Start: 2023-02-21 00:43:43 GMT Package: roary Version: 3.8.0+dfsg-1 Installed-Size: 634 Maintainer: Debian Med Packaging Team Architecture: all Depends: perl, bioperl, libarray-utils-perl, libenv-path-perl, libexception-class-perl, libfile-find-rule-perl, libfile-grep-perl, libfile-slurper-perl, libfile-which-perl, libfindbin-libs-perl, libgraph-perl, libgraph-readwrite-perl, liblog-log4perl-perl, libmoose-perl, libperlio-utf8-strict-perl, libtest-most-perl, libtest-file-perl, libtest-files-perl, libtest-output-perl, libtext-csv-perl, bedtools, cd-hit, ncbi-blast+, mcl, parallel, prank, r-base-core, r-cran-ggplot2, mafft, fasttree Description: high speed stand alone pan genome pipeline Homepage: http://sanger-pathogens.github.io/Roary/ Description-md5: 6d457fd706202fc2ef292eacf7b46029 Tag: field::biology, field::biology:bioinformatics, implemented-in::perl, interface::commandline, role::program, scope::utility, use::analysing, use::comparing Section: science Priority: optional Filename: pool/main/r/roary/roary_3.8.0+dfsg-1_all.deb Size: 170134 MD5sum: d2b5bd8c3cf60d6fabc08169c52a4d40 SHA256: 062eece678b4556ee0de3961c4789d1b51e2e860d582d72e19aedd6f8beef3db Executing: sudo env PYTHONPATH=/srv/piuparts.debian.org/lib/python3/dist-packages timeout -s INT -k 5m 80m /srv/piuparts.debian.org/sbin/piuparts --install-recommends --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --skip-logrotatefiles-test --warn-on-debsums-errors --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz -d stretch --no-upgrade-test --apt roary=3.8.0+dfsg-1 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.1.5 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --install-recommends --scriptsdir /etc/piuparts/scripts --no-eatmydata --allow-database --warn-on-leftovers-after-purge --skip-logrotatefiles-test --warn-on-debsums-errors --mirror 'http://deb.debian.org/debian/ main' --tmpdir /srv/piuparts.debian.org/tmp --arch amd64 -b /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz -d stretch --no-upgrade-test --apt roary=3.8.0+dfsg-1 0m0.0s INFO: Running on: Linux piu-slave-conova-01 5.10.0-21-amd64 #1 SMP Debian 5.10.162-1 (2023-01-21) x86_64 0m0.0s DEBUG: Created temporary directory /srv/piuparts.debian.org/tmp/tmpbtuj4qny 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmpbtuj4qny 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m1.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m1.2s DEBUG: Starting command: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny/proc'] 0m1.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny/proc'] 0m1.2s DEBUG: Starting command: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny/dev/pts'] 0m1.2s DEBUG: Command ok: ['mount', '-t', 'devpts', '-o', 'newinstance,noexec,nosuid,gid=5,mode=0620,ptmxmode=0666', 'devpts', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny/dev/pts'] 0m1.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny/dev/ptmx'] 0m1.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny/dev/ptmx'] 0m1.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny/dev/console'] 0m1.2s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/4', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny/dev/console'] 0m1.2s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny/dev/shm'] 0m1.2s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny/dev/shm'] 0m1.2s DEBUG: sources.list: deb http://deb.debian.org/debian/ stretch main 0m1.2s DEBUG: Created policy-rc.d and chmodded it. 0m1.2s DEBUG: Created resolv.conf. 0m1.2s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmpbtuj4qny/tmp/scripts/ 0m1.2s INFO: Running scripts post_chroot_unpack 0m1.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'apt-get', 'update'] 0m2.0s DUMP: Ign:1 http://deb.debian.org/debian stretch InRelease Hit:2 http://deb.debian.org/debian stretch Release Reading package lists... 0m2.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'apt-get', 'update'] 0m2.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'apt-get', '-yf', 'dist-upgrade'] 0m2.2s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'apt-get', '-yf', 'dist-upgrade'] 0m2.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.7s DUMP: 660e5103244a20b75ca08c3f8741e16e - 0m2.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.7s INFO: Running scripts post_setup 0m2.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/post_setup_dummy_users'] 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/post_setup_dummy_users'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/post_setup_forbid_home'] 0m3.7s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m3.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/post_setup_forbid_home'] 0m3.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.8s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' '/bin/sync' -> 'true' 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/post_setup_force-unsafe-io'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/post_setup_minimize'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/post_setup_minimize'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/post_setup_squeeze-backports'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/post_setup_zz_backports'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/post_setup_zz_backports'] 0m3.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'apt-get', 'clean'] 0m3.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'apt-get', 'clean'] 0m3.8s DEBUG: Recording chroot state 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', '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/tmpbtuj4qny', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'dpkg-divert', '--list'] 0m4.1s DUMP: local diversion of /bin/sync to /bin/sync.distrib diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'dpkg-divert', '--list'] 0m4.1s INFO: Running scripts is_testable 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/is_testable_uninstallable'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/is_testable_uninstallable'] 0m4.2s INFO: apt-cache does not know about any of the requested packages 0m4.2s INFO: Running scripts pre_test 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/pre_test_exceptions'] 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/pre_test_exceptions'] 0m4.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/pre_test_root_password'] 0m4.2s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m4.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/pre_test_root_password'] 0m4.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny'] 0m4.4s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny'] 0m4.7s DEBUG: No broken symlinks as far as we can find. 0m4.7s INFO: Running scripts pre_install 0m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/pre_install_database-server'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/pre_install_database-server'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/pre_install_exceptions'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/pre_install_exceptions'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/pre_install_extras'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/pre_install_extras'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/pre_install_foreign_architecture'] 0m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m4.8s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny'] 0m5.0s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny'] 0m5.4s DEBUG: No broken symlinks as far as we can find. 0m5.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'apt-cache', 'policy'] 0m6.0s 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: 0m6.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'apt-cache', 'policy'] 0m6.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'apt-cache', 'policy', 'roary'] 0m6.1s DUMP: roary: Installed: (none) Candidate: 3.8.0+dfsg-1 Version table: 3.8.0+dfsg-1 500 500 http://deb.debian.org/debian stretch/main amd64 Packages 0m6.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'apt-cache', 'policy', 'roary'] 0m6.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'apt-get', '-y', 'install', 'roary=3.8.0+dfsg-1'] 1m12.2s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: amap-align apache2-bin autotools-dev bedtools beignet-opencl-icd binutils bioperl bioperl-run blast2 blends-common bowtie build-essential bwa bzip2 bzip2-doc ca-certificates cd-hit cdbs clustalo clustalw cpp cpp-6 cron dbus dialign dialign-tx dialign-tx-data dirmngr dpkg-dev emboss emboss-data emboss-lib exim4 exim4-base exim4-config exim4-daemon-light exonerate fakeroot fasttree file fontconfig fontconfig-config fonts-dejavu-core fonts-droid-fallback fonts-lato fonts-liberation fonts-noto-mono fsa g++ g++-6 gawk gcc gcc-6 gfortran gfortran-6 ghostscript gnupg gnupg-agent gnupg-l10n graphviz gsfonts guile-2.0-libs hmmer hyphy-common hyphy-mpi icu-devtools infernal javascript-common kalign krb5-locales libace-perl libalgorithm-c3-perl libalgorithm-diff-perl libalgorithm-diff-xs-perl libalgorithm-merge-perl libalgorithm-munkres-perl libann0 libapache-dbi-perl libapache2-mod-perl2 libapache2-reload-perl libapparmor1 libapr1 libaprutil1 libaprutil1-dbd-sqlite3 libaprutil1-ldap libargtable2-0 libarray-compare-perl libarray-utils-perl libasan3 libassuan0 libatomic1 libauthen-sasl-perl libavahi-client3 libavahi-common-data libavahi-common3 libb-hooks-endofscope-perl libbio-asn1-entrezgene-perl libbio-perl-perl libbio-perl-run-perl libbit-vector-perl libblas-common libblas-dev libblas3 libbsd-resource-perl libbsd0 libbz2-dev libc-dev-bin libc6-dev libcache-cache-perl libcairo2 libcapture-tiny-perl libcarp-clan-perl libcc1-0 libcdt5 libcgi-fast-perl libcgi-pm-perl libcgraph6 libcilkrts5 libclass-c3-perl libclass-c3-xs-perl libclass-data-inheritable-perl libclass-inspector-perl libclass-load-perl libclass-load-xs-perl libclass-method-modifiers-perl libclass-tiny-perl libclass-xsaccessor-perl libclone-perl libconvert-binary-c-perl libconvert-binhex-perl libcrypt-rc4-perl libcups2 libcupsfilters1 libcupsimage2 libcurl3 libcurl3-gnutls libdata-optlist-perl libdata-stag-perl libdate-calc-perl libdate-calc-xs-perl libdate-manip-perl libdatrie1 libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libdbi-perl libdbus-1-3 libdevel-caller-perl libdevel-globaldestruction-perl libdevel-lexalias-perl libdevel-overloadinfo-perl libdevel-partialdump-perl libdevel-stacktrace-perl libdevel-symdump-perl libdigest-perl-md5-perl libdist-checkconflicts-perl libdivsufsort3 libdpkg-perl libdrm-amdgpu1 libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libelf1 libemail-date-format-perl libencode-locale-perl libenv-path-perl liberror-perl libeval-closure-perl libexception-class-perl libexpat1 libexporter-tiny-perl libfabric1 libfakeroot libfcgi-perl libffi6 libfile-basedir-perl libfile-desktopentry-perl libfile-fcntllock-perl libfile-find-rule-perl libfile-grep-perl libfile-listing-perl libfile-mimeinfo-perl libfile-slurp-tiny-perl libfile-slurper-perl libfile-which-perl libfindbin-libs-perl libfont-afm-perl libfontconfig1 libfontenc1 libfreetype6 libfreezethaw-perl libfribidi0 libgc1c2 libgcc-6-dev libgd-perl libgd3 libgdbm3 libgfortran-6-dev libgfortran3 libgl1-mesa-dri libgl1-mesa-glx libglapi-mesa libglib2.0-0 libglib2.0-data libgmp10 libgnutls30 libgomp1 libgpm2 libgraph-perl libgraph-readwrite-perl libgraphite2-3 libgraphviz-perl libgs9 libgs9-common libgsasl7 libgssapi-krb5-2 libgts-0.7-5 libgts-bin libgvc6 libgvpr2 libharfbuzz0b libhmsbeagle1v5 libhogweed4 libhpdf-2.2.1 libhtml-form-perl libhtml-format-perl libhtml-parser-perl libhtml-tableextract-perl libhtml-tagset-perl libhtml-tree-perl libhts1 libhttp-cookies-perl libhttp-daemon-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libhwloc-plugins libhwloc5 libibverbs1 libice6 libicu-dev libicu57 libidn11 libidn2-0 libijs-0.35 libimport-into-perl libio-all-perl libio-html-perl libio-pty-perl libio-sessiondata-perl libio-socket-ssl-perl libio-string-perl libio-stringy-perl libipc-run-perl libipc-shareable-perl libipc-sharelite-perl libipc-system-simple-perl libisl15 libitm1 libjbig0 libjbig2dec0 libjcode-pm-perl libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libjs-jquery libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libksba8 libkyotocabinet16v5 liblapack-dev liblapack3 liblcms2-2 libldap-2.4-2 libldap-common liblist-moreutils-perl libllvm3.9 liblocale-gettext-perl liblog-dispatch-perl liblog-log4perl-perl liblsan0 libltdl7 liblua5.2-0 liblwp-mediatypes-perl liblwp-protocol-https-perl liblzma-dev liblzo2-2 libmagic-mgc libmagic1 libmail-sendmail-perl libmailtools-perl libmailutils5 libmariadbclient18 libmath-derivative-perl libmath-spline-perl libmime-lite-perl libmime-tools-perl libmime-types-perl libmldbm-perl libmodule-implementation-perl libmodule-runtime-conflicts-perl libmodule-runtime-perl libmoo-perl libmoose-perl libmpc3 libmpfr4 libmpx2 libmro-compat-perl libnamespace-clean-perl libncurses5 libncurses5-dev libnet-dbus-perl libnet-http-perl libnet-smtp-ssl-perl libnet-ssleay-perl libnettle6 libnghttp2-14 libnl-3-200 libnl-route-3-200 libnpth0 libntlm0 libnuma1 libnumber-compare-perl libole-storage-lite-perl libopenjp2-7 libopenmpi2 libossp-uuid-perl libossp-uuid16 libp11-kit0 libpackage-deprecationmanager-perl libpackage-stash-perl libpackage-stash-xs-perl libpadwalker-perl libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libparams-classify-perl libparams-util-perl libparams-validate-perl libparse-recdescent-perl libparse-yapp-perl libpathplan4 libpciaccess0 libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libperl5.24 libperlio-utf8-strict-perl libpixman-1-0 libpng-dev libpng-tools libpng16-16 libpostscript-perl libpq5 libprocps6 libpsl5 libpsm-infinipath1 libpython-stdlib libpython2.7 libpython2.7-minimal libpython2.7-stdlib libquadmath0 librdmacm1 libreadline-dev libreadline7 librole-tiny-perl librtmp1 libruby2.3 libsasl2-2 libsasl2-modules libsasl2-modules-db libscalar-list-utils-perl libsensors4 libset-scalar-perl libsigsegv2 libsm6 libsoap-lite-perl libsort-naturally-perl libspiffy-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsqlite3-0 libssh2-1 libssl1.0.2 libssl1.1 libstatistics-descriptive-perl libstdc++-6-dev libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-uplevel-perl libsvg-graph-perl libsvg-perl libsys-hostname-long-perl libtask-weaken-perl libtasn1-6 libtcl8.6 libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-file-perl libtest-files-perl libtest-most-perl libtest-output-perl libtest-simple-perl libtest-warn-perl libtext-csv-perl libtext-csv-xs-perl libtext-diff-perl libtext-glob-perl libtext-iconv-perl libthai-data libthai0 libtie-ixhash-perl libtiff5 libtimedate-perl libtinfo-dev libtk8.6 libtree-dagnode-perl libtry-tiny-perl libtsan0 libtxc-dxtn-s2tc libtype-tiny-perl libtype-tiny-xs-perl libubsan0 libunicode-map-perl libunistring0 liburi-perl libvariable-magic-perl libwebp6 libwrap0 libwww-perl libwww-robotrules-perl libx11-6 libx11-data libx11-protocol-perl libx11-xcb1 libxau6 libxaw7 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-shape0 libxcb-shm0 libxcb-sync1 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxdot4 libxext6 libxfixes3 libxft2 libxi6 libxinerama1 libxml-dom-perl libxml-dom-xpath-perl libxml-filter-buffertext-perl libxml-libxml-perl libxml-libxslt-perl libxml-namespacesupport-perl libxml-parser-perl libxml-perl libxml-regexp-perl libxml-sax-base-perl libxml-sax-expat-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl libxml-writer-perl libxml-xpath-perl libxml-xpathengine-perl libxml2 libxmlrpc-lite-perl libxmu6 libxmuu1 libxpm4 libxrandr2 libxrender1 libxshmfence1 libxslt1.1 libxss1 libxt6 libxtst6 libxv1 libxxf86dga1 libxxf86vm1 libyaml-0-2 libyaml-libyaml-perl libyaml-perl linux-libc-dev littler lsb-base lynx lynx-common mafft mailutils mailutils-common make manpages manpages-dev maq mcl med-config menu mime-support mummer muscle mustang mysql-common ncbi-blast+ ncbi-blast+-legacy ncbi-data netbase ocl-icd-libopencl1 openmpi-bin openmpi-common openssl parallel patch perl perl-doc perl-modules-5.24 perl-openssl-defaults perl-tk phylip phyml pinentry-curses pkg-config poa poppler-data prank primer3 probalign probcons procps proda psmisc publicsuffix python python-minimal python2.7 python2.7-minimal r-base-core r-base-dev r-cran-assertthat r-cran-boot r-cran-class r-cran-cluster r-cran-codetools r-cran-colorspace r-cran-crayon r-cran-dichromat r-cran-digest r-cran-foreign r-cran-ggplot2 r-cran-gtable r-cran-kernsmooth 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-nnet r-cran-pkgkitten r-cran-plyr r-cran-rcolorbrewer r-cran-rcpp r-cran-reshape2 r-cran-rpart r-cran-scales r-cran-spatial r-cran-stringi r-cran-stringr r-cran-survival r-cran-tibble r-doc-html r-recommended rake raxml readline-common rename ruby ruby-did-you-mean ruby-minitest ruby-net-telnet ruby-power-assert ruby-test-unit ruby2.3 rubygems-integration samtools sgml-base shared-mime-info sim4 sysstat t-coffee tcpd tigr-glimmer tm-align tzdata ucf unzip wise wise-data x11-common x11-utils x11-xserver-utils xauth xdg-user-dirs xdg-utils xml-core xz-utils zip zlib1g-dev Suggested packages: apache2-doc apache2-suexec-pristine | apache2-suexec-custom filo binutils-doc groff-base gmap paml blends-doc bowtie-examples devscripts clustalx seaview cpp-doc gcc-6-locales anacron logrotate checksecurity default-dbus-session-bus | dbus-session-bus dbus-user-session libpam-systemd pinentry-gnome3 tor debian-keyring emboss-doc emboss-test embassy eximon4 exim4-doc-html | exim4-doc-info spf-tools-perl swaks fonts-noto g++-multilib g++-6-multilib gcc-6-doc libstdc++6-6-dbg gawk-doc gcc-multilib autoconf automake libtool flex bison gdb gcc-doc gcc-6-multilib libgcc1-dbg libgomp1-dbg libitm1-dbg libatomic1-dbg libasan3-dbg liblsan0-dbg libtsan0-dbg libubsan0-dbg libcilkrts5-dbg libmpx2-dbg libquadmath0-dbg gfortran-multilib gfortran-doc gfortran-6-multilib gfortran-6-doc libgfortran3-dbg libcoarrays-dev ghostscript-x parcimonie xloadimage scdaemon graphviz-doc hmmer-doc apache2 | lighttpd | httpd libdigest-hmac-perl libgssapi-perl libxml-sax-expatxs-perl liblapack-doc-man liblapack-doc glibc-doc cups-common libnet-daemon-perl libsql-statement-perl libgd-tools gnutls-bin gpm krb5-doc krb5-user libdata-dump-perl libhtml-element-extended-perl libhwloc-contrib-plugins icu-doc libdb-file-lock-perl libfile-readbackwards-perl liblcms2-utils libdbd-csv-perl liblog-dispatch-filerotate-perl librrds-perl libcrypt-ssleay-perl liblzma-doc libmojolicious-perl ncurses-doc uuid libscalar-number-perl pciutils readline-doc libsasl2-modules-gssapi-mit | libsasl2-modules-gssapi-heimdal libsasl2-modules-ldap libsasl2-modules-otp libsasl2-modules-sql lm-sensors libnet-jabber-perl libstdc++-6-doc libbareword-filehandles-perl libindirect-perl libmultidimensional-perl tcl8.6 tk8.6 libauthen-ntlm-perl libunicode-map8-perl libunicode-string-perl xml-twig-tools libyaml-shell-perl mailutils-mh mailutils-doc make-doc man-browser mcl-doc menu-l10n gksu | kde-runtime | ktsuss mustang-testdata ed diffutils-doc libterm-readline-gnu-perl | libterm-readline-perl-perl phylip-doc pinentry-doc poppler-utils fonts-japanese-mincho | fonts-ipafont-mincho fonts-japanese-gothic | fonts-ipafont-gothic fonts-arphic-ukai fonts-arphic-uming fonts-nanum ncbi-epcr probcons-extra python-doc python-tk python2.7-doc binfmt-support ess r-doc-info | r-doc-pdf r-mathlib r-base-html debhelper texlive-base texlive-latex-base texlive-generic-recommended texlive-fonts-recommended texlive-fonts-extra texlive-extra-utils texlive-latex-recommended texlive-latex-extra texinfo r-cran-kernlab r-cran-mvtnorm r-cran-vcd r-cran-shiny r-cran-testthat r-cran-hexbin r-cran-hmisc r-cran-mapproj r-cran-maps r-cran-maptools r-cran-multcomp r-cran-quantreg r-cran-knitr r-cran-getopt r-cran-abind r-cran-foreach r-cran-doparallel r-cran-iterators r-cran-inline r-cran-htmltools r-cran-htmlwidgets ri ruby-dev bundler sgml-base-doc isag boxshade t-coffee-examples pymol rasmol wise-doc mesa-utils nickle cairo-5c xorg-docs-core gvfs-bin The following NEW packages will be installed: amap-align apache2-bin autotools-dev bedtools beignet-opencl-icd binutils bioperl bioperl-run blast2 blends-common bowtie build-essential bwa bzip2 bzip2-doc ca-certificates cd-hit cdbs clustalo clustalw cpp cpp-6 cron dbus dialign dialign-tx dialign-tx-data dirmngr dpkg-dev emboss emboss-data emboss-lib exim4 exim4-base exim4-config exim4-daemon-light exonerate fakeroot fasttree file fontconfig fontconfig-config fonts-dejavu-core fonts-droid-fallback fonts-lato fonts-liberation fonts-noto-mono fsa g++ g++-6 gawk gcc gcc-6 gfortran gfortran-6 ghostscript gnupg gnupg-agent gnupg-l10n graphviz gsfonts guile-2.0-libs hmmer hyphy-common hyphy-mpi icu-devtools infernal javascript-common kalign krb5-locales libace-perl libalgorithm-c3-perl libalgorithm-diff-perl libalgorithm-diff-xs-perl libalgorithm-merge-perl libalgorithm-munkres-perl libann0 libapache-dbi-perl libapache2-mod-perl2 libapache2-reload-perl libapparmor1 libapr1 libaprutil1 libaprutil1-dbd-sqlite3 libaprutil1-ldap libargtable2-0 libarray-compare-perl libarray-utils-perl libasan3 libassuan0 libatomic1 libauthen-sasl-perl libavahi-client3 libavahi-common-data libavahi-common3 libb-hooks-endofscope-perl libbio-asn1-entrezgene-perl libbio-perl-perl libbio-perl-run-perl libbit-vector-perl libblas-common libblas-dev libblas3 libbsd-resource-perl libbsd0 libbz2-dev libc-dev-bin libc6-dev libcache-cache-perl libcairo2 libcapture-tiny-perl libcarp-clan-perl libcc1-0 libcdt5 libcgi-fast-perl libcgi-pm-perl libcgraph6 libcilkrts5 libclass-c3-perl libclass-c3-xs-perl libclass-data-inheritable-perl libclass-inspector-perl libclass-load-perl libclass-load-xs-perl libclass-method-modifiers-perl libclass-tiny-perl libclass-xsaccessor-perl libclone-perl libconvert-binary-c-perl libconvert-binhex-perl libcrypt-rc4-perl libcups2 libcupsfilters1 libcupsimage2 libcurl3 libcurl3-gnutls libdata-optlist-perl libdata-stag-perl libdate-calc-perl libdate-calc-xs-perl libdate-manip-perl libdatrie1 libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libdbi-perl libdbus-1-3 libdevel-caller-perl libdevel-globaldestruction-perl libdevel-lexalias-perl libdevel-overloadinfo-perl libdevel-partialdump-perl libdevel-stacktrace-perl libdevel-symdump-perl libdigest-perl-md5-perl libdist-checkconflicts-perl libdivsufsort3 libdpkg-perl libdrm-amdgpu1 libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libelf1 libemail-date-format-perl libencode-locale-perl libenv-path-perl liberror-perl libeval-closure-perl libexception-class-perl libexpat1 libexporter-tiny-perl libfabric1 libfakeroot libfcgi-perl libffi6 libfile-basedir-perl libfile-desktopentry-perl libfile-fcntllock-perl libfile-find-rule-perl libfile-grep-perl libfile-listing-perl libfile-mimeinfo-perl libfile-slurp-tiny-perl libfile-slurper-perl libfile-which-perl libfindbin-libs-perl libfont-afm-perl libfontconfig1 libfontenc1 libfreetype6 libfreezethaw-perl libfribidi0 libgc1c2 libgcc-6-dev libgd-perl libgd3 libgdbm3 libgfortran-6-dev libgfortran3 libgl1-mesa-dri libgl1-mesa-glx libglapi-mesa libglib2.0-0 libglib2.0-data libgmp10 libgnutls30 libgomp1 libgpm2 libgraph-perl libgraph-readwrite-perl libgraphite2-3 libgraphviz-perl libgs9 libgs9-common libgsasl7 libgssapi-krb5-2 libgts-0.7-5 libgts-bin libgvc6 libgvpr2 libharfbuzz0b libhmsbeagle1v5 libhogweed4 libhpdf-2.2.1 libhtml-form-perl libhtml-format-perl libhtml-parser-perl libhtml-tableextract-perl libhtml-tagset-perl libhtml-tree-perl libhts1 libhttp-cookies-perl libhttp-daemon-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libhwloc-plugins libhwloc5 libibverbs1 libice6 libicu-dev libicu57 libidn11 libidn2-0 libijs-0.35 libimport-into-perl libio-all-perl libio-html-perl libio-pty-perl libio-sessiondata-perl libio-socket-ssl-perl libio-string-perl libio-stringy-perl libipc-run-perl libipc-shareable-perl libipc-sharelite-perl libipc-system-simple-perl libisl15 libitm1 libjbig0 libjbig2dec0 libjcode-pm-perl libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libjs-jquery libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libksba8 libkyotocabinet16v5 liblapack-dev liblapack3 liblcms2-2 libldap-2.4-2 libldap-common liblist-moreutils-perl libllvm3.9 liblocale-gettext-perl liblog-dispatch-perl liblog-log4perl-perl liblsan0 libltdl7 liblua5.2-0 liblwp-mediatypes-perl liblwp-protocol-https-perl liblzma-dev liblzo2-2 libmagic-mgc libmagic1 libmail-sendmail-perl libmailtools-perl libmailutils5 libmariadbclient18 libmath-derivative-perl libmath-spline-perl libmime-lite-perl libmime-tools-perl libmime-types-perl libmldbm-perl libmodule-implementation-perl libmodule-runtime-conflicts-perl libmodule-runtime-perl libmoo-perl libmoose-perl libmpc3 libmpfr4 libmpx2 libmro-compat-perl libnamespace-clean-perl libncurses5 libncurses5-dev libnet-dbus-perl libnet-http-perl libnet-smtp-ssl-perl libnet-ssleay-perl libnettle6 libnghttp2-14 libnl-3-200 libnl-route-3-200 libnpth0 libntlm0 libnuma1 libnumber-compare-perl libole-storage-lite-perl libopenjp2-7 libopenmpi2 libossp-uuid-perl libossp-uuid16 libp11-kit0 libpackage-deprecationmanager-perl libpackage-stash-perl libpackage-stash-xs-perl libpadwalker-perl libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libparams-classify-perl libparams-util-perl libparams-validate-perl libparse-recdescent-perl libparse-yapp-perl libpathplan4 libpciaccess0 libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libperl5.24 libperlio-utf8-strict-perl libpixman-1-0 libpng-dev libpng-tools libpng16-16 libpostscript-perl libpq5 libprocps6 libpsl5 libpsm-infinipath1 libpython-stdlib libpython2.7 libpython2.7-minimal libpython2.7-stdlib libquadmath0 librdmacm1 libreadline-dev libreadline7 librole-tiny-perl librtmp1 libruby2.3 libsasl2-2 libsasl2-modules libsasl2-modules-db libscalar-list-utils-perl libsensors4 libset-scalar-perl libsigsegv2 libsm6 libsoap-lite-perl libsort-naturally-perl libspiffy-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsqlite3-0 libssh2-1 libssl1.0.2 libssl1.1 libstatistics-descriptive-perl libstdc++-6-dev libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-uplevel-perl libsvg-graph-perl libsvg-perl libsys-hostname-long-perl libtask-weaken-perl libtasn1-6 libtcl8.6 libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-file-perl libtest-files-perl libtest-most-perl libtest-output-perl libtest-simple-perl libtest-warn-perl libtext-csv-perl libtext-csv-xs-perl libtext-diff-perl libtext-glob-perl libtext-iconv-perl libthai-data libthai0 libtie-ixhash-perl libtiff5 libtimedate-perl libtinfo-dev libtk8.6 libtree-dagnode-perl libtry-tiny-perl libtsan0 libtxc-dxtn-s2tc libtype-tiny-perl libtype-tiny-xs-perl libubsan0 libunicode-map-perl libunistring0 liburi-perl libvariable-magic-perl libwebp6 libwrap0 libwww-perl libwww-robotrules-perl libx11-6 libx11-data libx11-protocol-perl libx11-xcb1 libxau6 libxaw7 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-shape0 libxcb-shm0 libxcb-sync1 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxdot4 libxext6 libxfixes3 libxft2 libxi6 libxinerama1 libxml-dom-perl libxml-dom-xpath-perl libxml-filter-buffertext-perl libxml-libxml-perl libxml-libxslt-perl libxml-namespacesupport-perl libxml-parser-perl libxml-perl libxml-regexp-perl libxml-sax-base-perl libxml-sax-expat-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl libxml-writer-perl libxml-xpath-perl libxml-xpathengine-perl libxml2 libxmlrpc-lite-perl libxmu6 libxmuu1 libxpm4 libxrandr2 libxrender1 libxshmfence1 libxslt1.1 libxss1 libxt6 libxtst6 libxv1 libxxf86dga1 libxxf86vm1 libyaml-0-2 libyaml-libyaml-perl libyaml-perl linux-libc-dev littler lsb-base lynx lynx-common mafft mailutils mailutils-common make manpages manpages-dev maq mcl med-config menu mime-support mummer muscle mustang mysql-common ncbi-blast+ ncbi-blast+-legacy ncbi-data netbase ocl-icd-libopencl1 openmpi-bin openmpi-common openssl parallel patch perl perl-doc perl-modules-5.24 perl-openssl-defaults perl-tk phylip phyml pinentry-curses pkg-config poa poppler-data prank primer3 probalign probcons procps proda psmisc publicsuffix python python-minimal python2.7 python2.7-minimal r-base-core r-base-dev r-cran-assertthat r-cran-boot r-cran-class r-cran-cluster r-cran-codetools r-cran-colorspace r-cran-crayon r-cran-dichromat r-cran-digest r-cran-foreign r-cran-ggplot2 r-cran-gtable r-cran-kernsmooth 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-nnet r-cran-pkgkitten r-cran-plyr r-cran-rcolorbrewer r-cran-rcpp r-cran-reshape2 r-cran-rpart r-cran-scales r-cran-spatial r-cran-stringi r-cran-stringr r-cran-survival r-cran-tibble r-doc-html r-recommended rake raxml readline-common rename roary ruby ruby-did-you-mean ruby-minitest ruby-net-telnet ruby-power-assert ruby-test-unit ruby2.3 rubygems-integration samtools sgml-base shared-mime-info sim4 sysstat t-coffee tcpd tigr-glimmer tm-align tzdata ucf unzip wise wise-data x11-common x11-utils x11-xserver-utils xauth xdg-user-dirs xdg-utils xml-core xz-utils zip zlib1g-dev 0 upgraded, 634 newly installed, 0 to remove and 0 not upgraded. Need to get 398 MB of archives. After this operation, 1761 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian stretch/main amd64 lsb-base all 9.20161125 [27.9 kB] Get:2 http://deb.debian.org/debian stretch/main amd64 cron amd64 3.0pl1-128+deb9u1 [95.4 kB] Get:3 http://deb.debian.org/debian stretch/main amd64 perl-modules-5.24 all 5.24.1-3+deb9u7 [2723 kB] Get:4 http://deb.debian.org/debian stretch/main amd64 libgdbm3 amd64 1.8.3-14 [30.0 kB] Get:5 http://deb.debian.org/debian stretch/main amd64 libperl5.24 amd64 5.24.1-3+deb9u7 [3527 kB] Get:6 http://deb.debian.org/debian stretch/main amd64 perl amd64 5.24.1-3+deb9u7 [218 kB] Get:7 http://deb.debian.org/debian stretch/main amd64 libpython2.7-minimal amd64 2.7.13-2+deb9u3 [389 kB] Get:8 http://deb.debian.org/debian stretch/main amd64 python2.7-minimal amd64 2.7.13-2+deb9u3 [1382 kB] Get:9 http://deb.debian.org/debian stretch/main amd64 python-minimal amd64 2.7.13-2 [40.5 kB] Get:10 http://deb.debian.org/debian stretch/main amd64 mime-support all 3.60 [36.7 kB] Get:11 http://deb.debian.org/debian stretch/main amd64 libexpat1 amd64 2.2.0-2+deb9u3 [83.7 kB] Get:12 http://deb.debian.org/debian stretch/main amd64 libffi6 amd64 3.2.1-6 [20.4 kB] Get:13 http://deb.debian.org/debian stretch/main amd64 readline-common all 7.0-3 [70.4 kB] Get:14 http://deb.debian.org/debian stretch/main amd64 libreadline7 amd64 7.0-3 [151 kB] Get:15 http://deb.debian.org/debian stretch/main amd64 libsqlite3-0 amd64 3.16.2-5+deb9u1 [572 kB] Get:16 http://deb.debian.org/debian stretch/main amd64 libssl1.1 amd64 1.1.0l-1~deb9u1 [1358 kB] Get:17 http://deb.debian.org/debian stretch/main amd64 libpython2.7-stdlib amd64 2.7.13-2+deb9u3 [1897 kB] Get:18 http://deb.debian.org/debian stretch/main amd64 python2.7 amd64 2.7.13-2+deb9u3 [285 kB] Get:19 http://deb.debian.org/debian stretch/main amd64 libpython-stdlib amd64 2.7.13-2 [20.0 kB] Get:20 http://deb.debian.org/debian stretch/main amd64 python amd64 2.7.13-2 [154 kB] Get:21 http://deb.debian.org/debian stretch/main amd64 libpng16-16 amd64 1.6.28-1+deb9u1 [280 kB] Get:22 http://deb.debian.org/debian stretch/main amd64 libfreetype6 amd64 2.6.3-3.2+deb9u1 [438 kB] Get:23 http://deb.debian.org/debian stretch/main amd64 ucf all 3.0036 [70.2 kB] Get:24 http://deb.debian.org/debian stretch/main amd64 fonts-dejavu-core all 2.37-1 [1068 kB] Get:25 http://deb.debian.org/debian stretch/main amd64 fonts-liberation all 1:1.07.4-2 [827 kB] Get:26 http://deb.debian.org/debian stretch/main amd64 fontconfig-config all 2.11.0-6.7 [271 kB] Get:27 http://deb.debian.org/debian stretch/main amd64 libfontconfig1 amd64 2.11.0-6.7+b1 [331 kB] Get:28 http://deb.debian.org/debian stretch/main amd64 fontconfig amd64 2.11.0-6.7+b1 [404 kB] Get:29 http://deb.debian.org/debian stretch/main amd64 fonts-droid-fallback all 1:6.0.1r16-1.1 [1807 kB] Get:30 http://deb.debian.org/debian stretch/main amd64 fonts-lato all 2.0-1 [2684 kB] Get:31 http://deb.debian.org/debian stretch/main amd64 libgmp10 amd64 2:6.1.2+dfsg-1 [253 kB] Get:32 http://deb.debian.org/debian stretch/main amd64 libmpfr4 amd64 3.1.5-1 [556 kB] Get:33 http://deb.debian.org/debian stretch/main amd64 libsigsegv2 amd64 2.10-5 [28.9 kB] Get:34 http://deb.debian.org/debian stretch/main amd64 gawk amd64 1:4.1.4+dfsg-1 [571 kB] Get:35 http://deb.debian.org/debian stretch/main amd64 