Start: 2023-04-15 17:37:25 GMT [stretch] Package: ruby-bio Version: 1.5.0-2 Installed-Size: 3031 Maintainer: Debian Ruby Extras Maintainers Architecture: all Depends: ruby | ruby-interpreter Recommends: blast2, hmmer, mafft, muscle, probcons, sim4, t-coffee Suggests: clustalw, emboss Description: Ruby tools for computational molecular biology Homepage: http://bioruby.org/ Description-md5: 9551e5ebe8c49f9d9485b7f15547f082 Ruby-Versions: all Section: ruby Priority: optional Filename: pool/main/r/ruby-bio/ruby-bio_1.5.0-2_all.deb Size: 700714 MD5sum: 5663504b90d48e9a1e161092c50c2114 SHA256: a8ddf161c996ae5f972b983ece41efbbd36eb00136b5da082f4fa8fc913dec4a [stretch-lts] Package: ruby-bio Version: 1.5.0-2 Installed-Size: 3031 Maintainer: Debian Ruby Extras Maintainers Architecture: all Depends: ruby | ruby-interpreter Recommends: blast2, hmmer, mafft, muscle, probcons, sim4, t-coffee Suggests: clustalw, emboss Description: Ruby tools for computational molecular biology Homepage: http://bioruby.org/ Description-md5: 9551e5ebe8c49f9d9485b7f15547f082 Ruby-Versions: all Section: ruby Priority: optional Filename: pool/main/r/ruby-bio/ruby-bio_1.5.0-2_all.deb Size: 700714 MD5sum: 5663504b90d48e9a1e161092c50c2114 SHA256: a8ddf161c996ae5f972b983ece41efbbd36eb00136b5da082f4fa8fc913dec4a Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --skip-logrotatefiles-test --warn-on-debsums-errors --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz -d stretch -d stretch-lts -B /srv/piuparts.debian.org/slave/refchroot/stretch2next/reference-chroot-metadata.dat --apt ruby-bio=1.5.0-2 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 --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --skip-logrotatefiles-test --warn-on-debsums-errors --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz -d stretch -d stretch-lts -B /srv/piuparts.debian.org/slave/refchroot/stretch2next/reference-chroot-metadata.dat --apt ruby-bio=1.5.0-2 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpkzgkp6f7 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpkzgkp6f7 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m1.7s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m1.7s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7/proc'] 0m1.7s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7/proc'] 0m1.7s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7/dev/pts'] 0m1.7s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7/dev/pts'] 0m1.7s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7/dev/ptmx'] 0m1.7s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7/dev/ptmx'] 0m1.7s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7/dev/console'] 0m1.8s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7/dev/console'] 0m1.8s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7/dev/shm'] 0m1.8s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7/dev/shm'] 0m1.8s DEBUG: sources.list: deb http://deb.debian.org/debian/ stretch main 0m1.8s DEBUG: Created policy-rc.d and chmodded it. 0m1.8s DEBUG: Created resolv.conf. 0m1.8s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpkzgkp6f7/tmp/scripts/ 0m1.8s INFO: Running scripts post_chroot_unpack 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'apt-get', 'update'] 0m3.0s DUMP: Ign:1 http://deb.debian.org/debian stretch InRelease Hit:2 http://deb.debian.org/debian stretch Release Reading package lists... 0m3.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'apt-get', 'update'] 0m3.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'apt-get', '-yf', 'dist-upgrade'] 0m3.4s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'apt-get', '-yf', 'dist-upgrade'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.7s DUMP: 660e5103244a20b75ca08c3f8741e16e - 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.7s INFO: Running scripts post_setup 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/post_setup_dummy_users'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/post_setup_dummy_users'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/post_setup_forbid_home'] 0m4.9s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/post_setup_forbid_home'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.9s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' '/bin/sync' -> 'true' 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/post_setup_minimize'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/post_setup_minimize'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/post_setup_zz_backports'] 0m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/post_setup_zz_backports'] 0m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.0s 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 0m5.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m5.0s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/stretch2next/reference-chroot-metadata.dat 0m5.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7'] 0m5.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7'] 0m5.2s INFO: Running scripts is_testable 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/is_testable_uninstallable'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/is_testable_uninstallable'] 0m5.2s INFO: Running scripts pre_test 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_test_exceptions'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_test_exceptions'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_test_root_password'] 0m5.3s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m5.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_test_root_password'] 0m5.