Start: 2022-12-17 08:41:21 GMT [stretch] Package: trinityrnaseq Source: trinityrnaseq (2.2.0+dfsg-2) Version: 2.2.0+dfsg-2+b1 Installed-Size: 8663 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.14), libgcc1 (>= 1:3.0), libgomp1 (>= 4.9), libhts1 (>= 1.0), libstdc++6 (>= 5.2), perl:any, jaligner, libcommons-collections4-java, libgetopt-java, libjung-free-java, bowtie, bowtie2, python, libwww-perl, default-jre-headless, samtools, jellyfish, r-base-core, r-cran-cluster, r-bioc-edger, r-bioc-qvalue, rsem, berkeley-express, trimmomatic, transdecoder, parafly, curl 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_2.2.0+dfsg-2+b1_amd64.deb Size: 1748158 MD5sum: 9b6f5af6d0dae2b9479a59f0267e1cbd SHA256: 16d49266252fa03e564134958ddec3aa54183dce6f8bf1102a7ba16567e26644 [buster] 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 --upgrade-before-dist-upgrade --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz -d stretch -d buster -B /srv/piuparts.debian.org/slave/refchroot/stretch2Xbuster/reference-chroot-metadata.dat --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 1.1.5 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --upgrade-before-dist-upgrade --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz -d stretch -d buster -B /srv/piuparts.debian.org/slave/refchroot/stretch2Xbuster/reference-chroot-metadata.dat --apt trinityrnaseq=2.6.6+dfsg-6 0m0.0s INFO: Running on: Linux piu-slave-ubc-01 5.10.0-19-amd64 #1 SMP Debian 5.10.149-2 (2022-10-21) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpfmkzlmxa 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpfmkzlmxa 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m1.4s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m1.4s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa/proc'] 0m1.4s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa/proc'] 0m1.4s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa/dev/pts'] 0m1.4s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa/dev/pts'] 0m1.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa/dev/ptmx'] 0m1.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa/dev/ptmx'] 0m1.4s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa/dev/console'] 0m1.4s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa/dev/console'] 0m1.4s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa/dev/shm'] 0m1.4s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa/dev/shm'] 0m1.4s DEBUG: sources.list: deb http://deb.debian.org/debian/ stretch main 0m1.4s DEBUG: Created policy-rc.d and chmodded it. 0m1.4s DEBUG: Created resolv.conf. 0m1.4s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpfmkzlmxa/tmp/scripts/ 0m1.5s INFO: Running scripts post_chroot_unpack 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'apt-get', 'update'] 0m2.5s DUMP: Ign:1 http://deb.debian.org/debian stretch InRelease Hit:2 http://deb.debian.org/debian stretch Release Reading package lists... 0m2.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'apt-get', 'update'] 0m2.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'apt-get', '-yf', 'dist-upgrade'] 0m2.9s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'apt-get', '-yf', 'dist-upgrade'] 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.2s DUMP: 660e5103244a20b75ca08c3f8741e16e - 0m3.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m3.2s INFO: Running scripts post_setup 0m3.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/post_setup_dummy_users'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/post_setup_dummy_users'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/post_setup_forbid_home'] 0m4.0s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/post_setup_forbid_home'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.0s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' '/bin/sync' -> 'true' 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/post_setup_minimize'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/post_setup_minimize'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/post_setup_zz_backports'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/post_setup_zz_backports'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.1s DUMP: install ok installed adduser adduser 3.115 install ok installed apt apt 1.4.10 install ok installed base-files base-files 9.9+deb9u13 install ok installed base-passwd base-passwd 3.5.43 install ok installed bash bash 4.4-5 install ok installed bsdutils bsdutils 1:2.29.2-1+deb9u1 install ok installed coreutils coreutils 8.26-3 install ok installed dash dash 0.5.8-2.4 install ok installed debconf debconf 1.5.61 install ok installed debian-archive-keyring debian-archive-keyring 2017.5+deb9u1 install ok installed debianutils debianutils 4.8.1.1 install ok installed diffutils diffutils 1:3.5-3 install ok installed dpkg dpkg 1.18.25 install ok installed e2fslibs:amd64 e2fslibs 1.43.4-2+deb9u1 install ok installed e2fsprogs e2fsprogs 1.43.4-2+deb9u1 install ok installed findutils findutils 4.6.0+git+20161106-2 install ok installed gcc-6-base:amd64 gcc-6-base 6.3.0-18+deb9u1 install ok installed gpgv gpgv 2.1.18-8~deb9u4 install ok installed grep grep 2.27-2 install ok installed gzip gzip 1.6-5+b1 install ok installed hostname hostname 3.18+b1 install ok installed init-system-helpers init-system-helpers 1.48 install ok installed libacl1:amd64 libacl1 2.2.52-3+b1 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.4.10 install ok installed libattr1:amd64 libattr1 1:2.4.47-2+b2 install ok installed libaudit-common libaudit-common 1:2.6.7-2 install ok installed libaudit1:amd64 libaudit1 1:2.6.7-2 install ok installed libblkid1:amd64 libblkid1 2.29.2-1+deb9u1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-8.1 install ok installed libc-bin libc-bin 2.24-11+deb9u4 install ok installed libc6:amd64 libc6 2.24-11+deb9u4 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.7-3+b1 install ok installed libcomerr2:amd64 libcomerr2 1.43.4-2+deb9u1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28-12+deb9u1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.227 install ok installed libfdisk1:amd64 libfdisk1 2.29.2-1+deb9u1 install ok installed libgcc1:amd64 libgcc1 1:6.3.0-18+deb9u1 install ok installed libgcrypt20:amd64 libgcrypt20 1.7.6-2+deb9u3 install ok installed libgpg-error0:amd64 libgpg-error0 1.26-2 install ok installed liblz4-1:amd64 liblz4-1 0.0~r131-2+b1 install ok installed liblzma5:amd64 liblzma5 5.2.2-1.2+b1 install ok installed libmount1:amd64 libmount1 2.29.2-1+deb9u1 install ok installed libncursesw5:amd64 libncursesw5 6.0+20161126-1+deb9u2 install ok installed libpam-modules:amd64 libpam-modules 1.1.8-3.6 install ok installed libpam-modules-bin libpam-modules-bin 1.1.8-3.6 install ok installed libpam-runtime libpam-runtime 1.1.8-3.6 install ok installed libpam0g:amd64 libpam0g 1.1.8-3.6 install ok installed libpcre3:amd64 libpcre3 2:8.39-3 install ok installed libselinux1:amd64 libselinux1 2.6-3+b3 install ok installed libsemanage-common libsemanage-common 2.6-2 install ok installed libsemanage1:amd64 libsemanage1 2.6-2 install ok installed libsepol1:amd64 libsepol1 2.6-2 install ok installed libsmartcols1:amd64 libsmartcols1 2.29.2-1+deb9u1 install ok installed libss2:amd64 libss2 1.43.4-2+deb9u1 install ok installed libstdc++6:amd64 libstdc++6 6.3.0-18+deb9u1 install ok installed libsystemd0:amd64 libsystemd0 232-25+deb9u12 install ok installed libtinfo5:amd64 libtinfo5 6.0+20161126-1+deb9u2 install ok installed libudev1:amd64 libudev1 232-25+deb9u12 install ok installed libustr-1.0-1:amd64 libustr-1.0-1 1.0.4-6 install ok installed libuuid1:amd64 libuuid1 2.29.2-1+deb9u1 install ok installed login login 1:4.4-4.1 install ok installed mawk mawk 1.3.3-17+b3 install ok installed mount mount 2.29.2-1+deb9u1 install ok installed multiarch-support multiarch-support 2.24-11+deb9u4 install ok installed ncurses-base ncurses-base 6.0+20161126-1+deb9u2 install ok installed ncurses-bin ncurses-bin 6.0+20161126-1+deb9u2 install ok installed passwd passwd 1:4.4-4.1 install ok installed perl-base perl-base 5.24.1-3+deb9u7 install ok installed sed sed 4.4-1 install ok installed sensible-utils sensible-utils 0.0.9+deb9u1 install ok installed sysvinit-utils sysvinit-utils 2.88dsf-59.9 install ok installed tar tar 1.29b-1.1 install ok installed util-linux util-linux 2.29.2-1+deb9u1 install ok installed zlib1g:amd64 zlib1g 1:1.2.8.dfsg-5 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.1s DEBUG: Loading chroot meta data from /srv/piuparts.debian.org/slave/refchroot/stretch2Xbuster/reference-chroot-metadata.dat 0m4.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa'] 0m4.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa'] 0m4.3s INFO: Running scripts is_testable 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/is_testable_uninstallable'] 0m4.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/is_testable_uninstallable'] 0m4.3s INFO: Running scripts pre_test 0m4.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_test_exceptions'] 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_test_exceptions'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_test_root_password'] 0m4.4s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m4.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_test_root_password'] 0m4.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'apt-cache', 'show', '--no-all-versions', 'trinityrnaseq'] 0m4.6s DUMP: Package: trinityrnaseq Source: trinityrnaseq (2.2.0+dfsg-2) Version: 2.2.0+dfsg-2+b1 Installed-Size: 8663 Maintainer: Debian Med Packaging Team Architecture: amd64 Depends: libc6 (>= 2.14), libgcc1 (>= 1:3.0), libgomp1 (>= 4.9), libhts1 (>= 1.0), libstdc++6 (>= 5.2), perl:any, jaligner, libcommons-collections4-java, libgetopt-java, libjung-free-java, bowtie, bowtie2, python, libwww-perl, default-jre-headless, samtools, jellyfish, r-base-core, r-cran-cluster, r-bioc-edger, r-bioc-qvalue, rsem, berkeley-express, trimmomatic, transdecoder, parafly, curl Recommends: trinityrnaseq-examples Suggests: collectl Description-en: RNA-Seq De novo Assembly Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes. Description-md5: 2ee7f38dbb99a040c33d6619f4f5668b Homepage: http://trinityrnaseq.github.io/ Section: science Priority: optional Filename: pool/main/t/trinityrnaseq/trinityrnaseq_2.2.0+dfsg-2+b1_amd64.deb Size: 1748158 MD5sum: 9b6f5af6d0dae2b9479a59f0267e1cbd SHA256: 16d49266252fa03e564134958ddec3aa54183dce6f8bf1102a7ba16567e26644 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'apt-cache', 'show', '--no-all-versions', 'trinityrnaseq'] 0m4.6s INFO: apt-cache knows about the following packages: trinityrnaseq 0m4.6s INFO: Running scripts pre_install 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_install_database-server'] 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_install_database-server'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_install_exceptions'] 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_install_exceptions'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_install_extras'] 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_install_extras'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'apt-cache', 'policy'] 0m4.7s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian stretch/main amd64 Packages release v=9.13,o=Debian,a=oldoldstable,n=stretch,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 0m4.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'apt-cache', 'policy'] 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'apt-cache', 'policy', 'trinityrnaseq'] 0m4.8s DUMP: trinityrnaseq: Installed: (none) Candidate: 2.2.0+dfsg-2+b1 Version table: 2.2.0+dfsg-2+b1 500 500 http://deb.debian.org/debian stretch/main amd64 Packages 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'apt-cache', 'policy', 'trinityrnaseq'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'apt-get', '-y', 'install', 'trinityrnaseq'] 0m59.1s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: adwaita-icon-theme berkeley-express bowtie bowtie2 ca-certificates ca-certificates-java cd-hit curl dconf-gsettings-backend dconf-service default-jre default-jre-headless fontconfig fontconfig-config fonts-dejavu-core glib-networking glib-networking-common glib-networking-services gnome-icon-theme gsettings-desktop-schemas gtk-update-icon-cache hicolor-icon-theme jaligner java-common jellyfish libasound2 libasound2-data libasyncns0 libatk-bridge2.0-0 libatk-wrapper-java libatk-wrapper-java-jni libatk1.0-0 libatk1.0-data libatomic1 libatspi2.0-0 libavahi-client3 libavahi-common-data libavahi-common3 libbamtools2.4.0 libblas-common libblas3 libboost-date-time1.62.0 libboost-filesystem1.62.0 libboost-program-options1.62.0 libboost-system1.62.0 libboost-thread1.62.0 libbsd0 libcairo-gobject2 libcairo2 libcap2 libcolord2 libcolt-free-java libcommons-collections4-java libconcurrent-java libcroco3 libcups2 libcurl3 libcurl3-gnutls libdatrie1 libdbus-1-3 libdconf1 libdrm2 libegl1-mesa libencode-locale-perl libepoxy0 libexpat1 libffi6 libfile-listing-perl libflac8 libfontconfig1 libfontenc1 libfreetype6 libgbm1 libgdbm3 libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common libgetopt-java libgfortran3 libgif7 libgl1-mesa-glx libglapi-mesa libglib2.0-0 libgmp10 libgnutls30 libgomp1 libgraphite2-3 libgssapi-krb5-2 libgtk-3-0 libgtk-3-common libgtk2.0-0 libgtk2.0-common libharfbuzz0b libhogweed4 libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhts1 libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libice6 libicu57 libidn11 libidn2-0 libio-html-perl libio-socket-ssl-perl libjbig0 libjbzip2-java libjellyfish-2.0-2 libjpeg62-turbo libjson-glib-1.0-0 libjson-glib-1.0-common libjung-free-java libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 libldap-common liblwp-mediatypes-perl liblwp-protocol-https-perl libncurses5 libnet-http-perl libnet-ssleay-perl libnettle6 libnghttp2-14 libnspr4 libnss3 libogg0 libp11-kit0 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpcsclite1 libperl5.24 libpixman-1-0 libpng16-16 libprotobuf10 libproxy1v5 libpsl5 libpulse0 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 libreadline7 librest-0.7-0 librsvg2-2 librsvg2-common librtmp1 libsasl2-2 libsasl2-modules-db libsm6 libsndfile1 libsoup-gnome2.4-1 libsoup2.4-1 libsqlite3-0 libssh2-1 libssl1.0.2 libssl1.1 libtasn1-6 libtbb2 libtcl8.6 libthai-data libthai0 libtiff5 libtimedate-perl libtk8.6 libunistring0 liburi-perl libvecmath-java libvorbis0a libvorbisenc2 libwayland-client0 libwayland-cursor0 libwayland-egl1-mesa libwayland-server0 libwrap0 libwww-perl libwww-robotrules-perl libx11-6 libx11-data libx11-xcb1 libxau6 libxaw7 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-shape0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxft2 libxi6 libxinerama1 libxkbcommon0 libxml2 libxmu6 libxmuu1 libxpm4 libxrandr2 libxrender1 libxshmfence1 libxss1 libxt6 libxtst6 libxv1 libxxf86dga1 libxxf86vm1 littler lsb-base mime-support netbase openjdk-8-jre openjdk-8-jre-headless openssl parafly perl perl-modules-5.24 perl-openssl-defaults python python-minimal python2.7 python2.7-minimal r-base-core r-bioc-edger r-bioc-limma r-bioc-qvalue r-cran-assertthat r-cran-cluster r-cran-colorspace r-cran-dichromat r-cran-digest r-cran-ggplot2 r-cran-gtable r-cran-labeling r-cran-lazyeval r-cran-littler r-cran-magrittr r-cran-mass r-cran-munsell r-cran-pkgkitten r-cran-plyr r-cran-rcolorbrewer r-cran-rcpp r-cran-reshape2 r-cran-scales r-cran-stringi r-cran-stringr r-cran-tibble readline-common rsem samtools shared-mime-info transdecoder trimmomatic tzdata ucf unzip x11-common x11-utils xdg-utils xkb-data zip Suggested packages: bowtie-examples bowtie2-examples libasound2-plugins alsa-utils colord libcommons-collections4-java-doc cups-common libgetopt-java-doc gnutls-bin krb5-doc krb5-user gvfs libdata-dump-perl liblcms2-utils libcrypt-ssleay-perl pcscd pulseaudio librsvg2-bin tcl8.6 tk8.6 libauthen-ntlm-perl icedtea-8-plugin 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 python-doc python-tk python2.7-doc binutils binfmt-support ess r-doc-info | r-doc-pdf r-mathlib r-base-html r-bioc-affy r-bioc-annotationdbi r-cran-biasedurn r-bioc-biobase r-cran-ellipse r-bioc-go.db r-cran-gplots r-cran-statmod r-cran-knitr r-cran-kernsmooth r-cran-kernlab r-cran-mvtnorm r-cran-vcd r-cran-shiny r-cran-hexbin r-cran-hmisc r-cran-lattice r-cran-mapproj r-cran-maps r-cran-maptools r-cran-mgcv r-cran-multcomp r-cran-nlme r-cran-testthat r-cran-quantreg r-cran-rpart r-cran-getopt r-cran-abind r-cran-foreach r-cran-doparallel r-cran-iterators r-cran-inline r-cran-htmltools r-cran-htmlwidgets readline-doc r-bioc-ebseq collectl mesa-utils gvfs-bin Recommended packages: med-config at-spi2-core dbus libgl1-mesa-dri libglib2.0-data xdg-user-dirs libgtk-3-bin libgail-common libgtk2.0-bin libhtml-format-perl krb5-locales libgpm2 publicsuffix libsasl2-modules tcpd libhtml-form-perl libhttp-daemon-perl libmailtools-perl xml-core bzip2 file xz-utils fonts-dejavu-extra rename r-recommended r-base-dev r-doc-html r-cran-crayon trinityrnaseq-examples libfile-mimeinfo-perl libnet-dbus-perl libx11-protocol-perl x11-xserver-utils The following NEW packages will be installed: adwaita-icon-theme berkeley-express bowtie bowtie2 ca-certificates ca-certificates-java cd-hit curl dconf-gsettings-backend dconf-service default-jre default-jre-headless fontconfig fontconfig-config fonts-dejavu-core glib-networking glib-networking-common glib-networking-services gnome-icon-theme gsettings-desktop-schemas gtk-update-icon-cache hicolor-icon-theme jaligner java-common jellyfish libasound2 libasound2-data libasyncns0 libatk-bridge2.0-0 libatk-wrapper-java libatk-wrapper-java-jni libatk1.0-0 libatk1.0-data libatomic1 libatspi2.0-0 libavahi-client3 libavahi-common-data libavahi-common3 libbamtools2.4.0 libblas-common libblas3 libboost-date-time1.62.0 libboost-filesystem1.62.0 libboost-program-options1.62.0 libboost-system1.62.0 libboost-thread1.62.0 libbsd0 libcairo-gobject2 libcairo2 libcap2 libcolord2 libcolt-free-java libcommons-collections4-java libconcurrent-java libcroco3 libcups2 libcurl3 libcurl3-gnutls libdatrie1 libdbus-1-3 libdconf1 libdrm2 libegl1-mesa libencode-locale-perl libepoxy0 libexpat1 libffi6 libfile-listing-perl libflac8 libfontconfig1 libfontenc1 libfreetype6 libgbm1 libgdbm3 libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common libgetopt-java libgfortran3 libgif7 libgl1-mesa-glx libglapi-mesa libglib2.0-0 libgmp10 libgnutls30 libgomp1 libgraphite2-3 libgssapi-krb5-2 libgtk-3-0 libgtk-3-common libgtk2.0-0 libgtk2.0-common libharfbuzz0b libhogweed4 libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhts1 libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libice6 libicu57 libidn11 libidn2-0 libio-html-perl libio-socket-ssl-perl libjbig0 libjbzip2-java libjellyfish-2.0-2 libjpeg62-turbo libjson-glib-1.0-0 libjson-glib-1.0-common libjung-free-java libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblapack3 liblcms2-2 libldap-2.4-2 libldap-common liblwp-mediatypes-perl liblwp-protocol-https-perl libncurses5 libnet-http-perl libnet-ssleay-perl libnettle6 libnghttp2-14 libnspr4 libnss3 libogg0 libp11-kit0 libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpcsclite1 libperl5.24 libpixman-1-0 libpng16-16 libprotobuf10 libproxy1v5 libpsl5 libpulse0 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 libreadline7 librest-0.7-0 librsvg2-2 librsvg2-common librtmp1 libsasl2-2 libsasl2-modules-db libsm6 libsndfile1 libsoup-gnome2.4-1 libsoup2.4-1 libsqlite3-0 libssh2-1 libssl1.0.2 libssl1.1 libtasn1-6 libtbb2 libtcl8.6 libthai-data libthai0 libtiff5 libtimedate-perl libtk8.6 libunistring0 liburi-perl libvecmath-java libvorbis0a libvorbisenc2 libwayland-client0 libwayland-cursor0 libwayland-egl1-mesa libwayland-server0 libwrap0 libwww-perl libwww-robotrules-perl libx11-6 libx11-data libx11-xcb1 libxau6 libxaw7 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-shape0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxft2 libxi6 libxinerama1 libxkbcommon0 libxml2 libxmu6 libxmuu1 libxpm4 libxrandr2 libxrender1 libxshmfence1 libxss1 libxt6 libxtst6 libxv1 libxxf86dga1 libxxf86vm1 littler lsb-base mime-support netbase openjdk-8-jre openjdk-8-jre-headless openssl parafly perl perl-modules-5.24 perl-openssl-defaults python python-minimal python2.7 python2.7-minimal r-base-core r-bioc-edger r-bioc-limma r-bioc-qvalue r-cran-assertthat r-cran-cluster r-cran-colorspace r-cran-dichromat r-cran-digest r-cran-ggplot2 r-cran-gtable r-cran-labeling r-cran-lazyeval r-cran-littler r-cran-magrittr r-cran-mass r-cran-munsell r-cran-pkgkitten r-cran-plyr r-cran-rcolorbrewer r-cran-rcpp r-cran-reshape2 r-cran-scales r-cran-stringi r-cran-stringr r-cran-tibble readline-common rsem samtools shared-mime-info transdecoder trimmomatic trinityrnaseq tzdata ucf unzip x11-common x11-utils xdg-utils xkb-data zip 0 upgraded, 279 newly installed, 0 to remove and 0 not upgraded. Need to get 163 MB of archives. After this operation, 511 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian stretch/main amd64 perl-modules-5.24 all 5.24.1-3+deb9u7 [2723 kB] Get:2 http://deb.debian.org/debian stretch/main amd64 libgdbm3 amd64 1.8.3-14 [30.0 kB] Get:3 http://deb.debian.org/debian stretch/main amd64 libperl5.24 amd64 5.24.1-3+deb9u7 [3527 kB] Get:4 http://deb.debian.org/debian stretch/main amd64 perl amd64 5.24.1-3+deb9u7 [218 kB] Get:5 http://deb.debian.org/debian stretch/main amd64 libpython2.7-minimal amd64 2.7.13-2+deb9u3 [389 kB] Get:6 http://deb.debian.org/debian stretch/main amd64 python2.7-minimal amd64 2.7.13-2+deb9u3 [1382 kB] Get:7 http://deb.debian.org/debian stretch/main amd64 python-minimal amd64 2.7.13-2 [40.5 kB] Get:8 http://deb.debian.org/debian stretch/main amd64 mime-support all 3.60 [36.7 kB] Get:9 http://deb.debian.org/debian stretch/main amd64 libexpat1 amd64 2.2.0-2+deb9u3 [83.7 kB] Get:10 http://deb.debian.org/debian stretch/main amd64 libffi6 amd64 3.2.1-6 [20.4 kB] Get:11 http://deb.debian.org/debian stretch/main amd64 readline-common all 7.0-3 [70.4 kB] Get:12 http://deb.debian.org/debian stretch/main amd64 libreadline7 amd64 7.0-3 [151 kB] Get:13 http://deb.debian.org/debian stretch/main amd64 libsqlite3-0 amd64 3.16.2-5+deb9u1 [572 kB] Get:14 http://deb.debian.org/debian stretch/main amd64 libssl1.1 amd64 1.1.0l-1~deb9u1 [1358 kB] Get:15 http://deb.debian.org/debian stretch/main amd64 libpython2.7-stdlib amd64 2.7.13-2+deb9u3 [1897 kB] Get:16 http://deb.debian.org/debian stretch/main amd64 python2.7 amd64 2.7.13-2+deb9u3 [285 kB] Get:17 http://deb.debian.org/debian stretch/main amd64 libpython-stdlib amd64 2.7.13-2 [20.0 kB] Get:18 http://deb.debian.org/debian stretch/main amd64 python amd64 2.7.13-2 [154 kB] Get:19 http://deb.debian.org/debian stretch/main amd64 libpng16-16 amd64 1.6.28-1+deb9u1 [280 kB] Get:20 http://deb.debian.org/debian stretch/main amd64 libfreetype6 amd64 2.6.3-3.2+deb9u1 [438 kB] Get:21 http://deb.debian.org/debian stretch/main amd64 ucf all 3.0036 [70.2 kB] Get:22 http://deb.debian.org/debian stretch/main amd64 fonts-dejavu-core all 2.37-1 [1068 kB] Get:23 http://deb.debian.org/debian stretch/main amd64 fontconfig-config all 2.11.0-6.7 [271 kB] Get:24 http://deb.debian.org/debian stretch/main amd64 libfontconfig1 amd64 2.11.0-6.7+b1 [331 kB] Get:25 http://deb.debian.org/debian stretch/main amd64 fontconfig amd64 2.11.0-6.7+b1 [404 kB] Get:26 http://deb.debian.org/debian stretch/main amd64 libogg0 amd64 1.3.2-1 [19.9 kB] Get:27 http://deb.debian.org/debian stretch/main amd64 libxau6 amd64 1:1.0.8-1 [20.7 kB] Get:28 http://deb.debian.org/debian stretch/main amd64 libbsd0 amd64 0.8.3-1 [83.0 kB] Get:29 http://deb.debian.org/debian stretch/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:30 http://deb.debian.org/debian stretch/main amd64 libxcb1 amd64 1.12-1 [133 kB] Get:31 http://deb.debian.org/debian stretch/main amd64 libx11-data all 2:1.6.4-3+deb9u1 [287 kB] Get:32 http://deb.debian.org/debian stretch/main amd64 libx11-6 amd64 2:1.6.4-3+deb9u1 [748 kB] Get:33 http://deb.debian.org/debian stretch/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get:34 http://deb.debian.org/debian