liblocale-gettext-perl amd64 1.07-3+b1 [18.7 kB] Get:36 http://deb.debian.org/debian stretch/main amd64 libpcrecpp0v5 amd64 2:8.39-3 [151 kB] Get:37 http://deb.debian.org/debian stretch/main amd64 libxau6 amd64 1:1.0.8-1 [20.7 kB] Get:38 http://deb.debian.org/debian stretch/main amd64 libbsd0 amd64 0.8.3-1 [83.0 kB] Get:39 http://deb.debian.org/debian stretch/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:40 http://deb.debian.org/debian stretch/main amd64 libxcb1 amd64 1.12-1 [133 kB] Get:41 http://deb.debian.org/debian stretch/main amd64 libx11-data all 2:1.6.4-3+deb9u1 [287 kB] Get:42 http://deb.debian.org/debian stretch/main amd64 libx11-6 amd64 2:1.6.4-3+deb9u1 [748 kB] Get:43 http://deb.debian.org/debian stretch/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get:44 http://deb.debian.org/debian stretch/main amd64 x11-common all 1:7.7+19 [251 kB] Get:45 http://deb.debian.org/debian stretch/main amd64 libxss1 amd64 1:1.2.2-1 [17.5 kB] Get:46 http://deb.debian.org/debian stretch/main amd64 poppler-data all 0.4.7-8 [1451 kB] Get:47 http://deb.debian.org/debian stretch/main amd64 sgml-base all 1.29 [14.8 kB] Get:48 http://deb.debian.org/debian stretch/main amd64 tzdata all 2020a-0+deb9u1 [278 kB] Get:49 http://deb.debian.org/debian stretch/main amd64 libassuan0 amd64 2.4.3-2 [42.5 kB] Get:50 http://deb.debian.org/debian stretch/main amd64 pinentry-curses amd64 1.0.0-2 [50.5 kB] Get:51 http://deb.debian.org/debian stretch/main amd64 libnpth0 amd64 1.3-1 [14.6 kB] Get:52 http://deb.debian.org/debian stretch/main amd64 gnupg-agent amd64 2.1.18-8~deb9u4 [554 kB] Get:53 http://deb.debian.org/debian stretch/main amd64 libksba8 amd64 1.3.5-2 [99.7 kB] Get:54 http://deb.debian.org/debian stretch/main amd64 gnupg amd64 2.1.18-8~deb9u4 [1128 kB] Get:55 http://deb.debian.org/debian stretch/main amd64 libprocps6 amd64 2:3.3.12-3+deb9u1 [58.5 kB] Get:56 http://deb.debian.org/debian stretch/main amd64 libssl1.0.2 amd64 1.0.2u-1~deb9u1 [1304 kB] Get:57 http://deb.debian.org/debian stretch/main amd64 netbase all 5.4 [19.1 kB] Get:58 http://deb.debian.org/debian stretch/main amd64 libncurses5 amd64 6.0+20161126-1+deb9u2 [93.4 kB] Get:59 http://deb.debian.org/debian stretch/main amd64 procps amd64 2:3.3.12-3+deb9u1 [250 kB] Get:60 http://deb.debian.org/debian stretch/main amd64 bzip2 amd64 1.0.6-8.1 [47.5 kB] Get:61 http://deb.debian.org/debian stretch/main amd64 libapparmor1 amd64 2.11.0-3+deb9u2 [78.9 kB] Get:62 http://deb.debian.org/debian stretch/main amd64 libdbus-1-3 amd64 1.10.32-0+deb9u1 [196 kB] Get:63 http://deb.debian.org/debian stretch/main amd64 dbus amd64 1.10.32-0+deb9u1 [213 kB] Get:64 http://deb.debian.org/debian stretch/main amd64 libmagic-mgc amd64 1:5.30-1+deb9u3 [222 kB] Get:65 http://deb.debian.org/debian stretch/main amd64 libmagic1 amd64 1:5.30-1+deb9u3 [111 kB] Get:66 http://deb.debian.org/debian stretch/main amd64 file amd64 1:5.30-1+deb9u3 [64.2 kB] Get:67 http://deb.debian.org/debian stretch/main amd64 krb5-locales all 1.15-1+deb9u1 [93.8 kB] Get:68 http://deb.debian.org/debian stretch/main amd64 libedit2 amd64 3.1-20160903-3 [84.8 kB] Get:69 http://deb.debian.org/debian stretch/main amd64 libgc1c2 amd64 1:7.4.2-8 [208 kB] Get:70 http://deb.debian.org/debian stretch/main amd64 libnettle6 amd64 3.3-1+b2 [192 kB] Get:71 http://deb.debian.org/debian stretch/main amd64 libhogweed4 amd64 3.3-1+b2 [136 kB] Get:72 http://deb.debian.org/debian stretch/main amd64 libidn11 amd64 1.33-1+deb9u1 [115 kB] Get:73 http://deb.debian.org/debian stretch/main amd64 libp11-kit0 amd64 0.23.3-2 [111 kB] Get:74 http://deb.debian.org/debian stretch/main amd64 libtasn1-6 amd64 4.10-1.1+deb9u1 [50.6 kB] Get:75 http://deb.debian.org/debian stretch/main amd64 libgnutls30 amd64 3.5.8-5+deb9u5 [896 kB] Get:76 http://deb.debian.org/debian stretch/main amd64 libgpm2 amd64 1.20.4-6.2+b1 [34.2 kB] Get:77 http://deb.debian.org/debian stretch/main amd64 libkeyutils1 amd64 1.5.9-9 [12.4 kB] Get:78 http://deb.debian.org/debian stretch/main amd64 libkrb5support0 amd64 1.15-1+deb9u1 [61.9 kB] Get:79 http://deb.debian.org/debian stretch/main amd64 libk5crypto3 amd64 1.15-1+deb9u1 [119 kB] Get:80 http://deb.debian.org/debian stretch/main amd64 libkrb5-3 amd64 1.15-1+deb9u1 [311 kB] Get:81 http://deb.debian.org/debian stretch/main amd64 libgssapi-krb5-2 amd64 1.15-1+deb9u1 [155 kB] Get:82 http://deb.debian.org/debian stretch/main amd64 libsasl2-modules-db amd64 2.1.27~101-g0780600+dfsg-3+deb9u1 [68.4 kB] Get:83 http://deb.debian.org/debian stretch/main amd64 libsasl2-2 amd64 2.1.27~101-g0780600+dfsg-3+deb9u1 [105 kB] Get:84 http://deb.debian.org/debian stretch/main amd64 libldap-common all 2.4.44+dfsg-5+deb9u4 [85.7 kB] Get:85 http://deb.debian.org/debian stretch/main amd64 libldap-2.4-2 amd64 2.4.44+dfsg-5+deb9u4 [219 kB] Get:86 http://deb.debian.org/debian stretch/main amd64 libwrap0 amd64 7.6.q-26 [58.2 kB] Get:87 http://deb.debian.org/debian stretch/main amd64 libicu57 amd64 57.1-6+deb9u4 [7699 kB] Get:88 http://deb.debian.org/debian stretch/main amd64 libxml2 amd64 2.9.4+dfsg1-2.2+deb9u2 [920 kB] Get:89 http://deb.debian.org/debian stretch/main amd64 manpages all 4.10-2 [1222 kB] Get:90 http://deb.debian.org/debian stretch/main amd64 xz-utils amd64 5.2.2-1.2+b1 [266 kB] Get:91 http://deb.debian.org/debian stretch/main amd64 amap-align amd64 2.2-6 [129 kB] Get:92 http://deb.debian.org/debian stretch/main amd64 libapr1 amd64 1.5.2-5 [96.6 kB] Get:93 http://deb.debian.org/debian stretch/main amd64 libaprutil1 amd64 1.5.4-3 [85.8 kB] Get:94 http://deb.debian.org/debian stretch/main amd64 libaprutil1-dbd-sqlite3 amd64 1.5.4-3 [19.3 kB] Get:95 http://deb.debian.org/debian stretch/main amd64 libaprutil1-ldap amd64 1.5.4-3 [17.4 kB] Get:96 http://deb.debian.org/debian stretch/main amd64 liblua5.2-0 amd64 5.2.4-1.1+b2 [110 kB] Get:97 http://deb.debian.org/debian stretch/main amd64 libnghttp2-14 amd64 1.18.1-1+deb9u1 [79.2 kB] Get:98 http://deb.debian.org/debian stretch/main amd64 apache2-bin amd64 2.4.25-3+deb9u9 [1185 kB] Get:99 http://deb.debian.org/debian stretch/main amd64 autotools-dev all 20161112.1 [73.4 kB] Get:100 http://deb.debian.org/debian stretch/main amd64 bedtools amd64 2.26.0+dfsg-3 [584 kB] Get:101 http://deb.debian.org/debian stretch/main amd64 binutils amd64 2.28-5 [3770 kB] Get:102 http://deb.debian.org/debian stretch/main amd64 libio-string-perl all 1.08-3 [12.3 kB] Get:103 http://deb.debian.org/debian stretch/main amd64 libdata-stag-perl all 0.14-2 [448 kB] Get:104 http://deb.debian.org/debian stretch/main amd64 libbio-perl-perl all 1.7.1-2 [4605 kB] Get:105 http://deb.debian.org/debian stretch/main amd64 bioperl all 1.7.1-2 [422 kB] Get:106 http://deb.debian.org/debian stretch/main amd64 libbio-perl-run-perl all 1.7.1-3 [816 kB] Get:107 http://deb.debian.org/debian stretch/main amd64 bioperl-run all 1.7.1-3 [44.2 kB] Get:108 http://deb.debian.org/debian stretch/main amd64 ncbi-data all 6.1.20170106+dfsg1-0+deb9u1 [3555 kB] Get:109 http://deb.debian.org/debian stretch/main amd64 libgomp1 amd64 6.3.0-18+deb9u1 [73.3 kB] Get:110 http://deb.debian.org/debian stretch/main amd64 ncbi-blast+ amd64 2.6.0-1 [9591 kB] Get:111 http://deb.debian.org/debian stretch/main amd64 ncbi-blast+-legacy all 2.6.0-1 [9604 B] Get:112 http://deb.debian.org/debian stretch/main amd64 blast2 all 1:2.6.0-1 [9084 B] Get:113 http://deb.debian.org/debian stretch/main amd64 menu amd64 2.1.47+b1 [380 kB] Get:114 http://deb.debian.org/debian stretch/main amd64 blends-common all 0.6.96 [23.3 kB] Get:115 http://deb.debian.org/debian stretch/main amd64 libc-dev-bin amd64 2.24-11+deb9u4 [259 kB] Get:116 http://deb.debian.org/debian stretch/main amd64 linux-libc-dev amd64 4.9.228-1 [1511 kB] Get:117 http://deb.debian.org/debian stretch/main amd64 libc6-dev amd64 2.24-11+deb9u4 [2364 kB] Get:118 http://deb.debian.org/debian stretch/main amd64 libisl15 amd64 0.18-1 [564 kB] Get:119 http://deb.debian.org/debian stretch/main amd64 libmpc3 amd64 1.0.3-1+b2 [39.9 kB] Get:120 http://deb.debian.org/debian stretch/main amd64 cpp-6 amd64 6.3.0-18+deb9u1 [6584 kB] Get:121 http://deb.debian.org/debian stretch/main amd64 cpp amd64 4:6.3.0-4 [18.7 kB] Get:122 http://deb.debian.org/debian stretch/main amd64 libcc1-0 amd64 6.3.0-18+deb9u1 [30.6 kB] Get:123 http://deb.debian.org/debian stretch/main amd64 libitm1 amd64 6.3.0-18+deb9u1 [27.3 kB] Get:124 http://deb.debian.org/debian stretch/main amd64 libatomic1 amd64 6.3.0-18+deb9u1 [8966 B] Get:125 http://deb.debian.org/debian stretch/main amd64 libasan3 amd64 6.3.0-18+deb9u1 [311 kB] Get:126 http://deb.debian.org/debian stretch/main amd64 liblsan0 amd64 6.3.0-18+deb9u1 [115 kB] Get:127 http://deb.debian.org/debian stretch/main amd64 libtsan0 amd64 6.3.0-18+deb9u1 [257 kB] Get:128 http://deb.debian.org/debian stretch/main amd64 libubsan0 amd64 6.3.0-18+deb9u1 [107 kB] Get:129 http://deb.debian.org/debian stretch/main amd64 libcilkrts5 amd64 6.3.0-18+deb9u1 [40.5 kB] Get:130 http://deb.debian.org/debian stretch/main amd64 libmpx2 amd64 6.3.0-18+deb9u1 [11.2 kB] Get:131 http://deb.debian.org/debian stretch/main amd64 libquadmath0 amd64 6.3.0-18+deb9u1 [131 kB] Get:132 http://deb.debian.org/debian stretch/main amd64 libgcc-6-dev amd64 6.3.0-18+deb9u1 [2296 kB] Get:133 http://deb.debian.org/debian stretch/main amd64 gcc-6 amd64 6.3.0-18+deb9u1 [6900 kB] Get:134 http://deb.debian.org/debian stretch/main amd64 gcc amd64 4:6.3.0-4 [5196 B] Get:135 http://deb.debian.org/debian stretch/main amd64 libstdc++-6-dev amd64 6.3.0-18+deb9u1 [1420 kB] Get:136 http://deb.debian.org/debian stretch/main amd64 g++-6 amd64 6.3.0-18+deb9u1 [7094 kB] Get:137 http://deb.debian.org/debian stretch/main amd64 g++ amd64 4:6.3.0-4 [1546 B] Get:138 http://deb.debian.org/debian stretch/main amd64 make amd64 4.1-9.1 [302 kB] Get:139 http://deb.debian.org/debian stretch/main amd64 libdpkg-perl all 1.18.25 [1287 kB] Get:140 http://deb.debian.org/debian stretch/main amd64 patch amd64 2.7.5-1+deb9u2 [112 kB] Get:141 http://deb.debian.org/debian stretch/main amd64 dpkg-dev all 1.18.25 [1595 kB] Get:142 http://deb.debian.org/debian stretch/main amd64 build-essential amd64 12.3 [7346 B] Get:143 http://deb.debian.org/debian stretch/main amd64 bwa amd64 0.7.15-2+deb9u1 [194 kB] Get:144 http://deb.debian.org/debian stretch/main amd64 bzip2-doc all 1.0.6-8.1 [307 kB] Get:145 http://deb.debian.org/debian stretch/main amd64 openssl amd64 1.1.0l-1~deb9u1 [749 kB] Get:146 http://deb.debian.org/debian stretch/main amd64 ca-certificates all 20200601~deb9u1 [160 kB] Get:147 http://deb.debian.org/debian stretch/main amd64 cd-hit amd64 4.6.6-2 [852 kB] Get:148 http://deb.debian.org/debian stretch/main amd64 cdbs all 0.4.150 [82.6 kB] Get:149 http://deb.debian.org/debian stretch/main amd64 libargtable2-0 amd64 13-1 [17.4 kB] Get:150 http://deb.debian.org/debian stretch/main amd64 clustalo amd64 1.2.4-1 [263 kB] Get:151 http://deb.debian.org/debian stretch/main amd64 clustalw amd64 2.1+lgpl-5 [286 kB] Get:152 http://deb.debian.org/debian stretch/main amd64 dialign amd64 2.2.1-8 [138 kB] Get:153 http://deb.debian.org/debian stretch/main amd64 dialign-tx-data all 1.0.2-9 [869 kB] Get:154 http://deb.debian.org/debian stretch/main amd64 dialign-tx amd64 1.0.2-9 [85.7 kB] Get:155 http://deb.debian.org/debian stretch/main amd64 dirmngr amd64 2.1.18-8~deb9u4 [597 kB] Get:156 http://deb.debian.org/debian stretch/main amd64 libjpeg62-turbo amd64 1:1.5.1-2 [134 kB] Get:157 http://deb.debian.org/debian stretch/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get:158 http://deb.debian.org/debian stretch/main amd64 libtiff5 amd64 4.0.8-2+deb9u5 [239 kB] Get:159 http://deb.debian.org/debian stretch/main amd64 libwebp6 amd64 0.5.2-1 [235 kB] Get:160 http://deb.debian.org/debian stretch/main amd64 libxpm4 amd64 1:3.5.12-1 [49.1 kB] Get:161 http://deb.debian.org/debian stretch/main amd64 libgd3 amd64 2.2.4-2+deb9u5 [132 kB] Get:162 http://deb.debian.org/debian stretch/main amd64 libhpdf-2.2.1 amd64 2.2.1-1.1+b1 [319 kB] Get:163 http://deb.debian.org/debian stretch/main amd64 mysql-common all 5.8+1.0.2 [5608 B] Get:164 http://deb.debian.org/debian stretch/main amd64 libmariadbclient18 amd64 10.1.45-0+deb9u1 [785 kB] Get:165 http://deb.debian.org/debian stretch/main amd64 libpq5 amd64 9.6.17-0+deb9u1 [137 kB] Get:166 http://deb.debian.org/debian stretch/main amd64 emboss-lib amd64 6.6.0+dfsg-6 [2773 kB] Get:167 http://deb.debian.org/debian stretch/main amd64 emboss-data all 6.6.0+dfsg-6 [61.1 MB] Get:168 http://deb.debian.org/debian stretch/main amd64 emboss amd64 6.6.0+dfsg-6 [1058 kB] Get:169 http://deb.debian.org/debian stretch/main amd64 exim4-config all 4.89-2+deb9u7 [377 kB] Get:170 http://deb.debian.org/debian stretch/main amd64 exim4-base amd64 4.89-2+deb9u7 [1094 kB] Get:171 http://deb.debian.org/debian stretch/main amd64 exim4-daemon-light amd64 4.89-2+deb9u7 [542 kB] Get:172 http://deb.debian.org/debian stretch/main amd64 exim4 all 4.89-2+deb9u7 [7860 B] Get:173 http://deb.debian.org/debian stretch/main amd64 libglib2.0-0 amd64 2.50.3-2+deb9u2 [2692 kB] Get:174 http://deb.debian.org/debian stretch/main amd64 exonerate amd64 2.4.0-2 [1476 kB] Get:175 http://deb.debian.org/debian stretch/main amd64 libfakeroot amd64 1.21-3.1 [45.7 kB] Get:176 http://deb.debian.org/debian stretch/main amd64 fakeroot amd64 1.21-3.1 [85.6 kB] Get:177 http://deb.debian.org/debian stretch/main amd64 fonts-noto-mono all 20161116-1 [79.2 kB] Get:178 http://deb.debian.org/debian stretch/main amd64 mummer amd64 3.23+dfsg-2 [809 kB] Get:179 http://deb.debian.org/debian stretch/main amd64 fsa amd64 1.15.9+dfsg-3 [753 kB] Get:180 http://deb.debian.org/debian stretch/main amd64 libgfortran3 amd64 6.3.0-18+deb9u1 [265 kB] Get:181 http://deb.debian.org/debian stretch/main amd64 libgfortran-6-dev amd64 6.3.0-18+deb9u1 [299 kB] Get:182 http://deb.debian.org/debian stretch/main amd64 gfortran-6 amd64 6.3.0-18+deb9u1 [6916 kB] Get:183 http://deb.debian.org/debian stretch/main amd64 gfortran amd64 4:6.3.0-4 [1356 B] Get:184 http://deb.debian.org/debian stretch/main amd64 libavahi-common-data amd64 0.6.32-2 [118 kB] Get:185 http://deb.debian.org/debian stretch/main amd64 libavahi-common3 amd64 0.6.32-2 [52.0 kB] Get:186 http://deb.debian.org/debian stretch/main amd64 libavahi-client3 amd64 0.6.32-2 [55.3 kB] Get:187 http://deb.debian.org/debian stretch/main amd64 libcups2 amd64 2.2.1-8+deb9u6 [307 kB] Get:188 http://deb.debian.org/debian stretch/main amd64 libcupsimage2 amd64 2.2.1-8+deb9u6 [122 kB] Get:189 http://deb.debian.org/debian stretch/main amd64 libijs-0.35 amd64 0.35-12 [18.4 kB] Get:190 http://deb.debian.org/debian stretch/main amd64 libjbig2dec0 amd64 0.13-4.1 [60.1 kB] Get:191 http://deb.debian.org/debian stretch/main amd64 liblcms2-2 amd64 2.8-4+deb9u1 [143 kB] Get:192 http://deb.debian.org/debian stretch/main amd64 libopenjp2-7 amd64 2.1.2-1.1+deb9u4 [122 kB] Get:193 http://deb.debian.org/debian stretch/main amd64 libpaper1 amd64 1.1.24+nmu5 [21.6 kB] Get:194 http://deb.debian.org/debian stretch/main amd64 libgs9-common all 9.26a~dfsg-0+deb9u6 [5143 kB] Get:195 http://deb.debian.org/debian stretch/main amd64 libgs9 amd64 9.26a~dfsg-0+deb9u6 [2213 kB] Get:196 http://deb.debian.org/debian stretch/main amd64 ghostscript amd64 9.26a~dfsg-0+deb9u6 [99.2 kB] Get:197 http://deb.debian.org/debian stretch/main amd64 libann0 amd64 1.1.2+doc-6 [24.9 kB] Get:198 http://deb.debian.org/debian stretch/main amd64 libcdt5 amd64 2.38.0-17 [59.6 kB] Get:199 http://deb.debian.org/debian stretch/main amd64 libcgraph6 amd64 2.38.0-17 [82.2 kB] Get:200 http://deb.debian.org/debian stretch/main amd64 libgts-0.7-5 amd64 0.7.6+darcs121130-4 [158 kB] Get:201 http://deb.debian.org/debian stretch/main amd64 libpixman-1-0 amd64 0.34.0-1 [530 kB] Get:202 http://deb.debian.org/debian stretch/main amd64 libxcb-render0 amd64 1.12-1 [105 kB] Get:203 http://deb.debian.org/debian stretch/main amd64 libxcb-shm0 amd64 1.12-1 [95.9 kB] Get:204 http://deb.debian.org/debian stretch/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get:205 http://deb.debian.org/debian stretch/main amd64 libcairo2 amd64 1.14.8-1 [771 kB] Get:206 http://deb.debian.org/debian stretch/main amd64 libltdl7 amd64 2.4.6-2 [389 kB] Get:207 http://deb.debian.org/debian stretch/main amd64 libthai-data all 0.1.26-1 [166 kB] Get:208 http://deb.debian.org/debian stretch/main amd64 libdatrie1 amd64 0.2.10-4+b1 [36.4 kB] Get:209 http://deb.debian.org/debian stretch/main amd64 libthai0 amd64 0.1.26-1 [52.1 kB] Get:210 http://deb.debian.org/debian stretch/main amd64 libpango-1.0-0 amd64 1.40.5-1 [320 kB] Get:211 http://deb.debian.org/debian stretch/main amd64 libgraphite2-3 amd64 1.3.10-1 [84.2 kB] Get:212 http://deb.debian.org/debian stretch/main amd64 libharfbuzz0b amd64 1.4.2-1 [671 kB] Get:213 http://deb.debian.org/debian stretch/main amd64 libpangoft2-1.0-0 amd64 1.40.5-1 [205 kB] Get:214 http://deb.debian.org/debian stretch/main amd64 libpangocairo-1.0-0 amd64 1.40.5-1 [193 kB] Get:215 http://deb.debian.org/debian stretch/main amd64 libpathplan4 amd64 2.38.0-17 [62.8 kB] Get:216 http://deb.debian.org/debian stretch/main amd64 libxdot4 amd64 2.38.0-17 [55.6 kB] Get:217 http://deb.debian.org/debian stretch/main amd64 libgvc6 amd64 2.38.0-17 [639 kB] Get:218 http://deb.debian.org/debian stretch/main amd64 libgvpr2 amd64 2.38.0-17 [211 kB] Get:219 http://deb.debian.org/debian stretch/main amd64 libice6 amd64 2:1.0.9-2 [58.7 kB] Get:220 http://deb.debian.org/debian stretch/main amd64 libsm6 amd64 2:1.2.2-1+b3 [33.3 kB] Get:221 http://deb.debian.org/debian stretch/main amd64 libxt6 amd64 1:1.1.5-1 [188 kB] Get:222 http://deb.debian.org/debian stretch/main amd64 libxmu6 amd64 2:1.1.2-2 [60.3 kB] Get:223 http://deb.debian.org/debian stretch/main amd64 libxaw7 amd64 2:1.0.13-1+b2 [201 kB] Get:224 http://deb.debian.org/debian stretch/main amd64 graphviz amd64 2.38.0-17 [802 kB] Get:225 http://deb.debian.org/debian stretch/main amd64 gsfonts all 1:8.11+urwcyr1.0.7~pre44-4.3 [3126 kB] Get:226 http://deb.debian.org/debian stretch/main amd64 libunistring0 amd64 0.9.6+really0.9.3-0.1 [279 kB] Get:227 http://deb.debian.org/debian stretch/main amd64 guile-2.0-libs amd64 2.0.13+1-4 [2232 kB] Get:228 http://deb.debian.org/debian stretch/main amd64 libdivsufsort3 amd64 2.0.1-2 [46.3 kB] Get:229 http://deb.debian.org/debian stretch/main amd64 hmmer amd64 3.1b2+dfsg-5 [1122 kB] Get:230 http://deb.debian.org/debian stretch/main amd64 hyphy-common all 2.2.7+dfsg-1 [619 kB] Get:231 http://deb.debian.org/debian stretch/main amd64 libidn2-0 amd64 0.16-1+deb9u1 [60.7 kB] Get:232 http://deb.debian.org/debian stretch/main amd64 libpsl5 amd64 0.17.0-3 [41.8 kB] Get:233 http://deb.debian.org/debian stretch/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-1+b1 [60.4 kB] Get:234 http://deb.debian.org/debian stretch/main amd64 libssh2-1 amd64 1.7.0-1+deb9u1 [139 kB] Get:235 http://deb.debian.org/debian stretch/main amd64 libcurl3-gnutls amd64 7.52.1-5+deb9u10 [290 kB] Get:236 http://deb.debian.org/debian stretch/main amd64 libnl-3-200 amd64 3.2.27-2 [61.5 kB] Get:237 http://deb.debian.org/debian stretch/main amd64 libnl-route-3-200 amd64 3.2.27-2 [136 kB] Get:238 http://deb.debian.org/debian stretch/main amd64 libibverbs1 amd64 1.2.1-2 [39.3 kB] Get:239 http://deb.debian.org/debian stretch/main amd64 libpsm-infinipath1 amd64 3.3+19.g67c0807.open-3 [169 kB] Get:240 http://deb.debian.org/debian stretch/main amd64 librdmacm1 amd64 1.1.0-2 [49.4 kB] Get:241 http://deb.debian.org/debian stretch/main amd64 libfabric1 amd64 1.4.0-1 [259 kB] Get:242 http://deb.debian.org/debian stretch/main amd64 libnuma1 amd64 2.0.11-2.1 [33.3 kB] Get:243 http://deb.debian.org/debian stretch/main amd64 libhwloc5 amd64 1.11.5-1 [105 kB] Get:244 http://deb.debian.org/debian stretch/main amd64 libpciaccess0 amd64 0.13.4-1+b2 [50.0 kB] Get:245 http://deb.debian.org/debian stretch/main amd64 ocl-icd-libopencl1 amd64 2.2.11-1 [36.8 kB] Get:246 http://deb.debian.org/debian stretch/main amd64 libhwloc-plugins amd64 1.11.5-1 [16.1 kB] Get:247 http://deb.debian.org/debian stretch/main amd64 libopenmpi2 amd64 2.0.2-2 [2008 kB] Get:248 http://deb.debian.org/debian stretch/main amd64 hyphy-mpi amd64 2.2.7+dfsg-1+b2 [920 kB] Get:249 http://deb.debian.org/debian stretch/main amd64 icu-devtools amd64 57.1-6+deb9u4 [178 kB] Get:250 http://deb.debian.org/debian stretch/main amd64 infernal amd64 1.1.2-1 [22.0 MB] Get:251 http://deb.debian.org/debian stretch/main amd64 javascript-common all 11 [6120 B] Get:252 http://deb.debian.org/debian stretch/main amd64 kalign amd64 1:2.03+20110620-3 [99.7 kB] Get:253 http://deb.debian.org/debian stretch/main amd64 liberror-perl all 0.17024-1 [26.9 kB] Get:254 http://deb.debian.org/debian stretch/main amd64 libipc-sharelite-perl amd64 0.17-4 [24.0 kB] Get:255 http://deb.debian.org/debian stretch/main amd64 libcache-cache-perl all 1.08-2 [76.6 kB] Get:256 http://deb.debian.org/debian stretch/main amd64 libace-perl amd64 1.92-4+b1 [286 kB] Get:257 http://deb.debian.org/debian stretch/main amd64 libalgorithm-c3-perl all 0.10-1 [12.0 kB] Get:258 http://deb.debian.org/debian stretch/main amd64 libalgorithm-diff-perl all 1.19.03-1 [48.7 kB] Get:259 http://deb.debian.org/debian stretch/main amd64 libalgorithm-diff-xs-perl amd64 0.04-4+b2 [11.6 kB] Get:260 http://deb.debian.org/debian stretch/main amd64 libalgorithm-merge-perl all 0.08-3 [12.7 kB] Get:261 http://deb.debian.org/debian stretch/main amd64 libalgorithm-munkres-perl all 0.08-3 [12.1 kB] Get:262 http://deb.debian.org/debian stretch/main amd64 libdevel-symdump-perl all 2.17-1 [17.0 kB] Get:263 http://deb.debian.org/debian stretch/main amd64 liburi-perl all 1.71-1 [88.6 kB] Get:264 http://deb.debian.org/debian stretch/main amd64 libencode-locale-perl all 1.05-1 [13.7 kB] Get:265 http://deb.debian.org/debian stretch/main amd64 libtimedate-perl all 2.3000-2+deb9u1 [37.9 kB] Get:266 http://deb.debian.org/debian stretch/main amd64 libhttp-date-perl all 6.02-1 [10.7 kB] Get:267 http://deb.debian.org/debian stretch/main amd64 libfile-listing-perl all 6.04-1 [10.3 kB] Get:268 http://deb.debian.org/debian stretch/main amd64 libhtml-tagset-perl all 3.20-3 [12.7 kB] Get:269 http://deb.debian.org/debian stretch/main amd64 libhtml-parser-perl amd64 3.72-3 [104 kB] Get:270 http://deb.debian.org/debian stretch/main amd64 libhtml-tree-perl all 5.03-2 [210 kB] Get:271 http://deb.debian.org/debian stretch/main amd64 libio-html-perl all 1.001-1 [17.6 kB] Get:272 http://deb.debian.org/debian stretch/main amd64 liblwp-mediatypes-perl all 6.02-1 [22.1 kB] Get:273 http://deb.debian.org/debian stretch/main amd64 libhttp-message-perl all 6.11-1 [75.9 kB] Get:274 http://deb.debian.org/debian stretch/main amd64 libhttp-cookies-perl all 6.01-1 [17.4 kB] Get:275 http://deb.debian.org/debian stretch/main amd64 libhttp-negotiate-perl all 6.00-2 [13.6 kB] Get:276 http://deb.debian.org/debian stretch/main amd64 perl-openssl-defaults amd64 3 [6782 B] Get:277 http://deb.debian.org/debian stretch/main amd64 libnet-ssleay-perl amd64 1.80-1 [285 kB] Get:278 http://deb.debian.org/debian stretch/main amd64 libio-socket-ssl-perl all 2.044-1 [195 kB] Get:279 http://deb.debian.org/debian stretch/main amd64 libnet-http-perl all 6.12-1 [23.8 kB] Get:280 http://deb.debian.org/debian stretch/main amd64 liblwp-protocol-https-perl all 6.06-2 [9582 B] Get:281 http://deb.debian.org/debian stretch/main amd64 libwww-robotrules-perl all 6.01-1 [14.3 kB] Get:282 http://deb.debian.org/debian stretch/main amd64 libwww-perl all 6.15-1 [195 kB] Get:283 http://deb.debian.org/debian stretch/main amd64 libapache2-mod-perl2 amd64 2.0.10-2+deb9u1 [886 kB] Get:284 http://deb.debian.org/debian stretch/main amd64 libdbi-perl amd64 1.636-1+b1 [766 kB] Get:285 http://deb.debian.org/debian stretch/main amd64 libapache-dbi-perl all 1.12-1 [54.6 kB] Get:286 http://deb.debian.org/debian stretch/main amd64 libapache2-reload-perl all 0.13-1 [17.4 kB] Get:287 http://deb.debian.org/debian stretch/main amd64 libclass-method-modifiers-perl all 2.12-1 [18.6 kB] Get:288 http://deb.debian.org/debian stretch/main amd64 libsub-exporter-progressive-perl all 0.001013-1 [7588 B] Get:289 http://deb.debian.org/debian stretch/main amd64 libdevel-globaldestruction-perl all 0.14-1 [8084 B] Get:290 http://deb.debian.org/debian stretch/main amd64 libparams-classify-perl amd64 0.013-6+b1 [24.4 kB] Get:291 http://deb.debian.org/debian stretch/main amd64 libmodule-runtime-perl all 0.014-2 [18.0 kB] Get:292 http://deb.debian.org/debian stretch/main amd64 libimport-into-perl all 1.002005-1 [11.6 kB] Get:293 http://deb.debian.org/debian stretch/main amd64 librole-tiny-perl all 2.000005-1 [19.0 kB] Get:294 http://deb.debian.org/debian stretch/main amd64 libstrictures-perl all 2.000003-1 [18.1 kB] Get:295 http://deb.debian.org/debian stretch/main amd64 libmoo-perl all 2.002005-1 [67.0 kB] Get:296 http://deb.debian.org/debian stretch/main amd64 libexporter-tiny-perl all 0.042-1 [32.4 kB] Get:297 http://deb.debian.org/debian stretch/main amd64 libtype-tiny-perl all 1.000005-1 [271 kB] Get:298 http://deb.debian.org/debian stretch/main amd64 libarray-compare-perl all 3.0.0-1 [14.0 kB] Get:299 http://deb.debian.org/debian stretch/main amd64 libarray-utils-perl all 0.5-1 [6254 B] Get:300 http://deb.debian.org/debian stretch/main amd64 libauthen-sasl-perl all 2.1600-1 [50.8 kB] Get:301 http://deb.debian.org/debian stretch/main amd64 libtry-tiny-perl all 0.28-1 [22.7 kB] Get:302 http://deb.debian.org/debian stretch/main amd64 libmodule-implementation-perl all 0.09-1 [12.9 kB] Get:303 http://deb.debian.org/debian stretch/main amd64 libvariable-magic-perl amd64 0.61-1 [45.1 kB] Get:304 http://deb.debian.org/debian stretch/main amd64 libb-hooks-endofscope-perl all 0.21-1 [16.3 kB] Get:305 http://deb.debian.org/debian stretch/main amd64 libbio-asn1-entrezgene-perl all 1.720-1 [38.5 kB] Get:306 http://deb.debian.org/debian stretch/main amd64 libcarp-clan-perl all 6.06-1 [12.9 kB] Get:307 http://deb.debian.org/debian stretch/main amd64 libbit-vector-perl amd64 7.4-1+b2 [146 kB] Get:308 http://deb.debian.org/debian stretch/main amd64 libblas-common amd64 3.7.0-2 [14.2 kB] Get:309 http://deb.debian.org/debian stretch/main amd64 libblas3 amd64 3.7.0-2 [155 kB] Get:310 http://deb.debian.org/debian stretch/main amd64 libblas-dev amd64 3.7.0-2 [162 kB] Get:311 http://deb.debian.org/debian stretch/main amd64 libbsd-resource-perl amd64 1.2910-1+b1 [33.7 kB] Get:312 http://deb.debian.org/debian stretch/main amd64 libbz2-dev amd64 1.0.6-8.1 [29.4 kB] Get:313 http://deb.debian.org/debian stretch/main amd64 libcapture-tiny-perl all 0.44-1 [25.4 kB] Get:314 http://deb.debian.org/debian stretch/main amd64 libcgi-pm-perl all 4.35-1 [222 kB] Get:315 http://deb.debian.org/debian stretch/main amd64 libfcgi-perl amd64 0.78-2 [38.2 kB] Get:316 http://deb.debian.org/debian stretch/main amd64 libcgi-fast-perl all 1:2.12-1 [11.2 kB] Get:317 http://deb.debian.org/debian stretch/main amd64 libclass-c3-perl all 0.32-1 [22.1 kB] Get:318 http://deb.debian.org/debian stretch/main amd64 libclass-c3-xs-perl amd64 0.14-1+b1 [16.3 kB] Get:319 http://deb.debian.org/debian stretch/main amd64 libclass-data-inheritable-perl all 0.08-2 [9296 B] Get:320 http://deb.debian.org/debian stretch/main amd64 libclass-inspector-perl all 1.31-1 [18.7 kB] Get:321 http://deb.debian.org/debian stretch/main amd64 libparams-util-perl amd64 1.07-3+b1 [22.7 kB] Get:322 http://deb.debian.org/debian stretch/main amd64 libsub-install-perl all 0.928-1 [11.4 kB] Get:323 http://deb.debian.org/debian stretch/main amd64 libdata-optlist-perl all 0.110-1 [10.6 kB] Get:324 http://deb.debian.org/debian stretch/main amd64 libpackage-stash-perl all 0.37-1 [20.8 kB] Get:325 http://deb.debian.org/debian stretch/main amd64 libclass-load-perl all 0.23-1 [15.9 kB] Get:326 http://deb.debian.org/debian stretch/main amd64 libclass-load-xs-perl amd64 0.09-2+b1 [14.4 kB] Get:327 http://deb.debian.org/debian stretch/main amd64 libclass-tiny-perl all 1.006-1 [18.8 kB] Get:328 http://deb.debian.org/debian stretch/main amd64 libclass-xsaccessor-perl amd64 1.19-2+b7 [36.7 kB] Get:329 http://deb.debian.org/debian stretch/main amd64 libclone-perl amd64 0.38-2+b1 [13.6 kB] Get:330 http://deb.debian.org/debian stretch/main amd64 libconvert-binary-c-perl amd64 0.78-1+b1 [271 kB] Get:331 http://deb.debian.org/debian stretch/main amd64 libconvert-binhex-perl all 1.125-1 [30.5 kB] Get:332 http://deb.debian.org/debian stretch/main amd64 libcrypt-rc4-perl all 2.02-2 [8150 B] Get:333 http://deb.debian.org/debian stretch/main amd64 libcupsfilters1 amd64 1.11.6-3+deb9u1 [129 kB] Get:334 http://deb.debian.org/debian stretch/main amd64 libcurl3 amd64 7.52.1-5+deb9u10 [292 kB] Get:335 http://deb.debian.org/debian stretch/main amd64 libdate-calc-perl all 6.4-1 [194 kB] Get:336 http://deb.debian.org/debian stretch/main amd64 libdate-calc-xs-perl amd64 6.4-1+b2 [54.3 kB] Get:337 http://deb.debian.org/debian stretch/main amd64 libdate-manip-perl all 6.57-1 [911 kB] Get:338 http://deb.debian.org/debian stretch/main amd64 libdbd-mysql-perl amd64 4.041-2 [114 kB] Get:339 http://deb.debian.org/debian stretch/main amd64 libdbd-pg-perl amd64 3.5.3-1+b2 [203 kB] Get:340 http://deb.debian.org/debian stretch/main amd64 libdbd-sqlite3-perl amd64 1.54-1 [164 kB] Get:341 http://deb.debian.org/debian stretch/main amd64 libpadwalker-perl amd64 2.2-2+b1 [19.7 kB] Get:342 http://deb.debian.org/debian stretch/main amd64 libdevel-caller-perl amd64 2.06-1+b4 [11.8 kB] Get:343 http://deb.debian.org/debian stretch/main amd64 libdevel-lexalias-perl amd64 0.05-1+b4 [8752 B] Get:344 http://deb.debian.org/debian stretch/main amd64 libmro-compat-perl all 0.12-1 [13.2 kB] Get:345 http://deb.debian.org/debian stretch/main amd64 libsub-identify-perl amd64 0.12-2+b1 [11.5 kB] Get:346 http://deb.debian.org/debian stretch/main amd64 libdevel-overloadinfo-perl all 0.004-1 [7270 B] Get:347 http://deb.debian.org/debian stretch/main amd64 libsub-name-perl amd64 0.21-1 [13.1 kB] Get:348 http://deb.debian.org/debian stretch/main amd64 libnamespace-clean-perl all 0.27-1 [17.3 kB] Get:349 http://deb.debian.org/debian stretch/main amd64 libsub-exporter-perl all 0.986-1 [49.9 kB] Get:350 http://deb.debian.org/debian stretch/main amd64 libdevel-partialdump-perl all 0.18-2 [14.6 kB] Get:351 http://deb.debian.org/debian stretch/main amd64 libdevel-stacktrace-perl all 2.0200-1 [27.3 kB] Get:352 http://deb.debian.org/debian stretch/main amd64 libdigest-perl-md5-perl all 1.9-1 [11.7 kB] Get:353 http://deb.debian.org/debian stretch/main amd64 libdist-checkconflicts-perl all 0.11-1 [10.8 kB] Get:354 http://deb.debian.org/debian stretch/main amd64 libdrm2 amd64 2.4.74-1 [36.2 kB] Get:355 http://deb.debian.org/debian stretch/main amd64 libdrm-amdgpu1 amd64 2.4.74-1 [26.4 kB] Get:356 http://deb.debian.org/debian stretch/main amd64 libdrm-intel1 amd64 2.4.74-1 [68.7 kB] Get:357 http://deb.debian.org/debian stretch/main amd64 libdrm-nouveau2 amd64 2.4.74-1 [25.1 kB] Get:358 http://deb.debian.org/debian stretch/main amd64 libdrm-radeon1 amd64 2.4.74-1 [30.2 kB] Get:359 http://deb.debian.org/debian stretch/main amd64 libelf1 amd64 0.168-1 [157 kB] Get:360 http://deb.debian.org/debian stretch/main amd64 libemail-date-format-perl all 1.005-1 [7050 B] Get:361 http://deb.debian.org/debian stretch/main amd64 libenv-path-perl all 0.19-1 [22.0 kB] Get:362 http://deb.debian.org/debian stretch/main amd64 libeval-closure-perl all 0.14-1 [11.5 kB] Get:363 http://deb.debian.org/debian stretch/main amd64 libexception-class-perl all 1.42-1 [31.5 kB] Get:364 http://deb.debian.org/debian stretch/main amd64 libipc-system-simple-perl all 1.25-3 [26.9 kB] Get:365 http://deb.debian.org/debian stretch/main amd64 libfile-basedir-perl all 0.07-1 [17.5 kB] Get:366 http://deb.debian.org/debian stretch/main amd64 libfile-desktopentry-perl all 0.22-1 [19.2 kB] Get:367 http://deb.debian.org/debian stretch/main amd64 libfile-fcntllock-perl amd64 0.22-3+b2 [35.3 kB] Get:368 http://deb.debian.org/debian stretch/main amd64 libnumber-compare-perl all 0.03-1 [7642 B] Get:369 http://deb.debian.org/debian stretch/main amd64 libtext-glob-perl all 0.10-1 [8362 B] Get:370 http://deb.debian.org/debian stretch/main amd64 libfile-find-rule-perl all 0.34-1 [30.6 kB] Get:371 http://deb.debian.org/debian stretch/main amd64 libfile-grep-perl all 0.02-1 [7654 B] Get:372 http://deb.debian.org/debian stretch/main amd64 shared-mime-info amd64 1.8-1+deb9u1 [731 kB] Get:373 http://deb.debian.org/debian stretch/main amd64 libfile-mimeinfo-perl all 0.27-1 [50.2 kB] Get:374 http://deb.debian.org/debian stretch/main amd64 