Start: 2024-01-29 04:39:01 GMT Package: trinityrnaseq Version: 2.6.6+dfsg-6 Installed-Size: 8883 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.27), libgcc1 (>= 1:3.0), libgomp1 (>= 4.9), libhts2 (>= 1.0), libstdc++6 (>= 5.2), zlib1g (>= 1:1.1.4), perl:any, jaligner, libcommons-collections4-java, libgetopt-java, libjung-free-java, bowtie, bowtie2, libwww-perl, default-jre-headless, samtools, jellyfish, r-base-core, r-cran-cluster, r-bioc-qvalue, rsem, berkeley-express, trimmomatic, transdecoder, parafly, curl, salmon, python3-numpy, ncbi-blast+ Recommends: trinityrnaseq-examples Suggests: collectl Description: RNA-Seq De novo Assembly Homepage: http://trinityrnaseq.github.io/ Description-md5: 2ee7f38dbb99a040c33d6619f4f5668b Section: science Priority: optional Filename: pool/main/t/trinityrnaseq/trinityrnaseq_2.6.6+dfsg-6_amd64.deb Size: 1838012 MD5sum: 66979c39ee852e06ed8c617e67274079 SHA256: 1401b390ee10ca788d291d399192915a55e19f1185dc935d01c08c93662638bb Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts-log-alternatives --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --warn-on-debsums-errors --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/buster-merged-usr_amd64.tar.gz -d buster --no-upgrade-test --apt trinityrnaseq=2.6.6+dfsg-6 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.2 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --scriptsdir /etc/piuparts/scripts-log-alternatives --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --warn-on-debsums-errors --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/buster-merged-usr_amd64.tar.gz -d buster --no-upgrade-test --apt trinityrnaseq=2.6.6+dfsg-6 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-27-amd64 #1 SMP Debian 5.10.205-2 (2023-12-31) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmph3a3epj4 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/buster-merged-usr_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmph3a3epj4 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/buster-merged-usr_amd64.tar.gz'] 0m1.9s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/buster-merged-usr_amd64.tar.gz'] 0m1.9s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmph3a3epj4/proc'] 0m1.9s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmph3a3epj4/proc'] 0m1.9s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmph3a3epj4/dev/pts'] 0m1.9s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmph3a3epj4/dev/pts'] 0m1.9s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmph3a3epj4/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmph3a3epj4/dev/ptmx'] 0m1.9s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmph3a3epj4/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmph3a3epj4/dev/ptmx'] 0m1.9s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmph3a3epj4/dev/console'] 0m1.9s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmph3a3epj4/dev/console'] 0m1.9s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmph3a3epj4/dev/shm'] 0m1.9s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmph3a3epj4/dev/shm'] 0m1.9s DEBUG: sources.list: deb http://deb.debian.org/debian/ buster main 0m1.9s DEBUG: Created policy-rc.d and chmodded it. 0m1.9s DEBUG: Created resolv.conf. 0m1.9s DEBUG: Copying scriptsdir /etc/piuparts/scripts-log-alternatives to /srv/piuparts.debian.org/tmp/tmph3a3epj4/tmp/scripts/ 0m1.9s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmph3a3epj4/tmp/scripts/ 0m1.9s INFO: Running scripts post_chroot_unpack 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'apt-get', 'update'] 0m3.4s DUMP: Hit:1 http://deb.debian.org/debian buster InRelease Reading package lists... 0m3.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'apt-get', 'update'] 0m3.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'apt-get', '-yf', 'dist-upgrade'] 0m3.9s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m3.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'apt-get', '-yf', 'dist-upgrade'] 0m3.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.2s DUMP: f6fc0f2636004ef589309651dfd778f4 - 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m4.2s INFO: Running scripts post_setup 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/post_setup_dummy_users'] 0m5.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/post_setup_dummy_users'] 0m5.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/post_setup_forbid_home'] 0m5.5s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/post_setup_forbid_home'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.6s 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' 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/post_setup_force-unsafe-io'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/post_setup_minimize'] 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/post_setup_minimize'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/post_setup_squeeze-backports'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/post_setup_zz_backports'] 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/post_setup_zz_backports'] 0m5.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'apt-get', 'clean'] 0m5.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'apt-get', 'clean'] 0m5.6s DEBUG: Recording chroot state 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m6.1s DUMP: install ok installed adduser adduser 3.118 install ok installed apt apt 1.8.2.3 install ok installed base-files base-files 10.3+deb10u13 install ok installed base-passwd base-passwd 3.5.46 install ok installed bash bash 5.0-4 install ok installed bsdutils bsdutils 1:2.33.1-0.1 install ok installed coreutils coreutils 8.30-3 install ok installed dash dash 0.5.10.2-5 install ok installed debconf debconf 1.5.71+deb10u1 install ok installed debian-archive-keyring debian-archive-keyring 2019.1+deb10u1 install ok installed debianutils debianutils 4.8.6.1 install ok installed diffutils diffutils 1:3.7-3 install ok installed dpkg dpkg 1.19.8 install ok installed e2fsprogs e2fsprogs 1.44.5-1+deb10u3 install ok installed fdisk fdisk 2.33.1-0.1 install ok installed findutils findutils 4.6.0+git+20190209-2 install ok installed gcc-8-base:amd64 gcc-8-base 8.3.0-6 install ok installed gpgv gpgv 2.2.12-1+deb10u2 install ok installed grep grep 3.3-1 install ok installed gzip gzip 1.9-3+deb10u1 install ok installed hostname hostname 3.21 install ok installed init-system-helpers init-system-helpers 1.56+nmu1 install ok installed libacl1:amd64 libacl1 2.2.53-4 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.8.2.3 install ok installed libattr1:amd64 libattr1 1:2.4.48-4 install ok installed libaudit-common libaudit-common 1:2.8.4-3 install ok installed libaudit1:amd64 libaudit1 1:2.8.4-3 install ok installed libblkid1:amd64 libblkid1 2.33.1-0.1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-9.2~deb10u1 install ok installed libc-bin libc-bin 2.28-10+deb10u1 install ok installed libc6:amd64 libc6 2.28-10+deb10u1 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2 install ok installed libcom-err2:amd64 libcom-err2 1.44.5-1+deb10u3 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.5 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.249 install ok installed libext2fs2:amd64 libext2fs2 1.44.5-1+deb10u3 install ok installed libfdisk1:amd64 libfdisk1 2.33.1-0.1 install ok installed libffi6:amd64 libffi6 3.2.1-9 install ok installed libgcc1:amd64 libgcc1 1:8.3.0-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.4-5+deb10u1 install ok installed libgmp10:amd64 libgmp10 2:6.1.2+dfsg-4+deb10u1 install ok installed libgnutls30:amd64 libgnutls30 3.6.7-4+deb10u8 install ok installed libgpg-error0:amd64 libgpg-error0 1.35-1 install ok installed libhogweed4:amd64 libhogweed4 3.4.1-1+deb10u1 install ok installed libidn2-0:amd64 libidn2-0 2.0.5-1+deb10u1 install ok installed liblz4-1:amd64 liblz4-1 1.8.3-1+deb10u1 install ok installed liblzma5:amd64 liblzma5 5.2.4-1+deb10u1 install ok installed libmount1:amd64 libmount1 2.33.1-0.1 install ok installed libncursesw6:amd64 libncursesw6 6.1+20181013-2+deb10u2 install ok installed libnettle6:amd64 libnettle6 3.4.1-1+deb10u1 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.15-2+deb10u1 install ok installed libpam-modules:amd64 libpam-modules 1.3.1-5 install ok installed libpam-modules-bin libpam-modules-bin 1.3.1-5 install ok installed libpam-runtime libpam-runtime 1.3.1-5 install ok installed libpam0g:amd64 libpam0g 1.3.1-5 install ok installed libpcre3:amd64 libpcre3 2:8.39-12 install ok installed libseccomp2:amd64 libseccomp2 2.3.3-4 install ok installed libselinux1:amd64 libselinux1 2.8-1+b1 install ok installed libsemanage-common libsemanage-common 2.8-2 install ok installed libsemanage1:amd64 libsemanage1 2.8-2 install ok installed libsepol1:amd64 libsepol1 2.8-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.33.1-0.1 install ok installed libss2:amd64 libss2 1.44.5-1+deb10u3 install ok installed libstdc++6:amd64 libstdc++6 8.3.0-6 install ok installed libsystemd0:amd64 libsystemd0 241-7~deb10u8 install ok installed libtasn1-6:amd64 libtasn1-6 4.13-3 install ok installed libtinfo6:amd64 libtinfo6 6.1+20181013-2+deb10u2 install ok installed libudev1:amd64 libudev1 241-7~deb10u8 install ok installed libunistring2:amd64 libunistring2 0.9.10-1 install ok installed libuuid1:amd64 libuuid1 2.33.1-0.1 install ok installed libzstd1:amd64 libzstd1 1.3.8+dfsg-3+deb10u2 install ok installed login login 1:4.5-1.1 install ok installed mawk mawk 1.3.3-17+b3 install ok installed mount mount 2.33.1-0.1 install ok installed ncurses-base ncurses-base 6.1+20181013-2+deb10u2 install ok installed ncurses-bin ncurses-bin 6.1+20181013-2+deb10u2 install ok installed passwd passwd 1:4.5-1.1 install ok installed perl-base perl-base 5.28.1-6+deb10u1 install ok installed sed sed 4.7-1 install ok installed sysvinit-utils sysvinit-utils 2.93-8 install ok installed tar tar 1.30+dfsg-6 install ok installed tzdata tzdata 2021a-0+deb10u6 install ok installed util-linux util-linux 2.33.1-0.1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-1+deb10u1 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'dpkg-divert', '--list'] 0m6.1s 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 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'dpkg-divert', '--list'] 0m6.1s INFO: Running scripts is_testable 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/is_testable_uninstallable'] 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/is_testable_uninstallable'] 0m6.1s INFO: apt-cache does not know about any of the requested packages 0m6.1s INFO: Running scripts pre_test 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/pre_test_exceptions'] 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/pre_test_exceptions'] 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/pre_test_root_password'] 0m6.1s DUMP: New password: Retype new password: passwd: password updated successfully 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/pre_test_root_password'] 0m6.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmph3a3epj4'] 0m6.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmph3a3epj4'] 0m7.1s DEBUG: No broken symlinks as far as we can find. 0m7.1s INFO: Running scripts pre_install 0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/pre_install_database-server'] 0m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/pre_install_database-server'] 0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/pre_install_exceptions'] 0m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/pre_install_exceptions'] 0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/pre_install_extras'] 0m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/pre_install_extras'] 0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/pre_install_foreign_architecture'] 0m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/pre_install_foreign_architecture'] 0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m7.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m7.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/pre_install_log_alternatives'] 0m7.2s DUMP: Adding 'local diversion of /usr/bin/update-alternatives to /usr/bin/update-alternatives.orig' dpkg-divert: warning: diverting file '/usr/bin/update-alternatives' from an Essential package with rename is dangerous, use --no-rename 0m7.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/pre_install_log_alternatives'] 0m7.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmph3a3epj4'] 0m7.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmph3a3epj4'] 0m8.1s DEBUG: No broken symlinks as far as we can find. 0m8.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'apt-cache', 'policy'] 0m9.0s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian buster/main amd64 Packages release v=10.13,o=Debian,a=oldoldstable,n=buster,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m9.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'apt-cache', 'policy'] 0m9.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'apt-cache', 'policy', 'trinityrnaseq'] 0m9.1s DUMP: trinityrnaseq: Installed: (none) Candidate: 2.6.6+dfsg-6 Version table: 2.6.6+dfsg-6 500 500 http://deb.debian.org/debian buster/main amd64 Packages 0m9.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'apt-cache', 'policy', 'trinityrnaseq'] 0m9.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'apt-get', '-y', 'install', 'trinityrnaseq=2.6.6+dfsg-6'] 1m28.0s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: berkeley-express bowtie bowtie2 ca-certificates ca-certificates-java curl default-jre default-jre-headless fontconfig fontconfig-config fonts-dejavu-core fonts-font-awesome fonts-lato fonts-roboto-slab jaligner java-common jellyfish libapache-pom-java libasound2 libasound2-data libatomic1 libavahi-client3 libavahi-common-data libavahi-common3 libbamtools2.5.1 libblas3 libboost-atomic1.67.0 libboost-chrono1.67.0 libboost-date-time1.67.0 libboost-filesystem1.67.0 libboost-iostreams1.67.0 libboost-program-options1.67.0 libboost-regex1.67.0 libboost-system1.67.0 libboost-thread1.67.0 libboost-timer1.67.0 libbsd0 libcairo2 libcolt-free-java libcommons-collections4-java libcommons-parent-java libconcurrent-java libcups2 libcurl3-gnutls libcurl4 libdatrie1 libdbus-1-3 libdeflate0 libdivsufsort3 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libelf1 libencode-locale-perl libexpat1 libfile-listing-perl libfontconfig1 libfreetype6 libfribidi0 libgdbm-compat4 libgdbm6 libgetopt-java libgfortran5 libgif7 libgl1 libgl1-mesa-dri libglapi-mesa libglib2.0-0 libglvnd0 libglx-mesa0 libglx0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhts2 libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libice6 libicu63 libio-html-perl libio-socket-ssl-perl libjbig0 libjbzip2-java libjellyfish-2.0-2 libjemalloc2 libjpeg62-turbo libjs-jquery libjs-modernizr libjs-sphinxdoc libjs-underscore libjung-free-java libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 libldap-common libllvm7 liblmdb0 liblwp-mediatypes-perl liblwp-protocol-https-perl libmbedcrypto3 libmbedtls12 libmbedx509-0 libmpdec2 libncurses6 libnet-http-perl libnet-ssleay-perl libnghttp2-14 libnspr4 libnss3 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpciaccess0 libpcsclite1 libperl5.28 libpixman-1-0 libpng16-16 libprotobuf17 libpsl5 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libquadmath0 libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libsm6 libsqlite3-0 libssh2-1 libssl1.1 libstaden-read13 libtbb2 libtcl8.6 libthai-data libthai0 libtiff5 libtimedate-perl libtk8.6 libtry-tiny-perl liburi-perl libvecmath-java libwebp6 libwww-perl libwww-robotrules-perl libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxft2 libxi6 libxrender1 libxshmfence1 libxss1 libxt6 libxtst6 libxxf86vm1 littler lsb-base mime-support ncbi-blast+ ncbi-data netbase openjdk-11-jre openjdk-11-jre-headless openssl parafly perl perl-modules-5.28 perl-openssl-defaults python python-minimal python2 python2-minimal python2.7 python2.7-minimal python3 python3-minimal python3-numpy python3-pkg-resources python3.7 python3.7-minimal r-base-core r-bioc-biocgenerics r-bioc-qvalue r-cran-assertthat r-cran-cli r-cran-cluster r-cran-colorspace r-cran-crayon r-cran-digest r-cran-fansi r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-labeling r-cran-lattice r-cran-lazyeval r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plyr r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-reshape2 r-cran-rlang r-cran-scales r-cran-stringi r-cran-stringr r-cran-tibble r-cran-utf8 r-cran-viridislite r-cran-withr readline-common rsem salmon samtools sensible-utils sphinx-rtd-theme-common transdecoder trimmomatic ucf unzip x11-common xdg-utils zip Suggested packages: bowtie-examples bowtie2-examples fonts-roboto libasound2-plugins alsa-utils libcommons-collections4-java-doc cups-common gdbm-l10n libgetopt-java-doc krb5-doc krb5-user libdata-dump-perl liblcms2-utils libcrypt-ssleay-perl pciutils pcscd lm-sensors tcl8.6 tk8.6 libauthen-ntlm-perl libnss-mdns fonts-dejavu-extra fonts-ipafont-gothic fonts-ipafont-mincho fonts-wqy-microhei | fonts-wqy-zenhei fonts-indic perl-doc libterm-readline-gnu-perl | libterm-readline-perl-perl make libb-debug-perl liblocale-codes-perl python-doc python-tk python2-doc python2.7-doc binutils binfmt-support python3-doc python3-tk python3-venv gcc gfortran python-numpy-doc python3-dev python3-pytest python3-numpy-dbg python3-setuptools python3.7-venv python3.7-doc ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-bioc-biobase r-bioc-s4vectors r-bioc-iranges r-bioc-genomicranges r-bioc-rsamtools r-bioc-annotationdbi r-bioc-affy r-bioc-deseq2 r-bioc-annotate r-cran-knitr r-cran-webshot r-cran-kernsmooth r-cran-kernlab r-cran-mvtnorm r-cran-vcd r-cran-shiny r-cran-shinyjs r-cran-dplyr r-cran-png r-cran-rmarkdown r-cran-viridis r-cran-rstudioapi r-cran-hmisc r-cran-maps r-cran-maptools r-cran-multcomp r-cran-quantreg r-cran-rpart r-cran-sf r-cran-svglite r-cran-dbi r-cran-rsqlite r-cran-r.utils r-cran-forcats libgdal-dev r-cran-getopt r-cran-testthat r-cran-foreach r-cran-doparallel r-cran-iterators r-cran-inline r-cran-dichromat r-cran-htmltools readline-doc r-bioc-ebseq collectl Recommended packages: med-config dbus libglib2.0-data shared-mime-info xdg-user-dirs libhtml-format-perl javascript-common krb5-locales libgpm2 publicsuffix libsasl2-modules libdata-dump-perl libhtml-form-perl libhttp-daemon-perl libmailtools-perl bzip2 file xz-utils libatk-wrapper-java-jni fonts-dejavu-extra