Start: 2019-02-14 15:48:45 UTC [testing] Package: ruby-fix-trinity-output Version: 1.0.0-1 Installed-Size: 29 Maintainer: Debian Ruby Extras Maintainers Architecture: all Depends: ruby | ruby-interpreter, ruby-trollop (>= 2.0) Description: Fix output fastq files from trinityrnaseq Homepage: http://rubygems.org/gems/fix-trinity-output Description-md5: 3f69f71932ea2f46698f4c8c3290ad8e Ruby-Versions: all Section: ruby Priority: optional Filename: pool/main/r/ruby-fix-trinity-output/ruby-fix-trinity-output_1.0.0-1_all.deb Size: 4734 MD5sum: 0ba9f29840214ce02ba379deae85cf68 SHA256: 9a6da7d1e104089e19df5e4813d7467a89adb618844625b581fb5a2b8e42f9af [sid] Package: ruby-fix-trinity-output Version: 1.0.0-2 Installed-Size: 30 Maintainer: Debian Ruby Extras Maintainers Architecture: all Depends: ruby | ruby-interpreter, ruby-trollop (>= 2.0) Description: Fix output fastq files from trinityrnaseq Homepage: http://rubygems.org/gems/fix-trinity-output Description-md5: 3f69f71932ea2f46698f4c8c3290ad8e Ruby-Versions: all Section: ruby Priority: optional Filename: pool/main/r/ruby-fix-trinity-output/ruby-fix-trinity-output_1.0.0-2_all.deb Size: 5040 MD5sum: 59b93806dcf47fe6e53f09134ef4df42 SHA256: 49f3061861ec92be6ea88e10ac470d8a15bbd73ec8267f54e2ac17f773900d4f Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python2.7/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://mirror.bm.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/buster_amd64.tar.gz -d testing -d sid -B reference-chroot-metadata.dat --apt ruby-fix-trinity-output=1.0.0-2 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 0.98~201902141516~0.97-23-ga308323a starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://mirror.bm.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/buster_amd64.tar.gz -d testing -d sid -B reference-chroot-metadata.dat --apt ruby-fix-trinity-output=1.0.0-2 0m0.0s INFO: Running on: Linux piu-slave-bm-a 4.9.0-8-amd64 #1 SMP Debian 4.9.130-2 (2018-10-27) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmp5wzv4k 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/buster_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmp5wzv4k 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/buster_amd64.tar.gz'] 0m2.6s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/buster_amd64.tar.gz'] 0m2.6s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp5wzv4k/proc'] 0m2.7s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmp5wzv4k/proc'] 0m2.7s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp5wzv4k/dev/pts'] 0m2.7s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmp5wzv4k/dev/pts'] 0m2.7s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp5wzv4k/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp5wzv4k/dev/ptmx'] 0m2.7s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmp5wzv4k/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmp5wzv4k/dev/ptmx'] 0m2.7s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/5', '/srv/piuparts.debian.org/tmp/tmp5wzv4k/dev/console'] 0m2.7s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/5', '/srv/piuparts.debian.org/tmp/tmp5wzv4k/dev/console'] 0m2.7s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp5wzv4k/dev/shm'] 0m2.8s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmp5wzv4k/dev/shm'] 0m2.8s DEBUG: sources.list: deb http://mirror.bm.debian.org/debian/ buster main 0m2.8s DEBUG: Created policy-rc.d and chmodded it. 0m2.8s DEBUG: Created resolv.conf. 0m2.8s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmp5wzv4k/tmp/scripts/ 0m2.8s INFO: Running scripts post_chroot_unpack 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m2.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'apt-get', 'update'] 0m6.8s DUMP: Get:1 http://mirror.bm.debian.org/debian buster InRelease [159 kB] Get:2 http://mirror.bm.debian.org/debian buster/main amd64 Packages [7995 kB] Fetched 8154 kB in 2s (3590 kB/s) Reading package lists... 0m6.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'apt-get', 'update'] 0m6.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'apt-get', '-yf', 'dist-upgrade'] 0m8.2s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m8.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'apt-get', '-yf', 'dist-upgrade'] 0m8.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m9.5s DUMP: 93fd9b1b97f5337158f8997e780a7fa7 - 0m9.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m9.5s INFO: Running scripts post_setup 0m9.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_setup_dummy_users'] 0m11.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_setup_dummy_users'] 0m11.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_setup_experimental'] 0m11.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_setup_experimental'] 0m11.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_setup_forbid_home'] 0m11.5s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m11.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_setup_forbid_home'] 0m11.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_setup_force-unsafe-io'] 0m11.6s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' dpkg-divert: warning: diverting file '/bin/sync' from an Essential package with rename is dangerous, use --no-rename '/bin/sync' -> 'true' 0m11.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_setup_force-unsafe-io'] 0m11.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_setup_minimize'] 0m11.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_setup_minimize'] 0m11.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_setup_squeeze-backports'] 0m11.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_setup_squeeze-backports'] 0m11.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_setup_zz_backports'] 0m11.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_setup_zz_backports'] 0m11.