libfile-slurp-tiny-perl all 0.003-1 [6852 B] Get:375 http://deb.debian.org/debian stretch/main amd64 libfile-slurper-perl all 0.009-1 [7850 B] Get:376 http://deb.debian.org/debian stretch/main amd64 libfile-which-perl all 1.21-1 [14.3 kB] Get:377 http://deb.debian.org/debian stretch/main amd64 libfindbin-libs-perl all 2.150-1 [28.7 kB] Get:378 http://deb.debian.org/debian stretch/main amd64 libfont-afm-perl all 1.20-2 [13.6 kB] Get:379 http://deb.debian.org/debian stretch/main amd64 libfontenc1 amd64 1:1.1.3-1+b2 [24.4 kB] Get:380 http://deb.debian.org/debian stretch/main amd64 libfreezethaw-perl all 0.5001-1 [18.2 kB] Get:381 http://deb.debian.org/debian stretch/main amd64 libfribidi0 amd64 0.19.7-1+deb9u1 [45.6 kB] Get:382 http://deb.debian.org/debian stretch/main amd64 libllvm3.9 amd64 1:3.9.1-9 [11.3 MB] Get:383 http://deb.debian.org/debian stretch/main amd64 libsensors4 amd64 1:3.4.0-4 [53.3 kB] Get:384 http://deb.debian.org/debian stretch/main amd64 libgl1-mesa-dri amd64 13.0.6-1+b2 [4536 kB] Get:385 http://deb.debian.org/debian stretch/main amd64 libglapi-mesa amd64 13.0.6-1+b2 [58.9 kB] Get:386 http://deb.debian.org/debian stretch/main amd64 libx11-xcb1 amd64 2:1.6.4-3+deb9u1 [183 kB] Get:387 http://deb.debian.org/debian stretch/main amd64 libxcb-dri2-0 amd64 1.12-1 [97.2 kB] Get:388 http://deb.debian.org/debian stretch/main amd64 libxcb-dri3-0 amd64 1.12-1 [95.6 kB] Get:389 http://deb.debian.org/debian stretch/main amd64 libxcb-glx0 amd64 1.12-1 [113 kB] Get:390 http://deb.debian.org/debian stretch/main amd64 libxcb-present0 amd64 1.12-1 [95.8 kB] Get:391 http://deb.debian.org/debian stretch/main amd64 libxcb-sync1 amd64 1.12-1 [99.2 kB] Get:392 http://deb.debian.org/debian stretch/main amd64 libxfixes3 amd64 1:5.0.3-1 [21.9 kB] Get:393 http://deb.debian.org/debian stretch/main amd64 libxdamage1 amd64 1:1.1.4-2+b3 [14.5 kB] Get:394 http://deb.debian.org/debian stretch/main amd64 libxshmfence1 amd64 1.2-1+b2 [7922 B] Get:395 http://deb.debian.org/debian stretch/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b2 [20.8 kB] Get:396 http://deb.debian.org/debian stretch/main amd64 libgl1-mesa-glx amd64 13.0.6-1+b2 [167 kB] Get:397 http://deb.debian.org/debian stretch/main amd64 libglib2.0-data all 2.50.3-2+deb9u2 [2517 kB] Get:398 http://deb.debian.org/debian stretch/main amd64 libgraph-perl all 1:0.96-2 [126 kB] Get:399 http://deb.debian.org/debian stretch/main amd64 libscalar-list-utils-perl amd64 1:1.47-1 [54.4 kB] Get:400 http://deb.debian.org/debian stretch/main amd64 libspiffy-perl all 0.41-1 [26.1 kB] Get:401 http://deb.debian.org/debian stretch/main amd64 libio-all-perl all 0.86-2 [73.4 kB] Get:402 http://deb.debian.org/debian stretch/main amd64 libparse-yapp-perl all 1.05-12 [50.5 kB] Get:403 http://deb.debian.org/debian stretch/main amd64 libxml-parser-perl amd64 2.44-2+b1 [212 kB] Get:404 http://deb.debian.org/debian stretch/main amd64 libxml-writer-perl all 0.625-1 [29.7 kB] Get:405 http://deb.debian.org/debian stretch/main amd64 libgraph-readwrite-perl all 2.09-1 [44.7 kB] Get:406 http://deb.debian.org/debian stretch/main amd64 libio-pty-perl amd64 1:1.08-1.1+b2 [33.6 kB] Get:407 http://deb.debian.org/debian stretch/main amd64 libipc-run-perl all 0.94-1+deb9u1 [99.1 kB] Get:408 http://deb.debian.org/debian stretch/main amd64 libparse-recdescent-perl all 1.967013+dfsg-1 [159 kB] Get:409 http://deb.debian.org/debian stretch/main amd64 libxml-twig-perl all 1:3.50-1 [179 kB] Get:410 http://deb.debian.org/debian stretch/main amd64 libxml-xpath-perl all 1.40-1 [69.2 kB] Get:411 http://deb.debian.org/debian stretch/main amd64 libgraphviz-perl all 2.22-1 [107 kB] Get:412 http://deb.debian.org/debian stretch/main amd64 libntlm0 amd64 1.4-8 [20.9 kB] Get:413 http://deb.debian.org/debian stretch/main amd64 libgsasl7 amd64 1.8.0-8+b2 [207 kB] Get:414 http://deb.debian.org/debian stretch/main amd64 libgts-bin amd64 0.7.6+darcs121130-4 [50.8 kB] Get:415 http://deb.debian.org/debian stretch/main amd64 beignet-opencl-icd amd64 1.3.0-4 [12.8 MB] Get:416 http://deb.debian.org/debian stretch/main amd64 libhmsbeagle1v5 amd64 2.1.2+20160831-5 [116 kB] Get:417 http://deb.debian.org/debian stretch/main amd64 libhtml-form-perl all 6.03-1 [23.9 kB] Get:418 http://deb.debian.org/debian stretch/main amd64 libhtml-format-perl all 2.12-1 [43.5 kB] Get:419 http://deb.debian.org/debian stretch/main amd64 libhtml-tableextract-perl all 2.13-1 [30.7 kB] Get:420 http://deb.debian.org/debian stretch/main amd64 libhts1 amd64 1.3.2-2 [257 kB] Get:421 http://deb.debian.org/debian stretch/main amd64 libhttp-daemon-perl all 6.01-1 [17.3 kB] Get:422 http://deb.debian.org/debian stretch/main amd64 libicu-dev amd64 57.1-6+deb9u4 [16.5 MB] Get:423 http://deb.debian.org/debian stretch/main amd64 libio-sessiondata-perl all 1.03-1 [5782 B] Get:424 http://deb.debian.org/debian stretch/main amd64 libio-stringy-perl all 2.111-2 [61.2 kB] Get:425 http://deb.debian.org/debian stretch/main amd64 libipc-shareable-perl all 0.61-1 [35.4 kB] Get:426 http://deb.debian.org/debian stretch/main amd64 libjcode-pm-perl amd64 2.06-1 [30.9 kB] Get:427 http://deb.debian.org/debian stretch/main amd64 libjpeg62-turbo-dev amd64 1:1.5.1-2 [210 kB] Get:428 http://deb.debian.org/debian stretch/main amd64 libjpeg-dev all 1:1.5.1-2 [56.1 kB] Get:429 http://deb.debian.org/debian stretch/main amd64 libjs-jquery all 3.1.1-2+deb9u1 [154 kB] Get:430 http://deb.debian.org/debian stretch/main amd64 liblzo2-2 amd64 2.08-1.2+b2 [55.0 kB] Get:431 http://deb.debian.org/debian stretch/main amd64 libkyotocabinet16v5 amd64 1.2.76-4.2+b1 [298 kB] Get:432 http://deb.debian.org/debian stretch/main amd64 liblapack3 amd64 3.7.0-2 [2141 kB] Get:433 http://deb.debian.org/debian stretch/main amd64 liblapack-dev amd64 3.7.0-2 [2170 kB] Get:434 http://deb.debian.org/debian stretch/main amd64 liblist-moreutils-perl amd64 0.416-1+b1 [63.0 kB] Get:435 http://deb.debian.org/debian stretch/main amd64 libparams-validate-perl amd64 1.26-1 [66.0 kB] Get:436 http://deb.debian.org/debian stretch/main amd64 liblog-dispatch-perl all 2.58-1 [72.5 kB] Get:437 http://deb.debian.org/debian stretch/main amd64 liblog-log4perl-perl all 1.48-1+deb9u1 [376 kB] Get:438 http://deb.debian.org/debian stretch/main amd64 liblzma-dev amd64 5.2.2-1.2+b1 [292 kB] Get:439 http://deb.debian.org/debian stretch/main amd64 libsys-hostname-long-perl all 1.5-1 [12.0 kB] Get:440 http://deb.debian.org/debian stretch/main amd64 libmail-sendmail-perl all 0.79.16-2 [24.9 kB] Get:441 http://deb.debian.org/debian stretch/main amd64 libnet-smtp-ssl-perl all 1.04-1 [6184 B] Get:442 http://deb.debian.org/debian stretch/main amd64 libmailtools-perl all 2.18-1 [88.5 kB] Get:443 http://deb.debian.org/debian stretch/main amd64 mailutils-common all 1:3.1.1-1 [642 kB] Get:444 http://deb.debian.org/debian stretch/main amd64 libpython2.7 amd64 2.7.13-2+deb9u3 [1071 kB] Get:445 http://deb.debian.org/debian stretch/main amd64 libmailutils5 amd64 1:3.1.1-1 [817 kB] Get:446 http://deb.debian.org/debian stretch/main amd64 libmath-derivative-perl all 0.04-2 [7208 B] Get:447 http://deb.debian.org/debian stretch/main amd64 libmath-spline-perl all 0.02-1 [7992 B] Get:448 http://deb.debian.org/debian stretch/main amd64 libmime-lite-perl all 3.030-2 [72.3 kB] Get:449 http://deb.debian.org/debian stretch/main amd64 libmime-tools-perl all 5.508-1 [212 kB] Get:450 http://deb.debian.org/debian stretch/main amd64 libmime-types-perl all 2.13-1 [61.7 kB] Get:451 http://deb.debian.org/debian stretch/main amd64 libmldbm-perl all 2.05-2 [18.4 kB] Get:452 http://deb.debian.org/debian stretch/main amd64 libmodule-runtime-conflicts-perl all 0.003-1 [6882 B] Get:453 http://deb.debian.org/debian stretch/main amd64 libpackage-deprecationmanager-perl all 0.17-1 [16.4 kB] Get:454 http://deb.debian.org/debian stretch/main amd64 libpackage-stash-xs-perl amd64 0.28-3+b1 [17.9 kB] Get:455 http://deb.debian.org/debian stretch/main amd64 libmoose-perl amd64 2.1807-1 [801 kB] Get:456 http://deb.debian.org/debian stretch/main amd64 libtinfo-dev amd64 6.0+20161126-1+deb9u2 [79.2 kB] Get:457 http://deb.debian.org/debian stretch/main amd64 libncurses5-dev amd64 6.0+20161126-1+deb9u2 [175 kB] Get:458 http://deb.debian.org/debian stretch/main amd64 libnet-dbus-perl amd64 1.1.0-4+b1 [179 kB] Get:459 http://deb.debian.org/debian stretch/main amd64 libole-storage-lite-perl all 0.19-1+deb9u1 [23.4 kB] Get:460 http://deb.debian.org/debian stretch/main amd64 libossp-uuid16 amd64 1.6.2-1.5+b4 [38.3 kB] Get:461 http://deb.debian.org/debian stretch/main amd64 libossp-uuid-perl amd64 1.6.2-1.5+b4 [28.7 kB] Get:462 http://deb.debian.org/debian stretch/main amd64 libpaper-utils amd64 1.1.24+nmu5 [17.6 kB] Get:463 http://deb.debian.org/debian stretch/main amd64 libpcre16-3 amd64 2:8.39-3 [258 kB] Get:464 http://deb.debian.org/debian stretch/main amd64 libpcre32-3 amd64 2:8.39-3 [248 kB] Get:465 http://deb.debian.org/debian stretch/main amd64 libpcre3-dev amd64 2:8.39-3 [647 kB] Get:466 http://deb.debian.org/debian stretch/main amd64 libperlio-utf8-strict-perl amd64 0.006-1+b2 [11.3 kB] Get:467 http://deb.debian.org/debian stretch/main amd64 zlib1g-dev amd64 1:1.2.8.dfsg-5 [205 kB] Get:468 http://deb.debian.org/debian stretch/main amd64 libpng-dev amd64 1.6.28-1+deb9u1 [250 kB] Get:469 http://deb.debian.org/debian stretch/main amd64 libpng-tools amd64 1.6.28-1+deb9u1 [133 kB] Get:470 http://deb.debian.org/debian stretch/main amd64 libpostscript-perl all 0.06-2 [31.4 kB] Get:471 http://deb.debian.org/debian stretch/main amd64 libreadline-dev amd64 7.0-3 [132 kB] Get:472 http://deb.debian.org/debian stretch/main amd64 libsasl2-modules amd64 2.1.27~101-g0780600+dfsg-3+deb9u1 [102 kB] Get:473 http://deb.debian.org/debian stretch/main amd64 libtask-weaken-perl all 1.04-1 [7990 B] Get:474 http://deb.debian.org/debian stretch/main amd64 libsoap-lite-perl all 1.20-1 [259 kB] Get:475 http://deb.debian.org/debian stretch/main amd64 libsort-naturally-perl all 1.03-1 [13.9 kB] Get:476 http://deb.debian.org/debian stretch/main amd64 libspreadsheet-writeexcel-perl all 2.40-1 [550 kB] Get:477 http://deb.debian.org/debian stretch/main amd64 libunicode-map-perl amd64 0.112-11+b3 [145 kB] Get:478 http://deb.debian.org/debian stretch/main amd64 libspreadsheet-parseexcel-perl all 0.6500-1 [159 kB] Get:479 http://deb.debian.org/debian stretch/main amd64 libstatistics-descriptive-perl all 3.0612-1 [41.9 kB] Get:480 http://deb.debian.org/debian stretch/main amd64 libsub-uplevel-perl all 0.2600-1 [16.1 kB] Get:481 http://deb.debian.org/debian stretch/main amd64 libsvg-perl all 2.64-1 [69.8 kB] Get:482 http://deb.debian.org/debian stretch/main amd64 libtree-dagnode-perl all 1.29-1 [60.6 kB] Get:483 http://deb.debian.org/debian stretch/main amd64 libsvg-graph-perl all 0.02-2 [130 kB] Get:484 http://deb.debian.org/debian stretch/main amd64 libtcl8.6 amd64 8.6.6+dfsg-1+b1 [985 kB] Get:485 http://deb.debian.org/debian stretch/main amd64 libtest-deep-perl all 1.126-1 [48.4 kB] Get:486 http://deb.debian.org/debian stretch/main amd64 libtext-diff-perl all 1.44-1 [27.4 kB] Get:487 http://deb.debian.org/debian stretch/main amd64 libtest-differences-perl all 0.64-1 [18.0 kB] Get:488 http://deb.debian.org/debian stretch/main amd64 libtest-exception-perl all 0.43-1 [18.7 kB] Get:489 http://deb.debian.org/debian stretch/main amd64 libtest-file-perl all 1.442-1 [19.8 kB] Get:490 http://deb.debian.org/debian stretch/main amd64 libtest-files-perl all 0.14-1 [11.2 kB] Get:491 http://deb.debian.org/debian stretch/main amd64 libtest-warn-perl all 0.32-1 [15.1 kB] Get:492 http://deb.debian.org/debian stretch/main amd64 libtest-simple-perl all 1.302075-1 [298 kB] Get:493 http://deb.debian.org/debian stretch/main amd64 libtest-most-perl all 0.35-1 [24.5 kB] Get:494 http://deb.debian.org/debian stretch/main amd64 libtest-output-perl all 1.03-1 [13.9 kB] Get:495 http://deb.debian.org/debian stretch/main amd64 libtext-csv-perl all 1.33-2 [50.5 kB] Get:496 http://deb.debian.org/debian stretch/main amd64 libtext-csv-xs-perl amd64 1.26-1 [114 kB] Get:497 http://deb.debian.org/debian stretch/main amd64 libtext-iconv-perl amd64 1.7-5+b4 [15.3 kB] Get:498 http://deb.debian.org/debian stretch/main amd64 libtie-ixhash-perl all 1.23-2 [11.7 kB] Get:499 http://deb.debian.org/debian stretch/main amd64 libxft2 amd64 2.3.2-1+b2 [56.5 kB] Get:500 http://deb.debian.org/debian stretch/main amd64 libtk8.6 amd64 8.6.6-1+b1 [754 kB] Get:501 http://deb.debian.org/debian stretch/main amd64 libtype-tiny-xs-perl amd64 0.012-1+b2 [26.8 kB] Get:502 http://deb.debian.org/debian stretch/main amd64 libx11-protocol-perl all 0.56-7 [150 kB] Get:503 http://deb.debian.org/debian stretch/main amd64 libxcb-shape0 amd64 1.12-1 [96.2 kB] Get:504 http://deb.debian.org/debian stretch/main amd64 libxcomposite1 amd64 1:0.4.4-2 [16.5 kB] Get:505 http://deb.debian.org/debian stretch/main amd64 libxcursor1 amd64 1:1.1.14-1+deb9u2 [34.9 kB] Get:506 http://deb.debian.org/debian stretch/main amd64 libxi6 amd64 2:1.7.9-1 [82.6 kB] Get:507 http://deb.debian.org/debian stretch/main amd64 libxinerama1 amd64 2:1.1.3-1+b3 [16.7 kB] Get:508 http://deb.debian.org/debian stretch/main amd64 libxml-perl all 0.08-2 [113 kB] Get:509 http://deb.debian.org/debian stretch/main amd64 libxml-regexp-perl all 0.04-1 [8370 B] Get:510 http://deb.debian.org/debian stretch/main amd64 libxml-dom-perl all 1.44-2 [179 kB] Get:511 http://deb.debian.org/debian stretch/main amd64 libxml-xpathengine-perl all 0.13-1 [39.1 kB] Get:512 http://deb.debian.org/debian stretch/main amd64 libxml-dom-xpath-perl all 0.14-2 [9622 B] Get:513 http://deb.debian.org/debian stretch/main amd64 libxml-namespacesupport-perl all 1.11-1 [14.8 kB] Get:514 http://deb.debian.org/debian stretch/main amd64 libxml-sax-base-perl all 1.07-1 [23.1 kB] Get:515 http://deb.debian.org/debian stretch/main amd64 libxml-sax-perl all 0.99+dfsg-2 [68.3 kB] Get:516 http://deb.debian.org/debian stretch/main amd64 libxml-filter-buffertext-perl all 1.01-5 [7354 B] Get:517 http://deb.debian.org/debian stretch/main amd64 libxml-libxml-perl amd64 2.0128+dfsg-1+deb9u1 [338 kB] Get:518 http://deb.debian.org/debian stretch/main amd64 libxslt1.1 amd64 1.1.29-2.1+deb9u2 [233 kB] Get:519 http://deb.debian.org/debian stretch/main amd64 libxml-libxslt-perl amd64 1.95-1+b1 [46.8 kB] Get:520 http://deb.debian.org/debian stretch/main amd64 libxml-sax-expat-perl all 0.40-2 [12.9 kB] Get:521 http://deb.debian.org/debian stretch/main amd64 libxml-sax-writer-perl all 0.56-1 [23.7 kB] Get:522 http://deb.debian.org/debian stretch/main amd64 libxml-simple-perl all 2.22-1 [71.8 kB] Get:523 http://deb.debian.org/debian stretch/main amd64 libxmlrpc-lite-perl all 0.717-1 [26.1 kB] Get:524 http://deb.debian.org/debian stretch/main amd64 libxmuu1 amd64 2:1.1.2-2 [23.5 kB] Get:525 http://deb.debian.org/debian stretch/main amd64 libxrandr2 amd64 2:1.5.1-1 [37.5 kB] Get:526 http://deb.debian.org/debian stretch/main amd64 libxtst6 amd64 2:1.2.3-1 [27.8 kB] Get:527 http://deb.debian.org/debian stretch/main amd64 libxv1 amd64 2:1.0.11-1 [24.6 kB] Get:528 http://deb.debian.org/debian stretch/main amd64 libxxf86dga1 amd64 2:1.1.4-1+b3 [22.1 kB] Get:529 http://deb.debian.org/debian stretch/main amd64 libyaml-0-2 amd64 0.1.7-2 [47.6 kB] Get:530 http://deb.debian.org/debian stretch/main amd64 libyaml-libyaml-perl amd64 0.63-2 [68.8 kB] Get:531 http://deb.debian.org/debian stretch/main amd64 libyaml-perl all 1.21-1 [64.8 kB] Get:532 http://deb.debian.org/debian stretch/main amd64 zip amd64 3.0-11+b1 [234 kB] Get:533 http://deb.debian.org/debian stretch/main amd64 unzip amd64 6.0-21+deb9u2 [172 kB] Get:534 http://deb.debian.org/debian stretch/main amd64 xdg-utils all 1.1.1-1+deb9u2 [71.5 kB] Get:535 http://deb.debian.org/debian stretch/main amd64 r-base-core amd64 3.3.3-1 [21.2 MB] Get:536 http://deb.debian.org/debian stretch/main amd64 r-cran-littler amd64 0.3.1-1 [59.1 kB] Get:537 http://deb.debian.org/debian stretch/main amd64 littler all 0.3.1-1 [11.7 kB] Get:538 http://deb.debian.org/debian stretch/main amd64 lynx-common all 2.8.9dev11-1 [1098 kB] Get:539 http://deb.debian.org/debian stretch/main amd64 mafft amd64 7.307-1 [889 kB] Get:540 http://deb.debian.org/debian stretch/main amd64 mailutils amd64 1:3.1.1-1 [573 kB] Get:541 http://deb.debian.org/debian stretch/main amd64 manpages-dev all 4.10-2 [2145 kB] Get:542 http://deb.debian.org/debian stretch/main amd64 maq amd64 0.7.1-7 [311 kB] Get:543 http://deb.debian.org/debian stretch/main amd64 mcl amd64 1:14-137-1+b1 [619 kB] Get:544 http://deb.debian.org/debian stretch/main amd64 muscle amd64 1:3.8.31+dfsg-2 [151 kB] Get:545 http://deb.debian.org/debian stretch/main amd64 mustang amd64 3.2.3-1 [113 kB] Get:546 http://deb.debian.org/debian stretch/main amd64 perl-doc all 5.24.1-3+deb9u7 [7145 kB] Get:547 http://deb.debian.org/debian stretch/main amd64 perl-tk amd64 1:804.033-1+b3 [1943 kB] Get:548 http://deb.debian.org/debian stretch/main amd64 phylip amd64 1:3.696+dfsg-5 [942 kB] Get:549 http://deb.debian.org/debian stretch/main amd64 openmpi-common all 2.0.2-2 [149 kB] Get:550 http://deb.debian.org/debian stretch/main amd64 openmpi-bin amd64 2.0.2-2 [186 kB] Get:551 http://deb.debian.org/debian stretch/main amd64 phyml amd64 3:3.2.0+dfsg-7+b1 [1298 kB] Get:552 http://deb.debian.org/debian stretch/main amd64 pkg-config amd64 0.29-4+b1 [63.3 kB] Get:553 http://deb.debian.org/debian stretch/main amd64 poa amd64 2.0+20060928-4+b1 [45.4 kB] Get:554 http://deb.debian.org/debian stretch/main amd64 prank amd64 0.0.150803-2 [374 kB] Get:555 http://deb.debian.org/debian stretch/main amd64 primer3 amd64 2.3.7-3 [173 kB] Get:556 http://deb.debian.org/debian stretch/main amd64 probalign amd64 1.4-5 [65.4 kB] Get:557 http://deb.debian.org/debian stretch/main amd64 probcons amd64 1.12-11 [107 kB] Get:558 http://deb.debian.org/debian stretch/main amd64 proda amd64 1.0-10 [60.1 kB] Get:559 http://deb.debian.org/debian stretch/main amd64 psmisc amd64 22.21-2.1+b2 [123 kB] Get:560 http://deb.debian.org/debian stretch/main amd64 xauth amd64 1:1.0.9-1+b2 [39.6 kB] Get:561 http://deb.debian.org/debian stretch/main amd64 r-base-dev all 3.3.3-1 [4402 B] Get:562 http://deb.debian.org/debian stretch/main amd64 r-cran-assertthat all 0.1-1 [43.3 kB] Get:563 http://deb.debian.org/debian stretch/main amd64 r-cran-boot all 1.3-18-2 [577 kB] Get:564 http://deb.debian.org/debian stretch/main amd64 r-cran-mass amd64 7.3-45-1 [1017 kB] Get:565 http://deb.debian.org/debian stretch/main amd64 r-cran-class amd64 7.3-14-1 [80.9 kB] Get:566 http://deb.debian.org/debian stretch/main amd64 r-cran-cluster amd64 2.0.5-1 [490 kB] Get:567 http://deb.debian.org/debian stretch/main amd64 r-cran-codetools all 0.2-15-1 [46.2 kB] Get:568 http://deb.debian.org/debian stretch/main amd64 r-cran-colorspace amd64 1.3-2-1 [388 kB] Get:569 http://deb.debian.org/debian stretch/main amd64 r-cran-crayon amd64 1.3.2-1 [705 kB] Get:570 http://deb.debian.org/debian stretch/main amd64 r-cran-dichromat all 2.0.0-3 [146 kB] Get:571 http://deb.debian.org/debian stretch/main amd64 r-cran-digest amd64 0.6.11-1 [112 kB] Get:572 http://deb.debian.org/debian stretch/main amd64 r-cran-foreign amd64 0.8.67-1 [211 kB] Get:573 http://deb.debian.org/debian stretch/main amd64 r-cran-gtable all 0.2.0-1 [65.1 kB] Get:574 http://deb.debian.org/debian stretch/main amd64 r-cran-pkgkitten all 0.1.4-1 [18.7 kB] Get:575 http://deb.debian.org/debian stretch/main amd64 r-cran-rcpp amd64 0.12.9-1 [2168 kB] Get:576 http://deb.debian.org/debian stretch/main amd64 r-cran-plyr amd64 1.8.4-1 [727 kB] Get:577 http://deb.debian.org/debian stretch/main amd64 r-cran-stringi amd64 1.1.2-1 [606 kB] Get:578 http://deb.debian.org/debian stretch/main amd64 r-cran-magrittr amd64 1.5-3 [147 kB] Get:579 http://deb.debian.org/debian stretch/main amd64 r-cran-stringr all 1.1.0-1 [117 kB] Get:580 http://deb.debian.org/debian stretch/main amd64 r-cran-reshape2 amd64 1.4.2-1 [87.5 kB] Get:581 http://deb.debian.org/debian stretch/main amd64 r-cran-rcolorbrewer all 1.1-2-1 [26.0 kB] Get:582 http://deb.debian.org/debian stretch/main amd64 r-cran-munsell all 0.4.3-1 [127 kB] Get:583 http://deb.debian.org/debian stretch/main amd64 r-cran-labeling all 0.3-1 [39.9 kB] Get:584 http://deb.debian.org/debian stretch/main amd64 r-cran-scales amd64 0.4.1-1 [200 kB] Get:585 http://deb.debian.org/debian stretch/main amd64 r-cran-lazyeval amd64 0.2.0-1 [112 kB] Get:586 http://deb.debian.org/debian stretch/main amd64 r-cran-tibble amd64 1.2-1 [121 kB] Get:587 http://deb.debian.org/debian stretch/main amd64 r-cran-ggplot2 all 2.2.1-2 [2658 kB] Get:588 http://deb.debian.org/debian stretch/main amd64 r-cran-kernsmooth amd64 2.23-15-2 [81.7 kB] Get:589 http://deb.debian.org/debian stretch/main amd64 r-cran-lattice amd64 0.20-34-1 [713 kB] Get:590 http://deb.debian.org/debian stretch/main amd64 r-cran-matrix amd64 1.2-7.1-1 [2311 kB] Get:591 http://deb.debian.org/debian stretch/main amd64 r-cran-nlme amd64 3.1.129-1 [2042 kB] Get:592 http://deb.debian.org/debian stretch/main amd64 r-cran-mgcv amd64 1.8-16-1 [2106 kB] Get:593 http://deb.debian.org/debian stretch/main amd64 r-cran-nnet amd64 7.3-12-1 [96.9 kB] Get:594 http://deb.debian.org/debian stretch/main amd64 r-cran-survival amd64 2.40-1-1 [4863 kB] Get:595 http://deb.debian.org/debian stretch/main amd64 r-cran-rpart amd64 4.1-10-2 [861 kB] Get:596 http://deb.debian.org/debian stretch/main amd64 r-cran-spatial amd64 7.3-11-1 [118 kB] Get:597 http://deb.debian.org/debian stretch/main amd64 r-doc-html all 3.3.3-1 [551 kB] Get:598 http://deb.debian.org/debian stretch/main amd64 r-recommended all 3.3.3-1 [2706 B] Get:599 http://deb.debian.org/debian stretch/main amd64 rubygems-integration all 1.11 [4994 B] Get:600 http://deb.debian.org/debian stretch/main amd64 ruby-did-you-mean all 1.0.0-2 [11.2 kB] Get:601 http://deb.debian.org/debian stretch/main amd64 ruby-minitest all 5.9.0-1 [51.1 kB] Get:602 http://deb.debian.org/debian stretch/main amd64 ruby-net-telnet all 0.1.1-2 [12.5 kB] Get:603 http://deb.debian.org/debian stretch/main amd64 ruby-power-assert all 0.3.0-1 [7902 B] Get:604 http://deb.debian.org/debian stretch/main amd64 ruby-test-unit all 3.1.7-2 [69.6 kB] Get:605 http://deb.debian.org/debian stretch/main amd64 libruby2.3 amd64 2.3.3-1+deb9u8 [3108 kB] Get:606 http://deb.debian.org/debian stretch/main amd64 ruby2.3 amd64 2.3.3-1+deb9u8 [189 kB] Get:607 http://deb.debian.org/debian stretch/main amd64 ruby amd64 1:2.3.3 [10.8 kB] Get:608 http://deb.debian.org/debian stretch/main amd64 rake all 10.5.0-2+deb9u1 [49.7 kB] Get:609 http://deb.debian.org/debian stretch/main amd64 raxml amd64 8.2.9+dfsg-1+b1 [1278 kB] Get:610 http://deb.debian.org/debian stretch/main amd64 rename all 0.20-4 [12.5 kB] Get:611 http://deb.debian.org/debian stretch/main amd64 sysstat amd64 11.4.3-2 [360 kB] Get:612 http://deb.debian.org/debian stretch/main amd64 parallel all 20161222-1 [307 kB] Get:613 http://deb.debian.org/debian stretch/main amd64 fasttree amd64 2.1.9-1 [132 kB] Get:614 http://deb.debian.org/debian stretch/main amd64 roary all 3.8.0+dfsg-1 [170 kB] Get:615 http://deb.debian.org/debian stretch/main amd64 samtools amd64 1.3.1-3 [254 kB] Get:616 http://deb.debian.org/debian stretch/main amd64 sim4 amd64 0.0.20121010-4 [396 kB] Get:617 http://deb.debian.org/debian stretch/main amd64 t-coffee amd64 11.00.8cbe486-5 [1918 kB] Get:618 http://deb.debian.org/debian stretch/main amd64 tcpd amd64 7.6.q-26 [23.3 kB] Get:619 http://deb.debian.org/debian stretch/main amd64 tigr-glimmer amd64 3.02b-1 [283 kB] Get:620 http://deb.debian.org/debian stretch/main amd64 tm-align amd64 20160521+dfsg-2 [868 kB] Get:621 http://deb.debian.org/debian stretch/main amd64 wise-data all 2.4.1-19 [108 kB] Get:622 http://deb.debian.org/debian stretch/main amd64 wise amd64 2.4.1-19 [993 kB] Get:623 http://deb.debian.org/debian stretch/main amd64 x11-utils amd64 7.7+3+b1 [202 kB] Get:624 http://deb.debian.org/debian stretch/main amd64 x11-xserver-utils amd64 7.7+7+b1 [167 kB] Get:625 http://deb.debian.org/debian stretch/main amd64 xdg-user-dirs amd64 0.15-2+b1 [52.2 kB] Get:626 http://deb.debian.org/debian stretch/main amd64 xml-core all 0.17 [23.2 kB] Get:627 http://deb.debian.org/debian stretch/main amd64 bowtie amd64 1.1.2-6 [1618 kB] Get:628 http://deb.debian.org/debian stretch/main amd64 gnupg-l10n all 2.1.18-8~deb9u4 [893 kB] Get:629 http://deb.debian.org/debian stretch/main amd64 libgd-perl amd64 2.53-3 [177 kB] Get:630 http://deb.debian.org/debian stretch/main amd64 libset-scalar-perl all 1.29-2 [31.4 kB] Get:631 http://deb.debian.org/debian stretch/main amd64 libtxc-dxtn-s2tc amd64 1.0+git20151227-2 [48.4 kB] Get:632 http://deb.debian.org/debian stretch/main amd64 lynx amd64 2.8.9dev11-1 [632 kB] Get:633 http://deb.debian.org/debian stretch/main amd64 med-config all 3.0.1 [17.1 kB] Get:634 http://deb.debian.org/debian stretch/main amd64 publicsuffix all 20190415.1030-0+deb9u1 [108 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 398 MB in 4s (82.9 MB/s) Selecting previously unselected package lsb-base. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 4411 files and directories currently installed.) Preparing to unpack .../00-lsb-base_9.20161125_all.deb ... Unpacking lsb-base (9.20161125) ... Selecting previously unselected package cron. Preparing to unpack .../01-cron_3.0pl1-128+deb9u1_amd64.deb ... Unpacking cron (3.0pl1-128+deb9u1) ... Selecting previously unselected package perl-modules-5.24. Preparing to unpack .../02-perl-modules-5.24_5.24.1-3+deb9u7_all.deb ... 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Setting up libgmp10:amd64 (2:6.1.2+dfsg-1) ... Setting up libmpfr4:amd64 (3.1.5-1) ... Setting up readline-common (7.0-3) ... Setting up libreadline7:amd64 (7.0-3) ... Setting up libsigsegv2:amd64 (2.10-5) ... Selecting previously unselected package gawk. (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 ... 7445 files and directories currently installed.) Preparing to unpack .../000-gawk_1%3a4.1.4+dfsg-1_amd64.deb ... Unpacking gawk (1:4.1.4+dfsg-1) ... 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Adding 'diversion of /usr/bin/parallel to /usr/bin/parallel.moreutils by parallel' Adding 'diversion of /usr/share/man/man1/parallel.1.gz to /usr/share/man/man1/parallel.moreutils.1.gz by parallel' Unpacking parallel (20161222-1) ... Selecting previously unselected package fasttree. Preparing to unpack .../579-fasttree_2.1.9-1_amd64.deb ... Unpacking fasttree (2.1.9-1) ... Selecting previously unselected package roary. Preparing to unpack .../580-roary_3.8.0+dfsg-1_all.deb ... Unpacking roary (3.8.0+dfsg-1) ... Selecting previously unselected package samtools. Preparing to unpack .../581-samtools_1.3.1-3_amd64.deb ... Unpacking samtools (1.3.1-3) ... Selecting previously unselected package sim4. Preparing to unpack .../582-sim4_0.0.20121010-4_amd64.deb ... Unpacking sim4 (0.0.20121010-4) ... Selecting previously unselected package t-coffee. Preparing to unpack .../583-t-coffee_11.00.8cbe486-5_amd64.deb ... Unpacking t-coffee (11.00.8cbe486-5) ... 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Selecting previously unselected package libtxc-dxtn-s2tc:amd64. Preparing to unpack .../597-libtxc-dxtn-s2tc_1.0+git20151227-2_amd64.deb ... Unpacking libtxc-dxtn-s2tc:amd64 (1.0+git20151227-2) ... Selecting previously unselected package lynx. Preparing to unpack .../598-lynx_2.8.9dev11-1_amd64.deb ... Unpacking lynx (2.8.9dev11-1) ... Selecting previously unselected package med-config. Preparing to unpack .../599-med-config_3.0.1_all.deb ... Unpacking med-config (3.0.1) ... Selecting previously unselected package publicsuffix. Preparing to unpack .../600-publicsuffix_20190415.1030-0+deb9u1_all.deb ... Unpacking publicsuffix (20190415.1030-0+deb9u1) ... Setting up libquadmath0:amd64 (6.3.0-18+deb9u1) ... Setting up tigr-glimmer (3.02b-1) ... Setting up cdbs (0.4.150) ... Setting up libgs9-common (9.26a~dfsg-0+deb9u6) ... Setting up libnpth0:amd64 (1.3-1) ... Setting up phylip (1:3.696+dfsg-5) ... Setting up libargtable2-0 (13-1) ... Setting up libncurses5:amd64 (6.0+20161126-1+deb9u2) ... Setting up libgomp1:amd64 (6.3.0-18+deb9u1) ... Setting up libjs-jquery (3.1.1-2+deb9u1) ... Setting up libatomic1:amd64 (6.3.0-18+deb9u1) ... Setting up libapr1:amd64 (1.5.2-5) ... Setting up prank (0.0.150803-2) ... Setting up perl-modules-5.24 (5.24.1-3+deb9u7) ... Setting up libgdbm3:amd64 (1.8.3-14) ... Setting up manpages (4.10-2) ... Setting up libperl5.24:amd64 (5.24.1-3+deb9u7) ... Setting up libnettle6:amd64 (3.3-1+b2) ... Setting up kalign (1:2.03+20110620-3) ... Setting up clustalo (1.2.4-1) ... Setting up libpathplan4 (2.38.0-17) ... Setting up fonts-droid-fallback (1:6.0.1r16-1.1) ... Setting up libexpat1:amd64 (2.2.0-2+deb9u3) ... Setting up libcc1-0:amd64 (6.3.0-18+deb9u1) ... Setting up bwa (0.7.15-2+deb9u1) ... Setting up make (4.1-9.1) ... Setting up libasan3:amd64 (6.3.0-18+deb9u1) ... Setting up maq (0.7.1-7) ... Setting up libopenjp2-7:amd64 (2.1.2-1.1+deb9u4) ... Setting up libxdot4 (2.38.0-17) ... Setting up libjpeg62-turbo:amd64 (1:1.5.1-2) ... Setting up libdivsufsort3:amd64 (2.0.1-2) ... Setting up psmisc (22.21-2.1+b2) ... Setting up libnghttp2-14:amd64 (1.18.1-1+deb9u1) ... Setting up bedtools (2.26.0+dfsg-3) ... Setting up exim4-config (4.89-2+deb9u7) ... Adding system-user for exim (v4) Setting up mime-support (3.60) ... Setting up gsfonts (1:8.11+urwcyr1.0.7~pre44-4.3) ... Setting up libpng16-16:amd64 (1.6.28-1+deb9u1) ... Setting up t-coffee (11.00.8cbe486-5) ... Setting up liblcms2-2:amd64 (2.8-4+deb9u1) ... Setting up libjbig0:amd64 (2.1-3.1+b2) ... Setting up libgpm2:amd64 (1.20.4-6.2+b1) ... Setting up libldap-common (2.4.44+dfsg-5+deb9u4) ... Setting up fonts-dejavu-core (2.37-1) ... Setting up poppler-data (0.4.7-8) ... Setting up libcilkrts5:amd64 (6.3.0-18+deb9u1) ... Setting up libblas-common (3.7.0-2) ... Setting up libpng-tools (1.6.28-1+deb9u1) ... Setting up libnuma1:amd64 (2.0.11-2.1) ... Setting up tzdata (2020a-0+deb9u1) ... Current default time zone: 'Etc/UTC' Local time is now: Tue Feb 21 00:44:44 UTC 2023. Universal Time is now: Tue Feb 21 00:44:44 UTC 2023. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up libelf1:amd64 (0.168-1) ... Setting up libubsan0:amd64 (6.3.0-18+deb9u1) ... Setting up libtsan0:amd64 (6.3.0-18+deb9u1) ... Setting up libgfortran3:amd64 (6.3.0-18+deb9u1) ... Setting up mysql-common (5.8+1.0.2) ... update-alternatives: using /etc/mysql/my.cnf.fallback to provide /etc/mysql/my.cnf (my.cnf) in auto mode Setting up libxshmfence1:amd64 (1.2-1+b2) ... Setting up libossp-uuid16:amd64 (1.6.2-1.5+b4) ... Setting up infernal (1.1.2-1) ... Setting up probcons (1.12-11) ... Setting up libsasl2-modules-db:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Setting up unzip (6.0-21+deb9u2) ... Setting up linux-libc-dev:amd64 (4.9.228-1) ... Setting up dialign (2.2.1-8) ... Setting up libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Setting up libtinfo-dev:amd64 (6.0+20161126-1+deb9u2) ... Setting up libgc1c2:amd64 (1:7.4.2-8) ... Setting up menu (2.1.47+b1) ... Setting up libdatrie1:amd64 (0.2.10-4+b1) ... Setting up libtiff5:amd64 (4.0.8-2+deb9u5) ... Setting up libtxc-dxtn-s2tc:amd64 (1.0+git20151227-2) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/s2tc/libtxc_dxtn.so to provide /usr/lib/x86_64-linux-gnu/libtxc_dxtn.so (libtxc-dxtn-x86_64-linux-gnu) in auto mode Setting up libksba8:amd64 (1.3.5-2) ... Setting up libmariadbclient18:amd64 (10.1.45-0+deb9u1) ... Setting up libglapi-mesa:amd64 (13.0.6-1+b2) ... Setting up sgml-base (1.29) ... Setting up gawk (1:4.1.4+dfsg-1) ... Setting up libicu57:amd64 (57.1-6+deb9u4) ... Setting up libbsd0:amd64 (0.8.3-1) ... Setting up fonts-liberation (1:1.07.4-2) ... Setting up libprocps6:amd64 (2:3.3.12-3+deb9u1) ... Setting up ucf (3.0036) ... Setting up libxml2:amd64 (2.9.4+dfsg1-2.2+deb9u2) ... Setting up zip (3.0-11+b1) ... Setting up tm-align (20160521+dfsg-2) ... Setting up libfreetype6:amd64 (2.6.3-3.2+deb9u1) ... Setting up libtasn1-6:amd64 (4.10-1.1+deb9u1) ... Setting up libmagic-mgc (1:5.30-1+deb9u3) ... Setting up fonts-noto-mono (20161116-1) ... Setting up gnupg-l10n (2.1.18-8~deb9u4) ... Setting up libdrm2:amd64 (2.4.74-1) ... Setting up bzip2 (1.0.6-8.1) ... Setting up libmagic1:amd64 (1:5.30-1+deb9u3) ... Setting up dialign-tx-data (1.0.2-9) ... Setting up lsb-base (9.20161125) ... Setting up libhogweed4:amd64 (3.3-1+b2) ... Setting up libgraphite2-3:amd64 (1.3.10-1) ... Setting up liblsan0:amd64 (6.3.0-18+deb9u1) ... Setting up procps (2:3.3.12-3+deb9u1) ... update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode Setting up fonts-lato (2.0-1) ... Setting up libxslt1.1:amd64 (1.1.29-2.1+deb9u2) ... Setting up sim4 (0.0.20121010-4) ... Setting up libpsm-infinipath1 (3.3+19.g67c0807.open-3) ... Setting up raxml (8.2.9+dfsg-1+b1) ... 