r-recommended r-base-dev r-doc-html r-cran-runit r-cran-testthat r-cran-mockery r-cran-sp r-cran-mapproj r-cran-hexbin r-cran-lubridate r-cran-domc r-cran-abind r-cran-bit64 r-cran-hms r-cran-htmltools r-cran-htmlwidgets r-cran-data.table r-cran-rsqlite r-cran-knitr r-cran-dplyr r-cran-mockr r-cran-dbi cwltool trinityrnaseq-examples libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-utils x11-xserver-utils The following NEW packages will be installed: berkeley-express bowtie bowtie2 ca-certificates ca-certificates-java curl default-jre default-jre-headless fontconfig fontconfig-config fonts-dejavu-core fonts-font-awesome fonts-lato fonts-roboto-slab jaligner java-common jellyfish libapache-pom-java libasound2 libasound2-data libatomic1 libavahi-client3 libavahi-common-data libavahi-common3 libbamtools2.5.1 libblas3 libboost-atomic1.67.0 libboost-chrono1.67.0 libboost-date-time1.67.0 libboost-filesystem1.67.0 libboost-iostreams1.67.0 libboost-program-options1.67.0 libboost-regex1.67.0 libboost-system1.67.0 libboost-thread1.67.0 libboost-timer1.67.0 libbsd0 libcairo2 libcolt-free-java libcommons-collections4-java libcommons-parent-java libconcurrent-java libcups2 libcurl3-gnutls libcurl4 libdatrie1 libdbus-1-3 libdeflate0 libdivsufsort3 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libelf1 libencode-locale-perl libexpat1 libfile-listing-perl libfontconfig1 libfreetype6 libfribidi0 libgdbm-compat4 libgdbm6 libgetopt-java libgfortran5 libgif7 libgl1 libgl1-mesa-dri libglapi-mesa libglib2.0-0 libglvnd0 libglx-mesa0 libglx0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhts2 libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libice6 libicu63 libio-html-perl libio-socket-ssl-perl libjbig0 libjbzip2-java libjellyfish-2.0-2 libjemalloc2 libjpeg62-turbo libjs-jquery libjs-modernizr libjs-sphinxdoc libjs-underscore libjung-free-java libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 libldap-common libllvm7 liblmdb0 liblwp-mediatypes-perl liblwp-protocol-https-perl libmbedcrypto3 libmbedtls12 libmbedx509-0 libmpdec2 libncurses6 libnet-http-perl libnet-ssleay-perl libnghttp2-14 libnspr4 libnss3 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpciaccess0 libpcsclite1 libperl5.28 libpixman-1-0 libpng16-16 libprotobuf17 libpsl5 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libquadmath0 libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libsm6 libsqlite3-0 libssh2-1 libssl1.1 libstaden-read13 libtbb2 libtcl8.6 libthai-data libthai0 libtiff5 libtimedate-perl libtk8.6 libtry-tiny-perl liburi-perl libvecmath-java libwebp6 libwww-perl libwww-robotrules-perl libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxft2 libxi6 libxrender1 libxshmfence1 libxss1 libxt6 libxtst6 libxxf86vm1 littler lsb-base mime-support ncbi-blast+ ncbi-data netbase openjdk-11-jre openjdk-11-jre-headless openssl parafly perl perl-modules-5.28 perl-openssl-defaults python python-minimal python2 python2-minimal python2.7 python2.7-minimal python3 python3-minimal python3-numpy python3-pkg-resources python3.7 python3.7-minimal r-base-core r-bioc-biocgenerics r-bioc-qvalue r-cran-assertthat r-cran-cli r-cran-cluster r-cran-colorspace r-cran-crayon r-cran-digest r-cran-fansi r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-labeling r-cran-lattice r-cran-lazyeval r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plyr r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-reshape2 r-cran-rlang r-cran-scales r-cran-stringi r-cran-stringr r-cran-tibble r-cran-utf8 r-cran-viridislite r-cran-withr readline-common rsem salmon samtools sensible-utils sphinx-rtd-theme-common transdecoder trimmomatic trinityrnaseq ucf unzip x11-common xdg-utils zip 0 upgraded, 269 newly installed, 0 to remove and 0 not upgraded. Need to get 246 MB of archives. After this operation, 910 MB of additional disk space will be used. 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buster/main amd64 mime-support all 3.62 [37.2 kB] Get:12 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u4 [108 kB] Get:13 http://deb.debian.org/debian buster/main amd64 readline-common all 7.0-5 [70.6 kB] Get:14 http://deb.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get:15 http://deb.debian.org/debian buster/main amd64 libsqlite3-0 amd64 3.27.2-3+deb10u1 [641 kB] Get:16 http://deb.debian.org/debian buster/main amd64 libpython2.7-stdlib amd64 2.7.16-2+deb10u1 [1912 kB] Get:17 http://deb.debian.org/debian buster/main amd64 python2.7 amd64 2.7.16-2+deb10u1 [305 kB] Get:18 http://deb.debian.org/debian buster/main amd64 libpython2-stdlib amd64 2.7.16-1 [20.8 kB] Get:19 http://deb.debian.org/debian buster/main amd64 libpython-stdlib amd64 2.7.16-1 [20.8 kB] Get:20 http://deb.debian.org/debian buster/main amd64 python2 amd64 2.7.16-1 [41.6 kB] Get:21 http://deb.debian.org/debian buster/main amd64 python amd64 2.7.16-1 [22.8 kB] Get:22 http://deb.debian.org/debian buster/main amd64 fonts-lato all 2.0-2 [2698 kB] Get:23 http://deb.debian.org/debian buster/main amd64 libpython3.7-minimal amd64 3.7.3-2+deb10u3 [589 kB] Get:24 http://deb.debian.org/debian buster/main amd64 python3.7-minimal amd64 3.7.3-2+deb10u3 [1737 kB] Get:25 http://deb.debian.org/debian buster/main amd64 python3-minimal amd64 3.7.3-1 [36.6 kB] Get:26 http://deb.debian.org/debian buster/main amd64 libmpdec2 amd64 2.4.2-2 [87.2 kB] Get:27 http://deb.debian.org/debian buster/main amd64 libpython3.7-stdlib amd64 3.7.3-2+deb10u3 [1734 kB] Get:28 http://deb.debian.org/debian buster/main amd64 python3.7 amd64 3.7.3-2+deb10u3 [330 kB] Get:29 http://deb.debian.org/debian buster/main amd64 libpython3-stdlib amd64 3.7.3-1 [20.0 kB] Get:30 http://deb.debian.org/debian buster/main amd64 python3 amd64 3.7.3-1 [61.5 kB] Get:31 http://deb.debian.org/debian buster/main amd64 netbase all 5.6 [19.4 kB] Get:32 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get:33 http://deb.debian.org/debian buster/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get:34 http://deb.debian.org/debian buster/main amd64 libbamtools2.5.1 amd64 2.5.1+dfsg-3 [154 kB] Get:35 http://deb.debian.org/debian buster/main amd64 libboost-atomic1.67.0 amd64 1.67.0-13+deb10u1 [226 kB] Get:36 http://deb.debian.org/debian buster/main amd64 libboost-system1.67.0 amd64 1.67.0-13+deb10u1 [229 kB] Get:37 http://deb.debian.org/debian buster/main amd64 libboost-chrono1.67.0 amd64 1.67.0-13+deb10u1 [234 kB] Get:38 http://deb.debian.org/debian buster/main amd64 libboost-date-time1.67.0 amd64 1.67.0-13+deb10u1 [239 kB] Get:39 http://deb.debian.org/debian buster/main amd64 libboost-filesystem1.67.0 amd64 1.67.0-13+deb10u1 [261 kB] Get:40 http://deb.debian.org/debian buster/main amd64 libboost-program-options1.67.0 amd64 1.67.0-13+deb10u1 [357 kB] Get:41 http://deb.debian.org/debian buster/main amd64 libboost-thread1.67.0 amd64 1.67.0-13+deb10u1 [268 kB] Get:42 http://deb.debian.org/debian buster/main amd64 libprotobuf17 amd64 3.6.1.3-2 [814 kB] Get:43 http://deb.debian.org/debian buster/main amd64 berkeley-express amd64 1.5.2+dfsg-1+b2 [237 kB] Get:44 http://deb.debian.org/debian buster/main amd64 libatomic1 amd64 8.3.0-6 [9032 B] Get:45 http://deb.debian.org/debian buster/main amd64 libtbb2 amd64 2018~U6-4 [147 kB] Get:46 http://deb.debian.org/debian buster/main amd64 bowtie amd64 1.2.2+dfsg-4 [1670 kB] Get:47 http://deb.debian.org/debian buster/main amd64 bowtie2 amd64 2.3.4.3-1 [1188 kB] Get:48 http://deb.debian.org/debian buster/main amd64 openssl amd64 1.1.1n-0+deb10u3 [855 kB] Get:49 http://deb.debian.org/debian buster/main amd64 ca-certificates all 20200601~deb10u2 [166 kB] Get:50 http://deb.debian.org/debian buster/main amd64 java-common all 0.71 [14.4 kB] Get:51 http://deb.debian.org/debian buster/main amd64 libavahi-common-data amd64 0.7-4+deb10u1 [122 kB] Get:52 http://deb.debian.org/debian buster/main amd64 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buster/main amd64 libgraphite2-3 amd64 1.3.13-7 [80.7 kB] Get:74 http://deb.debian.org/debian buster/main amd64 libharfbuzz0b amd64 2.3.1-1 [1187 kB] Get:75 http://deb.debian.org/debian buster/main amd64 libpcsclite1 amd64 1.8.24-1 [58.5 kB] Get:76 http://deb.debian.org/debian buster/main amd64 openjdk-11-jre-headless amd64 11.0.16+8-1~deb10u1 [37.3 MB] Get:77 http://deb.debian.org/debian buster/main amd64 default-jre-headless amd64 2:1.11-71 [10.9 kB] Get:78 http://deb.debian.org/debian buster/main amd64 ca-certificates-java all 20190405 [15.7 kB] Get:79 http://deb.debian.org/debian buster/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-1+deb10u2 [69.2 kB] Get:80 http://deb.debian.org/debian buster/main amd64 libsasl2-2 amd64 2.1.27+dfsg-1+deb10u2 [106 kB] Get:81 http://deb.debian.org/debian buster/main amd64 libldap-common all 2.4.47+dfsg-3+deb10u7 [90.1 kB] Get:82 http://deb.debian.org/debian buster/main amd64 libldap-2.4-2 amd64 2.4.47+dfsg-3+deb10u7 [224 kB] Get:83 http://deb.debian.org/debian buster/main amd64 libnghttp2-14 amd64 1.36.0-2+deb10u1 [85.0 kB] Get:84 http://deb.debian.org/debian buster/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get:85 http://deb.debian.org/debian buster/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [60.5 kB] Get:86 http://deb.debian.org/debian buster/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get:87 http://deb.debian.org/debian buster/main amd64 libcurl4 amd64 7.64.0-4+deb10u2 [332 kB] Get:88 http://deb.debian.org/debian buster/main amd64 curl amd64 7.64.0-4+deb10u2 [265 kB] Get:89 http://deb.debian.org/debian buster/main amd64 libglvnd0 amd64 1.1.0-1 [48.6 kB] Get:90 http://deb.debian.org/debian buster/main amd64 libxau6 amd64 1:1.0.8-1+b2 [19.9 kB] Get:91 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2+deb10u1 [99.5 kB] Get:92 http://deb.debian.org/debian buster/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:93 http://deb.debian.org/debian buster/main amd64 libxcb1 amd64 1.13.1-2 [137 kB] Get:94 http://deb.debian.org/debian buster/main amd64 libx11-data all 2:1.6.7-1+deb10u2 [299 kB] Get:95 http://deb.debian.org/debian buster/main amd64 libx11-6 amd64 2:1.6.7-1+deb10u2 [757 kB] Get:96 http://deb.debian.org/debian buster/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get:97 http://deb.debian.org/debian buster/main amd64 libdrm-common all 2.4.97-1 [13.8 kB] Get:98 http://deb.debian.org/debian buster/main amd64 libdrm2 amd64 2.4.97-1 [39.7 kB] Get:99 http://deb.debian.org/debian buster/main amd64 libglapi-mesa amd64 18.3.6-2+deb10u1 [66.3 kB] Get:100 http://deb.debian.org/debian buster/main amd64 libx11-xcb1 amd64 2:1.6.7-1+deb10u2 [191 kB] Get:101 http://deb.debian.org/debian buster/main amd64 libxcb-dri2-0 amd64 1.13.1-2 [101 kB] Get:102 http://deb.debian.org/debian buster/main amd64 libxcb-dri3-0 amd64 1.13.1-2 [100 kB] Get:103 http://deb.debian.org/debian buster/main amd64 libxcb-glx0 amd64 1.13.1-2 [116 kB] Get:104 http://deb.debian.org/debian buster/main amd64 libxcb-present0 amd64 1.13.1-2 [99.1 kB] Get:105 http://deb.debian.org/debian buster/main amd64 libxcb-sync1 amd64 1.13.1-2 [103 kB] Get:106 http://deb.debian.org/debian buster/main amd64 libxfixes3 amd64 1:5.0.3-1 [21.9 kB] Get:107 http://deb.debian.org/debian buster/main amd64 libxdamage1 amd64 1:1.1.4-3+b3 [14.9 kB] Get:108 http://deb.debian.org/debian buster/main amd64 libxshmfence1 amd64 1.3-1 [8820 B] Get:109 http://deb.debian.org/debian buster/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get:110 http://deb.debian.org/debian buster/main amd64 libdrm-amdgpu1 amd64 2.4.97-1 [27.3 kB] Get:111 http://deb.debian.org/debian buster/main amd64 libpciaccess0 amd64 0.14-1 [53.5 kB] Get:112 http://deb.debian.org/debian buster/main amd64 libdrm-intel1 amd64 2.4.97-1 [69.8 kB] Get:113 http://deb.debian.org/debian buster/main amd64 libdrm-nouveau2 amd64 2.4.97-1 [26.3 kB] Get:114 http://deb.debian.org/debian buster/main amd64 libdrm-radeon1 amd64 2.4.97-1 [31.1 kB] Get:115 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get:116 http://deb.debian.org/debian buster/main amd64 libedit2 amd64 3.1-20181209-1 [94.0 kB] Get:117 http://deb.debian.org/debian buster/main amd64 libllvm7 amd64 1:7.0.1-8+deb10u2 [13.1 MB] Get:118 http://deb.debian.org/debian buster/main amd64 libsensors-config all 1:3.5.0-3 [31.6 kB] Get:119 http://deb.debian.org/debian buster/main amd64 libsensors5 amd64 1:3.5.0-3 [52.6 kB] Get:120 http://deb.debian.org/debian buster/main amd64 libgl1-mesa-dri amd64 18.3.6-2+deb10u1 [6685 kB] Get:121 http://deb.debian.org/debian buster/main amd64 libglx-mesa0 amd64 18.3.6-2+deb10u1 [180 kB] Get:122 http://deb.debian.org/debian buster/main amd64 libglx0 amd64 1.1.0-1 [30.0 kB] Get:123 http://deb.debian.org/debian buster/main amd64 libgl1 amd64 1.1.0-1 [91.1 kB] Get:124 http://deb.debian.org/debian buster/main amd64 libgif7 amd64 5.1.4-3 [43.3 kB] Get:125 http://deb.debian.org/debian buster/main amd64 libxi6 amd64 2:1.7.9-1 [82.6 kB] Get:126 http://deb.debian.org/debian buster/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get:127 http://deb.debian.org/debian buster/main amd64 lsb-base all 10.2019051400 [28.4 kB] Get:128 http://deb.debian.org/debian buster/main amd64 x11-common all 1:7.7+19 [251 kB] Get:129 http://deb.debian.org/debian buster/main amd64 libxtst6 amd64 2:1.2.3-1 [27.8 kB] Get:130 http://deb.debian.org/debian buster/main amd64 openjdk-11-jre amd64 11.0.16+8-1~deb10u1 [174 kB] Get:131 http://deb.debian.org/debian buster/main amd64 default-jre amd64 2:1.11-71 [1044 B] Get:132 http://deb.debian.org/debian buster/main amd64 fontconfig amd64 2.13.1-2 [405 kB] Get:133 http://deb.debian.org/debian buster/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-1 [515 kB] Get:134 http://deb.debian.org/debian buster/main amd64 fonts-roboto-slab all 1.100263+20170512-1 [207 kB] Get:135 http://deb.debian.org/debian buster/main amd64 jaligner all 1.0+dfsg-6 [131 kB] Get:136 http://deb.debian.org/debian buster/main amd64 libjellyfish-2.0-2 amd64 2.2.10-2 [64.6 kB] Get:137 http://deb.debian.org/debian buster/main amd64 jellyfish amd64 2.2.10-2 [361 kB] Get:138 http://deb.debian.org/debian buster/main amd64 libapache-pom-java all 18-1 [4676 B] Get:139 http://deb.debian.org/debian buster/main amd64 libquadmath0 amd64 8.3.0-6 [133 kB] Get:140 http://deb.debian.org/debian buster/main amd64 libgfortran5 amd64 8.3.0-6 [581 kB] Get:141 http://deb.debian.org/debian buster/main amd64 libblas3 amd64 3.8.0-2 [148 kB] Get:142 http://deb.debian.org/debian buster/main amd64 libboost-iostreams1.67.0 amd64 1.67.0-13+deb10u1 [249 kB] Get:143 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u3 [8293 kB] Get:144 http://deb.debian.org/debian buster/main amd64 libboost-regex1.67.0 amd64 1.67.0-13+deb10u1 [485 kB] Get:145 http://deb.debian.org/debian buster/main amd64 libboost-timer1.67.0 amd64 1.67.0-13+deb10u1 [231 kB] Get:146 http://deb.debian.org/debian buster/main amd64 libpixman-1-0 amd64 0.36.0-1 [537 kB] Get:147 http://deb.debian.org/debian buster/main amd64 libxcb-render0 amd64 1.13.1-2 [109 kB] Get:148 http://deb.debian.org/debian buster/main amd64 libxcb-shm0 amd64 1.13.1-2 [99.2 kB] Get:149 http://deb.debian.org/debian buster/main amd64 libcairo2 amd64 1.16.0-4+deb10u1 [688 kB] Get:150 http://deb.debian.org/debian buster/main amd64 libconcurrent-java all 1.3.4-4 [133 kB] Get:151 http://deb.debian.org/debian buster/main amd64 libcolt-free-java all 1.2.0+dfsg-7 [434 kB] Get:152 http://deb.debian.org/debian buster/main amd64 libcommons-parent-java all 43-1 [10.8 kB] Get:153 http://deb.debian.org/debian buster/main amd64 libcommons-collections4-java all 4.2-1 [662 kB] Get:154 http://deb.debian.org/debian buster/main amd64 libcurl3-gnutls amd64 7.64.0-4+deb10u2 [330 kB] Get:155 http://deb.debian.org/debian buster/main amd64 libdatrie1 amd64 0.2.12-2 [39.3 kB] Get:156 http://deb.debian.org/debian buster/main amd64 libdeflate0 amd64 1.2-1 [55.4 kB] Get:157 http://deb.debian.org/debian buster/main amd64 libdivsufsort3 amd64 2.0.1-4 [44.5 kB] Get:158 http://deb.debian.org/debian buster/main amd64 libencode-locale-perl all 1.05-1 [13.7 kB] Get:159 http://deb.debian.org/debian buster/main amd64 libtimedate-perl all 2.3000-2+deb10u1 [38.1 kB] Get:160 http://deb.debian.org/debian buster/main amd64 libhttp-date-perl all 6.02-1 [10.7 kB] Get:161 http://deb.debian.org/debian buster/main amd64 libfile-listing-perl all 6.04-1 [10.3 kB] Get:162 http://deb.debian.org/debian buster/main amd64 libfribidi0 amd64 1.0.5-3.1+deb10u2 [63.9 kB] Get:163 http://deb.debian.org/debian buster/main amd64 libgetopt-java all 1.0.14+dfsg-4 [25.5 kB] Get:164 http://deb.debian.org/debian buster/main amd64 libgomp1 amd64 8.3.0-6 [75.8 kB] Get:165 http://deb.debian.org/debian buster/main amd64 libhtml-tagset-perl all 3.20-3 [12.7 kB] Get:166 http://deb.debian.org/debian buster/main amd64 liburi-perl all 1.76-1 [89.9 kB] Get:167 http://deb.debian.org/debian buster/main amd64 libhtml-parser-perl amd64 3.72-3+b3 [105 kB] Get:168 http://deb.debian.org/debian buster/main amd64 libhtml-tree-perl all 5.07-2 [213 kB] Get:169 http://deb.debian.org/debian buster/main amd64 libhts2 amd64 1.9-12~deb10u1 [305 kB] Get:170 http://deb.debian.org/debian buster/main amd64 libio-html-perl all 1.001-1 [17.6 kB] Get:171 http://deb.debian.org/debian buster/main amd64 liblwp-mediatypes-perl all 6.02-1 [22.1 kB] Get:172 http://deb.debian.org/debian buster/main amd64 libhttp-message-perl all 6.18-1 [77.8 kB] Get:173 http://deb.debian.org/debian buster/main amd64 libhttp-cookies-perl all 6.04-1 [17.8 kB] Get:174 http://deb.debian.org/debian buster/main amd64 libhttp-negotiate-perl all 6.01-1 [12.8 kB] Get:175 http://deb.debian.org/debian buster/main amd64 libice6 amd64 2:1.0.9-2 [58.7 kB] Get:176 http://deb.debian.org/debian buster/main amd64 perl-openssl-defaults amd64 3 [6782 B] Get:177 http://deb.debian.org/debian buster/main amd64 libnet-ssleay-perl amd64 1.85-2+deb10u1 [308 kB] Get:178 http://deb.debian.org/debian buster/main amd64 libio-socket-ssl-perl all 2.060-3 [207 kB] Get:179 http://deb.debian.org/debian buster/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get:180 http://deb.debian.org/debian buster/main amd64 libjbzip2-java all 0.9.1-5 [42.6 kB] Get:181 http://deb.debian.org/debian buster/main amd64 libjemalloc2 amd64 5.1.0-3 [225 kB] Get:182 http://deb.debian.org/debian buster/main amd64 libjs-jquery all 3.3.1~dfsg-3+deb10u1 [332 kB] Get:183 http://deb.debian.org/debian buster/main amd64 libjs-modernizr all 2.6.2+ds1-3 [46.7 kB] Get:184 http://deb.debian.org/debian buster/main amd64 libjs-underscore all 1.9.1~dfsg-1+deb10u1 [100.0 kB] Get:185 http://deb.debian.org/debian buster/main