stretch/main amd64 lsb-base all 9.20161125 [27.9 kB] Get:35 http://deb.debian.org/debian stretch/main amd64 x11-common all 1:7.7+19 [251 kB] Get:36 http://deb.debian.org/debian stretch/main amd64 libxss1 amd64 1:1.2.2-1 [17.5 kB] Get:37 http://deb.debian.org/debian stretch/main amd64 tzdata all 2020a-0+deb9u1 [278 kB] Get:38 http://deb.debian.org/debian stretch/main amd64 libssl1.0.2 amd64 1.0.2u-1~deb9u1 [1304 kB] Get:39 http://deb.debian.org/debian stretch/main amd64 netbase all 5.4 [19.1 kB] Get:40 http://deb.debian.org/debian stretch/main amd64 libcap2 amd64 1:2.25-1 [16.8 kB] Get:41 http://deb.debian.org/debian stretch/main amd64 libgmp10 amd64 2:6.1.2+dfsg-1 [253 kB] Get:42 http://deb.debian.org/debian stretch/main amd64 libnettle6 amd64 3.3-1+b2 [192 kB] Get:43 http://deb.debian.org/debian stretch/main amd64 libhogweed4 amd64 3.3-1+b2 [136 kB] Get:44 http://deb.debian.org/debian stretch/main amd64 libidn11 amd64 1.33-1+deb9u1 [115 kB] Get:45 http://deb.debian.org/debian stretch/main amd64 libp11-kit0 amd64 0.23.3-2 [111 kB] Get:46 http://deb.debian.org/debian stretch/main amd64 libtasn1-6 amd64 4.10-1.1+deb9u1 [50.6 kB] Get:47 http://deb.debian.org/debian stretch/main amd64 libgnutls30 amd64 3.5.8-5+deb9u5 [896 kB] Get:48 http://deb.debian.org/debian stretch/main amd64 libkeyutils1 amd64 1.5.9-9 [12.4 kB] Get:49 http://deb.debian.org/debian stretch/main amd64 libkrb5support0 amd64 1.15-1+deb9u1 [61.9 kB] Get:50 http://deb.debian.org/debian stretch/main amd64 libk5crypto3 amd64 1.15-1+deb9u1 [119 kB] Get:51 http://deb.debian.org/debian stretch/main amd64 libkrb5-3 amd64 1.15-1+deb9u1 [311 kB] Get:52 http://deb.debian.org/debian stretch/main amd64 libgssapi-krb5-2 amd64 1.15-1+deb9u1 [155 kB] Get:53 http://deb.debian.org/debian stretch/main amd64 libsasl2-modules-db amd64 2.1.27~101-g0780600+dfsg-3+deb9u1 [68.4 kB] Get:54 http://deb.debian.org/debian stretch/main amd64 libsasl2-2 amd64 2.1.27~101-g0780600+dfsg-3+deb9u1 [105 kB] Get:55 http://deb.debian.org/debian stretch/main amd64 libldap-common all 2.4.44+dfsg-5+deb9u4 [85.7 kB] Get:56 http://deb.debian.org/debian stretch/main amd64 libldap-2.4-2 amd64 2.4.44+dfsg-5+deb9u4 [219 kB] Get:57 http://deb.debian.org/debian stretch/main amd64 libwrap0 amd64 7.6.q-26 [58.2 kB] Get:58 http://deb.debian.org/debian stretch/main amd64 libicu57 amd64 57.1-6+deb9u4 [7699 kB] Get:59 http://deb.debian.org/debian stretch/main amd64 libxml2 amd64 2.9.4+dfsg1-2.2+deb9u2 [920 kB] Get:60 http://deb.debian.org/debian stretch/main amd64 hicolor-icon-theme all 0.15-1 [9550 B] Get:61 http://deb.debian.org/debian stretch/main amd64 libglib2.0-0 amd64 2.50.3-2+deb9u2 [2692 kB] Get:62 http://deb.debian.org/debian stretch/main amd64 libjpeg62-turbo amd64 1:1.5.1-2 [134 kB] Get:63 http://deb.debian.org/debian stretch/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get:64 http://deb.debian.org/debian stretch/main amd64 libtiff5 amd64 4.0.8-2+deb9u5 [239 kB] Get:65 http://deb.debian.org/debian stretch/main amd64 shared-mime-info amd64 1.8-1+deb9u1 [731 kB] Get:66 http://deb.debian.org/debian stretch/main amd64 libgdk-pixbuf2.0-common all 2.36.5-2+deb9u2 [311 kB] Get:67 http://deb.debian.org/debian stretch/main amd64 libgdk-pixbuf2.0-0 amd64 2.36.5-2+deb9u2 [170 kB] Get:68 http://deb.debian.org/debian stretch/main amd64 gtk-update-icon-cache amd64 3.22.11-1 [76.6 kB] Get:69 http://deb.debian.org/debian stretch/main amd64 libpixman-1-0 amd64 0.34.0-1 [530 kB] Get:70 http://deb.debian.org/debian stretch/main amd64 libxcb-render0 amd64 1.12-1 [105 kB] Get:71 http://deb.debian.org/debian stretch/main amd64 libxcb-shm0 amd64 1.12-1 [95.9 kB] Get:72 http://deb.debian.org/debian stretch/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get:73 http://deb.debian.org/debian stretch/main amd64 libcairo2 amd64 1.14.8-1 [771 kB] Get:74 http://deb.debian.org/debian stretch/main amd64 libcroco3 amd64 0.6.11-3 [143 kB] Get:75 http://deb.debian.org/debian stretch/main amd64 libthai-data all 0.1.26-1 [166 kB] Get:76 http://deb.debian.org/debian stretch/main amd64 libdatrie1 amd64 0.2.10-4+b1 [36.4 kB] Get:77 http://deb.debian.org/debian stretch/main amd64 libthai0 amd64 0.1.26-1 [52.1 kB] Get:78 http://deb.debian.org/debian stretch/main amd64 libpango-1.0-0 amd64 1.40.5-1 [320 kB] Get:79 http://deb.debian.org/debian stretch/main amd64 libgraphite2-3 amd64 1.3.10-1 [84.2 kB] Get:80 http://deb.debian.org/debian stretch/main amd64 libharfbuzz0b amd64 1.4.2-1 [671 kB] Get:81 http://deb.debian.org/debian stretch/main amd64 libpangoft2-1.0-0 amd64 1.40.5-1 [205 kB] Get:82 http://deb.debian.org/debian stretch/main amd64 libpangocairo-1.0-0 amd64 1.40.5-1 [193 kB] Get:83 http://deb.debian.org/debian stretch/main amd64 librsvg2-2 amd64 2.40.16-1+b1 [281 kB] Get:84 http://deb.debian.org/debian stretch/main amd64 librsvg2-common amd64 2.40.16-1+b1 [194 kB] Get:85 http://deb.debian.org/debian stretch/main amd64 adwaita-icon-theme all 3.22.0-1+deb9u1 [11.5 MB] Get:86 http://deb.debian.org/debian stretch/main amd64 libbamtools2.4.0 amd64 2.4.1+dfsg-1 [190 kB] Get:87 http://deb.debian.org/debian stretch/main amd64 libboost-date-time1.62.0 amd64 1.62.0+dfsg-4 [42.9 kB] Get:88 http://deb.debian.org/debian stretch/main amd64 libboost-system1.62.0 amd64 1.62.0+dfsg-4 [32.4 kB] Get:89 http://deb.debian.org/debian stretch/main amd64 libboost-filesystem1.62.0 amd64 1.62.0+dfsg-4 [63.2 kB] Get:90 http://deb.debian.org/debian stretch/main amd64 libboost-program-options1.62.0 amd64 1.62.0+dfsg-4 [159 kB] Get:91 http://deb.debian.org/debian stretch/main amd64 libboost-thread1.62.0 amd64 1.62.0+dfsg-4 [71.5 kB] Get:92 http://deb.debian.org/debian stretch/main amd64 libprotobuf10 amd64 3.0.0-9 [681 kB] Get:93 http://deb.debian.org/debian stretch/main amd64 berkeley-express amd64 1.5.1-3+b1 [234 kB] Get:94 http://deb.debian.org/debian stretch/main amd64 openssl amd64 1.1.0l-1~deb9u1 [749 kB] Get:95 http://deb.debian.org/debian stretch/main amd64 ca-certificates all 20200601~deb9u1 [160 kB] Get:96 http://deb.debian.org/debian stretch/main amd64 java-common all 0.58+deb9u1 [13.6 kB] Get:97 http://deb.debian.org/debian stretch/main amd64 libavahi-common-data amd64 0.6.32-2 [118 kB] Get:98 http://deb.debian.org/debian stretch/main amd64 libavahi-common3 amd64 0.6.32-2 [52.0 kB] Get:99 http://deb.debian.org/debian stretch/main amd64 libdbus-1-3 amd64 1.10.32-0+deb9u1 [196 kB] Get:100 http://deb.debian.org/debian stretch/main amd64 libavahi-client3 amd64 0.6.32-2 [55.3 kB] Get:101 http://deb.debian.org/debian stretch/main amd64 libcups2 amd64 2.2.1-8+deb9u6 [307 kB] Get:102 http://deb.debian.org/debian stretch/main amd64 liblcms2-2 amd64 2.8-4+deb9u1 [143 kB] Get:103 http://deb.debian.org/debian stretch/main amd64 libnspr4 amd64 2:4.12-6 [117 kB] Get:104 http://deb.debian.org/debian stretch/main amd64 libnss3 amd64 2:3.26.2-1.1+deb9u1 [1161 kB] Get:105 http://deb.debian.org/debian stretch/main amd64 libpcsclite1 amd64 1.8.20-1 [56.5 kB] Get:106 http://deb.debian.org/debian stretch/main amd64 libxi6 amd64 2:1.7.9-1 [82.6 kB] Get:107 http://deb.debian.org/debian stretch/main amd64 libxtst6 amd64 2:1.2.3-1 [27.8 kB] Get:108 http://deb.debian.org/debian stretch/main amd64 openjdk-8-jre-headless amd64 8u252-b09-1~deb9u1 [27.4 MB] Get:109 http://deb.debian.org/debian stretch/main amd64 default-jre-headless amd64 2:1.8-58+deb9u1 [10.1 kB] Get:110 http://deb.debian.org/debian stretch/main amd64 ca-certificates-java all 20170929~deb9u3 [15.1 kB] Get:111 http://deb.debian.org/debian stretch/main amd64 libgomp1 amd64 6.3.0-18+deb9u1 [73.3 kB] Get:112 http://deb.debian.org/debian stretch/main amd64 cd-hit amd64 4.6.6-2 [852 kB] Get:113 http://deb.debian.org/debian stretch/main amd64 libunistring0 amd64 0.9.6+really0.9.3-0.1 [279 kB] Get:114 http://deb.debian.org/debian stretch/main amd64 libidn2-0 amd64 0.16-1+deb9u1 [60.7 kB] Get:115 http://deb.debian.org/debian stretch/main amd64 libnghttp2-14 amd64 1.18.1-1+deb9u1 [79.2 kB] Get:116 http://deb.debian.org/debian stretch/main amd64 libpsl5 amd64 0.17.0-3 [41.8 kB] Get:117 http://deb.debian.org/debian stretch/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-1+b1 [60.4 kB] Get:118 http://deb.debian.org/debian stretch/main amd64 libssh2-1 amd64 1.7.0-1+deb9u1 [139 kB] Get:119 http://deb.debian.org/debian stretch/main amd64 libcurl3 amd64 7.52.1-5+deb9u10 [292 kB] Get:120 http://deb.debian.org/debian stretch/main amd64 curl amd64 7.52.1-5+deb9u10 [227 kB] Get:121 http://deb.debian.org/debian stretch/main amd64 libdconf1 amd64 0.26.0-2+b1 [37.6 kB] Get:122 http://deb.debian.org/debian stretch/main amd64 dconf-service amd64 0.26.0-2+b1 [34.7 kB] Get:123 http://deb.debian.org/debian stretch/main amd64 dconf-gsettings-backend amd64 0.26.0-2+b1 [26.4 kB] Get:124 http://deb.debian.org/debian stretch/main amd64 libxrandr2 amd64 2:1.5.1-1 [37.5 kB] Get:125 http://deb.debian.org/debian stretch/main amd64 libxinerama1 amd64 2:1.1.3-1+b3 [16.7 kB] Get:126 http://deb.debian.org/debian stretch/main amd64 libdrm2 amd64 2.4.74-1 [36.2 kB] Get:127 http://deb.debian.org/debian stretch/main amd64 libglapi-mesa amd64 13.0.6-1+b2 [58.9 kB] Get:128 http://deb.debian.org/debian stretch/main amd64 libx11-xcb1 amd64 2:1.6.4-3+deb9u1 [183 kB] Get:129 http://deb.debian.org/debian stretch/main amd64 libxcb-dri2-0 amd64 1.12-1 [97.2 kB] Get:130 http://deb.debian.org/debian stretch/main amd64 libxcb-dri3-0 amd64 1.12-1 [95.6 kB] Get:131 http://deb.debian.org/debian stretch/main amd64 libxcb-glx0 amd64 1.12-1 [113 kB] Get:132 http://deb.debian.org/debian stretch/main amd64 libxcb-present0 amd64 1.12-1 [95.8 kB] Get:133 http://deb.debian.org/debian stretch/main amd64 libxcb-sync1 amd64 1.12-1 [99.2 kB] Get:134 http://deb.debian.org/debian stretch/main amd64 libxfixes3 amd64 1:5.0.3-1 [21.9 kB] Get:135 http://deb.debian.org/debian stretch/main amd64 libxdamage1 amd64 1:1.1.4-2+b3 [14.5 kB] Get:136 http://deb.debian.org/debian stretch/main amd64 libxshmfence1 amd64 1.2-1+b2 [7922 B] Get:137 http://deb.debian.org/debian stretch/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get:138 http://deb.debian.org/debian stretch/main amd64 libgl1-mesa-glx amd64 13.0.6-1+b2 [167 kB] Get:139 http://deb.debian.org/debian stretch/main amd64 libgtk2.0-common all 2.24.31-2 [2693 kB] Get:140 http://deb.debian.org/debian stretch/main amd64 libatk1.0-data all 2.22.0-1 [172 kB] Get:141 http://deb.debian.org/debian stretch/main amd64 libatk1.0-0 amd64 2.22.0-1 [78.4 kB] Get:142 http://deb.debian.org/debian stretch/main amd64 libxcomposite1 amd64 1:0.4.4-2 [16.5 kB] Get:143 http://deb.debian.org/debian stretch/main amd64 libxcursor1 amd64 1:1.1.14-1+deb9u2 [34.9 kB] Get:144 http://deb.debian.org/debian stretch/main amd64 gnome-icon-theme all 3.12.0-2 [9890 kB] Get:145 http://deb.debian.org/debian stretch/main amd64 libgtk2.0-0 amd64 2.24.31-2 [1800 kB] Get:146 http://deb.debian.org/debian stretch/main amd64 libatspi2.0-0 amd64 2.22.0-6+deb9u1 [60.9 kB] Get:147 http://deb.debian.org/debian stretch/main amd64 libatk-bridge2.0-0 amd64 2.22.0-2 [56.3 kB] Get:148 http://deb.debian.org/debian stretch/main amd64 libcairo-gobject2 amd64 1.14.8-1 [336 kB] Get:149 http://deb.debian.org/debian stretch/main amd64 libgtk-3-common all 3.22.11-1 [3416 kB] Get:150 http://deb.debian.org/debian stretch/main amd64 libcolord2 amd64 1.3.3-2 [252 kB] Get:151 http://deb.debian.org/debian stretch/main amd64 libepoxy0 amd64 1.3.1-2 [176 kB] Get:152 http://deb.debian.org/debian stretch/main amd64 libjson-glib-1.0-common all 1.2.6-1 [166 kB] Get:153 http://deb.debian.org/debian stretch/main amd64 libjson-glib-1.0-0 amd64 1.2.6-1 [178 kB] Get:154 http://deb.debian.org/debian stretch/main amd64 libproxy1v5 amd64 0.4.14-2 [57.4 kB] Get:155 http://deb.debian.org/debian stretch/main amd64 glib-networking-common all 2.50.0-1+deb9u1 [49.2 kB] Get:156 http://deb.debian.org/debian stretch/main amd64 glib-networking-services amd64 2.50.0-1+deb9u1 [12.2 kB] Get:157 http://deb.debian.org/debian stretch/main amd64 gsettings-desktop-schemas all 3.22.0-1 [473 kB] Get:158 http://deb.debian.org/debian stretch/main amd64 glib-networking amd64 2.50.0-1+deb9u1 [57.0 kB] Get:159 http://deb.debian.org/debian stretch/main amd64 libsoup2.4-1 amd64 2.56.0-2+deb9u2 [296 kB] Get:160 http://deb.debian.org/debian stretch/main amd64 libsoup-gnome2.4-1 amd64 2.56.0-2+deb9u2 [16.4 kB] Get:161 http://deb.debian.org/debian stretch/main amd64 librest-0.7-0 amd64 0.8.0-2 [33.0 kB] Get:162 http://deb.debian.org/debian stretch/main amd64 libwayland-client0 amd64 1.12.0-1+deb9u1 [25.1 kB] Get:163 http://deb.debian.org/debian stretch/main amd64 libwayland-cursor0 amd64 1.12.0-1+deb9u1 [13.5 kB] Get:164 http://deb.debian.org/debian stretch/main amd64 libwayland-server0 amd64 1.12.0-1+deb9u1 [30.6 kB] Get:165 http://deb.debian.org/debian stretch/main amd64 libgbm1 amd64 13.0.6-1+b2 [59.2 kB] Get:166 http://deb.debian.org/debian stretch/main amd64 libxcb-xfixes0 amd64 1.12-1 [99.6 kB] Get:167 http://deb.debian.org/debian stretch/main amd64 libegl1-mesa amd64 13.0.6-1+b2 [112 kB] Get:168 http://deb.debian.org/debian stretch/main amd64 libwayland-egl1-mesa amd64 13.0.6-1+b2 [43.0 kB] Get:169 http://deb.debian.org/debian stretch/main amd64 xkb-data all 2.19-1+deb9u1 [650 kB] Get:170 http://deb.debian.org/debian stretch/main amd64 libxkbcommon0 amd64 0.7.1-2~deb9u1 [122 kB] Get:171 http://deb.debian.org/debian stretch/main amd64 libgtk-3-0 amd64 3.22.11-1 [2529 kB] Get:172 http://deb.debian.org/debian stretch/main amd64 libfontenc1 amd64 1:1.1.3-1+b2 [24.4 kB] Get:173 http://deb.debian.org/debian stretch/main amd64 libice6 amd64 2:1.0.9-2 [58.7 kB] Get:174 http://deb.debian.org/debian stretch/main amd64 libsm6 amd64 2:1.2.2-1+b3 [33.3 kB] Get:175 http://deb.debian.org/debian stretch/main amd64 libxt6 amd64 1:1.1.5-1 [188 kB] Get:176 http://deb.debian.org/debian stretch/main amd64 libxmu6 amd64 2:1.1.2-2 [60.3 kB] Get:177 http://deb.debian.org/debian stretch/main amd64 libxpm4 amd64 1:3.5.12-1 [49.1 kB] Get:178 http://deb.debian.org/debian stretch/main amd64 libxaw7 amd64 2:1.0.13-1+b2 [201 kB] Get:179 http://deb.debian.org/debian stretch/main amd64 libxcb-shape0 amd64 1.12-1 [96.2 kB] Get:180 http://deb.debian.org/debian stretch/main amd64 libxft2 amd64 2.3.2-1+b2 [56.5 kB] Get:181 http://deb.debian.org/debian stretch/main amd64 libxmuu1 amd64 2:1.1.2-2 [23.5 kB] Get:182 http://deb.debian.org/debian stretch/main amd64 libxv1 amd64 2:1.0.11-1 [24.6 kB] Get:183 http://deb.debian.org/debian stretch/main amd64 libxxf86dga1 amd64 2:1.1.4-1+b3 [22.1 kB] Get:184 http://deb.debian.org/debian stretch/main amd64 x11-utils amd64 7.7+3+b1 [202 kB] Get:185 http://deb.debian.org/debian stretch/main amd64 libatk-wrapper-java all 0.33.3-13+deb9u1 [44.1 kB] Get:186 http://deb.debian.org/debian stretch/main amd64 libatk-wrapper-java-jni amd64 0.33.3-13+deb9u1 [37.5 kB] Get:187 http://deb.debian.org/debian stretch/main amd64 libasound2-data all 1.1.3-5 [173 kB] Get:188 http://deb.debian.org/debian stretch/main amd64 libasound2 amd64 1.1.3-5 [497 kB] Get:189 http://deb.debian.org/debian stretch/main amd64 libgif7 amd64 5.1.4-0.4 [43.1 kB] Get:190 http://deb.debian.org/debian stretch/main amd64 libasyncns0 amd64 0.8-6 [12.5 kB] Get:191 http://deb.debian.org/debian stretch/main amd64 libflac8 amd64 1.3.2-1 [221 kB] Get:192 http://deb.debian.org/debian stretch/main amd64 libvorbis0a amd64 1.3.5-4+deb9u2 [91.7 kB] Get:193 http://deb.debian.org/debian stretch/main amd64 libvorbisenc2 amd64 1.3.5-4+deb9u2 [79.4 kB] Get:194 http://deb.debian.org/debian stretch/main amd64 libsndfile1 amd64 1.0.27-3 [248 kB] Get:195 http://deb.debian.org/debian stretch/main amd64 libpulse0 amd64 10.0-1+deb9u1 [283 kB] Get:196 http://deb.debian.org/debian stretch/main amd64 openjdk-8-jre amd64 8u252-b09-1~deb9u1 [69.8 kB] Get:197 http://deb.debian.org/debian stretch/main amd64 default-jre amd64 2:1.8-58+deb9u1 [930 B] Get:198 http://deb.debian.org/debian stretch/main amd64 jaligner all 1.0+dfsg-4 [128 kB] Get:199 http://deb.debian.org/debian stretch/main amd64 libjellyfish-2.0-2 amd64 2.2.6-1+b1 [62.2 kB] Get:200 http://deb.debian.org/debian stretch/main amd64 jellyfish amd64 2.2.6-1+b1 [349 kB] Get:201 http://deb.debian.org/debian stretch/main amd64 libatomic1 amd64 6.3.0-18+deb9u1 [8966 B] Get:202 http://deb.debian.org/debian stretch/main amd64 libblas-common amd64 3.7.0-2 [14.2 kB] Get:203 http://deb.debian.org/debian stretch/main amd64 libquadmath0 amd64 6.3.0-18+deb9u1 [131 kB] Get:204 http://deb.debian.org/debian stretch/main amd64 libgfortran3 amd64 6.3.0-18+deb9u1 [265 kB] Get:205 http://deb.debian.org/debian stretch/main amd64 libblas3 amd64 3.7.0-2 [155 kB] Get:206 http://deb.debian.org/debian stretch/main amd64 libconcurrent-java all 1.3.4-4 [133 kB] Get:207 http://deb.debian.org/debian stretch/main amd64 libcolt-free-java all 1.2.0+dfsg-4 [405 kB] Get:208 http://deb.debian.org/debian stretch/main amd64 libcommons-collections4-java all 4.1-1 [656 kB] Get:209 http://deb.debian.org/debian stretch/main amd64 libcurl3-gnutls amd64 7.52.1-5+deb9u10 [290 kB] Get:210 http://deb.debian.org/debian stretch/main amd64 libencode-locale-perl all 1.05-1 [13.7 kB] Get:211 http://deb.debian.org/debian stretch/main amd64 libtimedate-perl all 2.3000-2+deb9u1 [37.9 kB] Get:212 http://deb.debian.org/debian stretch/main amd64 libhttp-date-perl all 6.02-1 [10.7 kB] Get:213 http://deb.debian.org/debian stretch/main amd64 libfile-listing-perl all 6.04-1 [10.3 kB] Get:214 http://deb.debian.org/debian stretch/main amd64 libgetopt-java all 1.0.14+dfsg-3 [24.9 kB] Get:215 http://deb.debian.org/debian stretch/main amd64 libhtml-tagset-perl all 3.20-3 [12.7 kB] Get:216 http://deb.debian.org/debian stretch/main amd64 liburi-perl all 1.71-1 [88.6 kB] Get:217 http://deb.debian.org/debian stretch/main amd64 libhtml-parser-perl amd64 3.72-3 [104 kB] Get:218 http://deb.debian.org/debian stretch/main amd64 libhtml-tree-perl all 5.03-2 [210 kB] Get:219 http://deb.debian.org/debian stretch/main amd64 libhts1 amd64 1.3.2-2 [257 kB] Get:220 http://deb.debian.org/debian stretch/main amd64 libio-html-perl all 1.001-1 [17.6 kB] Get:221 http://deb.debian.org/debian stretch/main amd64 liblwp-mediatypes-perl all 6.02-1 [22.1 kB] Get:222 http://deb.debian.org/debian stretch/main amd64 libhttp-message-perl all 6.11-1 [75.9 kB] Get:223 http://deb.debian.org/debian stretch/main amd64 libhttp-cookies-perl all 6.01-1 [17.4 kB] Get:224 http://deb.debian.org/debian stretch/main amd64 libhttp-negotiate-perl all 6.00-2 [13.6 kB] Get:225 http://deb.debian.org/debian stretch/main amd64 perl-openssl-defaults amd64 3 [6782 B] Get:226 http://deb.debian.org/debian stretch/main amd64 libnet-ssleay-perl amd64 1.80-1 [285 kB] Get:227 http://deb.debian.org/debian stretch/main amd64 libio-socket-ssl-perl all 2.044-1 [195 kB] Get:228 http://deb.debian.org/debian stretch/main amd64 libvecmath-java all 1.5.2-5 [76.9 kB] Get:229 http://deb.debian.org/debian stretch/main amd64 libjung-free-java all 2.0.1+dfsg-1 [976 kB] Get:230 http://deb.debian.org/debian stretch/main amd64 liblapack3 amd64 3.7.0-2 [2141 kB] Get:231 http://deb.debian.org/debian stretch/main amd64 libnet-http-perl all 6.12-1 [23.8 kB] Get:232 http://deb.debian.org/debian stretch/main amd64 libwww-robotrules-perl all 6.01-1 [14.3 kB] Get:233 http://deb.debian.org/debian stretch/main amd64 libwww-perl all 6.15-1 [195 kB] Get:234 http://deb.debian.org/debian stretch/main amd64 liblwp-protocol-https-perl all 6.06-2 [9582 B] Get:235 http://deb.debian.org/debian stretch/main amd64 libncurses5 amd64 6.0+20161126-1+deb9u2 [93.4 kB] Get:236 http://deb.debian.org/debian stretch/main amd64 libpaper1 amd64 1.1.24+nmu5 [21.6 kB] Get:237 http://deb.debian.org/debian stretch/main amd64 libpaper-utils amd64 1.1.24+nmu5 [17.6 kB] Get:238 http://deb.debian.org/debian stretch/main amd64 libtcl8.6 amd64 8.6.6+dfsg-1+b1 [985 kB] Get:239 http://deb.debian.org/debian stretch/main amd64 libtk8.6 amd64 8.6.6-1+b1 [754 kB] Get:240 http://deb.debian.org/debian stretch/main amd64 zip amd64 3.0-11+b1 [234 kB] Get:241 http://deb.debian.org/debian stretch/main amd64 unzip amd64 6.0-21+deb9u2 [172 kB] Get:242 http://deb.debian.org/debian stretch/main amd64 xdg-utils all 1.1.1-1+deb9u2 [71.5 kB] Get:243 http://deb.debian.org/debian stretch/main amd64 r-base-core amd64 3.3.3-1 [21.2 MB] Get:244 http://deb.debian.org/debian stretch/main amd64 r-cran-littler amd64 0.3.1-1 [59.1 kB] Get:245 http://deb.debian.org/debian stretch/main amd64 littler all 0.3.1-1 [11.7 kB] Get:246 http://deb.debian.org/debian stretch/main amd64 parafly amd64 0.0.2013.01.21-3+b1 [16.4 kB] Get:247 http://deb.debian.org/debian stretch/main amd64 r-bioc-limma amd64 3.30.8+dfsg-1 [1055 kB] Get:248 http://deb.debian.org/debian stretch/main amd64 r-bioc-edger amd64 3.14.0+dfsg-1 [543 kB] Get:249 http://deb.debian.org/debian stretch/main amd64 r-cran-digest amd64 0.6.11-1 [112 kB] Get:250 http://deb.debian.org/debian stretch/main amd64 r-cran-gtable all 0.2.0-1 [65.1 kB] Get:251 http://deb.debian.org/debian stretch/main amd64 r-cran-mass amd64 7.3-45-1 [1017 kB] Get:252 http://deb.debian.org/debian stretch/main amd64 r-cran-pkgkitten all 0.1.4-1 [18.7 kB] Get:253 http://deb.debian.org/debian stretch/main amd64 r-cran-rcpp amd64 0.12.9-1 [2168 kB] Get:254 http://deb.debian.org/debian stretch/main amd64 r-cran-plyr amd64 1.8.4-1 [727 kB] Get:255 http://deb.debian.org/debian stretch/main amd64 r-cran-stringi amd64 1.1.2-1 [606 kB] Get:256 http://deb.debian.org/debian stretch/main amd64 r-cran-magrittr amd64 1.5-3 [147 kB] Get:257 http://deb.debian.org/debian stretch/main amd64 r-cran-stringr all 1.1.0-1 [117 kB] Get:258 http://deb.debian.org/debian stretch/main amd64 r-cran-reshape2 amd64 1.4.2-1 [87.5 kB] Get:259 http://deb.debian.org/debian stretch/main amd64 r-cran-rcolorbrewer all 1.1-2-1 [26.0 kB] Get:260 http://deb.debian.org/debian stretch/main amd64 r-cran-dichromat all 2.0.0-3 [146 kB] Get:261 http://deb.debian.org/debian stretch/main amd64 r-cran-colorspace amd64 1.3-2-1 [388 kB] Get:262 http://deb.debian.org/debian stretch/main amd64 r-cran-munsell all 0.4.3-1 [127 kB] Get:263 http://deb.debian.org/debian stretch/main amd64 r-cran-labeling all 0.3-1 [39.9 kB] Get:264 http://deb.debian.org/debian stretch/main amd64 r-cran-scales amd64 0.4.1-1 [200 kB] Get:265 http://deb.debian.org/debian stretch/main amd64 r-cran-assertthat all 0.1-1 [43.3 kB] Get:266 http://deb.debian.org/debian stretch/main amd64 r-cran-lazyeval amd64 0.2.0-1 [112 kB] Get:267 http://deb.debian.org/debian stretch/main amd64 r-cran-tibble amd64 1.2-1 [121 kB] Get:268 http://deb.debian.org/debian stretch/main amd64 r-cran-ggplot2 all 2.2.1-2 [2658 kB] Get:269 http://deb.debian.org/debian stretch/main amd64 r-bioc-qvalue all 2.6.0-1 [2788 kB] Get:270 http://deb.debian.org/debian stretch/main amd64 r-cran-cluster amd64 2.0.5-1 [490 kB] Get:271 http://deb.debian.org/debian stretch/main amd64 bowtie amd64 1.1.2-6 [1618 kB] Get:272 http://deb.debian.org/debian stretch/main amd64 libtbb2 amd64 4.3~20150611-2 [136 kB] Get:273 http://deb.debian.org/debian stretch/main amd64 bowtie2 amd64 2.3.0-2 [1166 kB] Get:274 http://deb.debian.org/debian stretch/main amd64 rsem amd64 1.2.31+dfsg-1 [765 kB] Get:275 http://deb.debian.org/debian stretch/main amd64 samtools amd64 1.3.1-3 [254 kB] Get:276 http://deb.debian.org/debian stretch/main amd64 transdecoder all 3.0.1+dfsg-1 [62.8 kB] Get:277 http://deb.debian.org/debian stretch/main amd64 libjbzip2-java all 0.9.1-3 [39.9 kB] Get:278 http://deb.debian.org/debian stretch/main amd64 trimmomatic all 0.36+dfsg-1 [116 kB] Get:279 http://deb.debian.org/debian stretch/main amd64 trinityrnaseq amd64 2.2.0+dfsg-2+b1 [1748 kB] debconf: delaying package configuration, since apt-utils is not installed 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Setting up perl (5.24.1-3+deb9u7) ... update-alternatives: using /usr/bin/prename to provide /usr/bin/rename (rename) in auto mode Setting up libprotobuf10:amd64 (3.0.0-9) ... Setting up libogg0:amd64 (1.3.2-1) ... Setting up libssl1.0.2:amd64 (1.0.2u-1~deb9u1) ... Setting up libatk1.0-data (2.22.0-1) ... Setting up libx11-xcb1:amd64 (2:1.6.4-3+deb9u1) ... Setting up libgmp10:amd64 (2:6.1.2+dfsg-1) ... Setting up libpixman-1-0:amd64 (0.34.0-1) ... Setting up libblas3 (3.7.0-2) ... update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide /usr/lib/libblas.so.3 (libblas.so.3) in auto mode Setting up libssh2-1:amd64 (1.7.0-1+deb9u1) ... Setting up liblwp-mediatypes-perl (6.02-1) ... Setting up libvecmath-java (1.5.2-5) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up libepoxy0:amd64 (1.3.1-2) ... Setting up libunistring0:amd64 (0.9.6+really0.9.3-0.1) ... Setting up liburi-perl (1.71-1) ... Setting up libssl1.1:amd64 (1.1.0l-1~deb9u1) ... Setting up openssl (1.1.0l-1~deb9u1) ... Setting up libsqlite3-0:amd64 (3.16.2-5+deb9u1) ... Setting up libfontenc1:amd64 (1:1.1.3-1+b2) ... Setting up libxkbcommon0:amd64 (0.7.1-2~deb9u1) ... Setting up libnet-http-perl (6.12-1) ... Setting up libffi6:amd64 (3.2.1-6) ... Setting up libtcl8.6:amd64 (8.6.6+dfsg-1+b1) ... Setting up libthai-data (0.1.26-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up libkeyutils1:amd64 (1.5.9-9) ... Setting up libvorbis0a:amd64 (1.3.5-4+deb9u2) ... Setting up x11-common (1:7.7+19) ... update-rc.d: warning: start and stop actions are no longer supported; falling back to defaults invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up xdg-utils (1.1.1-1+deb9u2) ... Setting up ca-certificates (20200601~deb9u1) ... Updating certificates in /etc/ssl/certs... 