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 amap-align (2.2-6) ... Setting up libenv-path-perl (0.19-1) ... Setting up libsys-hostname-long-perl (1.5-1) ... Setting up libfile-fcntllock-perl (0.22-3+b2) ... Setting up libssl1.0.2:amd64 (1.0.2u-1~deb9u1) ... Setting up libtext-glob-perl (0.10-1) ... Setting up libxml-sax-base-perl (1.07-1) ... Setting up libpackage-stash-xs-perl (0.28-3+b1) ... Setting up libjbig2dec0:amd64 (0.13-4.1) ... Setting up libstrictures-perl (2.000003-1) ... Setting up ruby-did-you-mean (1.0.0-2) ... Setting up libmpx2:amd64 (6.3.0-18+deb9u1) ... Setting up libisl15:amd64 (0.18-1) ... Setting up libyaml-0-2:amd64 (0.1.7-2) ... Setting up libx11-xcb1:amd64 (2:1.6.4-3+deb9u1) ... Setting up libntlm0:amd64 (1.4-8) ... Setting up ncbi-data (6.1.20170106+dfsg1-0+deb9u1) ... Setting up libpixman-1-0:amd64 (0.34.0-1) ... Setting up hmmer (3.1b2+dfsg-5) ... 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 patch (2.7.5-1+deb9u2) ... Setting up proda (1.0-10) ... Setting up libglib2.0-data (2.50.3-2+deb9u2) ... Setting up liblwp-mediatypes-perl (6.02-1) ... Setting up libmail-sendmail-perl (0.79.16-2) ... Setting up krb5-locales (1.15-1+deb9u1) ... Setting up openmpi-common (2.0.2-2) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Setting up wise-data (2.4.1-19) ... Setting up libsort-naturally-perl (1.03-1) ... Setting up libbsd-resource-perl (1.2910-1+b1) ... Setting up libxml-regexp-perl (0.04-1) ... Setting up publicsuffix (20190415.1030-0+deb9u1) ... Setting up fasttree (2.1.9-1) ... Setting up autotools-dev (20161112.1) ... Setting up libunistring0:amd64 (0.9.6+really0.9.3-0.1) ... Setting up bzip2-doc (1.0.6-8.1) ... Setting up libapparmor1:amd64 (2.11.0-3+deb9u2) ... Setting up liburi-perl (1.71-1) ... Setting up libssl1.1:amd64 (1.1.0l-1~deb9u1) ... Setting up xz-utils (5.2.2-1.2+b1) ... update-alternatives: using /usr/bin/xz to provide /usr/bin/lzma (lzma) in auto mode Setting up libtext-iconv-perl (1.7-5+b4) ... Setting up primer3 (2.3.7-3) ... Setting up libaprutil1:amd64 (1.5.4-3) ... Setting up libfakeroot:amd64 (1.21-3.1) ... Setting up libscalar-list-utils-perl (1:1.47-1) ... Setting up libltdl7:amd64 (2.4.6-2) ... Setting up openssl (1.1.0l-1~deb9u1) ... Setting up ruby-net-telnet (0.1.1-2) ... Setting up libreadline-dev:amd64 (7.0-3) ... Setting up mcl (1:14-137-1+b1) ... Setting up libijs-0.35:amd64 (0.35-12) ... Setting up libfile-grep-perl (0.02-1) ... Setting up libsqlite3-0:amd64 (3.16.2-5+deb9u1) ... Setting up libann0 (1.1.2+doc-6) ... Setting up libfontenc1:amd64 (1:1.1.3-1+b2) ... Setting up libdate-manip-perl (6.57-1) ... Setting up libio-string-perl (1.08-3) ... Setting up libmldbm-perl (2.05-2) ... Setting up libalgorithm-diff-perl (1.19.03-1) ... Setting up libfribidi0:amd64 (0.19.7-1+deb9u1) ... Setting up liblocale-gettext-perl (1.07-3+b1) ... Setting up probalign (1.4-5) ... Setting up libclone-perl (0.38-2+b1) ... Setting up emboss-data (6.6.0+dfsg-6) ... Setting up libpciaccess0:amd64 (0.13.4-1+b2) ... Setting up libclass-xsaccessor-perl (1.19-2+b7) ... Setting up libx11-protocol-perl (0.56-7) ... Setting up libxml-xpathengine-perl (0.13-1) ... Setting up libsensors4:amd64 (1:3.4.0-4) ... Setting up libpcrecpp0v5:amd64 (2:8.39-3) ... Setting up libpcre32-3:amd64 (2:8.39-3) ... Setting up libnet-http-perl (6.12-1) ... Setting up libnumber-compare-perl (0.03-1) ... Setting up libmpc3:amd64 (1.0.3-1+b2) ... Setting up libcrypt-rc4-perl (2.02-2) ... Setting up poa (2.0+20060928-4+b1) ... Setting up muscle (1:3.8.31+dfsg-2) ... Setting up binutils (2.28-5) ... Setting up libffi6:amd64 (3.2.1-6) ... Setting up cpp-6 (6.3.0-18+deb9u1) ... Setting up icu-devtools (57.1-6+deb9u4) ... Setting up libc-dev-bin (2.24-11+deb9u4) ... Setting up liblua5.2-0:amd64 (5.2.4-1.1+b2) ... Setting up libdrm-radeon1:amd64 (2.4.74-1) ... Setting up libpcre16-3:amd64 (2:8.39-3) ... Setting up libconvert-binary-c-perl (0.78-1+b1) ... Setting up libtcl8.6:amd64 (8.6.6+dfsg-1+b1) ... Setting up libthai-data (0.1.26-1) ... Setting up liblzma-dev:amd64 (5.2.2-1.2+b1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up xml-core (0.17) ... Setting up javascript-common (11) ... Setting up ocl-icd-libopencl1:amd64 (2.2.11-1) ... Setting up libkeyutils1:amd64 (1.5.9-9) ... Setting up libdrm-nouveau2:amd64 (2.4.74-1) ... Setting up libsasl2-modules:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Setting up libconvert-binhex-perl (1.125-1) ... Setting up libio-sessiondata-perl (1.03-1) ... Setting up libnl-3-200:amd64 (3.2.27-2) ... Setting up libsub-uplevel-perl (0.2600-1) ... Setting up libpadwalker-perl (2.2-2+b1) ... Setting up libparams-util-perl (1.07-3+b1) ... Setting up ruby-minitest (5.9.0-1) ... Setting up lynx-common (2.8.9dev11-1) ... 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 mustang (3.2.3-1) ... Setting up clustalw (2.1+lgpl-5) ... Setting up xdg-utils (1.1.1-1+deb9u2) ... Setting up libsub-name-perl (0.21-1) ... Setting up ca-certificates (20200601~deb9u1) ... Updating certificates in /etc/ssl/certs... 126 added, 0 removed; done. Setting up libtext-csv-perl (1.33-2) ... Setting up libalgorithm-munkres-perl (0.08-3) ... Setting up manpages-dev (4.10-2) ... Setting up libyaml-libyaml-perl (0.63-2) ... Setting up libc6-dev:amd64 (2.24-11+deb9u4) ... Setting up cron (3.0pl1-128+deb9u1) ... Adding group `crontab' (GID 151) ... Done. 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 libpostscript-perl (0.06-2) ... Setting up libparams-classify-perl (0.013-6+b1) ... Setting up libassuan0:amd64 (2.4.3-2) ... Setting up libfcgi-perl (0.78-2) ... Setting up xdg-user-dirs (0.15-2+b1) ... Setting up libwww-robotrules-perl (6.01-1) ... Setting up libcdt5 (2.38.0-17) ... Setting up libauthen-sasl-perl (2.1600-1) ... Setting up libdbi-perl (1.636-1+b1) ... Setting up libitm1:amd64 (6.3.0-18+deb9u1) ... Setting up libx11-data (2:1.6.4-3+deb9u1) ... Setting up libpython2.7-stdlib:amd64 (2.7.13-2+deb9u3) ... Setting up libdata-stag-perl (0.14-2) ... Setting up libxau6:amd64 (1:1.0.8-1) ... Setting up libfile-slurper-perl (0.009-1) ... Setting up libidn11:amd64 (1.33-1+deb9u1) ... Setting up libdbus-1-3:amd64 (1.10.32-0+deb9u1) ... Setting up libalgorithm-c3-perl (0.10-1) ... Setting up hyphy-common (2.2.7+dfsg-1) ... Setting up libclass-inspector-perl (1.31-1) ... Setting up liblzo2-2:amd64 (2.08-1.2+b2) ... Setting up r-doc-html (3.3.3-1) ... Setting up libclass-c3-perl (0.32-1) ... Setting up libwrap0:amd64 (7.6.q-26) ... Setting up ruby-power-assert (0.3.0-1) ... Setting up libavahi-common-data:amd64 (0.6.32-2) ... Setting up libcgraph6 (2.38.0-17) ... Setting up libspiffy-perl (0.41-1) ... Setting up mailutils-common (1:3.1.1-1) ... Setting up libtest-warn-perl (0.32-1) ... Setting up libtask-weaken-perl (1.04-1) ... Setting up netbase (5.4) ... Setting up libwebp6:amd64 (0.5.2-1) ... Setting up zlib1g-dev:amd64 (1:1.2.8.dfsg-5) ... Setting up libhtml-tagset-perl (3.20-3) ... Setting up libedit2:amd64 (3.1-20160903-3) ... Setting up libpaper1:amd64 (1.1.24+nmu5) ... Creating config file /etc/papersize with new version Setting up libclass-c3-xs-perl (0.14-1+b1) ... Setting up cpp (4:6.3.0-4) ... Setting up libsub-install-perl (0.928-1) ... Setting up libfindbin-libs-perl (2.150-1) ... Setting up libdevel-symdump-perl (2.17-1) ... Setting up mafft (7.307-1) ... Setting up libtest-deep-perl (1.126-1) ... Setting up libdata-optlist-perl (0.110-1) ... Setting up libio-stringy-perl (2.111-2) ... Setting up libparse-yapp-perl (1.05-12) ... Setting up libhpdf-2.2.1 (2.2.1-1.1+b1) ... Setting up cd-hit (4.6.6-2) ... Setting up libipc-sharelite-perl (0.17-4) ... Setting up libsub-exporter-progressive-perl (0.001013-1) ... Setting up libtry-tiny-perl (0.28-1) ... Setting up libfile-find-rule-perl (0.34-1) ... Setting up libfile-slurp-tiny-perl (0.003-1) ... Setting up libpaper-utils (1.1.24+nmu5) ... Setting up libclass-method-modifiers-perl (2.12-1) ... Setting up libfont-afm-perl (1.20-2) ... Setting up libpcre3-dev:amd64 (2:8.39-3) ... Setting up fontconfig-config (2.11.0-6.7) ... Setting up liblog-log4perl-perl (1.48-1+deb9u1) ... Setting up libbz2-dev:amd64 (1.0.6-8.1) ... Setting up libgcc-6-dev:amd64 (6.3.0-18+deb9u1) ... Setting up libidn2-0:amd64 (0.16-1+deb9u1) ... Setting up sysstat (11.4.3-2) ... Creating config file /etc/default/sysstat with new version update-alternatives: using /usr/bin/sar.sysstat to provide /usr/bin/sar (sar) in auto mode Setting up libstdc++-6-dev:amd64 (6.3.0-18+deb9u1) ... Setting up libclass-data-inheritable-perl (0.08-2) ... Setting up libdbd-sqlite3-perl (1.54-1) ... Setting up libbio-perl-perl (1.7.1-2) ... Setting up libxml-namespacesupport-perl (1.11-1) ... Setting up libio-pty-perl (1:1.08-1.1+b2) ... Setting up libdrm-amdgpu1:amd64 (2.4.74-1) ... Setting up libfile-which-perl (1.21-1) ... Setting up libencode-locale-perl (1.05-1) ... Setting up libtext-csv-xs-perl (1.26-1) ... Setting up ruby-test-unit (3.1.7-2) ... Setting up liberror-perl (0.17024-1) ... Setting up libaprutil1-dbd-sqlite3:amd64 (1.5.4-3) ... Setting up libvariable-magic-perl (0.61-1) ... Setting up libtimedate-perl (2.3000-2+deb9u1) ... Setting up rename (0.20-4) ... update-alternatives: using /usr/bin/file-rename to provide /usr/bin/rename (rename) in auto mode Setting up librole-tiny-perl (2.000005-1) ... Setting up libgraph-perl (1:0.96-2) ... Setting up libgvpr2 (2.38.0-17) ... Setting up libemail-date-format-perl (1.005-1) ... Setting up libbio-asn1-entrezgene-perl (1.720-1) ... Setting up perl-openssl-defaults:amd64 (3) ... Setting up libfreezethaw-perl (0.5001-1) ... Setting up perl-doc (5.24.1-3+deb9u7) ... Setting up libmodule-runtime-perl (0.014-2) ... Setting up libset-scalar-perl (1.29-2) ... Setting up libpsl5:amd64 (0.17.0-3) ... Setting up libsvg-perl (2.64-1) ... Setting up libipc-system-simple-perl (1.25-3) ... Setting up libfile-basedir-perl (0.07-1) ... Setting up libdevel-stacktrace-perl (2.0200-1) ... Setting up libclass-tiny-perl (1.006-1) ... Setting up mummer (3.23+dfsg-2) ... 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 libtext-diff-perl (1.44-1) ... Setting up libtest-exception-perl (0.43-1) ... Setting up libglib2.0-0:amd64 (2.50.3-2+deb9u2) ... No schema files found: doing nothing. Setting up dialign-tx (1.0.2-9) ... Setting up libcapture-tiny-perl (0.44-1) ... Setting up libio-html-perl (1.001-1) ... Setting up libexporter-tiny-perl (0.042-1) ... Setting up libllvm3.9:amd64 (1:3.9.1-9) ... Setting up libossp-uuid-perl (1.6.2-1.5+b4) ... Setting up libgfortran-6-dev:amd64 (6.3.0-18+deb9u1) ... Setting up libtie-ixhash-perl (1.23-2) ... Setting up exonerate (2.4.0-2) ... Setting up libcarp-clan-perl (6.06-1) ... Setting up libdpkg-perl (1.18.25) ... Setting up libmath-derivative-perl (0.04-2) ... Setting up python2.7 (2.7.13-2+deb9u3) ... Setting up libyaml-perl (1.21-1) ... Setting up libperlio-utf8-strict-perl (0.006-1+b2) ... Setting up libparse-recdescent-perl (1.967013+dfsg-1) ... Setting up libdigest-perl-md5-perl (1.9-1) ... Setting up libspreadsheet-writeexcel-perl (2.40-1) ... Setting up libharfbuzz0b:amd64 (1.4.2-1) ... Setting up libipc-shareable-perl (0.61-1) ... Setting up libnl-route-3-200:amd64 (3.2.27-2) ... Setting up libthai0:amd64 (0.1.26-1) ... Setting up libmro-compat-perl (0.12-1) ... Setting up libtype-tiny-xs-perl (0.012-1+b2) ... Setting up libicu-dev (57.1-6+deb9u4) ... Setting up libtest-simple-perl (1.302075-1) ... Setting up exim4-base (4.89-2+deb9u7) ... exim: DB upgrade, deleting hints-db Setting up libjcode-pm-perl (2.06-1) ... Setting up file (1:5.30-1+deb9u3) ... Setting up libarray-utils-perl (0.5-1) ... Setting up libsub-identify-perl (0.12-2+b1) ... Setting up fakeroot (1.21-3.1) ... update-alternatives: using /usr/bin/fakeroot-sysv to provide /usr/bin/fakeroot (fakeroot) in auto mode Setting up tcpd (7.6.q-26) ... Setting up libunicode-map-perl (0.112-11+b3) ... Setting up libhwloc5:amd64 (1.11.5-1) ... Setting up libkrb5support0:amd64 (1.15-1+deb9u1) ... Setting up libdevel-caller-perl (2.06-1+b4) ... Setting up libxml-writer-perl (0.625-1) ... Setting up libtest-file-perl (1.442-1) ... Setting up gcc-6 (6.3.0-18+deb9u1) ... Setting up libio-all-perl (0.86-2) ... Setting up fsa (1.15.9+dfsg-3) ... Setting up libmime-types-perl (2.13-1) ... Setting up libsub-exporter-perl (0.986-1) ... Setting up g++-6 (6.3.0-18+deb9u1) ... Setting up libncurses5-dev:amd64 (6.0+20161126-1+deb9u2) ... Setting up libpython-stdlib:amd64 (2.7.13-2) ... Setting up libhwloc-plugins (1.11.5-1) ... Setting up libalgorithm-merge-perl (0.08-3) ... Setting up pkg-config (0.29-4+b1) ... Setting up libdrm-intel1:amd64 (2.4.74-1) ... Setting up dpkg-dev (1.18.25) ... Setting up libalgorithm-diff-xs-perl (0.04-4+b2) ... Setting up libfile-desktopentry-perl (0.22-1) ... Setting up wise (2.4.1-19) ... Setting up guile-2.0-libs:amd64 (2.0.13+1-4) ... Setting up libp11-kit0:amd64 (0.23.3-2) ... Setting up libhtml-parser-perl (3.72-3) ... Setting up libpython2.7:amd64 (2.7.13-2+deb9u3) ... Setting up libipc-run-perl (0.94-1+deb9u1) ... Setting up bioperl (1.7.1-2) ... Setting up libcgi-pm-perl (4.35-1) ... Setting up libdevel-globaldestruction-perl (0.14-1) ... Setting up libice6:amd64 (2:1.0.9-2) ... Setting up libbit-vector-perl (7.4-1+b2) ... Setting up rubygems-integration (1.11) ... Setting up shared-mime-info (1.8-1+deb9u1) ... Setting up pinentry-curses (1.0.0-2) ... Setting up libavahi-common3:amd64 (0.6.32-2) ... Setting up libeval-closure-perl (0.14-1) ... Setting up libjpeg62-turbo-dev:amd64 (1:1.5.1-2) ... Setting up libpng-dev:amd64 (1.6.28-1+deb9u1) ... Setting up dbus (1.10.32-0+deb9u1) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up gnupg-agent (2.1.18-8~deb9u4) ... Setting up libdbd-mysql-perl (4.041-2) ... Setting up libfile-mimeinfo-perl (0.27-1) ... Setting up libbio-perl-run-perl (1.7.1-3) ... Setting up libkyotocabinet16v5:amd64 (1.2.76-4.2+b1) ... Setting up libdist-checkconflicts-perl (0.11-1) ... Setting up libtree-dagnode-perl (1.29-1) ... Setting up libxcb1:amd64 (1.12-1) ... Setting up python (2.7.13-2) ... Setting up libole-storage-lite-perl (0.19-1+deb9u1) ... Setting up libspreadsheet-parseexcel-perl (0.6500-1) ... Setting up libxml-sax-perl (0.99+dfsg-2) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up liblist-moreutils-perl (0.416-1+b1) ... Setting up libhtml-tableextract-perl (2.13-1) ... Setting up libdevel-lexalias-perl (0.05-1+b4) ... Setting up libibverbs1 (1.2.1-2) ... Setting up libxcb-present0:amd64 (1.12-1) ... Setting up libgts-0.7-5:amd64 (0.7.6+darcs121130-4) ... Setting up libfontconfig1:amd64 (2.11.0-6.7+b1) ... Setting up libstatistics-descriptive-perl (3.0612-1) ... 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 gfortran-6 (6.3.0-18+deb9u1) ... Setting up parallel (20161222-1) ... Setting up libhttp-date-perl (6.02-1) ... Setting up libxcb-render0:amd64 (1.12-1) ... Setting up libmath-spline-perl (0.02-1) ... Setting up bowtie (1.1.2-6) ... Setting up libtest-differences-perl (0.64-1) ... Setting up libimport-into-perl (1.002005-1) ... Setting up libcache-cache-perl (1.08-2) ... Setting up libmodule-implementation-perl (0.09-1) ... Setting up libexception-class-perl (1.42-1) ... Setting up libtest-files-perl (0.14-1) ... Setting up libnet-ssleay-perl (1.80-1) ... Setting up libtype-tiny-perl (1.000005-1) ... Setting up libtest-output-perl (1.03-1) ... Setting up gnupg (2.1.18-8~deb9u4) ... Setting up libgnutls30:amd64 (3.5.8-5+deb9u5) ... Setting up libx11-6:amd64 (2:1.6.4-3+deb9u1) ... Setting up libgl1-mesa-dri:amd64 (13.0.6-1+b2) ... Setting up libmodule-runtime-conflicts-perl (0.003-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-1+b1) ... Setting up librdmacm1 (1.1.0-2) ... Setting up gcc (4:6.3.0-4) ... Setting up libio-socket-ssl-perl (2.044-1) ... Setting up libxmuu1:amd64 (2:1.1.2-2) ... Setting up libcgi-fast-perl (1:2.12-1) ... Setting up libhtml-tree-perl (5.03-2) ... Setting up libparams-validate-perl (1.26-1) ... Setting up libxcb-sync1:amd64 (1.12-1) ... Setting up libjpeg-dev (1:1.5.1-2) ... Setting up libdate-calc-perl (6.4-1) ... Setting up libldap-2.4-2:amd64 (2.4.44+dfsg-5+deb9u4) ... Setting up libxml-filter-buffertext-perl (1.01-5) ... Setting up libace-perl (1.92-4+b1) ... Setting up bioperl-run (1.7.1-3) ... 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 libmoo-perl (2.002005-1) ... Setting up libhttp-message-perl (6.11-1) ... Setting up g++ (4:6.3.0-4) ... update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode Setting up libavahi-client3:amd64 (0.6.32-2) ... Setting up libkrb5-3:amd64 (1.15-1+deb9u1) ... Setting up libb-hooks-endofscope-perl (0.21-1) ... Setting up libgts-bin (0.7.6+darcs121130-4) ... Setting up exim4-daemon-light (4.89-2+deb9u7) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Initializing GnuTLS DH parameter file Setting up libxml-libxml-perl (2.0128+dfsg-1+deb9u1) ... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libxft2:amd64 (2.3.2-1+b2) ... Setting up libxml-sax-writer-perl (0.56-1) ... Setting up dirmngr (2.1.18-8~deb9u4) ... Setting up fontconfig (2.11.0-6.7+b1) ... Regenerating fonts cache... done. Setting up libhttp-negotiate-perl (6.00-2) ... Setting up libtest-most-perl (0.35-1) ... Setting up libaprutil1-ldap:amd64 (1.5.4-3) ... Setting up lynx (2.8.9dev11-1) ... update-alternatives: using /usr/bin/lynx to provide /usr/bin/www-browser (www-browser) in auto mode Setting up libpackage-stash-perl (0.37-1) ... Setting up gfortran (4:6.3.0-4) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode Setting up liblog-dispatch-perl (2.58-1) ... Setting up libsvg-graph-perl (0.02-2) ... Setting up libnet-smtp-ssl-perl (1.04-1) ... Setting up libhtml-format-perl (2.12-1) ... Setting up libxext6:amd64 (2:1.3.3-1+b2) ... Setting up libxfixes3:amd64 (1:5.0.3-1) ... Setting up libhttp-cookies-perl (6.01-1) ... Setting up libfabric1 (1.4.0-1) ... Setting up libblas-dev (3.7.0-2) ... update-alternatives: using /usr/lib/libblas/libblas.so to provide /usr/lib/libblas.so (libblas.so) in auto mode Setting up build-essential (12.3) ... Setting up libxss1:amd64 (1:1.2.2-1) ... Setting up libarray-compare-perl (3.0.0-1) ... Setting up ncbi-blast+ (2.6.0-1) ... Setting up libdate-calc-xs-perl (6.4-1+b2) ... Setting up apache2-bin (2.4.25-3+deb9u9) ... Setting up libgd3:amd64 (2.2.4-2+deb9u5) ... Setting up libhttp-daemon-perl (6.01-1) ... Setting up libdevel-overloadinfo-perl (0.004-1) ... Setting up libgd-perl (2.53-3) ... Setting up libxmu6:amd64 (2:1.1.2-2) ... Setting up libclass-load-perl (0.23-1) ... Setting up libgssapi-krb5-2:amd64 (1.15-1+deb9u1) ... Setting up xauth (1:1.0.9-1+b2) ... Setting up libpackage-deprecationmanager-perl (0.17-1) ... Setting up libxml-simple-perl (2.22-1) ... Setting up libxcursor1:amd64 (1:1.1.14-1+deb9u2) ... Setting up libpq5:amd64 (9.6.17-0+deb9u1) ... Setting up libxxf86dga1:amd64 (2:1.1.4-1+b3) ... Setting up libxml-libxslt-perl (1.95-1+b1) ... Setting up exim4 (4.89-2+deb9u7) ... Setting up perl-tk (1:804.033-1+b3) ... Setting up libpango-1.0-0:amd64 (1.40.5-1) ... Setting up emboss-lib (6.6.0+dfsg-6) ... Setting up libclass-load-xs-perl (0.09-2+b1) ... Setting up libhtml-form-perl (6.03-1) ... Setting up libxv1:amd64 (2:1.0.11-1) ... Setting up libopenmpi2:amd64 (2.0.2-2) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b2) ... Setting up libnamespace-clean-perl (0.27-1) ... Setting up beignet-opencl-icd:amd64 (1.3.0-4) ... 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 liblapack-dev (3.7.0-2) ... update-alternatives: using /usr/lib/lapack/liblapack.so to provide /usr/lib/liblapack.so (liblapack.so) in auto mode Setting up libgsasl7 (1.8.0-8+b2) ... Setting up libxaw7:amd64 (2:1.0.13-1+b2) ... Setting up libmailutils5:amd64 (1:3.1.1-1) ... Setting up ncbi-blast+-legacy (2.6.0-1) ... Setting up libcairo2:amd64 (1.14.8-1) ... Setting up libxinerama1:amd64 (2:1.1.3-1+b3) ... Setting up libmailtools-perl (2.18-1) ... 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 blast2 (1:2.6.0-1) ... Setting up libmoose-perl (2.1807-1) ... Setting up libhmsbeagle1v5 (2.1.2+20160831-5) ... Setting up libdbd-pg-perl (3.5.3-1+b2) ... Setting up mailutils (1:3.1.1-1) ... update-alternatives: using /usr/bin/frm.mailutils to provide /usr/bin/frm (frm) in auto mode update-alternatives: using /usr/bin/from.mailutils to provide /usr/bin/from (from) in auto mode update-alternatives: using /usr/bin/messages.mailutils to provide /usr/bin/messages (messages) in auto mode update-alternatives: using /usr/bin/movemail.mailutils to provide /usr/bin/movemail (movemail) in auto mode update-alternatives: using /usr/bin/readmsg.mailutils to provide /usr/bin/readmsg (readmsg) in auto mode update-alternatives: using /usr/bin/dotlock.mailutils to provide /usr/bin/dotlock (dotlock) in auto mode update-alternatives: using /usr/bin/mail.mailutils to provide /usr/bin/mailx (mailx) in auto mode Setting up openmpi-bin (2.0.2-2) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode Setting up libmime-lite-perl (3.030-2) ... Setting up libdevel-partialdump-perl (0.18-2) ... Setting up libxtst6:amd64 (2:1.2.3-1) ... Setting up libpangoft2-1.0-0:amd64 (1.40.5-1) ... Setting up libcupsimage2:amd64 (2.2.1-8+deb9u6) ... Setting up libgl1-mesa-glx:amd64 (13.0.6-1+b2) ... Setting up emboss (6.6.0+dfsg-6) ... Setting up x11-xserver-utils (7.7+7+b1) ... Setting up phyml (3:3.2.0+dfsg-7+b1) ... Setting up libgs9:amd64 (9.26a~dfsg-0+deb9u6) ... Setting up libmime-tools-perl (5.508-1) ... Setting up libhts1:amd64 (1.3.2-2) ... Setting up hyphy-mpi (2.2.7+dfsg-1+b2) ... Setting up x11-utils (7.7+3+b1) ... Setting up libpangocairo-1.0-0:amd64 (1.40.5-1) ... Setting up ghostscript (9.26a~dfsg-0+deb9u6) ... Setting up libcupsfilters1:amd64 (1.11.6-3+deb9u1) ... Setting up samtools (1.3.1-3) ... Setting up libgvc6 (2.38.0-17) ... 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 littler (0.3.1-1) ... Setting up r-cran-nnet (7.3-12-1) ... Setting up r-cran-crayon (1.3.2-1) ... Setting up r-cran-gtable (0.2.0-1) ... Setting up r-base-dev (3.3.3-1) ... 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-spatial (7.3-11-1) ... 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-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 graphviz (2.38.0-17) ... Setting up r-cran-boot (1.3-18-2) ... Setting up r-cran-codetools (0.2-15-1) ... Setting up r-cran-lattice (0.20-34-1) ... Setting up r-cran-lazyeval (0.2.0-1) ... Setting up r-cran-nlme (3.1.129-1) ... Setting up r-cran-foreign (0.8.67-1) ... Setting up r-cran-stringr (1.1.0-1) ... Setting up r-cran-class (7.3-14-1) ... Setting up r-cran-kernsmooth (2.23-15-2) ... 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-matrix (1.2-7.1-1) ... Setting up r-cran-mgcv (1.8-16-1) ... Setting up r-cran-ggplot2 (2.2.1-2) ... Setting up r-cran-survival (2.40-1-1) ... Setting up r-cran-rpart (4.1-10-2) ... Setting up r-recommended (3.3.3-1) ... Processing triggers for menu (2.1.47+b1) ... Setting up blends-common (0.6.96) ... Setting up med-config (3.0.1) ... Adding group `med' (GID 154) ... Done. Setting up liblwp-protocol-https-perl (6.06-2) ... Setting up ruby2.3 (2.3.3-1+deb9u8) ... Setting up ruby (1:2.3.3) ... Setting up libwww-perl (6.15-1) ... Setting up libapache2-mod-perl2 (2.0.10-2+deb9u1) ... Setting up rake (10.5.0-2+deb9u1) ... Setting up libxml-parser-perl (2.44-2+b1) ... Setting up libapache2-reload-perl (0.13-1) ... Setting up libgraph-readwrite-perl (2.09-1) ... Setting up libruby2.3:amd64 (2.3.3-1+deb9u8) ... Setting up libxml-sax-expat-perl (0.40-2) ... update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::Expat with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libapache-dbi-perl (1.12-1) ... Setting up libxml-twig-perl (1:3.50-1) ... Setting up libsoap-lite-perl (1.20-1) ... Setting up libxml-xpath-perl (1.40-1) ... Setting up libnet-dbus-perl (1.1.0-4+b1) ... Setting up roary (3.8.0+dfsg-1) ... Setting up libxml-perl (0.08-2) ... Setting up libxmlrpc-lite-perl (0.717-1) ... Setting up libxml-dom-perl (1.44-2) ... Setting up libgraphviz-perl (2.22-1) ... Setting up libxml-dom-xpath-perl (0.14-2) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... Processing triggers for sgml-base (1.29) ... 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. 1m12.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'apt-get', '-y', 'install', 'roary=3.8.0+dfsg-1'] 1m12.2s INFO: Running scripts post_install 1m12.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/post_install_exceptions'] 1m12.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/post_install_exceptions'] 1m12.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny'] 1m14.2s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny'] 1m17.7s DEBUG: No broken symlinks as far as we can find. 1m20.1s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', '-ac', '--ignore-obsolete'] 1m25.4s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', '-ac', '--ignore-obsolete'] 1m25.4s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m25.4s DUMP: 0.15.6 1m25.4s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m25.4s INFO: Running adequate version 0.15.6 now. 1m25.4s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'roary'] 1m25.5s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'roary'] 1m25.5s INFO: Running scripts pre_remove 1m25.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m25.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m25.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m25.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m25.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m37.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m37.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m37.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m37.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m37.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m37.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/pre_remove_exceptions'] 1m38.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/pre_remove_exceptions'] 1m38.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m38.0s DUMP: install ok installed adduser adduser 3.115 install ok installed amap-align amap-align 2.2-6 install ok installed apache2-bin apache2-bin 2.4.25-3+deb9u9 install ok installed apt apt 1.4.10 install ok installed autotools-dev autotools-dev 20161112.1 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 bedtools bedtools 2.26.0+dfsg-3 install ok installed beignet-opencl-icd:amd64 beignet-opencl-icd 1.3.0-4 install ok installed binutils binutils 2.28-5 install ok installed bioperl bioperl 1.7.1-2 install ok installed bioperl-run bioperl-run 1.7.1-3 install ok installed blast2 blast2 1:2.6.0-1 install ok installed blends-common blends-common 0.6.96 install ok installed bowtie bowtie 1.1.2-6 install ok installed bsdutils bsdutils 1:2.29.2-1+deb9u1 install ok installed build-essential build-essential 12.3 install ok installed bwa bwa 0.7.15-2+deb9u1 install ok installed bzip2 bzip2 1.0.6-8.1 install ok installed bzip2-doc bzip2-doc 1.0.6-8.1 install ok installed ca-certificates ca-certificates 20200601~deb9u1 install ok installed cd-hit cd-hit 4.6.6-2 install ok installed cdbs cdbs 0.4.150 install ok installed clustalo clustalo 1.2.4-1 install ok installed clustalw clustalw 2.1+lgpl-5 install ok installed coreutils coreutils 8.26-3 install ok installed cpp cpp 4:6.3.0-4 install ok installed cpp-6 cpp-6 6.3.0-18+deb9u1 install ok installed cron cron 3.0pl1-128+deb9u1 install ok installed dash dash 0.5.8-2.4 install ok installed dbus dbus 1.10.32-0+deb9u1 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 dialign dialign 2.2.1-8 install ok installed dialign-tx dialign-tx 1.0.2-9 install ok installed dialign-tx-data dialign-tx-data 1.0.2-9 install ok installed diffutils diffutils 1:3.5-3 install ok installed dirmngr dirmngr 2.1.18-8~deb9u4 install ok installed dpkg dpkg 1.18.25 install ok installed dpkg-dev dpkg-dev 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 emboss emboss 6.6.0+dfsg-6 install ok installed emboss-data emboss-data 6.6.0+dfsg-6 install ok installed emboss-lib emboss-lib 6.6.0+dfsg-6 install ok installed exim4 exim4 4.89-2+deb9u7 install ok installed exim4-base exim4-base 4.89-2+deb9u7 install ok installed exim4-config exim4-config 4.89-2+deb9u7 install ok installed exim4-daemon-light exim4-daemon-light 4.89-2+deb9u7 install ok installed exonerate exonerate 2.4.0-2 install ok installed fakeroot fakeroot 1.21-3.1 install ok installed fasttree fasttree 2.1.9-1 install ok installed file file 1:5.30-1+deb9u3 install ok installed findutils findutils 4.6.0+git+20161106-2 install ok installed fontconfig fontconfig 2.11.0-6.7+b1 install ok installed fontconfig-config fontconfig-config 2.11.0-6.7 install ok installed fonts-dejavu-core fonts-dejavu-core 2.37-1 install ok installed fonts-droid-fallback fonts-droid-fallback 1:6.0.1r16-1.1 install ok installed fonts-lato fonts-lato 2.0-1 install ok installed fonts-liberation fonts-liberation 1:1.07.4-2 install ok installed fonts-noto-mono fonts-noto-mono 20161116-1 install ok installed fsa fsa 1.15.9+dfsg-3 install ok installed g++ g++ 4:6.3.0-4 install ok installed g++-6 g++-6 6.3.0-18+deb9u1 install ok installed gawk gawk 1:4.1.4+dfsg-1 install ok installed gcc gcc 4:6.3.0-4 install ok installed gcc-6 gcc-6 6.3.0-18+deb9u1 install ok installed gcc-6-base:amd64 gcc-6-base 6.3.0-18+deb9u1 install ok installed gfortran gfortran 4:6.3.0-4 install ok installed gfortran-6 gfortran-6 6.3.0-18+deb9u1 install ok installed ghostscript ghostscript 9.26a~dfsg-0+deb9u6 install ok installed gnupg gnupg 2.1.18-8~deb9u4 install ok installed gnupg-agent gnupg-agent 2.1.18-8~deb9u4 install ok installed gnupg-l10n gnupg-l10n 2.1.18-8~deb9u4 install ok installed gpgv gpgv 2.1.18-8~deb9u4 install ok installed graphviz graphviz 2.38.0-17 install ok installed grep grep 2.27-2 install ok installed gsfonts gsfonts 1:8.11+urwcyr1.0.7~pre44-4.3 install ok installed guile-2.0-libs:amd64 guile-2.0-libs 2.0.13+1-4 install ok installed gzip gzip 1.6-5+b1 install ok installed hmmer hmmer 3.1b2+dfsg-5 install ok installed hostname hostname 3.18+b1 install ok installed hyphy-common hyphy-common 2.2.7+dfsg-1 install ok installed hyphy-mpi hyphy-mpi 2.2.7+dfsg-1+b2 install ok installed icu-devtools icu-devtools 57.1-6+deb9u4 install ok installed infernal infernal 1.1.2-1 install ok installed init-system-helpers init-system-helpers 1.48 install ok installed javascript-common javascript-common 11 install ok installed kalign kalign 1:2.03+20110620-3 install ok installed krb5-locales krb5-locales 1.15-1+deb9u1 install ok installed libace-perl libace-perl 1.92-4+b1 install ok installed libacl1:amd64 libacl1 2.2.52-3+b1 install ok installed libalgorithm-c3-perl libalgorithm-c3-perl 0.10-1 install ok installed libalgorithm-diff-perl libalgorithm-diff-perl 1.19.03-1 install ok installed libalgorithm-diff-xs-perl libalgorithm-diff-xs-perl 0.04-4+b2 install ok installed libalgorithm-merge-perl libalgorithm-merge-perl 0.08-3 install ok installed libalgorithm-munkres-perl libalgorithm-munkres-perl 0.08-3 install ok installed libann0 libann0 1.1.2+doc-6 install ok installed libapache-dbi-perl libapache-dbi-perl 1.12-1 install ok installed libapache2-mod-perl2 libapache2-mod-perl2 2.0.10-2+deb9u1 install ok installed libapache2-reload-perl libapache2-reload-perl 0.13-1 install ok installed libapparmor1:amd64 libapparmor1 2.11.0-3+deb9u2 install ok installed libapr1:amd64 libapr1 1.5.2-5 install ok installed libaprutil1:amd64 libaprutil1 1.5.4-3 install ok installed libaprutil1-dbd-sqlite3:amd64 libaprutil1-dbd-sqlite3 1.5.4-3 install ok installed libaprutil1-ldap:amd64 libaprutil1-ldap 1.5.4-3 install ok installed libapt-pkg5.0:amd64 libapt-pkg5.0 1.4.10 install ok installed libargtable2-0 libargtable2-0 13-1 install ok installed libarray-compare-perl libarray-compare-perl 3.0.0-1 install ok installed libarray-utils-perl libarray-utils-perl 0.5-1 install ok installed libasan3:amd64 libasan3 6.3.0-18+deb9u1 install ok installed libassuan0:amd64 libassuan0 2.4.3-2 install ok installed libatomic1:amd64 libatomic1 6.3.0-18+deb9u1 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 libauthen-sasl-perl