amd64 libjs-sphinxdoc all 1.8.4-1 [95.9 kB] Get:186 http://deb.debian.org/debian buster/main amd64 libvecmath-java all 1.5.2-7 [97.0 kB] Get:187 http://deb.debian.org/debian buster/main amd64 libjung-free-java all 2.0.1+dfsg-1 [976 kB] Get:188 http://deb.debian.org/debian buster/main amd64 liblapack3 amd64 3.8.0-2 [2110 kB] Get:189 http://deb.debian.org/debian buster/main amd64 liblmdb0 amd64 0.9.22-1 [45.0 kB] Get:190 http://deb.debian.org/debian buster/main amd64 libnet-http-perl all 6.18-1 [24.5 kB] Get:191 http://deb.debian.org/debian buster/main amd64 libtry-tiny-perl all 0.30-1 [23.3 kB] Get:192 http://deb.debian.org/debian buster/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get:193 http://deb.debian.org/debian buster/main amd64 libwww-perl all 6.36-2 [188 kB] Get:194 http://deb.debian.org/debian buster/main amd64 liblwp-protocol-https-perl all 6.07-2 [9242 B] Get:195 http://deb.debian.org/debian buster/main amd64 libmbedcrypto3 amd64 2.16.0-1 [209 kB] Get:196 http://deb.debian.org/debian buster/main amd64 libmbedx509-0 amd64 2.16.0-1 [91.4 kB] Get:197 http://deb.debian.org/debian buster/main amd64 libmbedtls12 amd64 2.16.0-1 [130 kB] Get:198 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get:199 http://deb.debian.org/debian buster/main amd64 libthai-data all 0.1.28-2 [170 kB] Get:200 http://deb.debian.org/debian buster/main amd64 libthai0 amd64 0.1.28-2 [54.1 kB] Get:201 http://deb.debian.org/debian buster/main amd64 libpango-1.0-0 amd64 1.42.4-8~deb10u1 [186 kB] Get:202 http://deb.debian.org/debian buster/main amd64 libpangoft2-1.0-0 amd64 1.42.4-8~deb10u1 [68.3 kB] Get:203 http://deb.debian.org/debian buster/main amd64 libpangocairo-1.0-0 amd64 1.42.4-8~deb10u1 [55.7 kB] Get:204 http://deb.debian.org/debian buster/main amd64 libpaper1 amd64 1.1.28 [21.3 kB] Get:205 http://deb.debian.org/debian buster/main amd64 libpaper-utils amd64 1.1.28 [18.0 kB] Get:206 http://deb.debian.org/debian buster/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get:207 http://deb.debian.org/debian buster/main amd64 libstaden-read13 amd64 1.14.11-6 [280 kB] Get:208 http://deb.debian.org/debian buster/main amd64 libtcl8.6 amd64 8.6.9+dfsg-2 [1005 kB] Get:209 http://deb.debian.org/debian buster/main amd64 libwebp6 amd64 0.6.1-2+deb10u1 [261 kB] Get:210 http://deb.debian.org/debian buster/main amd64 libtiff5 amd64 4.1.0+git191117-2~deb10u4 [271 kB] Get:211 http://deb.debian.org/debian buster/main amd64 libxft2 amd64 2.3.2-2 [57.2 kB] Get:212 http://deb.debian.org/debian buster/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get:213 http://deb.debian.org/debian buster/main amd64 libtk8.6 amd64 8.6.9-2 [768 kB] Get:214 http://deb.debian.org/debian buster/main amd64 libxt6 amd64 1:1.1.5-1+b3 [190 kB] Get:215 http://deb.debian.org/debian buster/main amd64 zip amd64 3.0-11+b1 [234 kB] Get:216 http://deb.debian.org/debian buster/main amd64 unzip amd64 6.0-23+deb10u2 [172 kB] Get:217 http://deb.debian.org/debian buster/main amd64 xdg-utils all 1.1.3-1+deb10u1 [73.7 kB] Get:218 http://deb.debian.org/debian buster/main amd64 r-base-core amd64 3.5.2-1 [23.9 MB] Get:219 http://deb.debian.org/debian buster/main amd64 r-cran-littler amd64 0.3.6-1 [308 kB] Get:220 http://deb.debian.org/debian buster/main amd64 littler all 0.3.6-1 [13.6 kB] Get:221 http://deb.debian.org/debian buster/main amd64 ncbi-data all 6.1.20170106+dfsg1-0+deb10u2 [3552 kB] Get:222 http://deb.debian.org/debian buster/main amd64 ncbi-blast+ amd64 2.8.1-1+deb10u1 [10.9 MB] Get:223 http://deb.debian.org/debian buster/main amd64 parafly amd64 0.0.2013.01.21-4 [15.8 kB] Get:224 http://deb.debian.org/debian buster/main amd64 python3-pkg-resources all 40.8.0-1 [153 kB] Get:225 http://deb.debian.org/debian buster/main amd64 python3-numpy amd64 1:1.16.2-1 [2119 kB] Get:226 http://deb.debian.org/debian buster/main amd64 r-bioc-biocgenerics all 0.28.0-2 [644 kB] Get:227 http://deb.debian.org/debian buster/main amd64 r-cran-digest amd64 0.6.18-1 [136 kB] Get:228 http://deb.debian.org/debian buster/main amd64 r-cran-gtable all 0.2.0-3 [93.6 kB] Get:229 http://deb.debian.org/debian buster/main amd64 r-cran-lazyeval amd64 0.2.1-3 [138 kB] Get:230 http://deb.debian.org/debian buster/main amd64 r-cran-mass amd64 7.3-51.1-1 [1100 kB] Get:231 http://deb.debian.org/debian buster/main amd64 r-cran-lattice amd64 0.20-38-1 [1121 kB] Get:232 http://deb.debian.org/debian buster/main amd64 r-cran-nlme amd64 3.1.137-1+b3 [2223 kB] Get:233 http://deb.debian.org/debian buster/main amd64 r-cran-matrix amd64 1.2-15-1 [3421 kB] Get:234 http://deb.debian.org/debian buster/main amd64 r-cran-mgcv amd64 1.8-27-1 [2665 kB] Get:235 http://deb.debian.org/debian buster/main amd64 r-cran-pkgkitten all 0.1.4-2 [22.4 kB] Get:236 http://deb.debian.org/debian buster/main amd64 r-cran-rcpp amd64 1.0.0-1 [3381 kB] Get:237 http://deb.debian.org/debian buster/main amd64 r-cran-plyr amd64 1.8.4-2 [813 kB] Get:238 http://deb.debian.org/debian buster/main amd64 r-cran-glue amd64 1.3.0-1 [92.0 kB] Get:239 http://deb.debian.org/debian buster/main amd64 r-cran-magrittr all 1.5-5 [152 kB] Get:240 http://deb.debian.org/debian buster/main amd64 r-cran-stringi amd64 1.2.4-2 [8702 kB] Get:241 http://deb.debian.org/debian buster/main amd64 r-cran-stringr all 1.4.0-1 [198 kB] Get:242 http://deb.debian.org/debian buster/main amd64 r-cran-reshape2 amd64 1.4.3-2 [114 kB] Get:243 http://deb.debian.org/debian buster/main amd64 r-cran-rlang amd64 0.3.1-2 [1083 kB] Get:244 http://deb.debian.org/debian buster/main amd64 r-cran-labeling all 0.3-3 [61.4 kB] Get:245 http://deb.debian.org/debian buster/main amd64 r-cran-colorspace amd64 1.4-0+dfsg-1 [1580 kB] Get:246 http://deb.debian.org/debian buster/main amd64 r-cran-munsell all 0.5.0-1 [235 kB] Get:247 http://deb.debian.org/debian buster/main amd64 r-cran-r6 all 2.4.0-1 [75.2 kB] Get:248 http://deb.debian.org/debian buster/main amd64 r-cran-rcolorbrewer all 1.1-2-2 [54.3 kB] Get:249 http://deb.debian.org/debian buster/main amd64 r-cran-viridislite all 0.3.0-3 [59.2 kB] Get:250 http://deb.debian.org/debian buster/main amd64 r-cran-scales amd64 1.0.0-2 [546 kB] Get:251 http://deb.debian.org/debian buster/main amd64 r-cran-assertthat all 0.2.0-2 [54.4 kB] Get:252 http://deb.debian.org/debian buster/main amd64 r-cran-crayon all 1.3.4-4 [750 kB] Get:253 http://deb.debian.org/debian buster/main amd64 r-cran-cli all 1.0.1-1 [519 kB] Get:254 http://deb.debian.org/debian buster/main amd64 r-cran-fansi amd64 0.4.0-1 [339 kB] Get:255 http://deb.debian.org/debian buster/main amd64 r-cran-utf8 amd64 1.1.4-1+b1 [131 kB] Get:256 http://deb.debian.org/debian buster/main amd64 r-cran-pillar all 1.3.1-1 [203 kB] Get:257 http://deb.debian.org/debian buster/main amd64 r-cran-pkgconfig all 2.0.2-1 [19.4 kB] Get:258 http://deb.debian.org/debian buster/main amd64 r-cran-tibble amd64 2.0.1-1 [656 kB] Get:259 http://deb.debian.org/debian buster/main amd64 r-cran-withr all 2.1.2-3 [152 kB] Get:260 http://deb.debian.org/debian buster/main amd64 r-cran-ggplot2 all 3.1.0-1 [3740 kB] Get:261 http://deb.debian.org/debian buster/main amd64 r-bioc-qvalue all 2.14.1-1 [2797 kB] Get:262 http://deb.debian.org/debian buster/main amd64 r-cran-cluster amd64 2.0.7-1-1+b3 [531 kB] Get:263 http://deb.debian.org/debian buster/main amd64 rsem amd64 1.3.1+dfsg-1 [36.1 MB] Get:264 http://deb.debian.org/debian buster/main amd64 sphinx-rtd-theme-common all 0.4.3+dfsg-1 [1021 kB] Get:265 http://deb.debian.org/debian buster/main amd64 salmon amd64 0.12.0+ds1-1+b1 [1354 kB] Get:266 http://deb.debian.org/debian buster/main amd64 samtools amd64 1.9-4 [443 kB] Get:267 http://deb.debian.org/debian buster/main amd64 transdecoder all 5.0.1-2 [187 kB] Get:268 http://deb.debian.org/debian buster/main amd64 trimmomatic all 0.38+dfsg-1 [757 kB] Get:269 http://deb.debian.org/debian buster/main amd64 trinityrnaseq amd64 2.6.6+dfsg-6 [1838 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 246 MB in 31s (7981 kB/s) Selecting previously unselected package perl-modules-5.28. (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 ... 6463 files and directories currently installed.) Preparing to unpack .../00-perl-modules-5.28_5.28.1-6+deb10u1_all.deb ... Unpacking perl-modules-5.28 (5.28.1-6+deb10u1) ... Selecting previously unselected package libgdbm6:amd64. Preparing to unpack .../01-libgdbm6_1.18.1-4_amd64.deb ... Unpacking libgdbm6:amd64 (1.18.1-4) ... Selecting previously unselected package libgdbm-compat4:amd64. 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Setting up libgfortran5:amd64 (8.3.0-6) ... Setting up libgif7:amd64 (5.1.4-3) ... Setting up sensible-utils (0.0.12) ... Setting up libxshmfence1:amd64 (1.3-1) ... Setting up libasound2:amd64 (1.1.8-1) ... Setting up libmbedcrypto3:amd64 (2.16.0-1) ... Setting up libthai-data (0.1.28-2) ... Setting up libssh2-1:amd64 (1.8.0-2.1) ... Setting up netbase (5.6) ... Setting up libboost-atomic1.67.0:amd64 (1.67.0-13+deb10u1) ... Setting up libkrb5-3:amd64 (1.17-3+deb10u4) ... Setting up libtiff5:amd64 (4.1.0+git191117-2~deb10u4) ... Setting up libprotobuf17:amd64 (3.6.1.3-2) ... Setting up libmpdec2:amd64 (2.4.2-2) ... Setting up libjs-jquery (3.3.1~dfsg-3+deb10u1) ... Setting up libboost-system1.67.0:amd64 (1.67.0-13+deb10u1) ... Setting up libdivsufsort3:amd64 (2.0.1-4) ... Setting up openssl (1.1.1n-0+deb10u3) ... Setting up libbsd0:amd64 (0.9.1-2+deb10u1) ... Setting up libdrm-common (2.4.97-1) ... Setting up libelf1:amd64 (0.176-1.1) ... Setting up readline-common (7.0-5) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-1) ... Setting up sphinx-rtd-theme-common (0.4.3+dfsg-1) ... Setting up xdg-utils (1.1.3-1+deb10u1) ... Setting up libreadline7:amd64 (7.0-5) ... Setting up libgdbm6:amd64 (1.18.1-4) ... Setting up libjs-underscore (1.9.1~dfsg-1+deb10u1) ... Setting up libice6:amd64 (2:1.0.9-2) ... Setting up parafly (0.0.2013.01.21-4) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libpython3.7-stdlib:amd64 (3.7.3-2+deb10u3) ... Setting up libxcb1:amd64 (1.13.1-2) ... Setting up libboost-regex1.67.0:amd64 (1.67.0-13+deb10u1) ... Setting up libboost-chrono1.67.0:amd64 (1.67.0-13+deb10u1) ... Setting up libboost-thread1.67.0:amd64 (1.67.0-13+deb10u1) ... Setting up libxcb-render0:amd64 (1.13.1-2) ... Setting up libmbedx509-0:amd64 (2.16.0-1) ... Setting up libxcb-glx0:amd64 (1.13.1-2) ... Setting up libedit2:amd64 (3.1-20181209-1) ... Setting up libcommons-parent-java (43-1) ... Setting up libtbb2:amd64 (2018~U6-4) ... Setting up libmbedtls12:amd64 (2.16.0-1) ... Setting up libavahi-common3:amd64 (0.7-4+deb10u1) ... Setting up libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u7) ... Setting up libnss3:amd64 (2:3.42.1-1+deb10u5) ... Setting up libxcb-shm0:amd64 (1.13.1-2) ... Setting up libpython2.7-stdlib:amd64 (2.7.16-2+deb10u1) ... Setting up libxcb-present0:amd64 (1.13.1-2) ... Setting up libthai0:amd64 (0.1.28-2) ... Setting up ca-certificates (20200601~deb10u2) ... Updating certificates in /etc/ssl/certs... 137 added, 0 removed; done. Setting up libblas3:amd64 (3.8.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode Setting up libfreetype6:amd64 (2.9.1-3+deb10u3) ... Setting up libxcb-sync1:amd64 (1.13.1-2) ... Setting up libgssapi-krb5-2:amd64 (1.17-3+deb10u4) ... Setting up libcommons-collections4-java (4.2-1) ... Setting up libgdbm-compat4:amd64 (1.18.1-4) ... Setting up ucf (3.0038+nmu1) ... Setting up libjs-sphinxdoc (1.8.4-1) ... Setting up libperl5.28:amd64 (5.28.1-6+deb10u1) ... Setting up libxcb-dri2-0:amd64 (1.13.1-2) ... Setting up libdrm2:amd64 (2.4.97-1) ... Setting up libboost-timer1.67.0:amd64 (1.67.0-13+deb10u1) ... Setting up libcurl4:amd64 (7.64.0-4+deb10u2) ... Setting up libllvm7:amd64 (1:7.0.1-8+deb10u2) ... Setting up libx11-6:amd64 (2:1.6.7-1+deb10u2) ... Setting up libharfbuzz0b:amd64 (2.3.1-1) ... Setting up libboost-filesystem1.67.0:amd64 (1.67.0-13+deb10u1) ... Setting up curl (7.64.0-4+deb10u2) ... Setting up libsm6:amd64 (2:1.2.3-1) ... Setting up libavahi-client3:amd64 (0.7-4+deb10u1) ... Setting up libpython3-stdlib:amd64 (3.7.3-1) ... Setting up libdrm-amdgpu1:amd64 (2.4.97-1) ... Setting up libxcb-dri3-0:amd64 (1.13.1-2) ... Setting up libpaper1:amd64 (1.1.28) ... Creating config file /etc/papersize with new version Setting up python3.7 (3.7.3-2+deb10u3) ... Setting up liblapack3:amd64 (3.8.0-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libdrm-nouveau2:amd64 (2.4.97-1) ... Setting up python2.7 (2.7.16-2+deb10u1) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up libpython2-stdlib:amd64 (2.7.16-1) ... Setting up libdrm-radeon1:amd64 (2.4.97-1) ... Setting up fontconfig-config (2.13.1-2) ... Setting up libdrm-intel1:amd64 (2.4.97-1) ... Setting up libgl1-mesa-dri:amd64 (18.3.6-2+deb10u1) ... Setting up libxext6:amd64 (2:1.3.3-1+b2) ... Setting up libcurl3-gnutls:amd64 (7.64.0-4+deb10u2) ... Setting up python3 (3.7.3-1) ... Setting up libpaper-utils (1.1.28) ... Setting up python2 (2.7.16-1) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up libpython-stdlib:amd64 (2.7.16-1) ... Setting up perl (5.28.1-6+deb10u1) ... Setting up libxfixes3:amd64 (1:5.0.3-1) ... Setting up libio-html-perl (1.001-1) ... Setting up libxt6:amd64 (1:1.1.5-1+b3) ... Setting up berkeley-express (1.5.2+dfsg-1+b2) ... Setting up libtimedate-perl (2.3000-2+deb10u1) ... Setting up libcups2:amd64 (2.2.10-6+deb10u6) ... Setting up libxss1:amd64 (1:1.2.3-1) ... Setting up libfontconfig1:amd64 (2.13.1-2) ... Setting up python (2.7.16-1) ... Setting up liburi-perl (1.76-1) ... Setting up libstaden-read13:amd64 (1.14.11-6) ... Setting up libnet-ssleay-perl (1.85-2+deb10u1) ... Setting up python3-pkg-resources (40.8.0-1) ... Setting up libhttp-date-perl (6.02-1) ... Setting up fontconfig (2.13.1-2) ... Regenerating fonts cache... done. Setting up libxft2:amd64 (2.3.2-2) ... Setting up libxdamage1:amd64 (1:1.1.4-3+b3) ... Setting up libfile-listing-perl (6.04-1) ... Setting up libxi6:amd64 (2:1.7.9-1) ... Setting up libhts2:amd64 (1.9-12~deb10u1) ... Setting up bowtie (1.2.2+dfsg-4) ... Setting up libxtst6:amd64 (2:1.2.3-1) ... Setting up libhtml-tagset-perl (3.20-3) ... Setting up libtk8.6:amd64 (8.6.9-2) ... Setting up libpango-1.0-0:amd64 (1.42.4-8~deb10u1) ... Setting up liblwp-mediatypes-perl (6.02-1) ... Setting up libtry-tiny-perl (0.30-1) ... Setting up libnet-http-perl (6.18-1) ... Setting up libencode-locale-perl (1.05-1) ... Setting up libcairo2:amd64 (1.16.0-4+deb10u1) ... Setting up samtools (1.9-4) ... Setting up bowtie2 (2.3.4.3-1) ... Setting up ncbi-blast+ (2.8.1-1+deb10u1) ... Setting up salmon (0.12.0+ds1-1+b1) ... Setting up python3-numpy (1:1.16.2-1) ... Setting up libwww-robotrules-perl (6.02-1) ... Setting up libhtml-parser-perl (3.72-3+b3) ... Setting up libpangoft2-1.0-0:amd64 (1.42.4-8~deb10u1) ... Setting up libio-socket-ssl-perl (2.060-3) ... Setting up libpangocairo-1.0-0:amd64 (1.42.4-8~deb10u1) ... Setting up libhttp-message-perl (6.18-1) ... Setting up libhttp-negotiate-perl (6.01-1) ... Setting up libglx-mesa0:amd64 (18.3.6-2+deb10u1) ... Setting up libglx0:amd64 (1.1.0-1) ... Setting up libhttp-cookies-perl (6.04-1) ... Setting up libhtml-tree-perl (5.07-2) ... Setting up libgl1:amd64 (1.1.0-1) ... Setting up r-base-core (3.5.2-1) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-crayon (1.3.4-4) ... Setting up r-cran-gtable (0.2.0-3) ... Setting up r-cran-labeling (0.3-3) ... Setting up r-cran-lattice (0.20-38-1) ... Setting up r-cran-nlme (3.1.137-1+b3) ... Setting up r-cran-viridislite (0.3.0-3) ... Setting up r-cran-cluster (2.0.7-1-1+b3) ... Setting up rsem (1.3.1+dfsg-1) ... Setting up r-cran-lazyeval (0.2.1-3) ... Setting up r-cran-r6 (2.4.0-1) ... Setting up r-cran-pkgkitten (0.1.4-2) ... Setting up r-cran-magrittr (1.5-5) ... Setting up r-cran-littler (0.3.6-1) ... Setting up transdecoder (5.0.1-2) ... Setting up r-cran-rcpp (1.0.0-1) ... Setting up r-bioc-biocgenerics (0.28.0-2) ... Setting up r-cran-rlang (0.3.1-2) ... Setting up r-cran-assertthat (0.2.0-2) ... Setting up littler (0.3.6-1) ... Setting up r-cran-withr (2.1.2-3) ... Setting up r-cran-digest (0.6.18-1) ... Setting up r-cran-fansi (0.4.0-1) ... Setting up r-cran-mass (7.3-51.1-1) ... Setting up r-cran-glue (1.3.0-1) ... Setting up r-cran-cli (1.0.1-1) ... Setting up r-cran-pkgconfig (2.0.2-1) ... Setting up r-cran-utf8 (1.1.4-1+b1) ... Setting up r-cran-colorspace (1.4-0+dfsg-1) ... Setting up r-cran-stringi (1.2.4-2) ... Setting up r-cran-plyr (1.8.4-2) ... Setting up r-cran-rcolorbrewer (1.1-2-2) ... Setting up r-cran-matrix (1.2-15-1) ... Setting up r-cran-mgcv (1.8-27-1) ... Setting up r-cran-pillar (1.3.1-1) ... Setting up r-cran-stringr (1.4.0-1) ... Setting up r-cran-munsell (0.5.0-1) ... Setting up r-cran-tibble (2.0.1-1) ... Setting up r-cran-reshape2 (1.4.3-2) ... Setting up r-cran-scales (1.0.0-2) ... Setting up r-cran-ggplot2 (3.1.0-1) ... Setting up r-bioc-qvalue (2.14.1-1) ... Setting up default-jre-headless (2:1.11-71) ... Setting up libwww-perl (6.36-2) ... Setting up openjdk-11-jre-headless:amd64 (11.0.16+8-1~deb10u1) ... update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode update-alternatives: using /usr/lib/jvm/java-11-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up libconcurrent-java (1.3.4-4) ... Setting up openjdk-11-jre:amd64 (11.0.16+8-1~deb10u1) ... Setting up jaligner (1.0+dfsg-6) ... Setting up default-jre (2:1.11-71) ... Setting up libcolt-free-java (1.2.0+dfsg-7) ... Setting up ca-certificates-java (20190405) ... head: cannot open '/etc/ssl/certs/java/cacerts' for reading: No such file or directory Adding debian:thawte_Primary_Root_CA_-_G3.pem Adding debian:thawte_Primary_Root_CA_-_G2.pem Adding debian:thawte_Primary_Root_CA.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:Verisign_Class_3_Public_Primary_Certification_Authority_-_G3.pem Adding debian:VeriSign_Universal_Root_Certification_Authority.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G5.pem Adding debian:VeriSign_Class_3_Public_Primary_Certification_Authority_-_G4.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:Trustis_FPS_Root_CA.pem Adding debian:TrustCor_RootCert_CA-2.pem Adding debian:TrustCor_RootCert_CA-1.pem Adding debian:TrustCor_ECA-1.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Taiwan_GRCA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G3.pem Adding debian:Staat_der_Nederlanden_Root_CA_-_G2.pem Adding debian:Staat_der_Nederlanden_EV_Root_CA.pem Adding debian:Sonera_Class_2_Root_CA.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Secure_Global_CA.pem Adding debian:SecureTrust_CA.