amd64 1:2.33.1-0.1 [121 kB] Get:3 http://deb.debian.org/debian buster/main amd64 debianutils amd64 4.8.6.1 [100 kB] Get:4 http://deb.debian.org/debian buster/main amd64 diffutils amd64 1:3.7-3 [371 kB] Get:5 http://deb.debian.org/debian buster/main amd64 findutils amd64 4.6.0+git+20190209-2 [684 kB] Get:6 http://deb.debian.org/debian buster/main amd64 grep amd64 3.3-1 [373 kB] Get:7 http://deb.debian.org/debian buster/main amd64 gzip amd64 1.9-3+deb10u1 [128 kB] Get:8 http://deb.debian.org/debian buster/main amd64 hostname amd64 3.21 [14.8 kB] Get:9 http://deb.debian.org/debian buster/main amd64 sed amd64 4.7-1 [310 kB] Get:10 http://deb.debian.org/debian buster/main amd64 tar amd64 1.30+dfsg-6 [780 kB] Get:11 http://deb.debian.org/debian buster/main amd64 libdebconfclient0 amd64 0.249 [49.1 kB] Get:12 http://deb.debian.org/debian buster/main amd64 base-passwd amd64 3.5.46 [56.7 kB] Get:13 http://deb.debian.org/debian buster/main amd64 init-system-helpers all 1.56+nmu1 [46.8 kB] Get:14 http://deb.debian.org/debian buster/main amd64 sysvinit-utils amd64 2.93-8 [78.4 kB] Get:15 http://deb.debian.org/debian buster/main amd64 debconf all 1.5.71+deb10u1 [145 kB] Get:16 http://deb.debian.org/debian buster/main amd64 libpam-runtime all 1.3.1-5 [211 kB] Get:17 http://deb.debian.org/debian buster/main amd64 libaudit-common all 1:2.8.4-3 [22.4 kB] Get:18 http://deb.debian.org/debian buster/main amd64 libcap-ng0 amd64 0.7.9-2 [14.3 kB] Get:19 http://deb.debian.org/debian buster/main amd64 libaudit1 amd64 1:2.8.4-3 [57.3 kB] Get:20 http://deb.debian.org/debian buster/main amd64 libpam0g amd64 1.3.1-5 [126 kB] Get:21 http://deb.debian.org/debian buster/main amd64 libpcre3 amd64 2:8.39-12 [341 kB] Get:22 http://deb.debian.org/debian buster/main amd64 libselinux1 amd64 2.8-1+b1 [86.9 kB] Get:23 http://deb.debian.org/debian buster/main amd64 libsepol1 amd64 2.8-1 [263 kB] Get:24 http://deb.debian.org/debian buster/main amd64 libsemanage-common all 2.8-2 [17.7 kB] Get:25 http://deb.debian.org/debian buster/main amd64 libsemanage1 amd64 2.8-2 [96.5 kB] Get:26 http://deb.debian.org/debian buster/main amd64 libbz2-1.0 amd64 1.0.6-9.2~deb10u1 [45.3 kB] Get:27 http://deb.debian.org/debian buster/main amd64 passwd amd64 1:4.5-1.1 [1005 kB] Get:28 http://deb.debian.org/debian buster/main amd64 adduser all 3.118 [240 kB] Get:29 http://deb.debian.org/debian buster/main amd64 debian-archive-keyring all 2019.1+deb10u1 [93.5 kB] Get:30 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get:31 http://deb.debian.org/debian buster/main amd64 libattr1 amd64 1:2.4.48-4 [21.3 kB] Get:32 http://deb.debian.org/debian buster/main amd64 libacl1 amd64 2.2.53-4 [30.4 kB] Get:33 http://deb.debian.org/debian buster/main amd64 libdb5.3 amd64 5.3.28+dfsg1-0.5 [683 kB] Get:34 http://deb.debian.org/debian buster/main amd64 libgcrypt20 amd64 1.8.4-5+deb10u1 [556 kB] Get:35 http://deb.debian.org/debian buster/main amd64 liblz4-1 amd64 1.8.3-1+deb10u1 [53.3 kB] Get:36 http://deb.debian.org/debian buster/main amd64 liblzma5 amd64 5.2.4-1+deb10u1 [153 kB] Get:37 http://deb.debian.org/debian buster/main amd64 zlib1g amd64 1:1.2.11.dfsg-1+deb10u1 [90.8 kB] Get:38 http://deb.debian.org/debian buster/main amd64 krb5-locales all 1.17-3+deb10u4 [95.6 kB] Get:39 http://deb.debian.org/debian buster/main amd64 libaec0 amd64 1.0.2-1 [20.1 kB] Get:40 http://deb.debian.org/debian buster/main amd64 libffi6 amd64 3.2.1-9 [20.8 kB] Get:41 http://deb.debian.org/debian buster/main amd64 libgmp10 amd64 2:6.1.2+dfsg-4+deb10u1 [251 kB] Get:42 http://deb.debian.org/debian buster/main amd64 libhogweed4 amd64 3.4.1-1+deb10u1 [141 kB] Get:43 http://deb.debian.org/debian buster/main amd64 libnettle6 amd64 3.4.1-1+deb10u1 [215 kB] Get:44 http://deb.debian.org/debian buster/main amd64 libidn11 amd64 1.33-2.2 [116 kB] Get:45 http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get:46 http://deb.debian.org/debian buster/main amd64 libldap-common all 2.4.47+dfsg-3+deb10u7 [90.1 kB] Get:47 http://deb.debian.org/debian buster/main amd64 libnghttp2-14 amd64 1.36.0-2+deb10u1 [85.0 kB] Get:48 http://deb.debian.org/debian buster/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [60.5 kB] Get:49 http://deb.debian.org/debian buster/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-1+deb10u2 [69.2 kB] Get:50 http://deb.debian.org/debian buster/main amd64 libsasl2-2 amd64 2.1.27+dfsg-1+deb10u2 [106 kB] Get:51 http://deb.debian.org/debian buster/main amd64 libsasl2-modules amd64 2.1.27+dfsg-1+deb10u2 [104 kB] Get:52 http://deb.debian.org/debian buster/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get:53 http://deb.debian.org/debian buster/main amd64 libsz2 amd64 1.0.2-1 [6676 B] Get:54 http://deb.debian.org/debian buster/main amd64 libtasn1-6 amd64 4.13-3 [51.9 kB] Get:55 http://deb.debian.org/debian buster/main amd64 multiarch-support amd64 2.28-10+deb10u1 [216 kB] Get:56 http://deb.debian.org/debian buster/main amd64 publicsuffix all 20220811.1734-0+deb10u1 [127 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 9482 kB in 0s (54.8 MB/s) (Reading database ... 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Preparing to unpack .../10-librtmp1_2.4+20151223.gitfa8646d.1-2_amd64.deb ... Unpacking librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) over (2.4+20151223.gitfa8646d.1-1+b1) ... Preparing to unpack .../11-libsasl2-modules-db_2.1.27+dfsg-1+deb10u2_amd64.deb ... Unpacking libsasl2-modules-db:amd64 (2.1.27+dfsg-1+deb10u2) over (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Preparing to unpack .../12-libsasl2-2_2.1.27+dfsg-1+deb10u2_amd64.deb ... Unpacking libsasl2-2:amd64 (2.1.27+dfsg-1+deb10u2) over (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Preparing to unpack .../13-libsasl2-modules_2.1.27+dfsg-1+deb10u2_amd64.deb ... Unpacking libsasl2-modules:amd64 (2.1.27+dfsg-1+deb10u2) over (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Preparing to unpack .../14-libssh2-1_1.8.0-2.1_amd64.deb ... Unpacking libssh2-1:amd64 (1.8.0-2.1) over (1.7.0-1+deb9u1) ... Preparing to unpack .../15-libsz2_1.0.2-1_amd64.deb ... Unpacking libsz2:amd64 (1.0.2-1) over (0.3.2-1) ... Preparing to unpack .../16-libtasn1-6_4.13-3_amd64.deb ... Unpacking libtasn1-6:amd64 (4.13-3) over (4.10-1.1+deb9u1) ... Preparing to unpack .../17-multiarch-support_2.28-10+deb10u1_amd64.deb ... Unpacking multiarch-support (2.28-10+deb10u1) over (2.24-11+deb9u4) ... Preparing to unpack .../18-publicsuffix_20220811.1734-0+deb10u1_all.deb ... Unpacking publicsuffix (20220811.1734-0+deb10u1) over (20190415.1030-0+deb9u1) ... Setting up libnettle6:amd64 (3.4.1-1+deb10u1) ... Setting up libaec0:amd64 (1.0.2-1) ... Setting up libnghttp2-14:amd64 (1.36.0-2+deb10u1) ... Setting up libldap-common (2.4.47+dfsg-3+deb10u7) ... Setting up multiarch-support (2.28-10+deb10u1) ... Setting up libsasl2-modules-db:amd64 (2.1.27+dfsg-1+deb10u2) ... Setting up libsasl2-2:amd64 (2.1.27+dfsg-1+deb10u2) ... Setting up libtasn1-6:amd64 (4.13-3) ... Setting up libgmp10:amd64 (2:6.1.2+dfsg-4+deb10u1) ... Setting up libssh2-1:amd64 (1.8.0-2.1) ... Setting up krb5-locales (1.17-3+deb10u4) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up publicsuffix (20220811.1734-0+deb10u1) ... Setting up libffi6:amd64 (3.2.1-9) ... Setting up libkeyutils1:amd64 (1.6-6) ... Setting up libsasl2-modules:amd64 (2.1.27+dfsg-1+deb10u2) ... Setting up libidn11:amd64 (1.33-2.2) ... Setting up libsz2:amd64 (1.0.2-1) ... Setting up libhogweed4:amd64 (3.4.1-1+deb10u1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... 