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m11.7s DUMP: install ok installed adduser adduser 3.118 install ok installed apt apt 1.8.0~rc2 install ok installed base-files base-files 10.1 install ok installed base-passwd base-passwd 3.5.45 install ok installed bash bash 5.0-2 install ok installed bsdutils bsdutils 1:2.33.1-0.1 install ok installed coreutils coreutils 8.30-1 install ok installed dash dash 0.5.10.2-5 install ok installed debconf debconf 1.5.70 install ok installed debian-archive-keyring debian-archive-keyring 2018.1 install ok installed debianutils debianutils 4.8.6.1 install ok installed diffutils diffutils 1:3.6-1 install ok installed dpkg dpkg 1.19.2 install ok installed e2fsprogs e2fsprogs 1.44.5-1 install ok installed fdisk fdisk 2.33.1-0.1 install ok installed findutils findutils 4.6.0+git+20190105-2 install ok installed gcc-8-base:amd64 gcc-8-base 8.2.0-16 install ok installed gpgv gpgv 2.2.12-1 install ok installed grep grep 3.3-1 install ok installed gzip gzip 1.9-3 install ok installed hostname hostname 3.21 install ok installed init-system-helpers init-system-helpers 1.56+nmu1 install ok installed libacl1:amd64 libacl1 2.2.52-3+b1 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.8.0~rc2 install ok installed libattr1:amd64 libattr1 1:2.4.47-2+b2 install ok installed libaudit-common libaudit-common 1:2.8.4-2 install ok installed libaudit1:amd64 libaudit1 1:2.8.4-2 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 install ok installed libc-bin libc-bin 2.28-6 install ok installed libc6:amd64 libc6 2.28-6 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2 install ok installed libcom-err2:amd64 libcom-err2 1.44.5-1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.3 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.246 install ok installed libext2fs2:amd64 libext2fs2 1.44.5-1 install ok installed libfdisk1:amd64 libfdisk1 2.33.1-0.1 install ok installed libffi6:amd64 libffi6 3.2.1-9 install ok installed libgcc1:amd64 libgcc1 1:8.2.0-16 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.4-5 install ok installed libgmp10:amd64 libgmp10 2:6.1.2+dfsg-4 install ok installed libgnutls30:amd64 libgnutls30 3.6.6-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.35-1 install ok installed libhogweed4:amd64 libhogweed4 3.4.1-1 install ok installed libidn2-0:amd64 libidn2-0 2.0.5-1 install ok installed liblz4-1:amd64 liblz4-1 1.8.3-1 install ok installed liblzma5:amd64 liblzma5 5.2.4-1 install ok installed libmount1:amd64 libmount1 2.33.1-0.1 install ok installed libncursesw6:amd64 libncursesw6 6.1+20181013-1 install ok installed libnettle6:amd64 libnettle6 3.4.1-1 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.14-2 install ok installed libpam-modules:amd64 libpam-modules 1.1.8-4 install ok installed libpam-modules-bin libpam-modules-bin 1.1.8-4 install ok installed libpam-runtime libpam-runtime 1.1.8-4 install ok installed libpam0g:amd64 libpam0g 1.1.8-4 install ok installed libpcre3:amd64 libpcre3 2:8.39-11 install ok installed libseccomp2:amd64 libseccomp2 2.3.3-3 install ok installed libselinux1:amd64 libselinux1 2.8-1+b1 install ok installed libsemanage-common libsemanage-common 2.8-2 install ok installed libsemanage1:amd64 libsemanage1 2.8-2 install ok installed libsepol1:amd64 libsepol1 2.8-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.33.1-0.1 install ok installed libss2:amd64 libss2 1.44.5-1 install ok installed libstdc++6:amd64 libstdc++6 8.2.0-16 install ok installed libsystemd0:amd64 libsystemd0 240-5 install ok installed libtasn1-6:amd64 libtasn1-6 4.13-3 install ok installed libtinfo6:amd64 libtinfo6 6.1+20181013-1 install ok installed libudev1:amd64 libudev1 240-5 install ok installed libunistring2:amd64 libunistring2 0.9.10-1 install ok installed libuuid1:amd64 libuuid1 2.33.1-0.1 install ok installed libzstd1:amd64 libzstd1 1.3.8+dfsg-3 install ok installed login login 1:4.5-1.1 install ok installed mawk mawk 1.3.3-17+b3 install ok installed mount mount 2.33.1-0.1 install ok installed ncurses-base ncurses-base 6.1+20181013-1 install ok installed ncurses-bin ncurses-bin 6.1+20181013-1 install ok installed passwd passwd 1:4.5-1.1 install ok installed perl-base perl-base 5.28.1-4 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.93-6 install ok installed tar tar 1.30+dfsg-5 install ok installed tzdata tzdata 2018i-1 install ok installed util-linux util-linux 2.33.1-0.1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-1 0m11.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m11.7s DEBUG: Loading chroot meta data from reference-chroot-metadata.dat 0m12.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5wzv4k'] 0m13.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5wzv4k'] 0m13.9s INFO: Running scripts is_testable 0m13.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/is_testable_uninstallable'] 0m14.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/is_testable_uninstallable'] 0m14.0s INFO: Running scripts pre_test 0m14.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_test_exceptions'] 0m14.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_test_exceptions'] 0m14.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_test_root_password'] 0m14.0s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m14.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_test_root_password'] 0m14.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'apt-cache', 'show', '--no-all-versions', 'ruby-fix-trinity-output'] 0m14.5s DUMP: Package: ruby-fix-trinity-output Version: 1.0.0-1 Installed-Size: 29 Maintainer: Debian Ruby Extras Maintainers Architecture: all Depends: ruby | ruby-interpreter, ruby-trollop (>= 2.0) Description-en: Fix output fastq files from trinityrnaseq trinityrnaseq outputs fastq files that have been 'corrected' . Unfortunately these files are no longer properly paired and therefore can't be used in most aligners such as bowtie2 and snap-aligner. This script attempts to fix that and produce 2 properly paired fastq files and a fastq file containing single reads Description-md5: 3f69f71932ea2f46698f4c8c3290ad8e Homepage: http://rubygems.org/gems/fix-trinity-output Ruby-Versions: all Section: ruby Priority: optional Filename: pool/main/r/ruby-fix-trinity-output/ruby-fix-trinity-output_1.0.0-1_all.deb Size: 4734 MD5sum: 0ba9f29840214ce02ba379deae85cf68 SHA256: 9a6da7d1e104089e19df5e4813d7467a89adb618844625b581fb5a2b8e42f9af 0m14.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'apt-cache', 'show', '--no-all-versions', 'ruby-fix-trinity-output'] 0m14.5s INFO: apt-cache knows about the following packages: ruby-fix-trinity-output 0m14.5s INFO: Running scripts pre_install 0m14.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_install_database-server'] 0m14.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_install_database-server'] 0m14.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_install_exceptions'] 0m14.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_install_exceptions'] 0m14.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_install_extras'] 0m14.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_install_extras'] 0m14.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_install_foreign_architecture'] 0m14.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_install_foreign_architecture'] 0m14.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m14.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m14.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'apt-cache', 'policy'] 0m14.7s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://mirror.bm.debian.org/debian buster/main amd64 Packages release o=Debian,a=testing,n=buster,l=Debian,c=main,b=amd64 origin mirror.bm.debian.org Pinned packages: 0m14.