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'apt-cache', 'show', '--no-all-versions', 'ruby-bio'] 0m5.5s DUMP: Package: ruby-bio Version: 1.5.0-2 Installed-Size: 3031 Maintainer: Debian Ruby Extras Maintainers Architecture: all Depends: ruby | ruby-interpreter Recommends: blast2, hmmer, mafft, muscle, probcons, sim4, t-coffee Suggests: clustalw, emboss Description-en: Ruby tools for computational molecular biology BioRuby project aims to implement an integrated environment for Bioinformatics with Ruby language. Design philosophy of the BioRuby library is KISS (keep it simple, stupid) to maximize the usability and the efficiency for biologists as a daily tool. The project was started in Japan and supported by University of Tokyo (Human Genome Center), Kyoto University (Bioinformatics Center) and the Open Bio Foundation. Description-md5: 9551e5ebe8c49f9d9485b7f15547f082 Homepage: http://bioruby.org/ Ruby-Versions: all Section: ruby Priority: optional Filename: pool/main/r/ruby-bio/ruby-bio_1.5.0-2_all.deb Size: 700714 MD5sum: 5663504b90d48e9a1e161092c50c2114 SHA256: a8ddf161c996ae5f972b983ece41efbbd36eb00136b5da082f4fa8fc913dec4a 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'apt-cache', 'show', '--no-all-versions', 'ruby-bio'] 0m5.5s INFO: apt-cache knows about the following packages: ruby-bio 0m5.5s INFO: Running scripts pre_install 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_install_database-server'] 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_install_database-server'] 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_install_exceptions'] 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_install_exceptions'] 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_install_extras'] 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_install_extras'] 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'apt-cache', 'policy'] 0m5.6s 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: 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'apt-cache', 'policy'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'apt-cache', 'policy', 'ruby-bio'] 0m5.7s DUMP: ruby-bio: Installed: (none) Candidate: 1.5.0-2 Version table: 1.5.0-2 500 500 http://deb.debian.org/debian stretch/main amd64 Packages 0m5.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'apt-cache', 'policy', 'ruby-bio'] 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'apt-get', '-y', 'install', 'ruby-bio'] 0m13.5s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: ca-certificates libffi6 libgdbm3 libgmp10 libncurses5 libreadline7 libruby2.3 libssl1.0.2 libssl1.1 libyaml-0-2 openssl rake readline-common ruby ruby-did-you-mean ruby-minitest ruby-net-telnet ruby-power-assert ruby-test-unit ruby2.3 rubygems-integration Suggested packages: readline-doc ri ruby-dev clustalw emboss bundler Recommended packages: libgpm2 zip blast2 hmmer mafft muscle probcons sim4 t-coffee fonts-lato libjs-jquery The following NEW packages will be installed: ca-certificates libffi6 libgdbm3 libgmp10 libncurses5 libreadline7 libruby2.3 libssl1.0.2 libssl1.1 libyaml-0-2 openssl rake readline-common ruby ruby-bio ruby-did-you-mean ruby-minitest ruby-net-telnet ruby-power-assert ruby-test-unit ruby2.3 rubygems-integration 0 upgraded, 22 newly installed, 0 to remove and 0 not upgraded. Need to get 8453 kB of archives. After this operation, 28.9 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian stretch/main amd64 libgdbm3 amd64 1.8.3-14 [30.0 kB] Get:2 http://deb.debian.org/debian stretch/main amd64 readline-common all 7.0-3 [70.4 kB] Get:3 http://deb.debian.org/debian stretch/main amd64 libreadline7 amd64 7.0-3 [151 kB] Get:4 http://deb.debian.org/debian stretch/main amd64 libssl1.0.2 amd64 1.0.2u-1~deb9u1 [1304 kB] Get:5 http://deb.debian.org/debian stretch/main amd64 libssl1.1 amd64 1.1.0l-1~deb9u1 [1358 kB] Get:6 http://deb.debian.org/debian stretch/main amd64 openssl amd64 1.1.0l-1~deb9u1 [749 kB] Get:7 http://deb.debian.org/debian stretch/main amd64 ca-certificates all 20200601~deb9u1 [160 kB] Get:8 http://deb.debian.org/debian stretch/main amd64 libffi6 amd64 3.2.1-6 [20.4 kB] Get:9 http://deb.debian.org/debian stretch/main amd64 libgmp10 amd64 2:6.1.2+dfsg-1 [253 kB] Get:10 http://deb.debian.org/debian stretch/main amd64 libncurses5 amd64 6.0+20161126-1+deb9u2 [93.4 kB] Get:11 http://deb.debian.org/debian stretch/main amd64 libyaml-0-2 amd64 0.1.7-2 [47.6 kB] Get:12 http://deb.debian.org/debian stretch/main amd64 rubygems-integration all 1.11 [4994 B] Get:13 http://deb.debian.org/debian stretch/main amd64 ruby-did-you-mean all 1.0.0-2 [11.2 kB] Get:14 http://deb.debian.org/debian stretch/main amd64 ruby-minitest all 5.9.0-1 [51.1 kB] Get:15 http://deb.debian.org/debian stretch/main amd64 ruby-net-telnet all 0.1.1-2 [12.5 kB] Get:16 http://deb.debian.org/debian stretch/main amd64 ruby-power-assert all 0.3.0-1 [7902 B] Get:17 http://deb.debian.org/debian stretch/main amd64 ruby-test-unit all 3.1.7-2 [69.6 kB] Get:18 http://deb.debian.org/debian stretch/main amd64 libruby2.3 amd64 2.3.3-1+deb9u8 [3108 kB] Get:19 http://deb.debian.org/debian stretch/main amd64 ruby2.3 amd64 2.3.3-1+deb9u8 [189 kB] Get:20 http://deb.debian.org/debian stretch/main amd64 ruby amd64 1:2.3.3 [10.8 kB] Get:21 http://deb.debian.org/debian stretch/main amd64 rake all 10.5.0-2+deb9u1 [49.7 kB] Get:22 http://deb.debian.org/debian stretch/main amd64 ruby-bio all 1.5.0-2 [701 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 8453 kB in 0s (25.0 MB/s) Selecting previously unselected package libgdbm3: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-libgdbm3_1.8.3-14_amd64.deb ... Unpacking