126 added, 0 removed; done. Setting up hicolor-icon-theme (0.15-1) ... Setting up libgetopt-java (1.0.14+dfsg-3) ... Setting up libwww-robotrules-perl (6.01-1) ... Setting up libx11-data (2:1.6.4-3+deb9u1) ... Setting up libpython2.7-stdlib:amd64 (2.7.13-2+deb9u3) ... Setting up libxau6:amd64 (1:1.0.8-1) ... Setting up libidn11:amd64 (1.33-1+deb9u1) ... Setting up libjellyfish-2.0-2 (2.2.6-1+b1) ... Setting up libdbus-1-3:amd64 (1.10.32-0+deb9u1) ... Setting up libboost-system1.62.0:amd64 (1.62.0+dfsg-4) ... Setting up libwrap0:amd64 (7.6.q-26) ... Setting up libavahi-common-data:amd64 (0.6.32-2) ... Setting up libwayland-server0:amd64 (1.12.0-1+deb9u1) ... Setting up netbase (5.4) ... Setting up libhtml-tagset-perl (3.20-3) ... Setting up libpaper1:amd64 (1.1.24+nmu5) ... Creating config file /etc/papersize with new version Setting up cd-hit (4.6.6-2) ... Setting up libpaper-utils (1.1.24+nmu5) ... Setting up fontconfig-config (2.11.0-6.7) ... Setting up libidn2-0:amd64 (0.16-1+deb9u1) ... Setting up libencode-locale-perl (1.05-1) ... Setting up libtimedate-perl (2.3000-2+deb9u1) ... Setting up libboost-thread1.62.0:amd64 (1.62.0+dfsg-4) ... Setting up perl-openssl-defaults:amd64 (3) ... Setting up libpsl5:amd64 (0.17.0-3) ... Setting up liblapack3 (3.7.0-2) ... update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide /usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode Setting up libglib2.0-0:amd64 (2.50.3-2+deb9u2) ... Setting up libio-html-perl (1.001-1) ... Setting up libwayland-client0:amd64 (1.12.0-1+deb9u1) ... Setting up libgbm1:amd64 (13.0.6-1+b2) ... Setting up transdecoder (3.0.1+dfsg-1) ... Setting up libflac8:amd64 (1.3.2-1) ... Setting up python2.7 (2.7.13-2+deb9u3) ... Setting up libnss3:amd64 (2:3.26.2-1.1+deb9u1) ... Setting up libharfbuzz0b:amd64 (1.4.2-1) ... Setting up glib-networking-services (2.50.0-1+deb9u1) ... Setting up libthai0:amd64 (0.1.26-1) ... Setting up libkrb5support0:amd64 (1.15-1+deb9u1) ... Setting up libjson-glib-1.0-0:amd64 (1.2.6-1) ... Setting up libhogweed4:amd64 (3.3-1+b2) ... Setting up libcroco3:amd64 (0.6.11-3) ... Setting up libpython-stdlib:amd64 (2.7.13-2) ... Setting up libatk1.0-0:amd64 (2.22.0-1) ... Setting up libp11-kit0:amd64 (0.23.3-2) ... Setting up libboost-filesystem1.62.0:amd64 (1.62.0+dfsg-4) ... Setting up libhtml-parser-perl (3.72-3) ... Setting up jellyfish (2.2.6-1+b1) ... Setting up libice6:amd64 (2:1.0.9-2) ... Setting up libdconf1:amd64 (0.26.0-2+b1) ... Setting up shared-mime-info (1.8-1+deb9u1) ... Setting up libavahi-common3:amd64 (0.6.32-2) ... Setting up libcolord2:amd64 (1.3.3-2) ... Setting up libvorbisenc2:amd64 (1.3.5-4+deb9u2) ... Setting up libxcb1:amd64 (1.12-1) ... Setting up libwayland-cursor0:amd64 (1.12.0-1+deb9u1) ... Setting up python (2.7.13-2) ... Setting up libxcb-present0:amd64 (1.12-1) ... Setting up libfontconfig1:amd64 (2.11.0-6.7+b1) ... Setting up libxcb-dri2-0:amd64 (1.12-1) ... Setting up libsm6:amd64 (2:1.2.2-1+b3) ... Setting up libxcb-dri3-0:amd64 (1.12-1) ... Setting up libk5crypto3:amd64 (1.15-1+deb9u1) ... Setting up libxcb-glx0:amd64 (1.12-1) ... Setting up libxcb-xfixes0:amd64 (1.12-1) ... Setting up libhttp-date-perl (6.02-1) ... Setting up libxcb-render0:amd64 (1.12-1) ... Setting up bowtie (1.1.2-6) ... Setting up berkeley-express (1.5.1-3+b1) ... Setting up dconf-service (0.26.0-2+b1) ... Setting up libnet-ssleay-perl (1.80-1) ... Setting up libgnutls30:amd64 (3.5.8-5+deb9u5) ... Setting up libx11-6:amd64 (2:1.6.4-3+deb9u1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-1+b1) ... Setting up libio-socket-ssl-perl (2.044-1) ... Setting up libxmuu1:amd64 (2:1.1.2-2) ... Setting up bowtie2 (2.3.0-2) ... Setting up libhtml-tree-perl (5.03-2) ... Setting up libxcb-sync1:amd64 (1.12-1) ... Setting up libsndfile1:amd64 (1.0.27-3) ... Setting up libldap-2.4-2:amd64 (2.4.44+dfsg-5+deb9u4) ... Setting up libfile-listing-perl (6.04-1) ... Setting up libxcomposite1:amd64 (1:0.4.4-2) ... Setting up libxcb-shm0:amd64 (1.12-1) ... Setting up libxpm4:amd64 (1:3.5.12-1) ... Setting up libxt6:amd64 (1:1.1.5-1) ... Setting up libxcb-shape0:amd64 (1.12-1) ... Setting up libxrender1:amd64 (1:0.9.10-1) ... Setting up libhttp-message-perl (6.11-1) ... Setting up libavahi-client3:amd64 (0.6.32-2) ... Setting up libkrb5-3:amd64 (1.15-1+deb9u1) ... Setting up libxft2:amd64 (2.3.2-1+b2) ... Setting up dconf-gsettings-backend:amd64 (0.26.0-2+b1) ... Setting up fontconfig (2.11.0-6.7+b1) ... Regenerating fonts cache... done. Setting up libhttp-negotiate-perl (6.00-2) ... Setting up libegl1-mesa:amd64 (13.0.6-1+b2) ... Setting up libxext6:amd64 (2:1.3.3-1+b2) ... Setting up libxfixes3:amd64 (1:5.0.3-1) ... Setting up gsettings-desktop-schemas (3.22.0-1) ... Setting up libhttp-cookies-perl (6.01-1) ... Setting up libgtk-3-common (3.22.11-1) ... Setting up libatspi2.0-0:amd64 (2.22.0-6+deb9u1) ... Setting up libxss1:amd64 (1:1.2.2-1) ... Setting up libgdk-pixbuf2.0-0:amd64 (2.36.5-2+deb9u2) ... Setting up libxmu6:amd64 (2:1.1.2-2) ... Setting up libgssapi-krb5-2:amd64 (1.15-1+deb9u1) ... Setting up gtk-update-icon-cache (3.22.11-1) ... Setting up libxcursor1:amd64 (1:1.1.14-1+deb9u2) ... Setting up libxxf86dga1:amd64 (2:1.1.4-1+b3) ... Setting up glib-networking:amd64 (2.50.0-1+deb9u1) ... Setting up libpango-1.0-0:amd64 (1.40.5-1) ... Setting up libwayland-egl1-mesa:amd64 (13.0.6-1+b2) ... Setting up libatk-bridge2.0-0:amd64 (2.22.0-2) ... Setting up libxv1:amd64 (2:1.0.11-1) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up libxrandr2:amd64 (2:1.5.1-1) ... Setting up libcups2:amd64 (2.2.1-8+deb9u6) ... Setting up libxi6:amd64 (2:1.7.9-1) ... Setting up libxaw7:amd64 (2:1.0.13-1+b2) ... Setting up libcairo2:amd64 (1.14.8-1) ... Setting up libxinerama1:amd64 (2:1.1.3-1+b3) ... Setting up libxdamage1:amd64 (1:1.1.4-2+b3) ... Setting up libcurl3:amd64 (7.52.1-5+deb9u10) ... Setting up libcurl3-gnutls:amd64 (7.52.1-5+deb9u10) ... Setting up libtk8.6:amd64 (8.6.6-1+b1) ... Setting up libcairo-gobject2:amd64 (1.14.8-1) ... Setting up libsoup2.4-1:amd64 (2.56.0-2+deb9u2) ... Setting up libsoup-gnome2.4-1:amd64 (2.56.0-2+deb9u2) ... Setting up libxtst6:amd64 (2:1.2.3-1) ... Setting up libpangoft2-1.0-0:amd64 (1.40.5-1) ... Setting up libgl1-mesa-glx:amd64 (13.0.6-1+b2) ... Setting up librest-0.7-0:amd64 (0.8.0-2) ... Setting up libhts1:amd64 (1.3.2-2) ... Setting up curl (7.52.1-5+deb9u10) ... Setting up x11-utils (7.7+3+b1) ... Setting up libpangocairo-1.0-0:amd64 (1.40.5-1) ... Setting up libpulse0:amd64 (10.0-1+deb9u1) ... Setting up samtools (1.3.1-3) ... Setting up libatk-wrapper-java (0.33.3-13+deb9u1) ... Setting up librsvg2-2:amd64 (2.40.16-1+b1) ... Setting up r-base-core (3.3.3-1) ... Creating config file /etc/R/Renviron with new version Setting up r-cran-littler (0.3.1-1) ... Setting up rsem (1.2.31+dfsg-1) ... Setting up littler (0.3.1-1) ... Setting up r-cran-gtable (0.2.0-1) ... Setting up librsvg2-common:amd64 (2.40.16-1+b1) ... Setting up r-cran-assertthat (0.1-1) ... Setting up r-cran-rcolorbrewer (1.1-2-1) ... Setting up r-cran-stringi (1.1.2-1) ... Setting up r-cran-pkgkitten (0.1.4-1) ... Setting up r-cran-rcpp (0.12.9-1) ... Setting up r-cran-labeling (0.3-1) ... Setting up r-cran-colorspace (1.3-2-1) ... Setting up r-cran-mass (7.3-45-1) ... Setting up r-cran-plyr (1.8.4-1) ... Setting up r-cran-digest (0.6.11-1) ... Setting up r-bioc-limma (3.30.8+dfsg-1) ... Setting up r-bioc-edger (3.14.0+dfsg-1) ... Setting up r-cran-magrittr (1.5-3) ... Setting up r-cran-cluster (2.0.5-1) ... Setting up r-cran-dichromat (2.0.0-3) ... Setting up adwaita-icon-theme (3.22.0-1+deb9u1) ... update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode Setting up libgtk2.0-0:amd64 (2.24.31-2) ... Setting up r-cran-lazyeval (0.2.0-1) ... Setting up r-cran-stringr (1.1.0-1) ... Setting up gnome-icon-theme (3.12.0-2) ... update-alternatives: using /usr/share/icons/gnome/scalable/places/debian-swirl.svg to provide /usr/share/icons/gnome/scalable/places/start-here.svg (start-here.svg) in auto mode Setting up libgtk-3-0:amd64 (3.22.11-1) ... Setting up libatk-wrapper-java-jni:amd64 (0.33.3-13+deb9u1) ... Setting up r-cran-munsell (0.4.3-1) ... Setting up r-cran-reshape2 (1.4.2-1) ... Setting up r-cran-scales (0.4.1-1) ... Setting up r-cran-tibble (1.2-1) ... Setting up r-cran-ggplot2 (2.2.1-2) ... Setting up r-bioc-qvalue (2.6.0-1) ... Setting up openjdk-8-jre-headless:amd64 (8u252-b09-1~deb9u1) ... update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/rmid to provide /usr/bin/rmid (rmid) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/jjs to provide /usr/bin/jjs (jjs) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/pack200 to provide /usr/bin/pack200 (pack200) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/unpack200 to provide /usr/bin/unpack200 (unpack200) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/orbd to provide /usr/bin/orbd (orbd) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/servertool to provide /usr/bin/servertool (servertool) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/tnameserv to provide /usr/bin/tnameserv (tnameserv) in auto mode update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up libconcurrent-java (1.3.4-4) ... Setting up ca-certificates-java (20170929~deb9u3) ... 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: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: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 liblwp-protocol-https-perl (6.06-2) ... Setting up openjdk-8-jre:amd64 (8u252-b09-1~deb9u1) ... update-alternatives: using /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/policytool to provide /usr/bin/policytool (policytool) in auto mode Setting up libcolt-free-java (1.2.0+dfsg-4) ... Setting up default-jre-headless (2:1.8-58+deb9u1) ... Setting up libwww-perl (6.15-1) ... Setting up libjung-free-java (2.0.1+dfsg-1) ... Setting up default-jre (2:1.8-58+deb9u1) ... Setting up jaligner (1.0+dfsg-4) ... Setting up trimmomatic (0.36+dfsg-1) ... Setting up trinityrnaseq (2.2.0+dfsg-2+b1) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Processing triggers for ca-certificates (20200601~deb9u1) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. done. Processing triggers for libgdk-pixbuf2.0-0:amd64 (2.36.5-2+deb9u2) ... 0m59.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'apt-get', '-y', 'install', 'trinityrnaseq'] 0m59.1s INFO: Running scripts post_install 0m59.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/post_install_exceptions'] 0m59.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/post_install_exceptions'] 0m59.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa'] 1m0.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa'] 1m0.1s DEBUG: Upgrading /srv/piuparts.debian.org/tmp/tmpfmkzlmxa to buster 1m0.1s DEBUG: sources.list: deb http://deb.debian.org/debian/ buster main 1m0.1s INFO: Running scripts pre_distupgrade 1m0.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 1m0.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_distupgrade_allow_unauthenticated'] 1m0.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_distupgrade_exceptions'] 1m0.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_distupgrade_exceptions'] 1m0.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 1m0.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_distupgrade_foreign_architecture_i386'] 1m0.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_distupgrade_zz_database-server'] 1m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_distupgrade_zz_database-server'] 1m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 1m0.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_distupgrade_zz_upgrade_early'] 1m0.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'apt-get', 'update'] 1m4.9s DUMP: Get:1 http://deb.debian.org/debian buster InRelease [122 kB] Get:2 http://deb.debian.org/debian buster/main amd64 Packages [7909 kB] Get:3 http://deb.debian.org/debian buster/main Translation-en [5969 kB] Fetched 14.0 MB in 3s (3794 kB/s) Reading package lists... 1m4.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'apt-get', 'update'] 1m4.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'apt-get', '-y', 'upgrade'] 1m37.6s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following package was automatically installed and is no longer required: cd-hit Use 'sudo apt autoremove' to remove it. The following packages have been kept back: apt bash berkeley-express curl dash dconf-gsettings-backend dconf-service default-jre default-jre-headless dpkg e2fslibs e2fsprogs glib-networking glib-networking-common glib-networking-services libapt-pkg5.0 libatomic1 libblas3 libcomerr2 libcommons-collections4-java libcups2 libcurl3-gnutls libdconf1 libdrm2 libegl1-mesa libgbm1 libgcc1 libgl1-mesa-glx libglapi-mesa libgnutls30 libgomp1 libgssapi-krb5-2 libgtk-3-0 libhtml-parser-perl libidn2-0 libio-socket-ssl-perl libk5crypto3 libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2 libncurses5 libncursesw5 libnet-ssleay-perl libpango-1.0-0 libpangoft2-1.0-0 libpsl5 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 libreadline7 libss2 libstdc++6 libtbb2 libtiff5 libtinfo5 libwayland-egl1-mesa libwww-perl libxml2 login mount ncurses-base ncurses-bin perl perl-base python python-minimal python2.7 python2.7-minimal r-base-core r-bioc-limma r-bioc-qvalue r-cran-assertthat r-cran-cluster r-cran-colorspace r-cran-dichromat r-cran-digest r-cran-ggplot2 r-cran-gtable r-cran-labeling r-cran-lazyeval r-cran-littler r-cran-magrittr r-cran-mass r-cran-munsell r-cran-pkgkitten r-cran-plyr r-cran-rcolorbrewer r-cran-rcpp r-cran-reshape2 r-cran-scales r-cran-stringi r-cran-stringr r-cran-tibble rsem samtools trinityrnaseq util-linux x11-utils The following packages will be upgraded: adduser adwaita-icon-theme base-files base-passwd bowtie bowtie2 bsdutils ca-certificates ca-certificates-java cd-hit coreutils debconf debian-archive-keyring debianutils diffutils findutils fontconfig fontconfig-config gnome-icon-theme gpgv grep gsettings-desktop-schemas gtk-update-icon-cache gzip hicolor-icon-theme hostname init-system-helpers jaligner java-common jellyfish libacl1 libasound2 libasound2-data libatk-bridge2.0-0 libatk-wrapper-java libatk-wrapper-java-jni libatk1.0-0 libatk1.0-data libatspi2.0-0 libattr1 libaudit-common libaudit1 libavahi-client3 libavahi-common-data libavahi-common3 libblkid1 libbsd0 libbz2-1.0 libc-bin libc6 libcairo-gobject2 libcairo2 libcap-ng0 libcap2 libcolord2 libcolt-free-java libcroco3 libdatrie1 libdb5.3 libdbus-1-3 libdebconfclient0 libepoxy0 libexpat1 libfdisk1 libffi6 libflac8 libfontconfig1 libfreetype6 libgcrypt20 libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common libgetopt-java libgif7 libglib2.0-0 libgmp10 libgpg-error0 libgraphite2-3 libgtk-3-common libgtk2.0-0 libgtk2.0-common libharfbuzz0b libhogweed4 libhtml-tree-perl libhttp-cookies-perl libhttp-message-perl libhttp-negotiate-perl libidn11 libjbzip2-java libjellyfish-2.0-2 libjpeg62-turbo libjson-glib-1.0-0 libjson-glib-1.0-common libkeyutils1 liblcms2-2 libldap-common liblwp-protocol-https-perl liblz4-1 liblzma5 libmount1 libnet-http-perl libnettle6 libnghttp2-14 libnspr4 libnss3 libogg0 libp11-kit0 libpam-modules libpam-modules-bin libpam-runtime libpam0g libpangocairo-1.0-0 libpaper-utils libpaper1 libpcre3 libpcsclite1 libpixman-1-0 libpng16-16 libproxy1v5 libpulse0 librest-0.7-0 librsvg2-2 librsvg2-common librtmp1 libsasl2-2 libsasl2-modules-db libselinux1 libsemanage-common libsemanage1 libsepol1 libsm6 libsmartcols1 libsndfile1 libsoup-gnome2.4-1 libsoup2.4-1 libsqlite3-0 libssh2-1 libssl1.1 libsystemd0 libtasn1-6 libtcl8.6 libthai-data libthai0 libtimedate-perl libtk8.6 libudev1 liburi-perl libuuid1 libvecmath-java libvorbis0a libvorbisenc2 libwayland-client0 libwayland-cursor0 libwayland-server0 libwrap0 libwww-robotrules-perl libx11-6 libx11-data libx11-xcb1 libxau6 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-shape0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcursor1 libxdamage1 libxft2 libxinerama1 libxkbcommon0 libxmu6 libxmuu1 libxshmfence1 libxss1 libxt6 littler lsb-base mime-support multiarch-support netbase openssl parafly passwd readline-common sed sensible-utils shared-mime-info sysvinit-utils tar transdecoder trimmomatic tzdata ucf unzip xdg-utils xkb-data zlib1g 201 upgraded, 0 newly installed, 0 to remove and 100 not upgraded. Need to get 77.6 MB of archives. After this operation, 10.9 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian buster/main amd64 base-files amd64 10.3+deb10u13 [69.9 kB] Get:2 http://deb.debian.org/debian buster/main amd64 bsdutils amd64 1:2.33.1-0.1 [121 kB] Get:3 http://deb.debian.org/debian buster/main amd64 libc6 amd64 2.28-10+deb10u1 [2863 kB] Get:4 http://deb.debian.org/debian buster/main amd64 libc-bin amd64 2.28-10+deb10u1 [795 kB] Get:5 http://deb.debian.org/debian buster/main amd64 coreutils amd64 8.30-3 [2708 kB] Get:6 http://deb.debian.org/debian buster/main amd64 debianutils amd64 4.8.6.1 [100 kB] Get:7 http://deb.debian.org/debian buster/main amd64 diffutils amd64 1:3.7-3 [371 kB] Get:8 http://deb.debian.org/debian buster/main amd64 findutils amd64 4.6.0+git+20190209-2 [684 kB] Get:9 http://deb.debian.org/debian buster/main amd64 grep amd64 3.3-1 [373 kB] Get:10 http://deb.debian.org/debian buster/main amd64 gzip amd64 1.9-3+deb10u1 [128 kB] Get:11 http://deb.debian.org/debian buster/main amd64 hostname amd64 3.21 [14.8 kB] Get:12 http://deb.debian.org/debian buster/main amd64 sed amd64 4.7-1 [310 kB] Get:13 http://deb.debian.org/debian buster/main amd64 tar amd64 1.30+dfsg-6 [780 kB] Get:14 http://deb.debian.org/debian buster/main amd64 libdebconfclient0 amd64 0.249 [49.1 kB] Get:15 http://deb.debian.org/debian buster/main amd64 base-passwd amd64 3.5.46 [56.7 kB] Get:16 http://deb.debian.org/debian buster/main amd64 init-system-helpers all 1.56+nmu1 [46.8 kB] Get:17 http://deb.debian.org/debian buster/main amd64 sysvinit-utils amd64 2.93-8 [78.4 kB] Get:18 http://deb.debian.org/debian buster/main amd64 debconf all 1.5.71+deb10u1 [145 kB] Get:19 http://deb.debian.org/debian buster/main amd64 libaudit-common all 1:2.8.4-3 [22.4 kB] Get:20 http://deb.debian.org/debian buster/main amd64 libcap-ng0 amd64 0.7.9-2 [14.3 kB] Get:21 http://deb.debian.org/debian buster/main amd64 libaudit1 amd64 1:2.8.4-3 [57.3 kB] Get:22 http://deb.debian.org/debian buster/main amd64 libpam0g amd64 1.3.1-5 [126 kB] Get:23 http://deb.debian.org/debian buster/main amd64 libpcre3 amd64 2:8.39-12 [341 kB] Get:24 http://deb.debian.org/debian buster/main amd64 libselinux1 amd64 2.8-1+b1 [86.9 kB] Get:25 http://deb.debian.org/debian buster/main amd64 libpam-modules-bin amd64 1.3.1-5 [107 kB] Get:26 http://deb.debian.org/debian buster/main amd64 libpam-modules amd64 1.3.1-5 [309 kB] Get:27 http://deb.debian.org/debian buster/main amd64 libgpg-error0 amd64 1.35-1 [71.1 kB] Get:28 http://deb.debian.org/debian buster/main amd64 libgcrypt20 amd64 1.8.4-5+deb10u1 [556 kB] Get:29 http://deb.debian.org/debian buster/main amd64 libsystemd0 amd64 241-7~deb10u8 [331 kB] Get:30 http://deb.debian.org/debian buster/main amd64 libpam-runtime all 1.3.1-5 [211 kB] Get:31 http://deb.debian.org/debian buster/main amd64 libsepol1 amd64 2.8-1 [263 kB] Get:32 http://deb.debian.org/debian buster/main amd64 libsemanage-common all 2.8-2 [17.7 kB] Get:33 http://deb.debian.org/debian buster/main amd64 libsemanage1 amd64 2.8-2 [96.5 kB] Get:34 http://deb.debian.org/debian buster/main amd64 libbz2-1.0 amd64 1.0.6-9.2~deb10u1 [45.3 kB] Get:35 http://deb.debian.org/debian buster/main amd64 passwd amd64 1:4.5-1.1 [1005 kB] Get:36 http://deb.debian.org/debian buster/main amd64 adduser all 3.118 [240 kB] Get:37 http://deb.debian.org/debian buster/main amd64 debian-archive-keyring all 2019.1+deb10u1 [93.5 kB] Get:38 http://deb.debian.org/debian buster/main amd64 zlib1g amd64 1:1.2.11.dfsg-1+deb10u1 [90.8 kB] Get:39 http://deb.debian.org/debian buster/main amd64 gpgv amd64 2.2.12-1+deb10u2 [584 kB] Get:40 http://deb.debian.org/debian buster/main amd64 sensible-utils all 0.0.12 [15.8 kB] Get:41 http://deb.debian.org/debian buster/main amd64 libattr1 amd64 1:2.4.48-4 [21.3 kB] Get:42 http://deb.debian.org/debian buster/main amd64 libacl1 amd64 2.2.53-4 [30.4 kB] Get:43 http://deb.debian.org/debian buster/main amd64 libuuid1 amd64 2.33.1-0.1 [78.3 kB] Get:44 http://deb.debian.org/debian buster/main amd64 libblkid1 amd64 2.33.1-0.1 [195 kB] Get:45 http://deb.debian.org/debian buster/main amd64 libdb5.3 amd64 5.3.28+dfsg1-0.5 [683 kB] Get:46 http://deb.debian.org/debian buster/main amd64 libfdisk1 amd64 2.33.1-0.1 [234 kB] Get:47 http://deb.debian.org/debian buster/main amd64 liblz4-1 amd64 1.8.3-1+deb10u1 [53.3 kB] Get:48 http://deb.debian.org/debian buster/main amd64 liblzma5 amd64 5.2.4-1+deb10u1 [153 kB] Get:49 http://deb.debian.org/debian buster/main amd64 libmount1 amd64 2.33.1-0.1 [207 kB] Get:50 http://deb.debian.org/debian buster/main amd64 libsmartcols1 amd64 2.33.1-0.1 [150 kB] Get:51 http://deb.debian.org/debian buster/main amd64 libudev1 amd64 241-7~deb10u8 [151 kB] Get:52 http://deb.debian.org/debian buster/main amd64 tzdata all 2021a-0+deb10u6 [265 kB] Get:53 http://deb.debian.org/debian buster/main amd64 netbase all 5.6 [19.4 kB] Get:54 http://deb.debian.org/debian buster/main amd64 readline-common all 7.0-5 [70.6 kB] Get:55 http://deb.debian.org/debian buster/main amd64 mime-support all 3.62 [37.2 kB] Get:56 http://deb.debian.org/debian buster/main amd64 ucf all 3.0038+nmu1 [69.0 kB] Get:57 http://deb.debian.org/debian buster/main amd64 hicolor-icon-theme all 0.17-2 [11.4 kB] Get:58 http://deb.debian.org/debian buster/main amd64 libffi6 amd64 3.2.1-9 [20.8 kB] Get:59 http://deb.debian.org/debian buster/main amd64 libglib2.0-0 amd64 2.58.3-2+deb10u3 [1259 kB] Get:60 http://deb.debian.org/debian buster/main amd64 libjpeg62-turbo amd64 1:1.5.2-2+deb10u1 [133 kB] Get:61 http://deb.debian.org/debian buster/main amd64 libpng16-16 amd64 1.6.36-6 [292 kB] Get:62 http://deb.debian.org/debian buster/main amd64 libx11-data all 2:1.6.7-1+deb10u2 [299 kB] Get:63 http://deb.debian.org/debian buster/main amd64 xkb-data all 2.26-2 [681 kB] Get:64 http://deb.debian.org/debian buster/main amd64 libxau6 amd64 1:1.0.8-1+b2 [19.9 kB] Get:65 http://deb.debian.org/debian buster/main amd64 libxcb1 amd64 1.13.1-2 [137 kB] Get:66 http://deb.debian.org/debian buster/main amd64 libx11-6 amd64 2:1.6.7-1+deb10u2 [757 kB] Get:67 http://deb.debian.org/debian buster/main amd64 shared-mime-info amd64 1.10-1 [766 kB] Get:68 http://deb.debian.org/debian buster/main amd64 libgdk-pixbuf2.0-0 amd64 2.38.1+dfsg-1 [177 kB] Get:69 http://deb.debian.org/debian buster/main amd64 libgdk-pixbuf2.0-common all 2.38.1+dfsg-1 [316 kB] Get:70 http://deb.debian.org/debian buster/main amd64 gtk-update-icon-cache amd64 3.24.5-1 [81.7 kB] Get:71 