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'apt-cache', 'policy'] 0m14.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'apt-cache', 'policy', 'ruby-fix-trinity-output'] 0m14.8s DUMP: ruby-fix-trinity-output: Installed: (none) Candidate: 1.0.0-1 Version table: 1.0.0-1 500 500 http://mirror.bm.debian.org/debian buster/main amd64 Packages 0m14.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'apt-cache', 'policy', 'ruby-fix-trinity-output'] 0m14.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'apt-get', '-y', 'install', 'ruby-fix-trinity-output'] 0m23.7s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: ca-certificates libgdbm-compat4 libgdbm6 libncurses6 libreadline7 libruby2.5 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 ruby-trollop ruby-xmlrpc ruby2.5 rubygems-integration Suggested packages: gdbm-l10n readline-doc ri ruby-dev bundler Recommended packages: libgpm2 zip fonts-lato libjs-jquery The following NEW packages will be installed: ca-certificates libgdbm-compat4 libgdbm6 libncurses6 libreadline7 libruby2.5 libssl1.1 libyaml-0-2 openssl rake readline-common ruby ruby-did-you-mean ruby-fix-trinity-output ruby-minitest ruby-net-telnet ruby-power-assert ruby-test-unit ruby-trollop ruby-xmlrpc ruby2.5 rubygems-integration 0 upgraded, 22 newly installed, 0 to remove and 0 not upgraded. Need to get 7114 kB of archives. After this operation, 23.9 MB of additional disk space will be used. Get:1 http://mirror.bm.debian.org/debian buster/main amd64 readline-common all 7.0-5 [70.6 kB] Get:2 http://mirror.bm.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1a-1 [1527 kB] Get:3 http://mirror.bm.debian.org/debian buster/main amd64 openssl amd64 1.1.1a-1 [836 kB] Get:4 http://mirror.bm.debian.org/debian buster/main amd64 ca-certificates all 20190110 [157 kB] Get:5 http://mirror.bm.debian.org/debian buster/main amd64 libgdbm6 amd64 1.18.1-2 [64.5 kB] Get:6 http://mirror.bm.debian.org/debian buster/main amd64 libgdbm-compat4 amd64 1.18.1-2 [44.0 kB] Get:7 http://mirror.bm.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-1 [102 kB] Get:8 http://mirror.bm.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get:9 http://mirror.bm.debian.org/debian buster/main amd64 rubygems-integration all 1.11 [4994 B] Get:10 http://mirror.bm.debian.org/debian buster/main amd64 ruby2.5 amd64 2.5.3-3 [393 kB] Get:11 http://mirror.bm.debian.org/debian buster/main amd64 ruby amd64 1:2.5.1 [11.3 kB] Get:12 http://mirror.bm.debian.org/debian buster/main amd64 rake all 12.3.1-3 [66.9 kB] Get:13 http://mirror.bm.debian.org/debian buster/main amd64 ruby-did-you-mean all 1.2.1-1 [14.4 kB] Get:14 http://mirror.bm.debian.org/debian buster/main amd64 ruby-minitest all 5.11.3-1 [54.8 kB] Get:15 http://mirror.bm.debian.org/debian buster/main amd64 ruby-net-telnet all 0.1.1-2 [12.5 kB] Get:16 http://mirror.bm.debian.org/debian buster/main amd64 ruby-power-assert all 1.1.1-1 [10.9 kB] Get:17 http://mirror.bm.debian.org/debian buster/main amd64 ruby-test-unit all 3.2.8-1 [72.4 kB] Get:18 http://mirror.bm.debian.org/debian buster/main amd64 ruby-xmlrpc all 0.3.0-2 [23.7 kB] Get:19 http://mirror.bm.debian.org/debian buster/main amd64 libyaml-0-2 amd64 0.2.1-1 [47.2 kB] Get:20 http://mirror.bm.debian.org/debian buster/main amd64 libruby2.5 amd64 2.5.3-3 [3429 kB] Get:21 http://mirror.bm.debian.org/debian buster/main amd64 ruby-trollop all 2.0-2 [16.8 kB] Get:22 http://mirror.bm.debian.org/debian buster/main amd64 ruby-fix-trinity-output all 1.0.0-1 [4734 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 7114 kB in 0s (31.9 MB/s) Selecting previously unselected package readline-common. (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 ... 6359 files and directories currently installed.) Preparing to unpack .../00-readline-common_7.0-5_all.deb ... Unpacking readline-common (7.0-5) ... Selecting previously unselected package libssl1.1:amd64. Preparing to unpack .../01-libssl1.1_1.1.1a-1_amd64.deb ... Unpacking libssl1.1:amd64 (1.1.1a-1) ... Selecting previously unselected package openssl. Preparing to unpack .../02-openssl_1.1.1a-1_amd64.deb ... Unpacking openssl (1.1.1a-1) ... Selecting previously unselected package ca-certificates. Preparing to unpack .../03-ca-certificates_20190110_all.deb ... Unpacking ca-certificates (20190110) ... Selecting previously unselected package libgdbm6:amd64. Preparing to unpack .../04-libgdbm6_1.18.1-2_amd64.deb ... Unpacking libgdbm6:amd64 (1.18.1-2) ... Selecting previously unselected package libgdbm-compat4:amd64. Preparing to unpack .../05-libgdbm-compat4_1.18.1-2_amd64.deb ... Unpacking libgdbm-compat4:amd64 (1.18.1-2) ... Selecting previously unselected package libncurses6:amd64. Preparing to unpack .../06-libncurses6_6.1+20181013-1_amd64.deb ... Unpacking libncurses6:amd64 (6.1+20181013-1) ... Selecting previously unselected package libreadline7:amd64. Preparing to unpack .../07-libreadline7_7.0-5_amd64.deb ... Unpacking libreadline7:amd64 (7.0-5) ... Selecting previously unselected package rubygems-integration. Preparing to unpack .../08-rubygems-integration_1.11_all.deb ... Unpacking rubygems-integration (1.11) ... Selecting previously unselected package ruby2.5. Preparing to unpack .../09-ruby2.5_2.5.3-3_amd64.deb ... Unpacking ruby2.5 (2.5.3-3) ... Selecting previously unselected package ruby. Preparing to unpack .../10-ruby_1%3a2.5.1_amd64.deb ... Unpacking ruby (1:2.5.1) ... Selecting previously unselected package rake. Preparing to unpack .../11-rake_12.3.1-3_all.deb ... Unpacking rake (12.3.1-3) ... Selecting previously unselected package ruby-did-you-mean. Preparing to unpack .../12-ruby-did-you-mean_1.2.1-1_all.deb ... Unpacking ruby-did-you-mean (1.2.1-1) ... Selecting previously unselected package ruby-minitest. Preparing to unpack .../13-ruby-minitest_5.11.3-1_all.deb ... Unpacking ruby-minitest (5.11.3-1) ... 