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GA_CA.pem Adding debian:Network_Solutions_Certificate_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:LuxTrust_Global_Root_2.pem Adding debian:Izenpe.com.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:ISRG_Root_X1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:Hongkong_Post_Root_CA_1.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2011.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Global_Chambersign_Root_-_2008.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R2.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GeoTrust_Universal_CA_2.pem Adding debian:GeoTrust_Universal_CA.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G3.pem Adding debian:GeoTrust_Primary_Certification_Authority_-_G2.pem Adding debian:GeoTrust_Primary_Certification_Authority.pem Adding debian:GeoTrust_Global_CA.pem Adding debian:GTS_Root_R4.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R1.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:EE_Certification_Centre_Root_CA.pem Adding debian:EC-ACC.pem Adding debian:E-Tugra_Certification_Authority.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DST_Root_CA_X3.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:Cybertrust_Global_Root.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:Chambers_of_Commerce_Root_-_2008.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certigna.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:ACCVRAIZ1.pem done. Setting up trimmomatic (0.38+dfsg-1) ... Setting up liblwp-protocol-https-perl (6.07-2) ... Setting up libjung-free-java (2.0.1+dfsg-1) ... Setting up trinityrnaseq (2.6.6+dfsg-6) ... Processing triggers for libc-bin (2.28-10+deb10u1) ... Processing triggers for ca-certificates (20200601~deb10u2) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. done. 1m28.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'apt-get', '-y', 'install', 'trinityrnaseq=2.6.6+dfsg-6'] 1m28.0s INFO: Running scripts post_install 1m28.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/post_install_exceptions'] 1m28.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/post_install_exceptions'] 1m28.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/post_install_log_alternatives'] 1m28.1s DUMP: Removing 'local diversion of /usr/bin/update-alternatives to /usr/bin/update-alternatives.orig' LOG-ALTERNATIVES: dpkg=python: piuparts=trinityrnaseq=2.6.6+dfsg-6: /usr/bin/update-alternatives --auto /usr/bin/python LOG-ALTERNATIVES: dpkg=python: piuparts=trinityrnaseq=2.6.6+dfsg-6: /usr/bin/update-alternatives --remove python /usr/bin/python1.5 LOG-ALTERNATIVES: dpkg=python: piuparts=trinityrnaseq=2.6.6+dfsg-6: /usr/bin/update-alternatives --remove python /usr/bin/python2.1 LOG-ALTERNATIVES: dpkg=python: piuparts=trinityrnaseq=2.6.6+dfsg-6: /usr/bin/update-alternatives --remove python /usr/bin/python2.2 LOG-ALTERNATIVES: dpkg=python3: piuparts=trinityrnaseq=2.6.6+dfsg-6: /usr/bin/update-alternatives --auto /usr/bin/python3 LOG-ALTERNATIVES: dpkg=libblas3: piuparts=trinityrnaseq=2.6.6+dfsg-6: /usr/bin/update-alternatives --install /usr/lib/x86_64-linux-gnu/libblas.so.3 libblas.so.3-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 10 LOG-ALTERNATIVES: dpkg=liblapack3: piuparts=trinityrnaseq=2.6.6+dfsg-6: /usr/bin/update-alternatives --install /usr/lib/x86_64-linux-gnu/liblapack.so.3 liblapack.so.3-x86_64-linux-gnu /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 10 LOG-ALTERNATIVES: dpkg=perl: piuparts=trinityrnaseq=2.6.6+dfsg-6: /usr/bin/update-alternatives --remove rename /usr/bin/prename LOG-ALTERNATIVES: dpkg=openjdk-11-jre-headless: piuparts=trinityrnaseq=2.6.6+dfsg-6: /usr/bin/update-alternatives --install /usr/bin/java java /usr/lib/jvm/java-11-openjdk-amd64/bin/java 1111 --slave /usr/share/man/man1/java.1.gz java.1.gz /usr/lib/jvm/java-11-openjdk-amd64/man/man1/java.1.gz LOG-ALTERNATIVES: dpkg=openjdk-11-jre-headless: piuparts=trinityrnaseq=2.6.6+dfsg-6: /usr/bin/update-alternatives --install /usr/bin/jjs jjs /usr/lib/jvm/java-11-openjdk-amd64/bin/jjs 1111 --slave /usr/share/man/man1/jjs.1.gz jjs.1.gz /usr/lib/jvm/java-11-openjdk-amd64/man/man1/jjs.1.gz LOG-ALTERNATIVES: dpkg=openjdk-11-jre-headless: piuparts=trinityrnaseq=2.6.6+dfsg-6: /usr/bin/update-alternatives --install /usr/bin/keytool keytool /usr/lib/jvm/java-11-openjdk-amd64/bin/keytool 1111 --slave /usr/share/man/man1/keytool.1.gz keytool.1.gz /usr/lib/jvm/java-11-openjdk-amd64/man/man1/keytool.1.gz LOG-ALTERNATIVES: dpkg=openjdk-11-jre-headless: piuparts=trinityrnaseq=2.6.6+dfsg-6: /usr/bin/update-alternatives --install /usr/bin/rmid rmid /usr/lib/jvm/java-11-openjdk-amd64/bin/rmid 1111 --slave /usr/share/man/man1/rmid.1.gz rmid.1.gz /usr/lib/jvm/java-11-openjdk-amd64/man/man1/rmid.1.gz LOG-ALTERNATIVES: dpkg=openjdk-11-jre-headless: piuparts=trinityrnaseq=2.6.6+dfsg-6: /usr/bin/update-alternatives --install /usr/bin/rmiregistry rmiregistry /usr/lib/jvm/java-11-openjdk-amd64/bin/rmiregistry 1111 --slave /usr/share/man/man1/rmiregistry.1.gz rmiregistry.1.gz /usr/lib/jvm/java-11-openjdk-amd64/man/man1/rmiregistry.1.gz LOG-ALTERNATIVES: dpkg=openjdk-11-jre-headless: piuparts=trinityrnaseq=2.6.6+dfsg-6: /usr/bin/update-alternatives --install /usr/bin/pack200 pack200 /usr/lib/jvm/java-11-openjdk-amd64/bin/pack200 1111 --slave /usr/share/man/man1/pack200.1.gz pack200.1.gz /usr/lib/jvm/java-11-openjdk-amd64/man/man1/pack200.1.gz LOG-ALTERNATIVES: dpkg=openjdk-11-jre-headless: piuparts=trinityrnaseq=2.6.6+dfsg-6: /usr/bin/update-alternatives --install /usr/bin/unpack200 unpack200 /usr/lib/jvm/java-11-openjdk-amd64/bin/unpack200 1111 --slave /usr/share/man/man1/unpack200.1.gz unpack200.1.gz /usr/lib/jvm/java-11-openjdk-amd64/man/man1/unpack200.1.gz LOG-ALTERNATIVES: dpkg=openjdk-11-jre-headless: piuparts=trinityrnaseq=2.6.6+dfsg-6: /usr/bin/update-alternatives --install /usr/bin/jexec jexec /usr/lib/jvm/java-11-openjdk-amd64/lib/jexec 1111 --slave /usr/share/binfmts/jar jexec-binfmt /usr/lib/jvm/java-11-openjdk-amd64/lib/jar.binfmt 1m28.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/post_install_log_alternatives'] 1m28.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmph3a3epj4'] 1m28.9s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmph3a3epj4'] 1m30.6s ERROR: WARN: Broken symlinks: /usr/lib/transdecoder/util/__pwm_tests/pasa_assemblies.fasta.gz -> ../../sample_data/pasa_example/pasa_assemblies.fasta.gz (transdecoder) /usr/lib/jvm/java-11-openjdk-amd64/lib/libatk-wrapper.so -> ../../../x86_64-linux-gnu/jni/libatk-wrapper.so (openjdk-11-jre:amd64) /usr/lib/jvm/java-11-openjdk-amd64/lib/security/blacklisted.certs -> /etc/java-11-openjdk/security/blacklisted.certs (openjdk-11-jre-headless:amd64) 1m30.6s INFO: /bin converted to /usr/bin by /usr merge 1m30.7s INFO: /lib converted to /usr/lib by /usr merge 1m30.7s INFO: /lib/init converted to /usr/lib/init by /usr merge 1m30.7s INFO: /lib/lsb converted to /usr/lib/lsb by /usr merge 1m30.7s INFO: /lib/lsb/init-functions.d converted to /usr/lib/lsb/init-functions.d by /usr merge 1m30.7s INFO: /lib/systemd converted to /usr/lib/systemd by /usr merge 1m30.7s INFO: /lib/systemd/system converted to /usr/lib/systemd/system by /usr merge 1m30.7s INFO: /lib/terminfo converted to /usr/lib/terminfo by /usr merge 1m30.7s INFO: /lib/terminfo/E converted to /usr/lib/terminfo/E by /usr merge 1m30.7s INFO: /lib/terminfo/a converted to /usr/lib/terminfo/a by /usr merge 1m30.7s INFO: /lib/terminfo/c converted to /usr/lib/terminfo/c by /usr merge 1m30.7s INFO: /lib/terminfo/d converted to /usr/lib/terminfo/d by /usr merge 1m30.7s INFO: /lib/terminfo/h converted to /usr/lib/terminfo/h by /usr merge 1m30.7s INFO: /lib/terminfo/l converted to /usr/lib/terminfo/l by /usr merge 1m30.7s INFO: /lib/terminfo/m converted to /usr/lib/terminfo/m by /usr merge 1m30.7s INFO: /lib/terminfo/p converted to /usr/lib/terminfo/p by /usr merge 1m30.7s INFO: /lib/terminfo/r converted to /usr/lib/terminfo/r by /usr merge 1m30.7s INFO: /lib/terminfo/s converted to /usr/lib/terminfo/s by /usr merge 1m30.7s INFO: /lib/terminfo/v converted to /usr/lib/terminfo/v by /usr merge 1m30.7s INFO: /lib/terminfo/w converted to /usr/lib/terminfo/w by /usr merge 1m30.7s INFO: /lib/terminfo/x converted to /usr/lib/terminfo/x by /usr merge 1m30.7s INFO: /lib/udev converted to /usr/lib/udev by /usr merge 1m30.7s INFO: /lib/udev/rules.d converted to /usr/lib/udev/rules.d by /usr merge 1m30.7s INFO: /lib/x86_64-linux-gnu converted to /usr/lib/x86_64-linux-gnu by /usr merge 1m30.7s INFO: /lib/x86_64-linux-gnu/security converted to /usr/lib/x86_64-linux-gnu/security by /usr merge 1m30.7s INFO: /lib64 converted to /usr/lib64 by /usr merge 1m30.7s INFO: /sbin converted to /usr/sbin by /usr merge 1m31.7s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', '-ac', '--ignore-obsolete'] 1m35.3s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', '-ac', '--ignore-obsolete'] 1m35.3s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m35.3s DUMP: 0.15.6 1m35.3s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m35.3s INFO: Running adequate version 0.15.6 now. 1m35.3s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'trinityrnaseq'] 1m35.4s DUMP: trinityrnaseq: py-file-not-bytecompiled /usr/lib/trinityrnaseq/Analysis/SuperTranscripts/pylib/TGLOBALS.py trinityrnaseq: py-file-not-bytecompiled /usr/lib/trinityrnaseq/Analysis/SuperTranscripts/pylib/__init__.py trinityrnaseq: py-file-not-bytecompiled /usr/lib/trinityrnaseq/util/misc/alt_GG_read_partitioning_JCornish/genwig2.py trinityrnaseq: py-file-not-bytecompiled /usr/lib/trinityrnaseq/util/support_scripts/tests/sample_data_tests.py trinityrnaseq: py-file-not-bytecompiled /usr/lib/trinityrnaseq/util/support_scripts/tests/test_prep.py trinityrnaseq: py-file-not-bytecompiled /usr/lib/trinityrnaseq/util/support_scripts/tests/tests.py 1m35.4s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'trinityrnaseq'] 1m35.4s ERROR: WARN: Inadequate results from running adequate! trinityrnaseq: py-file-not-bytecompiled /usr/lib/trinityrnaseq/Analysis/SuperTranscripts/pylib/TGLOBALS.py trinityrnaseq: py-file-not-bytecompiled /usr/lib/trinityrnaseq/Analysis/SuperTranscripts/pylib/__init__.py trinityrnaseq: py-file-not-bytecompiled /usr/lib/trinityrnaseq/util/misc/alt_GG_read_partitioning_JCornish/genwig2.py trinityrnaseq: py-file-not-bytecompiled /usr/lib/trinityrnaseq/util/support_scripts/tests/sample_data_tests.py trinityrnaseq: py-file-not-bytecompiled /usr/lib/trinityrnaseq/util/support_scripts/tests/test_prep.py trinityrnaseq: py-file-not-bytecompiled /usr/lib/trinityrnaseq/util/support_scripts/tests/tests.py 1m35.4s ERROR: WARN: Running adequate resulted in inadequate tags found: py-file-not-bytecompiled 1m35.4s INFO: Running scripts pre_remove 1m35.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m35.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m35.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m35.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m35.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m42.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m42.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m43.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m43.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m43.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m43.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/pre_remove_exceptions'] 1m43.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/pre_remove_exceptions'] 1m43.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m43.2s DUMP: install ok installed adduser adduser 3.118 install ok installed apt apt 1.8.2.3 install ok installed base-files base-files 10.3+deb10u13 install ok installed base-passwd base-passwd 3.5.46 install ok installed bash bash 5.0-4 install ok installed berkeley-express berkeley-express 1.5.2+dfsg-1+b2 install ok installed bowtie bowtie 1.2.2+dfsg-4 install ok installed bowtie2 bowtie2 2.3.4.3-1 install ok installed bsdutils bsdutils 1:2.33.1-0.1 install ok installed ca-certificates ca-certificates 20200601~deb10u2 install ok installed ca-certificates-java ca-certificates-java 20190405 install ok installed coreutils coreutils 8.30-3 install ok installed curl curl 7.64.0-4+deb10u2 install ok installed dash dash 0.5.10.2-5 install ok installed debconf debconf 1.5.71+deb10u1 install ok installed debian-archive-keyring debian-archive-keyring 2019.1+deb10u1 install ok installed debianutils debianutils 4.8.6.1 install ok installed default-jre default-jre 2:1.11-71 install ok installed default-jre-headless default-jre-headless 2:1.11-71 install ok installed diffutils diffutils 1:3.7-3 install ok installed dpkg dpkg 1.19.8 install ok installed e2fsprogs e2fsprogs 1.44.5-1+deb10u3 install ok installed fdisk fdisk 2.33.1-0.1 install ok installed findutils findutils 4.6.0+git+20190209-2 install ok installed fontconfig fontconfig 2.13.1-2 install ok installed fontconfig-config fontconfig-config 2.13.1-2 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-1 install ok installed fonts-font-awesome fonts-font-awesome 5.0.10+really4.7.0~dfsg-1 install ok installed fonts-lato fonts-lato 2.0-2 install ok installed fonts-roboto-slab fonts-roboto-slab 1.100263+20170512-1 install ok installed gcc-8-base:amd64 gcc-8-base 8.3.0-6 install ok installed gpgv gpgv 2.2.12-1+deb10u2 install ok installed grep grep 3.3-1 install ok installed gzip gzip 1.9-3+deb10u1 install ok installed hostname hostname 3.21 install ok installed init-system-helpers init-system-helpers 1.56+nmu1 install ok installed jaligner jaligner 1.0+dfsg-6 install ok installed java-common java-common 0.71 install ok installed jellyfish jellyfish 2.2.10-2 install ok installed libacl1:amd64 libacl1 2.2.53-4 install ok installed libapache-pom-java libapache-pom-java 18-1 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.8.2.3 install ok installed libasound2:amd64 libasound2 1.1.8-1 install ok installed libasound2-data libasound2-data 1.1.8-1 install ok installed libatomic1:amd64 libatomic1 8.3.0-6 install ok installed libattr1:amd64 libattr1 1:2.4.48-4 install ok installed libaudit-common libaudit-common 1:2.8.4-3 install ok installed libaudit1:amd64 libaudit1 1:2.8.4-3 install ok installed libavahi-client3:amd64 libavahi-client3 0.7-4+deb10u1 install ok installed libavahi-common-data:amd64 libavahi-common-data 0.7-4+deb10u1 install ok installed libavahi-common3:amd64 libavahi-common3 0.7-4+deb10u1 install ok installed libbamtools2.5.1:amd64 libbamtools2.5.1 2.5.1+dfsg-3 install ok installed libblas3:amd64 libblas3 3.8.0-2 install ok installed libblkid1:amd64 libblkid1 2.33.1-0.1 install ok installed libboost-atomic1.67.0:amd64 libboost-atomic1.67.0 1.67.0-13+deb10u1 install ok installed libboost-chrono1.67.0:amd64 libboost-chrono1.67.0 1.67.0-13+deb10u1 install ok installed libboost-date-time1.67.0:amd64 libboost-date-time1.67.0 1.67.0-13+deb10u1 install ok installed libboost-filesystem1.67.0:amd64 libboost-filesystem1.67.0 1.67.0-13+deb10u1 install ok installed libboost-iostreams1.67.0:amd64 libboost-iostreams1.67.0 1.67.0-13+deb10u1 install ok installed libboost-program-options1.67.0:amd64 libboost-program-options1.67.0 1.67.0-13+deb10u1 install ok installed libboost-regex1.67.0:amd64 libboost-regex1.67.0 1.67.0-13+deb10u1 install ok installed libboost-system1.67.0:amd64 libboost-system1.67.0 1.67.0-13+deb10u1 install ok installed libboost-thread1.67.0:amd64 libboost-thread1.67.0 1.67.0-13+deb10u1 install ok installed libboost-timer1.67.0:amd64 libboost-timer1.67.0 1.67.0-13+deb10u1 install ok installed libbsd0:amd64 libbsd0 0.9.1-2+deb10u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-9.2~deb10u1 install ok installed libc-bin libc-bin 2.28-10+deb10u1 install ok installed libc6:amd64 libc6 2.28-10+deb10u1 install ok installed libcairo2:amd64 libcairo2 1.16.0-4+deb10u1 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.9-2 install ok installed libcolt-free-java libcolt-free-java 1.2.0+dfsg-7 install ok installed libcom-err2:amd64 libcom-err2 1.44.5-1+deb10u3 install ok installed libcommons-collections4-java libcommons-collections4-java 4.2-1 install ok installed libcommons-parent-java libcommons-parent-java 43-1 install ok installed libconcurrent-java libconcurrent-java 1.3.4-4 install ok installed libcups2:amd64 libcups2 2.2.10-6+deb10u6 install ok installed libcurl3-gnutls:amd64 libcurl3-gnutls 7.64.0-4+deb10u2 install ok installed libcurl4:amd64 libcurl4 7.64.0-4+deb10u2 install ok installed libdatrie1:amd64 libdatrie1 0.2.12-2 install ok installed libdb5.3:amd64 libdb5.3 5.3.28+dfsg1-0.5 install ok installed libdbus-1-3:amd64 libdbus-1-3 1.12.20-0+deb10u1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.249 install ok installed libdeflate0:amd64 libdeflate0 1.2-1 install ok installed libdivsufsort3:amd64 libdivsufsort3 2.0.1-4 install ok installed libdrm-amdgpu1:amd64 libdrm-amdgpu1 2.4.97-1 install ok installed libdrm-common libdrm-common 2.4.97-1 install ok installed libdrm-intel1:amd64 libdrm-intel1 2.4.97-1 install ok installed libdrm-nouveau2:amd64 libdrm-nouveau2 2.4.97-1 install ok installed libdrm-radeon1:amd64 libdrm-radeon1 2.4.97-1 install ok installed libdrm2:amd64 libdrm2 2.4.97-1 install ok installed libedit2:amd64 libedit2 3.1-20181209-1 install ok installed libelf1:amd64 libelf1 0.176-1.1 install ok installed libencode-locale-perl libencode-locale-perl 1.05-1 install ok installed libexpat1:amd64 libexpat1 2.2.6-2+deb10u4 install ok installed libext2fs2:amd64 libext2fs2 1.44.5-1+deb10u3 install ok installed libfdisk1:amd64 libfdisk1 2.33.1-0.1 install ok installed libffi6:amd64 libffi6 3.2.1-9 install ok installed libfile-listing-perl libfile-listing-perl 6.04-1 install ok installed libfontconfig1:amd64 libfontconfig1 2.13.1-2 install ok installed libfreetype6:amd64 libfreetype6 2.9.1-3+deb10u3 install ok installed libfribidi0:amd64 libfribidi0 1.0.5-3.1+deb10u2 install ok installed libgcc1:amd64 libgcc1 1:8.3.0-6 install ok installed libgcrypt20:amd64 libgcrypt20 1.8.4-5+deb10u1 install ok installed libgdbm-compat4:amd64 libgdbm-compat4 1.18.1-4 install ok installed libgdbm6:amd64 libgdbm6 1.18.1-4 install ok installed libgetopt-java libgetopt-java 1.0.14+dfsg-4 install ok installed libgfortran5:amd64 libgfortran5 8.3.0-6 install ok installed libgif7:amd64 libgif7 5.1.4-3 install ok installed libgl1:amd64 libgl1 1.1.0-1 install ok installed libgl1-mesa-dri:amd64 libgl1-mesa-dri 18.3.6-2+deb10u1 install ok installed libglapi-mesa:amd64 libglapi-mesa 18.3.6-2+deb10u1 