Start: 2023-01-31 19:44:58 GMT Package: gbrowse Version: 2.56+dfsg-2 Installed-Size: 7015 Maintainer: Debian Med Packaging Team Architecture: all Depends: perl, apache2 (>= 2.4) | httpd-cgi, bioperl, libbio-graphics-perl (>= 2.31), libbio-coordinate-perl, libcgi-session-perl, libgd-gd2-noxpm-perl | libgd-gd2-perl, libio-string-perl, libjson-perl, libstatistics-descriptive-perl, libwww-perl, libhttp-daemon-perl, libterm-readkey-perl, sqlite3, libdbd-sqlite3-perl, libjs-prototype, libjs-scriptaculous, libvm-ec2-perl, lsb-base (>= 3.0-6) Recommends: apache2 (>= 2.4.6-4~) | httpd Suggests: gbrowse-data, gbrowse-calign, libfile-nfslock-perl Description: GMOD Generic Genome Browser Homepage: http://www.gbrowse.org/ Description-md5: 0aa2912bfc190ad55fe33a0ecfc2aabe Tag: field::biology, field::biology:bioinformatics, implemented-in::perl, interface::web, role::program, use::analysing, use::viewing, web::application, web::cgi Section: science Priority: optional Filename: pool/main/g/gbrowse/gbrowse_2.56+dfsg-2_all.deb Size: 2373492 MD5sum: a813d344ffc1119a68e1863da9f56ad9 SHA256: 286a0302c0219a68597d42ade3d50b505ae3c51307d5a654426618539a1c4525 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 gbrowse=2.56+dfsg-2 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: To quickly glance what went wrong, scroll down to the bottom of this logfile. 0m0.0s INFO: FAQ available at https://wiki.debian.org/piuparts/FAQ 0m0.0s INFO: The FAQ also explains how to contact us in case you think piuparts is wrong. 0m0.0s INFO: ------------------------------------------------------------------------------ 0m0.0s INFO: piuparts version 1.1.5 starting up. 0m0.0s INFO: Command line arguments: /srv/piuparts.debian.org/sbin/piuparts --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 gbrowse=2.56+dfsg-2 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/tmppkudj_pn 0m0.0s DEBUG: Unpacking /srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz into /srv/piuparts.debian.org/tmp/tmppkudj_pn 0m0.0s DEBUG: Starting command: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', '-zxf', '/srv/piuparts.debian.org/slave/basetgz/stretch_amd64.tar.gz'] 0m1.2s DEBUG: Command ok: ['tar', '-C', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', '-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/tmppkudj_pn/proc'] 0m1.2s DEBUG: Command ok: ['mount', '-t', 'proc', 'proc', '/srv/piuparts.debian.org/tmp/tmppkudj_pn/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/tmppkudj_pn/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/tmppkudj_pn/dev/pts'] 0m1.2s DEBUG: Starting command: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmppkudj_pn/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmppkudj_pn/dev/ptmx'] 0m1.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/srv/piuparts.debian.org/tmp/tmppkudj_pn/dev/pts/ptmx', '/srv/piuparts.debian.org/tmp/tmppkudj_pn/dev/ptmx'] 0m1.3s DEBUG: Starting command: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmppkudj_pn/dev/console'] 0m1.3s DEBUG: Command ok: ['mount', '-o', 'bind', '/dev/pts/2', '/srv/piuparts.debian.org/tmp/tmppkudj_pn/dev/console'] 0m1.3s DEBUG: Starting command: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmppkudj_pn/dev/shm'] 0m1.3s DEBUG: Command ok: ['mount', '-t', 'tmpfs', '-o', 'size=65536k', 'tmpfs', '/srv/piuparts.debian.org/tmp/tmppkudj_pn/dev/shm'] 0m1.3s DEBUG: sources.list: deb http://deb.debian.org/debian/ stretch main 0m1.3s DEBUG: Created policy-rc.d and chmodded it. 0m1.3s DEBUG: Created resolv.conf. 0m1.3s DEBUG: Copying scriptsdir /etc/piuparts/scripts to /srv/piuparts.debian.org/tmp/tmppkudj_pn/tmp/scripts/ 0m1.3s INFO: Running scripts post_chroot_unpack 0m1.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/post_chroot_unpack_allow_unauthenticated'] 0m1.