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_1.1.1-1_all.deb ... Unpacking ruby-power-assert (1.1.1-1) ... Selecting previously unselected package ruby-test-unit. Preparing to unpack .../16-ruby-test-unit_3.2.8-1_all.deb ... Unpacking ruby-test-unit (3.2.8-1) ... Selecting previously unselected package ruby-xmlrpc. Preparing to unpack .../17-ruby-xmlrpc_0.3.0-2_all.deb ... Unpacking ruby-xmlrpc (0.3.0-2) ... Selecting previously unselected package libyaml-0-2:amd64. Preparing to unpack .../18-libyaml-0-2_0.2.1-1_amd64.deb ... Unpacking libyaml-0-2:amd64 (0.2.1-1) ... Selecting previously unselected package libruby2.5:amd64. Preparing to unpack .../19-libruby2.5_2.5.3-3_amd64.deb ... Unpacking libruby2.5:amd64 (2.5.3-3) ... Selecting previously unselected package ruby-trollop. Preparing to unpack .../20-ruby-trollop_2.0-2_all.deb ... Unpacking ruby-trollop (2.0-2) ... Selecting previously unselected package ruby-fix-trinity-output. Preparing to unpack .../21-ruby-fix-trinity-output_1.0.0-1_all.deb ... Unpacking ruby-fix-trinity-output (1.0.0-1) ... Setting up readline-common (7.0-5) ... Setting up ruby-xmlrpc (0.3.0-2) ... Setting up libreadline7:amd64 (7.0-5) ... Setting up libgdbm6:amd64 (1.18.1-2) ... Setting up ruby-did-you-mean (1.2.1-1) ... Setting up libyaml-0-2:amd64 (0.2.1-1) ... Processing triggers for libc-bin (2.28-6) ... Setting up libssl1.1:amd64 (1.1.1a-1) ... Setting up openssl (1.1.1a-1) ... Setting up ruby-net-telnet (0.1.1-2) ... Setting up libgdbm-compat4:amd64 (1.18.1-2) ... Setting up ruby-minitest (5.11.3-1) ... Setting up ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 128 added, 0 removed; done. Setting up libncurses6:amd64 (6.1+20181013-1) ... Setting up ruby-power-assert (1.1.1-1) ... Setting up ruby-test-unit (3.2.8-1) ... Setting up rubygems-integration (1.11) ... Setting up rake (12.3.1-3) ... Setting up libruby2.5:amd64 (2.5.3-3) ... Setting up ruby2.5 (2.5.3-3) ... Setting up ruby (1:2.5.1) ... Setting up ruby-trollop (2.0-2) ... Setting up ruby-fix-trinity-output (1.0.0-1) ... Processing triggers for libc-bin (2.28-6) ... Processing triggers for ca-certificates (20190110) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. 0m23.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'apt-get', '-y', 'install', 'ruby-fix-trinity-output'] 0m23.7s INFO: Running scripts post_install 0m23.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_install_exceptions'] 0m23.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_install_exceptions'] 0m23.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5wzv4k'] 0m25.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5wzv4k'] 0m25.2s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmp5wzv4k to sid 0m25.2s DEBUG: sources.list: deb http://mirror.bm.debian.org/debian/ sid main 0m25.2s INFO: Running scripts pre_distupgrade 0m25.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m25.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 0m25.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_distupgrade_exceptions'] 0m25.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_distupgrade_exceptions'] 0m25.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m25.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 0m25.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m25.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_distupgrade_zz_database-server'] 0m25.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m25.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 0m25.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'apt-get', 'update'] 0m32.9s DUMP: Get:1 http://mirror.bm.debian.org/debian sid InRelease [243 kB] Get:2 http://mirror.bm.debian.org/debian sid/main amd64 Packages [8351 kB] Get:3 http://mirror.bm.debian.org/debian sid/main Translation-en [6321 kB] Fetched 14.9 MB in 6s (2643 kB/s) Reading package lists... 0m32.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'apt-get', 'update'] 0m32.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'apt-get', '-yf', 'dist-upgrade'] 0m41.3s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages will be upgraded: apt base-passwd dpkg gcc-8-base libapt-pkg5.0 libc-bin libc6 libdebconfclient0 libgcc1 libgdbm-compat4 libgdbm6 libncurses6 libncursesw6 libpam-modules libpam-modules-bin libpam-runtime libpam0g libseccomp2 libstdc++6 libtinfo6 ncurses-base ncurses-bin ruby-fix-trinity-output 23 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. Need to get 11.0 MB of archives. After this operation, 91.1 kB of additional disk space will be used. Get:1 http://mirror.bm.debian.org/debian sid/main amd64 dpkg amd64 1.19.4 [2157 kB] Get:2 http://mirror.bm.debian.org/debian sid/main amd64 ncurses-bin amd64 6.1+20181013-2 [406 kB] Get:3 http://mirror.bm.debian.org/debian sid/main amd64 gcc-8-base amd64 8.2.0-20 [189 kB] Get:4 http://mirror.bm.debian.org/debian sid/main amd64 libgcc1 amd64 1:8.2.0-20 [40.7 kB] Get:5 http://mirror.bm.debian.org/debian sid/main amd64 libstdc++6 amd64 8.2.0-20 [392 kB] Get:6 http://mirror.bm.debian.org/debian sid/main amd64 libc6 amd64 2.28-7 [2863 kB] Get:7 http://mirror.bm.debian.org/debian sid/main amd64 libapt-pkg5.0 amd64 1.8.0~rc3 [966 kB] Get:8 http://mirror.bm.debian.org/debian sid/main amd64 libseccomp2 amd64 2.3.3-4 [41.4 kB] Get:9 http://mirror.bm.debian.org/debian sid/main amd64 apt amd64 1.8.0~rc3 [1356 kB] Get:10 http://mirror.bm.debian.org/debian sid/main amd64 libdebconfclient0 amd64 0.247 [48.9 kB] Get:11 http://mirror.bm.debian.org/debian sid/main amd64 base-passwd amd64 3.5.46 [56.7 kB] Get:12 http://mirror.bm.debian.org/debian sid/main amd64 libc-bin amd64 2.28-7 [789 kB] Get:13 http://mirror.bm.debian.org/debian sid/main amd64 ncurses-base all 6.1+20181013-2 [258 kB] Get:14 http://mirror.bm.debian.org/debian sid/main amd64 libpam0g amd64 1.3.1-5 [126 kB] Get:15 http://mirror.bm.debian.org/debian sid/main amd64 libpam-modules-bin amd64 1.3.1-5 [107 kB] Get:16 http://mirror.bm.debian.org/debian sid/main amd64 libpam-modules amd64 1.3.1-5 [309 kB] Get:17 http://mirror.bm.debian.org/debian sid/main amd64 libpam-runtime all 1.3.1-5 [211 kB] Get:18 http://mirror.bm.debian.org/debian sid/main amd64 libncurses6 amd64 6.1+20181013-2 [102 kB] Get:19 http://mirror.bm.debian.org/debian sid/main amd64 libtinfo6 amd64 6.1+20181013-2 [325 kB] Get:20 http://mirror.bm.debian.org/debian sid/main amd64 libncursesw6 amd64 6.1+20181013-2 [132 kB] Get:21 http://mirror.bm.debian.org/debian sid/main amd64 libgdbm6 amd64 1.18.1-3 [64.5 kB] Get:22 http://mirror.bm.debian.org/debian sid/main amd64 libgdbm-compat4 amd64 1.18.1-3 [44.0 kB] Get:23 http://mirror.bm.debian.org/debian sid/main amd64 ruby-fix-trinity-output all 1.0.0-2 [5040 B] debconf: delaying package configuration, since apt-utils is not installed Fetched 11.0 MB in 0s (56.5 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 ... 7999 files and directories currently installed.) Preparing to unpack .../archives/dpkg_1.19.4_amd64.deb ... Unpacking dpkg (1.19.4) over (1.19.2) ... Setting up dpkg (1.19.4) ... Installing new version of config file /etc/cron.daily/dpkg ... (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 ... 7996 files and directories currently installed.) Preparing to unpack .../libc6_2.28-7_amd64.deb ... Unpacking libc6:amd64 (2.28-7) over (2.28-6) ... Setting up libc6:amd64 (2.28-7) ... (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 ... 