http://deb.debian.org/debian buster/main amd64 libexpat1 amd64 2.2.6-2+deb10u4 [108 kB] Get:72 http://deb.debian.org/debian buster/main amd64 libfreetype6 amd64 2.9.1-3+deb10u3 [380 kB] Get:73 http://deb.debian.org/debian buster/main amd64 libfontconfig1 amd64 2.13.1-2 [346 kB] Get:74 http://deb.debian.org/debian buster/main amd64 fontconfig-config all 2.13.1-2 [280 kB] Get:75 http://deb.debian.org/debian buster/main amd64 libpixman-1-0 amd64 0.36.0-1 [537 kB] Get:76 http://deb.debian.org/debian buster/main amd64 libxcb-render0 amd64 1.13.1-2 [109 kB] Get:77 http://deb.debian.org/debian buster/main amd64 libxcb-shm0 amd64 1.13.1-2 [99.2 kB] Get:78 http://deb.debian.org/debian buster/main amd64 libcairo2 amd64 1.16.0-4+deb10u1 [688 kB] Get:79 http://deb.debian.org/debian buster/main amd64 libcroco3 amd64 0.6.12-3 [145 kB] Get:80 http://deb.debian.org/debian buster/main amd64 libpangocairo-1.0-0 amd64 1.42.4-8~deb10u1 [55.7 kB] Get:81 http://deb.debian.org/debian buster/main amd64 librsvg2-common amd64 2.44.10-2.1+deb10u3 [23.6 kB] Get:82 http://deb.debian.org/debian buster/main amd64 librsvg2-2 amd64 2.44.10-2.1+deb10u3 [1258 kB] Get:83 http://deb.debian.org/debian buster/main amd64 adwaita-icon-theme all 3.30.1-1 [11.7 MB] Get:84 http://deb.debian.org/debian buster/main amd64 bowtie amd64 1.2.2+dfsg-4 [1670 kB] Get:85 http://deb.debian.org/debian buster/main amd64 bowtie2 amd64 2.3.4.3-1 [1188 kB] Get:86 http://deb.debian.org/debian buster/main amd64 libssl1.1 amd64 1.1.1n-0+deb10u3 [1551 kB] Get:87 http://deb.debian.org/debian buster/main amd64 openssl amd64 1.1.1n-0+deb10u3 [855 kB] Get:88 http://deb.debian.org/debian buster/main amd64 ca-certificates all 20200601~deb10u2 [166 kB] Get:89 http://deb.debian.org/debian buster/main amd64 libnspr4 amd64 2:4.20-1 [112 kB] Get:90 http://deb.debian.org/debian buster/main amd64 libsqlite3-0 amd64 3.27.2-3+deb10u1 [641 kB] Get:91 http://deb.debian.org/debian buster/main amd64 libnss3 amd64 2:3.42.1-1+deb10u5 [1160 kB] Get:92 http://deb.debian.org/debian buster/main amd64 ca-certificates-java all 20190405 [15.7 kB] Get:93 http://deb.debian.org/debian buster/main amd64 cd-hit amd64 4.6.8-2 [521 kB] Get:94 http://deb.debian.org/debian buster/main amd64 fontconfig amd64 2.13.1-2 [405 kB] Get:95 http://deb.debian.org/debian buster/main amd64 gnome-icon-theme all 3.12.0-3 [9869 kB] Get:96 http://deb.debian.org/debian buster/main amd64 gsettings-desktop-schemas all 3.28.1-1 [529 kB] Get:97 http://deb.debian.org/debian buster/main amd64 jaligner all 1.0+dfsg-6 [131 kB] Get:98 http://deb.debian.org/debian buster/main amd64 java-common all 0.71 [14.4 kB] Get:99 http://deb.debian.org/debian buster/main amd64 jellyfish amd64 2.2.10-2 [361 kB] Get:100 http://deb.debian.org/debian buster/main amd64 libjellyfish-2.0-2 amd64 2.2.10-2 [64.6 kB] Get:101 http://deb.debian.org/debian buster/main amd64 libasound2 amd64 1.1.8-1 [361 kB] Get:102 http://deb.debian.org/debian buster/main amd64 libasound2-data all 1.1.8-1 [59.6 kB] Get:103 http://deb.debian.org/debian buster/main amd64 libatk1.0-0 amd64 2.30.0-2 [50.6 kB] Get:104 http://deb.debian.org/debian buster/main amd64 libatk1.0-data all 2.30.0-2 [145 kB] Get:105 http://deb.debian.org/debian buster/main amd64 libdbus-1-3 amd64 1.12.20-0+deb10u1 [215 kB] Get:106 http://deb.debian.org/debian buster/main amd64 libatspi2.0-0 amd64 2.30.0-7 [65.0 kB] Get:107 http://deb.debian.org/debian buster/main amd64 libatk-bridge2.0-0 amd64 2.30.0-5 [61.6 kB] Get:108 http://deb.debian.org/debian buster/main amd64 libatk-wrapper-java all 0.33.3-22+deb10u1 [45.5 kB] Get:109 http://deb.debian.org/debian buster/main amd64 libcairo-gobject2 amd64 1.16.0-4+deb10u1 [125 kB] Get:110 http://deb.debian.org/debian buster/main amd64 libgtk2.0-common all 2.24.32-3 [2698 kB] Get:111 http://deb.debian.org/debian buster/main amd64 libxcursor1 amd64 1:1.1.15-2 [36.6 kB] Get:112 http://deb.debian.org/debian buster/main amd64 libxdamage1 amd64 1:1.1.4-3+b3 [14.9 kB] Get:113 http://deb.debian.org/debian buster/main amd64 libxinerama1 amd64 2:1.1.4-2 [17.7 kB] Get:114 http://deb.debian.org/debian buster/main amd64 libgtk2.0-0 amd64 2.24.32-3 [1809 kB] Get:115 http://deb.debian.org/debian buster/main amd64 libatk-wrapper-java-jni amd64 0.33.3-22+deb10u1 [39.5 kB] Get:116 http://deb.debian.org/debian buster/main amd64 libavahi-common-data amd64 0.7-4+deb10u1 [122 kB] Get:117 http://deb.debian.org/debian buster/main amd64 libavahi-common3 amd64 0.7-4+deb10u1 [54.4 kB] Get:118 http://deb.debian.org/debian buster/main amd64 libavahi-client3 amd64 0.7-4+deb10u1 [58.2 kB] Get:119 http://deb.debian.org/debian buster/main amd64 libbsd0 amd64 0.9.1-2+deb10u1 [99.5 kB] Get:120 http://deb.debian.org/debian buster/main amd64 libcap2 amd64 1:2.25-2 [17.6 kB] Get:121 http://deb.debian.org/debian buster/main amd64 liblcms2-2 amd64 2.9-3 [145 kB] Get:122 http://deb.debian.org/debian buster/main amd64 libcolord2 amd64 1.4.3-4 [141 kB] Get:123 http://deb.debian.org/debian buster/main amd64 libcolt-free-java all 1.2.0+dfsg-7 [434 kB] Get:124 http://deb.debian.org/debian buster/main amd64 libdatrie1 amd64 0.2.12-2 [39.3 kB] Get:125 http://deb.debian.org/debian buster/main amd64 libepoxy0 amd64 1.5.3-0.1 [190 kB] Get:126 http://deb.debian.org/debian buster/main amd64 libogg0 amd64 1.3.2-1+b1 [21.3 kB] Get:127 http://deb.debian.org/debian buster/main amd64 libflac8 amd64 1.3.2-3+deb10u2 [193 kB] Get:128 http://deb.debian.org/debian buster/main amd64 libgetopt-java all 1.0.14+dfsg-4 [25.5 kB] Get:129 http://deb.debian.org/debian buster/main amd64 libgif7 amd64 5.1.4-3 [43.3 kB] Get:130 http://deb.debian.org/debian buster/main amd64 libgmp10 amd64 2:6.1.2+dfsg-4+deb10u1 [251 kB] Get:131 http://deb.debian.org/debian buster/main amd64 libgraphite2-3 amd64 1.3.13-7 [80.7 kB] Get:132 http://deb.debian.org/debian buster/main amd64 libgtk-3-common all 3.24.5-1 [3678 kB] Get:133 http://deb.debian.org/debian buster/main amd64 libharfbuzz0b amd64 2.3.1-1 [1187 kB] Get:134 http://deb.debian.org/debian buster/main amd64 libhogweed4 amd64 3.4.1-1+deb10u1 [141 kB] Get:135 http://deb.debian.org/debian buster/main amd64 libnettle6 amd64 3.4.1-1+deb10u1 [215 kB] Get:136 http://deb.debian.org/debian buster/main amd64 libhtml-tree-perl all 5.07-2 [213 kB] Get:137 http://deb.debian.org/debian buster/main amd64 liburi-perl all 1.76-1 [89.9 kB] Get:138 http://deb.debian.org/debian buster/main amd64 libhttp-message-perl all 6.18-1 [77.8 kB] Get:139 http://deb.debian.org/debian buster/main amd64 libhttp-cookies-perl all 6.04-1 [17.8 kB] Get:140 http://deb.debian.org/debian buster/main amd64 libhttp-negotiate-perl all 6.01-1 [12.8 kB] Get:141 http://deb.debian.org/debian buster/main amd64 libidn11 amd64 1.33-2.2 [116 kB] Get:142 http://deb.debian.org/debian buster/main amd64 libjbzip2-java all 0.9.1-5 [42.6 kB] Get:143 http://deb.debian.org/debian buster/main amd64 libjson-glib-1.0-common all 1.4.4-2 [52.3 kB] Get:144 http://deb.debian.org/debian buster/main amd64 libjson-glib-1.0-0 amd64 1.4.4-2 [61.2 kB] Get:145 http://deb.debian.org/debian buster/main amd64 libkeyutils1 amd64 1.6-6 [15.0 kB] Get:146 http://deb.debian.org/debian buster/main amd64 libldap-common all 2.4.47+dfsg-3+deb10u7 [90.1 kB] Get:147 http://deb.debian.org/debian buster/main amd64 libnet-http-perl all 6.18-1 [24.5 kB] Get:148 http://deb.debian.org/debian buster/main amd64 liblwp-protocol-https-perl all 6.07-2 [9242 B] Get:149 http://deb.debian.org/debian buster/main amd64 libnghttp2-14 amd64 1.36.0-2+deb10u1 [85.0 kB] Get:150 http://deb.debian.org/debian buster/main amd64 libp11-kit0 amd64 0.23.15-2+deb10u1 [316 kB] Get:151 http://deb.debian.org/debian buster/main amd64 libpaper1 amd64 1.1.28 [21.3 kB] Get:152 http://deb.debian.org/debian buster/main amd64 libpaper-utils amd64 1.1.28 [18.0 kB] Get:153 http://deb.debian.org/debian buster/main amd64 libpcsclite1 amd64 1.8.24-1 [58.5 kB] Get:154 http://deb.debian.org/debian buster/main amd64 libproxy1v5 amd64 0.4.15-5+deb10u1 [56.1 kB] Get:155 http://deb.debian.org/debian buster/main amd64 libsm6 amd64 2:1.2.3-1 [35.1 kB] Get:156 http://deb.debian.org/debian buster/main amd64 libvorbisenc2 amd64 1.3.6-2 [80.2 kB] Get:157 http://deb.debian.org/debian buster/main amd64 libvorbis0a amd64 1.3.6-2 [93.5 kB] Get:158 http://deb.debian.org/debian buster/main amd64 libsndfile1 amd64 1.0.28-6+deb10u1 [253 kB] Get:159 http://deb.debian.org/debian buster/main amd64 libwrap0 amd64 7.6.q-28 [58.7 kB] Get:160 http://deb.debian.org/debian buster/main amd64 libx11-xcb1 amd64 2:1.6.7-1+deb10u2 [191 kB] Get:161 http://deb.debian.org/debian buster/main amd64 libpulse0 amd64 12.2-4+deb10u1 [281 kB] Get:162 http://deb.debian.org/debian buster/main amd64 libsoup2.4-1 amd64 2.64.2-2 [253 kB] Get:163 http://deb.debian.org/debian buster/main amd64 libsoup-gnome2.4-1 amd64 2.64.2-2 [18.0 kB] Get:164 http://deb.debian.org/debian buster/main amd64 librest-0.7-0 amd64 0.8.1-1 [33.7 kB] Get:165 http://deb.debian.org/debian buster/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2 [60.5 kB] Get:166 http://deb.debian.org/debian buster/main amd64 libsasl2-modules-db amd64 2.1.27+dfsg-1+deb10u2 [69.2 kB] Get:167 http://deb.debian.org/debian buster/main amd64 libsasl2-2 amd64 2.1.27+dfsg-1+deb10u2 [106 kB] Get:168 http://deb.debian.org/debian buster/main amd64 libssh2-1 amd64 1.8.0-2.1 [140 kB] Get:169 http://deb.debian.org/debian buster/main amd64 libtasn1-6 amd64 4.13-3 [51.9 kB] Get:170 http://deb.debian.org/debian buster/main amd64 libtcl8.6 amd64 8.6.9+dfsg-2 [1005 kB] Get:171 http://deb.debian.org/debian buster/main amd64 libthai-data all 0.1.28-2 [170 kB] Get:172 http://deb.debian.org/debian buster/main amd64 libthai0 amd64 0.1.28-2 [54.1 kB] Get:173 http://deb.debian.org/debian buster/main amd64 libtimedate-perl all 2.3000-2+deb10u1 [38.1 kB] Get:174 http://deb.debian.org/debian buster/main amd64 libxft2 amd64 2.3.2-2 [57.2 kB] Get:175 http://deb.debian.org/debian buster/main amd64 libxss1 amd64 1:1.2.3-1 [17.8 kB] Get:176 http://deb.debian.org/debian buster/main amd64 libtk8.6 amd64 8.6.9-2 [768 kB] Get:177 http://deb.debian.org/debian buster/main amd64 libvecmath-java all 1.5.2-7 [97.0 kB] Get:178 http://deb.debian.org/debian buster/main amd64 libwayland-client0 amd64 1.16.0-1 [26.4 kB] Get:179 http://deb.debian.org/debian buster/main amd64 libwayland-cursor0 amd64 1.16.0-1 [14.1 kB] Get:180 http://deb.debian.org/debian buster/main amd64 libwayland-server0 amd64 1.16.0-1 [32.5 kB] Get:181 http://deb.debian.org/debian buster/main amd64 libwww-robotrules-perl all 6.02-1 [12.9 kB] Get:182 http://deb.debian.org/debian buster/main amd64 libxcb-dri2-0 amd64 1.13.1-2 [101 kB] Get:183 http://deb.debian.org/debian buster/main amd64 libxcb-dri3-0 amd64 1.13.1-2 [100 kB] Get:184 http://deb.debian.org/debian buster/main amd64 libxcb-glx0 amd64 1.13.1-2 [116 kB] Get:185 http://deb.debian.org/debian buster/main amd64 libxcb-present0 amd64 1.13.1-2 [99.1 kB] Get:186 http://deb.debian.org/debian buster/main amd64 libxcb-shape0 amd64 1.13.1-2 [99.5 kB] Get:187 http://deb.debian.org/debian buster/main amd64 libxcb-sync1 amd64 1.13.1-2 [103 kB] Get:188 http://deb.debian.org/debian buster/main amd64 libxcb-xfixes0 amd64 1.13.1-2 [103 kB] Get:189 http://deb.debian.org/debian buster/main amd64 libxkbcommon0 amd64 0.8.2-1 [123 kB] Get:190 http://deb.debian.org/debian buster/main amd64 libxt6 amd64 1:1.1.5-1+b3 [190 kB] Get:191 http://deb.debian.org/debian buster/main amd64 libxmu6 amd64 2:1.1.2-2+b3 [60.8 kB] Get:192 http://deb.debian.org/debian buster/main amd64 libxmuu1 amd64 2:1.1.2-2+b3 [23.9 kB] Get:193 http://deb.debian.org/debian buster/main amd64 libxshmfence1 amd64 1.3-1 [8820 B] Get:194 http://deb.debian.org/debian buster/main amd64 littler all 0.3.6-1 [13.6 kB] Get:195 http://deb.debian.org/debian buster/main amd64 lsb-base all 10.2019051400 [28.4 kB] Get:196 http://deb.debian.org/debian buster/main amd64 multiarch-support amd64 2.28-10+deb10u1 [216 kB] Get:197 http://deb.debian.org/debian buster/main amd64 parafly amd64 0.0.2013.01.21-4 [15.8 kB] Get:198 http://deb.debian.org/debian buster/main amd64 transdecoder all 5.0.1-2 [187 kB] Get:199 http://deb.debian.org/debian buster/main amd64 trimmomatic all 0.38+dfsg-1 [757 kB] Get:200 http://deb.debian.org/debian buster/main amd64 unzip amd64 6.0-23+deb10u2 [172 kB] Get:201 http://deb.debian.org/debian buster/main amd64 xdg-utils all 1.1.3-1+deb10u1 [73.7 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 77.6 MB in 2s (30.6 MB/s) (Reading database ... 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Installing new version of config file /etc/apt/trusted.gpg.d/debian-archive-buster-security-automatic.gpg ... Installing new version of config file /etc/apt/trusted.gpg.d/debian-archive-buster-stable.gpg ... Installing new version of config file /etc/apt/trusted.gpg.d/debian-archive-stretch-automatic.gpg ... Installing new version of config file /etc/apt/trusted.gpg.d/debian-archive-stretch-security-automatic.gpg ... Installing new version of config file /etc/apt/trusted.gpg.d/debian-archive-stretch-stable.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-jessie-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-jessie-security-automatic.gpg ... Removing obsolete conffile /etc/apt/trusted.gpg.d/debian-archive-jessie-stable.gpg ... (Reading database ... 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(Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 29974 files and directories currently installed.) Preparing to unpack .../libfdisk1_2.33.1-0.1_amd64.deb ... Unpacking libfdisk1:amd64 (2.33.1-0.1) over (2.29.2-1+deb9u1) ... Setting up libfdisk1:amd64 (2.33.1-0.1) ... (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 ... 29974 files and directories currently installed.) Preparing to unpack .../liblz4-1_1.8.3-1+deb10u1_amd64.deb ... Unpacking liblz4-1:amd64 (1.8.3-1+deb10u1) over (0.0~r131-2+b1) ... Setting up liblz4-1:amd64 (1.8.3-1+deb10u1) ... (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 ... 29973 files and directories currently installed.) Preparing to unpack .../liblzma5_5.2.4-1+deb10u1_amd64.deb ... Unpacking liblzma5:amd64 (5.2.4-1+deb10u1) over (5.2.2-1.2+b1) ... Setting up liblzma5:amd64 (5.2.4-1+deb10u1) ... (Reading database ... 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Setting up libsndfile1:amd64 (1.0.28-6+deb10u1) ... Setting up libxcursor1:amd64 (1:1.1.15-2) ... Setting up libxcb-shm0:amd64 (1.13.1-2) ... Setting up libxt6:amd64 (1:1.1.5-1+b3) ... Setting up libxcb-shape0:amd64 (1.13.1-2) ... Setting up libavahi-client3:amd64 (0.7-4+deb10u1) ... Setting up libxft2:amd64 (2.3.2-2) ... Setting up fontconfig (2.13.1-2) ... Regenerating fonts cache... done. Setting up libcairo2:amd64 (1.16.0-4+deb10u1) ... Setting up libxinerama1:amd64 (2:1.1.4-2) ... Setting up libxdamage1:amd64 (1:1.1.4-3+b3) ... Setting up libatspi2.0-0:amd64 (2.30.0-7) ... Setting up libxss1:amd64 (1:1.2.3-1) ... Setting up libgdk-pixbuf2.0-0:amd64 (2.38.1+dfsg-1) ... Setting up libcairo-gobject2:amd64 (1.16.0-4+deb10u1) ... Setting up libpangocairo-1.0-0:amd64 (1.42.4-8~deb10u1) ... Setting up libpulse0:amd64 (12.2-4+deb10u1) ... Setting up libxmu6:amd64 (2:1.1.2-2+b3) ... Setting up gtk-update-icon-cache (3.24.5-1) ... Setting up libatk-bridge2.0-0:amd64 (2.30.0-5) ... Setting up librsvg2-2:amd64 (2.44.10-2.1+deb10u3) ... Setting up libtk8.6:amd64 (8.6.9-2) ... Setting up librsvg2-common:amd64 (2.44.10-2.1+deb10u3) ... Setting up adwaita-icon-theme (3.30.1-1) ... Setting up libgtk2.0-0:amd64 (2.24.32-3) ... Setting up gnome-icon-theme (3.12.0-3) ... Setting up libatk-wrapper-java-jni:amd64 (0.33.3-22+deb10u1) ... 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. Processing triggers for libgdk-pixbuf2.0-0:amd64 (2.38.1+dfsg-1) ... 1m37.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'apt-get', '-y', 'upgrade'] 1m37.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'apt-get', '-yf', 'dist-upgrade'] 2m26.8s DUMP: Reading package lists... Building dependency tree... Reading state information... Calculating upgrade... The following packages were automatically installed and are no longer required: cd-hit libasyncns0 libbamtools2.4.0 libblas-common libboost-date-time1.62.0 libboost-filesystem1.62.0 libboost-program-options1.62.0 libboost-system1.62.0 libboost-thread1.62.0 libegl-mesa0 libegl1 libegl1-mesa libflac8 libgbm1 libgdbm3 libgfortran3 libgl1-mesa-glx libhts1 libicu57 libogg0 libperl5.24 libprotobuf10 libpulse0 libsndfile1 libssl1.0.2 libunistring0 libvorbis0a libvorbisenc2 libwayland-egl1-mesa libwayland-server0 libwrap0 libxcb-xfixes0 openjdk-8-jre r-bioc-limma Use 'sudo apt autoremove' to remove them. The following packages will be REMOVED: libcurl3 r-bioc-edger The following NEW packages will be installed: dbus dbus-user-session dmsetup fdisk fonts-font-awesome fonts-lato fonts-roboto-slab gcc-8-base libapache-pom-java libapparmor1 libargon2-1 libbamtools2.5.1 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 libcom-err2 libcommons-parent-java libcryptsetup12 libcurl4 libdeflate0 libdevmapper1.02.1 libdivsufsort3 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libedit2 libegl-mesa0 libegl1 libelf1 libext2fs2 libfribidi0 libgdbm-compat4 libgdbm6 libgfortran5 libgl1 libgl1-mesa-dri libglvnd0 libglx-mesa0 libglx0 libhts2 libicu63 libip4tc0 libjemalloc2 libjs-jquery libjs-modernizr libjs-sphinxdoc libjs-underscore libjson-c3 libkmod2 libllvm7 liblmdb0 libmbedcrypto3 libmbedtls12 libmbedx509-0 libmpdec2 libncurses6 libncursesw6 libpam-systemd libpciaccess0 libperl5.28 libprotobuf17 libpython2-stdlib libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libseccomp2 libsensors-config libsensors5 libstaden-read13 libtinfo6 libtry-tiny-perl libunistring2 libwayland-egl1 libwebp6 libzstd1 ncbi-blast+ ncbi-data openjdk-11-jre openjdk-11-jre-headless perl-modules-5.28 python2 python2-minimal python3 python3-minimal python3-numpy python3-pkg-resources python3.7 python3.7-minimal r-bioc-biocgenerics r-cran-cli r-cran-crayon r-cran-fansi r-cran-glue r-cran-lattice r-cran-matrix r-cran-mgcv r-cran-nlme r-cran-pillar r-cran-pkgconfig r-cran-r6 r-cran-rlang r-cran-utf8 r-cran-viridislite r-cran-withr salmon sphinx-rtd-theme-common systemd systemd-sysv The following packages will be upgraded: apt bash berkeley-express curl dash dconf-gsettings-backend dconf-service default-jre default-jre-headless dpkg e2fslibs e2fsprogs glib-networking glib-networking-common glib-networking-services libapt-pkg5.0 libatomic1 libblas3 libcomerr2 libcommons-collections4-java libcups2 libcurl3-gnutls libdconf1 libdrm2 libegl1-mesa libgbm1 libgcc1 libgl1-mesa-glx libglapi-mesa libgnutls30 libgomp1 libgssapi-krb5-2 libgtk-3-0 libhtml-parser-perl libidn2-0 libio-socket-ssl-perl libk5crypto3 libkrb5-3 libkrb5support0 liblapack3 libldap-2.4-2 libncurses5 libncursesw5 libnet-ssleay-perl libpango-1.0-0 libpangoft2-1.0-0 libpsl5 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 libreadline7 libss2 libstdc++6 libtbb2 libtiff5 libtinfo5 libwayland-egl1-mesa libwww-perl libxml2 login mount ncurses-base ncurses-bin perl perl-base python python-minimal python2.7 python2.7-minimal r-base-core r-bioc-limma r-bioc-qvalue r-cran-assertthat r-cran-cluster r-cran-colorspace r-cran-dichromat r-cran-digest r-cran-ggplot2 r-cran-gtable r-cran-labeling r-cran-lazyeval r-cran-littler r-cran-magrittr r-cran-mass r-cran-munsell r-cran-pkgkitten r-cran-plyr r-cran-rcolorbrewer r-cran-rcpp r-cran-reshape2 r-cran-scales r-cran-stringi r-cran-stringr r-cran-tibble rsem samtools trinityrnaseq util-linux x11-utils 100 upgraded, 117 newly installed, 2 to remove and 0 not upgraded. Need to get 246 MB of archives. After this operation, 756 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian buster/main amd64 libtinfo6 amd64 6.1+20181013-2+deb10u2 [325 kB] Get:2 http://deb.debian.org/debian buster/main amd64 bash amd64 5.0-4 [1378 kB] Get:3 http://deb.debian.org/debian buster/main amd64 libzstd1 amd64 1.3.8+dfsg-3+deb10u2 [237 kB] Get:4 http://deb.debian.org/debian buster/main amd64 libunistring2 amd64 0.9.10-1 [381 kB] Get:5 http://deb.debian.org/debian buster/main amd64 libidn2-0 amd64 2.0.5-1+deb10u1 [76.7 kB] Get:6 http://deb.debian.org/debian buster/main amd64 libgnutls30 amd64 3.6.7-4+deb10u8 [1126 kB] Get:7 http://deb.debian.org/debian buster/main amd64 libseccomp2 amd64 2.3.3-4 [41.4 kB] Get:8 http://deb.debian.org/debian buster/main amd64 gcc-8-base amd64 8.3.0-6 [191 kB] Get:9 http://deb.debian.org/debian buster/main amd64 libgcc1 amd64 1:8.3.0-6 [40.6 kB] Get:10 http://deb.debian.org/debian buster/main amd64 libstdc++6 amd64 8.3.0-6 [395 kB] Get:11 http://deb.debian.org/debian buster/main amd64 libapt-pkg5.0 amd64 1.8.2.3 [967 kB] Get:12 http://deb.debian.org/debian buster/main amd64 apt amd64 1.8.2.3 [1418 kB] Get:13 http://deb.debian.org/debian buster/main amd64 dpkg amd64 1.19.8 [2210 kB] Get:14 http://deb.debian.org/debian buster/main amd64 dash amd64 0.5.10.2-5 [112 kB] Get:15 http://deb.debian.org/debian buster/main amd64 libcom-err2 amd64 1.44.5-1+deb10u3 [68.4 kB] Get:16 http://deb.debian.org/debian buster/main amd64 libcomerr2 amd64 1.44.5-1+deb10u3 [64.2 kB] Get:17 http://deb.debian.org/debian buster/main amd64 libext2fs2 amd64 1.44.5-1+deb10u3 [221 kB] Get:18 http://deb.debian.org/debian buster/main amd64 e2fslibs amd64 1.44.5-1+deb10u3 [64.2 kB] Get:19 http://deb.debian.org/debian buster/main amd64 e2fsprogs amd64 1.44.5-1+deb10u3 [576 kB] Get:20 http://deb.debian.org/debian buster/main amd64 libncursesw6 amd64 6.1+20181013-2+deb10u2 [132 kB] Get:21 http://deb.debian.org/debian buster/main amd64 fdisk amd64 2.33.1-0.1 [179 kB] Get:22 http://deb.debian.org/debian buster/main amd64 login amd64 1:4.5-1.1 [751 kB] Get:23 http://deb.debian.org/debian buster/main amd64 util-linux amd64 2.33.1-0.1 [1062 kB] Get:24 http://deb.debian.org/debian buster/main amd64 mount amd64 2.33.1-0.1 [174 kB] Get:25 http://deb.debian.org/debian buster/main amd64 ncurses-bin amd64 6.1+20181013-2+deb10u2 [406 kB] Get:26 http://deb.debian.org/debian buster/main amd64 libnet-ssleay-perl amd64 1.85-2+deb10u1 [308 kB] Get:27 http://deb.debian.org/debian buster/main amd64 libhtml-parser-perl amd64 3.72-3+b3 [105 kB] Get:28 http://deb.debian.org/debian buster/main amd64 perl-modules-5.28 all 5.28.1-6+deb10u1 [2873 kB] Get:29 http://deb.debian.org/debian buster/main amd64 libgdbm6 amd64 1.18.1-4 [64.7 kB] Get:30 http://deb.debian.org/debian buster/main amd64 libgdbm-compat4 amd64 1.18.1-4 [44.1 kB] Get:31 http://deb.debian.org/debian buster/main amd64 libperl5.28 amd64 5.28.1-6+deb10u1 [3894 kB] Get:32 http://deb.debian.org/debian buster/main amd64 perl amd64 5.28.1-6+deb10u1 [204 kB] Get:33 http://deb.debian.org/debian buster/main amd64 perl-base amd64 5.28.1-6+deb10u1 [1514 kB] Get:34 http://deb.debian.org/debian buster/main amd64 libncurses5 amd64 6.1+20181013-2+deb10u2 [96.2 kB] Get:35 http://deb.debian.org/debian buster/main amd64 libtinfo5 amd64 6.1+20181013-2+deb10u2 [321 kB] Get:36 http://deb.debian.org/debian buster/main amd64 libncursesw5 amd64 6.1+20181013-2+deb10u2 [118 kB] Get:37 http://deb.debian.org/debian buster/main amd64 ncurses-base all 6.1+20181013-2+deb10u2 [258 kB] Get:38 http://deb.debian.org/debian buster/main amd64 r-cran-labeling all 0.3-3 [61.4 kB] Get:39 http://deb.debian.org/debian buster/main amd64 r-cran-colorspace amd64 1.4-0+dfsg-1 [1580 kB] Get:40 http://deb.debian.org/debian buster/main amd64 r-cran-munsell all 0.5.0-1 [235 kB] Get:41 http://deb.debian.org/debian buster/main amd64 r-cran-r6 all 2.4.0-1 [75.2 kB] Get:42 http://deb.debian.org/debian buster/main amd64 r-cran-rcolorbrewer all 1.1-2-2 [54.3 kB] Get:43 http://deb.debian.org/debian buster/main amd64 libquadmath0 amd64 8.3.0-6 [133 kB] Get:44 http://deb.debian.org/debian buster/main amd64 libgfortran5 amd64 8.3.0-6 [581 kB] Get:45 http://deb.debian.org/debian buster/main amd64 libblas3 amd64 3.8.0-2 [148 kB] Get:46 http://deb.debian.org/debian buster/main amd64 libgomp1 amd64 8.3.0-6 [75.8 kB] Get:47 http://deb.debian.org/debian buster/main amd64 libicu63 amd64 63.1-6+deb10u3 [8293 kB] Get:48 http://deb.debian.org/debian buster/main amd64 liblapack3 amd64 3.8.0-2 [2110 kB] Get:49 http://deb.debian.org/debian