0m19.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'apt-get', '-y', 'upgrade'] 0m19.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'apt-get', '-yf', 'dist-upgrade'] 0m45.8s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: libgfortran3 libhts1 libidn11 libunistring0 Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libhdf5-100 The following NEW packages will be installed: bzip2 e2fsprogs-l10n fdisk file gcc-8-base gsfonts libblas3 libcom-err2 libdeflate0 libexpat1 libext2fs2 libfreetype6 libgdbm-compat4 libgdbm6 libgfortran5 libgpg-error-l10n libgpm2 libhdf5-103 libhts2 libimagequant0 libjbig0 libjpeg62-turbo liblapack3 liblcms2-2 liblmdb0 libmagic-mgc libmagic1 libmbedcrypto3 libmbedtls12 libmbedx509-0 libncursesw6 libperl5.28 libpng16-16 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libreadline7 libseccomp2 libsqlite3-0 libtiff5 libtinfo6 libunistring2 libwebp6 libwebpdemux2 libwebpmux3 libzstd1 mime-support ncbi-blast+ ncbi-data netbase perl perl-modules-5.28 python python-biopython python-biopython-doc python-minimal python-numpy python-olefile python-pil python-pkg-resources python-pysam python-renderpm python-reportlab python-reportlab-accel python2 python2-minimal python2.7 python2.7-minimal readline-common xz-utils The following packages will be upgraded: apt bash ca-certificates coreutils dash dpkg e2fslibs e2fsprogs gpgv libapt-pkg5.0 libblkid1 libc-bin libc6 libcomerr2 libcurl3-gnutls libfdisk1 libgcc1 libgnutls30 libgomp1 libgpg-error0 libgssapi-krb5-2 libidn2-0 libk5crypto3 libkrb5-3 libkrb5support0 libldap-2.4-2 libmount1 libncursesw5 libp11-kit0 libpam-modules libpam-modules-bin libpsl5 libquadmath0 libsmartcols1 libss2 libssl1.1 libstdc++6 libsystemd0 libtinfo5 libudev1 libuuid1 login mount nanopolish ncurses-base ncurses-bin openssl perl-base util-linux 49 upgraded, 71 newly installed, 1 to remove and 0 not upgraded. Need to get 88.6 MB of archives. After this operation, 238 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian buster/main amd64 libc6 amd64 2.28-10+deb10u1 [2863 kB] Get:2 http://deb.debian.org/debian buster/main amd64 libc-bin amd64 2.28-10+deb10u1 [795 kB] Get:3 http://deb.debian.org/debian buster/main amd64 gcc-8-base amd64 8.3.0-6 [191 kB] Get:4 http://deb.debian.org/debian buster/main amd64 libgcc1 amd64 1:8.3.0-6 [40.6 kB] Get:5 http://deb.debian.org/debian buster/main amd64 libtinfo6 amd64 6.1+20181013-2+deb10u2 [325 kB] Get:6 http://deb.debian.org/debian buster/main amd64 bash amd64 5.0-4 [1378 kB] Get:7 http://deb.debian.org/debian buster/main amd64 coreutils amd64 8.30-3 [2708 kB] Get:8 http://deb.debian.org/debian buster/main amd64 libzstd1 amd64 1.3.8+dfsg-3+deb10u2 [237 kB] Get:9 http://deb.debian.org/debian buster/main amd64 libunistring2 amd64 0.9.10-1 [381 kB] Get:10 http://deb.debian.org/debian buster/main amd64 libidn2-0 amd64 2.0.5-1+deb10u1 [76.7 kB] Get:11 http://deb.debian.org/debian buster/main amd64 libp11-kit0 amd64 0.23.15-2+deb10u1 [316 kB] Get:12 http://deb.debian.org/debian buster/main amd64 libgnutls30 amd64 3.6.7-4+deb10u8 [1126 kB] Get:13 http://deb.debian.org/debian buster/main amd64 libseccomp2 amd64 2.3.3-4 [41.4 kB] Get:14 http://deb.debian.org/debian buster/main amd64 libgpg-error0 amd64 1.35-1 [71.1 kB] Get:15 http://deb.debian.org/debian buster/main amd64 gpgv amd64 2.2.12-1+deb10u2 [584 kB] Get:16 http://deb.debian.org/debian buster/main amd64 libstdc++6 amd64 8.3.0-6 [395 kB] Get:17 http://deb.debian.org/debian buster/main amd64 libapt-pkg5.0 amd64 1.8.2.3 [967 kB] Get:18 http://deb.debian.org/debian buster/main amd64 apt amd64 1.8.2.3 [1418 kB] Get:19 http://deb.debian.org/debian buster/main amd64 libsystemd0 amd64 241-7~deb10u8 [331 kB] Get:20 http://deb.debian.org/debian buster/main amd64 libudev1 amd64 241-7~deb10u8 [151 kB] Get:21 http://deb.debian.org/debian buster/main amd64 dpkg amd64 1.19.8 [2210 kB] Get:22 http://deb.debian.org/debian buster/main amd64 dash amd64 0.5.10.2-5 [112 kB] Get:23 http://deb.debian.org/debian buster/main amd64 libcom-err2 amd64 1.44.5-1+deb10u3 [68.4 kB] Get:24 http://deb.debian.org/debian buster/main amd64 libcomerr2 amd64 1.44.5-1+deb10u3 [64.2 kB] Get:25 http://deb.debian.org/debian buster/main amd64 libext2fs2 amd64 1.44.5-1+deb10u3 [221 kB] Get:26 http://deb.debian.org/debian buster/main amd64 e2fslibs amd64 1.44.5-1+deb10u3 [64.2 kB] Get:27 http://deb.debian.org/debian buster/main amd64 e2fsprogs amd64 1.44.5-1+deb10u3 [576 kB] Get:28 http://deb.debian.org/debian buster/main amd64 libuuid1 amd64 2.33.1-0.1 [78.3 kB] Get:29 http://deb.debian.org/debian buster/main amd64 libblkid1 amd64 2.33.1-0.1 [195 kB] Get:30 http://deb.debian.org/debian buster/main amd64 libsmartcols1 amd64 2.33.1-0.1 [150 kB] Get:31 http://deb.debian.org/debian buster/main amd64 libfdisk1 amd64 2.33.1-0.1 [234 kB] Get:32 http://deb.debian.org/debian buster/main amd64 libncursesw6 amd64 6.1+20181013-2+deb10u2 [132 kB] Get:33 http://deb.debian.org/debian buster/main amd64 libmount1 amd64 2.33.1-0.1 [207 kB] Get:34 http://deb.debian.org/debian buster/main amd64 fdisk amd64 2.33.1-0.1 [179 kB] Get:35 http://deb.debian.org/debian buster/main amd64 login amd64 1:4.5-1.1 [751 kB] Get:36 http://deb.debian.org/debian buster/main amd64 util-linux amd64 2.33.1-0.1 [1062 kB] Get:37 http://deb.debian.org/debian buster/main amd64 mount amd64 2.33.1-0.1 [174 kB] Get:38 http://deb.debian.org/debian buster/main amd64 ncurses-bin amd64 6.1+20181013-2+deb10u2 [406 kB] Get:39 http://deb.debian.org/debian buster/main amd64 perl-base amd64 5.28.1-6+deb10u1 [1514 kB] Get:40 http://deb.debian.org/debian buster/main amd64 libtinfo5 amd64 6.1+20181013-2+deb10u2 [321 kB] Get:41 http://deb.debian.org/debian buster/main amd64 libncursesw5 amd64 6.1+20181013-2+deb10u2 [118 kB] Get:42 http://deb.debian.org/debian buster/main amd64 ncurses-base all 6.1+20181013-2+deb10u2 [258 kB] Get:43 http://deb.debian.org/debian buster/main amd64 libgomp1 amd64 8.3.0-6 [75.8 kB] Get:44 http://deb.debian.org/debian buster/main amd64 libquadmath0 amd64 8.3.0-6 [133 kB] Get:45 http://deb.debian.org/debian buster/main amd64 libgfortran5 amd64 8.3.0-6 [581 kB] Get:46 http://deb.debian.org/debian buster/main amd64 nanopolish amd64 0.11.0-2 [2215 kB] Get:47 http://deb.debian.org/debian buster/main amd64 libhdf5-103 amd64 1.10.4+repack-10 [1325 kB] Get:48 http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u4 [158 kB] Get:49 http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u4 [369 kB] Get:50 http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u4 [122 kB] Get:51 http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u4 [65.9 kB] Get:52 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1n-0+deb10u3 [1551 kB] Get:53 http://deb.debian.org/debian buster/main amd64 libldap-2.4-2 amd64 2.4.47+dfsg-3+deb10u7 [224 kB] Get:54 http://deb.debian.org/debian buster/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get:55 http://deb.debian.org/debian buster/main amd64 libcurl3-gnutls amd64 7.64.0-4+deb10u2 [330 kB] Get:56 http://deb.debian.org/debian buster/main amd64 libdeflate0 amd64 1.2-1 [55.4 kB] Get:57 http://deb.debian.org/debian buster/main amd64 libhts2 amd64 1.9-12~deb10u1 [305 kB] Get:58 http://deb.debian.org/debian buster/main amd64 libpython2.7-minimal amd64 2.7.16-2+deb10u1 [395 kB] Get:59 http://deb.debian.org/debian buster/main amd64 python2.7-minimal amd64 2.7.16-2+deb10u1 [1369 kB] Get:60 http://deb.debian.org/debian buster/main amd64 python2-minimal amd64 2.7.16-1 [41.4 kB] Get:61 http://deb.debian.org/debian buster/main amd64 python-minimal amd64 2.7.16-1 [21.0 kB] Get:62 http://deb.debian.org/debian buster/main amd64 mime-support all 3.62 [37.2 kB] Get:63 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u4 [108 kB] Get:64 http://deb.debian.org/debian buster/main amd64 readline-common all 7.0-5 [70.6 kB] Get:65 http://deb.