7996 files and directories currently installed.) Preparing to unpack .../libapt-pkg5.0_1.8.0~rc3_amd64.deb ... Unpacking libapt-pkg5.0:amd64 (1.8.0~rc3) over (1.8.0~rc2) ... Setting up libapt-pkg5.0:amd64 (1.8.0~rc3) ... (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 ... 7996 files and directories currently installed.) Preparing to unpack .../libseccomp2_2.3.3-4_amd64.deb ... Unpacking libseccomp2:amd64 (2.3.3-4) over (2.3.3-3) ... Setting up libseccomp2:amd64 (2.3.3-4) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 7996 files and directories currently installed.) Preparing to unpack .../apt_1.8.0~rc3_amd64.deb ... Unpacking apt (1.8.0~rc3) over (1.8.0~rc2) ... Setting up apt (1.8.0~rc3) ... (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 ... 8008 files and directories currently installed.) Preparing to unpack .../libdebconfclient0_0.247_amd64.deb ... Unpacking libdebconfclient0:amd64 (0.247) over (0.246) ... Setting up libdebconfclient0:amd64 (0.247) ... (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 ... 8008 files and directories currently installed.) Preparing to unpack .../base-passwd_3.5.46_amd64.deb ... Unpacking base-passwd (3.5.46) over (3.5.45) ... Setting up base-passwd (3.5.46) ... (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 ... 8008 files and directories currently installed.) Preparing to unpack .../libc-bin_2.28-7_amd64.deb ... Unpacking libc-bin (2.28-7) over (2.28-6) ... Setting up libc-bin (2.28-7) ... (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 ... 8008 files and directories currently installed.) Preparing to unpack .../ncurses-base_6.1+20181013-2_all.deb ... Unpacking ncurses-base (6.1+20181013-2) over (6.1+20181013-1) ... Setting up ncurses-base (6.1+20181013-2) ... (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 ... 8008 files and directories currently installed.) Preparing to unpack .../libpam0g_1.3.1-5_amd64.deb ... Unpacking libpam0g:amd64 (1.3.1-5) over (1.1.8-4) ... Setting up libpam0g:amd64 (1.3.1-5) ... Checking for services that may need to be restarted...Checking init scripts... Nothing to restart. (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 ... 8008 files and directories currently installed.) Preparing to unpack .../libpam-modules-bin_1.3.1-5_amd64.deb ... Unpacking libpam-modules-bin (1.3.1-5) over (1.1.8-4) ... Setting up libpam-modules-bin (1.3.1-5) ... (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 ... 8008 files and directories currently installed.) Preparing to unpack .../libpam-modules_1.3.1-5_amd64.deb ... Unpacking libpam-modules:amd64 (1.3.1-5) over (1.1.8-4) ... Setting up libpam-modules:amd64 (1.3.1-5) ... Installing new version of config file /etc/security/access.conf ... Installing new version of config file /etc/security/limits.conf ... (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 ... 8008 files and directories currently installed.) Preparing to unpack .../libpam-runtime_1.3.1-5_all.deb ... Unpacking libpam-runtime (1.3.1-5) over (1.1.8-4) ... Setting up libpam-runtime (1.3.1-5) ... (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 ... 8068 files and directories currently installed.) Preparing to unpack .../libncurses6_6.1+20181013-2_amd64.deb ... Unpacking libncurses6:amd64 (6.1+20181013-2) over (6.1+20181013-1) ... Preparing to unpack .../libtinfo6_6.1+20181013-2_amd64.deb ... Unpacking libtinfo6:amd64 (6.1+20181013-2) over (6.1+20181013-1) ... Setting up libtinfo6:amd64 (6.1+20181013-2) ... (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 ... 8068 files and directories currently installed.) Preparing to unpack .../libncursesw6_6.1+20181013-2_amd64.deb ... Unpacking libncursesw6:amd64 (6.1+20181013-2) over (6.1+20181013-1) ... Setting up libncursesw6:amd64 (6.1+20181013-2) ... (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 ... 8068 files and directories currently installed.) Preparing to unpack .../libgdbm6_1.18.1-3_amd64.deb ... Unpacking libgdbm6:amd64 (1.18.1-3) over (1.18.1-2) ... Preparing to unpack .../libgdbm-compat4_1.18.1-3_amd64.deb ... Unpacking libgdbm-compat4:amd64 (1.18.1-3) over (1.18.1-2) ... Preparing to unpack .../ruby-fix-trinity-output_1.0.0-2_all.deb ... Unpacking ruby-fix-trinity-output (1.0.0-2) over (1.0.0-1) ... Setting up libgdbm6:amd64 (1.18.1-3) ... Setting up libgdbm-compat4:amd64 (1.18.1-3) ... Setting up ruby-fix-trinity-output (1.0.0-2) ... Setting up libncurses6:amd64 (6.1+20181013-2) ... Processing triggers for libc-bin (2.28-7) ... 0m41.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'apt-get', '-yf', 'dist-upgrade'] 0m41.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m42.5s DUMP: 1142f1fc8824103226f5da3495fc52f5 - 0m42.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m42.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'apt-cache', 'show', '--no-all-versions', 'ruby-fix-trinity-output'] 0m43.0s DUMP: Package: ruby-fix-trinity-output Version: 1.0.0-2 Installed-Size: 30 Maintainer: Debian Ruby Extras Maintainers Architecture: all Depends: ruby | ruby-interpreter, ruby-trollop (>= 2.0) Description-en: Fix output fastq files from trinityrnaseq trinityrnaseq outputs fastq files that have been 'corrected' . Unfortunately these files are no longer properly paired and therefore can't be used in most aligners such as bowtie2 and snap-aligner. This script attempts to fix that and produce 2 properly paired fastq files and a fastq file containing single reads Description-md5: 3f69f71932ea2f46698f4c8c3290ad8e Homepage: http://rubygems.org/gems/fix-trinity-output Ruby-Versions: all Section: ruby Priority: optional Filename: pool/main/r/ruby-fix-trinity-output/ruby-fix-trinity-output_1.0.0-2_all.deb Size: 5040 MD5sum: 59b93806dcf47fe6e53f09134ef4df42 SHA256: 49f3061861ec92be6ea88e10ac470d8a15bbd73ec8267f54e2ac17f773900d4f 0m43.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'apt-cache', 'show', '--no-all-versions', 'ruby-fix-trinity-output'] 0m43.0s INFO: apt-cache knows about the following packages: ruby-fix-trinity-output 0m43.0s INFO: Running scripts pre_install 0m43.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_install_database-server'] 0m43.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_install_database-server'] 0m43.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_install_exceptions'] 0m43.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_install_exceptions'] 0m43.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_install_extras'] 0m43.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_install_extras'] 0m43.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_install_foreign_architecture'] 0m43.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_install_foreign_architecture'] 0m43.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m43.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m43.