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'apt-get', 'update'] 0m1.9s DUMP: Ign:1 http://deb.debian.org/debian stretch InRelease Hit:2 http://deb.debian.org/debian stretch Release Reading package lists... 0m1.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'apt-get', 'update'] 0m1.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'apt-get', '-yf', 'dist-upgrade'] 0m2.3s DUMP: Reading package lists... Building dependency tree... Calculating upgrade... 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 0m2.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'apt-get', '-yf', 'dist-upgrade'] 0m2.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.9s DUMP: 660e5103244a20b75ca08c3f8741e16e - 0m2.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'sh', '-c', 'apt-cache dumpavail | md5sum'] 0m2.9s INFO: Running scripts post_setup 0m2.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/post_setup_dummy_users'] 0m4.0s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/post_setup_dummy_users'] 0m4.0s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/post_setup_forbid_home'] 0m4.1s DUMP: Disabling /home Adding 'local diversion of /home to /home.distrib' 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/post_setup_forbid_home'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.1s DUMP: Enabling dpkg --force-unsafe-io. Adding 'local diversion of /bin/sync to /bin/sync.distrib' '/bin/sync' -> 'true' 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/post_setup_force-unsafe-io'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/post_setup_minimize'] 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/post_setup_minimize'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/post_setup_squeeze-backports'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/post_setup_zz_backports'] 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/post_setup_zz_backports'] 0m4.1s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'apt-get', 'clean'] 0m4.1s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'apt-get', 'clean'] 0m4.1s DEBUG: Recording chroot state 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.5s 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 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'dpkg-divert', '--list'] 0m4.5s 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 0m4.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'dpkg-divert', '--list'] 0m4.5s INFO: Running scripts is_testable 0m4.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/is_testable_uninstallable'] 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/is_testable_uninstallable'] 0m4.6s INFO: apt-cache does not know about any of the requested packages 0m4.6s INFO: Running scripts pre_test 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/pre_test_exceptions'] 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/pre_test_exceptions'] 0m4.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/pre_test_root_password'] 0m4.6s DUMP: Enter new UNIX password: Retype new UNIX password: passwd: password updated successfully 0m4.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/pre_test_root_password'] 0m4.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppkudj_pn'] 0m4.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppkudj_pn'] 0m5.2s DEBUG: No broken symlinks as far as we can find. 0m5.2s INFO: Running scripts pre_install 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/pre_install_database-server'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/pre_install_database-server'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/pre_install_exceptions'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/pre_install_exceptions'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/pre_install_extras'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/pre_install_extras'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/pre_install_foreign_architecture'] 0m5.