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get:66 http://deb.debian.org/debian buster/main amd64 libsqlite3-0 amd64 3.27.2-3+deb10u1 [641 kB] Get:67 http://deb.debian.org/debian buster/main amd64 libpython2.7-stdlib amd64 2.7.16-2+deb10u1 [1912 kB] Get:68 http://deb.debian.org/debian buster/main amd64 python2.7 amd64 2.7.16-2+deb10u1 [305 kB] Get:69 http://deb.debian.org/debian buster/main amd64 libpython2-stdlib amd64 2.7.16-1 [20.8 kB] Get:70 http://deb.debian.org/debian buster/main amd64 libpython-stdlib amd64 2.7.16-1 [20.8 kB] Get:71 http://deb.debian.org/debian buster/main amd64 python2 amd64 2.7.16-1 [41.6 kB] Get:72 http://deb.debian.org/debian buster/main amd64 python amd64 2.7.16-1 [22.8 kB] Get:73 http://deb.debian.org/debian buster/main amd64 libpam-modules-bin amd64 1.3.1-5 [107 kB] Get:74 http://deb.debian.org/debian buster/main amd64 libpam-modules amd64 1.3.1-5 [309 kB] Get:75 http://deb.debian.org/debian buster/main amd64 perl-modules-5.28 all 5.28.1-6+deb10u1 [2873 kB] Get:76 http://deb.debian.org/debian buster/main amd64 libgdbm6 amd64 1.18.1-4 [64.7 kB] Get:77 http://deb.debian.org/debian buster/main amd64 libgdbm-compat4 amd64 1.18.1-4 [44.1 kB] Get:78 http://deb.debian.org/debian buster/main amd64 libperl5.28 amd64 5.28.1-6+deb10u1 [3894 kB] Get:79 http://deb.debian.org/debian buster/main amd64 perl amd64 5.28.1-6+deb10u1 [204 kB] Get:80 http://deb.debian.org/debian buster/main amd64 libss2 amd64 1.44.5-1+deb10u3 [72.9 kB] Get:81 http://deb.debian.org/debian buster/main amd64 netbase all 5.6 [19.4 kB] Get:82 http://deb.debian.org/debian buster/main amd64 bzip2 amd64 1.0.6-9.2~deb10u1 [48.4 kB] Get:83 http://deb.debian.org/debian buster/main amd64 libmagic-mgc amd64 1:5.35-4+deb10u2 [242 kB] Get:84 http://deb.debian.org/debian buster/main amd64 libmagic1 amd64 1:5.35-4+deb10u2 [118 kB] Get:85 http://deb.debian.org/debian buster/main amd64 file amd64 1:5.35-4+deb10u2 [66.4 kB] Get:86 http://deb.debian.org/debian buster/main amd64 xz-utils amd64 5.2.4-1+deb10u1 [183 kB] Get:87 http://deb.debian.org/debian buster/main amd64 openssl amd64 1.1.1n-0+deb10u3 [855 kB] Get:88 http://deb.debian.org/debian buster/main amd64 ca-certificates all 20200601~deb10u2 [166 kB] Get:89 http://deb.debian.org/debian buster/main amd64 e2fsprogs-l10n all 1.44.5-1+deb10u3 [504 kB] Get:90 http://deb.debian.org/debian buster/main amd64 gsfonts all 1:8.11+urwcyr1.0.7~pre44-4.4 [3125 kB] Get:91 http://deb.debian.org/debian buster/main amd64 libblas3 amd64 3.8.0-2 [148 kB] Get:92 http://deb.debian.org/debian buster/main amd64 libpng16-16 amd64 1.6.36-6 [292 kB] Get:93 http://deb.debian.org/debian buster/main amd64 libfreetype6 amd64 2.9.1-3+deb10u3 [380 kB] Get:94 http://deb.debian.org/debian buster/main amd64 libgpg-error-l10n all 1.35-1 [97.6 kB] Get:95 http://deb.debian.org/debian buster/main amd64 libgpm2 amd64 1.20.7-5 [35.1 kB] Get:96 http://deb.debian.org/debian buster/main amd64 libimagequant0 amd64 2.12.2-1.1 [32.5 kB] Get:97 http://deb.debian.org/debian buster/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get:98 http://deb.debian.org/debian buster/main amd64 libjpeg62-turbo amd64 1:1.5.2-2+deb10u1 [133 kB] Get:99 http://deb.debian.org/debian buster/main amd64 liblapack3 amd64 3.8.0-2 [2110 kB] Get:100 http://deb.debian.org/debian buster/main amd64 liblcms2-2 amd64 2.9-3 [145 kB] Get:101 http://deb.debian.org/debian buster/main amd64 liblmdb0 amd64 0.9.22-1 [45.0 kB] Get:102 http://deb.debian.org/debian buster/main amd64 libmbedcrypto3 amd64 2.16.0-1 [209 kB] Get:103 http://deb.debian.org/debian buster/main amd64 libmbedx509-0 amd64 2.16.0-1 [91.4 kB] Get:104 http://deb.debian.org/debian buster/main amd64 libmbedtls12 amd64 2.16.0-1 [130 kB] Get:105 http://deb.debian.org/debian buster/main amd64 libwebp6 amd64 0.6.1-2+deb10u1 [261 kB] Get:106 http://deb.debian.org/debian buster/main amd64 libtiff5 amd64 4.1.0+git191117-2~deb10u4 [271 kB] Get:107 http://deb.debian.org/debian buster/main amd64 libwebpdemux2 amd64 0.6.1-2+deb10u1 [87.6 kB] Get:108 http://deb.debian.org/debian buster/main amd64 libwebpmux3 amd64 0.6.1-2+deb10u1 [97.8 kB] Get:109 http://deb.debian.org/debian buster/main amd64 ncbi-data all 6.1.20170106+dfsg1-0+deb10u2 [3552 kB] Get:110 http://deb.debian.org/debian buster/main amd64 ncbi-blast+ amd64 2.8.1-1+deb10u1 [10.9 MB] Get:111 http://deb.debian.org/debian buster/main amd64 python-pkg-resources all 40.8.0-1 [182 kB] Get:112 http://deb.debian.org/debian buster/main amd64 python-numpy amd64 1:1.16.2-1 [2101 kB] Get:113 http://deb.debian.org/debian buster/main amd64 python-pil amd64 5.4.1-2+deb10u3 [395 kB] Get:114 http://deb.debian.org/debian buster/main amd64 python-reportlab-accel amd64 3.5.13-1+deb10u1 [39.8 kB] Get:115 http://deb.debian.org/debian buster/main amd64 python-reportlab all 3.5.13-1+deb10u1 [545 kB] Get:116 http://deb.debian.org/debian buster/main amd64 python-biopython amd64 1.73+dfsg-1 [1334 kB] Get:117 http://deb.debian.org/debian buster/main amd64 python-biopython-doc all 1.73+dfsg-1 [14.1 MB] Get:118 http://deb.debian.org/debian buster/main amd64 python-olefile all 0.46-1 [35.9 kB] Get:119 http://deb.debian.org/debian buster/main amd64 python-pysam amd64 0.15.2+ds-2 [1629 kB] Get:120 http://deb.debian.org/debian buster/main amd64 python-renderpm amd64 3.5.13-1+deb10u1 [76.6 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 88.6 MB in 0s (129 MB/s) (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5091 files and directories currently installed.) Preparing to unpack .../libunistring2_0.9.10-1_amd64.deb ... Unpacking libunistring2:amd64 (0.9.10-1) ... Setting up libunistring2:amd64 (0.9.10-1) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5122 files and directories currently installed.) Preparing to unpack .../libp11-kit0_0.23.15-2+deb10u1_amd64.deb ... Unpacking libp11-kit0:amd64 (0.23.15-2+deb10u1) over (0.23.3-2) ... Setting up libp11-kit0:amd64 (0.23.15-2+deb10u1) ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 5170 files and directories currently installed.) Preparing to unpack .../libgomp1_8.3.0-6_amd64.deb ... Unpacking libgomp1:amd64 (8.3.0-6) over (6.3.0-18+deb9u1) ... Preparing to unpack .../libquadmath0_8.3.0-6_amd64.deb ... Unpacking libquadmath0:amd64 (8.3.0-6) over (6.3.0-18+deb9u1) ... Selecting previously unselected package libgfortran5:amd64. Preparing to unpack .../libgfortran5_8.3.0-6_amd64.deb ... Unpacking libgfortran5:amd64 (8.3.0-6) ... 