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'apt-cache', 'policy'] 0m43.2s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://mirror.bm.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin mirror.bm.debian.org Pinned packages: 0m43.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'apt-cache', 'policy'] 0m43.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'apt-cache', 'policy', 'ruby-fix-trinity-output'] 0m43.4s DUMP: ruby-fix-trinity-output: Installed: 1.0.0-2 Candidate: 1.0.0-2 Version table: *** 1.0.0-2 500 500 http://mirror.bm.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m43.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'apt-cache', 'policy', 'ruby-fix-trinity-output'] 0m43.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'apt-get', '-y', 'install', 'ruby-fix-trinity-output'] 0m44.8s DUMP: Reading package lists... Building dependency tree... Reading state information... ruby-fix-trinity-output is already the newest version (1.0.0-2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m44.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'apt-get', '-y', 'install', 'ruby-fix-trinity-output'] 0m44.8s INFO: Running scripts post_install 0m44.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_install_exceptions'] 0m44.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_install_exceptions'] 0m44.8s INFO: Running scripts post_distupgrade 0m44.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m44.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_distupgrade_base_cleanup'] 0m44.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_distupgrade_exceptions'] 0m44.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_distupgrade_exceptions'] 0m44.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_distupgrade_experimental'] 0m44.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_distupgrade_experimental'] 0m44.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m44.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 0m44.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_distupgrade_hack_debsums'] 0m44.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_distupgrade_hack_debsums'] 0m44.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m44.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_distupgrade_squeeze-backports'] 0m44.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_distupgrade_zz_backports'] 0m44.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_distupgrade_zz_backports'] 0m44.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5wzv4k'] 0m46.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5wzv4k'] 0m46.4s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5wzv4k'] 0m48.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5wzv4k'] 0m48.0s INFO: Running scripts pre_install 0m48.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_install_database-server'] 0m48.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_install_database-server'] 0m48.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_install_exceptions'] 0m48.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_install_exceptions'] 0m48.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_install_extras'] 0m48.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_install_extras'] 0m48.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_install_foreign_architecture'] 0m48.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_install_foreign_architecture'] 0m48.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m48.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m48.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'apt-cache', 'policy'] 0m48.2s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://mirror.bm.debian.org/debian sid/main amd64 Packages release o=Debian,a=unstable,n=sid,l=Debian,c=main,b=amd64 origin mirror.bm.debian.org Pinned packages: 0m48.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'apt-cache', 'policy'] 0m48.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'apt-cache', 'policy', 'ruby-fix-trinity-output'] 0m48.3s DUMP: ruby-fix-trinity-output: Installed: 1.0.0-2 Candidate: 1.0.0-2 Version table: *** 1.0.0-2 500 500 http://mirror.bm.debian.org/debian sid/main amd64 Packages 100 /var/lib/dpkg/status 0m48.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'apt-cache', 'policy', 'ruby-fix-trinity-output'] 0m48.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'apt-get', '-y', 'install', 'ruby-fix-trinity-output=1.0.0-2'] 0m49.8s DUMP: Reading package lists... Building dependency tree... Reading state information... ruby-fix-trinity-output is already the newest version (1.0.0-2). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m49.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'apt-get', '-y', 'install', 'ruby-fix-trinity-output=1.0.0-2'] 0m49.8s INFO: Running scripts post_install 0m49.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_install_exceptions'] 0m49.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_install_exceptions'] 0m49.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5wzv4k'] 0m51.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5wzv4k'] 0m51.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m51.4s DUMP: install ok installed adduser adduser 3.118 install ok installed apt apt 1.8.0~rc3 install ok installed base-files base-files 10.1 install ok installed base-passwd base-passwd 3.5.46 install ok installed bash bash 5.0-2 install ok installed bsdutils bsdutils 1:2.33.1-0.1 install ok installed ca-certificates ca-certificates 20190110 install ok installed coreutils coreutils 8.30-1 install ok installed dash dash 0.5.10.2-5 install ok installed debconf debconf 1.5.70 install ok installed debian-archive-keyring debian-archive-keyring 2018.1 install ok installed debianutils debianutils 4.8.6.1 install ok installed diffutils diffutils 1:3.6-1 install ok installed dpkg dpkg 1.19.4 install ok installed e2fsprogs e2fsprogs 1.44.5-1 install ok installed fdisk fdisk 2.33.1-0.1 install ok installed findutils findutils 4.6.0+git+20190105-2 install ok installed gcc-8-base:amd64 gcc-8-base 8.2.0-20 install ok installed gpgv gpgv 2.2.12-1 install ok installed grep grep 3.3-1 install ok installed gzip gzip 1.9-3 install ok installed hostname hostname 3.21 install ok installed init-system-helpers init-system-helpers 1.56+nmu1 install ok installed libacl1:amd64 libacl1 2.2.52-3+b1 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.8.0~rc3 install ok installed libattr1:amd64 libattr1 1:2.4.47-2+b2 install ok installed libaudit-common libaudit-common 1:2.8.4-2 install ok installed libaudit1:amd64 libaudit1 1:2.8.4-2 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 install ok installed libc-bin libc-bin 2.28-7 install ok installed libc6:amd64 libc6 