libgdbm3:amd64 (1.8.3-14) ... Selecting previously unselected package readline-common. Preparing to unpack .../01-readline-common_7.0-3_all.deb ... Unpacking readline-common (7.0-3) ... Selecting previously unselected package libreadline7:amd64. Preparing to unpack .../02-libreadline7_7.0-3_amd64.deb ... Unpacking libreadline7:amd64 (7.0-3) ... Selecting previously unselected package libssl1.0.2:amd64. Preparing to unpack .../03-libssl1.0.2_1.0.2u-1~deb9u1_amd64.deb ... Unpacking libssl1.0.2:amd64 (1.0.2u-1~deb9u1) ... Selecting previously unselected package libssl1.1:amd64. Preparing to unpack .../04-libssl1.1_1.1.0l-1~deb9u1_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.0l-1~deb9u1) ... Selecting previously unselected package openssl. Preparing to unpack .../05-openssl_1.1.0l-1~deb9u1_amd64.deb ... Unpacking openssl (1.1.0l-1~deb9u1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../06-ca-certificates_20200601~deb9u1_all.deb ... Unpacking ca-certificates (20200601~deb9u1) ... Selecting previously unselected package libffi6:amd64. Preparing to unpack .../07-libffi6_3.2.1-6_amd64.deb ... Unpacking libffi6:amd64 (3.2.1-6) ... Selecting previously unselected package libgmp10:amd64. Preparing to unpack .../08-libgmp10_2%3a6.1.2+dfsg-1_amd64.deb ... Unpacking libgmp10:amd64 (2:6.1.2+dfsg-1) ... Selecting previously unselected package libncurses5:amd64. Preparing to unpack .../09-libncurses5_6.0+20161126-1+deb9u2_amd64.deb ... Unpacking libncurses5:amd64 (6.0+20161126-1+deb9u2) ... Selecting previously unselected package libyaml-0-2:amd64. Preparing to unpack .../10-libyaml-0-2_0.1.7-2_amd64.deb ... Unpacking libyaml-0-2:amd64 (0.1.7-2) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../11-rubygems-integration_1.11_all.deb ... Unpacking rubygems-integration (1.11) ... Selecting previously unselected package ruby-did-you-mean. Preparing to unpack .../12-ruby-did-you-mean_1.0.0-2_all.deb ... Unpacking ruby-did-you-mean (1.0.0-2) ... Selecting previously unselected package ruby-minitest. Preparing to unpack .../13-ruby-minitest_5.9.0-1_all.deb ... Unpacking ruby-minitest (5.9.0-1) ... Selecting previously unselected package ruby-net-telnet. Preparing to unpack .../14-ruby-net-telnet_0.1.1-2_all.deb ... Unpacking ruby-net-telnet (0.1.1-2) ... Selecting previously unselected package ruby-power-assert. Preparing to unpack .../15-ruby-power-assert_0.3.0-1_all.deb ... Unpacking ruby-power-assert (0.3.0-1) ... Selecting previously unselected package ruby-test-unit. Preparing to unpack .../16-ruby-test-unit_3.1.7-2_all.deb ... Unpacking ruby-test-unit (3.1.7-2) ... Selecting previously unselected package libruby2.3:amd64. Preparing to unpack .../17-libruby2.3_2.3.3-1+deb9u8_amd64.deb ... Unpacking libruby2.3:amd64 (2.3.3-1+deb9u8) ... Selecting previously unselected package ruby2.3. Preparing to unpack .../18-ruby2.3_2.3.3-1+deb9u8_amd64.deb ... Unpacking ruby2.3 (2.3.3-1+deb9u8) ... Selecting previously unselected package ruby. Preparing to unpack .../19-ruby_1%3a2.3.3_amd64.deb ... Unpacking ruby (1:2.3.3) ... Selecting previously unselected package rake. Preparing to unpack .../20-rake_10.5.0-2+deb9u1_all.deb ... Unpacking rake (10.5.0-2+deb9u1) ... Selecting previously unselected package ruby-bio. Preparing to unpack .../21-ruby-bio_1.5.0-2_all.deb ... Unpacking ruby-bio (1.5.0-2) ... Setting up libncurses5:amd64 (6.0+20161126-1+deb9u2) ... Setting up readline-common (7.0-3) ... Setting up libgdbm3:amd64 (1.8.3-14) ... Setting up libreadline7:amd64 (7.0-3) ... Setting up libssl1.0.2:amd64 (1.0.2u-1~deb9u1) ... Setting up ruby-did-you-mean (1.0.0-2) ... Setting up libyaml-0-2:amd64 (0.1.7-2) ... Setting up libgmp10:amd64 (2:6.1.2+dfsg-1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up libssl1.1:amd64 (1.1.0l-1~deb9u1) ... Setting up openssl (1.1.0l-1~deb9u1) ... Setting up ruby-net-telnet (0.1.1-2) ... Setting up libffi6:amd64 (3.2.1-6) ... Setting up ruby-minitest (5.9.0-1) ... Setting up ca-certificates (20200601~deb9u1) ... Updating certificates in /etc/ssl/certs... 126 added, 0 removed; done. Setting up ruby-power-assert (0.3.0-1) ... Setting up ruby-test-unit (3.1.7-2) ... Setting up rubygems-integration (1.11) ... Setting up rake (10.5.0-2+deb9u1) ... Setting up libruby2.3:amd64 (2.3.3-1+deb9u8) ... Setting up ruby2.3 (2.3.3-1+deb9u8) ... Setting up ruby (1:2.3.3) ... Setting up ruby-bio (1.5.0-2) ... 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. 0m13.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'apt-get', '-y', 'install', 'ruby-bio'] 0m13.5s INFO: Running scripts post_install 0m13.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/post_install_exceptions'] 0m13.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/post_install_exceptions'] 0m13.5s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7'] 0m13.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7'] 0m13.9s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpkzgkp6f7 to stretch-lts 0m13.9s DEBUG: sources.list: deb http://deb.debian.org/debian/ stretch main deb http://security.debian.org stretch/updates main 0m13.9s INFO: Running scripts pre_distupgrade 0m13.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m13.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m13.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_distupgrade_exceptions'] 0m13.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_distupgrade_exceptions'] 0m13.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m13.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m13.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m14.