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Setting up e2fslibs:amd64 (1.44.5-1+deb10u3) ... Setting up libmagic-mgc (1:5.35-4+deb10u2) ... Setting up e2fsprogs-l10n (1.44.5-1+deb10u3) ... Setting up libssl1.1:amd64 (1.1.1n-0+deb10u3) ... Setting up libsqlite3-0:amd64 (3.27.2-3+deb10u1) ... Setting up libmagic1:amd64 (1:5.35-4+deb10u2) ... Setting up libdeflate0:amd64 (1.2-1) ... Setting up libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u7) ... Setting up file (1:5.35-4+deb10u2) ... Setting up libgomp1:amd64 (8.3.0-6) ... Setting up bzip2 (1.0.6-9.2~deb10u1) ... Setting up libjbig0:amd64 (2.1-3.1+b2) ... Setting up libkrb5support0:amd64 (1.17-3+deb10u4) ... Setting up libjpeg62-turbo:amd64 (1:1.5.2-2+deb10u1) ... Setting up gsfonts (1:8.11+urwcyr1.0.7~pre44-4.4) ... Setting up xz-utils (5.2.4-1+deb10u1) ... update-alternatives: using /usr/bin/xz to provide /usr/bin/lzma (lzma) in auto mode 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 libwebp6:amd64 (0.6.1-2+deb10u1) ... Setting up util-linux (2.33.1-0.1) ... update-alternatives: warning: alternative /usr/bin/pg (part of link group pager) doesn't exist; removing from list of alternatives Setting up libk5crypto3:amd64 (1.17-3+deb10u4) ... Setting up libgfortran5:amd64 (8.3.0-6) ... Setting up mount (2.33.1-0.1) ... Setting up libcomerr2:amd64 (1.44.5-1+deb10u3) ... Setting up python-biopython-doc (1.73+dfsg-1) ... Setting up libmbedcrypto3:amd64 (2.16.0-1) ... Setting up netbase (5.6) ... Setting up libkrb5-3:amd64 (1.17-3+deb10u4) ... Setting up libtiff5:amd64 (4.1.0+git191117-2~deb10u4) ... Setting up openssl (1.1.1n-0+deb10u3) ... Installing new version of config file /etc/ssl/openssl.cnf ... Setting up libwebpmux3:amd64 (0.6.1-2+deb10u1) ... Setting up libgpg-error-l10n (1.35-1) ... Setting up readline-common (7.0-5) ... Setting up libreadline7:amd64 (7.0-5) ... Setting up libgdbm6:amd64 (1.18.1-4) ... Setting up libmbedx509-0:amd64 (2.16.0-1) ... Setting up libwebpdemux2:amd64 (0.6.1-2+deb10u1) ... Setting up libmbedtls12:amd64 (2.16.0-1) ... Setting up libpython2.7-stdlib:amd64 (2.7.16-2+deb10u1) ... Setting up ca-certificates (20200601~deb10u2) ... Updating certificates in /etc/ssl/certs... 11 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 libfreetype6:amd64 (2.9.1-3+deb10u3) ... Setting up libhdf5-103:amd64 (1.10.4+repack-10) ... Setting up libgssapi-krb5-2:amd64 (1.17-3+deb10u4) ... Setting up libgdbm-compat4:amd64 (1.18.1-4) ... Setting up libperl5.28:amd64 (5.28.1-6+deb10u1) ... 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 python2.7 (2.7.16-2+deb10u1) ... Setting up libpython2-stdlib:amd64 (2.7.16-1) ... Setting up libcurl3-gnutls:amd64 (7.64.0-4+deb10u2) ... Setting up python2 (2.7.16-1) ... Setting up libpython-stdlib:amd64 (2.7.16-1) ... Setting up perl (5.28.1-6+deb10u1) ... Setting up python (2.7.16-1) ... Setting up libhts2:amd64 (1.9-12~deb10u1) ... Setting up python-pkg-resources (40.8.0-1) ... Setting up python-pil:amd64 (5.4.1-2+deb10u3) ... Setting up python-renderpm:amd64 (3.5.13-1+deb10u1) ... Setting up ncbi-blast+ (2.8.1-1+deb10u1) ... Setting up python-reportlab-accel:amd64 (3.5.13-1+deb10u1) ... Setting up python-olefile (0.46-1) ... Setting up nanopolish (0.11.0-2) ... Setting up python-pysam (0.15.2+ds-2) ... Setting up python-numpy (1:1.16.2-1) ... Setting up python-reportlab (3.5.13-1+deb10u1) ... Setting up python-biopython (1.73+dfsg-1) ... 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. 0m45.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'apt-get', '-yf', 'dist-upgrade'] 0m45.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m46.8s DUMP: f6fc0f2636004ef589309651dfd778f4 - 0m46.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m46.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'apt-cache', 'show', '--no-all-versions', 'nanopolish'] 0m47.0s DUMP: Package: nanopolish Version: 0.11.0-2 Installed-Size: 9781 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.27), libgcc1 (>= 1:3.3.1), libgomp1 (>= 4.9), libhdf5-103, libhts2 (>= 1.4.1), libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4), python:any Recommends: python-biopython, python-pysam Suggests: perl, make Description-en: consensus caller for nanopore sequencing data Nanopolish uses a signal-level hidden Markov model for consensus calling of nanopore genome sequencing data. It can perform signal-level analysis of Oxford Nanopore sequencing data. Nanopolish can calculate an improved consensus sequence for a draft genome assembly, detect base modifications, call SNPs and indels with respect to a reference genome and more. Description-md5: c65181cb6cafc3c3d9c0c69affe72640 Homepage: https://github.com/jts/nanopolish Section: science Priority: optional Filename: pool/main/n/nanopolish/nanopolish_0.11.0-2_amd64.deb Size: 2214776 MD5sum: b72ff98f6e32ed73516e13727f75bbee SHA256: f8782c56f1b4ba784f8fb3a81c46c2d68beb5e3f434aa605bce2473789ab4a47 0m47.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'apt-cache', 'show', '--no-all-versions', 'nanopolish'] 0m47.0s INFO: apt-cache knows about the following packages: nanopolish 0m47.0s INFO: Running scripts pre_install 0m47.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_install_database-server'] 0m47.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_install_database-server'] 0m47.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_install_exceptions'] 0m47.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_install_exceptions'] 0m47.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_install_extras'] 0m47.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_install_extras'] 0m47.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_install_foreign_architecture'] 0m47.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_install_foreign_architecture'] 0m47.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m47.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m47.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'apt-cache', 'policy'] 0m47.1s 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=oldstable,n=buster,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m47.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'apt-cache', 'policy'] 0m47.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'apt-cache', 'policy', 'nanopolish'] 0m47.1s DUMP: nanopolish: Installed: 0.11.0-2 Candidate: 0.11.0-2 Version table: *** 0.11.0-2 500 500 http://deb.debian.org/debian buster/main amd64 Packages 100 /var/lib/dpkg/status 0m47.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'apt-cache', 'policy', 'nanopolish'] 0m47.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'apt-get', '-y', 'install', 'nanopolish'] 0m47.4s DUMP: Reading package lists... Building dependency tree... Reading state information... nanopolish is already the newest version (0.11.0-2). The following packages were automatically installed and are no longer required: libgfortran3 libhts1 libidn11 libunistring0 Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m47.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'apt-get', '-y', 'install', 'nanopolish'] 0m47.4s INFO: Running scripts post_install 0m47.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/post_install_exceptions'] 0m47.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/post_install_exceptions'] 0m47.4s INFO: Running scripts post_distupgrade 0m47.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m47.