2.28-7 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2 install ok installed libcom-err2:amd64 libcom-err2 1.44.5-1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.3 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.247 install ok installed libext2fs2:amd64 libext2fs2 1.44.5-1 install ok installed libfdisk1:amd64 libfdisk1 2.33.1-0.1 install ok installed libffi6:amd64 libffi6 3.2.1-9 install ok installed libgcc1:amd64 libgcc1 1:8.2.0-20 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.4-5 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.18.1-3 install ok installed libgdbm6:amd64 libgdbm6 1.18.1-3 install ok installed libgmp10:amd64 libgmp10 2:6.1.2+dfsg-4 install ok installed libgnutls30:amd64 libgnutls30 3.6.6-2 install ok installed libgpg-error0:amd64 libgpg-error0 1.35-1 install ok installed libhogweed4:amd64 libhogweed4 3.4.1-1 install ok installed libidn2-0:amd64 libidn2-0 2.0.5-1 install ok installed liblz4-1:amd64 liblz4-1 1.8.3-1 install ok installed liblzma5:amd64 liblzma5 5.2.4-1 install ok installed libmount1:amd64 libmount1 2.33.1-0.1 install ok installed libncurses6:amd64 libncurses6 6.1+20181013-2 install ok installed libncursesw6:amd64 libncursesw6 6.1+20181013-2 install ok installed libnettle6:amd64 libnettle6 3.4.1-1 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.14-2 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 2:8.39-11 install ok installed libreadline7:amd64 libreadline7 7.0-5 install ok installed libruby2.5:amd64 libruby2.5 2.5.3-3 install ok installed libseccomp2:amd64 libseccomp2 2.3.3-4 install ok installed libselinux1:amd64 libselinux1 2.8-1+b1 install ok installed libsemanage-common libsemanage-common 2.8-2 install ok installed libsemanage1:amd64 libsemanage1 2.8-2 install ok installed libsepol1:amd64 libsepol1 2.8-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.33.1-0.1 install ok installed libss2:amd64 libss2 1.44.5-1 install ok installed libssl1.1:amd64 libssl1.1 1.1.1a-1 install ok installed libstdc++6:amd64 libstdc++6 8.2.0-20 install ok installed libsystemd0:amd64 libsystemd0 240-5 install ok installed libtasn1-6:amd64 libtasn1-6 4.13-3 install ok installed libtinfo6:amd64 libtinfo6 6.1+20181013-2 install ok installed libudev1:amd64 libudev1 240-5 install ok installed libunistring2:amd64 libunistring2 0.9.10-1 install ok installed libuuid1:amd64 libuuid1 2.33.1-0.1 install ok installed libyaml-0-2:amd64 libyaml-0-2 0.2.1-1 install ok installed libzstd1:amd64 libzstd1 1.3.8+dfsg-3 install ok installed login login 1:4.5-1.1 install ok installed mawk mawk 1.3.3-17+b3 install ok installed mount mount 2.33.1-0.1 install ok installed ncurses-base ncurses-base 6.1+20181013-2 install ok installed ncurses-bin ncurses-bin 6.1+20181013-2 install ok installed openssl openssl 1.1.1a-1 install ok installed passwd passwd 1:4.5-1.1 install ok installed perl-base perl-base 5.28.1-4 install ok installed rake rake 12.3.1-3 install ok installed readline-common readline-common 7.0-5 install ok installed ruby ruby 1:2.5.1 install ok installed ruby-did-you-mean ruby-did-you-mean 1.2.1-1 install ok installed ruby-fix-trinity-output ruby-fix-trinity-output 1.0.0-2 install ok installed ruby-minitest ruby-minitest 5.11.3-1 install ok installed ruby-net-telnet ruby-net-telnet 0.1.1-2 install ok installed ruby-power-assert ruby-power-assert 1.1.1-1 install ok installed ruby-test-unit ruby-test-unit 3.2.8-1 install ok installed ruby-trollop ruby-trollop 2.0-2 install ok installed ruby-xmlrpc ruby-xmlrpc 0.3.0-2 install ok installed ruby2.5 ruby2.5 2.5.3-3 install ok installed rubygems-integration rubygems-integration 1.11 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.93-6 install ok installed tar tar 1.30+dfsg-5 install ok installed tzdata tzdata 2018i-1 install ok installed util-linux util-linux 2.33.1-0.1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-1 0m51.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m52.7s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', '-ac', '--ignore-obsolete'] 0m54.3s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', '-ac', '--ignore-obsolete'] 0m54.3s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m54.3s DUMP: 0.15.1 0m54.3s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 0m54.3s INFO: Running adequate version 0.15.1 now. 0m54.3s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'ruby-fix-trinity-output'] 0m54.5s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'ruby-fix-trinity-output'] 0m54.5s INFO: Running scripts pre_remove 0m54.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m54.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 0m54.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m54.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 0m54.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m56.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 0m56.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m56.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 0m56.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m56.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 0m56.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_remove_exceptions'] 0m56.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/pre_remove_exceptions'] 0m56.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'apt-get', 'remove', 'libruby2.5:amd64', 'ruby-power-assert', 'openssl', 'ruby-xmlrpc', 'libgdbm6:amd64', 'libssl1.1:amd64', 'ruby-trollop', 'ruby-test-unit', 'rake', 'libyaml-0-2:amd64', 'ruby-minitest', 'ruby-did-you-mean', 'libncurses6:amd64', 'libreadline7:amd64', 'ca-certificates', 'rubygems-integration', 'readline-common', 'ruby-net-telnet', 'ruby2.5', 'ruby', 'libgdbm-compat4:amd64', 'ruby-fix-trinity-output'] 1m0.2s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: ca-certificates libgdbm-compat4 libgdbm6 libncurses6 libreadline7 libruby2.5 libssl1.1 libyaml-0-2 openssl rake readline-common ruby ruby-did-you-mean ruby-fix-trinity-output ruby-minitest ruby-net-telnet ruby-power-assert ruby-test-unit ruby-trollop ruby-xmlrpc ruby2.5 rubygems-integration 0 upgraded, 0 newly installed, 22 to remove and 0 not upgraded. After this operation, 23.9 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 ... 8068 files and directories currently installed.) Removing ruby-fix-trinity-output (1.0.0-2) ... Removing ruby-trollop (2.0-2) ... Removing libruby2.5:amd64 (2.5.3-3) ... Removing rake (12.3.1-3) ... Removing ruby (1:2.5.1) ... Removing libgdbm-compat4:amd64 (1.18.1-3) ... Removing libgdbm6:amd64 (1.18.1-3) ... Removing libncurses6:amd64 (6.1+20181013-2) ... Removing libreadline7:amd64 (7.0-5) ... Removing libyaml-0-2:amd64 (0.2.1-1) ... Removing readline-common (7.0-5) ... Removing ruby-did-you-mean (1.2.1-1) ... Removing ruby-minitest (5.11.3-1) ... Removing ruby-net-telnet (0.1.1-2) ... Removing ruby-test-unit (3.2.8-1) ... Removing ruby-power-assert (1.1.1-1) ... Removing ruby-xmlrpc (0.3.0-2) ... Removing ruby2.5 (2.5.3-3) ... Removing rubygems-integration (1.11) ... Removing ca-certificates (20190110) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing openssl (1.1.1a-1) ... Removing libssl1.1:amd64 (1.1.1a-1) ... Processing triggers for libc-bin (2.28-7) ... 