buster/main amd64 r-cran-littler amd64 0.3.6-1 [308 kB] Get:50 http://deb.debian.org/debian buster/main amd64 r-cran-pkgkitten all 0.1.4-2 [22.4 kB] Get:51 http://deb.debian.org/debian buster/main amd64 r-cran-rcpp amd64 1.0.0-1 [3381 kB] Get:52 http://deb.debian.org/debian buster/main amd64 r-cran-viridislite all 0.3.0-3 [59.2 kB] Get:53 http://deb.debian.org/debian buster/main amd64 r-cran-scales amd64 1.0.0-2 [546 kB] Get:54 http://deb.debian.org/debian buster/main amd64 r-cran-cluster amd64 2.0.7-1-1+b3 [531 kB] Get:55 http://deb.debian.org/debian buster/main amd64 r-cran-magrittr all 1.5-5 [152 kB] Get:56 http://deb.debian.org/debian buster/main amd64 libgssapi-krb5-2 amd64 1.17-3+deb10u4 [158 kB] Get:57 http://deb.debian.org/debian buster/main amd64 libkrb5-3 amd64 1.17-3+deb10u4 [369 kB] Get:58 http://deb.debian.org/debian buster/main amd64 libk5crypto3 amd64 1.17-3+deb10u4 [122 kB] Get:59 http://deb.debian.org/debian buster/main amd64 libkrb5support0 amd64 1.17-3+deb10u4 [65.9 kB] Get:60 http://deb.debian.org/debian buster/main amd64 libldap-2.4-2 amd64 2.4.47+dfsg-3+deb10u7 [224 kB] Get:61 http://deb.debian.org/debian buster/main amd64 libpsl5 amd64 0.20.2-2 [53.7 kB] Get:62 http://deb.debian.org/debian buster/main amd64 libcurl3-gnutls amd64 7.64.0-4+deb10u2 [330 kB] Get:63 http://deb.debian.org/debian buster/main amd64 libdeflate0 amd64 1.2-1 [55.4 kB] Get:64 http://deb.debian.org/debian buster/main amd64 libhts2 amd64 1.9-12~deb10u1 [305 kB] Get:65 http://deb.debian.org/debian buster/main amd64 libapache-pom-java all 18-1 [4676 B] Get:66 http://deb.debian.org/debian buster/main amd64 libcommons-parent-java all 43-1 [10.8 kB] Get:67 http://deb.debian.org/debian buster/main amd64 libcommons-collections4-java all 4.2-1 [662 kB] Get:68 http://deb.debian.org/debian buster/main amd64 libtry-tiny-perl all 0.30-1 [23.3 kB] Get:69 http://deb.debian.org/debian buster/main amd64 libwww-perl all 6.36-2 [188 kB] Get:70 http://deb.debian.org/debian buster/main amd64 libcups2 amd64 2.2.10-6+deb10u6 [325 kB] Get:71 http://deb.debian.org/debian buster/main amd64 openjdk-11-jre-headless amd64 11.0.16+8-1~deb10u1 [37.3 MB] Get:72 http://deb.debian.org/debian buster/main amd64 libdrm-common all 2.4.97-1 [13.8 kB] Get:73 http://deb.debian.org/debian buster/main amd64 libdrm2 amd64 2.4.97-1 [39.7 kB] Get:74 http://deb.debian.org/debian buster/main amd64 x11-utils amd64 7.7+4 [202 kB] Get:75 http://deb.debian.org/debian buster/main amd64 libgl1-mesa-glx amd64 18.3.6-2+deb10u1 [47.4 kB] Get:76 http://deb.debian.org/debian buster/main amd64 libglapi-mesa amd64 18.3.6-2+deb10u1 [66.3 kB] Get:77 http://deb.debian.org/debian buster/main amd64 libdrm-amdgpu1 amd64 2.4.97-1 [27.3 kB] Get:78 http://deb.debian.org/debian buster/main amd64 libpciaccess0 amd64 0.14-1 [53.5 kB] Get:79 http://deb.debian.org/debian buster/main amd64 libdrm-intel1 amd64 2.4.97-1 [69.8 kB] Get:80 http://deb.debian.org/debian buster/main amd64 libdrm-nouveau2 amd64 2.4.97-1 [26.3 kB] Get:81 http://deb.debian.org/debian buster/main amd64 libdrm-radeon1 amd64 2.4.97-1 [31.1 kB] Get:82 http://deb.debian.org/debian buster/main amd64 libelf1 amd64 0.176-1.1 [161 kB] Get:83 http://deb.debian.org/debian buster/main amd64 libedit2 amd64 3.1-20181209-1 [94.0 kB] Get:84 http://deb.debian.org/debian buster/main amd64 libllvm7 amd64 1:7.0.1-8+deb10u2 [13.1 MB] Get:85 http://deb.debian.org/debian buster/main amd64 libsensors-config all 1:3.5.0-3 [31.6 kB] Get:86 http://deb.debian.org/debian buster/main amd64 libsensors5 amd64 1:3.5.0-3 [52.6 kB] Get:87 http://deb.debian.org/debian buster/main amd64 libgl1-mesa-dri amd64 18.3.6-2+deb10u1 [6685 kB] Get:88 http://deb.debian.org/debian buster/main amd64 libglx-mesa0 amd64 18.3.6-2+deb10u1 [180 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 libglx0 amd64 1.1.0-1 [30.0 kB] Get:91 http://deb.debian.org/debian buster/main amd64 libgl1 amd64 1.1.0-1 [91.1 kB] Get:92 http://deb.debian.org/debian buster/main amd64 openjdk-11-jre amd64 11.0.16+8-1~deb10u1 [174 kB] Get:93 http://deb.debian.org/debian buster/main amd64 default-jre amd64 2:1.11-71 [1044 B] Get:94 http://deb.debian.org/debian buster/main amd64 default-jre-headless amd64 2:1.11-71 [10.9 kB] Get:95 http://deb.debian.org/debian buster/main amd64 libncurses6 amd64 6.1+20181013-2+deb10u2 [102 kB] Get:96 http://deb.debian.org/debian buster/main amd64 samtools amd64 1.9-4 [443 kB] Get:97 http://deb.debian.org/debian buster/main amd64 r-bioc-biocgenerics all 0.28.0-2 [644 kB] Get:98 http://deb.debian.org/debian buster/main amd64 r-cran-digest amd64 0.6.18-1 [136 kB] Get:99 http://deb.debian.org/debian buster/main amd64 r-cran-gtable all 0.2.0-3 [93.6 kB] Get:100 http://deb.debian.org/debian buster/main amd64 r-cran-lazyeval amd64 0.2.1-3 [138 kB] Get:101 http://deb.debian.org/debian buster/main amd64 r-cran-mass amd64 7.3-51.1-1 [1100 kB] Get:102 http://deb.debian.org/debian buster/main amd64 r-cran-lattice amd64 0.20-38-1 [1121 kB] Get:103 http://deb.debian.org/debian buster/main amd64 r-cran-nlme amd64 3.1.137-1+b3 [2223 kB] Get:104 http://deb.debian.org/debian buster/main amd64 r-cran-matrix amd64 1.2-15-1 [3421 kB] Get:105 http://deb.debian.org/debian buster/main amd64 r-cran-mgcv amd64 1.8-27-1 [2665 kB] Get:106 http://deb.debian.org/debian buster/main amd64 r-cran-plyr amd64 1.8.4-2 [813 kB] Get:107 http://deb.debian.org/debian buster/main amd64 r-cran-glue amd64 1.3.0-1 [92.0 kB] Get:108 http://deb.debian.org/debian buster/main amd64 r-cran-stringi amd64 1.2.4-2 [8702 kB] Get:109 http://deb.debian.org/debian buster/main amd64 r-cran-stringr all 1.4.0-1 [198 kB] Get:110 http://deb.debian.org/debian buster/main amd64 r-cran-reshape2 amd64 1.4.3-2 [114 kB] Get:111 http://deb.debian.org/debian buster/main amd64 r-cran-assertthat all 0.2.0-2 [54.4 kB] Get:112 http://deb.debian.org/debian buster/main amd64 r-cran-crayon all 1.3.4-4 [750 kB] Get:113 http://deb.debian.org/debian buster/main amd64 r-cran-cli all 1.0.1-1 [519 kB] Get:114 http://deb.debian.org/debian buster/main amd64 r-cran-fansi amd64 0.4.0-1 [339 kB] Get:115 http://deb.debian.org/debian buster/main amd64 r-cran-utf8 amd64 1.1.4-1+b1 [131 kB] Get:116 http://deb.debian.org/debian buster/main amd64 r-cran-tibble amd64 2.0.1-1 [656 kB] Get:117 http://deb.debian.org/debian buster/main amd64 r-cran-pillar all 1.3.1-1 [203 kB] Get:118 http://deb.debian.org/debian buster/main amd64 r-cran-pkgconfig all 2.0.2-1 [19.4 kB] Get:119 http://deb.debian.org/debian buster/main amd64 r-cran-rlang amd64 0.3.1-2 [1083 kB] Get:120 http://deb.debian.org/debian buster/main amd64 r-cran-withr all 2.1.2-3 [152 kB] Get:121 http://deb.debian.org/debian buster/main amd64 r-cran-ggplot2 all 3.1.0-1 [3740 kB] Get:122 http://deb.debian.org/debian buster/main amd64 r-bioc-qvalue all 2.14.1-1 [2797 kB] Get:123 http://deb.debian.org/debian buster/main amd64 python2.7 amd64 2.7.16-2+deb10u1 [305 kB] Get:124 http://deb.debian.org/debian buster/main amd64 libreadline7 amd64 7.0-5 [151 kB] Get:125 http://deb.debian.org/debian buster/main amd64 libpython2.7-stdlib amd64 2.7.16-2+deb10u1 [1912 kB] Get:126 http://deb.debian.org/debian buster/main amd64 python2.7-minimal amd64 2.7.16-2+deb10u1 [1369 kB] Get:127 http://deb.debian.org/debian buster/main amd64 libpython2.7-minimal amd64 2.7.16-2+deb10u1 [395 kB] Get:128 http://deb.debian.org/debian buster/main amd64 python2-minimal amd64 2.7.16-1 [41.4 kB] Get:129 http://deb.debian.org/debian buster/main amd64 python-minimal amd64 2.7.16-1 [21.0 kB] Get:130 http://deb.debian.org/debian buster/main amd64 python amd64 2.7.16-1 [22.8 kB] Get:131 http://deb.debian.org/debian buster/main amd64 libpython-stdlib amd64 2.7.16-1 [20.8 kB] Get:132 http://deb.debian.org/debian buster/main amd64 libpython2-stdlib amd64 2.7.16-1 [20.8 kB] Get:133 http://deb.debian.org/debian buster/main amd64 python2 amd64 2.7.16-1 [41.6 kB] Get:134 http://deb.debian.org/debian buster/main amd64 rsem amd64 1.3.1+dfsg-1 [36.1 MB] Get:135 http://deb.debian.org/debian buster/main amd64 libbamtools2.5.1 amd64 2.5.1+dfsg-3 [154 kB] Get:136 http://deb.debian.org/debian buster/main amd64 libboost-atomic1.67.0 amd64 1.67.0-13+deb10u1 [226 kB] Get:137 http://deb.debian.org/debian buster/main amd64 libboost-system1.67.0 amd64 1.67.0-13+deb10u1 [229 kB] Get:138 http://deb.debian.org/debian buster/main amd64 libboost-chrono1.67.0 amd64 1.67.0-13+deb10u1 [234 kB] Get:139 http://deb.debian.org/debian buster/main amd64 libboost-date-time1.67.0 amd64 1.67.0-13+deb10u1 [239 kB] Get:140 http://deb.debian.org/debian buster/main amd64 libboost-filesystem1.67.0 amd64 1.67.0-13+deb10u1 [261 kB] Get:141 http://deb.debian.org/debian buster/main amd64 libboost-program-options1.67.0 amd64 1.67.0-13+deb10u1 [357 kB] Get:142 http://deb.debian.org/debian buster/main amd64 libboost-thread1.67.0 amd64 1.67.0-13+deb10u1 [268 kB] Get:143 http://deb.debian.org/debian buster/main amd64 libprotobuf17 amd64 3.6.1.3-2 [814 kB] Get:144 http://deb.debian.org/debian buster/main amd64 berkeley-express amd64 1.5.2+dfsg-1+b2 [237 kB] Get:145 http://deb.debian.org/debian buster/main amd64 trinityrnaseq amd64 2.6.6+dfsg-6 [1838 kB] Get:146 http://deb.debian.org/debian buster/main amd64 r-bioc-limma amd64 3.38.3+dfsg-1 [1662 kB] Get:147 http://deb.debian.org/debian buster/main amd64 r-base-core amd64 3.5.2-1 [23.9 MB] Get:148 http://deb.debian.org/debian buster/main amd64 curl amd64 7.64.0-4+deb10u2 [265 kB] Get:149 http://deb.debian.org/debian buster/main amd64 libcurl4 amd64 7.64.0-4+deb10u2 [332 kB] Get:150 http://deb.debian.org/debian buster/main amd64 libboost-iostreams1.67.0 amd64 1.67.0-13+deb10u1 [249 kB] Get:151 http://deb.debian.org/debian buster/main amd64 libboost-regex1.67.0 amd64 1.67.0-13+deb10u1 [485 kB] Get:152 http://deb.debian.org/debian buster/main amd64 libboost-timer1.67.0 amd64 1.67.0-13+deb10u1 [231 kB] Get:153 http://deb.debian.org/debian buster/main amd64 libdivsufsort3 amd64 2.0.1-4 [44.5 kB] Get:154 http://deb.debian.org/debian buster/main amd64 libjemalloc2 amd64 5.1.0-3 [225 kB] Get:155 http://deb.debian.org/debian buster/main amd64 libstaden-read13 amd64 1.14.11-6 [280 kB] Get:156 http://deb.debian.org/debian buster/main amd64 libatomic1 amd64 8.3.0-6 [9032 B] Get:157 http://deb.debian.org/debian buster/main amd64 libtbb2 amd64 2018~U6-4 [147 kB] Get:158 http://deb.debian.org/debian buster/main amd64 libjs-jquery all 3.3.1~dfsg-3+deb10u1 [332 kB] Get:159 http://deb.debian.org/debian buster/main amd64 libjs-underscore all 1.9.1~dfsg-1+deb10u1 [100.0 kB] Get:160 http://deb.debian.org/debian buster/main amd64 libjs-sphinxdoc all 1.8.4-1 [95.9 kB] Get:161 http://deb.debian.org/debian buster/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-1 [515 kB] Get:162 http://deb.debian.org/debian buster/main amd64 fonts-lato all 2.0-2 [2698 kB] Get:163 http://deb.debian.org/debian buster/main amd64 fonts-roboto-slab all 1.100263+20170512-1 [207 kB] Get:164 http://deb.debian.org/debian buster/main amd64 libjs-modernizr all 2.6.2+ds1-3 [46.7 kB] Get:165 http://deb.debian.org/debian buster/main amd64 sphinx-rtd-theme-common all 0.4.3+dfsg-1 [1021 kB] Get:166 http://deb.debian.org/debian buster/main amd64 salmon amd64 0.12.0+ds1-1+b1 [1354 kB] Get:167 http://deb.debian.org/debian buster/main amd64 libpython3.7-minimal amd64 3.7.3-2+deb10u3 [589 kB] Get:168 http://deb.debian.org/debian buster/main amd64 python3.7-minimal amd64 3.7.3-2+deb10u3 [1737 kB] Get:169 http://deb.debian.org/debian buster/main amd64 python3-minimal amd64 3.7.3-1 [36.6 kB] Get:170 http://deb.debian.org/debian buster/main amd64 libmpdec2 amd64 2.4.2-2 [87.2 kB] Get:171 http://deb.debian.org/debian buster/main amd64 libpython3.7-stdlib amd64 3.7.3-2+deb10u3 [1734 kB] Get:172 http://deb.debian.org/debian buster/main amd64 python3.7 amd64 3.7.3-2+deb10u3 [330 kB] Get:173 http://deb.debian.org/debian buster/main amd64 libpython3-stdlib amd64 3.7.3-1 [20.0 kB] Get:174 http://deb.debian.org/debian buster/main amd64 python3 amd64 3.7.3-1 [61.5 kB] Get:175 http://deb.debian.org/debian buster/main amd64 python3-pkg-resources all 40.8.0-1 [153 kB] Get:176 http://deb.debian.org/debian buster/main amd64 python3-numpy amd64 1:1.16.2-1 [2119 kB] Get:177 http://deb.debian.org/debian buster/main amd64 ncbi-data all 6.1.20170106+dfsg1-0+deb10u2 [3552 kB] Get:178 http://deb.debian.org/debian buster/main amd64 liblmdb0 amd64 0.9.22-1 [45.0 kB] Get:179 http://deb.debian.org/debian buster/main amd64 libmbedcrypto3 amd64 2.16.0-1 [209 kB] Get:180 http://deb.debian.org/debian buster/main amd64 libmbedx509-0 amd64 2.16.0-1 [91.4 kB] Get:181 http://deb.debian.org/debian buster/main amd64 libmbedtls12 amd64 2.16.0-1 [130 kB] Get:182 http://deb.debian.org/debian buster/main amd64 ncbi-blast+ amd64 2.8.1-1+deb10u1 [10.9 MB] Get:183 http://deb.debian.org/debian buster/main amd64 libfribidi0 amd64 1.0.5-3.1+deb10u2 [63.9 kB] Get:184 http://deb.debian.org/debian buster/main amd64 libpango-1.0-0 amd64 1.42.4-8~deb10u1 [186 kB] Get:185 http://deb.debian.org/debian buster/main amd64 libwebp6 amd64 0.6.1-2+deb10u1 [261 kB] Get:186 http://deb.debian.org/debian buster/main amd64 libtiff5 amd64 4.1.0+git191117-2~deb10u4 [271 kB] Get:187 http://deb.debian.org/debian buster/main amd64 libapparmor1 amd64 2.13.2-10 [94.7 kB] Get:188 http://deb.debian.org/debian buster/main amd64 libargon2-1 amd64 0~20171227-0.2 [19.6 kB] Get:189 http://deb.debian.org/debian buster/main amd64 dmsetup amd64 2:1.02.155-3 [90.8 kB] Get:190 http://deb.debian.org/debian buster/main amd64 libdevmapper1.02.1 amd64 2:1.02.155-3 [141 kB] Get:191 http://deb.debian.org/debian buster/main amd64 libjson-c3 amd64 0.12.1+ds-2+deb10u1 [27.3 kB] Get:192 http://deb.debian.org/debian buster/main amd64 libcryptsetup12 amd64 2:2.1.0-5+deb10u2 [193 kB] Get:193 http://deb.debian.org/debian buster/main amd64 libip4tc0 amd64 1.8.2-4 [70.2 kB] Get:194 http://deb.debian.org/debian buster/main amd64 libkmod2 amd64 26-1 [52.7 kB] Get:195 http://deb.debian.org/debian buster/main amd64 systemd amd64 241-7~deb10u8 [3496 kB] Get:196 http://deb.debian.org/debian buster/main amd64 systemd-sysv amd64 241-7~deb10u8 [100 kB] Get:197 http://deb.debian.org/debian buster/main amd64 libss2 amd64 1.44.5-1+deb10u3 [72.9 kB] Get:198 http://deb.debian.org/debian buster/main amd64 dbus amd64 1.12.20-0+deb10u1 [236 kB] Get:199 http://deb.debian.org/debian buster/main amd64 libpam-systemd amd64 241-7~deb10u8 [209 kB] Get:200 http://deb.debian.org/debian buster/main amd64 dbus-user-session amd64 1.12.20-0+deb10u1 [94.5 kB] Get:201 http://deb.debian.org/debian buster/main amd64 dconf-gsettings-backend amd64 0.30.1-2 [28.9 kB] Get:202 http://deb.debian.org/debian buster/main amd64 dconf-service amd64 0.30.1-2 [36.4 kB] Get:203 http://deb.debian.org/debian buster/main amd64 libdconf1 amd64 0.30.1-2 [40.7 kB] Get:204 http://deb.debian.org/debian buster/main amd64 glib-networking-common all 2.58.0-2+deb10u2 [59.5 kB] Get:205 http://deb.debian.org/debian buster/main amd64 glib-networking amd64 2.58.0-2+deb10u2 [54.6 kB] Get:206 http://deb.debian.org/debian buster/main amd64 glib-networking-services amd64 2.58.0-2+deb10u2 [13.7 kB] Get:207 http://deb.debian.org/debian buster/main amd64 libpangoft2-1.0-0 amd64 1.42.4-8~deb10u1 [68.3 kB] Get:208 http://deb.debian.org/debian buster/main amd64 libwayland-egl1-mesa amd64 18.3.6-2+deb10u1 [47.4 kB] Get:209 http://deb.debian.org/debian buster/main amd64 libwayland-egl1 amd64 1.16.0-1 [8204 B] Get:210 http://deb.debian.org/debian buster/main amd64 libxml2 amd64 2.9.4+dfsg1-7+deb10u4 [689 kB] Get:211 http://deb.debian.org/debian buster/main amd64 libgtk-3-0 amd64 3.24.5-1 [2580 kB] Get:212 http://deb.debian.org/debian buster/main amd64 libegl1-mesa amd64 18.3.6-2+deb10u1 [47.4 kB] Get:213 http://deb.debian.org/debian buster/main amd64 libegl1 amd64 1.1.0-1 [33.6 kB] Get:214 http://deb.debian.org/debian buster/main amd64 libgbm1 amd64 18.3.6-2+deb10u1 [67.8 kB] Get:215 http://deb.debian.org/debian buster/main amd64 libegl-mesa0 amd64 18.3.6-2+deb10u1 [135 kB] Get:216 http://deb.debian.org/debian buster/main amd64 libio-socket-ssl-perl all 2.060-3 [207 kB] Get:217 http://deb.debian.org/debian buster/main amd64 r-cran-dichromat all 1:2.0-0-2 [148 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 246 MB in 10s (24.5 MB/s) Selecting previously unselected package libtinfo6:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 30472 files and directories currently installed.) Preparing to unpack .../libtinfo6_6.1+20181013-2+deb10u2_amd64.deb ... Unpacking libtinfo6:amd64 (6.1+20181013-2+deb10u2) ... Setting up libtinfo6:amd64 (6.1+20181013-2+deb10u2) ... (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 ... 30482 files and directories currently installed.) Preparing to unpack .../archives/bash_5.0-4_amd64.deb ... Unpacking bash (5.0-4) over (4.4-5) ... Setting up bash (5.0-4) ... Installing new version of config file /etc/bash.bashrc ... Installing new version of config file /etc/skel/.profile ... update-alternatives: using /usr/share/man/man7/bash-builtins.7.gz to provide /usr/share/man/man7/builtins.7.gz (builtins.7.gz) in auto mode Selecting previously unselected package libzstd1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 30483 files and directories currently installed.) Preparing to unpack .../libzstd1_1.3.8+dfsg-3+deb10u2_amd64.deb ... Unpacking libzstd1:amd64 (1.3.8+dfsg-3+deb10u2) ... Setting up libzstd1:amd64 (1.3.8+dfsg-3+deb10u2) ... Selecting previously unselected package libunistring2:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 30489 files and directories currently installed.) Preparing to unpack .../libunistring2_0.9.10-1_amd64.deb ... Unpacking libunistring2:amd64 (0.9.10-1) ... Setting up libunistring2:amd64 (0.9.10-1) ... (Reading database ... (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 ... 30495 files and directories currently installed.) Preparing to unpack .../libidn2-0_2.0.5-1+deb10u1_amd64.deb ... Unpacking libidn2-0:amd64 (2.0.5-1+deb10u1) over (0.16-1+deb9u1) ... Setting up libidn2-0:amd64 (2.0.5-1+deb10u1) ... (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 ... 30518 files and directories currently installed.) Preparing to unpack .../libgnutls30_3.6.7-4+deb10u8_amd64.deb ... Unpacking libgnutls30:amd64 (3.6.7-4+deb10u8) over (3.5.8-5+deb9u5) ... Setting up libgnutls30:amd64 (3.6.7-4+deb10u8) ... Selecting previously unselected package libseccomp2:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 30519 files and directories currently installed.) Preparing to unpack .../libseccomp2_2.3.3-4_amd64.deb ... Unpacking libseccomp2:amd64 (2.3.3-4) ... Setting up libseccomp2:amd64 (2.3.3-4) ... Selecting previously unselected package gcc-8-base:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 30525 files and directories currently installed.) Preparing to unpack .../gcc-8-base_8.3.0-6_amd64.deb ... Unpacking gcc-8-base:amd64 (8.3.0-6) ... Setting up gcc-8-base:amd64 (8.3.0-6) ... (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 ... 30531 files and directories currently installed.) Preparing to unpack .../libgcc1_1%3a8.3.0-6_amd64.deb ... Unpacking libgcc1:amd64 (1:8.3.0-6) over (1:6.3.0-18+deb9u1) ... Setting up libgcc1:amd64 (1:8.3.0-6) ... (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 ... 30531 files and directories currently installed.) Preparing to unpack .../libstdc++6_8.3.0-6_amd64.deb ... Unpacking libstdc++6:amd64 (8.3.0-6) over (6.3.0-18+deb9u1) ... Setting up libstdc++6:amd64 (8.3.0-6) ... (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 ... 30531 files and directories currently installed.) Preparing to unpack .../archives/apt_1.8.2.3_amd64.deb ... Unpacking apt (1.8.2.3) over (1.4.10) ... Preparing to unpack .../libapt-pkg5.0_1.8.2.3_amd64.deb ... Unpacking libapt-pkg5.0:amd64 (1.8.2.3) over (1.4.10) ... Setting up libapt-pkg5.0:amd64 (1.8.2.3) ... (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 ... 30559 files and directories currently installed.) Preparing to unpack .../archives/dpkg_1.19.8_amd64.deb ... Unpacking dpkg (1.19.8) over (1.18.25) ... Setting up dpkg (1.19.8) ... Installing new version of config file /etc/alternatives/README ... Installing new version of config file /etc/cron.daily/dpkg ... Installing new version of config file /etc/logrotate.d/dpkg ... (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 ... 30557 files and directories currently installed.) Preparing to unpack .../dash_0.5.10.2-5_amd64.deb ... Unpacking dash (0.5.10.2-5) over (0.5.8-2.4) ... Setting up dash (0.5.10.2-5) ... (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 30558 files and directories currently installed.) Preparing to unpack .../libcomerr2_1.44.5-1+deb10u3_amd64.deb ... Unpacking libcomerr2:amd64 (1.44.5-1+deb10u3) over (1.43.4-2+deb9u1) ... Selecting previously unselected package libcom-err2:amd64. Preparing to unpack .../libcom-err2_1.44.5-1+deb10u3_amd64.deb ... Unpacking libcom-err2:amd64 (1.44.5-1+deb10u3) ... Setting up libcom-err2:amd64 (1.44.5-1+deb10u3) ... (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 ... 30561 files and directories currently installed.) Preparing to unpack .../e2fslibs_1.44.5-1+deb10u3_amd64.deb ... Unpacking e2fslibs:amd64 (1.44.5-1+deb10u3) over (1.43.4-2+deb9u1) ... Selecting previously unselected package libext2fs2:amd64. Preparing to unpack .../libext2fs2_1.44.5-1+deb10u3_amd64.deb ... Unpacking libext2fs2:amd64 (1.44.5-1+deb10u3) ... Setting up libext2fs2:amd64 (1.44.5-1+deb10u3) ... (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 ... 30564 files and directories currently installed.) Preparing to unpack .../e2fsprogs_1.44.5-1+deb10u3_amd64.deb ... Unpacking e2fsprogs (1.44.5-1+deb10u3) over (1.43.4-2+deb9u1) ... Setting up e2fsprogs (1.44.5-1+deb10u3) ... Installing new version of config file /etc/mke2fs.conf ... Selecting previously unselected package libncursesw6:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 30547 files and directories currently installed.) Preparing to unpack .../libncursesw6_6.1+20181013-2+deb10u2_amd64.deb ... Unpacking libncursesw6:amd64 (6.1+20181013-2+deb10u2) ... Setting up libncursesw6:amd64 (6.1+20181013-2+deb10u2) ... (Reading database ... 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Setting up libpsl5:amd64 (0.20.2-2) ... Setting up apt (1.8.2.3) ... Installing new version of config file /etc/apt/apt.conf.d/01autoremove ... Installing new version of config file /etc/cron.daily/apt-compat ... Setting up fonts-lato (2.0-2) ... Setting up e2fslibs:amd64 (1.44.5-1+deb10u3) ... Setting up libglvnd0:amd64 (1.1.0-1) ... Setting up libedit2:amd64 (3.1-20181209-1) ... Setting up libsensors-config (1:3.5.0-3) ... Setting up libdeflate0:amd64 (1.2-1) ... Setting up fonts-roboto-slab (1.100263+20170512-1) ... Setting up libldap-2.4-2:amd64 (2.4.47+dfsg-3+deb10u7) ... Setting up libboost-date-time1.67.0:amd64 (1.67.0-13+deb10u1) ... Setting up libjemalloc2:amd64 (5.1.0-3) ... Setting up libgomp1:amd64 (8.3.0-6) ... Setting up libjs-modernizr (2.6.2+ds1-3) ... Setting up libncurses5:amd64 (6.1+20181013-2+deb10u2) ... Setting up libicu63:amd64 (63.1-6+deb10u3) ... Setting up libkrb5support0:amd64 (1.17-3+deb10u4) ... Setting up libdconf1:amd64 (0.30.1-2) ... 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Setting up libcups2:amd64 (2.2.10-6+deb10u6) ... 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 libboost-filesystem1.67.0:amd64 (1.67.0-13+deb10u1) ... Setting up curl (7.64.0-4+deb10u2) ... Setting up glib-networking:amd64 (2.58.0-2+deb10u2) ... Setting up libpangoft2-1.0-0:amd64 (1.42.4-8~deb10u1) ... Setting up libpython3-stdlib:amd64 (3.7.3-1) ... Setting up libdrm-amdgpu1:amd64 (2.4.97-1) ... 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 libgbm1:amd64 (18.3.6-2+deb10u1) ... Setting up libpython2-stdlib:amd64 (2.7.16-1) ... Setting up libdrm-radeon1:amd64 (2.4.97-1) ... Setting up libgtk-3-0:amd64 (3.24.5-1) ... Setting up libdrm-intel1:amd64 (2.4.97-1) ... 