libauthen-sasl-perl 2.1600-1 install ok installed libavahi-client3:amd64 libavahi-client3 0.6.32-2 install ok installed libavahi-common-data:amd64 libavahi-common-data 0.6.32-2 install ok installed libavahi-common3:amd64 libavahi-common3 0.6.32-2 install ok installed libb-hooks-endofscope-perl libb-hooks-endofscope-perl 0.21-1 install ok installed libbio-asn1-entrezgene-perl libbio-asn1-entrezgene-perl 1.720-1 install ok installed libbio-perl-perl libbio-perl-perl 1.7.1-2 install ok installed libbio-perl-run-perl libbio-perl-run-perl 1.7.1-3 install ok installed libbit-vector-perl libbit-vector-perl 7.4-1+b2 install ok installed libblas-common libblas-common 3.7.0-2 install ok installed libblas-dev libblas-dev 3.7.0-2 install ok installed libblas3 libblas3 3.7.0-2 install ok installed libblkid1:amd64 libblkid1 2.29.2-1+deb9u1 install ok installed libbsd-resource-perl libbsd-resource-perl 1.2910-1+b1 install ok installed libbsd0:amd64 libbsd0 0.8.3-1 install ok installed libbz2-1.0:amd64 libbz2-1.0 1.0.6-8.1 install ok installed libbz2-dev:amd64 libbz2-dev 1.0.6-8.1 install ok installed libc-bin libc-bin 2.24-11+deb9u4 install ok installed libc-dev-bin libc-dev-bin 2.24-11+deb9u4 install ok installed libc6:amd64 libc6 2.24-11+deb9u4 install ok installed libc6-dev:amd64 libc6-dev 2.24-11+deb9u4 install ok installed libcache-cache-perl libcache-cache-perl 1.08-2 install ok installed libcairo2:amd64 libcairo2 1.14.8-1 install ok installed libcap-ng0:amd64 libcap-ng0 0.7.7-3+b1 install ok installed libcapture-tiny-perl libcapture-tiny-perl 0.44-1 install ok installed libcarp-clan-perl libcarp-clan-perl 6.06-1 install ok installed libcc1-0:amd64 libcc1-0 6.3.0-18+deb9u1 install ok installed libcdt5 libcdt5 2.38.0-17 install ok installed libcgi-fast-perl libcgi-fast-perl 1:2.12-1 install ok installed libcgi-pm-perl libcgi-pm-perl 4.35-1 install ok installed libcgraph6 libcgraph6 2.38.0-17 install ok installed libcilkrts5:amd64 libcilkrts5 6.3.0-18+deb9u1 install ok installed libclass-c3-perl libclass-c3-perl 0.32-1 install ok installed libclass-c3-xs-perl libclass-c3-xs-perl 0.14-1+b1 install ok installed libclass-data-inheritable-perl libclass-data-inheritable-perl 0.08-2 install ok installed libclass-inspector-perl libclass-inspector-perl 1.31-1 install ok installed libclass-load-perl libclass-load-perl 0.23-1 install ok installed libclass-load-xs-perl libclass-load-xs-perl 0.09-2+b1 install ok installed libclass-method-modifiers-perl libclass-method-modifiers-perl 2.12-1 install ok installed libclass-tiny-perl libclass-tiny-perl 1.006-1 install ok installed libclass-xsaccessor-perl libclass-xsaccessor-perl 1.19-2+b7 install ok installed libclone-perl libclone-perl 0.38-2+b1 install ok installed libcomerr2:amd64 libcomerr2 1.43.4-2+deb9u1 install ok installed libconvert-binary-c-perl libconvert-binary-c-perl 0.78-1+b1 install ok installed libconvert-binhex-perl libconvert-binhex-perl 1.125-1 install ok installed libcrypt-rc4-perl libcrypt-rc4-perl 2.02-2 install ok installed libcups2:amd64 libcups2 2.2.1-8+deb9u6 install ok installed libcupsfilters1:amd64 libcupsfilters1 1.11.6-3+deb9u1 install ok installed libcupsimage2:amd64 libcupsimage2 2.2.1-8+deb9u6 install ok installed libcurl3:amd64 libcurl3 7.52.1-5+deb9u10 install ok installed libcurl3-gnutls:amd64 libcurl3-gnutls 7.52.1-5+deb9u10 install ok installed libdata-optlist-perl libdata-optlist-perl 0.110-1 install ok installed libdata-stag-perl libdata-stag-perl 0.14-2 install ok installed libdate-calc-perl libdate-calc-perl 6.4-1 install ok installed libdate-calc-xs-perl libdate-calc-xs-perl 6.4-1+b2 install ok installed libdate-manip-perl libdate-manip-perl 6.57-1 install ok installed libdatrie1:amd64 libdatrie1 0.2.10-4+b1 install ok installed libdb5.3:amd64 libdb5.3 5.3.28-12+deb9u1 install ok installed libdbd-mysql-perl libdbd-mysql-perl 4.041-2 install ok installed libdbd-pg-perl libdbd-pg-perl 3.5.3-1+b2 install ok installed libdbd-sqlite3-perl libdbd-sqlite3-perl 1.54-1 install ok installed libdbi-perl libdbi-perl 1.636-1+b1 install ok installed libdbus-1-3:amd64 libdbus-1-3 1.10.32-0+deb9u1 install ok installed libdebconfclient0:amd64 libdebconfclient0 0.227 install ok installed libdevel-caller-perl libdevel-caller-perl 2.06-1+b4 install ok installed libdevel-globaldestruction-perl libdevel-globaldestruction-perl 0.14-1 install ok installed libdevel-lexalias-perl libdevel-lexalias-perl 0.05-1+b4 install ok installed libdevel-overloadinfo-perl libdevel-overloadinfo-perl 0.004-1 install ok installed libdevel-partialdump-perl libdevel-partialdump-perl 0.18-2 install ok installed libdevel-stacktrace-perl libdevel-stacktrace-perl 2.0200-1 install ok installed libdevel-symdump-perl libdevel-symdump-perl 2.17-1 install ok installed libdigest-perl-md5-perl libdigest-perl-md5-perl 1.9-1 install ok installed libdist-checkconflicts-perl libdist-checkconflicts-perl 0.11-1 install ok installed libdivsufsort3:amd64 libdivsufsort3 2.0.1-2 install ok installed libdpkg-perl libdpkg-perl 1.18.25 install ok installed libdrm-amdgpu1:amd64 libdrm-amdgpu1 2.4.74-1 install ok installed libdrm-intel1:amd64 libdrm-intel1 2.4.74-1 install ok installed libdrm-nouveau2:amd64 libdrm-nouveau2 2.4.74-1 install ok installed libdrm-radeon1:amd64 libdrm-radeon1 2.4.74-1 install ok installed libdrm2:amd64 libdrm2 2.4.74-1 install ok installed libedit2:amd64 libedit2 3.1-20160903-3 install ok installed libelf1:amd64 libelf1 0.168-1 install ok installed libemail-date-format-perl libemail-date-format-perl 1.005-1 install ok installed libencode-locale-perl libencode-locale-perl 1.05-1 install ok installed libenv-path-perl libenv-path-perl 0.19-1 install ok installed liberror-perl liberror-perl 0.17024-1 install ok installed libeval-closure-perl libeval-closure-perl 0.14-1 install ok installed libexception-class-perl libexception-class-perl 1.42-1 install ok installed libexpat1:amd64 libexpat1 2.2.0-2+deb9u3 install ok installed libexporter-tiny-perl libexporter-tiny-perl 0.042-1 install ok installed libfabric1 libfabric1 1.4.0-1 install ok installed libfakeroot:amd64 libfakeroot 1.21-3.1 install ok installed libfcgi-perl libfcgi-perl 0.78-2 install ok installed libfdisk1:amd64 libfdisk1 2.29.2-1+deb9u1 install ok installed libffi6:amd64 libffi6 3.2.1-6 install ok installed libfile-basedir-perl libfile-basedir-perl 0.07-1 install ok installed libfile-desktopentry-perl libfile-desktopentry-perl 0.22-1 install ok installed libfile-fcntllock-perl libfile-fcntllock-perl 0.22-3+b2 install ok installed libfile-find-rule-perl libfile-find-rule-perl 0.34-1 install ok installed libfile-grep-perl libfile-grep-perl 0.02-1 install ok installed libfile-listing-perl libfile-listing-perl 6.04-1 install ok installed libfile-mimeinfo-perl libfile-mimeinfo-perl 0.27-1 install ok installed libfile-slurp-tiny-perl libfile-slurp-tiny-perl 0.003-1 install ok installed libfile-slurper-perl libfile-slurper-perl 0.009-1 install ok installed libfile-which-perl libfile-which-perl 1.21-1 install ok installed libfindbin-libs-perl libfindbin-libs-perl 2.150-1 install ok installed libfont-afm-perl libfont-afm-perl 1.20-2 install ok installed libfontconfig1:amd64 libfontconfig1 2.11.0-6.7+b1 install ok installed libfontenc1:amd64 libfontenc1 1:1.1.3-1+b2 install ok installed libfreetype6:amd64 libfreetype6 2.6.3-3.2+deb9u1 install ok installed libfreezethaw-perl libfreezethaw-perl 0.5001-1 install ok installed libfribidi0:amd64 libfribidi0 0.19.7-1+deb9u1 install ok installed libgc1c2:amd64 libgc1c2 1:7.4.2-8 install ok installed libgcc-6-dev:amd64 libgcc-6-dev 6.3.0-18+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 libgd-perl libgd-perl 2.53-3 install ok installed libgd3:amd64 libgd3 2.2.4-2+deb9u5 install ok installed libgdbm3:amd64 libgdbm3 1.8.3-14 install ok installed libgfortran-6-dev:amd64 libgfortran-6-dev 6.3.0-18+deb9u1 install ok installed libgfortran3:amd64 libgfortran3 6.3.0-18+deb9u1 install ok installed libgl1-mesa-dri:amd64 libgl1-mesa-dri 13.0.6-1+b2 install ok installed libgl1-mesa-glx:amd64 libgl1-mesa-glx 13.0.6-1+b2 install ok installed libglapi-mesa:amd64 libglapi-mesa 13.0.6-1+b2 install ok installed libglib2.0-0:amd64 libglib2.0-0 2.50.3-2+deb9u2 install ok installed libglib2.0-data libglib2.0-data 2.50.3-2+deb9u2 install ok installed libgmp10:amd64 libgmp10 2:6.1.2+dfsg-1 install ok installed libgnutls30:amd64 libgnutls30 3.5.8-5+deb9u5 install ok installed libgomp1:amd64 libgomp1 6.3.0-18+deb9u1 install ok installed libgpg-error0:amd64 libgpg-error0 1.26-2 install ok installed libgpm2:amd64 libgpm2 1.20.4-6.2+b1 install ok installed libgraph-perl libgraph-perl 1:0.96-2 install ok installed libgraph-readwrite-perl libgraph-readwrite-perl 2.09-1 install ok installed libgraphite2-3:amd64 libgraphite2-3 1.3.10-1 install ok installed libgraphviz-perl libgraphviz-perl 2.22-1 install ok installed libgs9:amd64 libgs9 9.26a~dfsg-0+deb9u6 install ok installed libgs9-common libgs9-common 9.26a~dfsg-0+deb9u6 install ok installed libgsasl7 libgsasl7 1.8.0-8+b2 install ok installed libgssapi-krb5-2:amd64 libgssapi-krb5-2 1.15-1+deb9u1 install ok installed libgts-0.7-5:amd64 libgts-0.7-5 0.7.6+darcs121130-4 install ok installed libgts-bin libgts-bin 0.7.6+darcs121130-4 install ok installed libgvc6 libgvc6 2.38.0-17 install ok installed libgvpr2 libgvpr2 2.38.0-17 install ok installed libharfbuzz0b:amd64 libharfbuzz0b 1.4.2-1 install ok installed libhmsbeagle1v5 libhmsbeagle1v5 2.1.2+20160831-5 install ok installed libhogweed4:amd64 libhogweed4 3.3-1+b2 install ok installed libhpdf-2.2.1 libhpdf-2.2.1 2.2.1-1.1+b1 install ok installed libhtml-form-perl libhtml-form-perl 6.03-1 install ok installed libhtml-format-perl libhtml-format-perl 2.12-1 install ok installed libhtml-parser-perl libhtml-parser-perl 3.72-3 install ok installed libhtml-tableextract-perl libhtml-tableextract-perl 2.13-1 install ok installed libhtml-tagset-perl libhtml-tagset-perl 3.20-3 install ok installed libhtml-tree-perl libhtml-tree-perl 5.03-2 install ok installed libhts1:amd64 libhts1 1.3.2-2 install ok installed libhttp-cookies-perl libhttp-cookies-perl 6.01-1 install ok installed libhttp-daemon-perl libhttp-daemon-perl 6.01-1 install ok installed libhttp-date-perl libhttp-date-perl 6.02-1 install ok installed libhttp-message-perl libhttp-message-perl 6.11-1 install ok installed libhttp-negotiate-perl libhttp-negotiate-perl 6.00-2 install ok installed libhwloc-plugins libhwloc-plugins 1.11.5-1 install ok installed libhwloc5:amd64 libhwloc5 1.11.5-1 install ok installed libibverbs1 libibverbs1 1.2.1-2 install ok installed libice6:amd64 libice6 2:1.0.9-2 install ok installed libicu-dev libicu-dev 57.1-6+deb9u4 install ok installed libicu57:amd64 libicu57 57.1-6+deb9u4 install ok installed libidn11:amd64 libidn11 1.33-1+deb9u1 install ok installed libidn2-0:amd64 libidn2-0 0.16-1+deb9u1 install ok installed libijs-0.35:amd64 libijs-0.35 0.35-12 install ok installed libimport-into-perl libimport-into-perl 1.002005-1 install ok installed libio-all-perl libio-all-perl 0.86-2 install ok installed libio-html-perl libio-html-perl 1.001-1 install ok installed libio-pty-perl libio-pty-perl 1:1.08-1.1+b2 install ok installed libio-sessiondata-perl libio-sessiondata-perl 1.03-1 install ok installed libio-socket-ssl-perl libio-socket-ssl-perl 2.044-1 install ok installed libio-string-perl libio-string-perl 1.08-3 install ok installed libio-stringy-perl libio-stringy-perl 2.111-2 install ok installed libipc-run-perl libipc-run-perl 0.94-1+deb9u1 install ok installed libipc-shareable-perl libipc-shareable-perl 0.61-1 install ok installed libipc-sharelite-perl libipc-sharelite-perl 0.17-4 install ok installed libipc-system-simple-perl libipc-system-simple-perl 1.25-3 install ok installed libisl15:amd64 libisl15 0.18-1 install ok installed libitm1:amd64 libitm1 6.3.0-18+deb9u1 install ok installed libjbig0:amd64 libjbig0 2.1-3.1+b2 install ok installed libjbig2dec0:amd64 libjbig2dec0 0.13-4.1 install ok installed libjcode-pm-perl libjcode-pm-perl 2.06-1 install ok installed libjpeg-dev libjpeg-dev 1:1.5.1-2 install ok installed libjpeg62-turbo:amd64 libjpeg62-turbo 1:1.5.1-2 install ok installed libjpeg62-turbo-dev:amd64 libjpeg62-turbo-dev 1:1.5.1-2 install ok installed libjs-jquery libjs-jquery 3.1.1-2+deb9u1 install ok installed libk5crypto3:amd64 libk5crypto3 1.15-1+deb9u1 install ok installed libkeyutils1:amd64 libkeyutils1 1.5.9-9 install ok installed libkrb5-3:amd64 libkrb5-3 1.15-1+deb9u1 install ok installed libkrb5support0:amd64 libkrb5support0 1.15-1+deb9u1 install ok installed libksba8:amd64 libksba8 1.3.5-2 install ok installed libkyotocabinet16v5:amd64 libkyotocabinet16v5 1.2.76-4.2+b1 install ok installed liblapack-dev liblapack-dev 3.7.0-2 install ok installed liblapack3 liblapack3 3.7.0-2 install ok installed liblcms2-2:amd64 liblcms2-2 2.8-4+deb9u1 install ok installed libldap-2.4-2:amd64 libldap-2.4-2 2.4.44+dfsg-5+deb9u4 install ok installed libldap-common libldap-common 2.4.44+dfsg-5+deb9u4 install ok installed liblist-moreutils-perl liblist-moreutils-perl 0.416-1+b1 install ok installed libllvm3.9:amd64 libllvm3.9 1:3.9.1-9 install ok installed liblocale-gettext-perl liblocale-gettext-perl 1.07-3+b1 install ok installed liblog-dispatch-perl liblog-dispatch-perl 2.58-1 install ok installed liblog-log4perl-perl liblog-log4perl-perl 1.48-1+deb9u1 install ok installed liblsan0:amd64 liblsan0 6.3.0-18+deb9u1 install ok installed libltdl7:amd64 libltdl7 2.4.6-2 install ok installed liblua5.2-0:amd64 liblua5.2-0 5.2.4-1.1+b2 install ok installed liblwp-mediatypes-perl liblwp-mediatypes-perl 6.02-1 install ok installed liblwp-protocol-https-perl liblwp-protocol-https-perl 6.06-2 install ok installed liblz4-1:amd64 liblz4-1 0.0~r131-2+b1 install ok installed liblzma-dev:amd64 liblzma-dev 5.2.2-1.2+b1 install ok installed liblzma5:amd64 liblzma5 5.2.2-1.2+b1 install ok installed liblzo2-2:amd64 liblzo2-2 2.08-1.2+b2 install ok installed libmagic-mgc libmagic-mgc 1:5.30-1+deb9u3 install ok installed libmagic1:amd64 libmagic1 1:5.30-1+deb9u3 install ok installed libmail-sendmail-perl libmail-sendmail-perl 0.79.16-2 install ok installed libmailtools-perl libmailtools-perl 2.18-1 install ok installed libmailutils5:amd64 libmailutils5 1:3.1.1-1 install ok installed libmariadbclient18:amd64 libmariadbclient18 10.1.45-0+deb9u1 install ok installed libmath-derivative-perl libmath-derivative-perl 0.04-2 install ok installed libmath-spline-perl libmath-spline-perl 0.02-1 install ok installed libmime-lite-perl libmime-lite-perl 3.030-2 install ok installed libmime-tools-perl libmime-tools-perl 5.508-1 install ok installed libmime-types-perl libmime-types-perl 2.13-1 install ok installed libmldbm-perl libmldbm-perl 2.05-2 install ok installed libmodule-implementation-perl libmodule-implementation-perl 0.09-1 install ok installed libmodule-runtime-conflicts-perl libmodule-runtime-conflicts-perl 0.003-1 install ok installed libmodule-runtime-perl libmodule-runtime-perl 0.014-2 install ok installed libmoo-perl libmoo-perl 2.002005-1 install ok installed libmoose-perl libmoose-perl 2.1807-1 install ok installed libmount1:amd64 libmount1 2.29.2-1+deb9u1 install ok installed libmpc3:amd64 libmpc3 1.0.3-1+b2 install ok installed libmpfr4:amd64 libmpfr4 3.1.5-1 install ok installed libmpx2:amd64 libmpx2 6.3.0-18+deb9u1 install ok installed libmro-compat-perl libmro-compat-perl 0.12-1 install ok installed libnamespace-clean-perl libnamespace-clean-perl 0.27-1 install ok installed libncurses5:amd64 libncurses5 6.0+20161126-1+deb9u2 install ok installed libncurses5-dev:amd64 libncurses5-dev 6.0+20161126-1+deb9u2 install ok installed libncursesw5:amd64 libncursesw5 6.0+20161126-1+deb9u2 install ok installed libnet-dbus-perl libnet-dbus-perl 1.1.0-4+b1 install ok installed libnet-http-perl libnet-http-perl 6.12-1 install ok installed libnet-smtp-ssl-perl libnet-smtp-ssl-perl 1.04-1 install ok installed libnet-ssleay-perl libnet-ssleay-perl 1.80-1 install ok installed libnettle6:amd64 libnettle6 3.3-1+b2 install ok installed libnghttp2-14:amd64 libnghttp2-14 1.18.1-1+deb9u1 install ok installed libnl-3-200:amd64 libnl-3-200 3.2.27-2 install ok installed libnl-route-3-200:amd64 libnl-route-3-200 3.2.27-2 install ok installed libnpth0:amd64 libnpth0 1.3-1 install ok installed libntlm0:amd64 libntlm0 1.4-8 install ok installed libnuma1:amd64 libnuma1 2.0.11-2.1 install ok installed libnumber-compare-perl libnumber-compare-perl 0.03-1 install ok installed libole-storage-lite-perl libole-storage-lite-perl 0.19-1+deb9u1 install ok installed libopenjp2-7:amd64 libopenjp2-7 2.1.2-1.1+deb9u4 install ok installed libopenmpi2:amd64 libopenmpi2 2.0.2-2 install ok installed libossp-uuid-perl libossp-uuid-perl 1.6.2-1.5+b4 install ok installed libossp-uuid16:amd64 libossp-uuid16 1.6.2-1.5+b4 install ok installed libp11-kit0:amd64 libp11-kit0 0.23.3-2 install ok installed libpackage-deprecationmanager-perl libpackage-deprecationmanager-perl 0.17-1 install ok installed libpackage-stash-perl libpackage-stash-perl 0.37-1 install ok installed libpackage-stash-xs-perl libpackage-stash-xs-perl 0.28-3+b1 install ok installed libpadwalker-perl libpadwalker-perl 2.2-2+b1 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 libpango-1.0-0:amd64 libpango-1.0-0 1.40.5-1 install ok installed libpangocairo-1.0-0:amd64 libpangocairo-1.0-0 1.40.5-1 install ok installed libpangoft2-1.0-0:amd64 libpangoft2-1.0-0 1.40.5-1 install ok installed libpaper-utils libpaper-utils 1.1.24+nmu5 install ok installed libpaper1:amd64 libpaper1 1.1.24+nmu5 install ok installed libparams-classify-perl libparams-classify-perl 0.013-6+b1 install ok installed libparams-util-perl libparams-util-perl 1.07-3+b1 install ok installed libparams-validate-perl libparams-validate-perl 1.26-1 install ok installed libparse-recdescent-perl libparse-recdescent-perl 1.967013+dfsg-1 install ok installed libparse-yapp-perl libparse-yapp-perl 1.05-12 install ok installed libpathplan4 libpathplan4 2.38.0-17 install ok installed libpciaccess0:amd64 libpciaccess0 0.13.4-1+b2 install ok installed libpcre16-3:amd64 libpcre16-3 2:8.39-3 install ok installed libpcre3:amd64 libpcre3 2:8.39-3 install ok installed libpcre3-dev:amd64 libpcre3-dev 2:8.39-3 install ok installed libpcre32-3:amd64 libpcre32-3 2:8.39-3 install ok installed libpcrecpp0v5:amd64 libpcrecpp0v5 2:8.39-3 install ok installed libperl5.24:amd64 libperl5.24 5.24.1-3+deb9u7 install ok installed libperlio-utf8-strict-perl libperlio-utf8-strict-perl 0.006-1+b2 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.34.0-1 install ok installed libpng-dev:amd64 libpng-dev 1.6.28-1+deb9u1 install ok installed libpng-tools libpng-tools 1.6.28-1+deb9u1 install ok installed libpng16-16:amd64 libpng16-16 1.6.28-1+deb9u1 install ok installed libpostscript-perl libpostscript-perl 0.06-2 install ok installed libpq5:amd64 libpq5 9.6.17-0+deb9u1 install ok installed libprocps6:amd64 libprocps6 2:3.3.12-3+deb9u1 install ok installed libpsl5:amd64 libpsl5 0.17.0-3 install ok installed libpsm-infinipath1 libpsm-infinipath1 3.3+19.g67c0807.open-3 install ok installed libpython-stdlib:amd64 libpython-stdlib 2.7.13-2 install ok installed libpython2.7:amd64 libpython2.7 2.7.13-2+deb9u3 install ok installed libpython2.7-minimal:amd64 libpython2.7-minimal 2.7.13-2+deb9u3 install ok installed libpython2.7-stdlib:amd64 libpython2.7-stdlib 2.7.13-2+deb9u3 install ok installed libquadmath0:amd64 libquadmath0 6.3.0-18+deb9u1 install ok installed librdmacm1 librdmacm1 1.1.0-2 install ok installed libreadline-dev:amd64 libreadline-dev 7.0-3 install ok installed libreadline7:amd64 libreadline7 7.0-3 install ok installed librole-tiny-perl librole-tiny-perl 2.000005-1 install ok installed librtmp1:amd64 librtmp1 2.4+20151223.gitfa8646d.1-1+b1 install ok installed libruby2.3:amd64 libruby2.3 2.3.3-1+deb9u8 install ok installed libsasl2-2:amd64 libsasl2-2 2.1.27~101-g0780600+dfsg-3+deb9u1 install ok installed libsasl2-modules:amd64 libsasl2-modules 2.1.27~101-g0780600+dfsg-3+deb9u1 install ok installed libsasl2-modules-db:amd64 libsasl2-modules-db 2.1.27~101-g0780600+dfsg-3+deb9u1 install ok installed libscalar-list-utils-perl libscalar-list-utils-perl 1:1.47-1 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 libsensors4:amd64 libsensors4 1:3.4.0-4 install ok installed libsepol1:amd64 libsepol1 2.6-2 install ok installed libset-scalar-perl libset-scalar-perl 1.29-2 install ok installed libsigsegv2:amd64 libsigsegv2 2.10-5 install ok installed libsm6:amd64 libsm6 2:1.2.2-1+b3 install ok installed libsmartcols1:amd64 libsmartcols1 2.29.2-1+deb9u1 install ok installed libsoap-lite-perl libsoap-lite-perl 1.20-1 install ok installed libsort-naturally-perl libsort-naturally-perl 1.03-1 install ok installed libspiffy-perl libspiffy-perl 0.41-1 install ok installed libspreadsheet-parseexcel-perl libspreadsheet-parseexcel-perl 0.6500-1 install ok installed libspreadsheet-writeexcel-perl libspreadsheet-writeexcel-perl 2.40-1 install ok installed libsqlite3-0:amd64 libsqlite3-0 3.16.2-5+deb9u1 install ok installed libss2:amd64 libss2 1.43.4-2+deb9u1 install ok installed libssh2-1:amd64 libssh2-1 1.7.0-1+deb9u1 install ok installed libssl1.0.2:amd64 libssl1.0.2 1.0.2u-1~deb9u1 install ok installed libssl1.1:amd64 libssl1.1 1.1.0l-1~deb9u1 install ok installed libstatistics-descriptive-perl libstatistics-descriptive-perl 3.0612-1 install ok installed libstdc++-6-dev:amd64 libstdc++-6-dev 6.3.0-18+deb9u1 install ok installed libstdc++6:amd64 libstdc++6 6.3.0-18+deb9u1 install ok installed libstrictures-perl libstrictures-perl 2.000003-1 install ok installed libsub-exporter-perl libsub-exporter-perl 0.986-1 install ok installed libsub-exporter-progressive-perl libsub-exporter-progressive-perl 0.001013-1 install ok installed libsub-identify-perl libsub-identify-perl 0.12-2+b1 install ok installed libsub-install-perl libsub-install-perl 0.928-1 install ok installed libsub-name-perl libsub-name-perl 0.21-1 install ok installed libsub-uplevel-perl libsub-uplevel-perl 0.2600-1 install ok installed libsvg-graph-perl libsvg-graph-perl 0.02-2 install ok installed libsvg-perl libsvg-perl 2.64-1 install ok installed libsys-hostname-long-perl libsys-hostname-long-perl 1.5-1 install ok installed libsystemd0:amd64 libsystemd0 232-25+deb9u12 install ok installed libtask-weaken-perl libtask-weaken-perl 1.04-1 install ok installed libtasn1-6:amd64 libtasn1-6 4.10-1.1+deb9u1 install ok installed libtcl8.6:amd64 libtcl8.6 8.6.6+dfsg-1+b1 install ok installed libtest-deep-perl libtest-deep-perl 1.126-1 install ok installed libtest-differences-perl libtest-differences-perl 0.64-1 install ok installed libtest-exception-perl libtest-exception-perl 0.43-1 install ok installed libtest-file-perl libtest-file-perl 1.442-1 install ok installed libtest-files-perl libtest-files-perl 0.14-1 install ok installed libtest-most-perl libtest-most-perl 0.35-1 install ok installed libtest-output-perl libtest-output-perl 1.03-1 install ok installed libtest-simple-perl libtest-simple-perl 1.302075-1 install ok installed libtest-warn-perl libtest-warn-perl 0.32-1 install ok installed libtext-csv-perl libtext-csv-perl 1.33-2 install ok installed libtext-csv-xs-perl libtext-csv-xs-perl 1.26-1 install ok installed libtext-diff-perl libtext-diff-perl 1.44-1 install ok installed libtext-glob-perl libtext-glob-perl 0.10-1 install ok installed libtext-iconv-perl libtext-iconv-perl 1.7-5+b4 install ok installed libthai-data libthai-data 0.1.26-1 install ok installed libthai0:amd64 libthai0 0.1.26-1 install ok installed libtie-ixhash-perl libtie-ixhash-perl 1.23-2 install ok installed libtiff5:amd64 libtiff5 4.0.8-2+deb9u5 install ok installed libtimedate-perl libtimedate-perl 2.3000-2+deb9u1 install ok installed libtinfo-dev:amd64 libtinfo-dev 6.0+20161126-1+deb9u2 install ok installed libtinfo5:amd64 libtinfo5 6.0+20161126-1+deb9u2 install ok installed libtk8.6:amd64 libtk8.6 8.6.6-1+b1 install ok installed libtree-dagnode-perl libtree-dagnode-perl 1.29-1 install ok installed libtry-tiny-perl libtry-tiny-perl 0.28-1 install ok installed libtsan0:amd64 libtsan0 6.3.0-18+deb9u1 install ok installed libtxc-dxtn-s2tc:amd64 libtxc-dxtn-s2tc 1.0+git20151227-2 install ok installed libtype-tiny-perl libtype-tiny-perl 1.000005-1 install ok installed libtype-tiny-xs-perl libtype-tiny-xs-perl 0.012-1+b2 install ok installed libubsan0:amd64 libubsan0 6.3.0-18+deb9u1 install ok installed libudev1:amd64 libudev1 232-25+deb9u12 install ok installed libunicode-map-perl libunicode-map-perl 0.112-11+b3 install ok installed libunistring0:amd64 libunistring0 0.9.6+really0.9.3-0.1 install ok installed liburi-perl liburi-perl 1.71-1 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 libvariable-magic-perl libvariable-magic-perl 0.61-1 install ok installed libwebp6:amd64 libwebp6 0.5.2-1 install ok installed libwrap0:amd64 libwrap0 7.6.q-26 install ok installed libwww-perl libwww-perl 6.15-1 install ok installed libwww-robotrules-perl libwww-robotrules-perl 6.01-1 install ok installed libx11-6:amd64 libx11-6 2:1.6.4-3+deb9u1 install ok installed libx11-data libx11-data 2:1.6.4-3+deb9u1 install ok installed libx11-protocol-perl libx11-protocol-perl 0.56-7 install ok installed libx11-xcb1:amd64 libx11-xcb1 2:1.6.4-3+deb9u1 install ok installed libxau6:amd64 libxau6 1:1.0.8-1 install ok installed libxaw7:amd64 libxaw7 2:1.0.13-1+b2 install ok installed libxcb-dri2-0:amd64 libxcb-dri2-0 1.12-1 install ok installed libxcb-dri3-0:amd64 libxcb-dri3-0 1.12-1 install ok installed libxcb-glx0:amd64 libxcb-glx0 1.12-1 install ok installed libxcb-present0:amd64 libxcb-present0 1.12-1 install ok installed libxcb-render0:amd64 libxcb-render0 1.12-1 install ok installed libxcb-shape0:amd64 libxcb-shape0 1.12-1 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.12-1 install ok installed libxcb-sync1:amd64 libxcb-sync1 1.12-1 install ok installed libxcb1:amd64 libxcb1 1.12-1 install ok installed libxcomposite1:amd64 libxcomposite1 1:0.4.4-2 install ok installed libxcursor1:amd64 libxcursor1 1:1.1.14-1+deb9u2 install ok installed libxdamage1:amd64 libxdamage1 1:1.1.4-2+b3 install ok installed libxdmcp6:amd64 libxdmcp6 1:1.1.2-3 install ok installed libxdot4 libxdot4 2.38.0-17 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 2.3.2-1+b2 install ok installed libxi6:amd64 libxi6 2:1.7.9-1 install ok installed libxinerama1:amd64 libxinerama1 2:1.1.3-1+b3 install ok installed libxml-dom-perl libxml-dom-perl 1.44-2 install ok installed libxml-dom-xpath-perl libxml-dom-xpath-perl 0.14-2 install ok installed libxml-filter-buffertext-perl libxml-filter-buffertext-perl 1.01-5 install ok installed libxml-libxml-perl libxml-libxml-perl 2.0128+dfsg-1+deb9u1 install ok installed libxml-libxslt-perl libxml-libxslt-perl 1.95-1+b1 install ok installed libxml-namespacesupport-perl libxml-namespacesupport-perl 1.11-1 install ok installed libxml-parser-perl libxml-parser-perl 2.44-2+b1 install ok installed libxml-perl libxml-perl 0.08-2 install ok installed libxml-regexp-perl libxml-regexp-perl 0.04-1 install ok installed libxml-sax-base-perl libxml-sax-base-perl 1.07-1 install ok installed libxml-sax-expat-perl libxml-sax-expat-perl 0.40-2 install ok installed libxml-sax-perl libxml-sax-perl 0.99+dfsg-2 install ok installed libxml-sax-writer-perl libxml-sax-writer-perl 0.56-1 install ok installed libxml-simple-perl libxml-simple-perl 2.22-1 install ok installed libxml-twig-perl libxml-twig-perl 1:3.50-1 install ok installed libxml-writer-perl libxml-writer-perl 0.625-1 install ok installed libxml-xpath-perl libxml-xpath-perl 1.40-1 install ok installed libxml-xpathengine-perl libxml-xpathengine-perl 0.13-1 install ok installed libxml2:amd64 libxml2 2.9.4+dfsg1-2.2+deb9u2 install ok installed libxmlrpc-lite-perl libxmlrpc-lite-perl 0.717-1 install ok installed libxmu6:amd64 libxmu6 2:1.1.2-2 install ok installed libxmuu1:amd64 libxmuu1 2:1.1.2-2 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 1.2-1+b2 install ok installed libxslt1.1:amd64 libxslt1.1 1.1.29-2.1+deb9u2 install ok installed libxss1:amd64 libxss1 1:1.2.2-1 install ok installed libxt6:amd64 libxt6 1:1.1.5-1 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 libyaml-0-2:amd64 libyaml-0-2 0.1.7-2 install ok installed libyaml-libyaml-perl libyaml-libyaml-perl 0.63-2 install ok installed libyaml-perl libyaml-perl 1.21-1 install ok installed linux-libc-dev:amd64 linux-libc-dev 4.9.228-1 install ok installed littler littler 0.3.1-1 install ok installed login login 1:4.4-4.1 install ok installed lsb-base lsb-base 9.20161125 install ok installed lynx lynx 2.8.9dev11-1 install ok installed lynx-common lynx-common 2.8.9dev11-1 install ok installed mafft mafft 7.307-1 install ok installed mailutils mailutils 1:3.1.1-1 install ok installed mailutils-common mailutils-common 1:3.1.1-1 install ok installed make make 4.1-9.1 install ok installed manpages manpages 4.10-2 install ok installed manpages-dev manpages-dev 4.10-2 install ok installed maq maq 0.7.1-7 install ok installed mawk mawk 1.3.3-17+b3 install ok installed mcl mcl 1:14-137-1+b1 install ok installed med-config med-config 3.0.1 install ok installed menu menu 2.1.47+b1 install ok installed mime-support mime-support 3.60 install ok installed mount mount 2.29.2-1+deb9u1 install ok installed multiarch-support multiarch-support 2.24-11+deb9u4 install ok installed mummer mummer 3.23+dfsg-2 install ok installed muscle muscle 1:3.8.31+dfsg-2 install ok installed mustang mustang 3.2.3-1 install ok installed mysql-common mysql-common 5.8+1.0.2 install ok installed ncbi-blast+ ncbi-blast+ 2.6.0-1 install ok installed ncbi-blast+-legacy ncbi-blast+-legacy 2.6.0-1 install ok installed ncbi-data ncbi-data 6.1.20170106+dfsg1-0+deb9u1 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 netbase netbase 5.4 install ok installed ocl-icd-libopencl1:amd64 ocl-icd-libopencl1 2.2.11-1 install ok installed openmpi-bin openmpi-bin 2.0.2-2 install ok installed openmpi-common openmpi-common 2.0.2-2 install ok installed openssl openssl 1.1.0l-1~deb9u1 install ok installed parallel parallel 20161222-1 install ok installed passwd passwd 1:4.4-4.1 install ok installed patch patch 2.7.5-1+deb9u2 install ok installed perl perl 5.24.1-3+deb9u7 install ok installed perl-base perl-base 5.24.1-3+deb9u7 install ok installed perl-doc perl-doc 5.24.1-3+deb9u7 install ok installed perl-modules-5.24 perl-modules-5.24 5.24.1-3+deb9u7 install ok installed perl-openssl-defaults:amd64 perl-openssl-defaults 3 install ok installed perl-tk perl-tk 1:804.033-1+b3 install ok installed phylip phylip 1:3.696+dfsg-5 install ok installed phyml phyml 3:3.2.0+dfsg-7+b1 install ok installed pinentry-curses pinentry-curses 1.0.0-2 install ok installed pkg-config pkg-config 0.29-4+b1 install ok installed poa poa 2.0+20060928-4+b1 install ok installed poppler-data poppler-data 0.4.7-8 install ok installed prank prank 0.0.150803-2 install ok installed primer3 primer3 2.3.7-3 install ok installed probalign probalign 1.4-5 install ok installed probcons probcons 1.12-11 install ok installed procps procps 2:3.3.12-3+deb9u1 install ok installed proda proda 1.0-10 install ok installed psmisc psmisc 22.21-2.1+b2 install ok installed publicsuffix publicsuffix 20190415.1030-0+deb9u1 install ok installed python python 2.7.13-2 install ok installed python-minimal python-minimal 2.7.13-2 install ok installed python2.7 python2.7 2.7.13-2+deb9u3 install ok installed python2.7-minimal python2.7-minimal 2.7.13-2+deb9u3 install ok installed r-base-core r-base-core 3.3.3-1 install ok installed r-base-dev r-base-dev 3.3.3-1 install ok installed r-cran-assertthat r-cran-assertthat 0.1-1 install ok installed r-cran-boot r-cran-boot 1.3-18-2 install ok installed r-cran-class r-cran-class 7.3-14-1 install ok installed r-cran-cluster r-cran-cluster 2.0.5-1 install ok installed r-cran-codetools r-cran-codetools 0.2-15-1 install ok installed r-cran-colorspace r-cran-colorspace 1.3-2-1 install ok installed r-cran-crayon r-cran-crayon 1.3.2-1 install ok installed r-cran-dichromat r-cran-dichromat 2.0.0-3 install ok installed r-cran-digest r-cran-digest 0.6.11-1 install ok installed r-cran-foreign r-cran-foreign 0.8.67-1 install ok installed r-cran-ggplot2 r-cran-ggplot2 2.2.1-2 install ok installed r-cran-gtable r-cran-gtable 0.2.0-1 install ok installed r-cran-kernsmooth r-cran-kernsmooth 2.23-15-2 install ok installed r-cran-labeling r-cran-labeling 0.3-1 install ok installed r-cran-lattice r-cran-lattice 0.20-34-1 install ok installed r-cran-lazyeval r-cran-lazyeval 0.2.0-1 install ok installed r-cran-littler r-cran-littler 0.3.1-1 install ok installed r-cran-magrittr r-cran-magrittr 1.5-3 install ok installed r-cran-mass r-cran-mass 7.3-45-1 install ok installed r-cran-matrix r-cran-matrix 1.2-7.1-1 install ok installed r-cran-mgcv r-cran-mgcv 1.8-16-1 install ok installed r-cran-munsell r-cran-munsell 0.4.3-1 install ok installed r-cran-nlme r-cran-nlme 3.1.129-1 install ok installed r-cran-nnet r-cran-nnet 7.3-12-1 install ok installed r-cran-pkgkitten r-cran-pkgkitten 0.1.4-1 install ok installed r-cran-plyr r-cran-plyr 1.8.4-1 install ok installed r-cran-rcolorbrewer r-cran-rcolorbrewer 1.1-2-1 install ok installed r-cran-rcpp r-cran-rcpp 0.12.9-1 install ok installed r-cran-reshape2 r-cran-reshape2 1.4.2-1 install ok installed r-cran-rpart r-cran-rpart 4.1-10-2 install ok installed r-cran-scales r-cran-scales 0.4.1-1 install ok installed r-cran-spatial r-cran-spatial 7.3-11-1 install ok installed r-cran-stringi r-cran-stringi 1.1.2-1 install ok installed r-cran-stringr r-cran-stringr 1.1.0-1 install ok installed r-cran-survival r-cran-survival 2.40-1-1 install ok installed r-cran-tibble r-cran-tibble 1.2-1 install ok installed r-doc-html r-doc-html 3.3.3-1 install ok installed r-recommended r-recommended 3.3.3-1 install ok installed rake rake 10.5.0-2+deb9u1 install ok installed raxml raxml 8.2.9+dfsg-1+b1 install ok installed readline-common readline-common 7.0-3 install ok installed rename rename 0.20-4 install ok installed roary roary 3.8.0+dfsg-1 install ok installed ruby ruby 1:2.3.3 install ok installed ruby-did-you-mean ruby-did-you-mean 1.0.0-2 install ok installed ruby-minitest ruby-minitest 5.9.0-1 install ok installed ruby-net-telnet ruby-net-telnet 0.1.1-2 install ok installed ruby-power-assert ruby-power-assert 0.3.0-1 install ok installed ruby-test-unit ruby-test-unit 3.1.7-2 install ok installed ruby2.3 ruby2.3 2.3.3-1+deb9u8 install ok installed rubygems-integration rubygems-integration 1.11 install ok installed samtools samtools 1.3.1-3 install ok installed sed sed 4.4-1 install ok installed sensible-utils sensible-utils 0.0.9+deb9u1 install ok installed sgml-base sgml-base 1.29 install ok installed shared-mime-info shared-mime-info 1.8-1+deb9u1 install ok installed sim4 sim4 0.0.20121010-4 install ok installed sysstat sysstat 11.4.3-2 install ok installed sysvinit-utils sysvinit-utils 2.88dsf-59.9 install ok installed t-coffee t-coffee 11.00.8cbe486-5 install ok installed tar tar 1.29b-1.1 install ok installed tcpd tcpd 7.6.q-26 install ok installed tigr-glimmer tigr-glimmer 3.02b-1 install ok installed tm-align tm-align 20160521+dfsg-2 install ok installed tzdata tzdata 2020a-0+deb9u1 install ok installed ucf ucf 3.0036 install ok installed unzip unzip 6.0-21+deb9u2 install ok installed util-linux util-linux 2.29.2-1+deb9u1 install ok installed wise wise 2.4.1-19 install ok installed wise-data wise-data 2.4.1-19 install ok installed x11-common x11-common 1:7.7+19 install ok installed x11-utils x11-utils 7.7+3+b1 install ok installed x11-xserver-utils x11-xserver-utils 7.7+7+b1 install ok installed xauth xauth 1:1.0.9-1+b2 install ok installed xdg-user-dirs xdg-user-dirs 0.15-2+b1 install ok installed xdg-utils xdg-utils 1.1.1-1+deb9u2 install ok installed xml-core xml-core 0.17 install ok installed xz-utils xz-utils 5.2.2-1.2+b1 install ok installed zip zip 3.0-11+b1 install ok installed zlib1g:amd64 zlib1g 1:1.2.8.dfsg-5 install ok installed zlib1g-dev:amd64 zlib1g-dev 1:1.2.8.dfsg-5 1m38.