install ok installed libglib2.0-0:amd64 libglib2.0-0 2.58.3-2+deb10u3 install ok installed libglvnd0:amd64 libglvnd0 1.1.0-1 install ok installed libglx-mesa0:amd64 libglx-mesa0 18.3.6-2+deb10u1 install ok installed libglx0:amd64 libglx0 1.1.0-1 install ok installed libgmp10:amd64 libgmp10 2:6.1.2+dfsg-4+deb10u1 install ok installed libgnutls30:amd64 libgnutls30 3.6.7-4+deb10u8 install ok installed libgomp1:amd64 libgomp1 8.3.0-6 install ok installed libgpg-error0:amd64 libgpg-error0 1.35-1 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.13-7 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.17-3+deb10u4 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 2.3.1-1 install ok installed libhogweed4:amd64 libhogweed4 3.4.1-1+deb10u1 install ok installed libhtml-parser-perl libhtml-parser-perl 3.72-3+b3 install ok installed libhtml-tagset-perl libhtml-tagset-perl 3.20-3 install ok installed libhtml-tree-perl libhtml-tree-perl 5.07-2 install ok installed libhts2:amd64 libhts2 1.9-12~deb10u1 install ok installed libhttp-cookies-perl libhttp-cookies-perl 6.04-1 install ok installed libhttp-date-perl libhttp-date-perl 6.02-1 install ok installed libhttp-message-perl libhttp-message-perl 6.18-1 install ok installed libhttp-negotiate-perl libhttp-negotiate-perl 6.01-1 install ok installed libice6:amd64 libice6 2:1.0.9-2 install ok installed libicu63:amd64 libicu63 63.1-6+deb10u3 install ok installed libidn2-0:amd64 libidn2-0 2.0.5-1+deb10u1 install ok installed libio-html-perl libio-html-perl 1.001-1 install ok installed libio-socket-ssl-perl libio-socket-ssl-perl 2.060-3 install ok installed libjbig0:amd64 libjbig0 2.1-3.1+b2 install ok installed libjbzip2-java libjbzip2-java 0.9.1-5 install ok installed libjellyfish-2.0-2:amd64 libjellyfish-2.0-2 2.2.10-2 install ok installed libjemalloc2:amd64 libjemalloc2 5.1.0-3 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:1.5.2-2+deb10u1 install ok installed libjs-jquery libjs-jquery 3.3.1~dfsg-3+deb10u1 install ok installed libjs-modernizr libjs-modernizr 2.6.2+ds1-3 install ok installed libjs-sphinxdoc libjs-sphinxdoc 1.8.4-1 install ok installed libjs-underscore libjs-underscore 1.9.1~dfsg-1+deb10u1 install ok installed libjung-free-java libjung-free-java 2.0.1+dfsg-1 install ok installed libk5crypto3:amd64 libk5crypto3 1.17-3+deb10u4 install ok installed libkeyutils1:amd64 libkeyutils1 1.6-6 install ok installed libkrb5-3:amd64 libkrb5-3 1.17-3+deb10u4 install ok installed libkrb5support0:amd64 libkrb5support0 1.17-3+deb10u4 install ok installed liblapack3:amd64 liblapack3 3.8.0-2 install ok installed liblcms2-2:amd64 liblcms2-2 2.9-3 install ok installed libldap-2.4-2:amd64 libldap-2.4-2 2.4.47+dfsg-3+deb10u7 install ok installed libldap-common libldap-common 2.4.47+dfsg-3+deb10u7 install ok installed libllvm7:amd64 libllvm7 1:7.0.1-8+deb10u2 install ok installed liblmdb0:amd64 liblmdb0 0.9.22-1 install ok installed liblwp-mediatypes-perl liblwp-mediatypes-perl 6.02-1 install ok installed liblwp-protocol-https-perl liblwp-protocol-https-perl 6.07-2 install ok installed liblz4-1:amd64 liblz4-1 1.8.3-1+deb10u1 install ok installed liblzma5:amd64 liblzma5 5.2.4-1+deb10u1 install ok installed libmbedcrypto3:amd64 libmbedcrypto3 2.16.0-1 install ok installed libmbedtls12:amd64 libmbedtls12 2.16.0-1 install ok installed libmbedx509-0:amd64 libmbedx509-0 2.16.0-1 install ok installed libmount1:amd64 libmount1 2.33.1-0.1 install ok installed libmpdec2:amd64 libmpdec2 2.4.2-2 install ok installed libncurses6:amd64 libncurses6 6.1+20181013-2+deb10u2 install ok installed libncursesw6:amd64 libncursesw6 6.1+20181013-2+deb10u2 install ok installed libnet-http-perl libnet-http-perl 6.18-1 install ok installed libnet-ssleay-perl libnet-ssleay-perl 1.85-2+deb10u1 install ok installed libnettle6:amd64 libnettle6 3.4.1-1+deb10u1 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.36.0-2+deb10u1 install ok installed libnspr4:amd64 libnspr4 2:4.20-1 install ok installed libnss3:amd64 libnss3 2:3.42.1-1+deb10u5 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.15-2+deb10u1 install ok installed libpam-modules:amd64 libpam-modules 1.3.1-5 install ok installed libpam-modules-bin libpam-modules-bin 1.3.1-5 install ok installed libpam-runtime libpam-runtime 1.3.1-5 install ok installed libpam0g:amd64 libpam0g 1.3.1-5 install ok installed libpango-1.0-0:amd64 libpango-1.0-0 1.42.4-8~deb10u1 install ok installed libpangocairo-1.0-0:amd64 libpangocairo-1.0-0 1.42.4-8~deb10u1 install ok installed libpangoft2-1.0-0:amd64 libpangoft2-1.0-0 1.42.4-8~deb10u1 install ok installed libpaper-utils libpaper-utils 1.1.28 install ok installed libpaper1:amd64 libpaper1 1.1.28 install ok installed libpciaccess0:amd64 libpciaccess0 0.14-1 install ok installed libpcre3:amd64 libpcre3 2:8.39-12 install ok installed libpcsclite1:amd64 libpcsclite1 1.8.24-1 install ok installed libperl5.28:amd64 libperl5.28 5.28.1-6+deb10u1 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.36.0-1 install ok installed libpng16-16:amd64 libpng16-16 1.6.36-6 install ok installed libprotobuf17:amd64 libprotobuf17 3.6.1.3-2 install ok installed libpsl5:amd64 libpsl5 0.20.2-2 install ok installed libpython-stdlib:amd64 libpython-stdlib 2.7.16-1 install ok installed libpython2-stdlib:amd64 libpython2-stdlib 2.7.16-1 install ok installed libpython2.7-minimal:amd64 libpython2.7-minimal 2.7.16-2+deb10u1 install ok installed libpython2.7-stdlib:amd64 libpython2.7-stdlib 2.7.16-2+deb10u1 install ok installed libpython3-stdlib:amd64 libpython3-stdlib 3.7.3-1 install ok installed libpython3.7-minimal:amd64 libpython3.7-minimal 3.7.3-2+deb10u3 install ok installed libpython3.7-stdlib:amd64 libpython3.7-stdlib 3.7.3-2+deb10u3 install ok installed libquadmath0:amd64 libquadmath0 8.3.0-6 install ok installed libreadline7:amd64 libreadline7 7.0-5 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-2 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.27+dfsg-1+deb10u2 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.27+dfsg-1+deb10u2 install ok installed libseccomp2:amd64 libseccomp2 2.3.3-4 install ok installed libselinux1:amd64 libselinux1 2.8-1+b1 install ok installed libsemanage-common libsemanage-common 2.8-2 install ok installed libsemanage1:amd64 libsemanage1 2.8-2 install ok installed libsensors-config libsensors-config 1:3.5.0-3 install ok installed libsensors5:amd64 libsensors5 1:3.5.0-3 install ok installed libsepol1:amd64 libsepol1 2.8-1 install ok installed libsm6:amd64 libsm6 2:1.2.3-1 install ok installed libsmartcols1:amd64 libsmartcols1 2.33.1-0.1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.27.2-3+deb10u1 install ok installed libss2:amd64 libss2 1.44.5-1+deb10u3 install ok installed libssh2-1:amd64 libssh2-1 1.8.0-2.1 install ok installed libssl1.1:amd64 libssl1.1 1.1.1n-0+deb10u3 install ok installed libstaden-read13:amd64 libstaden-read13 1.14.11-6 install ok installed libstdc++6:amd64 libstdc++6 8.3.0-6 install ok installed libsystemd0:amd64 libsystemd0 241-7~deb10u8 install ok installed libtasn1-6:amd64 libtasn1-6 4.13-3 install ok installed libtbb2:amd64 libtbb2 2018~U6-4 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.9+dfsg-2 install ok installed libthai-data libthai-data 0.1.28-2 install ok installed libthai0:amd64 libthai0 0.1.28-2 install ok installed libtiff5:amd64 libtiff5 4.1.0+git191117-2~deb10u4 install ok installed libtimedate-perl libtimedate-perl 2.3000-2+deb10u1 install ok installed libtinfo6:amd64 libtinfo6 6.1+20181013-2+deb10u2 install ok installed libtk8.6:amd64 libtk8.6 8.6.9-2 install ok installed libtry-tiny-perl libtry-tiny-perl 0.30-1 install ok installed libudev1:amd64 libudev1 241-7~deb10u8 install ok installed libunistring2:amd64 libunistring2 0.9.10-1 install ok installed liburi-perl liburi-perl 1.76-1 install ok installed libuuid1:amd64 libuuid1 2.33.1-0.1 install ok installed libvecmath-java libvecmath-java 1.5.2-7 install ok installed libwebp6:amd64 libwebp6 0.6.1-2+deb10u1 install ok installed libwww-perl libwww-perl 6.36-2 install ok installed libwww-robotrules-perl libwww-robotrules-perl 6.02-1 install ok installed libx11-6:amd64 libx11-6 2:1.6.7-1+deb10u2 install ok installed libx11-data libx11-data 2:1.6.7-1+deb10u2 install ok installed libx11-xcb1:amd64 libx11-xcb1 2:1.6.7-1+deb10u2 install ok installed libxau6:amd64 libxau6 1:1.0.8-1+b2 install ok installed libxcb-dri2-0:amd64 libxcb-dri2-0 1.13.1-2 install ok installed libxcb-dri3-0:amd64 libxcb-dri3-0 1.13.1-2 install ok installed libxcb-glx0:amd64 libxcb-glx0 1.13.1-2 install ok installed libxcb-present0:amd64 libxcb-present0 1.13.1-2 install ok installed libxcb-render0:amd64 libxcb-render0 1.13.1-2 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.13.1-2 install ok installed libxcb-sync1:amd64 libxcb-sync1 1.13.1-2 install ok installed libxcb1:amd64 libxcb1 1.13.1-2 install ok installed libxdamage1:amd64 libxdamage1 1:1.1.4-3+b3 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3 install ok installed libxext6:amd64 libxext6 2:1.3.3-1+b2 install ok installed libxfixes3:amd64 libxfixes3 1:5.0.3-1 install ok installed libxft2:amd64 libxft2 2.3.2-2 install ok installed libxi6:amd64 libxi6 2:1.7.9-1 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1 install ok installed libxshmfence1:amd64 libxshmfence1 1.3-1 install ok installed libxss1:amd64 libxss1 1:1.2.3-1 install ok installed libxt6:amd64 libxt6 1:1.1.5-1+b3 install ok installed libxtst6:amd64 libxtst6 2:1.2.3-1 install ok installed libxxf86vm1:amd64 libxxf86vm1 1:1.1.4-1+b2 install ok installed libzstd1:amd64 libzstd1 1.3.8+dfsg-3+deb10u2 install ok installed littler littler 0.3.6-1 install ok installed login login 1:4.5-1.1 install ok installed lsb-base lsb-base 10.2019051400 install ok installed mawk mawk 1.3.3-17+b3 install ok installed mime-support mime-support 3.62 install ok installed mount mount 2.33.1-0.1 install ok installed ncbi-blast+ ncbi-blast+ 2.8.1-1+deb10u1 install ok installed ncbi-data ncbi-data 6.1.20170106+dfsg1-0+deb10u2 install ok installed ncurses-base ncurses-base 6.1+20181013-2+deb10u2 install ok installed ncurses-bin ncurses-bin 6.1+20181013-2+deb10u2 install ok installed netbase netbase 5.6 install ok installed openjdk-11-jre:amd64 openjdk-11-jre 11.0.16+8-1~deb10u1 install ok installed openjdk-11-jre-headless:amd64 openjdk-11-jre-headless 11.0.16+8-1~deb10u1 install ok installed openssl openssl 1.1.1n-0+deb10u3 install ok installed parafly parafly 0.0.2013.01.21-4 install ok installed passwd passwd 1:4.5-1.1 install ok installed perl perl 5.28.1-6+deb10u1 install ok installed perl-base perl-base 5.28.1-6+deb10u1 install ok installed perl-modules-5.28 perl-modules-5.28 5.28.1-6+deb10u1 install ok installed perl-openssl-defaults:amd64 perl-openssl-defaults 3 install ok installed python python 2.7.16-1 install ok installed python-minimal python-minimal 2.7.16-1 install ok installed python2 python2 2.7.16-1 install ok installed python2-minimal python2-minimal 2.7.16-1 install ok installed python2.7 python2.7 2.7.16-2+deb10u1 install ok installed python2.7-minimal python2.7-minimal 2.7.16-2+deb10u1 install ok installed python3 python3 3.7.3-1 install ok installed python3-minimal python3-minimal 3.7.3-1 install ok installed python3-numpy python3-numpy 1:1.16.2-1 install ok installed python3-pkg-resources python3-pkg-resources 40.8.0-1 install ok installed python3.7 python3.7 3.7.3-2+deb10u3 install ok installed python3.7-minimal python3.7-minimal 3.7.3-2+deb10u3 install ok installed r-base-core r-base-core 3.5.2-1 install ok installed r-bioc-biocgenerics r-bioc-biocgenerics 0.28.0-2 install ok installed r-bioc-qvalue r-bioc-qvalue 2.14.1-1 install ok installed r-cran-assertthat r-cran-assertthat 0.2.0-2 install ok installed r-cran-cli r-cran-cli 1.0.1-1 install ok installed r-cran-cluster r-cran-cluster 2.0.7-1-1+b3 install ok installed r-cran-colorspace r-cran-colorspace 1.4-0+dfsg-1 install ok installed r-cran-crayon r-cran-crayon 1.3.4-4 install ok installed r-cran-digest r-cran-digest 0.6.18-1 install ok installed r-cran-fansi r-cran-fansi 0.4.0-1 install ok installed r-cran-ggplot2 r-cran-ggplot2 3.1.0-1 install ok installed r-cran-glue r-cran-glue 1.3.0-1 install ok installed r-cran-gtable r-cran-gtable 0.2.0-3 install ok installed r-cran-labeling r-cran-labeling 0.3-3 install ok installed r-cran-lattice r-cran-lattice 0.20-38-1 install ok installed r-cran-lazyeval r-cran-lazyeval 0.2.1-3 install ok installed r-cran-littler r-cran-littler 0.3.6-1 install ok installed r-cran-magrittr r-cran-magrittr 1.5-5 install ok installed r-cran-mass r-cran-mass 7.3-51.1-1 install ok installed r-cran-matrix r-cran-matrix 1.2-15-1 install ok installed r-cran-mgcv r-cran-mgcv 1.8-27-1 install ok installed r-cran-munsell r-cran-munsell 0.5.0-1 install ok installed r-cran-nlme r-cran-nlme 3.1.137-1+b3 install ok installed r-cran-pillar r-cran-pillar 1.3.1-1 install ok installed r-cran-pkgconfig r-cran-pkgconfig 2.0.2-1 install ok installed r-cran-pkgkitten r-cran-pkgkitten 0.1.4-2 install ok installed r-cran-plyr r-cran-plyr 1.8.4-2 install ok installed r-cran-r6 r-cran-r6 2.4.0-1 install ok installed r-cran-rcolorbrewer r-cran-rcolorbrewer 1.1-2-2 install ok installed r-cran-rcpp r-cran-rcpp 1.0.0-1 install ok installed r-cran-reshape2 r-cran-reshape2 1.4.3-2 install ok installed r-cran-rlang r-cran-rlang 0.3.1-2 install ok installed r-cran-scales r-cran-scales 1.0.0-2 install ok installed r-cran-stringi r-cran-stringi 1.2.4-2 install ok installed r-cran-stringr r-cran-stringr 1.4.0-1 install ok installed r-cran-tibble r-cran-tibble 2.0.1-1 install ok installed r-cran-utf8 r-cran-utf8 1.1.4-1+b1 install ok installed r-cran-viridislite r-cran-viridislite 0.3.0-3 install ok installed r-cran-withr r-cran-withr 2.1.2-3 install ok installed readline-common readline-common 7.0-5 install ok installed rsem rsem 1.3.1+dfsg-1 install ok installed salmon salmon 0.12.0+ds1-1+b1 install ok installed samtools samtools 1.9-4 install ok installed sed sed 4.7-1 install ok installed sensible-utils sensible-utils 0.0.12 install ok installed sphinx-rtd-theme-common sphinx-rtd-theme-common 0.4.3+dfsg-1 install ok installed sysvinit-utils sysvinit-utils 2.93-8 install ok installed tar tar 1.30+dfsg-6 install ok installed transdecoder transdecoder 5.0.1-2 install ok installed trimmomatic trimmomatic 0.38+dfsg-1 install ok installed trinityrnaseq trinityrnaseq 2.6.6+dfsg-6 install ok installed tzdata tzdata 2021a-0+deb10u6 install ok installed ucf ucf 3.0038+nmu1 install ok installed unzip unzip 6.0-23+deb10u2 install ok installed util-linux util-linux 2.33.1-0.1 install ok installed x11-common x11-common 1:7.7+19 install ok installed xdg-utils xdg-utils 1.1.3-1+deb10u1 install ok installed zip zip 3.0-11+b1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-1+deb10u1 1m43.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m43.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'apt-get', 'remove', 'berkeley-express', 'bowtie', 'bowtie2', 'ca-certificates', 'ca-certificates-java', 'curl', 'default-jre', 'default-jre-headless', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-font-awesome', 'fonts-lato', 'fonts-roboto-slab', 'jaligner', 'java-common', 'jellyfish', 'libapache-pom-java', 'libasound2:amd64', 'libasound2-data', 'libatomic1:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbamtools2.5.1:amd64', 'libblas3:amd64', 'libboost-atomic1.67.0:amd64', 'libboost-chrono1.67.0:amd64', 'libboost-date-time1.67.0:amd64', 'libboost-filesystem1.67.0:amd64', 'libboost-iostreams1.67.0:amd64', 'libboost-program-options1.67.0:amd64', 'libboost-regex1.67.0:amd64', 'libboost-system1.67.0:amd64', 'libboost-thread1.67.0:amd64', 'libboost-timer1.67.0:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcolt-free-java', 'libcommons-collections4-java', 'libcommons-parent-java', 'libconcurrent-java', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdatrie1:amd64', 'libdbus-1-3:amd64', 'libdeflate0:amd64', 'libdivsufsort3:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm-nouveau2:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1:amd64', 'libencode-locale-perl', 'libexpat1:amd64', 'libfile-listing-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgetopt-java', 'libgfortran5:amd64', 'libgif7:amd64', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhtml-parser-perl', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhts2:amd64', 'libhttp-cookies-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libice6:amd64', 'libicu63:amd64', 'libio-html-perl', 'libio-socket-ssl-perl', 'libjbig0:amd64', 'libjbzip2-java', 'libjellyfish-2.0-2:amd64', 'libjemalloc2:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-modernizr', 'libjs-sphinxdoc', 'libjs-underscore', 'libjung-free-java', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libllvm7:amd64', 'liblmdb0:amd64', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'libmbedcrypto3:amd64', 'libmbedtls12:amd64', 'libmbedx509-0:amd64', 'libmpdec2:amd64', 'libncurses6:amd64', 'libnet-http-perl', 'libnet-ssleay-perl', 'libnghttp2-14:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.28:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libprotobuf17:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libpython3-stdlib:amd64', 'libpython3.7-minimal:amd64', 'libpython3.