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m14.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m14.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m14.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'apt-get', 'update'] 0m15.4s DUMP: Get:1 http://security.debian.org stretch/updates InRelease [59.1 kB] Ign:2 http://deb.debian.org/debian stretch InRelease Hit:3 http://deb.debian.org/debian stretch Release Get:4 http://security.debian.org stretch/updates/main amd64 Packages [782 kB] Get:5 http://security.debian.org stretch/updates/main Translation-en [368 kB] Fetched 1209 kB in 0s (2203 kB/s) Reading package lists... 0m15.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'apt-get', 'update'] 0m15.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'apt-get', '-yf', 'dist-upgrade'] 0m26.7s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt ca-certificates debian-archive-keyring dpkg e2fslibs e2fsprogs gzip libapt-pkg5.0 libcomerr2 libgcrypt20 libgmp10 liblz4-1 liblzma5 libruby2.3 libss2 libssl1.0.2 libssl1.1 libsystemd0 libudev1 login openssl passwd ruby2.3 tar zlib1g 25 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 16.7 MB of archives. After this operation, 81.9 kB of additional disk space will be used. Get:1 http://security.debian.org stretch/updates/main amd64 tar amd64 1.29b-1.1+deb9u1 [760 kB] Get:2 http://security.debian.org stretch/updates/main amd64 dpkg amd64 1.18.26 [2117 kB] Get:3 http://security.debian.org stretch/updates/main amd64 e2fslibs amd64 1.43.4-2+deb9u2 [208 kB] Get:4 http://security.debian.org stretch/updates/main amd64 e2fsprogs amd64 1.43.4-2+deb9u2 [948 kB] Get:5 http://security.debian.org stretch/updates/main amd64 gzip amd64 1.6-5+deb9u1 [114 kB] Get:6 http://security.debian.org stretch/updates/main amd64 login amd64 1:4.4-4.1+deb9u1 [790 kB] Get:7 http://security.debian.org stretch/updates/main amd64 debian-archive-keyring all 2017.5+deb9u2 [92.4 kB] Get:8 http://security.debian.org stretch/updates/main amd64 liblz4-1 amd64 0.0~r131-2+deb9u1 [33.2 kB] Get:9 http://security.debian.org stretch/updates/main amd64 liblzma5 amd64 5.2.2-1.2+deb9u1 [234 kB] Get:10 http://security.debian.org stretch/updates/main amd64 zlib1g amd64 1:1.2.8.dfsg-5+deb9u1 [87.8 kB] Get:11 http://security.debian.org stretch/updates/main amd64 libapt-pkg5.0 amd64 1.4.11 [917 kB] Get:12 http://security.debian.org stretch/updates/main amd64 apt amd64 1.4.11 [1232 kB] Get:13 http://security.debian.org stretch/updates/main amd64 libsystemd0 amd64 232-25+deb9u14 [282 kB] Get:14 http://security.debian.org stretch/updates/main amd64 libcomerr2 amd64 1.43.4-2+deb9u2 [63.8 kB] Get:15 http://security.debian.org stretch/updates/main amd64 libss2 amd64 1.43.4-2+deb9u2 [68.0 kB] Get:16 http://security.debian.org stretch/updates/main amd64 passwd amd64 1:4.4-4.1+deb9u1 [997 kB] Get:17 http://security.debian.org stretch/updates/main amd64 libudev1 amd64 232-25+deb9u14 [126 kB] Get:18 http://security.debian.org stretch/updates/main amd64 libgcrypt20 amd64 1.7.6-2+deb9u4 [523 kB] Get:19 http://security.debian.org stretch/updates/main amd64 libssl1.0.2 amd64 1.0.2u-1~deb9u7 [1305 kB] Get:20 http://security.debian.org stretch/updates/main amd64 libssl1.1 amd64 1.1.0l-1~deb9u6 [1360 kB] Get:21 http://security.debian.org stretch/updates/main amd64 openssl amd64 1.1.0l-1~deb9u6 [749 kB] Get:22 http://security.debian.org stretch/updates/main amd64 ca-certificates all 20200601~deb9u2 [168 kB] Get:23 http://security.debian.org stretch/updates/main amd64 libgmp10 amd64 2:6.1.2+dfsg-1+deb9u1 [253 kB] Get:24 http://security.debian.org stretch/updates/main amd64 libruby2.3 amd64 2.3.3-1+deb9u11 [3111 kB] Get:25 http://security.debian.org stretch/updates/main amd64 ruby2.3 amd64 2.3.3-1+deb9u11 [189 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 16.7 MB in 0s (47.5 MB/s) (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 6428 files and directories currently installed.) Preparing to unpack .../tar_1.29b-1.1+deb9u1_amd64.deb ... Unpacking tar (1.29b-1.1+deb9u1) over (1.29b-1.1) ... Setting up tar (1.29b-1.1+deb9u1) ... (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 ... 6428 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.43.4-2+deb9u2_amd64.deb ... Unpacking e2fsprogs (1.43.4-2+deb9u2) over (1.43.4-2+deb9u1) ... Setting up e2fsprogs (1.43.4-2+deb9u2) ... (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 ... 6428 files and directories currently installed.) Preparing to unpack .../zlib1g_1%3a1.2.8.dfsg-5+deb9u1_amd64.deb ... Unpacking zlib1g:amd64 (1:1.2.8.dfsg-5+deb9u1) over (1:1.2.8.dfsg-5) ... Setting up zlib1g:amd64 (1:1.2.8.dfsg-5+deb9u1) ... (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 ... 6428 files and directories currently installed.) Preparing to unpack .../libapt-pkg5.0_1.4.11_amd64.deb ... Unpacking libapt-pkg5.0:amd64 (1.4.11) over (1.4.10) ... Setting up libapt-pkg5.0:amd64 (1.4.11) ... (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 ... 6428 files and directories currently installed.) Preparing to unpack .../archives/apt_1.4.11_amd64.deb ... Unpacking apt (1.4.11) over (1.4.10) ... Setting up apt (1.4.11) ... (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 ... 6428 files and directories currently installed.) Preparing to unpack .../libsystemd0_232-25+deb9u14_amd64.deb ... Unpacking libsystemd0:amd64 (232-25+deb9u14) over (232-25+deb9u12) ... Setting up libsystemd0:amd64 (232-25+deb9u14) ... (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 ... 