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/pre_install_foreign_architecture_i386'] 0m5.2s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppkudj_pn'] 0m5.5s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppkudj_pn'] 0m5.7s DEBUG: No broken symlinks as far as we can find. 0m5.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'apt-cache', 'policy'] 0m6.3s 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: 0m6.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'apt-cache', 'policy'] 0m6.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'apt-cache', 'policy', 'gbrowse'] 0m6.4s DUMP: gbrowse: Installed: (none) Candidate: 2.56+dfsg-2 Version table: 2.56+dfsg-2 500 500 http://deb.debian.org/debian stretch/main amd64 Packages 0m6.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'apt-cache', 'policy', 'gbrowse'] 0m6.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'apt-get', '-y', 'install', 'gbrowse=2.56+dfsg-2'] 0m53.9s DUMP: Reading package lists... Building dependency tree... The following additional packages will be installed: amap-align apache2 apache2-bin apache2-data apache2-utils bedtools beignet-opencl-icd bioperl bioperl-run blast2 blends-common bowtie bwa bzip2 ca-certificates clustalo clustalw dbus dialign dialign-tx dialign-tx-data emboss emboss-data emboss-lib exonerate file fontconfig fontconfig-config fonts-dejavu-core fonts-droid-fallback fonts-lato fonts-liberation fonts-noto-mono fsa gawk ghostscript graphviz gsfonts hmmer hyphy-common hyphy-mpi infernal javascript-common kalign krb5-locales libace-perl libalgorithm-diff-perl libalgorithm-diff-xs-perl libalgorithm-munkres-perl libann0 libanyevent-cachedns-perl libanyevent-http-perl libanyevent-perl libapache-dbi-perl libapache2-mod-perl2 libapache2-reload-perl libapparmor1 libapr1 libaprutil1 libaprutil1-dbd-sqlite3 libaprutil1-ldap libargtable2-0 libarray-compare-perl libasync-interrupt-perl libauthen-sasl-perl libavahi-client3 libavahi-common-data libavahi-common3 libbio-asn1-entrezgene-perl libbio-coordinate-perl libbio-graphics-perl libbio-perl-perl libbio-perl-run-perl libbio-scf-perl libbit-vector-perl libbsd-resource-perl libbsd0 libcache-cache-perl libcairo2 libcarp-clan-perl libcdt5 libcgi-fast-perl libcgi-pm-perl libcgi-session-perl libcgraph6 libclass-inspector-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libcommon-sense-perl libconvert-binary-c-perl libconvert-binhex-perl libcrypt-rc4-perl libcups2 libcupsfilters1 libcupsimage2 libcurl3-gnutls 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-symdump-perl libdigest-perl-md5-perl libdivsufsort3 libdrm-intel1 libdrm2 libencode-locale-perl liberror-perl libev-perl libexpat1 libexporter-tiny-perl libfabric1 libfcgi-perl libffi6 libfile-listing-perl libfile-slurp-tiny-perl libfont-afm-perl libfontconfig1 libfreetype6 libfreezethaw-perl libgd-perl libgd-svg-perl libgd3 libgdbm3 libgfortran3 libglib2.0-0 libglib2.0-data libgmp10 libgnutls30 libgomp1 libgpm2 libgraph-perl libgraphite2-3 libgraphviz-perl libgs9 libgs9-common libgssapi-krb5-2 libgts-0.7-5 libgts-bin libguard-perl 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 libicu57 libidn11 libidn2-0 libijs-0.35 libimport-into-perl libio-html-perl libio-pty-perl libio-sessiondata-perl libio-socket-ssl-perl libio-string-perl libio-stringy-perl libipc-run-perl libipc-sharelite-perl libjbig0 libjbig2dec0 libjcode-pm-perl libjpeg62-turbo libjs-jquery libjs-prototype libjs-scriptaculous libjson-perl libjson-xs-perl libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblcms2-2 libldap-2.4-2 libldap-common liblist-moreutils-perl libltdl7 liblua5.2-0 liblwp-mediatypes-perl liblwp-protocol-https-perl libmagic-mgc libmagic1 libmailtools-perl libmariadbclient18 libmath-derivative-perl libmath-spline-perl libmime-tools-perl libmldbm-perl libmodule-runtime-perl libmoo-perl libmpfr4 libncurses5 