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 libgl1-mesa-dri:amd64 (18.3.6-2+deb10u1) ... Setting up libcurl3-gnutls:amd64 (7.64.0-4+deb10u2) ... Setting up dconf-service (0.30.1-2) ... Setting up python3 (3.7.3-1) ... Setting up python2 (2.7.16-1) ... Setting up libpython-stdlib:amd64 (2.7.16-1) ... Setting up perl (5.28.1-6+deb10u1) ... update-alternatives: warning: alternative /usr/bin/prename (part of link group rename) doesn't exist; removing from list of alternatives update-alternatives: warning: /etc/alternatives/rename is dangling; it will be updated with best choice Removing obsolete conffile /etc/perl/sitecustomize.pl ... Setting up libegl-mesa0:amd64 (18.3.6-2+deb10u1) ... Setting up r-base-core (3.5.2-1) ... Installing new version of config file /etc/R/Makeconf ... Installing new version of config file /etc/R/Renviron.site ... Installing new version of config file /etc/R/Rprofile.site ... Installing new version of config file /etc/R/ldpaths ... Installing new version of config file /etc/R/repositories ... Replacing 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 berkeley-express (1.5.2+dfsg-1+b2) ... Setting up r-cran-viridislite (0.3.0-3) ... Setting up libhtml-parser-perl (3.72-3+b3) ... Setting up r-cran-cluster (2.0.7-1-1+b3) ... Setting up libegl1:amd64 (1.1.0-1) ... 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 python (2.7.16-1) ... Setting up r-cran-magrittr (1.5-5) ... Setting up libwayland-egl1-mesa:amd64 (18.3.6-2+deb10u1) ... Setting up libstaden-read13:amd64 (1.14.11-6) ... Setting up r-cran-littler (0.3.6-1) ... Setting up libnet-ssleay-perl (1.85-2+deb10u1) ... Setting up python3-pkg-resources (40.8.0-1) ... Setting up r-cran-rcpp (1.0.0-1) ... 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Setting up r-bioc-qvalue (2.14.1-1) ... Setting up trinityrnaseq (2.6.6+dfsg-6) ... Processing triggers for mime-support (3.62) ... Processing triggers for hicolor-icon-theme (0.17-2) ... Processing triggers for libglib2.0-0:amd64 (2.58.3-2+deb10u3) ... Processing triggers for libc-bin (2.28-10+deb10u1) ... Processing triggers for systemd (241-7~deb10u8) ... Processing triggers for fontconfig (2.13.1-2) ... 2m26.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'apt-get', '-yf', 'dist-upgrade'] 2m26.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 2m28.0s DUMP: f6fc0f2636004ef589309651dfd778f4 - 2m28.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 2m28.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'apt-cache', 'show', '--no-all-versions', 'trinityrnaseq'] 2m28.2s DUMP: 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-en: RNA-Seq De novo Assembly Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes. Description-md5: 2ee7f38dbb99a040c33d6619f4f5668b Homepage: http://trinityrnaseq.github.io/ Section: science Priority: optional Filename: pool/main/t/trinityrnaseq/trinityrnaseq_2.6.6+dfsg-6_amd64.deb Size: 1838012 MD5sum: 66979c39ee852e06ed8c617e67274079 SHA256: 1401b390ee10ca788d291d399192915a55e19f1185dc935d01c08c93662638bb 2m28.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'apt-cache', 'show', '--no-all-versions', 'trinityrnaseq'] 2m28.2s INFO: apt-cache knows about the following packages: trinityrnaseq 2m28.2s INFO: Running scripts pre_install 2m28.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_install_database-server'] 2m28.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_install_database-server'] 2m28.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_install_exceptions'] 2m28.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_install_exceptions'] 2m28.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_install_extras'] 2m28.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_install_extras'] 2m28.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_install_foreign_architecture'] 2m28.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_install_foreign_architecture'] 2m28.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m28.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m28.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'apt-cache', 'policy'] 2m28.3s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian buster/main amd64 Packages release v=10.13,o=Debian,a=oldstable,n=buster,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 2m28.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'apt-cache', 'policy'] 2m28.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'apt-cache', 'policy', 'trinityrnaseq'] 2m28.3s DUMP: trinityrnaseq: Installed: 2.6.6+dfsg-6 Candidate: 2.6.6+dfsg-6 Version table: *** 2.6.6+dfsg-6 500 500 http://deb.debian.org/debian buster/main amd64 Packages 100 /var/lib/dpkg/status 2m28.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'apt-cache', 'policy', 'trinityrnaseq'] 2m28.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'apt-get', '-y', 'install', 'trinityrnaseq'] 2m28.8s DUMP: Reading package lists... Building dependency tree... Reading state information... trinityrnaseq is already the newest version (2.6.6+dfsg-6). The following packages were automatically installed and are no longer required: cd-hit libasyncns0 libbamtools2.4.0 libblas-common libboost-date-time1.62.0 libboost-filesystem1.62.0 libboost-program-options1.62.0 libboost-system1.62.0 libboost-thread1.62.0 libegl-mesa0 libegl1 libegl1-mesa libflac8 libgbm1 libgdbm3 libgfortran3 libgl1-mesa-glx libhts1 libicu57 libncurses5 libogg0 libperl5.24 libprotobuf10 libpulse0 libsndfile1 libssl1.0.2 libunistring0 libvorbis0a libvorbisenc2 libwayland-egl1-mesa libwayland-server0 libwrap0 libxcb-xfixes0 openjdk-8-jre r-bioc-limma Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 2m28.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'apt-get', '-y', 'install', 'trinityrnaseq'] 2m28.8s INFO: Running scripts post_install 2m28.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/post_install_exceptions'] 2m28.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/post_install_exceptions'] 2m28.8s INFO: Running scripts post_distupgrade 2m28.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/post_distupgrade_base_cleanup'] 2m28.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/post_distupgrade_base_cleanup'] 2m28.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/post_distupgrade_exceptions'] 2m28.8s DUMP: Normalized /etc/ca-certificates.conf removed empty directory '/etc/dbus-1/system.d' mode of '/var/lib/polkit-1' changed from 0755 (rwxr-xr-x) to 0700 (rwx------) 2m28.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/post_distupgrade_exceptions'] 2m28.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 2m28.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/post_distupgrade_force-unsafe-io'] 2m28.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/post_distupgrade_squeeze-backports'] 2m28.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/post_distupgrade_squeeze-backports'] 2m28.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/post_distupgrade_zz_backports'] 2m28.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/post_distupgrade_zz_backports'] 2m28.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa'] 2m30.1s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa'] 2m30.1s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa'] 2m31.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa'] 2m31.5s INFO: Running scripts pre_install 2m31.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_install_database-server'] 2m31.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_install_database-server'] 2m31.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_install_exceptions'] 2m31.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_install_exceptions'] 2m31.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_install_extras'] 2m31.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_install_extras'] 2m31.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_install_foreign_architecture'] 2m31.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_install_foreign_architecture'] 2m31.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m31.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_install_foreign_architecture_i386'] 2m31.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'apt-cache', 'policy'] 2m31.6s DUMP: Package files: 100 /var/lib/dpkg/status release a=now 500 http://deb.debian.org/debian buster/main amd64 Packages release v=10.13,o=Debian,a=oldstable,n=buster,l=Debian,c=main,b=amd64 origin deb.debian.org Pinned packages: 2m31.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'apt-cache', 'policy'] 2m31.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'apt-cache', 'policy', 'trinityrnaseq'] 2m31.6s DUMP: trinityrnaseq: Installed: 2.6.6+dfsg-6 Candidate: 2.6.6+dfsg-6 Version table: *** 2.6.6+dfsg-6 500 500 http://deb.debian.org/debian buster/main amd64 Packages 100 /var/lib/dpkg/status 2m31.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'apt-cache', 'policy', 'trinityrnaseq'] 2m31.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'apt-get', '-y', 'install', 'trinityrnaseq=2.6.6+dfsg-6'] 2m32.0s DUMP: Reading package lists... Building dependency tree... Reading state information... trinityrnaseq is already the newest version (2.6.6+dfsg-6). The following packages were automatically installed and are no longer required: cd-hit libasyncns0 libbamtools2.4.0 libblas-common libboost-date-time1.62.0 libboost-filesystem1.62.0 libboost-program-options1.62.0 libboost-system1.62.0 libboost-thread1.62.0 libegl-mesa0 libegl1 libegl1-mesa libflac8 libgbm1 libgdbm3 libgfortran3 libgl1-mesa-glx libhts1 libicu57 libncurses5 libogg0 libperl5.24 libprotobuf10 libpulse0 libsndfile1 libssl1.0.2 libunistring0 libvorbis0a libvorbisenc2 libwayland-egl1-mesa libwayland-server0 libwrap0 libxcb-xfixes0 openjdk-8-jre r-bioc-limma Use 'sudo apt autoremove' to remove them. 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 2m32.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'apt-get', '-y', 'install', 'trinityrnaseq=2.6.6+dfsg-6'] 2m32.0s INFO: Running scripts post_install 2m32.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/post_install_exceptions'] 2m32.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/post_install_exceptions'] 2m32.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa'] 2m33.3s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa'] 2m35.3s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', '-ac', '--ignore-obsolete'] 2m39.9s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', '-ac', '--ignore-obsolete'] 2m39.9s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 2m39.9s DUMP: 0.15.6 2m39.9s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 2m39.9s INFO: Running adequate version 0.15.6 now. 2m39.9s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'trinityrnaseq'] 2m40.0s 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 2m40.0s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'trinityrnaseq'] 2m40.0s 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 2m40.0s ERROR: WARN: Running adequate resulted in inadequate tags found: py-file-not-bytecompiled 2m40.0s INFO: Running scripts pre_remove 2m40.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 2m40.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 2m40.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 2m40.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 2m40.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 2m50.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 2m50.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 2m50.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 2m50.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 2m50.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 2m50.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_remove_exceptions'] 2m50.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/pre_remove_exceptions'] 2m50.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 2m50.5s DUMP: install ok installed adduser adduser 3.118 install ok installed adwaita-icon-theme adwaita-icon-theme 3.30.1-1 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 cd-hit cd-hit 4.6.8-2 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 dbus dbus 1.12.20-0+deb10u1 install ok installed dbus-user-session dbus-user-session 1.12.20-0+deb10u1 install ok installed dconf-gsettings-backend:amd64 dconf-gsettings-backend 0.30.1-2 install ok installed dconf-service dconf-service 0.30.1-2 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 dmsetup dmsetup 2:1.02.155-3 install ok installed dpkg dpkg 1.19.8 install ok installed e2fslibs:amd64 e2fslibs 1.44.5-1+deb10u3 install ok installed e2fsprogs e2fsprogs 1.44.5-1+deb10u3 install ok installed 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-6-base:amd64 gcc-6-base 6.3.0-18+deb9u1 install ok installed gcc-8-base:amd64 gcc-8-base 8.3.0-6 install ok installed glib-networking:amd64 glib-networking 2.58.0-2+deb10u2 install ok installed glib-networking-common glib-networking-common 2.58.0-2+deb10u2 install ok installed glib-networking-services glib-networking-services 2.58.0-2+deb10u2 install ok installed gnome-icon-theme gnome-icon-theme 3.12.0-3 install ok installed gpgv gpgv 2.2.12-1+deb10u2 install ok installed grep grep 3.3-1 install ok installed gsettings-desktop-schemas gsettings-desktop-schemas 3.28.1-1 install ok installed gtk-update-icon-cache gtk-update-icon-cache 3.24.5-1 install ok installed gzip gzip 1.9-3+deb10u1 install ok installed hicolor-icon-theme hicolor-icon-theme 0.17-2 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 libapparmor1:amd64 libapparmor1 2.13.2-10 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.8.2.3 install ok installed libargon2-1:amd64 libargon2-1 0~20171227-0.2 install ok installed libasound2:amd64 libasound2 1.1.8-1 install ok installed libasound2-data libasound2-data 1.1.8-1 install ok installed libasyncns0:amd64 libasyncns0 0.8-6 install ok installed libatk-bridge2.0-0:amd64 libatk-bridge2.0-0 2.30.0-5 install ok installed libatk-wrapper-java libatk-wrapper-java 0.33.3-22+deb10u1 install ok installed libatk-wrapper-java-jni:amd64 libatk-wrapper-java-jni 0.33.3-22+deb10u1 install ok installed libatk1.0-0:amd64 libatk1.0-0 2.30.0-2 install ok installed libatk1.0-data libatk1.0-data 2.30.0-2 install ok installed libatomic1:amd64 libatomic1 8.3.0-6 install ok installed libatspi2.0-0:amd64 libatspi2.0-0 2.30.0-7 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 libbamtools2.4.0 libbamtools2.4.0 2.4.1+dfsg-1 install ok installed libbamtools2.5.1:amd64 libbamtools2.5.1 2.5.1+dfsg-3 install ok installed libblas-common libblas-common 3.7.0-2 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-time1.62.0:amd64 libboost-date-time1.62.0 1.62.0+dfsg-4 install ok installed libboost-date-time1.67.0:amd64 libboost-date-time1.67.0 1.67.0-13+deb10u1 install ok installed libboost-filesystem1.62.0:amd64 libboost-filesystem1.62.0 1.62.0+dfsg-4 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-options1.62.0:amd64 libboost-program-options1.62.0 1.62.0+dfsg-4 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-system1.62.0:amd64 libboost-system1.62.0 1.62.0+dfsg-4 install ok installed libboost-system1.67.0:amd64 libboost-system1.67.0 1.67.0-13+deb10u1 install ok installed libboost-thread1.62.0:amd64 libboost-thread1.62.0 1.62.0+dfsg-4 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 libcairo-gobject2:amd64 libcairo-gobject2 1.16.0-4+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 libcap2:amd64 libcap2 1:2.25-2 install ok installed libcolord2:amd64 libcolord2 1.4.3-4 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 libcomerr2:amd64 libcomerr2 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 libcroco3:amd64 libcroco3 0.6.12-3 install ok installed libcryptsetup12:amd64 libcryptsetup12 2:2.1.0-5+deb10u2 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 libdconf1:amd64 libdconf1 0.30.1-2 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.249 install ok installed libdeflate0:amd64 libdeflate0 1.2-1 install ok installed libdevmapper1.02.1:amd64 libdevmapper1.02.1 2:1.02.155-3 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 libegl-mesa0:amd64 libegl-mesa0 18.3.6-2+deb10u1 install ok installed libegl1:amd64 libegl1 1.1.0-1 install ok installed libegl1-mesa:amd64 libegl1-mesa 18.3.6-2+deb10u1 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 libepoxy0:amd64 libepoxy0 1.5.3-0.1 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 libflac8:amd64 libflac8 1.3.2-3+deb10u2 install ok installed libfontconfig1:amd64 libfontconfig1 2.13.1-2 install ok installed libfontenc1:amd64 libfontenc1 1:1.1.3-1+b2 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 libgbm1:amd64 libgbm1 18.3.6-2+deb10u1 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 libgdbm3:amd64 libgdbm3 1.8.3-14 install ok installed libgdbm6:amd64 libgdbm6 1.18.1-4 install ok installed libgdk-pixbuf2.0-0:amd64 libgdk-pixbuf2.0-0 2.38.1+dfsg-1 install ok installed libgdk-pixbuf2.0-common libgdk-pixbuf2.0-common 2.38.1+dfsg-1 install ok installed libgetopt-java libgetopt-java 1.0.14+dfsg-4 install ok installed libgfortran3:amd64 libgfortran3 6.3.0-18+deb9u1 install ok installed libgfortran5:amd64 libgfortran5 8.3.0-6 install ok installed 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 libgl1-mesa-glx:amd64 libgl1-mesa-glx 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 libgtk-3-0:amd64 libgtk-3-0 3.24.5-1 install ok installed libgtk-3-common libgtk-3-common 3.24.5-1 install ok installed libgtk2.0-0:amd64 libgtk2.0-0 2.24.32-3 install ok installed libgtk2.0-common libgtk2.0-common 2.24.32-3 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 libhts1:amd64 libhts1 1.3.2-2 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 libicu57:amd64 libicu57 57.1-6+deb9u4 install ok installed libicu63:amd64 libicu63 63.1-6+deb10u3 install ok installed libidn11:amd64 libidn11 1.33-2.2 install ok installed libidn2-0:amd64 libidn2-0 2.0.5-1+deb10u1 install ok installed 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 libip4tc0:amd64 libip4tc0 1.8.2-4 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 libjson-c3:amd64 libjson-c3 0.12.1+ds-2+deb10u1 install ok installed libjson-glib-1.0-0:amd64 libjson-glib-1.0-0 1.4.4-2 install ok installed libjson-glib-1.0-common libjson-glib-1.0-common 1.4.4-2 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 libkmod2:amd64 libkmod2 26-1 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 libncurses5:amd64 libncurses5 6.1+20181013-2+deb10u2 install ok installed libncurses6:amd64 libncurses6 6.1+20181013-2+deb10u2 install ok installed libncursesw5:amd64 libncursesw5 6.1+20181013-2+deb10u2 install ok installed libncursesw6:amd64 libncursesw6 6.1+20181013-2+deb10u2 install ok installed 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 libogg0:amd64 libogg0 1.3.2-1+b1 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 libpam-systemd:amd64 libpam-systemd 241-7~deb10u8 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 libperl5.24:amd64 libperl5.24 5.24.1-3+deb9u7 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 libprotobuf10:amd64 libprotobuf10 3.0.0-9 install ok installed libprotobuf17:amd64 libprotobuf17 3.6.1.3-2 install ok installed libproxy1v5:amd64 libproxy1v5 0.4.15-5+deb10u1 install ok installed libpsl5:amd64 libpsl5 0.20.2-2 install ok installed libpulse0:amd64 libpulse0 12.2-4+deb10u1 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 librest-0.7-0:amd64 librest-0.7-0 0.8.1-1 install ok installed librsvg2-2:amd64 librsvg2-2 2.44.10-2.1+deb10u3 install ok installed librsvg2-common:amd64 librsvg2-common 2.44.10-2.1+deb10u3 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 libsndfile1:amd64 libsndfile1 1.0.28-6+deb10u1 install ok installed libsoup-gnome2.4-1:amd64 libsoup-gnome2.4-1 2.64.2-2 install ok installed libsoup2.4-1:amd64 libsoup2.4-1 2.64.2-2 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 libssl1.0.2:amd64 libssl1.0.2 1.0.2u-1~deb9u1 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 libtinfo5:amd64 libtinfo5 6.1+20181013-2+deb10u2 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 libunistring0:amd64 libunistring0 0.9.6+really0.9.3-0.1 install ok installed libunistring2:amd64 libunistring2 0.9.10-1 install ok installed liburi-perl liburi-perl 1.76-1 install ok installed libustr-1.0-1:amd64 libustr-1.0-1 1.0.4-6 install ok installed libuuid1:amd64 libuuid1 2.33.1-0.1 install ok installed libvecmath-java libvecmath-java 1.5.2-7 install ok installed libvorbis0a:amd64 libvorbis0a 1.3.6-2 install ok installed libvorbisenc2:amd64 libvorbisenc2 1.3.6-2 install ok installed libwayland-client0:amd64 libwayland-client0 1.16.0-1 install ok installed libwayland-cursor0:amd64 libwayland-cursor0 1.16.0-1 install ok installed libwayland-egl1:amd64 libwayland-egl1 1.16.0-1 install ok installed libwayland-egl1-mesa:amd64 libwayland-egl1-mesa 18.3.6-2+deb10u1 install ok installed libwayland-server0:amd64 libwayland-server0 1.16.0-1 install ok installed libwebp6:amd64 libwebp6 0.6.1-2+deb10u1 install ok installed libwrap0:amd64 libwrap0 7.6.q-28 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 libxaw7:amd64 libxaw7 2:1.0.13-1+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-shape0:amd64 libxcb-shape0 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 libxcb-xfixes0:amd64 libxcb-xfixes0 1.13.1-2 install ok installed libxcb1:amd64 libxcb1 1.13.1-2 install ok installed libxcomposite1:amd64 libxcomposite1 1:0.4.4-2 install ok installed libxcursor1:amd64 libxcursor1 1:1.1.15-2 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 libxinerama1:amd64 libxinerama1 2:1.1.4-2 install ok installed libxkbcommon0:amd64 libxkbcommon0 0.8.2-1 install ok installed libxml2:amd64 libxml2 2.9.4+dfsg1-7+deb10u4 install ok installed libxmu6:amd64 libxmu6 2:1.1.2-2+b3 install ok installed libxmuu1:amd64 libxmuu1 2:1.1.2-2+b3 install ok installed libxpm4:amd64 libxpm4 1:3.5.12-1 install ok installed libxrandr2:amd64 libxrandr2 2:1.5.1-1 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 libxv1:amd64 libxv1 2:1.0.11-1 install ok installed libxxf86dga1:amd64 libxxf86dga1 2:1.1.4-1+b3 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 multiarch-support multiarch-support 2.28-10+deb10u1 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 openjdk-8-jre:amd64 openjdk-8-jre 8u252-b09-1~deb9u1 install ok installed openjdk-8-jre-headless:amd64 openjdk-8-jre-headless 8u252-b09-1~deb9u1 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-5.24 perl-modules-5.24 5.24.1-3+deb9u7 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-limma r-bioc-limma 3.38.3+dfsg-1 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-dichromat r-cran-dichromat 1:2.0-0-2 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 shared-mime-info shared-mime-info 1.10-1 install ok installed sphinx-rtd-theme-common sphinx-rtd-theme-common 0.4.3+dfsg-1 install ok installed systemd systemd 241-7~deb10u8 install ok installed systemd-sysv systemd-sysv 241-7~deb10u8 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 x11-utils x11-utils 7.7+4 install ok installed xdg-utils xdg-utils 1.1.3-1+deb10u1 install ok installed xkb-data xkb-data 2.26-2 install ok installed zip zip 3.0-11+b1 install ok installed zlib1g:amd64 zlib1g 1:1.2.11.dfsg-1+deb10u1 2m50.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 2m50.