6428 files and directories currently installed.) Preparing to unpack .../libcomerr2_1.43.4-2+deb9u2_amd64.deb ... Unpacking libcomerr2:amd64 (1.43.4-2+deb9u2) over (1.43.4-2+deb9u1) ... Setting up libcomerr2:amd64 (1.43.4-2+deb9u2) ... (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 ... 6428 files and directories currently installed.) Preparing to unpack .../libss2_1.43.4-2+deb9u2_amd64.deb ... Unpacking libss2:amd64 (1.43.4-2+deb9u2) over (1.43.4-2+deb9u1) ... Setting up libss2:amd64 (1.43.4-2+deb9u2) ... (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 ... 6428 files and directories currently installed.) Preparing to unpack .../passwd_1%3a4.4-4.1+deb9u1_amd64.deb ... Unpacking passwd (1:4.4-4.1+deb9u1) over (1:4.4-4.1) ... Setting up passwd (1:4.4-4.1+deb9u1) ... (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 ... 6428 files and directories currently installed.) Preparing to unpack .../libudev1_232-25+deb9u14_amd64.deb ... Unpacking libudev1:amd64 (232-25+deb9u14) over (232-25+deb9u12) ... Setting up libudev1:amd64 (232-25+deb9u14) ... (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 ... 6428 files and directories currently installed.) Preparing to unpack .../libgcrypt20_1.7.6-2+deb9u4_amd64.deb ... Unpacking libgcrypt20:amd64 (1.7.6-2+deb9u4) over (1.7.6-2+deb9u3) ... Setting up libgcrypt20:amd64 (1.7.6-2+deb9u4) ... (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 ... 6428 files and directories currently installed.) Preparing to unpack .../0-libssl1.0.2_1.0.2u-1~deb9u7_amd64.deb ... Unpacking libssl1.0.2:amd64 (1.0.2u-1~deb9u7) over (1.0.2u-1~deb9u1) ... Preparing to unpack .../1-libssl1.1_1.1.0l-1~deb9u6_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.0l-1~deb9u6) over (1.1.0l-1~deb9u1) ... Preparing to unpack .../2-openssl_1.1.0l-1~deb9u6_amd64.deb ... Unpacking openssl (1.1.0l-1~deb9u6) over (1.1.0l-1~deb9u1) ... Preparing to unpack .../3-ca-certificates_20200601~deb9u2_all.deb ... Unpacking ca-certificates (20200601~deb9u2) over (20200601~deb9u1) ... Preparing to unpack .../4-libgmp10_2%3a6.1.2+dfsg-1+deb9u1_amd64.deb ... Unpacking libgmp10:amd64 (2:6.1.2+dfsg-1+deb9u1) over (2:6.1.2+dfsg-1) ... Preparing to unpack .../5-libruby2.3_2.3.3-1+deb9u11_amd64.deb ... Unpacking libruby2.3:amd64 (2.3.3-1+deb9u11) over (2.3.3-1+deb9u8) ... Preparing to unpack .../6-ruby2.3_2.3.3-1+deb9u11_amd64.deb ... Unpacking ruby2.3 (2.3.3-1+deb9u11) over (2.3.3-1+deb9u8) ... Setting up libssl1.0.2:amd64 (1.0.2u-1~deb9u7) ... Setting up libgmp10:amd64 (2:6.1.2+dfsg-1+deb9u1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up libssl1.1:amd64 (1.1.0l-1~deb9u6) ... Setting up openssl (1.1.0l-1~deb9u6) ... Setting up libruby2.3:amd64 (2.3.3-1+deb9u11) ... Setting up ca-certificates (20200601~deb9u2) ... Updating certificates in /etc/ssl/certs... 11 added, 0 removed; done. Setting up ruby2.3 (2.3.3-1+deb9u11) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Processing triggers for ca-certificates (20200601~deb9u2) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 0m26.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'apt-get', '-yf', 'dist-upgrade'] 0m26.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m27.0s DUMP: f0660a0a38f941b755664f52e8306b99 - 0m27.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m27.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'apt-cache', 'show', '--no-all-versions', 'ruby-bio'] 0m27.2s DUMP: Package: ruby-bio Version: 1.5.0-2 Installed-Size: 3031 Maintainer: Debian Ruby Extras Maintainers Architecture: all Depends: ruby | ruby-interpreter Recommends: blast2, hmmer, mafft, muscle, probcons, sim4, t-coffee Suggests: clustalw, emboss Description-en: Ruby tools for computational molecular biology BioRuby project aims to implement an integrated environment for Bioinformatics with Ruby language. Design philosophy of the BioRuby library is KISS (keep it simple, stupid) to maximize the usability and the efficiency for biologists as a daily tool. The project was started in Japan and supported by University of Tokyo (Human Genome Center), Kyoto University (Bioinformatics Center) and the Open Bio Foundation. Description-md5: 9551e5ebe8c49f9d9485b7f15547f082 Homepage: http://bioruby.org/ Ruby-Versions: all Section: ruby Priority: optional Filename: pool/main/r/ruby-bio/ruby-bio_1.5.0-2_all.deb Size: 700714 MD5sum: 5663504b90d48e9a1e161092c50c2114 SHA256: a8ddf161c996ae5f972b983ece41efbbd36eb00136b5da082f4fa8fc913dec4a 0m27.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'apt-cache', 'show', '--no-all-versions', 'ruby-bio'] 0m27.2s INFO: apt-cache knows about the following packages: ruby-bio 0m27.2s INFO: Running scripts pre_install 0m27.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_install_database-server'] 0m27.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_install_database-server'] 0m27.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_install_exceptions'] 0m27.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_install_exceptions'] 0m27.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_install_extras'] 0m27.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_install_extras'] 0m27.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_install_foreign_architecture'] 0m27.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_install_foreign_architecture'] 0m27.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m27.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m27.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'apt-cache', 'policy'] 0m27.3s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://security.debian.org stretch/updates/main amd64 Packages release v=9,o=Debian,a=oldoldstable,n=stretch,l=Debian-Security,c=main,b=amd64 origin security.debian.org 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: 0m27.