libnet-http-perl libnet-smtp-ssl-perl libnet-ssleay-perl libnettle6 libnghttp2-14 libnl-3-200 libnl-route-3-200 libnuma1 libole-storage-lite-perl libopenjp2-7 libopenmpi2 libossp-uuid-perl libossp-uuid16 libp11-kit0 libpadwalker-perl libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libparams-classify-perl libparse-recdescent-perl libpathplan4 libpciaccess0 libperl5.24 libpixman-1-0 libpng16-16 libpostscript-perl libpq5 libprocps6 libpsl5 libpsm-infinipath1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 librdmacm1 libreadline7 librole-tiny-perl librtmp1 libruby2.3 libsasl2-2 libsasl2-modules libsasl2-modules-db libset-scalar-perl libsigsegv2 libsm6 libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsqlite3-0 libssh2-1 libssl1.0.2 libssl1.1 libstaden-read11 libstatistics-descriptive-perl libstrictures-perl libstring-approx-perl libsub-exporter-progressive-perl libsub-name-perl libsvg-graph-perl libsvg-perl libtask-weaken-perl libtasn1-6 libterm-readkey-perl libtext-iconv-perl libthai-data libthai0 libtie-ixhash-perl libtiff5 libtimedate-perl libtree-dagnode-perl libtype-tiny-perl libtype-tiny-xs-perl libtypes-serialiser-perl libunicode-map-perl libunistring0 liburi-perl libvm-ec2-perl libwebp6 libwww-perl libwww-robotrules-perl libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxdot4 libxext6 libxfixes3 libxft2 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 libxpm4 libxrender1 libxslt1.1 libxt6 libyaml-0-2 libyaml-libyaml-perl libyaml-perl lsb-base lynx lynx-common mafft maq 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 perl perl-doc perl-modules-5.24 perl-openssl-defaults perl-tk phylip phyml poa poppler-data prank primer3 probalign probcons procps proda psmisc publicsuffix python python-minimal python2.7 python2.7-minimal 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 sqlite3 ssl-cert t-coffee tigr-glimmer tm-align ucf unzip wise wise-data x11-common xdg-user-dirs xml-core xz-utils zip Suggested packages: apache2-doc apache2-suexec-pristine | apache2-suexec-custom filo groff-base gmap paml blends-doc bowtie-examples bzip2-doc clustalx seaview default-dbus-session-bus | dbus-session-bus emboss-doc emboss-test embassy fonts-noto gawk-doc gbrowse-data gbrowse-calign libfile-nfslock-perl ghostscript-x graphviz-doc hmmer-doc libevent-perl libio-async-perl libpoe-perl libdigest-hmac-perl libgssapi-perl libxml-sax-expatxs-perl 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 liblcms2-utils libcrypt-ssleay-perl uuid libscalar-number-perl pciutils libsasl2-modules-gssapi-mit | libsasl2-modules-gssapi-heimdal libsasl2-modules-ldap libsasl2-modules-otp libsasl2-modules-sql libmime-lite-perl libnet-jabber-perl libbareword-filehandles-perl libindirect-perl libmultidimensional-perl libdevel-stacktrace-perl libauthen-ntlm-perl libunicode-map8-perl libunicode-string-perl xml-twig-tools libyaml-shell-perl menu-l10n gksu | kde-runtime | ktsuss mustang-testdata gfortran libterm-readline-gnu-perl | libterm-readline-perl-perl make man-browser phylip-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 binutils binfmt-support readline-doc ri ruby-dev bundler sgml-base-doc sqlite3-doc openssl-blacklist boxshade t-coffee-examples pymol rasmol wise-doc debhelper The following NEW packages will be installed: amap-align apache2 apache2-bin apache2-data apache2-utils bedtools beignet-opencl-icd bioperl bioperl-run blast2 blends-common bowtie bwa bzip2 ca-certificates clustalo clustalw dbus dialign dialign-tx dialign-tx-data emboss emboss-data emboss-lib exonerate file fontconfig fontconfig-config fonts-dejavu-core fonts-droid-fallback fonts-lato fonts-liberation fonts-noto-mono fsa gawk gbrowse ghostscript graphviz gsfonts hmmer hyphy-common hyphy-mpi infernal javascript-common kalign krb5-locales libace-perl libalgorithm-diff-perl libalgorithm-diff-xs-perl libalgorithm-munkres-perl libann0 