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m47.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/post_distupgrade_exceptions'] 0m47.5s DUMP: Normalized /etc/ca-certificates.conf Running pam-auth-update... 0m47.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/post_distupgrade_exceptions'] 0m47.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m47.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m47.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m47.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m47.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/post_distupgrade_zz_backports'] 0m47.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/post_distupgrade_zz_backports'] 0m47.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmphddufz4b'] 0m48.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmphddufz4b'] 0m48.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmphddufz4b'] 0m48.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmphddufz4b'] 0m48.6s INFO: Running scripts pre_install 0m48.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_install_database-server'] 0m48.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_install_database-server'] 0m48.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_install_exceptions'] 0m48.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_install_exceptions'] 0m48.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_install_extras'] 0m48.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_install_extras'] 0m48.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_install_foreign_architecture'] 0m48.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_install_foreign_architecture'] 0m48.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m48.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m48.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'apt-cache', 'policy'] 0m48.7s 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=oldstable,n=buster,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m48.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'apt-cache', 'policy'] 0m48.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'apt-cache', 'policy', 'nanopolish'] 0m48.7s DUMP: nanopolish: Installed: 0.11.0-2 Candidate: 0.11.0-2 Version table: *** 0.11.0-2 500 500 http://deb.debian.org/debian buster/main amd64 Packages 100 /var/lib/dpkg/status 0m48.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'apt-cache', 'policy', 'nanopolish'] 0m48.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'apt-get', '-y', 'install', 'nanopolish=0.11.0-2'] 0m49.0s DUMP: Reading package lists... Building dependency tree... Reading state information... nanopolish is already the newest version (0.11.0-2). The following packages were automatically installed and are no longer required: libgfortran3 libhts1 libidn11 libunistring0 Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m49.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'apt-get', '-y', 'install', 'nanopolish=0.11.0-2'] 0m49.0s INFO: Running scripts post_install 0m49.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/post_install_exceptions'] 0m49.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/post_install_exceptions'] 0m49.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmphddufz4b'] 0m49.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmphddufz4b'] 0m50.3s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmphddufz4b', '-ac', '--ignore-obsolete'] 0m51.6s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmphddufz4b', '-ac', '--ignore-obsolete'] 0m51.6s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m51.6s DUMP: 0.15.6 0m51.6s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m51.6s INFO: Running adequate version 0.15.6 now. 0m51.6s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'nanopolish'] 0m51.8s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'nanopolish'] 0m51.8s INFO: Running scripts pre_remove 0m51.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m51.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m51.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m51.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m51.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m53.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m53.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m53.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m53.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m53.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m53.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_remove_exceptions'] 0m53.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/pre_remove_exceptions'] 0m53.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m53.4s 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 bzip2 bzip2 1.0.6-9.2~deb10u1 install ok installed ca-certificates ca-certificates 20200601~deb10u2 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 e2fslibs:amd64 e2fslibs 1.44.5-1+deb10u3 install ok installed e2fsprogs e2fsprogs 1.44.5-1+deb10u3 install ok installed e2fsprogs-l10n e2fsprogs-l10n 1.44.5-1+deb10u3 install ok installed fdisk fdisk 2.33.1-0.1 install ok installed file file 1:5.35-4+deb10u2 install ok installed findutils findutils 4.6.0+git+20190209-2 install ok installed gcc-6-base:amd64 gcc-6-base 6.3.0-18+deb9u1 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 gsfonts gsfonts 1:8.11+urwcyr1.0.7~pre44-4.4 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 krb5-locales krb5-locales 1.17-3+deb10u4 install ok installed libacl1:amd64 libacl1 2.2.53-4 install ok installed libaec0:amd64 libaec0 1.0.2-1 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 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 libcomerr2:amd64 libcomerr2 1.44.5-1+deb10u3 install ok installed libcurl3-gnutls:amd64 libcurl3-gnutls 7.64.0-4+deb10u2 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+deb10u4 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 libfreetype6:amd64 libfreetype6 2.9.1-3+deb10u3 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 libgdbm-compat4:amd64 libgdbm-compat4 1.18.1-4 install ok installed libgdbm6:amd64 libgdbm6 1.18.1-4 install ok installed libgfortran3:amd64 libgfortran3 6.3.0-18+deb9u1 install ok installed libgfortran5:amd64 libgfortran5 8.3.0-6 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 libgomp1:amd64 libgomp1 8.3.0-6 install ok installed libgpg-error-l10n libgpg-error-l10n 1.35-1 install ok installed libgpg-error0:amd64 libgpg-error0 1.35-1 install ok installed libgpm2:amd64 libgpm2 1.20.7-5 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.17-3+deb10u4 install ok installed libhdf5-103:amd64 libhdf5-103 1.10.4+repack-10 install ok installed libhogweed4:amd64 libhogweed4 3.4.1-1+deb10u1 install ok installed libhts1:amd64 libhts1 1.3.2-2 install ok installed libhts2:amd64 libhts2 1.9-12~deb10u1 install ok installed libidn11:amd64 libidn11 1.33-2.2 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 libk5crypto3:amd64 libk5crypto3 1.17-3+deb10u4 install ok installed libkeyutils1:amd64 libkeyutils1 1.6-6 install ok installed libkrb5-3:amd64 libkrb5-3 1.17-3+deb10u4 install ok installed libkrb5support0:amd64 libkrb5support0 1.17-3+deb10u4 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 liblmdb0:amd64 liblmdb0 