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m38.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'apt-get', 'remove', 'amap-align', 'apache2-bin', 'autotools-dev', 'bedtools', 'beignet-opencl-icd:amd64', 'binutils', 'bioperl', 'bioperl-run', 'blast2', 'blends-common', 'bowtie', 'build-essential', 'bwa', 'bzip2', 'bzip2-doc', 'ca-certificates', 'cd-hit', 'cdbs', 'clustalo', 'clustalw', 'cpp', 'cpp-6', 'cron', 'dbus', 'dialign', 'dialign-tx', 'dialign-tx-data', 'dirmngr', 'dpkg-dev', 'emboss', 'emboss-data', 'emboss-lib', 'exim4', 'exim4-base', 'exim4-config', 'exim4-daemon-light', 'exonerate', 'fakeroot', 'fasttree', 'file', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-droid-fallback', 'fonts-lato', 'fonts-liberation', 'fonts-noto-mono', 'fsa', 'g++-', 'g++-6', 'gawk', 'gcc', 'gcc-6', 'gfortran', 'gfortran-6', 'ghostscript', 'gnupg', 'gnupg-agent', 'gnupg-l10n', 'graphviz', 'gsfonts', 'guile-2.0-libs:amd64', 'hmmer', 'hyphy-common', 'hyphy-mpi', 'icu-devtools', 'infernal', 'javascript-common', 'kalign', 'krb5-locales', 'libace-perl', 'libalgorithm-c3-perl', 'libalgorithm-diff-perl', 'libalgorithm-diff-xs-perl', 'libalgorithm-merge-perl', 'libalgorithm-munkres-perl', 'libann0', 'libapache-dbi-perl', 'libapache2-mod-perl2', 'libapache2-reload-perl', 'libapparmor1:amd64', 'libapr1:amd64', 'libaprutil1:amd64', 'libaprutil1-dbd-sqlite3:amd64', 'libaprutil1-ldap:amd64', 'libargtable2-0', 'libarray-compare-perl', 'libarray-utils-perl', 'libasan3:amd64', 'libassuan0:amd64', 'libatomic1:amd64', 'libauthen-sasl-perl', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libb-hooks-endofscope-perl', 'libbio-asn1-entrezgene-perl', 'libbio-perl-perl', 'libbio-perl-run-perl', 'libbit-vector-perl', 'libblas-common', 'libblas-dev', 'libblas3', 'libbsd-resource-perl', 'libbsd0:amd64', 'libbz2-dev:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcache-cache-perl', 'libcairo2:amd64', 'libcapture-tiny-perl', 'libcarp-clan-perl', 'libcc1-0:amd64', 'libcdt5', 'libcgi-fast-perl', 'libcgi-pm-perl', 'libcgraph6', 'libcilkrts5:amd64', 'libclass-c3-perl', 'libclass-c3-xs-perl', 'libclass-data-inheritable-perl', 'libclass-inspector-perl', 'libclass-load-perl', 'libclass-load-xs-perl', 'libclass-method-modifiers-perl', 'libclass-tiny-perl', 'libclass-xsaccessor-perl', 'libclone-perl', 'libconvert-binary-c-perl', 'libconvert-binhex-perl', 'libcrypt-rc4-perl', 'libcups2:amd64', 'libcupsfilters1:amd64', 'libcupsimage2:amd64', 'libcurl3:amd64', 'libcurl3-gnutls:amd64', 'libdata-optlist-perl', 'libdata-stag-perl', 'libdate-calc-perl', 'libdate-calc-xs-perl', 'libdate-manip-perl', 'libdatrie1:amd64', 'libdbd-mysql-perl', 'libdbd-pg-perl', 'libdbd-sqlite3-perl', 'libdbi-perl', 'libdbus-1-3:amd64', 'libdevel-caller-perl', 'libdevel-globaldestruction-perl', 'libdevel-lexalias-perl', 'libdevel-overloadinfo-perl', 'libdevel-partialdump-perl', 'libdevel-stacktrace-perl', 'libdevel-symdump-perl', 'libdigest-perl-md5-perl', 'libdist-checkconflicts-perl', 'libdivsufsort3:amd64', 'libdpkg-perl', 'libdrm-amdgpu1:amd64', 'libdrm-intel1:amd64', 'libdrm-nouveau2:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1:amd64', 'libemail-date-format-perl', 'libencode-locale-perl', 'libenv-path-perl', 'liberror-perl', 'libeval-closure-perl', 'libexception-class-perl', 'libexpat1:amd64', 'libexporter-tiny-perl', 'libfabric1', 'libfakeroot:amd64', 'libfcgi-perl', 'libffi6:amd64', 'libfile-basedir-perl', 'libfile-desktopentry-perl', 'libfile-fcntllock-perl', 'libfile-find-rule-perl', 'libfile-grep-perl', 'libfile-listing-perl', 'libfile-mimeinfo-perl', 'libfile-slurp-tiny-perl', 'libfile-slurper-perl', 'libfile-which-perl', 'libfindbin-libs-perl', 'libfont-afm-perl', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfreezethaw-perl', 'libfribidi0:amd64', 'libgc1c2:amd64', 'libgcc-6-dev:amd64', 'libgd-perl', 'libgd3:amd64', 'libgdbm3:amd64', 'libgfortran-6-dev:amd64', 'libgfortran3:amd64', 'libgl1-mesa-dri:amd64', 'libgl1-mesa-glx:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0:amd64', 'libglib2.0-data', 'libgmp10:amd64', 'libgnutls30:amd64', 'libgomp1:amd64', 'libgpm2:amd64', 'libgraph-perl', 'libgraph-readwrite-perl', 'libgraphite2-3:amd64', 'libgraphviz-perl', 'libgs9:amd64', 'libgs9-common', 'libgsasl7', 'libgssapi-krb5-2:amd64', 'libgts-0.7-5:amd64', 'libgts-bin', 'libgvc6', 'libgvpr2', 'libharfbuzz0b:amd64', 'libhmsbeagle1v5', 'libhogweed4:amd64', 'libhpdf-2.2.1', 'libhtml-form-perl', 'libhtml-format-perl', 'libhtml-parser-perl', 'libhtml-tableextract-perl', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhts1:amd64', 'libhttp-cookies-perl', 'libhttp-daemon-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libhwloc-plugins', 'libhwloc5:amd64', 'libibverbs1', 'libice6:amd64', 'libicu-dev', 'libicu57:amd64', 'libidn11:amd64', 'libidn2-0:amd64', 'libijs-0.35:amd64', 'libimport-into-perl', 'libio-all-perl', 'libio-html-perl', 'libio-pty-perl', 'libio-sessiondata-perl', 'libio-socket-ssl-perl', 'libio-string-perl', 'libio-stringy-perl', 'libipc-run-perl', 'libipc-shareable-perl', 'libipc-sharelite-perl', 'libipc-system-simple-perl', 'libisl15:amd64', 'libitm1:amd64', 'libjbig0:amd64', 'libjbig2dec0:amd64', 'libjcode-pm-perl', 'libjpeg-dev', 'libjpeg62-turbo:amd64', 'libjpeg62-turbo-dev:amd64', 'libjs-jquery', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libksba8:amd64', 'libkyotocabinet16v5:amd64', 'liblapack-dev', 'liblapack3', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'liblist-moreutils-perl', 'libllvm3.9:amd64', 'liblocale-gettext-perl', 'liblog-dispatch-perl', 'liblog-log4perl-perl', 'liblsan0:amd64', 'libltdl7:amd64', 'liblua5.2-0:amd64', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'liblzma-dev:amd64', 'liblzo2-2:amd64', 'libmagic-mgc', 'libmagic1:amd64', 'libmail-sendmail-perl', 'libmailtools-perl', 'libmailutils5:amd64', 'libmariadbclient18:amd64', 'libmath-derivative-perl', 'libmath-spline-perl', 'libmime-lite-perl', 'libmime-tools-perl', 'libmime-types-perl', 'libmldbm-perl', 'libmodule-implementation-perl', 'libmodule-runtime-conflicts-perl', 'libmodule-runtime-perl', 'libmoo-perl', 'libmoose-perl', 'libmpc3:amd64', 'libmpfr4:amd64', 'libmpx2:amd64', 'libmro-compat-perl', 'libnamespace-clean-perl', 'libncurses5:amd64', 'libncurses5-dev:amd64', 'libnet-dbus-perl', 'libnet-http-perl', 'libnet-smtp-ssl-perl', 'libnet-ssleay-perl', 'libnettle6:amd64', 'libnghttp2-14:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnpth0:amd64', 'libntlm0:amd64', 'libnuma1:amd64', 'libnumber-compare-perl', 'libole-storage-lite-perl', 'libopenjp2-7:amd64', 'libopenmpi2:amd64', 'libossp-uuid-perl', 'libossp-uuid16:amd64', 'libp11-kit0:amd64', 'libpackage-deprecationmanager-perl', 'libpackage-stash-perl', 'libpackage-stash-xs-perl', 'libpadwalker-perl', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libparams-classify-perl', 'libparams-util-perl', 'libparams-validate-perl', 'libparse-recdescent-perl', 'libparse-yapp-perl', 'libpathplan4', 'libpciaccess0:amd64', 'libpcre16-3:amd64', 'libpcre3-dev:amd64', 'libpcre32-3:amd64', 'libpcrecpp0v5:amd64', 'libperl5.24:amd64', 'libperlio-utf8-strict-perl', 'libpixman-1-0:amd64', 'libpng-dev:amd64', 'libpng-tools', 'libpng16-16:amd64', 'libpostscript-perl', 'libpq5:amd64', 'libprocps6:amd64', 'libpsl5:amd64', 'libpsm-infinipath1', 'libpython-stdlib:amd64', 'libpython2.7:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'librdmacm1', 'libreadline-dev:amd64', 'libreadline7:amd64', 'librole-tiny-perl', 'librtmp1:amd64', 'libruby2.3:amd64', 'libsasl2-2:amd64', 'libsasl2-modules:amd64', 'libsasl2-modules-db:amd64', 'libscalar-list-utils-perl', 'libsensors4:amd64', 'libset-scalar-perl', 'libsigsegv2:amd64', 'libsm6:amd64', 'libsoap-lite-perl', 'libsort-naturally-perl', 'libspiffy-perl', 'libspreadsheet-parseexcel-perl', 'libspreadsheet-writeexcel-perl', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.0.2:amd64', 'libssl1.1:amd64', 'libstatistics-descriptive-perl', 'libstdc++-6-dev:amd64', 'libstrictures-perl', 'libsub-exporter-perl', 'libsub-exporter-progressive-perl', 'libsub-identify-perl', 'libsub-install-perl', 'libsub-name-perl', 'libsub-uplevel-perl', 'libsvg-graph-perl', 'libsvg-perl', 'libsys-hostname-long-perl', 'libtask-weaken-perl', 'libtasn1-6:amd64', 'libtcl8.6:amd64', 'libtest-deep-perl', 'libtest-differences-perl', 'libtest-exception-perl', 'libtest-file-perl', 'libtest-files-perl', 'libtest-most-perl', 'libtest-output-perl', 'libtest-simple-perl', 'libtest-warn-perl', 'libtext-csv-perl', 'libtext-csv-xs-perl', 'libtext-diff-perl', 'libtext-glob-perl', 'libtext-iconv-perl', 'libthai-data', 'libthai0:amd64', 'libtie-ixhash-perl', 'libtiff5:amd64', 'libtimedate-perl', 'libtinfo-dev:amd64', 'libtk8.6:amd64', 'libtree-dagnode-perl', 'libtry-tiny-perl', 'libtsan0:amd64', 'libtxc-dxtn-s2tc:amd64', 'libtype-tiny-perl', 'libtype-tiny-xs-perl', 'libubsan0:amd64', 'libunicode-map-perl', 'libunistring0:amd64', 'liburi-perl', 'libvariable-magic-perl', 'libwebp6:amd64', 'libwrap0:amd64', 'libwww-perl', 'libwww-robotrules-perl', 'libx11-6:amd64', 'libx11-data', 'libx11-protocol-perl', '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', 'libxcb1:amd64', 'libxcomposite1:amd64', 'libxcursor1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxdot4', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxinerama1:amd64', 'libxml-dom-perl', 'libxml-dom-xpath-perl', 'libxml-filter-buffertext-perl', 'libxml-libxml-perl', 'libxml-libxslt-perl', 'libxml-namespacesupport-perl', 'libxml-parser-perl', 'libxml-perl', 'libxml-regexp-perl', 'libxml-sax-base-perl', 'libxml-sax-expat-perl', 'libxml-sax-perl', 'libxml-sax-writer-perl', 'libxml-simple-perl', 'libxml-twig-perl', 'libxml-writer-perl', 'libxml-xpath-perl', 'libxml-xpathengine-perl', 'libxml2:amd64', 'libxmlrpc-lite-perl', 'libxmu6:amd64', 'libxmuu1:amd64', 'libxpm4:amd64', 'libxrandr2:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libxt6:amd64', 'libxtst6:amd64', 'libxv1:amd64', 'libxxf86dga1:amd64', 'libxxf86vm1:amd64', 'libyaml-0-2:amd64', 'libyaml-libyaml-perl', 'libyaml-perl', 'linux-libc-dev:amd64', 'littler', 'lsb-base', 'lynx', 'lynx-common', 'mafft', 'mailutils', 'mailutils-common', 'make', 'manpages', 'manpages-dev', 'maq', 'mcl', 'med-config', 'menu', 'mime-support', 'mummer', 'muscle', 'mustang', 'mysql-common', 'ncbi-blast+-', 'ncbi-blast+-legacy', 'ncbi-data', 'netbase', 'ocl-icd-libopencl1:amd64', 'openmpi-bin', 'openmpi-common', 'openssl', 'parallel', 'patch', 'perl', 'perl-doc', 'perl-modules-5.24', 'perl-openssl-defaults:amd64', 'perl-tk', 'phylip', 'phyml', 'pinentry-curses', 'pkg-config', 'poa', 'poppler-data', 'prank', 'primer3', 'probalign', 'probcons', 'procps', 'proda', 'psmisc', 'publicsuffix', 'python', 'python-minimal', 'python2.7', 'python2.7-minimal', 'r-base-core', 'r-base-dev', 'r-cran-assertthat', 'r-cran-boot', 'r-cran-class', 'r-cran-cluster', 'r-cran-codetools', 'r-cran-colorspace', 'r-cran-crayon', 'r-cran-dichromat', 'r-cran-digest', 'r-cran-foreign', 'r-cran-ggplot2', 'r-cran-gtable', 'r-cran-kernsmooth', '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-nnet', 'r-cran-pkgkitten', 'r-cran-plyr', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-reshape2', 'r-cran-rpart', 'r-cran-scales', 'r-cran-spatial', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-survival', 'r-cran-tibble', 'r-doc-html', 'r-recommended', 'rake', 'raxml', 'readline-common', 'rename', 'ruby', 'ruby-did-you-mean', 'ruby-minitest', 'ruby-net-telnet', 'ruby-power-assert', 'ruby-test-unit', 'ruby2.3', 'rubygems-integration', 'samtools', 'sgml-base', 'shared-mime-info', 'sim4', 'sysstat', 't-coffee', 'tcpd', 'tigr-glimmer', 'tm-align', 'tzdata', 'ucf', 'unzip', 'wise', 'wise-data', 'x11-common', 'x11-utils', 'x11-xserver-utils', 'xauth', 'xdg-user-dirs', 'xdg-utils', 'xml-core', 'xz-utils', 'zip', 'zlib1g-dev:amd64', 'roary'] 1m45.2s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: amap-align apache2-bin autotools-dev bedtools beignet-opencl-icd binutils bioperl bioperl-run blast2 blends-common bowtie build-essential bwa bzip2 bzip2-doc ca-certificates cd-hit cdbs clustalo clustalw cpp cpp-6 cron dbus dialign dialign-tx dialign-tx-data dirmngr dpkg-dev emboss emboss-data emboss-lib exim4 exim4-base exim4-config exim4-daemon-light exonerate fakeroot fasttree file fontconfig fontconfig-config fonts-dejavu-core fonts-droid-fallback fonts-lato fonts-liberation fonts-noto-mono fsa g++ g++-6 gawk gcc gcc-6 gfortran gfortran-6 ghostscript gnupg gnupg-agent gnupg-l10n graphviz gsfonts guile-2.0-libs hmmer hyphy-common hyphy-mpi icu-devtools infernal javascript-common kalign krb5-locales libace-perl libalgorithm-c3-perl libalgorithm-diff-perl libalgorithm-diff-xs-perl libalgorithm-merge-perl libalgorithm-munkres-perl libann0 libapache-dbi-perl libapache2-mod-perl2 libapache2-reload-perl libapparmor1 libapr1 libaprutil1 libaprutil1-dbd-sqlite3 libaprutil1-ldap libargtable2-0 libarray-compare-perl libarray-utils-perl libasan3 libassuan0 libatomic1 libauthen-sasl-perl libavahi-client3 libavahi-common-data libavahi-common3 libb-hooks-endofscope-perl libbio-asn1-entrezgene-perl libbio-perl-perl libbio-perl-run-perl libbit-vector-perl libblas-common libblas-dev libblas3 libbsd-resource-perl libbsd0 libbz2-dev libc-dev-bin libc6-dev libcache-cache-perl libcairo2 libcapture-tiny-perl libcarp-clan-perl libcc1-0 libcdt5 libcgi-fast-perl libcgi-pm-perl libcgraph6 libcilkrts5 libclass-c3-perl libclass-c3-xs-perl libclass-data-inheritable-perl libclass-inspector-perl libclass-load-perl libclass-load-xs-perl libclass-method-modifiers-perl libclass-tiny-perl libclass-xsaccessor-perl libclone-perl libconvert-binary-c-perl libconvert-binhex-perl libcrypt-rc4-perl libcups2 libcupsfilters1 libcupsimage2 libcurl3 libcurl3-gnutls libdata-optlist-perl libdata-stag-perl libdate-calc-perl libdate-calc-xs-perl libdate-manip-perl libdatrie1 libdbd-mysql-perl libdbd-pg-perl libdbd-sqlite3-perl libdbi-perl libdbus-1-3 libdevel-caller-perl libdevel-globaldestruction-perl libdevel-lexalias-perl libdevel-overloadinfo-perl libdevel-partialdump-perl libdevel-stacktrace-perl libdevel-symdump-perl libdigest-perl-md5-perl libdist-checkconflicts-perl libdivsufsort3 libdpkg-perl libdrm-amdgpu1 libdrm-intel1 libdrm-nouveau2 libdrm-radeon1 libdrm2 libedit2 libelf1 libemail-date-format-perl libencode-locale-perl libenv-path-perl liberror-perl libeval-closure-perl libexception-class-perl libexpat1 libexporter-tiny-perl libfabric1 libfakeroot libfcgi-perl libffi6 libfile-basedir-perl libfile-desktopentry-perl libfile-fcntllock-perl libfile-find-rule-perl libfile-grep-perl libfile-listing-perl libfile-mimeinfo-perl libfile-slurp-tiny-perl libfile-slurper-perl libfile-which-perl libfindbin-libs-perl libfont-afm-perl libfontconfig1 libfontenc1 libfreetype6 libfreezethaw-perl libfribidi0 libgc1c2 libgcc-6-dev libgd-perl libgd3 libgdbm3 libgfortran-6-dev libgfortran3 libgl1-mesa-dri libgl1-mesa-glx libglapi-mesa libglib2.0-0 libglib2.0-data libgmp10 libgnutls30 libgomp1 libgpm2 libgraph-perl libgraph-readwrite-perl libgraphite2-3 libgraphviz-perl libgs9 libgs9-common libgsasl7 libgssapi-krb5-2 libgts-0.7-5 libgts-bin libgvc6 libgvpr2 libharfbuzz0b libhmsbeagle1v5 libhogweed4 libhpdf-2.2.1 libhtml-form-perl libhtml-format-perl libhtml-parser-perl libhtml-tableextract-perl libhtml-tagset-perl libhtml-tree-perl libhts1 libhttp-cookies-perl libhttp-daemon-perl libhttp-date-perl libhttp-message-perl libhttp-negotiate-perl libhwloc-plugins libhwloc5 libibverbs1 libice6 libicu-dev libicu57 libidn11 libidn2-0 libijs-0.35 libimport-into-perl libio-all-perl libio-html-perl libio-pty-perl libio-sessiondata-perl libio-socket-ssl-perl libio-string-perl libio-stringy-perl libipc-run-perl libipc-shareable-perl libipc-sharelite-perl libipc-system-simple-perl libisl15 libitm1 libjbig0 libjbig2dec0 libjcode-pm-perl libjpeg-dev libjpeg62-turbo libjpeg62-turbo-dev libjs-jquery libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 libksba8 libkyotocabinet16v5 liblapack-dev liblapack3 liblcms2-2 libldap-2.4-2 libldap-common liblist-moreutils-perl libllvm3.9 liblocale-gettext-perl liblog-dispatch-perl liblog-log4perl-perl liblsan0 libltdl7 liblua5.2-0 liblwp-mediatypes-perl liblwp-protocol-https-perl liblzma-dev liblzo2-2 libmagic-mgc libmagic1 libmail-sendmail-perl libmailtools-perl libmailutils5 libmariadbclient18 libmath-derivative-perl libmath-spline-perl libmime-lite-perl libmime-tools-perl libmime-types-perl libmldbm-perl libmodule-implementation-perl libmodule-runtime-conflicts-perl libmodule-runtime-perl libmoo-perl libmoose-perl libmpc3 libmpfr4 libmpx2 libmro-compat-perl libnamespace-clean-perl libncurses5 libncurses5-dev libnet-dbus-perl libnet-http-perl libnet-smtp-ssl-perl libnet-ssleay-perl libnettle6 libnghttp2-14 libnl-3-200 libnl-route-3-200 libnpth0 libntlm0 libnuma1 libnumber-compare-perl libole-storage-lite-perl libopenjp2-7 libopenmpi2 libossp-uuid-perl libossp-uuid16 libp11-kit0 libpackage-deprecationmanager-perl libpackage-stash-perl libpackage-stash-xs-perl libpadwalker-perl libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libparams-classify-perl libparams-util-perl libparams-validate-perl libparse-recdescent-perl libparse-yapp-perl libpathplan4 libpciaccess0 libpcre16-3 libpcre3-dev libpcre32-3 libpcrecpp0v5 libperl5.24 libperlio-utf8-strict-perl libpixman-1-0 libpng-dev libpng-tools libpng16-16 libpostscript-perl libpq5 libprocps6 libpsl5 libpsm-infinipath1 libpython-stdlib libpython2.7 libpython2.7-minimal libpython2.7-stdlib libquadmath0 librdmacm1 libreadline-dev libreadline7 librole-tiny-perl librtmp1 libruby2.3 libsasl2-2 libsasl2-modules libsasl2-modules-db libscalar-list-utils-perl libsensors4 libset-scalar-perl libsigsegv2 libsm6 libsoap-lite-perl libsort-naturally-perl libspiffy-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsqlite3-0 libssh2-1 libssl1.0.2 libssl1.1 libstatistics-descriptive-perl libstdc++-6-dev libstrictures-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsub-uplevel-perl libsvg-graph-perl libsvg-perl libsys-hostname-long-perl libtask-weaken-perl libtasn1-6 libtcl8.6 libtest-deep-perl libtest-differences-perl libtest-exception-perl libtest-file-perl libtest-files-perl libtest-most-perl libtest-output-perl libtest-simple-perl libtest-warn-perl libtext-csv-perl libtext-csv-xs-perl libtext-diff-perl libtext-glob-perl libtext-iconv-perl libthai-data libthai0 libtie-ixhash-perl libtiff5 libtimedate-perl libtinfo-dev libtk8.6 libtree-dagnode-perl libtry-tiny-perl libtsan0 libtxc-dxtn-s2tc libtype-tiny-perl libtype-tiny-xs-perl libubsan0 libunicode-map-perl libunistring0 liburi-perl libvariable-magic-perl libwebp6 libwrap0 libwww-perl libwww-robotrules-perl libx11-6 libx11-data libx11-protocol-perl libx11-xcb1 libxau6 libxaw7 libxcb-dri2-0 libxcb-dri3-0 libxcb-glx0 libxcb-present0 libxcb-render0 libxcb-shape0 libxcb-shm0 libxcb-sync1 libxcb1 libxcomposite1 libxcursor1 libxdamage1 libxdmcp6 libxdot4 libxext6 libxfixes3 libxft2 libxi6 libxinerama1 libxml-dom-perl libxml-dom-xpath-perl libxml-filter-buffertext-perl libxml-libxml-perl libxml-libxslt-perl libxml-namespacesupport-perl libxml-parser-perl libxml-perl libxml-regexp-perl libxml-sax-base-perl libxml-sax-expat-perl libxml-sax-perl libxml-sax-writer-perl libxml-simple-perl libxml-twig-perl libxml-writer-perl libxml-xpath-perl libxml-xpathengine-perl libxml2 libxmlrpc-lite-perl libxmu6 libxmuu1 libxpm4 libxrandr2 libxrender1 libxshmfence1 libxslt1.1 libxss1 libxt6 libxtst6 libxv1 libxxf86dga1 libxxf86vm1 libyaml-0-2 libyaml-libyaml-perl libyaml-perl linux-libc-dev littler lsb-base lynx lynx-common mafft mailutils mailutils-common make manpages manpages-dev maq mcl med-config menu mime-support mummer muscle mustang mysql-common ncbi-blast+ ncbi-blast+-legacy ncbi-data netbase ocl-icd-libopencl1 openmpi-bin openmpi-common openssl parallel patch perl perl-doc perl-modules-5.24 perl-openssl-defaults perl-tk phylip phyml pinentry-curses pkg-config poa poppler-data prank primer3 probalign probcons procps proda psmisc publicsuffix python python-minimal python2.7 python2.7-minimal r-base-core r-base-dev r-cran-assertthat r-cran-boot r-cran-class r-cran-cluster r-cran-codetools r-cran-colorspace r-cran-crayon r-cran-dichromat r-cran-digest r-cran-foreign r-cran-ggplot2 r-cran-gtable r-cran-kernsmooth 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-nnet r-cran-pkgkitten r-cran-plyr r-cran-rcolorbrewer r-cran-rcpp r-cran-reshape2 r-cran-rpart r-cran-scales r-cran-spatial r-cran-stringi r-cran-stringr r-cran-survival r-cran-tibble r-doc-html r-recommended rake raxml readline-common rename roary ruby ruby-did-you-mean ruby-minitest ruby-net-telnet ruby-power-assert ruby-test-unit ruby2.3 rubygems-integration samtools sgml-base shared-mime-info sim4 sysstat t-coffee tcpd tigr-glimmer tm-align tzdata ucf unzip wise wise-data x11-common x11-utils x11-xserver-utils xauth xdg-user-dirs xdg-utils xml-core xz-utils zip zlib1g-dev 0 upgraded, 0 newly installed, 634 to remove and 0 not upgraded. After this operation, 1761 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 ... 43104 files and directories currently installed.) Removing amap-align (2.2-6) ... Removing libapache2-reload-perl (0.13-1) ... Removing libapache-dbi-perl (1.12-1) ... Removing libapache2-mod-perl2 (2.0.10-2+deb9u1) ... Removing apache2-bin (2.4.25-3+deb9u9) ... Removing autotools-dev (20161112.1) ... Removing roary (3.8.0+dfsg-1) ... Removing bedtools (2.26.0+dfsg-3) ... Removing phyml (3:3.2.0+dfsg-7+b1) ... Removing libhmsbeagle1v5 (2.1.2+20160831-5) ... Removing beignet-opencl-icd:amd64 (1.3.0-4) ... Removing r-base-dev (3.3.3-1) ... Removing build-essential (12.3) ... Removing g++ (4:6.3.0-4) ... Removing liblapack-dev (3.7.0-2) ... Removing libblas-dev (3.7.0-2) ... Removing gfortran (4:6.3.0-4) ... Removing gcc (4:6.3.0-4) ... Removing dpkg-dev (1.18.25) ... Removing bioperl-run (1.7.1-3) ... Removing bioperl (1.7.1-2) ... Removing blast2 (1:2.6.0-1) ... Removing med-config (3.0.1) ... Removing blends-common (0.6.96) ... Removing bowtie (1.1.2-6) ... Removing bwa (0.7.15-2+deb9u1) ... Removing bzip2 (1.0.6-8.1) ... Removing bzip2-doc (1.0.6-8.1) ... Removing r-recommended (3.3.3-1) ... Removing r-cran-rpart (4.1-10-2) ... Removing r-cran-survival (2.40-1-1) ... Removing r-cran-mgcv (1.8-16-1) ... Removing r-cran-matrix (1.2-7.1-1) ... Removing cd-hit (4.6.6-2) ... Removing cdbs (0.4.150) ... Removing clustalo (1.2.4-1) ... Removing clustalw (2.1+lgpl-5) ... Removing x11-xserver-utils (7.7+7+b1) ... Removing cpp (4:6.3.0-4) ... Removing exim4 (4.89-2+deb9u7) ... Removing mailutils (1:3.1.1-1) ... Removing exim4-daemon-light (4.89-2+deb9u7) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing exim4-base (4.89-2+deb9u7) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing cron (3.0pl1-128+deb9u1) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing dbus (1.10.32-0+deb9u1) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. Removing dialign (2.2.1-8) ... Removing dialign-tx (1.0.2-9) ... Removing dialign-tx-data (1.0.2-9) ... Removing dirmngr (2.1.18-8~deb9u4) ... Removing emboss (6.6.0+dfsg-6) ... Removing emboss-data (6.6.0+dfsg-6) ... Removing emboss-lib (6.6.0+dfsg-6) ... Removing exim4-config (4.89-2+deb9u7) ... Removing fsa (1.15.9+dfsg-3) ... Removing exonerate (2.4.0-2) ... Removing fakeroot (1.21-3.1) ... update-alternatives: using /usr/bin/fakeroot-tcp to provide /usr/bin/fakeroot (fakeroot) in auto mode Removing fasttree (2.1.9-1) ... Removing file (1:5.30-1+deb9u3) ... Removing libgraphviz-perl (2.22-1) ... Removing graphviz (2.38.0-17) ... Removing libgvc6 (2.38.0-17) ... Removing x11-utils (7.7+3+b1) ... Removing perl-tk (1:804.033-1+b3) ... Removing fonts-dejavu-core (2.37-1) ... Removing fonts-droid-fallback (1:6.0.1r16-1.1) ... Removing fonts-lato (2.0-1) ... Removing fonts-noto-mono (20161116-1) ... Removing g++-6 (6.3.0-18+deb9u1) ... Removing mummer (3.23+dfsg-2) ... Removing gawk (1:4.1.4+dfsg-1) ... update-alternatives: using /usr/bin/mawk to provide /usr/bin/awk (awk) in auto mode Removing gfortran-6 (6.3.0-18+deb9u1) ... Removing ghostscript (9.26a~dfsg-0+deb9u6) ... Removing gnupg (2.1.18-8~deb9u4) ... Removing gnupg-agent (2.1.18-8~deb9u4) ... Removing gnupg-l10n (2.1.18-8~deb9u4) ... Removing gsfonts (1:8.11+urwcyr1.0.7~pre44-4.3) ... Removing libmailutils5:amd64 (1:3.1.1-1) ... Removing guile-2.0-libs:amd64 (2.0.13+1-4) ... Removing hmmer (3.1b2+dfsg-5) ... Removing hyphy-mpi (2.2.7+dfsg-1+b2) ... Removing hyphy-common (2.2.7+dfsg-1) ... Removing libicu-dev (57.1-6+deb9u4) ... Removing icu-devtools (57.1-6+deb9u4) ... Removing infernal (1.1.2-1) ... Removing javascript-common (11) ... Removing kalign (1:2.03+20110620-3) ... Removing krb5-locales (1.15-1+deb9u1) ... Removing libace-perl (1.92-4+b1) ... Removing libmoose-perl (2.1807-1) ... Removing libdevel-overloadinfo-perl (0.004-1) ... Removing libmro-compat-perl (0.12-1) ... Removing libclass-c3-perl (0.32-1) ... Removing libalgorithm-c3-perl (0.10-1) ... Removing libtest-files-perl (0.14-1) ... Removing libtest-most-perl (0.35-1) ... Removing libtest-differences-perl (0.64-1) ... Removing libtext-diff-perl (1.44-1) ... Removing libalgorithm-merge-perl (0.08-3) ... Removing libalgorithm-diff-xs-perl (0.04-4+b2) ... Removing libalgorithm-munkres-perl (0.08-3) ... Removing libann0 (1.1.2+doc-6) ... Removing libapparmor1:amd64 (2.11.0-3+deb9u2) ... Removing libaprutil1-ldap:amd64 (1.5.4-3) ... Removing libaprutil1-dbd-sqlite3:amd64 (1.5.4-3) ... Removing libaprutil1:amd64 (1.5.4-3) ... Removing libapr1:amd64 (1.5.2-5) ... Removing libargtable2-0 (13-1) ... Removing libarray-compare-perl (3.0.0-1) ... Removing libarray-utils-perl (0.5-1) ... Removing libstdc++-6-dev:amd64 (6.3.0-18+deb9u1) ... Removing libgfortran-6-dev:amd64 (6.3.0-18+deb9u1) ... Removing pinentry-curses (1.0.0-2) ... Removing libassuan0:amd64 (2.4.3-2) ... Removing libauthen-sasl-perl (2.1600-1) ... Removing libgs9:amd64 (9.26a~dfsg-0+deb9u6) ... Removing libcupsfilters1:amd64 (1.11.6-3+deb9u1) ... Removing libdevel-partialdump-perl (0.18-2) ... Removing libnamespace-clean-perl (0.27-1) ... Removing libb-hooks-endofscope-perl (0.21-1) ... Removing libbio-asn1-entrezgene-perl (1.720-1) ... Removing libbio-perl-run-perl (1.7.1-3) ... Removing libbio-perl-perl (1.7.1-2) ... Removing libdate-calc-xs-perl (6.4-1+b2) ... Removing libdate-calc-perl (6.4-1) ... Removing libbit-vector-perl (7.4-1+b2) ... Removing r-cran-ggplot2 (2.2.1-2) ... Removing r-cran-tibble (1.2-1) ... Removing r-cran-scales (0.4.1-1) ... Removing littler (0.3.1-1) ... Removing r-cran-kernsmooth (2.23-15-2) ... Removing libbsd-resource-perl (1.2910-1+b1) ... Removing lynx (2.8.9dev11-1) ... Removing xauth (1:1.0.9-1+b2) ... Removing libbz2-dev:amd64 (1.0.6-8.1) ... Removing libpng-dev:amd64 (1.6.28-1+deb9u1) ... Removing zlib1g-dev:amd64 (1:1.2.8.dfsg-5) ... Removing libncurses5-dev:amd64 (6.0+20161126-1+deb9u2) ... Removing libpcre3-dev:amd64 (2:8.39-3) ... Removing libjpeg-dev (1:1.5.1-2) ... Removing libjpeg62-turbo-dev:amd64 (1:1.5.1-2) ... Removing libc6-dev:amd64 (2.24-11+deb9u4) ... Removing libc-dev-bin (2.24-11+deb9u4) ... Removing libcache-cache-perl (1.08-2) ... Removing libtest-output-perl (1.03-1) ... Removing libcapture-tiny-perl (0.44-1) ... Removing libcarp-clan-perl (6.06-1) ... Removing libgvpr2 (2.38.0-17) ... Removing libcgraph6 (2.38.0-17) ... Removing libcdt5 (2.38.0-17) ... Removing libcgi-fast-perl (1:2.12-1) ... Removing libcgi-pm-perl (4.35-1) ... Removing libclass-c3-xs-perl (0.14-1+b1) ... Removing libexception-class-perl (1.42-1) ... Removing libclass-data-inheritable-perl (0.08-2) ... Removing libxmlrpc-lite-perl (0.717-1) ... Removing libsoap-lite-perl (1.20-1) ... Removing libclass-inspector-perl (1.31-1) ... Removing libclass-load-xs-perl (0.09-2+b1) ... Removing libclass-load-perl (0.23-1) ... Removing libmoo-perl (2.002005-1) ... Removing librole-tiny-perl (2.000005-1) ... Removing libclass-method-modifiers-perl (2.12-1) ... Removing libclass-tiny-perl (1.006-1) ... Removing libclass-xsaccessor-perl (1.19-2+b7) ... Removing libclone-perl (0.38-2+b1) ... Removing libconvert-binary-c-perl (0.78-1+b1) ... Removing libmime-tools-perl (5.508-1) ... Removing libconvert-binhex-perl (1.125-1) ... Removing libspreadsheet-parseexcel-perl (0.6500-1) ... Removing libcrypt-rc4-perl (2.02-2) ... Removing libcupsimage2:amd64 (2.2.1-8+deb9u6) ... Removing samtools (1.3.1-3) ... Removing libhts1:amd64 (1.3.2-2) ... Removing libcurl3-gnutls:amd64 (7.52.1-5+deb9u10) ... Removing libeval-closure-perl (0.14-1) ... Removing libsub-exporter-perl (0.986-1) ... Removing libdata-optlist-perl (0.110-1) ... Removing libdata-stag-perl (0.14-2) ... Removing libdate-manip-perl (6.57-1) ... Removing libdbd-mysql-perl (4.041-2) ... Removing libdbd-pg-perl (3.5.3-1+b2) ... Removing libdbd-sqlite3-perl (1.54-1) ... Removing libdbi-perl (1.636-1+b1) ... Removing libnet-dbus-perl (1.1.0-4+b1) ... Removing libdevel-lexalias-perl (0.05-1+b4) ... Removing libdevel-caller-perl (2.06-1+b4) ... Removing liblog-dispatch-perl (2.58-1) ... Removing libdevel-globaldestruction-perl (0.14-1) ... Removing libdevel-stacktrace-perl (2.0200-1) ... Removing libdevel-symdump-perl (2.17-1) ... Removing libdigest-perl-md5-perl (1.9-1) ... Removing libmodule-runtime-conflicts-perl (0.003-1) ... Removing libdist-checkconflicts-perl (0.11-1) ... Removing libdivsufsort3:amd64 (2.0.1-2) ... Removing pkg-config (0.29-4+b1) ... Removing libdpkg-perl (1.18.25) ... Removing libgl1-mesa-dri:amd64 (13.0.6-1+b2) ... Removing libdrm-amdgpu1:amd64 (2.4.74-1) ... Removing libdrm-intel1:amd64 (2.4.74-1) ... Removing libdrm-nouveau2:amd64 (2.4.74-1) ... Removing libdrm-radeon1:amd64 (2.4.74-1) ... Removing libgl1-mesa-glx:amd64 (13.0.6-1+b2) ... Removing libdrm2:amd64 (2.4.74-1) ... Removing libllvm3.9:amd64 (1:3.9.1-9) ... Removing libedit2:amd64 (3.1-20160903-3) ... Removing libelf1:amd64 (0.168-1) ... Removing libmime-lite-perl (3.030-2) ... Removing libemail-date-format-perl (1.005-1) ... Removing libxml-simple-perl (2.22-1) ... Removing libxml-sax-expat-perl (0.40-2) ... update-perl-sax-parsers: Unregistering Perl SAX parser XML::SAX::Expat with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Removing libxml-xpath-perl (1.40-1) ... Removing libxml-dom-xpath-perl (0.14-2) ... Removing libxml-dom-perl (1.44-2) ... Removing libenv-path-perl (0.19-1) ... Removing liberror-perl (0.17024-1) ... Removing ncbi-blast+-legacy (2.6.0-1) ... Removing ncbi-blast+ (2.6.0-1) ... Removing python (2.7.13-2) ... Removing python2.7 (2.7.13-2+deb9u3) ... Removing libpython2.7:amd64 (2.7.13-2+deb9u3) ... Removing libtype-tiny-perl (1.000005-1) ... Removing libsvg-graph-perl (0.02-2) ... Removing libstatistics-descriptive-perl (3.0612-1) ... Removing liblist-moreutils-perl (0.416-1+b1) ... Removing libexporter-tiny-perl (0.042-1) ... Removing openmpi-bin (2.0.2-2) ... Removing libopenmpi2:amd64 (2.0.2-2) ... Removing libfabric1 (1.4.0-1) ... Removing libfakeroot:amd64 (1.21-3.1) ... Removing libfcgi-perl (0.78-2) ... Removing libpq5:amd64 (9.6.17-0+deb9u1) ... Removing wise (2.4.1-19) ... Removing libfile-mimeinfo-perl (0.27-1) ... Removing libfile-desktopentry-perl (0.22-1) ... Removing libfile-basedir-perl (0.07-1) ... Removing libfile-fcntllock-perl (0.22-3+b2) ... Removing libfile-find-rule-perl (0.34-1) ... Removing libfile-grep-perl (0.02-1) ... Removing libtree-dagnode-perl (1.29-1) ... Removing libfile-slurp-tiny-perl (0.003-1) ... Removing libfile-slurper-perl (0.009-1) ... Removing libfile-which-perl (1.21-1) ... Removing libfindbin-libs-perl (2.150-1) ... Removing libhtml-format-perl (2.12-1) ... Removing libfont-afm-perl (1.20-2) ... Removing libfontenc1:amd64 (1:1.1.3-1+b2) ... Removing libgd-perl (2.53-3) ... Removing libgd3:amd64 (2.2.4-2+deb9u5) ... Removing libfreezethaw-perl (0.5001-1) ... Removing libfribidi0:amd64 (0.19.7-1+deb9u1) ... Removing libgc1c2:amd64 (1:7.4.2-8) ... Removing rename (0.20-4) ... update-alternatives: using /usr/bin/prename to provide /usr/bin/rename (rename) in auto mode Removing parallel (20161222-1) ... Removing 'diversion of /usr/bin/parallel to /usr/bin/parallel.moreutils by parallel' Removing 'diversion of /usr/share/man/man1/parallel.1.gz to /usr/share/man/man1/parallel.moreutils.1.gz by parallel' Removing perl-doc (5.24.1-3+deb9u7) ... Removing 'diversion of /usr/bin/perldoc to /usr/bin/perldoc.stub by perl-doc' Removing mafft (7.307-1) ... Removing tm-align (20160521+dfsg-2) ... Removing r-cran-nlme (3.1.129-1) ... Removing libglapi-mesa:amd64 (13.0.6-1+b2) ... Removing libglib2.0-data (2.50.3-2+deb9u2) ... Removing libgpm2:amd64 (1.20.4-6.2+b1) ... Removing libgraph-readwrite-perl (2.09-1) ... Removing libgraph-perl (1:0.96-2) ... Removing libgs9-common (9.26a~dfsg-0+deb9u6) ... Removing libgsasl7 (1.8.0-8+b2) ... Removing libgts-bin (0.7.6+darcs121130-4) ... 