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'apt-get', 'remove', 'adwaita-icon-theme', 'berkeley-express', 'bowtie', 'bowtie2', 'ca-certificates', 'ca-certificates-java', 'cd-hit', 'curl', 'dbus', 'dbus-user-session', 'dconf-gsettings-backend:amd64', 'dconf-service', 'default-jre', 'default-jre-headless', 'dmsetup', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-font-awesome', 'fonts-lato', 'fonts-roboto-slab', 'glib-networking:amd64', 'glib-networking-common', 'glib-networking-services', 'gnome-icon-theme', 'gsettings-desktop-schemas', 'gtk-update-icon-cache', 'hicolor-icon-theme', 'jaligner', 'java-common', 'jellyfish', 'libapache-pom-java', 'libapparmor1:amd64', 'libargon2-1:amd64', 'libasound2:amd64', 'libasound2-data', 'libasyncns0:amd64', 'libatk-bridge2.0-0:amd64', 'libatk-wrapper-java', 'libatk-wrapper-java-jni:amd64', 'libatk1.0-0:amd64', 'libatk1.0-data', 'libatomic1:amd64', 'libatspi2.0-0:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbamtools2.4.0', 'libbamtools2.5.1:amd64', 'libblas-common', 'libblas3:amd64', 'libboost-atomic1.67.0:amd64', 'libboost-chrono1.67.0:amd64', 'libboost-date-time1.62.0:amd64', 'libboost-date-time1.67.0:amd64', 'libboost-filesystem1.62.0:amd64', 'libboost-filesystem1.67.0:amd64', 'libboost-iostreams1.67.0:amd64', 'libboost-program-options1.62.0:amd64', 'libboost-program-options1.67.0:amd64', 'libboost-regex1.67.0:amd64', 'libboost-system1.62.0:amd64', 'libboost-system1.67.0:amd64', 'libboost-thread1.62.0:amd64', 'libboost-thread1.67.0:amd64', 'libboost-timer1.67.0:amd64', 'libbsd0:amd64', 'libcairo-gobject2:amd64', 'libcairo2:amd64', 'libcap2:amd64', 'libcolord2:amd64', 'libcolt-free-java', 'libcommons-collections4-java', 'libcommons-parent-java', 'libconcurrent-java', 'libcroco3:amd64', 'libcryptsetup12:amd64', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdatrie1:amd64', 'libdbus-1-3:amd64', 'libdconf1:amd64', 'libdeflate0:amd64', 'libdevmapper1.02.1:amd64', 'libdivsufsort3:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm-nouveau2:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libedit2:amd64', 'libegl-mesa0:amd64', 'libegl1:amd64', 'libegl1-mesa:amd64', 'libelf1:amd64', 'libencode-locale-perl', 'libepoxy0:amd64', 'libexpat1:amd64', 'libfile-listing-perl', 'libflac8:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgbm1:amd64', 'libgdbm-compat4:amd64', 'libgdbm3:amd64', 'libgdbm6:amd64', 'libgdk-pixbuf2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgetopt-java', 'libgfortran3:amd64', 'libgfortran5:amd64', 'libgif7:amd64', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libgl1-mesa-glx:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libgtk-3-0:amd64', 'libgtk-3-common', 'libgtk2.0-0:amd64', 'libgtk2.0-common', 'libharfbuzz0b:amd64', 'libhtml-parser-perl', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhts1:amd64', 'libhts2:amd64', 'libhttp-cookies-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libice6:amd64', 'libicu57:amd64', 'libicu63:amd64', 'libidn11:amd64', 'libio-html-perl', 'libio-socket-ssl-perl', 'libip4tc0:amd64', 'libjbig0:amd64', 'libjbzip2-java', 'libjellyfish-2.0-2:amd64', 'libjemalloc2:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-modernizr', 'libjs-sphinxdoc', 'libjs-underscore', 'libjson-c3:amd64', 'libjson-glib-1.0-0:amd64', 'libjson-glib-1.0-common', 'libjung-free-java', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkmod2: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', 'libncurses5:amd64', 'libncurses6:amd64', 'libnet-http-perl', 'libnet-ssleay-perl', 'libnghttp2-14:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libogg0:amd64', 'libpam-systemd:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.24:amd64', 'libperl5.28:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libprotobuf10:amd64', 'libprotobuf17:amd64', 'libproxy1v5:amd64', 'libpsl5:amd64', 'libpulse0: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', 'librest-0.7-0:amd64', 'librsvg2-2:amd64', 'librsvg2-common:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libsm6:amd64', 'libsndfile1:amd64', 'libsoup-gnome2.4-1:amd64', 'libsoup2.4-1:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.0.2: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', 'libunistring0:amd64', 'liburi-perl', 'libvecmath-java', 'libvorbis0a:amd64', 'libvorbisenc2:amd64', 'libwayland-client0:amd64', 'libwayland-cursor0:amd64', 'libwayland-egl1:amd64', 'libwayland-egl1-mesa:amd64', 'libwayland-server0:amd64', 'libwebp6:amd64', 'libwrap0:amd64', 'libwww-perl', 'libwww-robotrules-perl', 'libx11-6:amd64', 'libx11-data', 'libx11-xcb1:amd64', 'libxau6:amd64', 'libxaw7:amd64', 'libxcb-dri2-0:amd64', 'libxcb-dri3-0:amd64', 'libxcb-glx0:amd64', 'libxcb-present0:amd64', 'libxcb-render0:amd64', 'libxcb-shape0:amd64', 'libxcb-shm0:amd64', 'libxcb-sync1:amd64', 'libxcb-xfixes0:amd64', 'libxcb1:amd64', 'libxcomposite1:amd64', 'libxcursor1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxinerama1:amd64', 'libxkbcommon0:amd64', 'libxml2:amd64', 'libxmu6:amd64', 'libxmuu1:amd64', 'libxpm4:amd64', 'libxrandr2:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxss1:amd64', 'libxt6:amd64', 'libxtst6:amd64', 'libxv1:amd64', 'libxxf86dga1:amd64', 'libxxf86vm1:amd64', 'littler', 'lsb-base', 'mime-support', 'ncbi-blast+-', 'ncbi-data', 'netbase', 'openjdk-11-jre:amd64', 'openjdk-11-jre-headless:amd64', 'openjdk-8-jre:amd64', 'openjdk-8-jre-headless:amd64', 'openssl', 'parafly', 'perl', 'perl-modules-5.24', '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-limma', 'r-bioc-qvalue', 'r-cran-assertthat', 'r-cran-cli', 'r-cran-cluster', 'r-cran-colorspace', 'r-cran-crayon', 'r-cran-dichromat', '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', 'shared-mime-info', 'sphinx-rtd-theme-common', 'systemd', 'systemd-sysv', 'transdecoder', 'trimmomatic', 'tzdata', 'ucf', 'unzip', 'x11-common', 'x11-utils', 'xdg-utils', 'xkb-data', 'zip', 'trinityrnaseq'] 2m56.2s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: adwaita-icon-theme berkeley-express bowtie bowtie2 ca-certificates ca-certificates-java cd-hit curl dbus dbus-user-session dconf-gsettings-backend dconf-service default-jre default-jre-headless dmsetup fontconfig fontconfig-config fonts-dejavu-core fonts-font-awesome fonts-lato fonts-roboto-slab glib-networking glib-networking-common glib-networking-services gnome-icon-theme gsettings-desktop-schemas gtk-update-icon-cache hicolor-icon-theme jaligner java-common jellyfish libapache-pom-java libapparmor1 libargon2-1 libasound2 libasound2-data libasyncns0 libatk-bridge2.0-0 libatk-wrapper-java libatk-wrapper-java-jni libatk1.0-0 libatk1.0-data libatomic1 libatspi2.0-0 libavahi-client3 libavahi-common-data libavahi-common3 libbamtools2.4.0 libbamtools2.5.1 libblas-common libblas3 libboost-atomic1.67.0 libboost-chrono1.67.0 libboost-date-time1.62.0 libboost-date-time1.67.0 libboost-filesystem1.62.0 libboost-filesystem1.67.0 libboost-iostreams1.67.0 libboost-program-options1.62.0 libboost-program-options1.67.0 libboost-regex1.67.0 libboost-system1.62.0 libboost-system1.67.0 libboost-thread1.62.0 libboost-thread1.67.0 libboost-timer1.67.0 libbsd0 libcairo-gobject2 libcairo2 libcap2 libcolord2 libcolt-free-java libcommons-collections4-java libcommons-parent-java libconcurrent-java libcroco3 libcryptsetup12 libcups2 libcurl3-gnutls libcurl4 libdatrie1 libdbus-1-3 libdconf1 libdeflate0 libdevmapper1.02.1 libdivsufsort3 libdrm-amdgpu1 libdrm-common libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libegl-mesa0 libegl1 libegl1-mesa libelf1 libencode-locale-perl libepoxy0 libexpat1 libfile-listing-perl libflac8 libfontconfig1 libfontenc1 libfreetype6 libfribidi0 libgbm1 libgdbm-compat4 libgdbm3 libgdbm6 libgdk-pixbuf2.0-0 libgdk-pixbuf2.0-common libgetopt-java libgfortran3 libgfortran5 libgif7 libgl1 libgl1-mesa-dri libgl1-mesa-glx libglapi-mesa libglib2.0-0 libglvnd0 libglx-mesa0 libglx0 libgomp1 libgraphite2-3 libgssapi-krb5-2 libgtk-3-0 libgtk-3-common libgtk2.0-0 libgtk2.0-common libharfbuzz0b libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl libhts1 libhts2 libhttp-cookies-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libice6 libicu57 libicu63 libidn11 libio-html-perl libio-socket-ssl-perl libip4tc0 libjbig0 libjbzip2-java libjellyfish-2.0-2 libjemalloc2 libjpeg62-turbo libjs-jquery libjs-modernizr libjs-sphinxdoc libjs-underscore libjson-c3 libjson-glib-1.0-0 libjson-glib-1.0-common libjung-free-java libk5crypto3 libkeyutils1 libkmod2 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 libncurses5 libncurses6 libnet-http-perl libnet-ssleay-perl libnghttp2-14 libnspr4 libnss3 libogg0 libpam-systemd libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libpciaccess0 libpcsclite1 libperl5.24 libperl5.28 libpixman-1-0 libpng16-16 libprotobuf10 libprotobuf17 libproxy1v5 libpsl5 libpulse0 libpython-stdlib libpython2-stdlib libpython2.7-minimal libpython2.7-stdlib libpython3-stdlib libpython3.7-minimal libpython3.7-stdlib libquadmath0 libreadline7 librest-0.7-0 librsvg2-2 librsvg2-common librtmp1 libsasl2-2 libsasl2-modules-db libsensors-config libsensors5 libsm6 libsndfile1 libsoup-gnome2.4-1 libsoup2.4-1 libsqlite3-0 libssh2-1 libssl1.0.2 libssl1.1 libstaden-read13 libtbb2 libtcl8.6 libthai-data libthai0 libtiff5 libtimedate-perl libtk8.6 libtry-tiny-perl libunistring0 liburi-perl libvecmath-java libvorbis0a libvorbisenc2 libwayland-client0 libwayland-cursor0 libwayland-egl1 libwayland-egl1-mesa libwayland-server0 libwebp6 libwrap0 libwww-perl libwww-robotrules-perl libx11-6 libx11-data libx11-xcb1 libxau6 libxaw7 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-shape0 libxcb-shm0 libxcb-sync1 libxcb-xfixes0 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxext6 libxfixes3 libxft2 libxi6 libxinerama1 libxkbcommon0 libxml2 libxmu6 libxmuu1 libxpm4 libxrandr2 libxrender1 libxshmfence1 libxss1 libxt6 libxtst6 libxv1 libxxf86dga1 libxxf86vm1 littler lsb-base mime-support ncbi-blast+ ncbi-data netbase openjdk-11-jre openjdk-11-jre-headless openjdk-8-jre openjdk-8-jre-headless openssl parafly perl perl-modules-5.24 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-limma r-bioc-qvalue r-cran-assertthat r-cran-cli r-cran-cluster r-cran-colorspace r-cran-crayon r-cran-dichromat 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 shared-mime-info sphinx-rtd-theme-common systemd systemd-sysv transdecoder trimmomatic trinityrnaseq tzdata ucf unzip x11-common x11-utils xdg-utils xkb-data zip 0 upgraded, 0 newly installed, 377 to remove and 0 not upgraded. After this operation, 1262 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 ... 37719 files and directories currently installed.) Removing openjdk-8-jre:amd64 (8u252-b09-1~deb9u1) ... Removing libatk-wrapper-java-jni:amd64 (0.33.3-22+deb10u1) ... Removing libgtk-3-0:amd64 (3.24.5-1) ... Removing libgtk2.0-0:amd64 (2.24.32-3) ... Removing adwaita-icon-theme (3.30.1-1) ... 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 openjdk-8-jre-headless:amd64 (8u252-b09-1~deb9u1) ... 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 cd-hit (4.6.8-2) ... Removing curl (7.64.0-4+deb10u2) ... Removing libgtk-3-common (3.24.5-1) ... Removing librest-0.7-0:amd64 (0.8.1-1) ... Removing libsoup-gnome2.4-1:amd64 (2.64.2-2) ... Removing libsoup2.4-1:amd64 (2.64.2-2) ... Removing glib-networking:amd64 (2.58.0-2+deb10u2) ... Removing gsettings-desktop-schemas (3.28.1-1) ... Removing dconf-gsettings-backend:amd64 (0.30.1-2) ... Removing dconf-service (0.30.1-2) ... Removing dbus-user-session (1.12.20-0+deb10u1) ... Removing libpam-systemd:amd64 (241-7~deb10u8) ... Removing dbus (1.12.20-0+deb10u1) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of stop. Removing systemd-sysv (241-7~deb10u8) ... Removing systemd (241-7~deb10u8) ... Removing libcryptsetup12:amd64 (2:2.1.0-5+deb10u2) ... Removing gnome-icon-theme (3.12.0-3) ... update-alternatives: using /usr/share/icons/gnome/scalable/places/gnome-foot.svg to provide /usr/share/icons/gnome/scalable/places/start-here.svg (start-here.svg) in auto mode update-alternatives: warning: skip creation of /usr/share/icons/gnome/256x256/places/start-here.png because associated file /usr/share/icons/gnome/256x256/places/gnome-foot.png (of link group start-here.svg) doesn't exist Removing librsvg2-common:amd64 (2.44.10-2.1+deb10u3) ... Removing librsvg2-2:amd64 (2.44.10-2.1+deb10u3) ... Removing libatk-wrapper-java (0.33.3-22+deb10u1) ... Removing x11-utils (7.7+4) ... 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 glib-networking-services (2.58.0-2+deb10u2) ... Removing glib-networking-common (2.58.0-2+deb10u2) ... Removing gtk-update-icon-cache (3.24.5-1) ... Removing hicolor-icon-theme (0.17-2) ... 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 libapparmor1:amd64 (2.13.2-10) ... Removing libargon2-1:amd64 (0~20171227-0.2) ... Removing libpulse0:amd64 (12.2-4+deb10u1) ... Removing libasyncns0:amd64 (0.8-6) ... Removing libatk-bridge2.0-0:amd64 (2.30.0-5) ... Removing libatk1.0-0:amd64 (2.30.0-2) ... Removing libatk1.0-data (2.30.0-2) ... Removing libtbb2:amd64 (2018~U6-4) ... Removing libatomic1:amd64 (8.3.0-6) ... Removing libatspi2.0-0:amd64 (2.30.0-7) ... Removing libbamtools2.4.0 (2.4.1+dfsg-1) ... Removing libbamtools2.5.1:amd64 (2.5.1+dfsg-3) ... Removing libblas-common (3.7.0-2) ... 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-time1.62.0:amd64 (1.62.0+dfsg-4) ... Removing libboost-date-time1.67.0:amd64 (1.67.0-13+deb10u1) ... Removing libboost-filesystem1.62.0:amd64 (1.62.0+dfsg-4) ... 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-options1.62.0:amd64 (1.62.0+dfsg-4) ... 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-thread1.62.0:amd64 (1.62.0+dfsg-4) ... Removing libboost-system1.62.0:amd64 (1.62.0+dfsg-4) ... Removing libboost-system1.67.0:amd64 (1.67.0-13+deb10u1) ... 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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 libssl1.0.2:amd64 (1.0.2u-1~deb9u1) ... Removing libunistring0:amd64 (0.9.6+really0.9.3-0.1) ... Removing libvecmath-java (1.5.2-7) ... Removing libwayland-cursor0:amd64 (1.16.0-1) ... Removing libwayland-client0:amd64 (1.16.0-1) ... Removing libwayland-egl1:amd64 (1.16.0-1) ... Removing libwayland-server0:amd64 (1.16.0-1) ... Removing libwrap0:amd64 (7.6.q-28) ... Removing libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Removing libxxf86dga1:amd64 (2:1.1.4-1+b3) ... 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-shape0:amd64 (1.13.1-2) ... Removing libxcb-sync1:amd64 (1.13.1-2) ... Removing libxcb-xfixes0:amd64 (1.13.1-2) ... Removing libxcomposite1:amd64 (1:0.4.4-2) ... Removing libxcursor1:amd64 (1:1.1.15-2) ... Removing libxdamage1:amd64 (1:1.1.4-3+b3) ... Removing libxv1:amd64 (2:1.0.11-1) ... Removing libxfixes3:amd64 (1:5.0.3-1) ... Removing libxtst6:amd64 (2:1.2.3-1) ... Removing libxi6:amd64 (2:1.7.9-1) ... Removing libxinerama1:amd64 (2:1.1.4-2) ... Removing libxkbcommon0:amd64 (0.8.2-1) ... Removing libxmuu1:amd64 (2:1.1.2-2+b3) ... Removing libxpm4:amd64 (1:3.5.12-1) ... Removing libxrandr2:amd64 (2:1.5.1-1) ... Removing libxshmfence1:amd64 (1.3-1) ... Removing ncbi-data (6.1.20170106+dfsg1-0+deb10u2) ... Removing perl-modules-5.24 (5.24.1-3+deb9u7) ... Removing python2-minimal (2.7.16-1) ... Removing r-bioc-limma (3.38.3+dfsg-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-dichromat (1:2.0-0-2) ... 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 xkb-data (2.26-2) ... Removing r-cran-rcpp (1.0.0-1) ... Removing r-cran-littler (0.3.6-1) ... Removing libcurl3-gnutls:amd64 (7.64.0-4+deb10u2) ... 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 liblapack3:amd64 (3.8.0-2) ... Removing libblas3:amd64 (3.8.0-2) ... Removing libxt6:amd64 (1:1.1.5-1+b3) ... Removing libcairo2:amd64 (1.16.0-4+deb10u1) ... Removing libcurl4:amd64 (7.64.0-4+deb10u2) ... Removing libthai0:amd64 (0.1.28-2) ... Removing libdatrie1:amd64 (0.2.12-2) ... Removing libtk8.6:amd64 (8.6.9-2) ... 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 readline-common (7.0-5) ... Removing tzdata (2021a-0+deb10u6) ... Removing unzip (6.0-23+deb10u2) ... Removing xdg-utils (1.1.3-1+deb10u1) ... Removing zip (3.0-11+b1) ... Removing libxft2:amd64 (2.3.2-2) ... Removing libice6:amd64 (2:1.0.9-2) ... Removing libxext6:amd64 (2:1.3.3-1+b2) ... Removing libxrender1:amd64 (1:0.9.10-1) ... Removing x11-common (1:7.7+19) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing lsb-base (10.2019051400) ... Removing libx11-6:amd64 (2:1.6.7-1+deb10u2) ... Removing libx11-data (2:1.6.7-1+deb10u2) ... Removing libxcb1:amd64 (1.13.1-2) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libbsd0:amd64 (0.9.1-2+deb10u1) ... Removing libxau6:amd64 (1:1.0.8-1+b2) ... Removing dmsetup (2:1.02.155-3) ... Removing libdevmapper1.02.1:amd64 (2:1.02.155-3) ... Removing libwww-perl (6.36-2) ... Removing liblwp-protocol-https-perl (6.07-2) ... Removing libhttp-negotiate-perl (6.01-1) ... Removing libfile-listing-perl (6.04-1) ... Removing libwww-robotrules-perl (6.02-1) ... Removing libtry-tiny-perl (0.30-1) ... Removing libnet-http-perl (6.18-1) ... 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 libnet-ssleay-perl (1.85-2+deb10u1) ... Removing perl-openssl-defaults:amd64 (3) ... Removing netbase (5.6) ... Removing ca-certificates-java (20190405) ... Removing openjdk-11-jre-headless:amd64 (11.0.16+8-1~deb10u1) ... Removing ca-certificates (20200601~deb10u2) ... Removing dangling symlinks from /etc/ssl/certs... done. 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 libhttp-message-perl (6.18-1) ... Removing libencode-locale-perl (1.05-1) ... Removing libexpat1:amd64 (2.2.6-2+deb10u4) ... Removing libharfbuzz0b:amd64 (2.3.1-1) ... Removing libfreetype6:amd64 (2.9.1-3+deb10u3) ... Removing liburi-perl (1.76-1) ... 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 libhttp-date-perl (6.02-1) ... Removing libio-html-perl (1.001-1) ... 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 liblwp-mediatypes-perl (6.02-1) ... Removing libnss3:amd64 (2:3.42.1-1+deb10u5) ... Removing libnspr4:amd64 (2:4.20-1) ... Removing libpcsclite1:amd64 (1.8.24-1) ... Removing libpng16-16:amd64 (1.6.36-6) ... 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 ucf (3.0038+nmu1) ... 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) ... 2m56.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'apt-get', 'remove', 'adwaita-icon-theme', 'berkeley-express', 'bowtie', 'bowtie2', 'ca-certificates', 'ca-certificates-java', 'cd-hit', 'curl', 'dbus', 'dbus-user-session', 'dconf-gsettings-backend:amd64', 'dconf-service', 'default-jre', 'default-jre-headless', 'dmsetup', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-font-awesome', 'fonts-lato', 'fonts-roboto-slab', 'glib-networking:amd64', 'glib-networking-common', 'glib-networking-services', 'gnome-icon-theme', 'gsettings-desktop-schemas', 'gtk-update-icon-cache', 'hicolor-icon-theme', 'jaligner', 'java-common', 'jellyfish', 'libapache-pom-java', 'libapparmor1:amd64', 'libargon2-1:amd64', 'libasound2:amd64', 'libasound2-data', 'libasyncns0:amd64', 'libatk-bridge2.0-0:amd64', 'libatk-wrapper-java', 'libatk-wrapper-java-jni:amd64', 'libatk1.0-0:amd64', 'libatk1.0-data', 'libatomic1:amd64', 'libatspi2.0-0:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbamtools2.4.0', 'libbamtools2.5.1:amd64', 'libblas-common', 'libblas3:amd64', 'libboost-atomic1.67.0:amd64', 'libboost-chrono1.67.0:amd64', 'libboost-date-time1.62.0:amd64', 'libboost-date-time1.67.0:amd64', 'libboost-filesystem1.62.0:amd64', 'libboost-filesystem1.67.0:amd64', 'libboost-iostreams1.67.0:amd64', 'libboost-program-options1.62.0:amd64', 'libboost-program-options1.67.0:amd64', 'libboost-regex1.67.0:amd64', 'libboost-system1.62.0:amd64', 'libboost-system1.67.0:amd64', 'libboost-thread1.62.0:amd64', 'libboost-thread1.67.0:amd64', 'libboost-timer1.67.0:amd64', 'libbsd0:amd64', 'libcairo-gobject2:amd64', 'libcairo2:amd64', 'libcap2:amd64', 'libcolord2:amd64', 'libcolt-free-java', 'libcommons-collections4-java', 'libcommons-parent-java', 'libconcurrent-java', 'libcroco3:amd64', 'libcryptsetup12:amd64', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdatrie1:amd64', 'libdbus-1-3:amd64', 'libdconf1:amd64', 'libdeflate0:amd64', 'libdevmapper1.02.1:amd64', 'libdivsufsort3:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm-nouveau2:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libedit2:amd64', 'libegl-mesa0:amd64', 'libegl1:amd64', 'libegl1-mesa:amd64', 'libelf1:amd64', 'libencode-locale-perl', 'libepoxy0:amd64', 'libexpat1:amd64', 'libfile-listing-perl', 'libflac8:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgbm1:amd64', 'libgdbm-compat4:amd64', 'libgdbm3:amd64', 'libgdbm6:amd64', 'libgdk-pixbuf2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgetopt-java', 'libgfortran3:amd64', 'libgfortran5:amd64', 'libgif7:amd64', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libgl1-mesa-glx:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libgtk-3-0:amd64', 'libgtk-3-common', 'libgtk2.0-0:amd64', 'libgtk2.0-common', 'libharfbuzz0b:amd64', 'libhtml-parser-perl', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhts1:amd64', 'libhts2:amd64', 'libhttp-cookies-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libice6:amd64', 'libicu57:amd64', 'libicu63:amd64', 'libidn11:amd64', 'libio-html-perl', 'libio-socket-ssl-perl', 'libip4tc0:amd64', 'libjbig0:amd64', 'libjbzip2-java', 'libjellyfish-2.0-2:amd64', 'libjemalloc2:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-modernizr', 'libjs-sphinxdoc', 'libjs-underscore', 'libjson-c3:amd64', 'libjson-glib-1.0-0:amd64', 'libjson-glib-1.0-common', 'libjung-free-java', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkmod2: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', 'libncurses5:amd64', 'libncurses6:amd64', 'libnet-http-perl', 'libnet-ssleay-perl', 'libnghttp2-14:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libogg0:amd64', 'libpam-systemd:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.24:amd64', 'libperl5.28:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libprotobuf10:amd64', 'libprotobuf17:amd64', 'libproxy1v5:amd64', 'libpsl5:amd64', 'libpulse0: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', 'librest-0.7-0:amd64', 'librsvg2-2:amd64', 'librsvg2-common:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libsm6:amd64', 'libsndfile1:amd64', 'libsoup-gnome2.4-1:amd64', 'libsoup2.4-1:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.0.2: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', 'libunistring0:amd64', 'liburi-perl', 'libvecmath-java', 'libvorbis0a:amd64', 'libvorbisenc2:amd64', 'libwayland-client0:amd64', 'libwayland-cursor0:amd64', 'libwayland-egl1:amd64', 'libwayland-egl1-mesa:amd64', 'libwayland-server0:amd64', 'libwebp6:amd64', 'libwrap0:amd64', 'libwww-perl', 'libwww-robotrules-perl', 'libx11-6:amd64', 'libx11-data', 'libx11-xcb1:amd64', 'libxau6:amd64', 'libxaw7:amd64', 'libxcb-dri2-0:amd64', 'libxcb-dri3-0:amd64', 'libxcb-glx0:amd64', 'libxcb-present0:amd64', 'libxcb-render0:amd64', 'libxcb-shape0:amd64', 'libxcb-shm0:amd64', 'libxcb-sync1:amd64', 'libxcb-xfixes0:amd64', 'libxcb1:amd64', 'libxcomposite1:amd64', 'libxcursor1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxinerama1:amd64', 'libxkbcommon0:amd64', 'libxml2:amd64', 'libxmu6:amd64', 'libxmuu1:amd64', 'libxpm4:amd64', 'libxrandr2:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxss1:amd64', 'libxt6:amd64', 'libxtst6:amd64', 'libxv1:amd64', 'libxxf86dga1:amd64', 'libxxf86vm1:amd64', 'littler', 'lsb-base', 'mime-support', 'ncbi-blast+-', 'ncbi-data', 'netbase', 'openjdk-11-jre:amd64', 'openjdk-11-jre-headless:amd64', 'openjdk-8-jre:amd64', 'openjdk-8-jre-headless:amd64', 'openssl', 'parafly', 'perl', 'perl-modules-5.24', '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-limma', 'r-bioc-qvalue', 'r-cran-assertthat', 'r-cran-cli', 'r-cran-cluster', 'r-cran-colorspace', 'r-cran-crayon', 'r-cran-dichromat', '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', 'shared-mime-info', 'sphinx-rtd-theme-common', 'systemd', 'systemd-sysv', 'transdecoder', 'trimmomatic', 'tzdata', 'ucf', 'unzip', 'x11-common', 'x11-utils', 'xdg-utils', 'xkb-data', 'zip', 'trinityrnaseq'] 2m56.2s INFO: Running scripts post_remove 2m56.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/post_remove_exceptions'] 2m56.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/post_remove_exceptions'] 2m56.