libanyevent-cachedns-perl libanyevent-http-perl libanyevent-perl libapache-dbi-perl libapache2-mod-perl2 libapache2-reload-perl libapparmor1 libapr1 libaprutil1 libaprutil1-dbd-sqlite3 libaprutil1-ldap libargtable2-0 libarray-compare-perl libasync-interrupt-perl libauthen-sasl-perl libavahi-client3 libavahi-common-data libavahi-common3 libbio-asn1-entrezgene-perl libbio-coordinate-perl libbio-graphics-perl libbio-perl-perl libbio-perl-run-perl libbio-scf-perl libbit-vector-perl libbsd-resource-perl libbsd0 libcache-cache-perl libcairo2 libcarp-clan-perl libcdt5 libcgi-fast-perl libcgi-pm-perl libcgi-session-perl libcgraph6 libclass-inspector-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libcommon-sense-perl libconvert-binary-c-perl libconvert-binhex-perl libcrypt-rc4-perl libcups2 libcupsfilters1 libcupsimage2 libcurl3-gnutls 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-symdump-perl libdigest-perl-md5-perl libdivsufsort3 libdrm-intel1 libdrm2 libencode-locale-perl liberror-perl libev-perl libexpat1 libexporter-tiny-perl libfabric1 libfcgi-perl libffi6 libfile-listing-perl libfile-slurp-tiny-perl libfont-afm-perl libfontconfig1 libfreetype6 libfreezethaw-perl libgd-perl libgd-svg-perl libgd3 libgdbm3 libgfortran3 libglib2.0-0 libglib2.0-data libgmp10 libgnutls30 libgomp1 libgpm2 libgraph-perl libgraphite2-3 libgraphviz-perl libgs9 libgs9-common libgssapi-krb5-2 libgts-0.7-5 libgts-bin libguard-perl 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 libicu57 libidn11 libidn2-0 libijs-0.35 libimport-into-perl libio-html-perl libio-pty-perl libio-sessiondata-perl libio-socket-ssl-perl libio-string-perl libio-stringy-perl libipc-run-perl libipc-sharelite-perl libjbig0 libjbig2dec0 libjcode-pm-perl libjpeg62-turbo libjs-jquery libjs-prototype libjs-scriptaculous libjson-perl libjson-xs-perl libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblcms2-2 libldap-2.4-2 libldap-common liblist-moreutils-perl libltdl7 liblua5.2-0 liblwp-mediatypes-perl liblwp-protocol-https-perl libmagic-mgc libmagic1 libmailtools-perl libmariadbclient18 libmath-derivative-perl libmath-spline-perl libmime-tools-perl libmldbm-perl libmodule-runtime-perl libmoo-perl libmpfr4 libncurses5 libnet-http-perl libnet-smtp-ssl-perl libnet-ssleay-perl libnettle6 libnghttp2-14 libnl-3-200 libnl-route-3-200 libnuma1 libole-storage-lite-perl libopenjp2-7 libopenmpi2 libossp-uuid-perl libossp-uuid16 libp11-kit0 libpadwalker-perl libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libparams-classify-perl libparse-recdescent-perl libpathplan4 libpciaccess0 libperl5.24 libpixman-1-0 libpng16-16 libpostscript-perl libpq5 libprocps6 libpsl5 libpsm-infinipath1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 librdmacm1 libreadline7 librole-tiny-perl librtmp1 libruby2.3 libsasl2-2 libsasl2-modules libsasl2-modules-db libset-scalar-perl libsigsegv2 libsm6 libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsqlite3-0 libssh2-1 libssl1.0.2 libssl1.1 libstaden-read11 libstatistics-descriptive-perl libstrictures-perl libstring-approx-perl libsub-exporter-progressive-perl libsub-name-perl libsvg-graph-perl libsvg-perl libtask-weaken-perl libtasn1-6 libterm-readkey-perl libtext-iconv-perl libthai-data libthai0 libtie-ixhash-perl libtiff5 libtimedate-perl libtree-dagnode-perl libtype-tiny-perl libtype-tiny-xs-perl libtypes-serialiser-perl libunicode-map-perl libunistring0 liburi-perl libvm-ec2-perl libwebp6 libwww-perl libwww-robotrules-perl libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxdot4 libxext6 libxfixes3 libxft2 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 libxpm4 libxrender1 libxslt1.1 libxt6 libyaml-0-2 libyaml-libyaml-perl libyaml-perl lsb-base lynx lynx-common mafft maq 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 perl perl-doc perl-modules-5.24 perl-openssl-defaults perl-tk phylip phyml poa poppler-data prank