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Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Removing libxml-sax-perl (0.99+dfsg-2) ... update-perl-sax-parsers: Unregistering Perl SAX parser XML::SAX::PurePerl with priority 50... update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... Removing libxml-namespacesupport-perl (1.11-1) ... Removing libxml-perl (0.08-2) ... Removing libxml-regexp-perl (0.04-1) ... Removing libxml-sax-base-perl (1.07-1) ... Removing libxml-twig-perl (1:3.50-1) ... Removing libxml-writer-perl (0.625-1) ... Removing libxml-xpathengine-perl (0.13-1) ... Removing libxmuu1:amd64 (2:1.1.2-2) ... Removing libxpm4:amd64 (1:3.5.12-1) ... Removing libxrandr2:amd64 (2:1.5.1-1) ... Removing libxshmfence1:amd64 (1.2-1+b2) ... Removing libxslt1.1:amd64 (1.1.29-2.1+deb9u2) ... Removing libxv1:amd64 (2:1.0.11-1) ... Removing libyaml-libyaml-perl (0.63-2) ... Removing libyaml-perl (1.21-1) ... Removing linux-libc-dev:amd64 (4.9.228-1) ... 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Removing libxml2:amd64 (2.9.4+dfsg1-2.2+deb9u2) ... Removing libisl15:amd64 (0.18-1) ... Removing libitm1:amd64 (6.3.0-18+deb9u1) ... Removing liblsan0:amd64 (6.3.0-18+deb9u1) ... Removing libmpx2:amd64 (6.3.0-18+deb9u1) ... Removing libpython2.7-minimal:amd64 (2.7.13-2+deb9u3) ... Removing libsqlite3-0:amd64 (3.16.2-5+deb9u1) ... Removing libtsan0:amd64 (6.3.0-18+deb9u1) ... Removing libubsan0:amd64 (6.3.0-18+deb9u1) ... Removing mime-support (3.60) ... Removing r-cran-pkgkitten (0.1.4-1) ... Removing r-base-core (3.3.3-1) ... Removing libpangocairo-1.0-0:amd64 (1.40.5-1) ... Removing libpangoft2-1.0-0:amd64 (1.40.5-1) ... Removing libpango-1.0-0:amd64 (1.40.5-1) ... Removing fontconfig (2.11.0-6.7+b1) ... Removing libtk8.6:amd64 (8.6.6-1+b1) ... Removing libxft2:amd64 (2.3.2-1+b2) ... Removing liblapack3 (3.7.0-2) ... Removing libblas3 (3.7.0-2) ... Removing libblas-common (3.7.0-2) ... Removing libcairo2:amd64 (1.14.8-1) ... Removing libcurl3:amd64 (7.52.1-5+deb9u10) ... Removing libthai0:amd64 (0.1.26-1) ... Removing libdatrie1:amd64 (0.2.10-4+b1) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-1+b1) ... Removing libldap-2.4-2:amd64 (2.4.44+dfsg-5+deb9u4) ... Removing libgnutls30:amd64 (3.5.8-5+deb9u5) ... Removing libp11-kit0:amd64 (0.23.3-2) ... Removing libgfortran3:amd64 (6.3.0-18+deb9u1) ... Removing libhogweed4:amd64 (3.3-1+b2) ... Removing libgomp1:amd64 (6.3.0-18+deb9u1) ... Removing libharfbuzz0b:amd64 (1.4.2-1) ... Removing libgraphite2-3:amd64 (1.3.10-1) ... Removing libgssapi-krb5-2:amd64 (1.15-1+deb9u1) ... Removing libxt6:amd64 (1:1.1.5-1) ... Removing libsm6:amd64 (2:1.2.2-1+b3) ... Removing libice6:amd64 (2:1.0.9-2) ... Removing libicu57:amd64 (57.1-6+deb9u4) ... Removing libidn11:amd64 (1.33-1+deb9u1) ... Removing libpsl5:amd64 (0.17.0-3) ... Removing libidn2-0:amd64 (0.16-1+deb9u1) ... Removing libtiff5:amd64 (4.0.8-2+deb9u5) ... Removing libjbig0:amd64 (2.1-3.1+b2) ... Removing libjpeg62-turbo:amd64 (1:1.5.1-2) ... Removing libkrb5-3:amd64 (1.15-1+deb9u1) ... Removing libk5crypto3:amd64 (1.15-1+deb9u1) ... Removing libkrb5support0:amd64 (1.15-1+deb9u1) ... Removing libkeyutils1:amd64 (1.5.9-9) ... Removing libldap-common (2.4.44+dfsg-5+deb9u4) ... Removing libnettle6:amd64 (3.3-1+b2) ... Removing libnghttp2-14:amd64 (1.18.1-1+deb9u1) ... Removing libpaper-utils (1.1.24+nmu5) ... Removing libpaper1:amd64 (1.1.24+nmu5) ... Removing libpixman-1-0:amd64 (0.34.0-1) ... Removing libquadmath0:amd64 (6.3.0-18+deb9u1) ... Removing libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Removing libsasl2-modules-db:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Removing libssh2-1:amd64 (1.7.0-1+deb9u1) ... Removing libtasn1-6:amd64 (4.10-1.1+deb9u1) ... Removing libtcl8.6:amd64 (8.6.6+dfsg-1+b1) ... Removing libthai-data (0.1.26-1) ... Removing libunistring0:amd64 (0.9.6+really0.9.3-0.1) ... Removing libxcb-render0:amd64 (1.12-1) ... Removing libxcb-shm0:amd64 (1.12-1) ... Removing libxrender1:amd64 (1:0.9.10-1) ... Removing libxss1:amd64 (1:1.2.2-1) ... 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 (9.20161125) ... Removing tzdata (2020a-0+deb9u1) ... Removing unzip (6.0-21+deb9u2) ... Removing xdg-utils (1.1.1-1+deb9u2) ... Removing zip (3.0-11+b1) ... Removing libfontconfig1:amd64 (2.11.0-6.7+b1) ... Removing fontconfig-config (2.11.0-6.7) ... Removing fonts-liberation (1:1.07.4-2) ... Removing libexpat1:amd64 (2.2.0-2+deb9u3) ... Removing libglib2.0-0:amd64 (2.50.3-2+deb9u2) ... Removing libfreetype6:amd64 (2.6.3-3.2+deb9u1) ... Removing libpng16-16:amd64 (1.6.28-1+deb9u1) ... Removing libxext6:amd64 (2:1.3.3-1+b2) ... Removing ucf (3.0036) ... Removing libx11-6:amd64 (2:1.6.4-3+deb9u1) ... Removing libxcb1:amd64 (1.12-1) ... Removing libxdmcp6:amd64 (1:1.1.2-3) ... Removing libbsd0:amd64 (0.8.3-1) ... Removing libx11-data (2:1.6.4-3+deb9u1) ... Removing libxau6:amd64 (1:1.0.8-1) ... Removing rake (10.5.0-2+deb9u1) ... Removing ruby (1:2.3.3) ... Removing ruby2.3 (2.3.3-1+deb9u8) ... Removing libruby2.3:amd64 (2.3.3-1+deb9u8) ... Removing rubygems-integration (1.11) ... Removing libwww-perl (6.15-1) ... Removing libhttp-negotiate-perl (6.00-2) ... Removing libffi6:amd64 (3.2.1-6) ... Removing libfile-listing-perl (6.04-1) ... Removing libgmp10:amd64 (2:6.1.2+dfsg-1) ... Removing libhtml-tree-perl (5.03-2) ... Removing libhtml-parser-perl (3.72-3) ... Removing libhtml-tagset-perl (3.20-3) ... Removing libhttp-cookies-perl (6.01-1) ... Removing liblwp-protocol-https-perl (6.06-2) ... Removing libio-socket-ssl-perl (2.044-1) ... Removing libncurses5:amd64 (6.0+20161126-1+deb9u2) ... Removing libnet-http-perl (6.12-1) ... Removing libnet-ssleay-perl (1.80-1) ... Removing libreadline7:amd64 (7.0-3) ... Removing libssl1.0.2:amd64 (1.0.2u-1~deb9u1) ... Removing perl-openssl-defaults:amd64 (3) ... Removing libwww-robotrules-perl (6.01-1) ... Removing libyaml-0-2:amd64 (0.1.7-2) ... Removing netbase (5.4) ... Removing readline-common (7.0-3) ... Removing ruby-did-you-mean (1.0.0-2) ... Removing ruby-minitest (5.9.0-1) ... Removing ruby-net-telnet (0.1.1-2) ... Removing ruby-test-unit (3.1.7-2) ... Removing ruby-power-assert (0.3.0-1) ... Removing ca-certificates (20200601~deb9u1) ... Removing dangling symlinks from /etc/ssl/certs... done. Removing libhttp-message-perl (6.11-1) ... Removing libencode-locale-perl (1.05-1) ... Removing libhttp-date-perl (6.02-1) ... Removing libio-html-perl (1.001-1) ... Removing liblwp-mediatypes-perl (6.02-1) ... Removing openssl (1.1.0l-1~deb9u1) ... Removing libssl1.1:amd64 (1.1.0l-1~deb9u1) ... Removing libtimedate-perl (2.3000-2+deb9u1) ... Removing liburi-perl (1.71-1) ... Removing perl (5.24.1-3+deb9u7) ... Removing libperl5.24:amd64 (5.24.1-3+deb9u7) ... Removing libgdbm3:amd64 (1.8.3-14) ... Removing perl-modules-5.24 (5.24.1-3+deb9u7) ... Processing triggers for libc-bin (2.24-11+deb9u4) ... 1m45.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'apt-get', 'remove', 'amap-align', 'apache2-bin', 'autotools-dev', 'bedtools', 'beignet-opencl-icd:amd64', 'binutils', 'bioperl', 'bioperl-run', 'blast2', 'blends-common', 'bowtie', 'build-essential', 'bwa', 'bzip2', 'bzip2-doc', 'ca-certificates', 'cd-hit', 'cdbs', 'clustalo', 'clustalw', 'cpp', 'cpp-6', 'cron', 'dbus', 'dialign', 'dialign-tx', 'dialign-tx-data', 'dirmngr', 'dpkg-dev', 'emboss', 'emboss-data', 'emboss-lib', 'exim4', 'exim4-base', 'exim4-config', 'exim4-daemon-light', 'exonerate', 'fakeroot', 'fasttree', 'file', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-droid-fallback', 'fonts-lato', 'fonts-liberation', 'fonts-noto-mono', 'fsa', 'g++-', 'g++-6', 'gawk', 'gcc', 'gcc-6', 'gfortran', 'gfortran-6', 'ghostscript', 'gnupg', 'gnupg-agent', 'gnupg-l10n', 'graphviz', 'gsfonts', 'guile-2.0-libs:amd64', 'hmmer', 'hyphy-common', 'hyphy-mpi', 'icu-devtools', 'infernal', 'javascript-common', 'kalign', 'krb5-locales', 'libace-perl', 'libalgorithm-c3-perl', 'libalgorithm-diff-perl', 'libalgorithm-diff-xs-perl', 'libalgorithm-merge-perl', 'libalgorithm-munkres-perl', 'libann0', 'libapache-dbi-perl', 'libapache2-mod-perl2', 'libapache2-reload-perl', 'libapparmor1:amd64', 'libapr1:amd64', 'libaprutil1:amd64', 'libaprutil1-dbd-sqlite3:amd64', 'libaprutil1-ldap:amd64', 'libargtable2-0', 'libarray-compare-perl', 'libarray-utils-perl', 'libasan3:amd64', 'libassuan0:amd64', 'libatomic1:amd64', 'libauthen-sasl-perl', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libb-hooks-endofscope-perl', 'libbio-asn1-entrezgene-perl', 'libbio-perl-perl', 'libbio-perl-run-perl', 'libbit-vector-perl', 'libblas-common', 'libblas-dev', 'libblas3', 'libbsd-resource-perl', 'libbsd0:amd64', 'libbz2-dev:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcache-cache-perl', 'libcairo2:amd64', 'libcapture-tiny-perl', 'libcarp-clan-perl', 'libcc1-0:amd64', 'libcdt5', 'libcgi-fast-perl', 'libcgi-pm-perl', 'libcgraph6', 'libcilkrts5:amd64', 'libclass-c3-perl', 'libclass-c3-xs-perl', 'libclass-data-inheritable-perl', 'libclass-inspector-perl', 'libclass-load-perl', 'libclass-load-xs-perl', 'libclass-method-modifiers-perl', 'libclass-tiny-perl', 'libclass-xsaccessor-perl', 'libclone-perl', 'libconvert-binary-c-perl', 'libconvert-binhex-perl', 'libcrypt-rc4-perl', 'libcups2:amd64', 'libcupsfilters1:amd64', 'libcupsimage2:amd64', 'libcurl3:amd64', 'libcurl3-gnutls:amd64', 'libdata-optlist-perl', 'libdata-stag-perl', 'libdate-calc-perl', 'libdate-calc-xs-perl', 'libdate-manip-perl', 'libdatrie1:amd64', 'libdbd-mysql-perl', 'libdbd-pg-perl', 'libdbd-sqlite3-perl', 'libdbi-perl', 'libdbus-1-3:amd64', 'libdevel-caller-perl', 'libdevel-globaldestruction-perl', 'libdevel-lexalias-perl', 'libdevel-overloadinfo-perl', 'libdevel-partialdump-perl', 'libdevel-stacktrace-perl', 'libdevel-symdump-perl', 'libdigest-perl-md5-perl', 'libdist-checkconflicts-perl', 'libdivsufsort3:amd64', 'libdpkg-perl', 'libdrm-amdgpu1:amd64', 'libdrm-intel1:amd64', 'libdrm-nouveau2:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1:amd64', 'libemail-date-format-perl', 'libencode-locale-perl', 'libenv-path-perl', 'liberror-perl', 'libeval-closure-perl', 'libexception-class-perl', 'libexpat1:amd64', 'libexporter-tiny-perl', 'libfabric1', 'libfakeroot:amd64', 'libfcgi-perl', 'libffi6:amd64', 'libfile-basedir-perl', 'libfile-desktopentry-perl', 'libfile-fcntllock-perl', 'libfile-find-rule-perl', 'libfile-grep-perl', 'libfile-listing-perl', 'libfile-mimeinfo-perl', 'libfile-slurp-tiny-perl', 'libfile-slurper-perl', 'libfile-which-perl', 'libfindbin-libs-perl', 'libfont-afm-perl', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfreezethaw-perl', 'libfribidi0:amd64', 'libgc1c2:amd64', 'libgcc-6-dev:amd64', 'libgd-perl', 'libgd3:amd64', 'libgdbm3:amd64', 'libgfortran-6-dev:amd64', 'libgfortran3:amd64', 'libgl1-mesa-dri:amd64', 'libgl1-mesa-glx:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0:amd64', 'libglib2.0-data', 'libgmp10:amd64', 'libgnutls30:amd64', 'libgomp1:amd64', 'libgpm2:amd64', 'libgraph-perl', 'libgraph-readwrite-perl', 'libgraphite2-3:amd64', 'libgraphviz-perl', 'libgs9:amd64', 'libgs9-common', 'libgsasl7', 'libgssapi-krb5-2:amd64', 'libgts-0.7-5:amd64', 'libgts-bin', 'libgvc6', 'libgvpr2', 'libharfbuzz0b:amd64', 'libhmsbeagle1v5', 'libhogweed4:amd64', 'libhpdf-2.2.1', 'libhtml-form-perl', 'libhtml-format-perl', 'libhtml-parser-perl', 'libhtml-tableextract-perl', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhts1:amd64', 'libhttp-cookies-perl', 'libhttp-daemon-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libhwloc-plugins', 'libhwloc5:amd64', 'libibverbs1', 'libice6:amd64', 'libicu-dev', 'libicu57:amd64', 'libidn11:amd64', 'libidn2-0:amd64', 'libijs-0.35:amd64', 'libimport-into-perl', 'libio-all-perl', 'libio-html-perl', 'libio-pty-perl', 'libio-sessiondata-perl', 'libio-socket-ssl-perl', 'libio-string-perl', 'libio-stringy-perl', 'libipc-run-perl', 'libipc-shareable-perl', 'libipc-sharelite-perl', 'libipc-system-simple-perl', 'libisl15:amd64', 'libitm1:amd64', 'libjbig0:amd64', 'libjbig2dec0:amd64', 'libjcode-pm-perl', 'libjpeg-dev', 'libjpeg62-turbo:amd64', 'libjpeg62-turbo-dev:amd64', 'libjs-jquery', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libksba8:amd64', 'libkyotocabinet16v5:amd64', 'liblapack-dev', 'liblapack3', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'liblist-moreutils-perl', 'libllvm3.9:amd64', 'liblocale-gettext-perl', 'liblog-dispatch-perl', 'liblog-log4perl-perl', 'liblsan0:amd64', 'libltdl7:amd64', 'liblua5.2-0:amd64', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'liblzma-dev:amd64', 'liblzo2-2:amd64', 'libmagic-mgc', 'libmagic1:amd64', 'libmail-sendmail-perl', 'libmailtools-perl', 'libmailutils5:amd64', 'libmariadbclient18:amd64', 'libmath-derivative-perl', 'libmath-spline-perl', 'libmime-lite-perl', 'libmime-tools-perl', 'libmime-types-perl', 'libmldbm-perl', 'libmodule-implementation-perl', 'libmodule-runtime-conflicts-perl', 'libmodule-runtime-perl', 'libmoo-perl', 'libmoose-perl', 'libmpc3:amd64', 'libmpfr4:amd64', 'libmpx2:amd64', 'libmro-compat-perl', 'libnamespace-clean-perl', 'libncurses5:amd64', 'libncurses5-dev:amd64', 'libnet-dbus-perl', 'libnet-http-perl', 'libnet-smtp-ssl-perl', 'libnet-ssleay-perl', 'libnettle6:amd64', 'libnghttp2-14:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnpth0:amd64', 'libntlm0:amd64', 'libnuma1:amd64', 'libnumber-compare-perl', 'libole-storage-lite-perl', 'libopenjp2-7:amd64', 'libopenmpi2:amd64', 'libossp-uuid-perl', 'libossp-uuid16:amd64', 'libp11-kit0:amd64', 'libpackage-deprecationmanager-perl', 'libpackage-stash-perl', 'libpackage-stash-xs-perl', 'libpadwalker-perl', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libparams-classify-perl', 'libparams-util-perl', 'libparams-validate-perl', 'libparse-recdescent-perl', 'libparse-yapp-perl', 'libpathplan4', 'libpciaccess0:amd64', 'libpcre16-3:amd64', 'libpcre3-dev:amd64', 'libpcre32-3:amd64', 'libpcrecpp0v5:amd64', 'libperl5.24:amd64', 'libperlio-utf8-strict-perl', 'libpixman-1-0:amd64', 'libpng-dev:amd64', 'libpng-tools', 'libpng16-16:amd64', 'libpostscript-perl', 'libpq5:amd64', 'libprocps6:amd64', 'libpsl5:amd64', 'libpsm-infinipath1', 'libpython-stdlib:amd64', 'libpython2.7:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'librdmacm1', 'libreadline-dev:amd64', 'libreadline7:amd64', 'librole-tiny-perl', 'librtmp1:amd64', 'libruby2.3:amd64', 'libsasl2-2:amd64', 'libsasl2-modules:amd64', 'libsasl2-modules-db:amd64', 'libscalar-list-utils-perl', 'libsensors4:amd64', 'libset-scalar-perl', 'libsigsegv2:amd64', 'libsm6:amd64', 'libsoap-lite-perl', 'libsort-naturally-perl', 'libspiffy-perl', 'libspreadsheet-parseexcel-perl', 'libspreadsheet-writeexcel-perl', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.0.2:amd64', 'libssl1.1:amd64', 'libstatistics-descriptive-perl', 'libstdc++-6-dev:amd64', 'libstrictures-perl', 'libsub-exporter-perl', 'libsub-exporter-progressive-perl', 'libsub-identify-perl', 'libsub-install-perl', 'libsub-name-perl', 'libsub-uplevel-perl', 'libsvg-graph-perl', 'libsvg-perl', 'libsys-hostname-long-perl', 'libtask-weaken-perl', 'libtasn1-6:amd64', 'libtcl8.6:amd64', 'libtest-deep-perl', 'libtest-differences-perl', 'libtest-exception-perl', 'libtest-file-perl', 'libtest-files-perl', 'libtest-most-perl', 'libtest-output-perl', 'libtest-simple-perl', 'libtest-warn-perl', 'libtext-csv-perl', 'libtext-csv-xs-perl', 'libtext-diff-perl', 'libtext-glob-perl', 'libtext-iconv-perl', 'libthai-data', 'libthai0:amd64', 'libtie-ixhash-perl', 'libtiff5:amd64', 'libtimedate-perl', 'libtinfo-dev:amd64', 'libtk8.6:amd64', 'libtree-dagnode-perl', 'libtry-tiny-perl', 'libtsan0:amd64', 'libtxc-dxtn-s2tc:amd64', 'libtype-tiny-perl', 'libtype-tiny-xs-perl', 'libubsan0:amd64', 'libunicode-map-perl', 'libunistring0:amd64', 'liburi-perl', 'libvariable-magic-perl', 'libwebp6:amd64', 'libwrap0:amd64', 'libwww-perl', 'libwww-robotrules-perl', 'libx11-6:amd64', 'libx11-data', 'libx11-protocol-perl', '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', 'libxcb1:amd64', 'libxcomposite1:amd64', 'libxcursor1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxdot4', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxinerama1:amd64', 'libxml-dom-perl', 'libxml-dom-xpath-perl', 'libxml-filter-buffertext-perl', 'libxml-libxml-perl', 'libxml-libxslt-perl', 'libxml-namespacesupport-perl', 'libxml-parser-perl', 'libxml-perl', 'libxml-regexp-perl', 'libxml-sax-base-perl', 'libxml-sax-expat-perl', 'libxml-sax-perl', 'libxml-sax-writer-perl', 'libxml-simple-perl', 'libxml-twig-perl', 'libxml-writer-perl', 'libxml-xpath-perl', 'libxml-xpathengine-perl', 'libxml2:amd64', 'libxmlrpc-lite-perl', 'libxmu6:amd64', 'libxmuu1:amd64', 'libxpm4:amd64', 'libxrandr2:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libxt6:amd64', 'libxtst6:amd64', 'libxv1:amd64', 'libxxf86dga1:amd64', 'libxxf86vm1:amd64', 'libyaml-0-2:amd64', 'libyaml-libyaml-perl', 'libyaml-perl', 'linux-libc-dev:amd64', 'littler', 'lsb-base', 'lynx', 'lynx-common', 'mafft', 'mailutils', 'mailutils-common', 'make', 'manpages', 'manpages-dev', 'maq', 'mcl', 'med-config', 'menu', 'mime-support', 'mummer', 'muscle', 'mustang', 'mysql-common', 'ncbi-blast+-', 'ncbi-blast+-legacy', 'ncbi-data', 'netbase', 'ocl-icd-libopencl1:amd64', 'openmpi-bin', 'openmpi-common', 'openssl', 'parallel', 'patch', 'perl', 'perl-doc', 'perl-modules-5.24', 'perl-openssl-defaults:amd64', 'perl-tk', 'phylip', 'phyml', 'pinentry-curses', 'pkg-config', 'poa', 'poppler-data', 'prank', 'primer3', 'probalign', 'probcons', 'procps', 'proda', 'psmisc', 'publicsuffix', 'python', 'python-minimal', 'python2.7', 'python2.7-minimal', 'r-base-core', 'r-base-dev', 'r-cran-assertthat', 'r-cran-boot', 'r-cran-class', 'r-cran-cluster', 'r-cran-codetools', 'r-cran-colorspace', 'r-cran-crayon', 'r-cran-dichromat', 'r-cran-digest', 'r-cran-foreign', 'r-cran-ggplot2', 'r-cran-gtable', 'r-cran-kernsmooth', '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-nnet', 'r-cran-pkgkitten', 'r-cran-plyr', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-reshape2', 'r-cran-rpart', 'r-cran-scales', 'r-cran-spatial', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-survival', 'r-cran-tibble', 'r-doc-html', 'r-recommended', 'rake', 'raxml', 'readline-common', 'rename', 'ruby', 'ruby-did-you-mean', 'ruby-minitest', 'ruby-net-telnet', 'ruby-power-assert', 'ruby-test-unit', 'ruby2.3', 'rubygems-integration', 'samtools', 'sgml-base', 'shared-mime-info', 'sim4', 'sysstat', 't-coffee', 'tcpd', 'tigr-glimmer', 'tm-align', 'tzdata', 'ucf', 'unzip', 'wise', 'wise-data', 'x11-common', 'x11-utils', 'x11-xserver-utils', 'xauth', 'xdg-user-dirs', 'xdg-utils', 'xml-core', 'xz-utils', 'zip', 'zlib1g-dev:amd64', 'roary'] 1m45.2s INFO: Running scripts post_remove 1m45.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/post_remove_exceptions'] 1m45.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/post_remove_exceptions'] 1m45.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'dpkg', '--purge', 'amap-align', 'apache2-bin', 'autotools-dev', 'bedtools', 'beignet-opencl-icd:amd64', 'binutils', 'bioperl', 'bioperl-run', 'blast2', 'blends-common', 'bowtie', 'build-essential', 'bwa', 'bzip2', 'bzip2-doc', 'ca-certificates', 'cd-hit', 'cdbs', 'clustalo', 'clustalw', 'cpp', 'cpp-6', 'cron', 'dbus', 'dialign', 'dialign-tx', 'dialign-tx-data', 'dirmngr', 'dpkg-dev', 'emboss', 'emboss-data', 'emboss-lib', 'exim4', 'exim4-base', 'exim4-config', 'exim4-daemon-light', 'exonerate', 'fakeroot', 'fasttree', 'file', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-droid-fallback', 'fonts-lato', 'fonts-liberation', 'fonts-noto-mono', 'fsa', 'g++', 'g++-6', 'gawk', 'gcc', 'gcc-6', 'gfortran', 'gfortran-6', 'ghostscript', 'gnupg', 'gnupg-agent', 'gnupg-l10n', 'graphviz', 'gsfonts', 'guile-2.0-libs:amd64', 'hmmer', 'hyphy-common', 'hyphy-mpi', 'icu-devtools', 'infernal', 'javascript-common', 'kalign', 'krb5-locales', 'libace-perl', 'libalgorithm-c3-perl', 'libalgorithm-diff-perl', 'libalgorithm-diff-xs-perl', 'libalgorithm-merge-perl', 'libalgorithm-munkres-perl', 'libann0', 'libapache-dbi-perl', 'libapache2-mod-perl2', 'libapache2-reload-perl', 'libapparmor1:amd64', 'libapr1:amd64', 'libaprutil1:amd64', 'libaprutil1-dbd-sqlite3:amd64', 'libaprutil1-ldap:amd64', 'libargtable2-0', 'libarray-compare-perl', 'libarray-utils-perl', 'libasan3:amd64', 'libassuan0:amd64', 'libatomic1:amd64', 'libauthen-sasl-perl', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libb-hooks-endofscope-perl', 'libbio-asn1-entrezgene-perl', 'libbio-perl-perl', 'libbio-perl-run-perl', 'libbit-vector-perl', 'libblas-common', 'libblas-dev', 'libblas3', 'libbsd-resource-perl', 'libbsd0:amd64', 'libbz2-dev:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcache-cache-perl', 'libcairo2:amd64', 'libcapture-tiny-perl', 'libcarp-clan-perl', 'libcc1-0:amd64', 'libcdt5', 'libcgi-fast-perl', 'libcgi-pm-perl', 'libcgraph6', 'libcilkrts5:amd64', 'libclass-c3-perl', 'libclass-c3-xs-perl', 'libclass-data-inheritable-perl', 'libclass-inspector-perl', 'libclass-load-perl', 'libclass-load-xs-perl', 'libclass-method-modifiers-perl', 'libclass-tiny-perl', 'libclass-xsaccessor-perl', 'libclone-perl', 'libconvert-binary-c-perl', 'libconvert-binhex-perl', 'libcrypt-rc4-perl', 'libcups2:amd64', 'libcupsfilters1:amd64', 'libcupsimage2:amd64', 'libcurl3:amd64', 'libcurl3-gnutls:amd64', 'libdata-optlist-perl', 'libdata-stag-perl', 'libdate-calc-perl', 'libdate-calc-xs-perl', 'libdate-manip-perl', 'libdatrie1:amd64', 'libdbd-mysql-perl', 'libdbd-pg-perl', 'libdbd-sqlite3-perl', 'libdbi-perl', 'libdbus-1-3:amd64', 'libdevel-caller-perl', 'libdevel-globaldestruction-perl', 'libdevel-lexalias-perl', 'libdevel-overloadinfo-perl', 'libdevel-partialdump-perl', 'libdevel-stacktrace-perl', 'libdevel-symdump-perl', 'libdigest-perl-md5-perl', 'libdist-checkconflicts-perl', 'libdivsufsort3:amd64', 'libdpkg-perl', 'libdrm-amdgpu1:amd64', 'libdrm-intel1:amd64', 'libdrm-nouveau2:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1:amd64', 'libemail-date-format-perl', 'libencode-locale-perl', 'libenv-path-perl', 'liberror-perl', 'libeval-closure-perl', 'libexception-class-perl', 'libexpat1:amd64', 'libexporter-tiny-perl', 'libfabric1', 'libfakeroot:amd64', 'libfcgi-perl', 'libffi6:amd64', 'libfile-basedir-perl', 'libfile-desktopentry-perl', 'libfile-fcntllock-perl', 'libfile-find-rule-perl', 'libfile-grep-perl', 'libfile-listing-perl', 'libfile-mimeinfo-perl', 'libfile-slurp-tiny-perl', 'libfile-slurper-perl', 'libfile-which-perl', 'libfindbin-libs-perl', 'libfont-afm-perl', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfreezethaw-perl', 'libfribidi0:amd64', 'libgc1c2:amd64', 'libgcc-6-dev:amd64', 'libgd-perl', 'libgd3:amd64', 'libgdbm3:amd64', 'libgfortran-6-dev:amd64', 'libgfortran3:amd64', 'libgl1-mesa-dri:amd64', 'libgl1-mesa-glx:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0:amd64', 'libglib2.0-data', 'libgmp10:amd64', 'libgnutls30:amd64', 'libgomp1:amd64', 'libgpm2:amd64', 'libgraph-perl', 'libgraph-readwrite-perl', 'libgraphite2-3:amd64', 'libgraphviz-perl', 'libgs9:amd64', 'libgs9-common', 'libgsasl7', 'libgssapi-krb5-2:amd64', 'libgts-0.7-5:amd64', 'libgts-bin', 'libgvc6', 'libgvpr2', 'libharfbuzz0b:amd64', 'libhmsbeagle1v5', 'libhogweed4:amd64', 'libhpdf-2.2.1', 'libhtml-form-perl', 'libhtml-format-perl', 'libhtml-parser-perl', 'libhtml-tableextract-perl', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhts1:amd64', 'libhttp-cookies-perl', 'libhttp-daemon-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libhwloc-plugins', 'libhwloc5:amd64', 'libibverbs1', 'libice6:amd64', 'libicu-dev', 'libicu57:amd64', 'libidn11:amd64', 'libidn2-0:amd64', 'libijs-0.35:amd64', 'libimport-into-perl', 'libio-all-perl', 'libio-html-perl', 'libio-pty-perl', 'libio-sessiondata-perl', 'libio-socket-ssl-perl', 'libio-string-perl', 'libio-stringy-perl', 'libipc-run-perl', 'libipc-shareable-perl', 'libipc-sharelite-perl', 'libipc-system-simple-perl', 'libisl15:amd64', 'libitm1:amd64', 'libjbig0:amd64', 'libjbig2dec0:amd64', 'libjcode-pm-perl', 'libjpeg-dev', 'libjpeg62-turbo:amd64', 'libjpeg62-turbo-dev:amd64', 'libjs-jquery', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libksba8:amd64', 'libkyotocabinet16v5:amd64', 'liblapack-dev', 'liblapack3', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'liblist-moreutils-perl', 'libllvm3.9:amd64', 'liblocale-gettext-perl', 'liblog-dispatch-perl', 'liblog-log4perl-perl', 'liblsan0:amd64', 'libltdl7:amd64', 'liblua5.2-0:amd64', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'liblzma-dev:amd64', 'liblzo2-2:amd64', 'libmagic-mgc', 'libmagic1:amd64', 'libmail-sendmail-perl', 'libmailtools-perl', 'libmailutils5:amd64', 'libmariadbclient18:amd64', 'libmath-derivative-perl', 'libmath-spline-perl', 'libmime-lite-perl', 'libmime-tools-perl', 'libmime-types-perl', 'libmldbm-perl', 'libmodule-implementation-perl', 'libmodule-runtime-conflicts-perl', 'libmodule-runtime-perl', 'libmoo-perl', 'libmoose-perl', 'libmpc3:amd64', 'libmpfr4:amd64', 'libmpx2:amd64', 'libmro-compat-perl', 'libnamespace-clean-perl', 'libncurses5:amd64', 'libncurses5-dev:amd64', 'libnet-dbus-perl', 'libnet-http-perl', 'libnet-smtp-ssl-perl', 'libnet-ssleay-perl', 'libnettle6:amd64', 'libnghttp2-14:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnpth0:amd64', 'libntlm0:amd64', 'libnuma1:amd64', 'libnumber-compare-perl', 'libole-storage-lite-perl', 'libopenjp2-7:amd64', 'libopenmpi2:amd64', 'libossp-uuid-perl', 'libossp-uuid16:amd64', 'libp11-kit0:amd64', 'libpackage-deprecationmanager-perl', 'libpackage-stash-perl', 'libpackage-stash-xs-perl', 'libpadwalker-perl', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libparams-classify-perl', 'libparams-util-perl', 'libparams-validate-perl', 'libparse-recdescent-perl', 'libparse-yapp-perl', 'libpathplan4', 'libpciaccess0:amd64', 'libpcre16-3:amd64', 'libpcre3-dev:amd64', 'libpcre32-3:amd64', 'libpcrecpp0v5:amd64', 'libperl5.24:amd64', 'libperlio-utf8-strict-perl', 'libpixman-1-0:amd64', 'libpng-dev:amd64', 'libpng-tools', 'libpng16-16:amd64', 'libpostscript-perl', 'libpq5:amd64', 'libprocps6:amd64', 'libpsl5:amd64', 'libpsm-infinipath1', 'libpython-stdlib:amd64', 'libpython2.7:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'librdmacm1', 'libreadline-dev:amd64', 'libreadline7:amd64', 'librole-tiny-perl', 'librtmp1:amd64', 'libruby2.3:amd64', 'libsasl2-2:amd64', 'libsasl2-modules:amd64', 'libsasl2-modules-db:amd64', 'libscalar-list-utils-perl', 'libsensors4:amd64', 'libset-scalar-perl', 'libsigsegv2:amd64', 'libsm6:amd64', 'libsoap-lite-perl', 'libsort-naturally-perl', 'libspiffy-perl', 'libspreadsheet-parseexcel-perl', 'libspreadsheet-writeexcel-perl', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.0.2:amd64', 'libssl1.1:amd64', 'libstatistics-descriptive-perl', 'libstdc++-6-dev:amd64', 'libstrictures-perl', 'libsub-exporter-perl', 'libsub-exporter-progressive-perl', 'libsub-identify-perl', 'libsub-install-perl', 'libsub-name-perl', 'libsub-uplevel-perl', 'libsvg-graph-perl', 'libsvg-perl', 'libsys-hostname-long-perl', 'libtask-weaken-perl', 'libtasn1-6:amd64', 'libtcl8.6:amd64', 'libtest-deep-perl', 'libtest-differences-perl', 'libtest-exception-perl', 'libtest-file-perl', 'libtest-files-perl', 'libtest-most-perl', 'libtest-output-perl', 'libtest-simple-perl', 'libtest-warn-perl', 'libtext-csv-perl', 'libtext-csv-xs-perl', 'libtext-diff-perl', 'libtext-glob-perl', 'libtext-iconv-perl', 'libthai-data', 'libthai0:amd64', 'libtie-ixhash-perl', 'libtiff5:amd64', 'libtimedate-perl', 'libtinfo-dev:amd64', 'libtk8.6:amd64', 'libtree-dagnode-perl', 'libtry-tiny-perl', 'libtsan0:amd64', 'libtxc-dxtn-s2tc:amd64', 'libtype-tiny-perl', 'libtype-tiny-xs-perl', 'libubsan0:amd64', 'libunicode-map-perl', 'libunistring0:amd64', 'liburi-perl', 'libvariable-magic-perl', 'libwebp6:amd64', 'libwrap0:amd64', 'libwww-perl', 'libwww-robotrules-perl', 'libx11-6:amd64', 'libx11-data', 'libx11-protocol-perl', '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', 'libxcb1:amd64', 'libxcomposite1:amd64', 'libxcursor1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxdot4', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxinerama1:amd64', 'libxml-dom-perl', 'libxml-dom-xpath-perl', 'libxml-filter-buffertext-perl', 'libxml-libxml-perl', 'libxml-libxslt-perl', 'libxml-namespacesupport-perl', 'libxml-parser-perl', 'libxml-perl', 'libxml-regexp-perl', 'libxml-sax-base-perl', 'libxml-sax-expat-perl', 'libxml-sax-perl', 'libxml-sax-writer-perl', 'libxml-simple-perl', 'libxml-twig-perl', 'libxml-writer-perl', 'libxml-xpath-perl', 'libxml-xpathengine-perl', 'libxml2:amd64', 'libxmlrpc-lite-perl', 'libxmu6:amd64', 'libxmuu1:amd64', 'libxpm4:amd64', 'libxrandr2:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libxt6:amd64', 'libxtst6:amd64', 'libxv1:amd64', 'libxxf86dga1:amd64', 'libxxf86vm1:amd64', 'libyaml-0-2:amd64', 'libyaml-libyaml-perl', 'libyaml-perl', 'linux-libc-dev:amd64', 'littler', 'lsb-base', 'lynx', 'lynx-common', 'mafft', 'mailutils', 'mailutils-common', 'make', 'manpages', 'manpages-dev', 'maq', 'mcl', 'med-config', 'menu', 'mime-support', 'mummer', 'muscle', 'mustang', 'mysql-common', 'ncbi-blast+', 'ncbi-blast+-legacy', 'ncbi-data', 'netbase', 'ocl-icd-libopencl1:amd64', 'openmpi-bin', 'openmpi-common', 'openssl', 'parallel', 'patch', 'perl', 'perl-doc', 'perl-modules-5.24', 'perl-openssl-defaults:amd64', 'perl-tk', 'phylip', 'phyml', 'pinentry-curses', 'pkg-config', 'poa', 'poppler-data', 'prank', 'primer3', 'probalign', 'probcons', 'procps', 'proda', 'psmisc', 'publicsuffix', 'python', 'python-minimal', 'python2.7', 'python2.7-minimal', 'r-base-core', 'r-base-dev', 'r-cran-assertthat', 'r-cran-boot', 'r-cran-class', 'r-cran-cluster', 'r-cran-codetools', 'r-cran-colorspace', 'r-cran-crayon', 'r-cran-dichromat', 'r-cran-digest', 'r-cran-foreign', 'r-cran-ggplot2', 'r-cran-gtable', 'r-cran-kernsmooth', '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-nnet', 'r-cran-pkgkitten', 'r-cran-plyr', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-reshape2', 'r-cran-rpart', 'r-cran-scales', 'r-cran-spatial', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-survival', 'r-cran-tibble', 'r-doc-html', 'r-recommended', 'rake', 'raxml', 'readline-common', 'rename', 'ruby', 'ruby-did-you-mean', 'ruby-minitest', 'ruby-net-telnet', 'ruby-power-assert', 'ruby-test-unit', 'ruby2.3', 'rubygems-integration', 'samtools', 'sgml-base', 'shared-mime-info', 'sim4', 'sysstat', 't-coffee', 'tcpd', 'tigr-glimmer', 'tm-align', 'tzdata', 'ucf', 'unzip', 'wise', 'wise-data', 'x11-common', 'x11-utils', 'x11-xserver-utils', 'xauth', 'xdg-user-dirs', 'xdg-utils', 'xml-core', 'xz-utils', 'zip', 'zlib1g-dev:amd64'] 1m48.2s DUMP: dpkg: warning: ignoring request to remove amap-align which isn't installed dpkg: warning: ignoring request to remove apache2-bin which isn't installed dpkg: warning: ignoring request to remove autotools-dev which isn't installed dpkg: warning: ignoring request to remove bedtools which isn't installed (Reading database ... 