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libsm6:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libstaden-read13:amd64', 'libtbb2:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtimedate-perl', 'libtk8.6:amd64', 'libtry-tiny-perl', 'liburi-perl', 'libvecmath-java', 'libwebp6:amd64', 'libwww-perl', 'libwww-robotrules-perl', 'libx11-6:amd64', 'libx11-data', 'libx11-xcb1:amd64', 'libxau6:amd64', 'libxcb-dri2-0:amd64', 'libxcb-dri3-0:amd64', 'libxcb-glx0:amd64', 'libxcb-present0:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb-sync1:amd64', 'libxcb1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxss1:amd64', 'libxt6:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'littler', 'lsb-base', 'mime-support', 'ncbi-blast+-', 'ncbi-data', 'netbase', 'openjdk-11-jre:amd64', 'openjdk-11-jre-headless:amd64', 'openssl', 'parafly', 'perl', 'perl-modules-5.28', 'perl-openssl-defaults:amd64', 'python', 'python-minimal', 'python2', 'python2-minimal', 'python2.7', 'python2.7-minimal', 'python3', 'python3-minimal', 'python3-numpy', 'python3-pkg-resources', 'python3.7', 'python3.7-minimal', 'r-base-core', 'r-bioc-biocgenerics', 'r-bioc-qvalue', 'r-cran-assertthat', 'r-cran-cli', 'r-cran-cluster', 'r-cran-colorspace', 'r-cran-crayon', 'r-cran-digest', 'r-cran-fansi', 'r-cran-ggplot2', 'r-cran-glue', 'r-cran-gtable', 'r-cran-labeling', 'r-cran-lattice', 'r-cran-lazyeval', 'r-cran-littler', 'r-cran-magrittr', 'r-cran-mass', 'r-cran-matrix', 'r-cran-mgcv', 'r-cran-munsell', 'r-cran-nlme', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-plyr', 'r-cran-r6', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-reshape2', 'r-cran-rlang', 'r-cran-scales', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-tibble', 'r-cran-utf8', 'r-cran-viridislite', 'r-cran-withr', 'readline-common', 'rsem', 'salmon', 'samtools', 'sensible-utils', 'sphinx-rtd-theme-common', 'transdecoder', 'trimmomatic', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'trinityrnaseq'] 1m47.6s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: berkeley-express bowtie bowtie2 ca-certificates ca-certificates-java curl default-jre default-jre-headless fontconfig fontconfig-config fonts-dejavu-core fonts-font-awesome fonts-lato fonts-roboto-slab jaligner java-common jellyfish libapache-pom-java libasound2 libasound2-data libatomic1 libavahi-client3 libavahi-common-data libavahi-common3 libbamtools2.5.1 libblas3 libboost-atomic1.67.0 libboost-chrono1.67.0 libboost-date-time1.67.0 libboost-filesystem1.67.0 libboost-iostreams1.67.0 libboost-program-options1.67.0 libboost-regex1.67.0 libboost-system1.67.0 libboost-thread1.67.0 libboost-timer1.67.0 libbsd0 libcairo2 libcolt-free-java libcommons-collections4-java libcommons-parent-java libconcurrent-java libcups2 libcurl3-gnutls libcurl4 libdatrie1 libdbus-1-3 libdeflate0 libdivsufsort3 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libelf1 libencode-locale-perl libexpat1 libfile-listing-perl libfontconfig1 libfreetype6 libfribidi0 libgdbm-compat4 libgdbm6 libgetopt-java libgfortran5 libgif7 libgl1 libgl1-mesa-dri libglapi-mesa libglib2.0-0 libglvnd0 libglx-mesa0 libglx0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libharfbuzz0b libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhts2 libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libice6 libicu63 libio-html-perl libio-socket-ssl-perl libjbig0 libjbzip2-java libjellyfish-2.0-2 libjemalloc2 libjpeg62-turbo libjs-jquery libjs-modernizr libjs-sphinxdoc libjs-underscore libjung-free-java libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 libldap-common libllvm7 liblmdb0 liblwp-mediatypes-perl liblwp-protocol-https-perl libmbedcrypto3 libmbedtls12 libmbedx509-0 libmpdec2 libncurses6 libnet-http-perl libnet-ssleay-perl libnghttp2-14 libnspr4 libnss3 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpciaccess0 libpcsclite1 libperl5.28 libpixman-1-0 libpng16-16 libprotobuf17 libpsl5 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libquadmath0 libreadline7 librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libsm6 libsqlite3-0 libssh2-1 libssl1.1 libstaden-read13 libtbb2 libtcl8.6 libthai-data libthai0 libtiff5 libtimedate-perl libtk8.6 libtry-tiny-perl liburi-perl libvecmath-java libwebp6 libwww-perl libwww-robotrules-perl libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-shm0 libxcb-sync1 libxcb1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxft2 libxi6 libxrender1 libxshmfence1 libxss1 libxt6 libxtst6 libxxf86vm1 littler lsb-base mime-support ncbi-blast+ ncbi-data netbase openjdk-11-jre openjdk-11-jre-headless openssl parafly perl perl-modules-5.28 perl-openssl-defaults python python-minimal python2 python2-minimal python2.7 python2.7-minimal python3 python3-minimal python3-numpy python3-pkg-resources python3.7 python3.7-minimal r-base-core r-bioc-biocgenerics r-bioc-qvalue r-cran-assertthat r-cran-cli r-cran-cluster r-cran-colorspace r-cran-crayon r-cran-digest r-cran-fansi r-cran-ggplot2 r-cran-glue r-cran-gtable r-cran-labeling r-cran-lattice r-cran-lazyeval r-cran-littler r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig r-cran-pkgkitten r-cran-plyr r-cran-r6 r-cran-rcolorbrewer r-cran-rcpp r-cran-reshape2 r-cran-rlang r-cran-scales r-cran-stringi r-cran-stringr r-cran-tibble r-cran-utf8 r-cran-viridislite r-cran-withr readline-common rsem salmon samtools sensible-utils sphinx-rtd-theme-common transdecoder trimmomatic trinityrnaseq ucf unzip x11-common xdg-utils zip 0 upgraded, 0 newly installed, 269 to remove and 0 not upgraded. After this operation, 910 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 ... 20322 files and directories currently installed.) Removing trinityrnaseq (2.6.6+dfsg-6) ... Removing berkeley-express (1.5.2+dfsg-1+b2) ... Removing rsem (1.3.1+dfsg-1) ... Removing bowtie (1.2.2+dfsg-4) ... Removing bowtie2 (2.3.4.3-1) ... Removing trimmomatic (0.38+dfsg-1) ... Removing default-jre (2:1.11-71) ... Removing openjdk-11-jre:amd64 (11.0.16+8-1~deb10u1) ... Removing libjung-free-java (2.0.1+dfsg-1) ... Removing libcolt-free-java (1.2.0+dfsg-7) ... Removing libconcurrent-java (1.3.4-4) ... Removing jaligner (1.0+dfsg-6) ... Removing default-jre-headless (2:1.11-71) ... Removing transdecoder (5.0.1-2) ... Removing r-bioc-qvalue (2.14.1-1) ... Removing r-cran-ggplot2 (3.1.0-1) ... Removing r-cran-mgcv (1.8-27-1) ... Removing r-cran-matrix (1.2-15-1) ... Removing curl (7.64.0-4+deb10u2) ... Removing salmon (0.12.0+ds1-1+b1) ... Removing sphinx-rtd-theme-common (0.4.3+dfsg-1) ... Removing fonts-font-awesome (5.0.10+really4.7.0~dfsg-1) ... dpkg: warning: while removing fonts-font-awesome, directory '/usr/share/fonts/woff/font-awesome' not empty so not removed dpkg: warning: while removing fonts-font-awesome, directory '/usr/share/fonts/truetype/font-awesome' not empty so not removed dpkg: warning: while removing fonts-font-awesome, directory '/usr/share/fonts/svg/font-awesome' not empty so not removed dpkg: warning: while removing fonts-font-awesome, directory '/usr/share/fonts/opentype/font-awesome' not empty so not removed dpkg: warning: while removing fonts-font-awesome, directory '/usr/share/fonts/eot/font-awesome' not empty so not removed Removing fonts-lato (2.0-2) ... dpkg: warning: while removing fonts-lato, directory '/usr/share/fonts/truetype/lato' not empty so not removed Removing fonts-roboto-slab (1.100263+20170512-1) ... dpkg: warning: while removing fonts-roboto-slab, directory '/usr/share/fonts/truetype/roboto/slab' not empty so not removed Removing jellyfish (2.2.10-2) ... Removing libcommons-collections4-java (4.2-1) ... Removing libcommons-parent-java (43-1) ... Removing libapache-pom-java (18-1) ... Removing libtbb2:amd64 (2018~U6-4) ... Removing libatomic1:amd64 (8.3.0-6) ... Removing libbamtools2.5.1:amd64 (2.5.1+dfsg-3) ... Removing python3-numpy (1:1.16.2-1) ... Removing r-cran-scales (1.0.0-2) ... Removing r-cran-reshape2 (1.4.3-2) ... Removing littler (0.3.6-1) ... Removing libboost-thread1.67.0:amd64 (1.67.0-13+deb10u1) ... Removing libboost-atomic1.67.0:amd64 (1.67.0-13+deb10u1) ... Removing libboost-timer1.67.0:amd64 (1.67.0-13+deb10u1) ... Removing libboost-chrono1.67.0:amd64 (1.67.0-13+deb10u1) ... Removing libboost-date-time1.67.0:amd64 (1.67.0-13+deb10u1) ... Removing libboost-filesystem1.67.0:amd64 (1.67.0-13+deb10u1) ... Removing libboost-iostreams1.67.0:amd64 (1.67.0-13+deb10u1) ... Removing libboost-program-options1.67.0:amd64 (1.67.0-13+deb10u1) ... Removing libboost-regex1.67.0:amd64 (1.67.0-13+deb10u1) ... Removing libboost-system1.67.0:amd64 (1.67.0-13+deb10u1) ... Removing libgl1:amd64 (1.1.0-1) ... Removing libglx0:amd64 (1.1.0-1) ... Removing libglx-mesa0:amd64 (18.3.6-2+deb10u1) ... Removing libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Removing libstaden-read13:amd64 (1.14.11-6) ... Removing samtools (1.9-4) ... Removing libhts2:amd64 (1.9-12~deb10u1) ... Removing libcurl3-gnutls:amd64 (7.64.0-4+deb10u2) ... Removing libdeflate0:amd64 (1.2-1) ... Removing libdivsufsort3:amd64 (2.0.1-4) ... Removing libgl1-mesa-dri:amd64 (18.3.6-2+deb10u1) ... Removing libdrm-amdgpu1:amd64 (2.4.97-1) ... Removing libdrm-radeon1:amd64 (2.4.97-1) ... Removing libdrm-nouveau2:amd64 (2.4.97-1) ... Removing libdrm-intel1:amd64 (2.4.97-1) ... Removing libllvm7:amd64 (1:7.0.1-8+deb10u2) ... Removing libedit2:amd64 (3.1-20181209-1) ... Removing libelf1:amd64 (0.176-1.1) ... Removing python3-pkg-resources (40.8.0-1) ... Removing python3 (3.7.3-1) ... Removing python3.7 (3.7.3-2+deb10u3) ... Removing python3-minimal (3.7.3-1) ... Removing python3.7-minimal (3.7.3-2+deb10u3) ... Removing ncbi-blast+ (2.8.1-1+deb10u1) ... Removing python (2.7.16-1) ... Removing libgetopt-java (1.0.14+dfsg-4) ... Removing r-cran-nlme (3.1.137-1+b3) ... Removing r-cran-cluster (2.0.7-1-1+b3) ... Removing libgif7:amd64 (5.1.4-3) ... Removing libglapi-mesa:amd64 (18.3.6-2+deb10u1) ... Removing libglvnd0:amd64 (1.1.0-1) ... Removing parafly (0.0.2013.01.21-4) ... Removing libjbzip2-java (0.9.1-5) ... Removing libjellyfish-2.0-2:amd64 (2.2.10-2) ... Removing libjemalloc2:amd64 (5.1.0-3) ... Removing libjs-sphinxdoc (1.8.4-1) ... Removing libjs-jquery (3.3.1~dfsg-3+deb10u1) ... Removing libjs-modernizr (2.6.2+ds1-3) ... Removing libjs-underscore (1.9.1~dfsg-1+deb10u1) ... Removing liblmdb0:amd64 (0.9.22-1) ... Removing libmbedtls12:amd64 (2.16.0-1) ... Removing libmbedx509-0:amd64 (2.16.0-1) ... Removing libmbedcrypto3:amd64 (2.16.0-1) ... Removing libpython3-stdlib:amd64 (3.7.3-1) ... Removing libpython3.7-stdlib:amd64 (3.7.3-2+deb10u3) ... find: '/usr/lib/python3': No such file or directory Removing libmpdec2:amd64 (2.4.2-2) ... Removing libncurses6:amd64 (6.1+20181013-2+deb10u2) ... Removing libpciaccess0:amd64 (0.14-1) ... Removing libprotobuf17:amd64 (3.6.1.3-2) ... Removing libpython-stdlib:amd64 (2.7.16-1) ... Removing python2 (2.7.16-1) ... Removing libpython2-stdlib:amd64 (2.7.16-1) ... Removing python-minimal (2.7.16-1) ... Removing libpython3.7-minimal:amd64 (3.7.3-2+deb10u3) ... find: '/usr/lib/python3': No such file or directory Removing libsensors5:amd64 (1:3.5.0-3) ... Removing libsensors-config (1:3.5.0-3) ... Removing libvecmath-java (1.5.2-7) ... Removing libx11-xcb1:amd64 (2:1.6.7-1+deb10u2) ... Removing libxcb-dri2-0:amd64 (1.13.1-2) ... Removing libxcb-dri3-0:amd64 (1.13.1-2) ... Removing libxcb-glx0:amd64 (1.13.1-2) ... Removing libxcb-present0:amd64 (1.13.1-2) ... Removing libxcb-sync1:amd64 (1.13.1-2) ... Removing libxdamage1:amd64 (1:1.1.4-3+b3) ... Removing libxtst6:amd64 (2:1.2.3-1) ... Removing libxfixes3:amd64 (1:5.0.3-1) ... Removing libxi6:amd64 (2:1.7.9-1) ... Removing libxshmfence1:amd64 (1.3-1) ... Removing ncbi-data (6.1.20170106+dfsg1-0+deb10u2) ... Removing python2-minimal (2.7.16-1) ... Removing r-bioc-biocgenerics (0.28.0-2) ... Removing r-cran-tibble (2.0.1-1) ... Removing r-cran-pillar (1.3.1-1) ... Removing r-cran-cli (1.0.1-1) ... Removing r-cran-assertthat (0.2.0-2) ... Removing r-cran-munsell (0.5.0-1) ... Removing r-cran-colorspace (1.4-0+dfsg-1) ... Removing r-cran-crayon (1.3.4-4) ... Removing r-cran-digest (0.6.18-1) ... Removing r-cran-fansi (0.4.0-1) ... Removing r-cran-stringr (1.4.0-1) ... Removing r-cran-glue (1.3.0-1) ... Removing r-cran-gtable (0.2.0-3) ... Removing r-cran-labeling (0.3-3) ... Removing r-cran-lattice (0.20-38-1) ... Removing r-cran-lazyeval (0.2.1-3) ... Removing r-cran-magrittr (1.5-5) ... Removing r-cran-mass (7.3-51.1-1) ... Removing r-cran-pkgconfig (2.0.2-1) ... Removing r-cran-plyr (1.8.4-2) ... Removing r-cran-r6 (2.4.0-1) ... Removing r-cran-rcolorbrewer (1.1-2-2) ... Removing r-cran-rlang (0.3.1-2) ... Removing r-cran-stringi (1.2.4-2) ... Removing r-cran-utf8 (1.1.4-1+b1) ... Removing r-cran-viridislite (0.3.0-3) ... Removing r-cran-withr (2.1.2-3) ... Removing r-cran-rcpp (1.0.0-1) ... Removing r-cran-littler (0.3.6-1) ... Removing libdrm2:amd64 (2.4.97-1) ... Removing libdrm-common (2.4.97-1) ... Removing python2.7 (2.7.16-2+deb10u1) ... Removing libpython2.7-stdlib:amd64 (2.7.16-2+deb10u1) ... Removing python2.7-minimal (2.7.16-2+deb10u1) ... Removing libpython2.7-minimal:amd64 (2.7.16-2+deb10u1) ... find: '/usr/lib/python2.7': No such file or directory Removing mime-support (3.62) ... Removing r-cran-pkgkitten (0.1.4-2) ... Removing r-base-core (3.5.2-1) ... Removing libpangocairo-1.0-0:amd64 (1.42.4-8~deb10u1) ... Removing libpangoft2-1.0-0:amd64 (1.42.4-8~deb10u1) ... Removing libpango-1.0-0:amd64 (1.42.4-8~deb10u1) ... Removing fontconfig (2.13.1-2) ... Removing libtk8.6:amd64 (8.6.9-2) ... Removing libxft2:amd64 (2.3.2-2) ... Removing libcairo2:amd64 (1.16.0-4+deb10u1) ... Removing liblapack3:amd64 (3.8.0-2) ... Removing libblas3:amd64 (3.8.0-2) ... Removing libxt6:amd64 (1:1.1.5-1+b3) ... Removing libcurl4:amd64 (7.64.0-4+deb10u2) ... Removing libthai0:amd64 (0.1.28-2) ... Removing libdatrie1:amd64 (0.2.12-2) ... Removing libfribidi0:amd64 (1.0.5-3.1+deb10u2) ... Removing libgfortran5:amd64 (8.3.0-6) ... Removing libgomp1:amd64 (8.3.0-6) ... Removing libicu63:amd64 (63.1-6+deb10u3) ... Removing libtiff5:amd64 (4.1.0+git191117-2~deb10u4) ... Removing libjbig0:amd64 (2.1-3.1+b2) ... Removing libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u7) ... Removing libldap-common (2.4.47+dfsg-3+deb10u7) ... Removing libnghttp2-14:amd64 (1.36.0-2+deb10u1) ... Removing libpaper-utils (1.1.28) ... Removing libpaper1:amd64 (1.1.28) ... Removing libpixman-1-0:amd64 (0.36.0-1) ... Removing libpsl5:amd64 (0.20.2-2) ... Removing libquadmath0:amd64 (8.3.0-6) ... Removing libreadline7:amd64 (7.0-5) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-2) ... Removing libsasl2-2:amd64 (2.1.27+dfsg-1+deb10u2) ... Removing libsasl2-modules-db:amd64 (2.1.27+dfsg-1+deb10u2) ... Removing libsm6:amd64 (2:1.2.3-1) ... Removing libssh2-1:amd64 (1.8.0-2.1) ... Removing libtcl8.6:amd64 (8.6.9+dfsg-2) ... Removing libthai-data (0.1.28-2) ... Removing libwebp6:amd64 (0.6.1-2+deb10u1) ... Removing libxcb-render0:amd64 (1.13.1-2) ... Removing libxcb-shm0:amd64 (1.13.1-2) ... Removing libxss1:amd64 (1:1.2.3-1) ... Removing libxext6:amd64 (2:1.3.3-1+b2) ... Removing libxrender1:amd64 (1:0.9.10-1) ... Removing readline-common (7.0-5) ... Removing unzip (6.0-23+deb10u2) ... Removing xdg-utils (1.1.3-1+deb10u1) ... Removing zip (3.0-11+b1) ... Removing libx11-6:amd64 (2:1.6.7-1+deb10u2) ... Removing libxcb1:amd64 (1.13.1-2) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libice6:amd64 (2:1.0.9-2) ... Removing libbsd0:amd64 (0.9.1-2+deb10u1) ... Removing libx11-data (2:1.6.7-1+deb10u2) ... Removing libxau6:amd64 (1:1.0.8-1+b2) ... Removing x11-common (1:7.7+19) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing lsb-base (10.2019051400) ... Removing openjdk-11-jre-headless:amd64 (11.0.16+8-1~deb10u1) ... Removing libfontconfig1:amd64 (2.13.1-2) ... Removing fontconfig-config (2.13.1-2) ... Removing fonts-dejavu-core (2.37-1) ... Removing java-common (0.71) ... Removing libasound2:amd64 (1.1.8-1) ... Removing libasound2-data (1.1.8-1) ... Removing libcups2:amd64 (2.2.10-6+deb10u6) ... Removing libavahi-client3:amd64 (0.7-4+deb10u1) ... Removing libavahi-common3:amd64 (0.7-4+deb10u1) ... Removing libavahi-common-data:amd64 (0.7-4+deb10u1) ... Removing libdbus-1-3:amd64 (1.12.20-0+deb10u1) ... Removing libwww-perl (6.36-2) ... Removing liblwp-protocol-https-perl (6.07-2) ... Removing libhttp-negotiate-perl (6.01-1) ... Removing libexpat1:amd64 (2.2.6-2+deb10u4) ... Removing libfile-listing-perl (6.04-1) ... Removing libharfbuzz0b:amd64 (2.3.1-1) ... Removing libfreetype6:amd64 (2.9.1-3+deb10u3) ... Removing libwww-robotrules-perl (6.02-1) ... Removing libtry-tiny-perl (0.30-1) ... Removing libnet-http-perl (6.18-1) ... Removing libglib2.0-0:amd64 (2.58.3-2+deb10u3) ... Removing libgraphite2-3:amd64 (1.3.13-7) ... Removing libgssapi-krb5-2:amd64 (1.17-3+deb10u4) ... Removing libhtml-tree-perl (5.07-2) ... Removing libhtml-parser-perl (3.72-3+b3) ... Removing libhtml-tagset-perl (3.20-3) ... Removing libhttp-cookies-perl (6.04-1) ... Removing libio-socket-ssl-perl (2.060-3) ... Removing libjpeg62-turbo:amd64 (1:1.5.2-2+deb10u1) ... Removing libkrb5-3:amd64 (1.17-3+deb10u4) ... Removing libk5crypto3:amd64 (1.17-3+deb10u4) ... Removing libkrb5support0:amd64 (1.17-3+deb10u4) ... Removing libkeyutils1:amd64 (1.6-6) ... Removing liblcms2-2:amd64 (2.9-3) ... Removing libnet-ssleay-perl (1.85-2+deb10u1) ... Removing libpcsclite1:amd64 (1.8.24-1) ... Removing libpng16-16:amd64 (1.6.36-6) ... Removing perl-openssl-defaults:amd64 (3) ... Removing netbase (5.6) ... Removing ucf (3.0038+nmu1) ... Removing sensible-utils (0.0.12) ... Removing ca-certificates-java (20190405) ... Removing ca-certificates (20200601~deb10u2) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing libhttp-message-perl (6.18-1) ... Removing libencode-locale-perl (1.05-1) ... Removing liburi-perl (1.76-1) ... Removing libhttp-date-perl (6.02-1) ... Removing libio-html-perl (1.001-1) ... Removing liblwp-mediatypes-perl (6.02-1) ... Removing libnss3:amd64 (2:3.42.1-1+deb10u5) ... Removing libnspr4:amd64 (2:4.20-1) ... Removing libsqlite3-0:amd64 (3.27.2-3+deb10u1) ... Removing openssl (1.1.1n-0+deb10u3) ... Removing libssl1.1:amd64 (1.1.1n-0+deb10u3) ... Removing libtimedate-perl (2.3000-2+deb10u1) ... Removing perl (5.28.1-6+deb10u1) ... Removing libperl5.28:amd64 (5.28.1-6+deb10u1) ... Removing libgdbm-compat4:amd64 (1.18.1-4) ... Removing libgdbm6:amd64 (1.18.1-4) ... Removing perl-modules-5.28 (5.28.1-6+deb10u1) ... Processing triggers for libc-bin (2.28-10+deb10u1) ... 1m47.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'apt-get', 'remove', 'berkeley-express', 'bowtie', 'bowtie2', 'ca-certificates', 'ca-certificates-java', 'curl', 'default-jre', 'default-jre-headless', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-font-awesome', 'fonts-lato', 'fonts-roboto-slab', 'jaligner', 'java-common', 'jellyfish', 'libapache-pom-java', 'libasound2:amd64', 'libasound2-data', 'libatomic1:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbamtools2.5.1:amd64', 'libblas3:amd64', 'libboost-atomic1.67.0:amd64', 'libboost-chrono1.67.0:amd64', 'libboost-date-time1.67.0:amd64', 'libboost-filesystem1.67.0:amd64', 'libboost-iostreams1.67.0:amd64', 'libboost-program-options1.67.0:amd64', 'libboost-regex1.67.0:amd64', 'libboost-system1.67.0:amd64', 'libboost-thread1.67.0:amd64', 'libboost-timer1.67.0:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcolt-free-java', 'libcommons-collections4-java', 'libcommons-parent-java', 'libconcurrent-java', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdatrie1:amd64', 'libdbus-1-3:amd64', 'libdeflate0:amd64', 'libdivsufsort3:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm-nouveau2:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1:amd64', 'libencode-locale-perl', 'libexpat1:amd64', 'libfile-listing-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgetopt-java', 'libgfortran5:amd64', 'libgif7:amd64', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhtml-parser-perl', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhts2:amd64', 'libhttp-cookies-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libice6:amd64', 'libicu63:amd64', 'libio-html-perl', 'libio-socket-ssl-perl', 'libjbig0:amd64', 'libjbzip2-java', 'libjellyfish-2.0-2:amd64', 'libjemalloc2:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-modernizr', 'libjs-sphinxdoc', 'libjs-underscore', 'libjung-free-java', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libllvm7:amd64', 'liblmdb0:amd64', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'libmbedcrypto3:amd64', 'libmbedtls12:amd64', 'libmbedx509-0:amd64', 'libmpdec2:amd64', 'libncurses6:amd64', 'libnet-http-perl', 'libnet-ssleay-perl', 'libnghttp2-14:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.28:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libprotobuf17:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libpython3-stdlib:amd64', 'libpython3.7-minimal:amd64', 'libpython3.