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'dpkg', '--purge', 'adwaita-icon-theme', 'berkeley-express', 'bowtie', 'bowtie2', 'ca-certificates', 'ca-certificates-java', 'cd-hit', 'curl', 'dbus', 'dbus-user-session', 'dconf-gsettings-backend:amd64', 'dconf-service', 'default-jre', 'default-jre-headless', 'dmsetup', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-font-awesome', 'fonts-lato', 'fonts-roboto-slab', 'glib-networking:amd64', 'glib-networking-common', 'glib-networking-services', 'gnome-icon-theme', 'gsettings-desktop-schemas', 'gtk-update-icon-cache', 'hicolor-icon-theme', 'jaligner', 'java-common', 'jellyfish', 'libapache-pom-java', 'libapparmor1:amd64', 'libargon2-1:amd64', 'libasound2:amd64', 'libasound2-data', 'libasyncns0:amd64', 'libatk-bridge2.0-0:amd64', 'libatk-wrapper-java', 'libatk-wrapper-java-jni:amd64', 'libatk1.0-0:amd64', 'libatk1.0-data', 'libatomic1:amd64', 'libatspi2.0-0:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbamtools2.4.0', 'libbamtools2.5.1:amd64', 'libblas-common', 'libblas3:amd64', 'libboost-atomic1.67.0:amd64', 'libboost-chrono1.67.0:amd64', 'libboost-date-time1.62.0:amd64', 'libboost-date-time1.67.0:amd64', 'libboost-filesystem1.62.0:amd64', 'libboost-filesystem1.67.0:amd64', 'libboost-iostreams1.67.0:amd64', 'libboost-program-options1.62.0:amd64', 'libboost-program-options1.67.0:amd64', 'libboost-regex1.67.0:amd64', 'libboost-system1.62.0:amd64', 'libboost-system1.67.0:amd64', 'libboost-thread1.62.0:amd64', 'libboost-thread1.67.0:amd64', 'libboost-timer1.67.0:amd64', 'libbsd0:amd64', 'libcairo-gobject2:amd64', 'libcairo2:amd64', 'libcap2:amd64', 'libcolord2:amd64', 'libcolt-free-java', 'libcommons-collections4-java', 'libcommons-parent-java', 'libconcurrent-java', 'libcroco3:amd64', 'libcryptsetup12:amd64', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdatrie1:amd64', 'libdbus-1-3:amd64', 'libdconf1:amd64', 'libdeflate0:amd64', 'libdevmapper1.02.1:amd64', 'libdivsufsort3:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm-nouveau2:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libedit2:amd64', 'libegl-mesa0:amd64', 'libegl1:amd64', 'libegl1-mesa:amd64', 'libelf1:amd64', 'libencode-locale-perl', 'libepoxy0:amd64', 'libexpat1:amd64', 'libfile-listing-perl', 'libflac8:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgbm1:amd64', 'libgdbm-compat4:amd64', 'libgdbm3:amd64', 'libgdbm6:amd64', 'libgdk-pixbuf2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgetopt-java', 'libgfortran3:amd64', 'libgfortran5:amd64', 'libgif7:amd64', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libgl1-mesa-glx:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libgtk-3-0:amd64', 'libgtk-3-common', 'libgtk2.0-0:amd64', 'libgtk2.0-common', 'libharfbuzz0b:amd64', 'libhtml-parser-perl', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhts1:amd64', 'libhts2:amd64', 'libhttp-cookies-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libice6:amd64', 'libicu57:amd64', 'libicu63:amd64', 'libidn11:amd64', 'libio-html-perl', 'libio-socket-ssl-perl', 'libip4tc0:amd64', 'libjbig0:amd64', 'libjbzip2-java', 'libjellyfish-2.0-2:amd64', 'libjemalloc2:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-modernizr', 'libjs-sphinxdoc', 'libjs-underscore', 'libjson-c3:amd64', 'libjson-glib-1.0-0:amd64', 'libjson-glib-1.0-common', 'libjung-free-java', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkmod2: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', 'libncurses5:amd64', 'libncurses6:amd64', 'libnet-http-perl', 'libnet-ssleay-perl', 'libnghttp2-14:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libogg0:amd64', 'libpam-systemd:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.24:amd64', 'libperl5.28:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libprotobuf10:amd64', 'libprotobuf17:amd64', 'libproxy1v5:amd64', 'libpsl5:amd64', 'libpulse0: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', 'librest-0.7-0:amd64', 'librsvg2-2:amd64', 'librsvg2-common:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libsm6:amd64', 'libsndfile1:amd64', 'libsoup-gnome2.4-1:amd64', 'libsoup2.4-1:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.0.2: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', 'libunistring0:amd64', 'liburi-perl', 'libvecmath-java', 'libvorbis0a:amd64', 'libvorbisenc2:amd64', 'libwayland-client0:amd64', 'libwayland-cursor0:amd64', 'libwayland-egl1:amd64', 'libwayland-egl1-mesa:amd64', 'libwayland-server0:amd64', 'libwebp6:amd64', 'libwrap0:amd64', 'libwww-perl', 'libwww-robotrules-perl', 'libx11-6:amd64', 'libx11-data', 'libx11-xcb1:amd64', 'libxau6:amd64', 'libxaw7:amd64', 'libxcb-dri2-0:amd64', 'libxcb-dri3-0:amd64', 'libxcb-glx0:amd64', 'libxcb-present0:amd64', 'libxcb-render0:amd64', 'libxcb-shape0:amd64', 'libxcb-shm0:amd64', 'libxcb-sync1:amd64', 'libxcb-xfixes0:amd64', 'libxcb1:amd64', 'libxcomposite1:amd64', 'libxcursor1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxinerama1:amd64', 'libxkbcommon0:amd64', 'libxml2:amd64', 'libxmu6:amd64', 'libxmuu1:amd64', 'libxpm4:amd64', 'libxrandr2:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxss1:amd64', 'libxt6:amd64', 'libxtst6:amd64', 'libxv1:amd64', 'libxxf86dga1:amd64', 'libxxf86vm1:amd64', 'littler', 'lsb-base', 'mime-support', 'ncbi-blast+', 'ncbi-data', 'netbase', 'openjdk-11-jre:amd64', 'openjdk-11-jre-headless:amd64', 'openjdk-8-jre:amd64', 'openjdk-8-jre-headless:amd64', 'openssl', 'parafly', 'perl', 'perl-modules-5.24', '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-limma', 'r-bioc-qvalue', 'r-cran-assertthat', 'r-cran-cli', 'r-cran-cluster', 'r-cran-colorspace', 'r-cran-crayon', 'r-cran-dichromat', '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', 'shared-mime-info', 'sphinx-rtd-theme-common', 'systemd', 'systemd-sysv', 'transdecoder', 'trimmomatic', 'tzdata', 'ucf', 'unzip', 'x11-common', 'x11-utils', 'xdg-utils', 'xkb-data', 'zip'] 2m57.9s DUMP: (Reading database ... 4803 files and directories currently installed.) Purging configuration files for adwaita-icon-theme (3.30.1-1) ... 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 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 cd-hit which isn't installed dpkg: warning: ignoring request to remove curl which isn't installed Purging configuration files for dbus (1.12.20-0+deb10u1) ... rmdir: failed to remove '/var/run/dbus': No such file or directory Purging configuration files for dbus-user-session (1.12.20-0+deb10u1) ... dpkg: warning: ignoring request to remove dconf-gsettings-backend which isn't installed dpkg: warning: ignoring request to remove dconf-service 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 dpkg: warning: ignoring request to remove dmsetup 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 glib-networking which isn't installed dpkg: warning: ignoring request to remove glib-networking-common which isn't installed dpkg: warning: ignoring request to remove glib-networking-services which isn't installed dpkg: warning: ignoring request to remove gnome-icon-theme which isn't installed dpkg: warning: ignoring request to remove gsettings-desktop-schemas which isn't installed dpkg: warning: ignoring request to remove gtk-update-icon-cache which isn't installed dpkg: warning: ignoring request to remove hicolor-icon-theme 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 libapparmor1 which isn't installed dpkg: warning: ignoring request to remove libargon2-1 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 libasyncns0 which isn't installed dpkg: warning: ignoring request to remove libatk-bridge2.0-0 which isn't installed dpkg: warning: ignoring request to remove libatk-wrapper-java which isn't installed dpkg: warning: ignoring request to remove libatk-wrapper-java-jni which isn't installed dpkg: warning: ignoring request to remove libatk1.0-0 which isn't installed dpkg: warning: ignoring request to remove libatk1.0-data which isn't installed dpkg: warning: ignoring request to remove libatomic1 which isn't installed dpkg: warning: ignoring request to remove libatspi2.0-0 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 libbamtools2.4.0 which isn't installed dpkg: warning: ignoring request to remove libbamtools2.5.1 which isn't installed dpkg: warning: ignoring request to remove libblas-common 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-time1.62.0 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-filesystem1.62.0 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-options1.62.0 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-system1.62.0 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-thread1.62.0 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 libcairo-gobject2 which isn't installed dpkg: warning: ignoring request to remove libcairo2 which isn't installed dpkg: warning: ignoring request to remove libcap2 which isn't installed dpkg: warning: ignoring request to remove libcolord2 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 libcroco3 which isn't installed dpkg: warning: ignoring request to remove libcryptsetup12 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 libdconf1 which isn't installed dpkg: warning: ignoring request to remove libdeflate0 which isn't installed dpkg: warning: ignoring request to remove libdevmapper1.02.1 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 libegl-mesa0 which isn't installed dpkg: warning: ignoring request to remove libegl1 which isn't installed dpkg: warning: ignoring request to remove libegl1-mesa 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 libepoxy0 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 libflac8 which isn't installed dpkg: warning: ignoring request to remove libfontconfig1 which isn't installed dpkg: warning: ignoring request to remove libfontenc1 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 libgbm1 which isn't installed dpkg: warning: ignoring request to remove libgdbm-compat4 which isn't installed dpkg: warning: ignoring request to remove libgdbm3 which isn't installed dpkg: warning: ignoring request to remove libgdbm6 which isn't installed Purging configuration files for libgdk-pixbuf2.0-0:amd64 (2.38.1+dfsg-1) ... dpkg: warning: ignoring request to remove libgdk-pixbuf2.0-common which isn't installed dpkg: warning: ignoring request to remove libgetopt-java which isn't installed dpkg: warning: ignoring request to remove libgfortran3 which isn't installed dpkg: warning: ignoring request to remove libgfortran5 which isn't installed dpkg: warning: ignoring request to remove 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 libgl1-mesa-glx which isn't installed 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) ... Purging configuration files for libgtk-3-0:amd64 (3.24.5-1) ... Purging configuration files for libgtk-3-common (3.24.5-1) ... Purging configuration files for libgtk2.0-0:amd64 (2.24.32-3) ... Purging configuration files for libgtk2.0-common (2.24.32-3) ... 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 libhts1 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 libicu57 which isn't installed dpkg: warning: ignoring request to remove libicu63 which isn't installed dpkg: warning: ignoring request to remove libidn11 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 libip4tc0 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 libjson-c3 which isn't installed dpkg: warning: ignoring request to remove libjson-glib-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libjson-glib-1.0-common 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 libkmod2 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 libncurses5 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 libogg0 which isn't installed dpkg: warning: ignoring request to remove libpam-systemd 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 libperl5.24 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 libprotobuf10 which isn't installed dpkg: warning: ignoring request to remove libprotobuf17 which isn't installed dpkg: warning: ignoring request to remove libproxy1v5 which isn't installed dpkg: warning: ignoring request to remove libpsl5 which isn't installed Purging configuration files for libpulse0:amd64 (12.2-4+deb10u1) ... 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 librest-0.7-0 which isn't installed dpkg: warning: ignoring request to remove librsvg2-2 which isn't installed dpkg: warning: ignoring request to remove librsvg2-common 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 libsndfile1 which isn't installed dpkg: warning: ignoring request to remove libsoup-gnome2.4-1 which isn't installed dpkg: warning: ignoring request to remove libsoup2.4-1 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 libssl1.0.2:amd64 (1.0.2u-1~deb9u1) ... 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 libunistring0 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 libvorbis0a which isn't installed dpkg: warning: ignoring request to remove libvorbisenc2 which isn't installed dpkg: warning: ignoring request to remove libwayland-client0 which isn't installed dpkg: warning: ignoring request to remove libwayland-cursor0 which isn't installed dpkg: warning: ignoring request to remove libwayland-egl1 which isn't installed dpkg: warning: ignoring request to remove libwayland-egl1-mesa which isn't installed dpkg: warning: ignoring request to remove libwayland-server0 which isn't installed dpkg: warning: ignoring request to remove libwebp6 which isn't installed Purging configuration files for libwrap0:amd64 (7.6.q-28) ... 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 libxaw7 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-shape0 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 libxcb-xfixes0 which isn't installed dpkg: warning: ignoring request to remove libxcb1 which isn't installed dpkg: warning: ignoring request to remove libxcomposite1 which isn't installed dpkg: warning: ignoring request to remove libxcursor1 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 libxinerama1 which isn't installed dpkg: warning: ignoring request to remove libxkbcommon0 which isn't installed dpkg: warning: ignoring request to remove libxml2 which isn't installed dpkg: warning: ignoring request to remove libxmu6 which isn't installed dpkg: warning: ignoring request to remove libxmuu1 which isn't installed dpkg: warning: ignoring request to remove libxpm4 which isn't installed dpkg: warning: ignoring request to remove libxrandr2 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 libxv1 which isn't installed dpkg: warning: ignoring request to remove libxxf86dga1 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) ... dpkg: warning: ignoring request to remove openjdk-8-jre which isn't installed Purging configuration files for openjdk-8-jre-headless:amd64 (8u252-b09-1~deb9u1) ... 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-5.24 which isn't installed 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-limma 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-dichromat 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 Purging configuration files for shared-mime-info (1.10-1) ... dpkg: warning: ignoring request to remove sphinx-rtd-theme-common which isn't installed Purging configuration files for systemd (241-7~deb10u8) ... dpkg: warning: ignoring request to remove systemd-sysv 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 tzdata (2021a-0+deb10u6) ... 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) ... Purging configuration files for x11-utils (7.7+4) ... dpkg: warning: ignoring request to remove xdg-utils which isn't installed dpkg: warning: ignoring request to remove xkb-data which isn't installed dpkg: warning: ignoring request to remove zip which isn't installed 2m57.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'dpkg', '--purge', 'adwaita-icon-theme', 'berkeley-express', 'bowtie', 'bowtie2', 'ca-certificates', 'ca-certificates-java', 'cd-hit', 'curl', 'dbus', 'dbus-user-session', 'dconf-gsettings-backend:amd64', 'dconf-service', 'default-jre', 'default-jre-headless', 'dmsetup', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-font-awesome', 'fonts-lato', 'fonts-roboto-slab', 'glib-networking:amd64', 'glib-networking-common', 'glib-networking-services', 'gnome-icon-theme', 'gsettings-desktop-schemas', 'gtk-update-icon-cache', 'hicolor-icon-theme', 'jaligner', 'java-common', 'jellyfish', 'libapache-pom-java', 'libapparmor1:amd64', 'libargon2-1:amd64', 'libasound2:amd64', 'libasound2-data', 'libasyncns0:amd64', 'libatk-bridge2.0-0:amd64', 'libatk-wrapper-java', 'libatk-wrapper-java-jni:amd64', 'libatk1.0-0:amd64', 'libatk1.0-data', 'libatomic1:amd64', 'libatspi2.0-0:amd64', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbamtools2.4.0', 'libbamtools2.5.1:amd64', 'libblas-common', 'libblas3:amd64', 'libboost-atomic1.67.0:amd64', 'libboost-chrono1.67.0:amd64', 'libboost-date-time1.62.0:amd64', 'libboost-date-time1.67.0:amd64', 'libboost-filesystem1.62.0:amd64', 'libboost-filesystem1.67.0:amd64', 'libboost-iostreams1.67.0:amd64', 'libboost-program-options1.62.0:amd64', 'libboost-program-options1.67.0:amd64', 'libboost-regex1.67.0:amd64', 'libboost-system1.62.0:amd64', 'libboost-system1.67.0:amd64', 'libboost-thread1.62.0:amd64', 'libboost-thread1.67.0:amd64', 'libboost-timer1.67.0:amd64', 'libbsd0:amd64', 'libcairo-gobject2:amd64', 'libcairo2:amd64', 'libcap2:amd64', 'libcolord2:amd64', 'libcolt-free-java', 'libcommons-collections4-java', 'libcommons-parent-java', 'libconcurrent-java', 'libcroco3:amd64', 'libcryptsetup12:amd64', 'libcups2:amd64', 'libcurl3-gnutls:amd64', 'libcurl4:amd64', 'libdatrie1:amd64', 'libdbus-1-3:amd64', 'libdconf1:amd64', 'libdeflate0:amd64', 'libdevmapper1.02.1:amd64', 'libdivsufsort3:amd64', 'libdrm-amdgpu1:amd64', 'libdrm-common', 'libdrm-intel1:amd64', 'libdrm-nouveau2:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libedit2:amd64', 'libegl-mesa0:amd64', 'libegl1:amd64', 'libegl1-mesa:amd64', 'libelf1:amd64', 'libencode-locale-perl', 'libepoxy0:amd64', 'libexpat1:amd64', 'libfile-listing-perl', 'libflac8:amd64', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfribidi0:amd64', 'libgbm1:amd64', 'libgdbm-compat4:amd64', 'libgdbm3:amd64', 'libgdbm6:amd64', 'libgdk-pixbuf2.0-0:amd64', 'libgdk-pixbuf2.0-common', 'libgetopt-java', 'libgfortran3:amd64', 'libgfortran5:amd64', 'libgif7:amd64', 'libgl1:amd64', 'libgl1-mesa-dri:amd64', 'libgl1-mesa-glx:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0:amd64', 'libglvnd0:amd64', 'libglx-mesa0:amd64', 'libglx0:amd64', 'libgomp1:amd64', 'libgraphite2-3:amd64', 'libgssapi-krb5-2:amd64', 'libgtk-3-0:amd64', 'libgtk-3-common', 'libgtk2.0-0:amd64', 'libgtk2.0-common', 'libharfbuzz0b:amd64', 'libhtml-parser-perl', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhts1:amd64', 'libhts2:amd64', 'libhttp-cookies-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libice6:amd64', 'libicu57:amd64', 'libicu63:amd64', 'libidn11:amd64', 'libio-html-perl', 'libio-socket-ssl-perl', 'libip4tc0:amd64', 'libjbig0:amd64', 'libjbzip2-java', 'libjellyfish-2.0-2:amd64', 'libjemalloc2:amd64', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-modernizr', 'libjs-sphinxdoc', 'libjs-underscore', 'libjson-c3:amd64', 'libjson-glib-1.0-0:amd64', 'libjson-glib-1.0-common', 'libjung-free-java', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkmod2: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', 'libncurses5:amd64', 'libncurses6:amd64', 'libnet-http-perl', 'libnet-ssleay-perl', 'libnghttp2-14:amd64', 'libnspr4:amd64', 'libnss3:amd64', 'libogg0:amd64', 'libpam-systemd:amd64', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libpciaccess0:amd64', 'libpcsclite1:amd64', 'libperl5.24:amd64', 'libperl5.28:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libprotobuf10:amd64', 'libprotobuf17:amd64', 'libproxy1v5:amd64', 'libpsl5:amd64', 'libpulse0: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', 'librest-0.7-0:amd64', 'librsvg2-2:amd64', 'librsvg2-common:amd64', 'librtmp1:amd64', 'libsasl2-2:amd64', 'libsasl2-modules-db:amd64', 'libsensors-config', 'libsensors5:amd64', 'libsm6:amd64', 'libsndfile1:amd64', 'libsoup-gnome2.4-1:amd64', 'libsoup2.4-1:amd64', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.0.2: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', 'libunistring0:amd64', 'liburi-perl', 'libvecmath-java', 'libvorbis0a:amd64', 'libvorbisenc2:amd64', 'libwayland-client0:amd64', 'libwayland-cursor0:amd64', 'libwayland-egl1:amd64', 'libwayland-egl1-mesa:amd64', 'libwayland-server0:amd64', 'libwebp6:amd64', 'libwrap0:amd64', 'libwww-perl', 'libwww-robotrules-perl', 'libx11-6:amd64', 'libx11-data', 'libx11-xcb1:amd64', 'libxau6:amd64', 'libxaw7:amd64', 'libxcb-dri2-0:amd64', 'libxcb-dri3-0:amd64', 'libxcb-glx0:amd64', 'libxcb-present0:amd64', 'libxcb-render0:amd64', 'libxcb-shape0:amd64', 'libxcb-shm0:amd64', 'libxcb-sync1:amd64', 'libxcb-xfixes0:amd64', 'libxcb1:amd64', 'libxcomposite1:amd64', 'libxcursor1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxinerama1:amd64', 'libxkbcommon0:amd64', 'libxml2:amd64', 'libxmu6:amd64', 'libxmuu1:amd64', 'libxpm4:amd64', 'libxrandr2:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxss1:amd64', 'libxt6:amd64', 'libxtst6:amd64', 'libxv1:amd64', 'libxxf86dga1:amd64', 'libxxf86vm1:amd64', 'littler', 'lsb-base', 'mime-support', 'ncbi-blast+', 'ncbi-data', 'netbase', 'openjdk-11-jre:amd64', 'openjdk-11-jre-headless:amd64', 'openjdk-8-jre:amd64', 'openjdk-8-jre-headless:amd64', 'openssl', 'parafly', 'perl', 'perl-modules-5.24', '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-limma', 'r-bioc-qvalue', 'r-cran-assertthat', 'r-cran-cli', 'r-cran-cluster', 'r-cran-colorspace', 'r-cran-crayon', 'r-cran-dichromat', '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', 'shared-mime-info', 'sphinx-rtd-theme-common', 'systemd', 'systemd-sysv', 'transdecoder', 'trimmomatic', 'tzdata', 'ucf', 'unzip', 'x11-common', 'x11-utils', 'xdg-utils', 'xkb-data', 'zip'] 2m57.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'dpkg', '--purge', 'trinityrnaseq'] 2m57.9s DUMP: dpkg: warning: ignoring request to remove trinityrnaseq which isn't installed 2m57.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'dpkg', '--purge', 'trinityrnaseq'] 2m57.9s INFO: Running scripts post_purge 2m57.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/post_purge_exceptions'] 2m57.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/post_purge_exceptions'] 2m57.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'dpkg', '--purge', '--pending'] 2m57.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'dpkg', '--purge', '--pending'] 2m57.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'dpkg', '--remove', '--pending'] 2m57.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'dpkg', '--remove', '--pending'] 2m57.9s INFO: Running scripts post_test 2m57.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/post_test_exceptions'] 2m57.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'tmp/scripts/post_test_exceptions'] 2m57.9s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa'] 2m58.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa'] 2m58.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'dpkg-divert', '--list'] 2m58.2s DUMP: local diversion of /bin/sync to /bin/sync.distrib diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 2m58.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'dpkg-divert', '--list'] 2m58.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'apt-get', 'clean'] 2m58.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa', 'apt-get', 'clean'] 2m58.4s DEBUG: Recording chroot state 2m58.8s 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-lato, fonts-font-awesome, fonts-dejavu-core /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-lato, fonts-font-awesome, fonts-dejavu-core /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 2m59.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa/dev/shm'] 2m59.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa/dev/shm'] 2m59.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa/dev/console'] 2m59.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa/dev/console'] 2m59.1s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa/dev/ptmx'] 2m59.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa/dev/ptmx'] 2m59.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa/dev/pts'] 2m59.2s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa/dev/pts'] 2m59.2s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa/proc'] 2m59.3s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa/proc'] 2m59.3s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa'] 2m59.4s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpfmkzlmxa'] 2m59.4s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpfmkzlmxa 2m59.4s INFO: PASS: Upgrading between Debian distributions. 2m59.4s INFO: PASS: All tests. 2m59.4s INFO: piuparts run ends. ret=0 End: 2022-12-17 08:44:20 GMT