4682 files and directories currently installed.) Purging configuration files for beignet-opencl-icd:amd64 (1.3.0-4) ... dpkg: warning: ignoring request to remove binutils which isn't installed dpkg: warning: ignoring request to remove bioperl which isn't installed dpkg: warning: ignoring request to remove bioperl-run which isn't installed dpkg: warning: ignoring request to remove blast2 which isn't installed Purging configuration files for blends-common (0.6.96) ... dpkg: warning: ignoring request to remove bowtie which isn't installed dpkg: warning: ignoring request to remove build-essential which isn't installed dpkg: warning: ignoring request to remove bwa which isn't installed dpkg: warning: ignoring request to remove bzip2 which isn't installed dpkg: warning: ignoring request to remove bzip2-doc which isn't installed Purging configuration files for ca-certificates (20200601~deb9u1) ... Removing dangling symlinks from /etc/ssl/certs... done. dpkg: warning: ignoring request to remove cd-hit which isn't installed dpkg: warning: ignoring request to remove cdbs which isn't installed dpkg: warning: ignoring request to remove clustalo which isn't installed Purging configuration files for clustalw (2.1+lgpl-5) ... dpkg: warning: ignoring request to remove cpp which isn't installed dpkg: warning: ignoring request to remove cpp-6 which isn't installed Purging configuration files for cron (3.0pl1-128+deb9u1) ... Purging configuration files for dbus (1.10.32-0+deb9u1) ... rmdir: failed to remove '/var/run/dbus': No such file or directory dpkg: warning: ignoring request to remove dialign which isn't installed dpkg: warning: ignoring request to remove dialign-tx which isn't installed dpkg: warning: ignoring request to remove dialign-tx-data which isn't installed Purging configuration files for dirmngr (2.1.18-8~deb9u4) ... Purging configuration files for dpkg-dev (1.18.25) ... dpkg: warning: ignoring request to remove emboss which isn't installed dpkg: warning: ignoring request to remove emboss-data which isn't installed dpkg: warning: ignoring request to remove emboss-lib which isn't installed Purging configuration files for exim4 (4.89-2+deb9u7) ... Purging configuration files for exim4-base (4.89-2+deb9u7) ... Purging configuration files for exim4-config (4.89-2+deb9u7) ... dpkg-statoverride: warning: no override present Purging configuration files for exim4-daemon-light (4.89-2+deb9u7) ... dpkg: warning: ignoring request to remove exonerate which isn't installed dpkg: warning: ignoring request to remove fakeroot which isn't installed dpkg: warning: ignoring request to remove fasttree which isn't installed dpkg: warning: ignoring request to remove file which isn't installed Purging configuration files for fontconfig (2.11.0-6.7+b1) ... Purging configuration files for fontconfig-config (2.11.0-6.7) ... Purging configuration files for fonts-dejavu-core (2.37-1) ... Purging configuration files for fonts-droid-fallback (1:6.0.1r16-1.1) ... dpkg: warning: ignoring request to remove fonts-lato which isn't installed dpkg: warning: ignoring request to remove fonts-liberation which isn't installed Purging configuration files for fonts-noto-mono (20161116-1) ... dpkg: warning: ignoring request to remove fsa which isn't installed dpkg: warning: ignoring request to remove g++ which isn't installed dpkg: warning: ignoring request to remove g++-6 which isn't installed dpkg: warning: ignoring request to remove gawk which isn't installed dpkg: warning: ignoring request to remove gcc which isn't installed dpkg: warning: ignoring request to remove gcc-6 which isn't installed dpkg: warning: ignoring request to remove gfortran which isn't installed dpkg: warning: ignoring request to remove gfortran-6 which isn't installed dpkg: warning: ignoring request to remove ghostscript which isn't installed dpkg: warning: ignoring request to remove gnupg which isn't installed Purging configuration files for gnupg-agent (2.1.18-8~deb9u4) ... dpkg: warning: ignoring request to remove gnupg-l10n which isn't installed Purging configuration files for graphviz (2.38.0-17) ... Purging configuration files for gsfonts (1:8.11+urwcyr1.0.7~pre44-4.3) ... dpkg: warning: ignoring request to remove guile-2.0-libs which isn't installed dpkg: warning: ignoring request to remove hmmer which isn't installed dpkg: warning: ignoring request to remove hyphy-common which isn't installed dpkg: warning: ignoring request to remove hyphy-mpi which isn't installed dpkg: warning: ignoring request to remove icu-devtools which isn't installed dpkg: warning: ignoring request to remove infernal which isn't installed Purging configuration files for javascript-common (11) ... dpkg: warning: ignoring request to remove kalign which isn't installed dpkg: warning: ignoring request to remove krb5-locales which isn't installed dpkg: warning: ignoring request to remove libace-perl which isn't installed dpkg: warning: ignoring request to remove libalgorithm-c3-perl which isn't installed dpkg: warning: ignoring request to remove libalgorithm-diff-perl which isn't installed dpkg: warning: 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to remove libtk8.6 which isn't installed dpkg: warning: ignoring request to remove libtree-dagnode-perl which isn't installed dpkg: warning: ignoring request to remove libtry-tiny-perl which isn't installed dpkg: warning: ignoring request to remove libtsan0 which isn't installed dpkg: warning: ignoring request to remove libtxc-dxtn-s2tc which isn't installed dpkg: warning: ignoring request to remove libtype-tiny-perl which isn't installed dpkg: warning: ignoring request to remove libtype-tiny-xs-perl which isn't installed dpkg: warning: ignoring request to remove libubsan0 which isn't installed dpkg: warning: ignoring request to remove libunicode-map-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 libvariable-magic-perl which isn't installed dpkg: warning: ignoring request to remove libwebp6 which isn't installed Purging configuration files for libwrap0:amd64 (7.6.q-26) ... 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-protocol-perl which isn't installed dpkg: warning: ignoring request to remove libx11-xcb1 which isn't installed Purging configuration files for libxau6:amd64 (1:1.0.8-1) ... 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 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 libxdot4 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 libxml-dom-perl which isn't installed dpkg: warning: ignoring request to remove libxml-dom-xpath-perl which isn't installed dpkg: warning: ignoring request to remove libxml-filter-buffertext-perl which isn't installed dpkg: warning: ignoring request to remove libxml-libxml-perl which isn't installed dpkg: warning: ignoring request to remove libxml-libxslt-perl which isn't installed dpkg: warning: ignoring request to remove libxml-namespacesupport-perl which isn't installed dpkg: warning: ignoring request to remove libxml-parser-perl which isn't installed dpkg: warning: ignoring request to remove libxml-perl which isn't installed dpkg: warning: ignoring request to remove libxml-regexp-perl which isn't installed dpkg: warning: ignoring request to remove libxml-sax-base-perl which isn't installed dpkg: warning: ignoring request to remove libxml-sax-expat-perl which isn't installed Purging configuration files for libxml-sax-perl (0.99+dfsg-2) ... dpkg: warning: ignoring request to remove libxml-sax-writer-perl which isn't installed dpkg: warning: ignoring request to remove libxml-simple-perl which isn't installed dpkg: warning: ignoring request to remove libxml-twig-perl which isn't installed dpkg: warning: ignoring request to remove libxml-writer-perl which isn't installed dpkg: warning: ignoring request to remove libxml-xpath-perl which isn't installed dpkg: warning: ignoring request to remove libxml-xpathengine-perl which isn't installed dpkg: warning: ignoring request to remove libxml2 which isn't installed dpkg: warning: ignoring request to remove libxmlrpc-lite-perl 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 libxslt1.1 which isn't installed Purging configuration files for libxss1:amd64 (1:1.2.2-1) ... 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 libyaml-0-2 which isn't installed dpkg: warning: ignoring request to remove libyaml-libyaml-perl which isn't installed dpkg: warning: ignoring request to remove libyaml-perl which isn't installed dpkg: warning: ignoring request to remove linux-libc-dev 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 lynx (2.8.9dev11-1) ... Purging configuration files for lynx-common (2.8.9dev11-1) ... dpkg: warning: ignoring request to remove mafft which isn't installed dpkg: warning: ignoring request to remove mailutils which isn't installed dpkg: warning: ignoring request to remove mailutils-common which isn't installed dpkg: warning: ignoring request to remove make which isn't installed dpkg: warning: ignoring request to remove manpages which isn't installed dpkg: warning: ignoring request to remove manpages-dev which isn't installed dpkg: warning: ignoring request to remove maq which isn't installed dpkg: warning: ignoring request to remove mcl which isn't installed Purging configuration files for med-config (3.0.1) ... Purging configuration files for menu (2.1.47+b1) ... Purging configuration files for mime-support (3.60) ... dpkg: warning: ignoring request to remove mummer which isn't installed dpkg: warning: ignoring request to remove muscle which isn't installed dpkg: warning: ignoring request to remove mustang which isn't installed Purging configuration files for mysql-common (5.8+1.0.2) ... dpkg: warning: ignoring request to remove ncbi-blast+ which isn't installed dpkg: warning: ignoring request to remove ncbi-blast+-legacy which isn't installed Purging configuration files for ncbi-data (6.1.20170106+dfsg1-0+deb9u1) ... Purging configuration files for netbase (5.4) ... dpkg: warning: ignoring request to remove ocl-icd-libopencl1 which isn't installed Purging configuration files for openmpi-bin (2.0.2-2) ... dpkg: warning: ignoring request to remove openmpi-common which isn't installed Purging configuration files for openssl (1.1.0l-1~deb9u1) ... Purging configuration files for parallel (20161222-1) ... dpkg: warning: ignoring request to remove patch which isn't installed Purging configuration files for perl (5.24.1-3+deb9u7) ... Purging configuration files for perl-doc (5.24.1-3+deb9u7) ... dpkg: warning: ignoring request to remove perl-modules-5.24 which isn't installed dpkg: warning: ignoring request to remove perl-openssl-defaults which isn't installed dpkg: warning: ignoring request to remove perl-tk which isn't installed dpkg: warning: ignoring request to remove phylip which isn't installed dpkg: warning: ignoring request to remove phyml which isn't installed dpkg: warning: ignoring request to remove pinentry-curses which isn't installed Purging configuration files for pkg-config (0.29-4+b1) ... dpkg: warning: ignoring request to remove poa which isn't installed Purging configuration files for poppler-data (0.4.7-8) ... dpkg: warning: ignoring request to remove prank which isn't installed Purging configuration files for primer3 (2.3.7-3) ... dpkg: warning: ignoring request to remove probalign which isn't installed dpkg: warning: ignoring request to remove probcons which isn't installed Purging configuration files for procps (2:3.3.12-3+deb9u1) ... dpkg: warning: ignoring request to remove proda which isn't installed Purging configuration files for psmisc (22.21-2.1+b2) ... dpkg: warning: ignoring request to remove publicsuffix which isn't installed Purging configuration files for python (2.7.13-2) ... dpkg: warning: ignoring request to remove python-minimal which isn't installed dpkg: warning: ignoring request to remove python2.7 which isn't installed Purging configuration files for python2.7-minimal (2.7.13-2+deb9u3) ... Purging configuration files for r-base-core (3.3.3-1) ... dpkg: warning: ignoring request to remove r-base-dev 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-boot which isn't installed dpkg: warning: ignoring request to remove r-cran-class 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-codetools 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-foreign 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-gtable which isn't installed dpkg: warning: ignoring request to remove r-cran-kernsmooth 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-nnet 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-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-rpart 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-spatial 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-survival which isn't installed dpkg: warning: ignoring request to remove r-cran-tibble which isn't installed dpkg: warning: ignoring request to remove r-doc-html which isn't installed dpkg: warning: ignoring request to remove r-recommended which isn't installed dpkg: warning: ignoring request to remove rake which isn't installed dpkg: warning: ignoring request to remove raxml which isn't installed Purging configuration files for readline-common (7.0-3) ... dpkg: warning: ignoring request to remove rename which isn't installed dpkg: warning: ignoring request to remove ruby which isn't installed dpkg: warning: ignoring request to remove ruby-did-you-mean which isn't installed dpkg: warning: ignoring request to remove ruby-minitest which isn't installed dpkg: warning: ignoring request to remove ruby-net-telnet which isn't installed dpkg: warning: ignoring request to remove ruby-power-assert which isn't installed dpkg: warning: ignoring request to remove ruby-test-unit which isn't installed dpkg: warning: ignoring request to remove ruby2.3 which isn't installed dpkg: warning: ignoring request to remove rubygems-integration which isn't installed dpkg: warning: ignoring request to remove samtools which isn't installed Purging configuration files for sgml-base (1.29) ... Purging configuration files for shared-mime-info (1.8-1+deb9u1) ... dpkg: warning: ignoring request to remove sim4 which isn't installed Purging configuration files for sysstat (11.4.3-2) ... dpkg: warning: ignoring request to remove t-coffee which isn't installed dpkg: warning: ignoring request to remove tcpd which isn't installed dpkg: warning: ignoring request to remove tigr-glimmer which isn't installed dpkg: warning: ignoring request to remove tm-align which isn't installed Purging configuration files for tzdata (2020a-0+deb9u1) ... Purging configuration files for ucf (3.0036) ... Purging configuration files for unzip (6.0-21+deb9u2) ... dpkg: warning: ignoring request to remove wise which isn't installed dpkg: warning: ignoring request to remove wise-data which isn't installed Purging configuration files for x11-common (1:7.7+19) ... Purging configuration files for x11-utils (7.7+3+b1) ... Purging configuration files for x11-xserver-utils (7.7+7+b1) ... dpkg: warning: ignoring request to remove xauth which isn't installed Purging configuration files for xdg-user-dirs (0.15-2+b1) ... dpkg: warning: ignoring request to remove xdg-utils which isn't installed Purging configuration files for xml-core (0.17) ... dpkg: warning: ignoring request to remove xz-utils which isn't installed dpkg: warning: ignoring request to remove zip which isn't installed dpkg: warning: ignoring request to remove zlib1g-dev which isn't installed 1m48.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'dpkg', '--purge', 'amap-align', 'apache2-bin', 'autotools-dev', 'bedtools', 'beignet-opencl-icd:amd64', 'binutils', 'bioperl', 'bioperl-run', 'blast2', 'blends-common', 'bowtie', 'build-essential', 'bwa', 'bzip2', 'bzip2-doc', 'ca-certificates', 'cd-hit', 'cdbs', 'clustalo', 'clustalw', 'cpp', 'cpp-6', 'cron', 'dbus', 'dialign', 'dialign-tx', 'dialign-tx-data', 'dirmngr', 'dpkg-dev', 'emboss', 'emboss-data', 'emboss-lib', 'exim4', 'exim4-base', 'exim4-config', 'exim4-daemon-light', 'exonerate', 'fakeroot', 'fasttree', 'file', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-droid-fallback', 'fonts-lato', 'fonts-liberation', 'fonts-noto-mono', 'fsa', 'g++', 'g++-6', 'gawk', 'gcc', 'gcc-6', 'gfortran', 'gfortran-6', 'ghostscript', 'gnupg', 'gnupg-agent', 'gnupg-l10n', 'graphviz', 'gsfonts', 'guile-2.0-libs:amd64', 'hmmer', 'hyphy-common', 'hyphy-mpi', 'icu-devtools', 'infernal', 'javascript-common', 'kalign', 'krb5-locales', 'libace-perl', 'libalgorithm-c3-perl', 'libalgorithm-diff-perl', 'libalgorithm-diff-xs-perl', 'libalgorithm-merge-perl', 'libalgorithm-munkres-perl', 'libann0', 'libapache-dbi-perl', 'libapache2-mod-perl2', 'libapache2-reload-perl', 'libapparmor1:amd64', 'libapr1:amd64', 'libaprutil1:amd64', 'libaprutil1-dbd-sqlite3:amd64', 'libaprutil1-ldap:amd64', 'libargtable2-0', 'libarray-compare-perl', 'libarray-utils-perl', 'libasan3:amd64', 'libassuan0:amd64', 'libatomic1:amd64', 'libauthen-sasl-perl', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libb-hooks-endofscope-perl', 'libbio-asn1-entrezgene-perl', 'libbio-perl-perl', 'libbio-perl-run-perl', 'libbit-vector-perl', 'libblas-common', 'libblas-dev', 'libblas3', 'libbsd-resource-perl', 'libbsd0:amd64', 'libbz2-dev:amd64', 'libc-dev-bin', 'libc6-dev:amd64', 'libcache-cache-perl', 'libcairo2:amd64', 'libcapture-tiny-perl', 'libcarp-clan-perl', 'libcc1-0:amd64', 'libcdt5', 'libcgi-fast-perl', 'libcgi-pm-perl', 'libcgraph6', 'libcilkrts5:amd64', 'libclass-c3-perl', 'libclass-c3-xs-perl', 'libclass-data-inheritable-perl', 'libclass-inspector-perl', 'libclass-load-perl', 'libclass-load-xs-perl', 'libclass-method-modifiers-perl', 'libclass-tiny-perl', 'libclass-xsaccessor-perl', 'libclone-perl', 'libconvert-binary-c-perl', 'libconvert-binhex-perl', 'libcrypt-rc4-perl', 'libcups2:amd64', 'libcupsfilters1:amd64', 'libcupsimage2:amd64', 'libcurl3:amd64', 'libcurl3-gnutls:amd64', 'libdata-optlist-perl', 'libdata-stag-perl', 'libdate-calc-perl', 'libdate-calc-xs-perl', 'libdate-manip-perl', 'libdatrie1:amd64', 'libdbd-mysql-perl', 'libdbd-pg-perl', 'libdbd-sqlite3-perl', 'libdbi-perl', 'libdbus-1-3:amd64', 'libdevel-caller-perl', 'libdevel-globaldestruction-perl', 'libdevel-lexalias-perl', 'libdevel-overloadinfo-perl', 'libdevel-partialdump-perl', 'libdevel-stacktrace-perl', 'libdevel-symdump-perl', 'libdigest-perl-md5-perl', 'libdist-checkconflicts-perl', 'libdivsufsort3:amd64', 'libdpkg-perl', 'libdrm-amdgpu1:amd64', 'libdrm-intel1:amd64', 'libdrm-nouveau2:amd64', 'libdrm-radeon1:amd64', 'libdrm2:amd64', 'libedit2:amd64', 'libelf1:amd64', 'libemail-date-format-perl', 'libencode-locale-perl', 'libenv-path-perl', 'liberror-perl', 'libeval-closure-perl', 'libexception-class-perl', 'libexpat1:amd64', 'libexporter-tiny-perl', 'libfabric1', 'libfakeroot:amd64', 'libfcgi-perl', 'libffi6:amd64', 'libfile-basedir-perl', 'libfile-desktopentry-perl', 'libfile-fcntllock-perl', 'libfile-find-rule-perl', 'libfile-grep-perl', 'libfile-listing-perl', 'libfile-mimeinfo-perl', 'libfile-slurp-tiny-perl', 'libfile-slurper-perl', 'libfile-which-perl', 'libfindbin-libs-perl', 'libfont-afm-perl', 'libfontconfig1:amd64', 'libfontenc1:amd64', 'libfreetype6:amd64', 'libfreezethaw-perl', 'libfribidi0:amd64', 'libgc1c2:amd64', 'libgcc-6-dev:amd64', 'libgd-perl', 'libgd3:amd64', 'libgdbm3:amd64', 'libgfortran-6-dev:amd64', 'libgfortran3:amd64', 'libgl1-mesa-dri:amd64', 'libgl1-mesa-glx:amd64', 'libglapi-mesa:amd64', 'libglib2.0-0:amd64', 'libglib2.0-data', 'libgmp10:amd64', 'libgnutls30:amd64', 'libgomp1:amd64', 'libgpm2:amd64', 'libgraph-perl', 'libgraph-readwrite-perl', 'libgraphite2-3:amd64', 'libgraphviz-perl', 'libgs9:amd64', 'libgs9-common', 'libgsasl7', 'libgssapi-krb5-2:amd64', 'libgts-0.7-5:amd64', 'libgts-bin', 'libgvc6', 'libgvpr2', 'libharfbuzz0b:amd64', 'libhmsbeagle1v5', 'libhogweed4:amd64', 'libhpdf-2.2.1', 'libhtml-form-perl', 'libhtml-format-perl', 'libhtml-parser-perl', 'libhtml-tableextract-perl', 'libhtml-tagset-perl', 'libhtml-tree-perl', 'libhts1:amd64', 'libhttp-cookies-perl', 'libhttp-daemon-perl', 'libhttp-date-perl', 'libhttp-message-perl', 'libhttp-negotiate-perl', 'libhwloc-plugins', 'libhwloc5:amd64', 'libibverbs1', 'libice6:amd64', 'libicu-dev', 'libicu57:amd64', 'libidn11:amd64', 'libidn2-0:amd64', 'libijs-0.35:amd64', 'libimport-into-perl', 'libio-all-perl', 'libio-html-perl', 'libio-pty-perl', 'libio-sessiondata-perl', 'libio-socket-ssl-perl', 'libio-string-perl', 'libio-stringy-perl', 'libipc-run-perl', 'libipc-shareable-perl', 'libipc-sharelite-perl', 'libipc-system-simple-perl', 'libisl15:amd64', 'libitm1:amd64', 'libjbig0:amd64', 'libjbig2dec0:amd64', 'libjcode-pm-perl', 'libjpeg-dev', 'libjpeg62-turbo:amd64', 'libjpeg62-turbo-dev:amd64', 'libjs-jquery', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'libksba8:amd64', 'libkyotocabinet16v5:amd64', 'liblapack-dev', 'liblapack3', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'liblist-moreutils-perl', 'libllvm3.9:amd64', 'liblocale-gettext-perl', 'liblog-dispatch-perl', 'liblog-log4perl-perl', 'liblsan0:amd64', 'libltdl7:amd64', 'liblua5.2-0:amd64', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'liblzma-dev:amd64', 'liblzo2-2:amd64', 'libmagic-mgc', 'libmagic1:amd64', 'libmail-sendmail-perl', 'libmailtools-perl', 'libmailutils5:amd64', 'libmariadbclient18:amd64', 'libmath-derivative-perl', 'libmath-spline-perl', 'libmime-lite-perl', 'libmime-tools-perl', 'libmime-types-perl', 'libmldbm-perl', 'libmodule-implementation-perl', 'libmodule-runtime-conflicts-perl', 'libmodule-runtime-perl', 'libmoo-perl', 'libmoose-perl', 'libmpc3:amd64', 'libmpfr4:amd64', 'libmpx2:amd64', 'libmro-compat-perl', 'libnamespace-clean-perl', 'libncurses5:amd64', 'libncurses5-dev:amd64', 'libnet-dbus-perl', 'libnet-http-perl', 'libnet-smtp-ssl-perl', 'libnet-ssleay-perl', 'libnettle6:amd64', 'libnghttp2-14:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnpth0:amd64', 'libntlm0:amd64', 'libnuma1:amd64', 'libnumber-compare-perl', 'libole-storage-lite-perl', 'libopenjp2-7:amd64', 'libopenmpi2:amd64', 'libossp-uuid-perl', 'libossp-uuid16:amd64', 'libp11-kit0:amd64', 'libpackage-deprecationmanager-perl', 'libpackage-stash-perl', 'libpackage-stash-xs-perl', 'libpadwalker-perl', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libparams-classify-perl', 'libparams-util-perl', 'libparams-validate-perl', 'libparse-recdescent-perl', 'libparse-yapp-perl', 'libpathplan4', 'libpciaccess0:amd64', 'libpcre16-3:amd64', 'libpcre3-dev:amd64', 'libpcre32-3:amd64', 'libpcrecpp0v5:amd64', 'libperl5.24:amd64', 'libperlio-utf8-strict-perl', 'libpixman-1-0:amd64', 'libpng-dev:amd64', 'libpng-tools', 'libpng16-16:amd64', 'libpostscript-perl', 'libpq5:amd64', 'libprocps6:amd64', 'libpsl5:amd64', 'libpsm-infinipath1', 'libpython-stdlib:amd64', 'libpython2.7:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'librdmacm1', 'libreadline-dev:amd64', 'libreadline7:amd64', 'librole-tiny-perl', 'librtmp1:amd64', 'libruby2.3:amd64', 'libsasl2-2:amd64', 'libsasl2-modules:amd64', 'libsasl2-modules-db:amd64', 'libscalar-list-utils-perl', 'libsensors4:amd64', 'libset-scalar-perl', 'libsigsegv2:amd64', 'libsm6:amd64', 'libsoap-lite-perl', 'libsort-naturally-perl', 'libspiffy-perl', 'libspreadsheet-parseexcel-perl', 'libspreadsheet-writeexcel-perl', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.0.2:amd64', 'libssl1.1:amd64', 'libstatistics-descriptive-perl', 'libstdc++-6-dev:amd64', 'libstrictures-perl', 'libsub-exporter-perl', 'libsub-exporter-progressive-perl', 'libsub-identify-perl', 'libsub-install-perl', 'libsub-name-perl', 'libsub-uplevel-perl', 'libsvg-graph-perl', 'libsvg-perl', 'libsys-hostname-long-perl', 'libtask-weaken-perl', 'libtasn1-6:amd64', 'libtcl8.6:amd64', 'libtest-deep-perl', 'libtest-differences-perl', 'libtest-exception-perl', 'libtest-file-perl', 'libtest-files-perl', 'libtest-most-perl', 'libtest-output-perl', 'libtest-simple-perl', 'libtest-warn-perl', 'libtext-csv-perl', 'libtext-csv-xs-perl', 'libtext-diff-perl', 'libtext-glob-perl', 'libtext-iconv-perl', 'libthai-data', 'libthai0:amd64', 'libtie-ixhash-perl', 'libtiff5:amd64', 'libtimedate-perl', 'libtinfo-dev:amd64', 'libtk8.6:amd64', 'libtree-dagnode-perl', 'libtry-tiny-perl', 'libtsan0:amd64', 'libtxc-dxtn-s2tc:amd64', 'libtype-tiny-perl', 'libtype-tiny-xs-perl', 'libubsan0:amd64', 'libunicode-map-perl', 'libunistring0:amd64', 'liburi-perl', 'libvariable-magic-perl', 'libwebp6:amd64', 'libwrap0:amd64', 'libwww-perl', 'libwww-robotrules-perl', 'libx11-6:amd64', 'libx11-data', 'libx11-protocol-perl', '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', 'libxcb1:amd64', 'libxcomposite1:amd64', 'libxcursor1:amd64', 'libxdamage1:amd64', 'libxdmcp6:amd64', 'libxdot4', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2:amd64', 'libxi6:amd64', 'libxinerama1:amd64', 'libxml-dom-perl', 'libxml-dom-xpath-perl', 'libxml-filter-buffertext-perl', 'libxml-libxml-perl', 'libxml-libxslt-perl', 'libxml-namespacesupport-perl', 'libxml-parser-perl', 'libxml-perl', 'libxml-regexp-perl', 'libxml-sax-base-perl', 'libxml-sax-expat-perl', 'libxml-sax-perl', 'libxml-sax-writer-perl', 'libxml-simple-perl', 'libxml-twig-perl', 'libxml-writer-perl', 'libxml-xpath-perl', 'libxml-xpathengine-perl', 'libxml2:amd64', 'libxmlrpc-lite-perl', 'libxmu6:amd64', 'libxmuu1:amd64', 'libxpm4:amd64', 'libxrandr2:amd64', 'libxrender1:amd64', 'libxshmfence1:amd64', 'libxslt1.1:amd64', 'libxss1:amd64', 'libxt6:amd64', 'libxtst6:amd64', 'libxv1:amd64', 'libxxf86dga1:amd64', 'libxxf86vm1:amd64', 'libyaml-0-2:amd64', 'libyaml-libyaml-perl', 'libyaml-perl', 'linux-libc-dev:amd64', 'littler', 'lsb-base', 'lynx', 'lynx-common', 'mafft', 'mailutils', 'mailutils-common', 'make', 'manpages', 'manpages-dev', 'maq', 'mcl', 'med-config', 'menu', 'mime-support', 'mummer', 'muscle', 'mustang', 'mysql-common', 'ncbi-blast+', 'ncbi-blast+-legacy', 'ncbi-data', 'netbase', 'ocl-icd-libopencl1:amd64', 'openmpi-bin', 'openmpi-common', 'openssl', 'parallel', 'patch', 'perl', 'perl-doc', 'perl-modules-5.24', 'perl-openssl-defaults:amd64', 'perl-tk', 'phylip', 'phyml', 'pinentry-curses', 'pkg-config', 'poa', 'poppler-data', 'prank', 'primer3', 'probalign', 'probcons', 'procps', 'proda', 'psmisc', 'publicsuffix', 'python', 'python-minimal', 'python2.7', 'python2.7-minimal', 'r-base-core', 'r-base-dev', 'r-cran-assertthat', 'r-cran-boot', 'r-cran-class', 'r-cran-cluster', 'r-cran-codetools', 'r-cran-colorspace', 'r-cran-crayon', 'r-cran-dichromat', 'r-cran-digest', 'r-cran-foreign', 'r-cran-ggplot2', 'r-cran-gtable', 'r-cran-kernsmooth', '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-nnet', 'r-cran-pkgkitten', 'r-cran-plyr', 'r-cran-rcolorbrewer', 'r-cran-rcpp', 'r-cran-reshape2', 'r-cran-rpart', 'r-cran-scales', 'r-cran-spatial', 'r-cran-stringi', 'r-cran-stringr', 'r-cran-survival', 'r-cran-tibble', 'r-doc-html', 'r-recommended', 'rake', 'raxml', 'readline-common', 'rename', 'ruby', 'ruby-did-you-mean', 'ruby-minitest', 'ruby-net-telnet', 'ruby-power-assert', 'ruby-test-unit', 'ruby2.3', 'rubygems-integration', 'samtools', 'sgml-base', 'shared-mime-info', 'sim4', 'sysstat', 't-coffee', 'tcpd', 'tigr-glimmer', 'tm-align', 'tzdata', 'ucf', 'unzip', 'wise', 'wise-data', 'x11-common', 'x11-utils', 'x11-xserver-utils', 'xauth', 'xdg-user-dirs', 'xdg-utils', 'xml-core', 'xz-utils', 'zip', 'zlib1g-dev:amd64'] 1m48.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'dpkg', '--purge', 'roary'] 1m48.2s DUMP: dpkg: warning: ignoring request to remove roary which isn't installed 1m48.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'dpkg', '--purge', 'roary'] 1m48.2s INFO: Running scripts post_purge 1m48.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/post_purge_exceptions'] 1m48.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/post_purge_exceptions'] 1m48.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'dpkg', '--purge', '--pending'] 1m48.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'dpkg', '--purge', '--pending'] 1m48.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'dpkg', '--remove', '--pending'] 1m48.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'dpkg', '--remove', '--pending'] 1m48.3s INFO: Running scripts post_test 1m48.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/post_test_exceptions'] 1m48.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'tmp/scripts/post_test_exceptions'] 1m48.3s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny'] 1m48.6s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny'] 1m49.2s DEBUG: No broken symlinks as far as we can find. 1m49.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'dpkg-divert', '--list'] 1m49.3s DUMP: local diversion of /bin/sync to /bin/sync.distrib diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 1m49.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'dpkg-divert', '--list'] 1m49.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'apt-get', 'clean'] 1m49.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny', 'apt-get', 'clean'] 1m49.3s DEBUG: Recording chroot state 1m49.7s INFO: PASS: Installation and purging test. 1m49.9s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny/dev/shm'] 1m50.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny/dev/shm'] 1m50.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny/dev/console'] 1m50.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny/dev/console'] 1m50.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny/dev/ptmx'] 1m50.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny/dev/ptmx'] 1m50.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny/dev/pts'] 1m50.0s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny/dev/pts'] 1m50.0s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny/proc'] 1m50.1s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny/proc'] 1m50.1s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny'] 1m50.2s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmpbtuj4qny'] 1m50.2s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmpbtuj4qny 1m50.2s INFO: PASS: All tests. 1m50.2s INFO: piuparts run ends. ret=0 End: 2023-02-21 00:45:33 GMT