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libsm6:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libstaden-read13:amd64', 'libtbb2:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtimedate-perl', 'libtk8.6:amd64', 'libtry-tiny-perl', 'liburi-perl', 'libvecmath-java', 'libwebp6:amd64', 'libwww-perl', 'libwww-robotrules-perl', 'libx11-6:amd64', 'libx11-data', 'libx11-xcb1:amd64', 'libxau6:amd64', 'libxcb-dri2-0:amd64', 'libxcb-dri3-0:amd64', 'libxcb-glx0:amd64', 'libxcb-present0:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb-sync1:amd64', 'libxcb1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxss1:amd64', 'libxt6:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'littler', 'lsb-base', 'mime-support', 'ncbi-blast+-', 'ncbi-data', 'netbase', 'openjdk-11-jre:amd64', 'openjdk-11-jre-headless:amd64', 'openssl', 'parafly', 'perl', 'perl-modules-5.28', 'perl-openssl-defaults:amd64', 'python', 'python-minimal', 'python2', 'python2-minimal', 'python2.7', 'python2.7-minimal', 'python3', 'python3-minimal', 'python3-numpy', 'python3-pkg-resources', 'python3.7', 'python3.7-minimal', 'r-base-core', 'r-bioc-biocgenerics', 'r-bioc-qvalue', 'r-cran-assertthat', 'r-cran-cli', 'r-cran-cluster', 'r-cran-colorspace', 'r-cran-crayon', 'r-cran-digest', 'r-cran-fansi', 'r-cran-ggplot2', 'r-cran-glue', 'r-cran-gtable', 'r-cran-labeling', 'r-cran-lattice', 'r-cran-lazyeval', 'r-cran-littler', 'r-cran-magrittr', 'r-cran-mass', 'r-cran-matrix', 'r-cran-mgcv', 'r-cran-munsell', 'r-cran-nlme', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-plyr', 'r-cran-r6', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-reshape2', 'r-cran-rlang', 'r-cran-scales', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-tibble', 'r-cran-utf8', 'r-cran-viridislite', 'r-cran-withr', 'readline-common', 'rsem', 'salmon', 'samtools', 'sensible-utils', 'sphinx-rtd-theme-common', 'transdecoder', 'trimmomatic', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip', 'trinityrnaseq'] 1m47.6s INFO: Running scripts post_remove 1m47.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/post_remove_exceptions'] 1m47.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/post_remove_exceptions'] 1m47.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'dpkg', '--purge', 'berkeley-express', 'bowtie', 'bowtie2', 'ca-certificates', 'ca-certificates-java', 'curl', 'default-jre', 'default-jre-headless', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-font-awesome', 'fonts-lato', 'fonts-roboto-slab', 'jaligner', 'java-common', 'jellyfish', 'libapache-pom-java', 'libasound2:amd64', 'libasound2-data', 'libatomic1:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbamtools2.5.1:amd64', 'libblas3:amd64', 'libboost-atomic1.67.0:amd64', 'libboost-chrono1.67.0:amd64', 'libboost-date-time1.67.0:amd64', 'libboost-filesystem1.67.0:amd64', 'libboost-iostreams1.67.0:amd64', 'libboost-program-options1.67.0:amd64', 'libboost-regex1.67.0:amd64', 'libboost-system1.67.0:amd64', 'libboost-thread1.67.0:amd64', 'libboost-timer1.67.0:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcolt-free-java', 'libcommons-collections4-java', 'libcommons-parent-java', 'libconcurrent-java', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdatrie1:amd64', 'libdbus-1-3:amd64', 'libdeflate0:amd64', 'libdivsufsort3:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm-nouveau2:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1:amd64', 'libencode-locale-perl', 'libexpat1:amd64', 'libfile-listing-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgetopt-java', 'libgfortran5:amd64', 'libgif7:amd64', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhtml-parser-perl', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhts2:amd64', 'libhttp-cookies-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libice6:amd64', 'libicu63:amd64', 'libio-html-perl', 'libio-socket-ssl-perl', 'libjbig0:amd64', 'libjbzip2-java', 'libjellyfish-2.0-2:amd64', 'libjemalloc2:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-modernizr', 'libjs-sphinxdoc', 'libjs-underscore', 'libjung-free-java', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libllvm7:amd64', 'liblmdb0:amd64', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'libmbedcrypto3:amd64', 'libmbedtls12:amd64', 'libmbedx509-0:amd64', 'libmpdec2:amd64', 'libncurses6:amd64', 'libnet-http-perl', 'libnet-ssleay-perl', 'libnghttp2-14:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.28:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libprotobuf17:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libpython3-stdlib:amd64', 'libpython3.7-minimal:amd64', 'libpython3.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libsm6:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libstaden-read13:amd64', 'libtbb2:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtimedate-perl', 'libtk8.6:amd64', 'libtry-tiny-perl', 'liburi-perl', 'libvecmath-java', 'libwebp6:amd64', 'libwww-perl', 'libwww-robotrules-perl', 'libx11-6:amd64', 'libx11-data', 'libx11-xcb1:amd64', 'libxau6:amd64', 'libxcb-dri2-0:amd64', 'libxcb-dri3-0:amd64', 'libxcb-glx0:amd64', 'libxcb-present0:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb-sync1:amd64', 'libxcb1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxss1:amd64', 'libxt6:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'littler', 'lsb-base', 'mime-support', 'ncbi-blast+', 'ncbi-data', 'netbase', 'openjdk-11-jre:amd64', 'openjdk-11-jre-headless:amd64', 'openssl', 'parafly', 'perl', 'perl-modules-5.28', 'perl-openssl-defaults:amd64', 'python', 'python-minimal', 'python2', 'python2-minimal', 'python2.7', 'python2.7-minimal', 'python3', 'python3-minimal', 'python3-numpy', 'python3-pkg-resources', 'python3.7', 'python3.7-minimal', 'r-base-core', 'r-bioc-biocgenerics', 'r-bioc-qvalue', 'r-cran-assertthat', 'r-cran-cli', 'r-cran-cluster', 'r-cran-colorspace', 'r-cran-crayon', 'r-cran-digest', 'r-cran-fansi', 'r-cran-ggplot2', 'r-cran-glue', 'r-cran-gtable', 'r-cran-labeling', 'r-cran-lattice', 'r-cran-lazyeval', 'r-cran-littler', 'r-cran-magrittr', 'r-cran-mass', 'r-cran-matrix', 'r-cran-mgcv', 'r-cran-munsell', 'r-cran-nlme', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-plyr', 'r-cran-r6', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-reshape2', 'r-cran-rlang', 'r-cran-scales', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-tibble', 'r-cran-utf8', 'r-cran-viridislite', 'r-cran-withr', 'readline-common', 'rsem', 'salmon', 'samtools', 'sensible-utils', 'sphinx-rtd-theme-common', 'transdecoder', 'trimmomatic', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip'] 1m48.9s DUMP: dpkg: warning: ignoring request to remove berkeley-express which isn't installed dpkg: warning: ignoring request to remove bowtie which isn't installed dpkg: warning: ignoring request to remove bowtie2 which isn't installed (Reading database ... 6567 files and directories currently installed.) Purging configuration files for ca-certificates (20200601~deb10u2) ... Removing dangling symlinks from /etc/ssl/certs... done. Purging configuration files for ca-certificates-java (20190405) ... dpkg: warning: ignoring request to remove curl which isn't installed dpkg: warning: ignoring request to remove default-jre which isn't installed dpkg: warning: ignoring request to remove default-jre-headless which isn't installed Purging configuration files for fontconfig (2.13.1-2) ... Purging configuration files for fontconfig-config (2.13.1-2) ... Purging configuration files for fonts-dejavu-core (2.37-1) ... dpkg: warning: while removing fonts-dejavu-core, directory '/usr/share/fonts/truetype/dejavu' not empty so not removed dpkg: warning: ignoring request to remove fonts-font-awesome which isn't installed dpkg: warning: ignoring request to remove fonts-lato which isn't installed dpkg: warning: ignoring request to remove fonts-roboto-slab which isn't installed dpkg: warning: ignoring request to remove jaligner which isn't installed Purging configuration files for java-common (0.71) ... dpkg: warning: ignoring request to remove jellyfish which isn't installed dpkg: warning: ignoring request to remove libapache-pom-java which isn't installed dpkg: warning: ignoring request to remove libasound2 which isn't installed dpkg: warning: ignoring request to remove libasound2-data which isn't installed dpkg: warning: ignoring request to remove libatomic1 which isn't installed dpkg: warning: ignoring request to remove libavahi-client3 which isn't installed dpkg: warning: ignoring request to remove libavahi-common-data which isn't installed dpkg: warning: ignoring request to remove libavahi-common3 which isn't installed dpkg: warning: ignoring request to remove libbamtools2.5.1 which isn't installed dpkg: warning: ignoring request to remove libblas3 which isn't installed dpkg: warning: ignoring request to remove libboost-atomic1.67.0 which isn't installed dpkg: warning: ignoring request to remove libboost-chrono1.67.0 which isn't installed dpkg: warning: ignoring request to remove libboost-date-time1.67.0 which isn't installed dpkg: warning: ignoring request to remove libboost-filesystem1.67.0 which isn't installed dpkg: warning: ignoring request to remove libboost-iostreams1.67.0 which isn't installed dpkg: warning: ignoring request to remove libboost-program-options1.67.0 which isn't installed dpkg: warning: ignoring request to remove libboost-regex1.67.0 which isn't installed dpkg: warning: ignoring request to remove libboost-system1.67.0 which isn't installed dpkg: warning: ignoring request to remove libboost-thread1.67.0 which isn't installed dpkg: warning: ignoring request to remove libboost-timer1.67.0 which isn't installed dpkg: warning: ignoring request to remove libbsd0 which isn't installed dpkg: warning: ignoring request to remove libcairo2 which isn't installed dpkg: warning: ignoring request to remove libcolt-free-java which isn't installed dpkg: warning: ignoring request to remove libcommons-collections4-java which isn't installed dpkg: warning: ignoring request to remove libcommons-parent-java which isn't installed dpkg: warning: ignoring request to remove libconcurrent-java which isn't installed dpkg: warning: ignoring request to remove libcups2 which isn't installed dpkg: warning: ignoring request to remove libcurl3-gnutls which isn't installed dpkg: warning: ignoring request to remove libcurl4 which isn't installed dpkg: warning: ignoring request to remove libdatrie1 which isn't installed dpkg: warning: ignoring request to remove libdbus-1-3 which isn't installed dpkg: warning: ignoring request to remove libdeflate0 which isn't installed dpkg: warning: ignoring request to remove libdivsufsort3 which isn't installed dpkg: warning: ignoring request to remove libdrm-amdgpu1 which isn't installed dpkg: warning: ignoring request to remove libdrm-common which isn't installed dpkg: warning: ignoring request to remove libdrm-intel1 which isn't installed dpkg: warning: ignoring request to remove libdrm-nouveau2 which isn't installed dpkg: warning: ignoring request to remove libdrm-radeon1 which isn't installed dpkg: warning: ignoring request to remove libdrm2 which isn't installed dpkg: warning: ignoring request to remove libedit2 which isn't installed dpkg: warning: ignoring request to remove libelf1 which isn't installed dpkg: warning: ignoring request to remove libencode-locale-perl which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libfile-listing-perl which isn't installed dpkg: warning: ignoring request to remove libfontconfig1 which isn't installed dpkg: warning: ignoring request to remove libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libfribidi0 which isn't installed dpkg: warning: ignoring request to remove libgdbm-compat4 which isn't installed dpkg: warning: ignoring request to remove libgdbm6 which isn't installed dpkg: warning: ignoring request to remove libgetopt-java which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed dpkg: warning: ignoring request to remove libgif7 which isn't installed dpkg: warning: ignoring request to remove libgl1 which isn't installed Purging configuration files for libgl1-mesa-dri:amd64 (18.3.6-2+deb10u1) ... dpkg: warning: ignoring request to remove libglapi-mesa which isn't installed Purging configuration files for libglib2.0-0:amd64 (2.58.3-2+deb10u3) ... dpkg: warning: ignoring request to remove libglvnd0 which isn't installed dpkg: warning: ignoring request to remove libglx-mesa0 which isn't installed dpkg: warning: ignoring request to remove libglx0 which isn't installed dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.17-3+deb10u4) ... dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed dpkg: warning: ignoring request to remove libhtml-parser-perl which isn't installed dpkg: warning: ignoring request to remove libhtml-tagset-perl which isn't installed dpkg: warning: ignoring request to remove libhtml-tree-perl which isn't installed dpkg: warning: ignoring request to remove libhts2 which isn't installed dpkg: warning: ignoring request to remove libhttp-cookies-perl which isn't installed dpkg: warning: ignoring request to remove libhttp-date-perl which isn't installed dpkg: warning: ignoring request to remove libhttp-message-perl which isn't installed dpkg: warning: ignoring request to remove libhttp-negotiate-perl which isn't installed dpkg: warning: ignoring request to remove libice6 which isn't installed dpkg: warning: ignoring request to remove libicu63 which isn't installed dpkg: warning: ignoring request to remove libio-html-perl which isn't installed dpkg: warning: ignoring request to remove libio-socket-ssl-perl which isn't installed dpkg: warning: ignoring request to remove libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjbzip2-java which isn't installed dpkg: warning: ignoring request to remove libjellyfish-2.0-2 which isn't installed dpkg: warning: ignoring request to remove libjemalloc2 which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed dpkg: warning: ignoring request to remove libjs-jquery which isn't installed dpkg: warning: ignoring request to remove libjs-modernizr which isn't installed dpkg: warning: ignoring request to remove libjs-sphinxdoc which isn't installed dpkg: warning: ignoring request to remove libjs-underscore which isn't installed dpkg: warning: ignoring request to remove libjung-free-java which isn't installed dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove liblapack3 which isn't installed dpkg: warning: ignoring request to remove liblcms2-2 which isn't installed dpkg: warning: ignoring request to remove libldap-2.4-2 which isn't installed Purging configuration files for libldap-common (2.4.47+dfsg-3+deb10u7) ... dpkg: warning: ignoring request to remove libllvm7 which isn't installed dpkg: warning: ignoring request to remove liblmdb0 which isn't installed dpkg: warning: ignoring request to remove liblwp-mediatypes-perl which isn't installed dpkg: warning: ignoring request to remove liblwp-protocol-https-perl which isn't installed dpkg: warning: ignoring request to remove libmbedcrypto3 which isn't installed dpkg: warning: ignoring request to remove libmbedtls12 which isn't installed dpkg: warning: ignoring request to remove libmbedx509-0 which isn't installed dpkg: warning: ignoring request to remove libmpdec2 which isn't installed dpkg: warning: ignoring request to remove libncurses6 which isn't installed dpkg: warning: ignoring request to remove libnet-http-perl which isn't installed dpkg: warning: ignoring request to remove libnet-ssleay-perl which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed dpkg: warning: ignoring request to remove libnspr4 which isn't installed dpkg: warning: ignoring request to remove libnss3 which isn't installed dpkg: warning: ignoring request to remove libpango-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpangocairo-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpangoft2-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpaper-utils which isn't installed Purging configuration files for libpaper1:amd64 (1.1.28) ... dpkg: warning: ignoring request to remove libpciaccess0 which isn't installed dpkg: warning: ignoring request to remove libpcsclite1 which isn't installed dpkg: warning: ignoring request to remove libperl5.28 which isn't installed dpkg: warning: ignoring request to remove libpixman-1-0 which isn't installed dpkg: warning: ignoring request to remove libpng16-16 which isn't installed dpkg: warning: ignoring request to remove libprotobuf17 which isn't installed dpkg: warning: ignoring request to remove libpsl5 which isn't installed dpkg: warning: ignoring request to remove libpython-stdlib which isn't installed dpkg: warning: ignoring request to remove libpython2-stdlib which isn't installed Purging configuration files for libpython2.7-minimal:amd64 (2.7.16-2+deb10u1) ... dpkg: warning: ignoring request to remove libpython2.7-stdlib which isn't installed dpkg: warning: ignoring request to remove libpython3-stdlib which isn't installed Purging configuration files for libpython3.7-minimal:amd64 (3.7.3-2+deb10u3) ... dpkg: warning: ignoring request to remove libpython3.7-stdlib which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed dpkg: warning: ignoring request to remove libreadline7 which isn't installed dpkg: warning: ignoring request to remove librtmp1 which isn't installed dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed dpkg: warning: ignoring request to remove libsasl2-modules-db which isn't installed Purging configuration files for libsensors-config (1:3.5.0-3) ... dpkg: warning: ignoring request to remove libsensors5 which isn't installed dpkg: warning: ignoring request to remove libsm6 which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libssh2-1 which isn't installed Purging configuration files for libssl1.1:amd64 (1.1.1n-0+deb10u3) ... dpkg: warning: ignoring request to remove libstaden-read13 which isn't installed dpkg: warning: ignoring request to remove libtbb2 which isn't installed dpkg: warning: ignoring request to remove libtcl8.6 which isn't installed dpkg: warning: ignoring request to remove libthai-data which isn't installed dpkg: warning: ignoring request to remove libthai0 which isn't installed dpkg: warning: ignoring request to remove libtiff5 which isn't installed dpkg: warning: ignoring request to remove libtimedate-perl which isn't installed dpkg: warning: ignoring request to remove libtk8.6 which isn't installed dpkg: warning: ignoring request to remove libtry-tiny-perl which isn't installed dpkg: warning: ignoring request to remove liburi-perl which isn't installed dpkg: warning: ignoring request to remove libvecmath-java which isn't installed dpkg: warning: ignoring request to remove libwebp6 which isn't installed dpkg: warning: ignoring request to remove libwww-perl which isn't installed dpkg: warning: ignoring request to remove libwww-robotrules-perl which isn't installed dpkg: warning: ignoring request to remove libx11-6 which isn't installed dpkg: warning: ignoring request to remove libx11-data which isn't installed dpkg: warning: ignoring request to remove libx11-xcb1 which isn't installed dpkg: warning: ignoring request to remove libxau6 which isn't installed dpkg: warning: ignoring request to remove libxcb-dri2-0 which isn't installed dpkg: warning: ignoring request to remove libxcb-dri3-0 which isn't installed dpkg: warning: ignoring request to remove libxcb-glx0 which isn't installed dpkg: warning: ignoring request to remove libxcb-present0 which isn't installed dpkg: warning: ignoring request to remove libxcb-render0 which isn't installed dpkg: warning: ignoring request to remove libxcb-shm0 which isn't installed dpkg: warning: ignoring request to remove libxcb-sync1 which isn't installed dpkg: warning: ignoring request to remove libxcb1 which isn't installed dpkg: warning: ignoring request to remove libxdamage1 which isn't installed dpkg: warning: ignoring request to remove libxdmcp6 which isn't installed dpkg: warning: ignoring request to remove libxext6 which isn't installed dpkg: warning: ignoring request to remove libxfixes3 which isn't installed dpkg: warning: ignoring request to remove libxft2 which isn't installed dpkg: warning: ignoring request to remove libxi6 which isn't installed dpkg: warning: ignoring request to remove libxrender1 which isn't installed dpkg: warning: ignoring request to remove libxshmfence1 which isn't installed dpkg: warning: ignoring request to remove libxss1 which isn't installed dpkg: warning: ignoring request to remove libxt6 which isn't installed dpkg: warning: ignoring request to remove libxtst6 which isn't installed dpkg: warning: ignoring request to remove libxxf86vm1 which isn't installed dpkg: warning: ignoring request to remove littler which isn't installed dpkg: warning: ignoring request to remove lsb-base which isn't installed Purging configuration files for mime-support (3.62) ... dpkg: warning: ignoring request to remove ncbi-blast+ which isn't installed Purging configuration files for ncbi-data (6.1.20170106+dfsg1-0+deb10u2) ... Purging configuration files for netbase (5.6) ... dpkg: warning: ignoring request to remove openjdk-11-jre which isn't installed Purging configuration files for openjdk-11-jre-headless:amd64 (11.0.16+8-1~deb10u1) ... Purging configuration files for openssl (1.1.1n-0+deb10u3) ... dpkg: warning: ignoring request to remove parafly which isn't installed Purging configuration files for perl (5.28.1-6+deb10u1) ... dpkg: warning: ignoring request to remove perl-modules-5.28 which isn't installed dpkg: warning: ignoring request to remove perl-openssl-defaults which isn't installed Purging configuration files for python (2.7.16-1) ... dpkg: warning: ignoring request to remove python-minimal which isn't installed dpkg: warning: ignoring request to remove python2 which isn't installed dpkg: warning: ignoring request to remove python2-minimal which isn't installed dpkg: warning: ignoring request to remove python2.7 which isn't installed Purging configuration files for python2.7-minimal (2.7.16-2+deb10u1) ... Purging configuration files for python3 (3.7.3-1) ... dpkg: warning: ignoring request to remove python3-minimal which isn't installed dpkg: warning: ignoring request to remove python3-numpy which isn't installed dpkg: warning: ignoring request to remove python3-pkg-resources which isn't installed dpkg: warning: ignoring request to remove python3.7 which isn't installed Purging configuration files for python3.7-minimal (3.7.3-2+deb10u3) ... Purging configuration files for r-base-core (3.5.2-1) ... dpkg: warning: ignoring request to remove r-bioc-biocgenerics which isn't installed dpkg: warning: ignoring request to remove r-bioc-qvalue which isn't installed dpkg: warning: ignoring request to remove r-cran-assertthat which isn't installed dpkg: warning: ignoring request to remove r-cran-cli which isn't installed dpkg: warning: ignoring request to remove r-cran-cluster which isn't installed dpkg: warning: ignoring request to remove r-cran-colorspace which isn't installed dpkg: warning: ignoring request to remove r-cran-crayon which isn't installed dpkg: warning: ignoring request to remove r-cran-digest which isn't installed dpkg: warning: ignoring request to remove r-cran-fansi which isn't installed dpkg: warning: ignoring request to remove r-cran-ggplot2 which isn't installed dpkg: warning: ignoring request to remove r-cran-glue which isn't installed dpkg: warning: ignoring request to remove r-cran-gtable which isn't installed dpkg: warning: ignoring request to remove r-cran-labeling which isn't installed dpkg: warning: ignoring request to remove r-cran-lattice which isn't installed dpkg: warning: ignoring request to remove r-cran-lazyeval which isn't installed dpkg: warning: ignoring request to remove r-cran-littler which isn't installed dpkg: warning: ignoring request to remove r-cran-magrittr which isn't installed dpkg: warning: ignoring request to remove r-cran-mass which isn't installed dpkg: warning: ignoring request to remove r-cran-matrix which isn't installed dpkg: warning: ignoring request to remove r-cran-mgcv which isn't installed dpkg: warning: ignoring request to remove r-cran-munsell which isn't installed dpkg: warning: ignoring request to remove r-cran-nlme which isn't installed dpkg: warning: ignoring request to remove r-cran-pillar which isn't installed dpkg: warning: ignoring request to remove r-cran-pkgconfig which isn't installed dpkg: warning: ignoring request to remove r-cran-pkgkitten which isn't installed dpkg: warning: ignoring request to remove r-cran-plyr which isn't installed dpkg: warning: ignoring request to remove r-cran-r6 which isn't installed dpkg: warning: ignoring request to remove r-cran-rcolorbrewer which isn't installed dpkg: warning: ignoring request to remove r-cran-rcpp which isn't installed dpkg: warning: ignoring request to remove r-cran-reshape2 which isn't installed dpkg: warning: ignoring request to remove r-cran-rlang which isn't installed dpkg: warning: ignoring request to remove r-cran-scales which isn't installed dpkg: warning: ignoring request to remove r-cran-stringi which isn't installed dpkg: warning: ignoring request to remove r-cran-stringr which isn't installed dpkg: warning: ignoring request to remove r-cran-tibble which isn't installed dpkg: warning: ignoring request to remove r-cran-utf8 which isn't installed dpkg: warning: ignoring request to remove r-cran-viridislite which isn't installed dpkg: warning: ignoring request to remove r-cran-withr which isn't installed Purging configuration files for readline-common (7.0-5) ... dpkg: warning: ignoring request to remove rsem which isn't installed dpkg: warning: ignoring request to remove salmon which isn't installed dpkg: warning: ignoring request to remove samtools which isn't installed dpkg: warning: ignoring request to remove sensible-utils which isn't installed dpkg: warning: ignoring request to remove sphinx-rtd-theme-common which isn't installed dpkg: warning: ignoring request to remove transdecoder which isn't installed dpkg: warning: ignoring request to remove trimmomatic which isn't installed Purging configuration files for ucf (3.0038+nmu1) ... Purging configuration files for unzip (6.0-23+deb10u2) ... Purging configuration files for x11-common (1:7.7+19) ... dpkg: warning: ignoring request to remove xdg-utils which isn't installed dpkg: warning: ignoring request to remove zip which isn't installed 1m48.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'dpkg', '--purge', 'berkeley-express', 'bowtie', 'bowtie2', 'ca-certificates', 'ca-certificates-java', 'curl', 'default-jre', 'default-jre-headless', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-font-awesome', 'fonts-lato', 'fonts-roboto-slab', 'jaligner', 'java-common', 'jellyfish', 'libapache-pom-java', 'libasound2:amd64', 'libasound2-data', 'libatomic1:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbamtools2.5.1:amd64', 'libblas3:amd64', 'libboost-atomic1.67.0:amd64', 'libboost-chrono1.67.0:amd64', 'libboost-date-time1.67.0:amd64', 'libboost-filesystem1.67.0:amd64', 'libboost-iostreams1.67.0:amd64', 'libboost-program-options1.67.0:amd64', 'libboost-regex1.67.0:amd64', 'libboost-system1.67.0:amd64', 'libboost-thread1.67.0:amd64', 'libboost-timer1.67.0:amd64', 'libbsd0:amd64', 'libcairo2:amd64', 'libcolt-free-java', 'libcommons-collections4-java', 'libcommons-parent-java', 'libconcurrent-java', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdatrie1:amd64', 'libdbus-1-3:amd64', 'libdeflate0:amd64', 'libdivsufsort3:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm-nouveau2:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1:amd64', 'libencode-locale-perl', 'libexpat1:amd64', 'libfile-listing-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgdbm-compat4:amd64', 'libgdbm6:amd64', 'libgetopt-java', 'libgfortran5:amd64', 'libgif7:amd64', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libharfbuzz0b:amd64', 'libhtml-parser-perl', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhts2:amd64', 'libhttp-cookies-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libice6:amd64', 'libicu63:amd64', 'libio-html-perl', 'libio-socket-ssl-perl', 'libjbig0:amd64', 'libjbzip2-java', 'libjellyfish-2.0-2:amd64', 'libjemalloc2:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-modernizr', 'libjs-sphinxdoc', 'libjs-underscore', 'libjung-free-java', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblapack3:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'libllvm7:amd64', 'liblmdb0:amd64', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'libmbedcrypto3:amd64', 'libmbedtls12:amd64', 'libmbedx509-0:amd64', 'libmpdec2:amd64', 'libncurses6:amd64', 'libnet-http-perl', 'libnet-ssleay-perl', 'libnghttp2-14:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.28:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libprotobuf17:amd64', 'libpsl5:amd64', 'libpython-stdlib:amd64', 'libpython2-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libpython3-stdlib:amd64', 'libpython3.7-minimal:amd64', 'libpython3.7-stdlib:amd64', 'libquadmath0:amd64', 'libreadline7:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libsm6:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.1:amd64', 'libstaden-read13:amd64', 'libtbb2:amd64', 'libtcl8.6:amd64', 'libthai-data', 'libthai0:amd64', 'libtiff5:amd64', 'libtimedate-perl', 'libtk8.6:amd64', 'libtry-tiny-perl', 'liburi-perl', 'libvecmath-java', 'libwebp6:amd64', 'libwww-perl', 'libwww-robotrules-perl', 'libx11-6:amd64', 'libx11-data', 'libx11-xcb1:amd64', 'libxau6:amd64', 'libxcb-dri2-0:amd64', 'libxcb-dri3-0:amd64', 'libxcb-glx0:amd64', 'libxcb-present0:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb-sync1:amd64', 'libxcb1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxss1:amd64', 'libxt6:amd64', 'libxtst6:amd64', 'libxxf86vm1:amd64', 'littler', 'lsb-base', 'mime-support', 'ncbi-blast+', 'ncbi-data', 'netbase', 'openjdk-11-jre:amd64', 'openjdk-11-jre-headless:amd64', 'openssl', 'parafly', 'perl', 'perl-modules-5.28', 'perl-openssl-defaults:amd64', 'python', 'python-minimal', 'python2', 'python2-minimal', 'python2.7', 'python2.7-minimal', 'python3', 'python3-minimal', 'python3-numpy', 'python3-pkg-resources', 'python3.7', 'python3.7-minimal', 'r-base-core', 'r-bioc-biocgenerics', 'r-bioc-qvalue', 'r-cran-assertthat', 'r-cran-cli', 'r-cran-cluster', 'r-cran-colorspace', 'r-cran-crayon', 'r-cran-digest', 'r-cran-fansi', 'r-cran-ggplot2', 'r-cran-glue', 'r-cran-gtable', 'r-cran-labeling', 'r-cran-lattice', 'r-cran-lazyeval', 'r-cran-littler', 'r-cran-magrittr', 'r-cran-mass', 'r-cran-matrix', 'r-cran-mgcv', 'r-cran-munsell', 'r-cran-nlme', 'r-cran-pillar', 'r-cran-pkgconfig', 'r-cran-pkgkitten', 'r-cran-plyr', 'r-cran-r6', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-reshape2', 'r-cran-rlang', 'r-cran-scales', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-tibble', 'r-cran-utf8', 'r-cran-viridislite', 'r-cran-withr', 'readline-common', 'rsem', 'salmon', 'samtools', 'sensible-utils', 'sphinx-rtd-theme-common', 'transdecoder', 'trimmomatic', 'ucf', 'unzip', 'x11-common', 'xdg-utils', 'zip'] 1m48.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'dpkg', '--purge', 'trinityrnaseq'] 1m48.9s DUMP: dpkg: warning: ignoring request to remove trinityrnaseq which isn't installed 1m48.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'dpkg', '--purge', 'trinityrnaseq'] 1m48.9s INFO: Running scripts post_purge 1m48.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/post_purge_exceptions'] 1m48.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/post_purge_exceptions'] 1m48.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'dpkg', '--purge', '--pending'] 1m48.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'dpkg', '--purge', '--pending'] 1m48.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'dpkg', '--remove', '--pending'] 1m48.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'dpkg', '--remove', '--pending'] 1m48.9s INFO: Running scripts post_test 1m48.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/post_test_exceptions'] 1m49.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'tmp/scripts/post_test_exceptions'] 1m49.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmph3a3epj4'] 1m49.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmph3a3epj4'] 1m49.9s DEBUG: No broken symlinks as far as we can find. 1m49.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'dpkg-divert', '--list'] 1m49.9s 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 1m49.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'dpkg-divert', '--list'] 1m49.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'apt-get', 'clean'] 1m50.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmph3a3epj4', 'apt-get', 'clean'] 1m50.0s DEBUG: Recording chroot state 1m50.6s INFO: Warning: Package purging left files on system: /usr/local/share/fonts/ not owned /usr/local/share/fonts/.uuid not owned /usr/share/fonts/ owned by: fonts-roboto-slab, fonts-font-awesome, fonts-dejavu-core, fonts-lato /usr/share/fonts/.uuid not owned /usr/share/fonts/eot/ owned by: fonts-font-awesome /usr/share/fonts/eot/.uuid not owned /usr/share/fonts/eot/font-awesome/ owned by: fonts-font-awesome /usr/share/fonts/eot/font-awesome/.uuid not owned /usr/share/fonts/opentype/ owned by: fonts-font-awesome /usr/share/fonts/opentype/.uuid not owned /usr/share/fonts/opentype/font-awesome/ owned by: fonts-font-awesome /usr/share/fonts/opentype/font-awesome/.uuid not owned /usr/share/fonts/svg/ owned by: fonts-font-awesome /usr/share/fonts/svg/.uuid not owned /usr/share/fonts/svg/font-awesome/ owned by: fonts-font-awesome /usr/share/fonts/svg/font-awesome/.uuid not owned /usr/share/fonts/truetype/ owned by: fonts-roboto-slab, fonts-font-awesome, fonts-dejavu-core, fonts-lato /usr/share/fonts/truetype/.uuid not owned /usr/share/fonts/truetype/dejavu/ owned by: fonts-dejavu-core /usr/share/fonts/truetype/dejavu/.uuid not owned /usr/share/fonts/truetype/font-awesome/ owned by: fonts-font-awesome /usr/share/fonts/truetype/font-awesome/.uuid not owned /usr/share/fonts/truetype/lato/ owned by: fonts-lato /usr/share/fonts/truetype/lato/.uuid not owned /usr/share/fonts/truetype/roboto/ owned by: fonts-roboto-slab /usr/share/fonts/truetype/roboto/.uuid not owned /usr/share/fonts/truetype/roboto/slab/ owned by: fonts-roboto-slab /usr/share/fonts/truetype/roboto/slab/.uuid not owned /usr/share/fonts/woff/ owned by: fonts-font-awesome /usr/share/fonts/woff/.uuid not owned /usr/share/fonts/woff/font-awesome/ owned by: fonts-font-awesome /usr/share/fonts/woff/font-awesome/.uuid not owned 1m50.6s INFO: PASS: Installation and purging test. 1m50.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmph3a3epj4/dev/shm'] 1m50.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmph3a3epj4/dev/shm'] 1m50.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmph3a3epj4/dev/console'] 1m50.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmph3a3epj4/dev/console'] 1m50.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmph3a3epj4/dev/ptmx'] 1m50.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmph3a3epj4/dev/ptmx'] 1m50.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmph3a3epj4/dev/pts'] 1m50.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmph3a3epj4/dev/pts'] 1m50.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmph3a3epj4/proc'] 1m51.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmph3a3epj4/proc'] 1m51.0s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmph3a3epj4'] 1m51.1s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmph3a3epj4'] 1m51.1s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmph3a3epj4 1m51.1s INFO: PASS: All tests. 1m51.1s INFO: piuparts run ends. ret=0 End: 2024-01-29 04:40:52 GMT