0.9.22-1 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 libmagic-mgc libmagic-mgc 1:5.35-4+deb10u2 install ok installed libmagic1:amd64 libmagic1 1:5.35-4+deb10u2 install ok installed libmbedcrypto3:amd64 libmbedcrypto3 2.16.0-1 install ok installed libmbedtls12:amd64 libmbedtls12 2.16.0-1 install ok installed libmbedx509-0:amd64 libmbedx509-0 2.16.0-1 install ok installed libmount1:amd64 libmount1 2.33.1-0.1 install ok installed libncursesw5:amd64 libncursesw5 6.1+20181013-2+deb10u2 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 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 libpcre3:amd64 libpcre3 2:8.39-12 install ok installed libperl5.28:amd64 libperl5.28 5.28.1-6+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 libpython-stdlib:amd64 libpython-stdlib 2.7.16-1 install ok installed libpython2-stdlib:amd64 libpython2-stdlib 2.7.16-1 install ok installed libpython2.7-minimal:amd64 libpython2.7-minimal 2.7.16-2+deb10u1 install ok installed libpython2.7-stdlib:amd64 libpython2.7-stdlib 2.7.16-2+deb10u1 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:amd64 libsasl2-modules 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 libsmartcols1:amd64 libsmartcols1 2.33.1-0.1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.27.2-3+deb10u1 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+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 libsz2:amd64 libsz2 1.0.2-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.13-3 install ok installed libtiff5:amd64 libtiff5 4.1.0+git191117-2~deb10u4 install ok installed libtinfo5:amd64 libtinfo5 6.1+20181013-2+deb10u2 install ok installed libtinfo6:amd64 libtinfo6 6.1+20181013-2+deb10u2 install ok installed libudev1:amd64 libudev1 241-7~deb10u8 install ok installed libunistring0:amd64 libunistring0 0.9.6+really0.9.3-0.1 install ok installed libunistring2:amd64 libunistring2 0.9.10-1 install ok installed libustr-1.0-1:amd64 libustr-1.0-1 1.0.4-6 install ok installed libuuid1:amd64 libuuid1 2.33.1-0.1 install ok installed libwebp6:amd64 libwebp6 0.6.1-2+deb10u1 install ok installed libwebpdemux2:amd64 libwebpdemux2 0.6.1-2+deb10u1 install ok installed libwebpmux3:amd64 libwebpmux3 0.6.1-2+deb10u1 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 mime-support mime-support 3.62 install ok installed mount mount 2.33.1-0.1 install ok installed multiarch-support multiarch-support 2.28-10+deb10u1 install ok installed nanopolish nanopolish 0.11.0-2 install ok installed ncbi-blast+ ncbi-blast+ 2.8.1-1+deb10u1 install ok installed ncbi-data ncbi-data 6.1.20170106+dfsg1-0+deb10u2 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 netbase netbase 5.6 install ok installed openssl openssl 1.1.1n-0+deb10u3 install ok installed passwd passwd 1:4.5-1.1 install ok installed perl perl 5.28.1-6+deb10u1 install ok installed perl-base perl-base 5.28.1-6+deb10u1 install ok installed perl-modules-5.28 perl-modules-5.28 5.28.1-6+deb10u1 install ok installed publicsuffix publicsuffix 20220811.1734-0+deb10u1 install ok installed python python 2.7.16-1 install ok installed python-biopython python-biopython 1.73+dfsg-1 install ok installed python-biopython-doc python-biopython-doc 1.73+dfsg-1 install ok installed python-minimal python-minimal 2.7.16-1 install ok installed python-numpy python-numpy 1:1.16.2-1 install ok installed python-olefile python-olefile 0.46-1 install ok installed python-pil:amd64 python-pil 5.4.1-2+deb10u3 install ok installed python-pkg-resources python-pkg-resources 40.8.0-1 install ok installed python-pysam python-pysam 0.15.2+ds-2 install ok installed python-renderpm:amd64 python-renderpm 3.5.13-1+deb10u1 install ok installed python-reportlab python-reportlab 3.5.13-1+deb10u1 install ok installed python-reportlab-accel:amd64 python-reportlab-accel 3.5.13-1+deb10u1 install ok installed python2 python2 2.7.16-1 install ok installed python2-minimal python2-minimal 2.7.16-1 install ok installed python2.7 python2.7 2.7.16-2+deb10u1 install ok installed python2.7-minimal python2.7-minimal 2.7.16-2+deb10u1 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 util-linux util-linux 2.33.1-0.1 install ok installed xz-utils xz-utils 5.2.4-1+deb10u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-1+deb10u1 0m53.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m53.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'apt-get', 'remove', 'bzip2', 'file', 'gsfonts', 'krb5-locales', 'libaec0:amd64', 'libblas3:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfreetype6:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran3:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-103:amd64', 'libhts1:amd64', 'libhts2:amd64', 'libidn11:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'liblmdb0:amd64', 'libmagic-mgc', 'libmagic1:amd64', 'libmbedcrypto3:amd64', 'libmbedtls12:amd64', 'libmbedx509-0:amd64', 'libnghttp2-14:amd64', 'libperl5.28:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libsz2:amd64', 'libtiff5:amd64', 'libunistring0:amd64', 'libwebp6:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'mime-support', 'ncbi-blast+-', 'ncbi-data', 'netbase', 'perl', 'perl-modules-5.28', 'publicsuffix', 'python', 'python-biopython', 'python-biopython-doc', 'python-minimal', 'python-numpy', 'python-olefile', 'python-pil:amd64', 'python-pkg-resources', 'python-pysam', 'python-renderpm:amd64', 'python-reportlab', 'python-reportlab-accel:amd64', 'python2', 'python2-minimal', 'python2.7', 'python2.7-minimal', 'readline-common', 'xz-utils', 'nanopolish'] 0m54.6s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: bzip2 file gsfonts krb5-locales libaec0 libblas3 libcurl3-gnutls libdeflate0 libexpat1 libfreetype6 libgdbm-compat4 libgdbm6 libgfortran3 libgfortran5 libgomp1 libgssapi-krb5-2 libhdf5-103 libhts1 libhts2 libidn11 libimagequant0 libjbig0 libjpeg62-turbo libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 libldap-common liblmdb0 libmagic-mgc libmagic1 libmbedcrypto3 libmbedtls12 libmbedx509-0 libnghttp2-14 libperl5.28 libpng16-16 libpsl5 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 libreadline7 librtmp1 libsasl2-2 libsasl2-modules libsasl2-modules-db libsqlite3-0 libssh2-1 libsz2 libtiff5 libunistring0 libwebp6 libwebpdemux2 libwebpmux3 mime-support nanopolish ncbi-blast+ ncbi-data netbase perl perl-modules-5.28 publicsuffix python python-biopython python-biopython-doc python-minimal python-numpy python-olefile python-pil python-pkg-resources python-pysam python-renderpm python-reportlab python-reportlab-accel python2 python2-minimal python2.7 python2.7-minimal readline-common xz-utils 0 upgraded, 0 newly installed, 85 to remove and 0 not upgraded. After this operation, 240 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 ... 