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'apt-cache', 'policy'] 0m27.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'apt-cache', 'policy', 'ruby-bio'] 0m27.4s DUMP: ruby-bio: Installed: 1.5.0-2 Candidate: 1.5.0-2 Version table: *** 1.5.0-2 500 500 http://deb.debian.org/debian stretch/main amd64 Packages 100 /var/lib/dpkg/status 0m27.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'apt-cache', 'policy', 'ruby-bio'] 0m27.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'apt-get', '-y', 'install', 'ruby-bio'] 0m27.8s DUMP: Reading package lists... Building dependency tree... Reading state information... ruby-bio is already the newest version (1.5.0-2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m27.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'apt-get', '-y', 'install', 'ruby-bio'] 0m27.8s INFO: Running scripts post_install 0m27.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/post_install_exceptions'] 0m27.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/post_install_exceptions'] 0m27.8s INFO: Running scripts post_distupgrade 0m27.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m27.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m27.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/post_distupgrade_exceptions'] 0m27.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/post_distupgrade_exceptions'] 0m27.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m27.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m27.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m27.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m27.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/post_distupgrade_zz_backports'] 0m27.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/post_distupgrade_zz_backports'] 0m27.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7'] 0m28.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7'] 0m28.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7'] 0m28.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7'] 0m28.5s INFO: Running scripts pre_install 0m28.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_install_database-server'] 0m28.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_install_database-server'] 0m28.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_install_exceptions'] 0m28.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_install_exceptions'] 0m28.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_install_extras'] 0m28.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_install_extras'] 0m28.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_install_foreign_architecture'] 0m28.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_install_foreign_architecture'] 0m28.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m28.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m28.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'apt-cache', 'policy'] 0m28.6s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://security.debian.org stretch/updates/main amd64 Packages release v=9,o=Debian,a=oldoldstable,n=stretch,l=Debian-Security,c=main,b=amd64 origin security.debian.org 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: 0m28.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'apt-cache', 'policy'] 0m28.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'apt-cache', 'policy', 'ruby-bio'] 0m28.7s DUMP: ruby-bio: Installed: 1.5.0-2 Candidate: 1.5.0-2 Version table: *** 1.5.0-2 500 500 http://deb.debian.org/debian stretch/main amd64 Packages 100 /var/lib/dpkg/status 0m28.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'apt-cache', 'policy', 'ruby-bio'] 0m28.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'apt-get', '-y', 'install', 'ruby-bio=1.5.0-2'] 0m29.1s DUMP: Reading package lists... Building dependency tree... Reading state information... ruby-bio is already the newest version (1.5.0-2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m29.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'apt-get', '-y', 'install', 'ruby-bio=1.5.0-2'] 0m29.1s INFO: Running scripts post_install 0m29.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/post_install_exceptions'] 0m29.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/post_install_exceptions'] 0m29.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7'] 0m29.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7'] 0m29.9s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', '-ac', '--ignore-obsolete'] 0m30.7s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', '-ac', '--ignore-obsolete'] 0m30.7s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m30.7s DUMP: 0.15.6 0m30.7s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m30.7s INFO: Running adequate version 0.15.6 now. 0m30.7s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'ruby-bio'] 0m30.9s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'ruby-bio'] 0m30.9s INFO: Running scripts pre_remove 0m30.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m31.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m31.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m31.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m31.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m31.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m31.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m31.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m31.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m32.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m32.