primer3 probalign probcons procps proda psmisc publicsuffix python python-minimal python2.7 python2.7-minimal 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 sqlite3 ssl-cert t-coffee tigr-glimmer tm-align ucf unzip wise wise-data x11-common xdg-user-dirs xml-core xz-utils zip 0 upgraded, 412 newly installed, 0 to remove and 0 not upgraded. Need to get 248 MB of archives. After this operation, 1154 MB of additional disk space will be used. Get:1 http://deb.debian.org/debian stretch/main amd64 perl-modules-5.24 all 5.24.1-3+deb9u7 [2723 kB] Get:2 http://deb.debian.org/debian stretch/main amd64 libgdbm3 amd64 1.8.3-14 [30.0 kB] Get:3 http://deb.debian.org/debian stretch/main amd64 libperl5.24 amd64 5.24.1-3+deb9u7 [3527 kB] Get:4 http://deb.debian.org/debian stretch/main amd64 perl amd64 5.24.1-3+deb9u7 [218 kB] Get:5 http://deb.debian.org/debian stretch/main amd64 libpython2.7-minimal amd64 2.7.13-2+deb9u3 [389 kB] Get:6 http://deb.debian.org/debian stretch/main amd64 python2.7-minimal amd64 2.7.13-2+deb9u3 [1382 kB] Get:7 http://deb.debian.org/debian stretch/main amd64 python-minimal amd64 2.7.13-2 [40.5 kB] Get:8 http://deb.debian.org/debian stretch/main amd64 mime-support all 3.60 [36.7 kB] Get:9 http://deb.debian.org/debian stretch/main amd64 libexpat1 amd64 2.2.0-2+deb9u3 [83.7 kB] Get:10 http://deb.debian.org/debian stretch/main amd64 libffi6 amd64 3.2.1-6 [20.4 kB] Get:11 http://deb.debian.org/debian stretch/main amd64 readline-common all 7.0-3 [70.4 kB] Get:12 http://deb.debian.org/debian stretch/main amd64 libreadline7 amd64 7.0-3 [151 kB] Get:13 http://deb.debian.org/debian stretch/main amd64 libsqlite3-0 amd64 3.16.2-5+deb9u1 [572 kB] Get:14 http://deb.debian.org/debian stretch/main amd64 libssl1.1 amd64 1.1.0l-1~deb9u1 [1358 kB] Get:15 http://deb.debian.org/debian stretch/main amd64 libpython2.7-stdlib amd64 2.7.13-2+deb9u3 [1897 kB] Get:16 http://deb.debian.org/debian stretch/main amd64 python2.7 amd64 2.7.13-2+deb9u3 [285 kB] Get:17 http://deb.debian.org/debian stretch/main amd64 libpython-stdlib amd64 2.7.13-2 [20.0 kB] Get:18 http://deb.debian.org/debian stretch/main amd64 python amd64 2.7.13-2 [154 kB] Get:19 http://deb.debian.org/debian stretch/main amd64 lsb-base all 9.20161125 [27.9 kB] Get:20 http://deb.debian.org/debian stretch/main amd64 libncurses5 amd64 6.0+20161126-1+deb9u2 [93.4 kB] Get:21 http://deb.debian.org/debian stretch/main amd64 libprocps6 amd64 2:3.3.12-3+deb9u1 [58.5 kB] Get:22 http://deb.debian.org/debian stretch/main amd64 procps amd64 2:3.3.12-3+deb9u1 [250 kB] Get:23 http://deb.debian.org/debian stretch/main amd64 libapr1 amd64 1.5.2-5 [96.6 kB] Get:24 http://deb.debian.org/debian stretch/main amd64 libaprutil1 amd64 1.5.4-3 [85.8 kB] Get:25 http://deb.debian.org/debian stretch/main amd64 libaprutil1-dbd-sqlite3 amd64 1.5.4-3 [19.3 kB] Get:26 http://deb.debian.org/debian stretch/main amd64 libgmp10 amd64 2:6.1.2+dfsg-1 [253 kB] Get:27 http://deb.debian.org/debian stretch/main amd64 libnettle6 amd64 3.3-1+b2 [192 kB] Get:28 http://deb.debian.org/debian stretch/main amd64 libhogweed4 amd64 3.3-1+b2 [136 kB] Get:29 http://deb.debian.org/debian stretch/main amd64 libidn11 amd64 1.33-1+deb9u1 [115 kB] Get:30 http://deb.debian.org/debian stretch/main amd64 libp11-kit0 amd64 0.23.3-2 [111 kB] Get:31 http://deb.debian.org/debian stretch/main amd64 libtasn1-6 amd64 4.10-1.1+deb9u1 [50.6 kB] Get:32 http://deb.debian.org/debian stretch/main amd64 libgnutls30 amd64 3.5.8-5+deb9u5 [896 kB] Get:33 http://deb.debian.org/debian stretch/main amd64 libsasl2-modules-db amd64 2.1.27~101-g0780600+dfsg-3+deb9u1 [68.4 kB] Get:34 http://deb.debian.org/debian stretch/main amd64 libsasl2-2 amd64 2.1.27~101-g0780600+dfsg-3+deb9u1 [105 kB] Get:35 http://deb.debian.org/debian stretch/main amd64 libldap-common all 2.4.44+dfsg-5+deb9u4 [85.7 kB] Get:36 http://deb.debian.org/debian stretch/main amd64 