1m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'apt-get', 'remove', 'libruby2.5:amd64', 'ruby-power-assert', 'openssl', 'ruby-xmlrpc', 'libgdbm6:amd64', 'libssl1.1:amd64', 'ruby-trollop', 'ruby-test-unit', 'rake', 'libyaml-0-2:amd64', 'ruby-minitest', 'ruby-did-you-mean', 'libncurses6:amd64', 'libreadline7:amd64', 'ca-certificates', 'rubygems-integration', 'readline-common', 'ruby-net-telnet', 'ruby2.5', 'ruby', 'libgdbm-compat4:amd64', 'ruby-fix-trinity-output'] 1m0.2s INFO: Running scripts post_remove 1m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_remove_exceptions'] 1m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_remove_exceptions'] 1m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_remove_extras'] 1m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_remove_extras'] 1m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'dpkg', '--purge', 'libruby2.5:amd64', 'ruby-power-assert', 'openssl', 'ruby-xmlrpc', 'libgdbm6:amd64', 'libssl1.1:amd64', 'ruby-trollop', 'ruby-test-unit', 'rake', 'libyaml-0-2:amd64', 'ruby-minitest', 'ruby-did-you-mean', 'libncurses6:amd64', 'libreadline7:amd64', 'ca-certificates', 'rubygems-integration', 'readline-common', 'ruby-net-telnet', 'ruby2.5', 'ruby', 'libgdbm-compat4:amd64'] 1m0.6s DUMP: dpkg: warning: ignoring request to remove libruby2.5 which isn't installed dpkg: warning: ignoring request to remove ruby-power-assert which isn't installed (Reading database ... 6431 files and directories currently installed.) Purging configuration files for openssl (1.1.1a-1) ... dpkg: warning: while removing openssl, directory '/etc/ssl/certs' not empty so not removed dpkg: warning: ignoring request to remove ruby-xmlrpc which isn't installed dpkg: warning: ignoring request to remove libgdbm6 which isn't installed Purging configuration files for libssl1.1:amd64 (1.1.1a-1) ... dpkg: warning: ignoring request to remove ruby-trollop which isn't installed dpkg: warning: ignoring request to remove ruby-test-unit which isn't installed dpkg: warning: ignoring request to remove rake which isn't installed dpkg: warning: ignoring request to remove libyaml-0-2 which isn't installed dpkg: warning: ignoring request to remove ruby-minitest which isn't installed dpkg: warning: ignoring request to remove ruby-did-you-mean which isn't installed dpkg: warning: ignoring request to remove libncurses6 which isn't installed dpkg: warning: ignoring request to remove libreadline7 which isn't installed Purging configuration files for ca-certificates (20190110) ... Removing dangling symlinks from /etc/ssl/certs... done. dpkg: warning: ignoring request to remove rubygems-integration which isn't installed Purging configuration files for readline-common (7.0-5) ... dpkg: warning: ignoring request to remove ruby-net-telnet which isn't installed dpkg: warning: ignoring request to remove ruby2.5 which isn't installed dpkg: warning: ignoring request to remove ruby which isn't installed dpkg: warning: ignoring request to remove libgdbm-compat4 which isn't installed 1m0.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'dpkg', '--purge', 'libruby2.5:amd64', 'ruby-power-assert', 'openssl', 'ruby-xmlrpc', 'libgdbm6:amd64', 'libssl1.1:amd64', 'ruby-trollop', 'ruby-test-unit', 'rake', 'libyaml-0-2:amd64', 'ruby-minitest', 'ruby-did-you-mean', 'libncurses6:amd64', 'libreadline7:amd64', 'ca-certificates', 'rubygems-integration', 'readline-common', 'ruby-net-telnet', 'ruby2.5', 'ruby', 'libgdbm-compat4:amd64'] 1m0.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'dpkg', '--purge', 'ruby-fix-trinity-output'] 1m0.6s DUMP: dpkg: warning: ignoring request to remove ruby-fix-trinity-output which isn't installed 1m0.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'dpkg', '--purge', 'ruby-fix-trinity-output'] 1m0.6s INFO: Running scripts post_purge 1m0.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_purge_exceptions'] 1m0.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_purge_exceptions'] 1m0.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'dpkg', '--purge', '--pending'] 1m0.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'dpkg', '--purge', '--pending'] 1m0.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'dpkg', '--remove', '--pending'] 1m0.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'dpkg', '--remove', '--pending'] 1m0.7s INFO: Running scripts post_test 1m0.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_test_exceptions'] 1m0.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'tmp/scripts/post_test_exceptions'] 1m0.7s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5wzv4k'] 1m2.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmp5wzv4k'] 1m2.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'dpkg-divert', '--list'] 1m2.2s DUMP: local diversion of /bin/sync to /bin/sync.distrib diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 1m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'dpkg-divert', '--list'] 1m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'apt-get', 'clean'] 1m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmp5wzv4k', 'apt-get', 'clean'] 1m2.2s DEBUG: Recording chroot state 1m6.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp5wzv4k/dev/shm'] 1m6.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp5wzv4k/dev/shm'] 1m6.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp5wzv4k/dev/console'] 1m6.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp5wzv4k/dev/console'] 1m6.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp5wzv4k/dev/ptmx'] 1m6.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp5wzv4k/dev/ptmx'] 1m6.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp5wzv4k/dev/pts'] 1m6.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp5wzv4k/dev/pts'] 1m6.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmp5wzv4k/proc'] 1m6.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmp5wzv4k/proc'] 1m6.2s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp5wzv4k'] 1m6.4s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmp5wzv4k'] 1m6.4s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmp5wzv4k 1m6.5s INFO: PASS: Upgrading between Debian distributions. 1m6.5s INFO: PASS: All tests. 1m6.5s INFO: piuparts run ends. ret=0 End: 2019-02-14 15:49:52 UTC