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_remove_exceptions'] 0m32.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/pre_remove_exceptions'] 0m32.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m32.1s DUMP: install ok installed adduser adduser 3.115 install ok installed apt apt 1.4.11 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 ca-certificates ca-certificates 20200601~deb9u2 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+deb9u2 install ok installed debianutils debianutils 4.8.1.1 install ok installed diffutils diffutils 1:3.5-3 install ok installed dpkg dpkg 1.18.26 install ok installed e2fslibs:amd64 e2fslibs 1.43.4-2+deb9u2 install ok installed e2fsprogs e2fsprogs 1.43.4-2+deb9u2 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+deb9u1 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 1.4.11 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+deb9u2 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 libffi6:amd64 libffi6 3.2.1-6 install ok installed libgcc1:amd64 libgcc1 1:6.3.0-18+deb9u1 install ok installed libgcrypt20:amd64 libgcrypt20 1.7.6-2+deb9u4 install ok installed libgdbm3:amd64 libgdbm3 1.8.3-14 install ok installed libgmp10:amd64 libgmp10 2:6.1.2+dfsg-1+deb9u1 install ok installed libgpg-error0:amd64 libgpg-error0 1.26-2 install ok installed liblz4-1:amd64 liblz4-1 0.0~r131-2+deb9u1 install ok installed liblzma5:amd64 liblzma5 5.2.2-1.2+deb9u1 install ok installed libmount1:amd64 libmount1 2.29.2-1+deb9u1 install ok installed libncurses5:amd64 libncurses5 6.0+20161126-1+deb9u2 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 libreadline7:amd64 libreadline7 7.0-3 install ok installed libruby2.3:amd64 libruby2.3 2.3.3-1+deb9u11 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+deb9u2 install ok installed libssl1.0.2:amd64 libssl1.0.2 1.0.2u-1~deb9u7 install ok installed libssl1.1:amd64 libssl1.1 1.1.0l-1~deb9u6 install ok installed libstdc++6:amd64 libstdc++6 6.3.0-18+deb9u1 install ok installed libsystemd0:amd64 libsystemd0 232-25+deb9u14 install ok installed libtinfo5:amd64 libtinfo5 6.0+20161126-1+deb9u2 install ok installed libudev1:amd64 libudev1 232-25+deb9u14 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 libyaml-0-2:amd64 libyaml-0-2 0.1.7-2 install ok installed login login 1:4.4-4.1+deb9u1 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 openssl openssl 1.1.0l-1~deb9u6 install ok installed passwd passwd 1:4.4-4.1+deb9u1 install ok installed perl-base perl-base 5.24.1-3+deb9u7 install ok installed rake rake 10.5.0-2+deb9u1 install ok installed readline-common readline-common 7.0-3 install ok installed ruby ruby 1:2.3.3 install ok installed ruby-bio ruby-bio 1.5.0-2 install ok installed ruby-did-you-mean ruby-did-you-mean 1.0.0-2 install ok installed ruby-minitest ruby-minitest 5.9.0-1 install ok installed ruby-net-telnet ruby-net-telnet 0.1.1-2 install ok installed ruby-power-assert ruby-power-assert 0.3.0-1 install ok installed ruby-test-unit ruby-test-unit 3.1.7-2 install ok installed ruby2.3 ruby2.3 2.3.3-1+deb9u11 install ok installed rubygems-integration rubygems-integration 1.11 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+deb9u1 install ok installed util-linux util-linux 2.29.2-1+deb9u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.8.dfsg-5+deb9u1 0m32.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m32.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'apt-get', 'remove', 'ca-certificates', 'libffi6:amd64', 'libgdbm3:amd64', 'libgmp10:amd64', 'libncurses5:amd64', 'libreadline7:amd64', 'libruby2.3:amd64', 'libssl1.0.2:amd64', 'libssl1.1:amd64', 'libyaml-0-2:amd64', 'openssl', 'rake', 'readline-common', 'ruby', 'ruby-did-you-mean', 'ruby-minitest', 'ruby-net-telnet', 'ruby-power-assert', 'ruby-test-unit', 'ruby2.3', 'rubygems-integration', 'ruby-bio'] 0m33.6s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: ca-certificates libffi6 libgdbm3 libgmp10 libncurses5 libreadline7 libruby2.3 libssl1.0.2 libssl1.1 libyaml-0-2 openssl rake readline-common ruby ruby-bio ruby-did-you-mean ruby-minitest ruby-net-telnet ruby-power-assert ruby-test-unit ruby2.3 rubygems-integration 0 upgraded, 0 newly installed, 22 to remove and 0 not upgraded. After this operation, 28.9 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 ... 6439 files and directories currently installed.) Removing ruby-bio (1.5.0-2) ... Removing libruby2.3:amd64 (2.3.3-1+deb9u11) ... Removing rake (10.5.0-2+deb9u1) ... Removing ruby (1:2.3.3) ... Removing libffi6:amd64 (3.2.1-6) ... Removing libgdbm3:amd64 (1.8.3-14) ... Removing libncurses5:amd64 (6.0+20161126-1+deb9u2) ... Removing libreadline7:amd64 (7.0-3) ... Removing libssl1.0.2:amd64 (1.0.2u-1~deb9u7) ... Removing libyaml-0-2:amd64 (0.1.7-2) ... Removing readline-common (7.0-3) ... Removing ruby-did-you-mean (1.0.0-2) ... Removing ruby-minitest (5.9.0-1) ... Removing ruby-net-telnet (0.1.1-2) ... Removing ruby-test-unit (3.1.7-2) ... Removing ruby-power-assert (0.3.0-1) ... Removing ruby2.3 (2.3.3-1+deb9u11) ... Removing rubygems-integration (1.11) ... Removing ca-certificates (20200601~deb9u2) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing libgmp10:amd64 (2:6.1.2+dfsg-1+deb9u1) ... Removing openssl (1.1.0l-1~deb9u6) ... Removing libssl1.1:amd64 (1.1.0l-1~deb9u6) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... 0m33.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'apt-get', 'remove', 'ca-certificates', 'libffi6:amd64', 'libgdbm3:amd64', 'libgmp10:amd64', 'libncurses5:amd64', 'libreadline7:amd64', 'libruby2.3:amd64', 'libssl1.0.2:amd64', 'libssl1.1:amd64', 'libyaml-0-2:amd64', 'openssl', 'rake', 'readline-common', 'ruby', 'ruby-did-you-mean', 'ruby-minitest', 'ruby-net-telnet', 'ruby-power-assert', 'ruby-test-unit', 'ruby2.3', 'rubygems-integration', 'ruby-bio'] 0m33.6s INFO: Running scripts post_remove 0m33.