libldap-2.4-2 amd64 2.4.44+dfsg-5+deb9u4 [219 kB] Get:37 http://deb.debian.org/debian stretch/main amd64 libaprutil1-ldap amd64 1.5.4-3 [17.4 kB] Get:38 http://deb.debian.org/debian stretch/main amd64 liblua5.2-0 amd64 5.2.4-1.1+b2 [110 kB] Get:39 http://deb.debian.org/debian stretch/main amd64 libnghttp2-14 amd64 1.18.1-1+deb9u1 [79.2 kB] Get:40 http://deb.debian.org/debian stretch/main amd64 libssl1.0.2 amd64 1.0.2u-1~deb9u1 [1304 kB] Get:41 http://deb.debian.org/debian stretch/main amd64 libicu57 amd64 57.1-6+deb9u4 [7699 kB] Get:42 http://deb.debian.org/debian stretch/main amd64 libxml2 amd64 2.9.4+dfsg1-2.2+deb9u2 [920 kB] Get:43 http://deb.debian.org/debian stretch/main amd64 apache2-bin amd64 2.4.25-3+deb9u9 [1185 kB] Get:44 http://deb.debian.org/debian stretch/main amd64 apache2-utils amd64 2.4.25-3+deb9u9 [218 kB] Get:45 http://deb.debian.org/debian stretch/main amd64 apache2-data all 2.4.25-3+deb9u9 [162 kB] Get:46 http://deb.debian.org/debian stretch/main amd64 apache2 amd64 2.4.25-3+deb9u9 [237 kB] Get:47 http://deb.debian.org/debian stretch/main amd64 libpng16-16 amd64 1.6.28-1+deb9u1 [280 kB] Get:48 http://deb.debian.org/debian stretch/main amd64 libfreetype6 amd64 2.6.3-3.2+deb9u1 [438 kB] Get:49 http://deb.debian.org/debian stretch/main amd64 ucf all 3.0036 [70.2 kB] Get:50 http://deb.debian.org/debian stretch/main amd64 fonts-dejavu-core all 2.37-1 [1068 kB] Get:51 http://deb.debian.org/debian stretch/main amd64 fonts-liberation all 1:1.07.4-2 [827 kB] Get:52 http://deb.debian.org/debian stretch/main amd64 fontconfig-config all 2.11.0-6.7 [271 kB] Get:53 http://deb.debian.org/debian stretch/main amd64 libfontconfig1 amd64 2.11.0-6.7+b1 [331 kB] Get:54 http://deb.debian.org/debian stretch/main amd64 fontconfig amd64 2.11.0-6.7+b1 [404 kB] Get:55 http://deb.debian.org/debian stretch/main amd64 fonts-droid-fallback all 1:6.0.1r16-1.1 [1807 kB] Get:56 http://deb.debian.org/debian stretch/main amd64 fonts-lato all 2.0-1 [2684 kB] Get:57 http://deb.debian.org/debian stretch/main amd64 libmpfr4 amd64 3.1.5-1 [556 kB] Get:58 http://deb.debian.org/debian stretch/main amd64 libsigsegv2 amd64 2.10-5 [28.9 kB] Get:59 http://deb.debian.org/debian stretch/main amd64 gawk amd64 1:4.1.4+dfsg-1 [571 kB] Get:60 http://deb.debian.org/debian stretch/main amd64 libxau6 amd64 1:1.0.8-1 [20.7 kB] Get:61 http://deb.debian.org/debian stretch/main amd64 poppler-data all 0.4.7-8 [1451 kB] Get:62 http://deb.debian.org/debian stretch/main amd64 sgml-base all 1.29 [14.8 kB] Get:63 http://deb.debian.org/debian stretch/main amd64 netbase all 5.4 [19.1 kB] Get:64 http://deb.debian.org/debian stretch/main amd64 bzip2 amd64 1.0.6-8.1 [47.5 kB] Get:65 http://deb.debian.org/debian stretch/main amd64 libapparmor1 amd64 2.11.0-3+deb9u2 [78.9 kB] Get:66 http://deb.debian.org/debian stretch/main amd64 libdbus-1-3 amd64 1.10.32-0+deb9u1 [196 kB] Get:67 http://deb.debian.org/debian stretch/main amd64 dbus amd64 1.10.32-0+deb9u1 [213 kB] Get:68 http://deb.debian.org/debian stretch/main amd64 libmagic-mgc amd64 1:5.30-1+deb9u3 [222 kB] Get:69 http://deb.debian.org/debian stretch/main amd64 libmagic1 amd64 1:5.30-1+deb9u3 [111 kB] Get:70 http://deb.debian.org/debian stretch/main amd64 file amd64 1:5.30-1+deb9u3 [64.2 kB] Get:71 http://deb.debian.org/debian stretch/main amd64 krb5-locales all 1.15-1+deb9u1 [93.8 kB] Get:72 http://deb.debian.org/debian stretch/main amd64 libgpm2 amd64 1.20.4-6.2+b1 [34.2 kB] Get:73 http://deb.debian.org/debian stretch/main amd64 libkeyutils1 amd64 1.5.9-9 [12.4 kB] Get:74 http://deb.debian.org/debian stretch/main amd64 libkrb5support0 amd64 1.15-1+deb9u1 [61.9 kB] Get:75 http://deb.debian.org/debian stretch/main amd64 libk5crypto3 amd64 1.15-1+deb9u1 [119 kB] Get:76 http://deb.debian.org/debian stretch/main amd64 libkrb5-3 amd64 1.15-1+deb9u1 [311 kB] Get:77 http://deb.debian.org/debian stretch/main amd64 libgssapi-krb5-2 