11760 files and directories currently installed.) Removing bzip2 (1.0.6-9.2~deb10u1) ... Removing file (1:5.35-4+deb10u2) ... Removing python-renderpm:amd64 (3.5.13-1+deb10u1) ... Removing gsfonts (1:8.11+urwcyr1.0.7~pre44-4.4) ... Removing krb5-locales (1.17-3+deb10u4) ... Removing nanopolish (0.11.0-2) ... Removing libhdf5-103:amd64 (1.10.4+repack-10) ... Removing libsz2:amd64 (1.0.2-1) ... Removing libaec0:amd64 (1.0.2-1) ... Removing python-biopython (1.73+dfsg-1) ... Removing python-numpy (1:1.16.2-1) ... Removing liblapack3:amd64 (3.8.0-2) ... Removing libblas3:amd64 (3.8.0-2) ... Removing libhts1:amd64 (1.3.2-2) ... Removing python-pysam (0.15.2+ds-2) ... Removing libhts2:amd64 (1.9-12~deb10u1) ... Removing libcurl3-gnutls:amd64 (7.64.0-4+deb10u2) ... Removing libdeflate0:amd64 (1.2-1) ... Removing python-reportlab (3.5.13-1+deb10u1) ... Removing python-reportlab-accel:amd64 (3.5.13-1+deb10u1) ... Removing python-pkg-resources (40.8.0-1) ... Removing python-pil:amd64 (5.4.1-2+deb10u3) ... Removing python-olefile (0.46-1) ... Removing libfreetype6:amd64 (2.9.1-3+deb10u3) ... Removing ncbi-blast+ (2.8.1-1+deb10u1) ... Removing perl (5.28.1-6+deb10u1) ... Removing libperl5.28:amd64 (5.28.1-6+deb10u1) ... Removing libgdbm-compat4:amd64 (1.18.1-4) ... Removing libgdbm6:amd64 (1.18.1-4) ... Removing libgfortran3:amd64 (6.3.0-18+deb9u1) ... Removing libgfortran5:amd64 (8.3.0-6) ... Removing libgomp1:amd64 (8.3.0-6) ... Removing libgssapi-krb5-2:amd64 (1.17-3+deb10u4) ... Removing libidn11:amd64 (1.33-2.2) ... Removing libimagequant0:amd64 (2.12.2-1.1) ... Removing libtiff5:amd64 (4.1.0+git191117-2~deb10u4) ... Removing libjbig0:amd64 (2.1-3.1+b2) ... Removing libjpeg62-turbo:amd64 (1:1.5.2-2+deb10u1) ... Removing libkrb5-3:amd64 (1.17-3+deb10u4) ... Removing libk5crypto3:amd64 (1.17-3+deb10u4) ... Removing libkrb5support0:amd64 (1.17-3+deb10u4) ... 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 liblmdb0:amd64 (0.9.22-1) ... Removing libmagic1:amd64 (1:5.35-4+deb10u2) ... Removing libmagic-mgc (1:5.35-4+deb10u2) ... Removing libmbedtls12:amd64 (2.16.0-1) ... Removing libmbedx509-0:amd64 (2.16.0-1) ... Removing libmbedcrypto3:amd64 (2.16.0-1) ... Removing libnghttp2-14:amd64 (1.36.0-2+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: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 libunistring0:amd64 (0.9.6+really0.9.3-0.1) ... Removing libwebpmux3:amd64 (0.6.1-2+deb10u1) ... Removing libwebpdemux2:amd64 (0.6.1-2+deb10u1) ... Removing libwebp6:amd64 (0.6.1-2+deb10u1) ... Removing ncbi-data (6.1.20170106+dfsg1-0+deb10u2) ... Removing netbase (5.6) ... Removing perl-modules-5.28 (5.28.1-6+deb10u1) ... Removing publicsuffix (20220811.1734-0+deb10u1) ... Removing python-biopython-doc (1.73+dfsg-1) ... Removing xz-utils (5.2.4-1+deb10u1) ... Removing python (2.7.16-1) ... Removing python2 (2.7.16-1) ... Removing python2.7 (2.7.16-2+deb10u1) ... Removing libpython-stdlib:amd64 (2.7.16-1) ... Removing libpython2-stdlib:amd64 (2.7.16-1) ... Removing python-minimal (2.7.16-1) ... Removing python2-minimal (2.7.16-1) ... Removing python2.7-minimal (2.7.16-2+deb10u1) ... Removing libpython2.7-stdlib:amd64 (2.7.16-2+deb10u1) ... Removing libexpat1:amd64 (2.2.6-2+deb10u4) ... Removing libpython2.7-minimal:amd64 (2.7.16-2+deb10u1) ... find: '/usr/lib/python2.7': No such file or directory Removing libreadline7:amd64 (7.0-5) ... Removing libsqlite3-0:amd64 (3.27.2-3+deb10u1) ... Removing mime-support (3.62) ... Removing readline-common (7.0-5) ... Processing triggers for libc-bin (2.28-10+deb10u1) ... 0m54.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'apt-get', 'remove', 'bzip2', 'file', 'gsfonts', 'krb5-locales', 'libaec0:amd64', 'libblas3:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfreetype6:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran3:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-103:amd64', 'libhts1:amd64', 'libhts2:amd64', 'libidn11:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'liblmdb0:amd64', 'libmagic-mgc', 'libmagic1:amd64', 'libmbedcrypto3:amd64', 'libmbedtls12:amd64', 'libmbedx509-0:amd64', 'libnghttp2-14:amd64', 'libperl5.28:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libsz2:amd64', 'libtiff5:amd64', 'libunistring0:amd64', 'libwebp6:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'mime-support', 'ncbi-blast+-', 'ncbi-data', 'netbase', 'perl', 'perl-modules-5.28', 'publicsuffix', 'python', 'python-biopython', 'python-biopython-doc', 'python-minimal', 'python-numpy', 'python-olefile', 'python-pil:amd64', 'python-pkg-resources', 'python-pysam', 'python-renderpm:amd64', 'python-reportlab', 'python-reportlab-accel:amd64', 'python2', 'python2-minimal', 'python2.7', 'python2.7-minimal', 'readline-common', 'xz-utils', 'nanopolish'] 0m54.6s INFO: Running scripts post_remove 0m54.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/post_remove_exceptions'] 0m54.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/post_remove_exceptions'] 0m54.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'dpkg', '--purge', 'bzip2', 'file', 'gsfonts', 'krb5-locales', 'libaec0:amd64', 'libblas3:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfreetype6:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran3:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-103:amd64', 'libhts1:amd64', 'libhts2:amd64', 'libidn11:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'liblmdb0:amd64', 'libmagic-mgc', 'libmagic1:amd64', 'libmbedcrypto3:amd64', 'libmbedtls12:amd64', 'libmbedx509-0:amd64', 'libnghttp2-14:amd64', 'libperl5.28:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libsz2:amd64', 'libtiff5:amd64', 'libunistring0:amd64', 'libwebp6:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'mime-support', 'ncbi-blast+', 'ncbi-data', 'netbase', 'perl', 'perl-modules-5.28', 'publicsuffix', 'python', 'python-biopython', 'python-biopython-doc', 'python-minimal', 'python-numpy', 'python-olefile', 'python-pil:amd64', 'python-pkg-resources', 'python-pysam', 'python-renderpm:amd64', 'python-reportlab', 'python-reportlab-accel:amd64', 'python2', 'python2-minimal', 'python2.7', 'python2.7-minimal', 'readline-common', 'xz-utils'] 0m54.7s DUMP: dpkg: warning: ignoring request to remove bzip2 which isn't installed dpkg: warning: ignoring request to remove file which isn't installed (Reading database ... 5030 files and directories currently installed.) Purging configuration files for gsfonts (1:8.11+urwcyr1.0.7~pre44-4.4) ... dpkg: warning: ignoring request to remove krb5-locales which isn't installed dpkg: warning: ignoring request to remove libaec0 which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libcurl3-gnutls 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 libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libgdbm-compat4 which isn't installed dpkg: warning: ignoring request to remove libgdbm6 which isn't installed dpkg: warning: ignoring request to remove libgfortran3 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed dpkg: warning: ignoring request to remove libgomp1 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.17-3+deb10u4) ... dpkg: warning: ignoring request to remove libhdf5-103 which isn't installed dpkg: warning: ignoring request to remove libhts1 which isn't installed dpkg: warning: ignoring request to remove libhts2 which isn't installed dpkg: warning: ignoring request to remove libidn11 which isn't installed dpkg: warning: ignoring request to remove libimagequant0 which isn't installed dpkg: warning: ignoring request to remove libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove liblcms2-2 which isn't installed dpkg: warning: ignoring request to remove 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 liblmdb0 which isn't installed dpkg: warning: ignoring request to remove libmagic-mgc which isn't installed Purging configuration files for libmagic1:amd64 (1:5.35-4+deb10u2) ... dpkg: warning: ignoring request to remove libmbedcrypto3 which isn't installed dpkg: warning: ignoring request to remove libmbedtls12 which isn't installed dpkg: warning: ignoring request to remove libmbedx509-0 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libperl5.28 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 libpython-stdlib which isn't installed dpkg: warning: ignoring request to remove libpython2-stdlib which isn't installed Purging configuration files for libpython2.7-minimal:amd64 (2.7.16-2+deb10u1) ... dpkg: warning: ignoring request to remove libpython2.7-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 Purging configuration files for libsasl2-modules:amd64 (2.1.27+dfsg-1+deb10u2) ... dpkg: warning: ignoring request to remove libsasl2-modules-db which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libssh2-1 which isn't installed dpkg: warning: ignoring request to remove libsz2 which isn't installed dpkg: warning: ignoring request to remove libtiff5 which isn't installed dpkg: warning: ignoring request to remove libunistring0 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 Purging configuration files for mime-support (3.62) ... dpkg: warning: ignoring request to remove ncbi-blast+ which isn't installed Purging configuration files for ncbi-data (6.1.20170106+dfsg1-0+deb10u2) ... Purging configuration files for netbase (5.6) ... Purging configuration files for perl (5.28.1-6+deb10u1) ... dpkg: warning: ignoring request to remove perl-modules-5.28 which isn't installed dpkg: warning: ignoring request to remove publicsuffix which isn't installed Purging configuration files for python (2.7.16-1) ... dpkg: warning: ignoring request to remove python-biopython which isn't installed dpkg: warning: ignoring request to remove python-biopython-doc which isn't installed dpkg: warning: ignoring request to remove python-minimal which isn't installed dpkg: warning: ignoring request to remove python-numpy which isn't installed dpkg: warning: ignoring request to remove python-olefile which isn't installed dpkg: warning: ignoring request to remove python-pil which isn't installed dpkg: warning: ignoring request to remove python-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python-pysam which isn't installed dpkg: warning: ignoring request to remove python-renderpm which isn't installed dpkg: warning: ignoring request to remove python-reportlab which isn't installed dpkg: warning: ignoring request to remove python-reportlab-accel which isn't installed dpkg: warning: ignoring request to remove python2 which isn't installed dpkg: warning: ignoring request to remove python2-minimal which isn't installed dpkg: warning: ignoring request to remove python2.7 which isn't installed Purging configuration files for python2.7-minimal (2.7.16-2+deb10u1) ... Purging configuration files for readline-common (7.0-5) ... dpkg: warning: ignoring request to remove xz-utils which isn't installed 0m54.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'dpkg', '--purge', 'bzip2', 'file', 'gsfonts', 'krb5-locales', 'libaec0:amd64', 'libblas3:amd64', 'libcurl3-gnutls:amd64', 'libdeflate0:amd64', 'libexpat1:amd64', 'libfreetype6:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgfortran3:amd64', 'libgfortran5:amd64', 'libgomp1:amd64', 'libgssapi-krb5-2:amd64', 'libhdf5-103:amd64', 'libhts1:amd64', 'libhts2:amd64', 'libidn11:amd64', 'libimagequant0:amd64', 'libjbig0:amd64', 'libjpeg62-turbo:amd64', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'liblmdb0:amd64', 'libmagic-mgc', 'libmagic1:amd64', 'libmbedcrypto3:amd64', 'libmbedtls12:amd64', 'libmbedx509-0:amd64', 'libnghttp2-14:amd64', 'libperl5.28:amd64', 'libpng16-16:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules:amd64', 'libsasl2-modules-db:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libsz2:amd64', 'libtiff5:amd64', 'libunistring0:amd64', 'libwebp6:amd64', 'libwebpdemux2:amd64', 'libwebpmux3:amd64', 'mime-support', 'ncbi-blast+', 'ncbi-data', 'netbase', 'perl', 'perl-modules-5.28', 'publicsuffix', 'python', 'python-biopython', 'python-biopython-doc', 'python-minimal', 'python-numpy', 'python-olefile', 'python-pil:amd64', 'python-pkg-resources', 'python-pysam', 'python-renderpm:amd64', 'python-reportlab', 'python-reportlab-accel:amd64', 'python2', 'python2-minimal', 'python2.7', 'python2.7-minimal', 'readline-common', 'xz-utils'] 0m54.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'dpkg', '--purge', 'nanopolish'] 0m54.7s DUMP: dpkg: warning: ignoring request to remove nanopolish which isn't installed 0m54.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'dpkg', '--purge', 'nanopolish'] 0m54.7s INFO: Running scripts post_purge 0m54.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/post_purge_exceptions'] 0m54.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/post_purge_exceptions'] 0m54.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'dpkg', '--purge', '--pending'] 0m54.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'dpkg', '--purge', '--pending'] 0m54.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'dpkg', '--remove', '--pending'] 0m54.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'dpkg', '--remove', '--pending'] 0m54.7s INFO: Running scripts post_test 0m54.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/post_test_exceptions'] 0m54.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'tmp/scripts/post_test_exceptions'] 0m54.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmphddufz4b'] 0m55.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmphddufz4b'] 0m55.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'dpkg-divert', '--list'] 0m55.0s 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 0m55.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'dpkg-divert', '--list'] 0m55.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'apt-get', 'clean'] 0m55.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmphddufz4b', 'apt-get', 'clean'] 0m55.1s DEBUG: Recording chroot state 0m55.5s INFO: Warning: Package purging left files on system: /etc/ca-certificates.conf.dpkg-old not owned 0m55.7s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmphddufz4b/dev/shm'] 0m55.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmphddufz4b/dev/shm'] 0m55.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmphddufz4b/dev/console'] 0m55.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmphddufz4b/dev/console'] 0m55.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmphddufz4b/dev/ptmx'] 0m55.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmphddufz4b/dev/ptmx'] 0m55.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmphddufz4b/dev/pts'] 0m55.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmphddufz4b/dev/pts'] 0m55.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmphddufz4b/proc'] 0m55.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmphddufz4b/proc'] 0m55.9s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmphddufz4b'] 0m55.9s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmphddufz4b'] 0m55.9s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmphddufz4b 0m55.9s INFO: PASS: Upgrading between Debian distributions. 0m55.9s INFO: PASS: All tests. 0m55.9s INFO: piuparts run ends. ret=0 End: 2022-12-07 10:40:06 GMT