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/post_remove_exceptions'] 0m33.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/post_remove_exceptions'] 0m33.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'dpkg', '--purge', 'ca-certificates', 'libffi6:amd64', 'libgdbm3:amd64', 'libgmp10:amd64', 'libncurses5:amd64', 'libreadline7:amd64', 'libruby2.3:amd64', 'libssl1.0.2:amd64', 'libssl1.1:amd64', 'libyaml-0-2:amd64', 'openssl', 'rake', 'readline-common', 'ruby', 'ruby-did-you-mean', 'ruby-minitest', 'ruby-net-telnet', 'ruby-power-assert', 'ruby-test-unit', 'ruby2.3', 'rubygems-integration'] 0m34.0s DUMP: (Reading database ... 4414 files and directories currently installed.) Purging configuration files for ca-certificates (20200601~deb9u2) ... Removing dangling symlinks from /etc/ssl/certs... done. dpkg: warning: ignoring request to remove libffi6 which isn't installed dpkg: warning: ignoring request to remove libgdbm3 which isn't installed dpkg: warning: ignoring request to remove libgmp10 which isn't installed dpkg: warning: ignoring request to remove libncurses5 which isn't installed dpkg: warning: ignoring request to remove libreadline7 which isn't installed dpkg: warning: ignoring request to remove libruby2.3 which isn't installed Purging configuration files for libssl1.0.2:amd64 (1.0.2u-1~deb9u7) ... Purging configuration files for libssl1.1:amd64 (1.1.0l-1~deb9u6) ... dpkg: warning: ignoring request to remove libyaml-0-2 which isn't installed Purging configuration files for openssl (1.1.0l-1~deb9u6) ... dpkg: warning: ignoring request to remove rake which isn't installed Purging configuration files for readline-common (7.0-3) ... dpkg: warning: ignoring request to remove ruby which isn't installed dpkg: warning: ignoring request to remove ruby-did-you-mean which isn't installed dpkg: warning: ignoring request to remove ruby-minitest which isn't installed dpkg: warning: ignoring request to remove ruby-net-telnet which isn't installed dpkg: warning: ignoring request to remove ruby-power-assert which isn't installed dpkg: warning: ignoring request to remove ruby-test-unit which isn't installed dpkg: warning: ignoring request to remove ruby2.3 which isn't installed dpkg: warning: ignoring request to remove rubygems-integration which isn't installed 0m34.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'dpkg', '--purge', 'ca-certificates', 'libffi6:amd64', 'libgdbm3:amd64', 'libgmp10:amd64', 'libncurses5:amd64', 'libreadline7:amd64', 'libruby2.3:amd64', 'libssl1.0.2:amd64', 'libssl1.1:amd64', 'libyaml-0-2:amd64', 'openssl', 'rake', 'readline-common', 'ruby', 'ruby-did-you-mean', 'ruby-minitest', 'ruby-net-telnet', 'ruby-power-assert', 'ruby-test-unit', 'ruby2.3', 'rubygems-integration'] 0m34.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'dpkg', '--purge', 'ruby-bio'] 0m34.0s DUMP: dpkg: warning: ignoring request to remove ruby-bio which isn't installed 0m34.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'dpkg', '--purge', 'ruby-bio'] 0m34.0s INFO: Running scripts post_purge 0m34.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/post_purge_exceptions'] 0m34.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/post_purge_exceptions'] 0m34.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'dpkg', '--purge', '--pending'] 0m34.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'dpkg', '--purge', '--pending'] 0m34.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'dpkg', '--remove', '--pending'] 0m34.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'dpkg', '--remove', '--pending'] 0m34.1s INFO: Running scripts post_test 0m34.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/post_test_exceptions'] 0m34.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'tmp/scripts/post_test_exceptions'] 0m34.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7'] 0m34.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7'] 0m34.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'dpkg-divert', '--list'] 0m34.4s 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 0m34.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'dpkg-divert', '--list'] 0m34.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'apt-get', 'clean'] 0m34.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7', 'apt-get', 'clean'] 0m34.4s DEBUG: Recording chroot state 0m35.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7/dev/shm'] 0m35.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7/dev/shm'] 0m35.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7/dev/console'] 0m35.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7/dev/console'] 0m35.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7/dev/ptmx'] 0m35.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7/dev/ptmx'] 0m35.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7/dev/pts'] 0m35.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7/dev/pts'] 0m35.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7/proc'] 0m35.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7/proc'] 0m35.1s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7'] 0m35.2s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpkzgkp6f7'] 0m35.2s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpkzgkp6f7 0m35.2s INFO: PASS: Upgrading between Debian distributions. 0m35.2s INFO: PASS: All tests. 0m35.2s INFO: piuparts run ends. ret=0 End: 2023-04-15 17:38:01 GMT