amd64 1.15-1+deb9u1 [155 kB] Get:78 http://deb.debian.org/debian stretch/main amd64 xz-utils amd64 5.2.2-1.2+b1 [266 kB] Get:79 http://deb.debian.org/debian stretch/main amd64 amap-align amd64 2.2-6 [129 kB] Get:80 http://deb.debian.org/debian stretch/main amd64 bedtools amd64 2.26.0+dfsg-3 [584 kB] Get:81 http://deb.debian.org/debian stretch/main amd64 libio-string-perl all 1.08-3 [12.3 kB] Get:82 http://deb.debian.org/debian stretch/main amd64 libdata-stag-perl all 0.14-2 [448 kB] Get:83 http://deb.debian.org/debian stretch/main amd64 libbio-perl-perl all 1.7.1-2 [4605 kB] Get:84 http://deb.debian.org/debian stretch/main amd64 bioperl all 1.7.1-2 [422 kB] Get:85 http://deb.debian.org/debian stretch/main amd64 libbio-perl-run-perl all 1.7.1-3 [816 kB] Get:86 http://deb.debian.org/debian stretch/main amd64 bioperl-run all 1.7.1-3 [44.2 kB] Get:87 http://deb.debian.org/debian stretch/main amd64 ncbi-data all 6.1.20170106+dfsg1-0+deb9u1 [3555 kB] Get:88 http://deb.debian.org/debian stretch/main amd64 libgomp1 amd64 6.3.0-18+deb9u1 [73.3 kB] Get:89 http://deb.debian.org/debian stretch/main amd64 ncbi-blast+ amd64 2.6.0-1 [9591 kB] Get:90 http://deb.debian.org/debian stretch/main amd64 ncbi-blast+-legacy all 2.6.0-1 [9604 B] Get:91 http://deb.debian.org/debian stretch/main amd64 blast2 all 1:2.6.0-1 [9084 B] Get:92 http://deb.debian.org/debian stretch/main amd64 menu amd64 2.1.47+b1 [380 kB] Get:93 http://deb.debian.org/debian stretch/main amd64 blends-common all 0.6.96 [23.3 kB] Get:94 http://deb.debian.org/debian stretch/main amd64 bwa amd64 0.7.15-2+deb9u1 [194 kB] Get:95 http://deb.debian.org/debian stretch/main amd64 openssl amd64 1.1.0l-1~deb9u1 [749 kB] Get:96 http://deb.debian.org/debian stretch/main amd64 ca-certificates all 20200601~deb9u1 [160 kB] Get:97 http://deb.debian.org/debian stretch/main amd64 libargtable2-0 amd64 13-1 [17.4 kB] Get:98 http://deb.debian.org/debian stretch/main amd64 clustalo amd64 1.2.4-1 [263 kB] Get:99 http://deb.debian.org/debian stretch/main amd64 clustalw amd64 2.1+lgpl-5 [286 kB] Get:100 http://deb.debian.org/debian stretch/main amd64 dialign amd64 2.2.1-8 [138 kB] Get:101 http://deb.debian.org/debian stretch/main amd64 dialign-tx-data all 1.0.2-9 [869 kB] Get:102 http://deb.debian.org/debian stretch/main amd64 dialign-tx amd64 1.0.2-9 [85.7 kB] Get:103 http://deb.debian.org/debian stretch/main amd64 libjpeg62-turbo amd64 1:1.5.1-2 [134 kB] Get:104 http://deb.debian.org/debian stretch/main amd64 libjbig0 amd64 2.1-3.1+b2 [31.0 kB] Get:105 http://deb.debian.org/debian stretch/main amd64 libtiff5 amd64 4.0.8-2+deb9u5 [239 kB] Get:106 http://deb.debian.org/debian stretch/main amd64 libwebp6 amd64 0.5.2-1 [235 kB] Get:107 http://deb.debian.org/debian stretch/main amd64 libbsd0 amd64 0.8.3-1 [83.0 kB] Get:108 http://deb.debian.org/debian stretch/main amd64 libxdmcp6 amd64 1:1.1.2-3 [26.3 kB] Get:109 http://deb.debian.org/debian stretch/main amd64 libxcb1 amd64 1.12-1 [133 kB] Get:110 http://deb.debian.org/debian stretch/main amd64 libx11-data all 2:1.6.4-3+deb9u1 [287 kB] Get:111 http://deb.debian.org/debian stretch/main amd64 libx11-6 amd64 2:1.6.4-3+deb9u1 [748 kB] Get:112 http://deb.debian.org/debian stretch/main amd64 libxpm4 amd64 1:3.5.12-1 [49.1 kB] Get:113 http://deb.debian.org/debian stretch/main amd64 libgd3 amd64 2.2.4-2+deb9u5 [132 kB] Get:114 http://deb.debian.org/debian stretch/main amd64 libhpdf-2.2.1 amd64 2.2.1-1.1+b1 [319 kB] Get:115 http://deb.debian.org/debian stretch/main amd64 mysql-common all 5.8+1.0.2 [5608 B] Get:116 http://deb.debian.org/debian stretch/main amd64 libmariadbclient18 amd64 10.1.45-0+deb9u1 [785 kB] Get:117 http://deb.debian.org/debian stretch/main amd64 libpq5 amd64 9.6.17-0+deb9u1 [137 kB] Get:118 http://deb.debian.org/debian stretch/main amd64 emboss-lib amd64 6.6.0+dfsg-6 [2773 kB] Get:119 http://deb.debian.org/debian stretch/main amd64 emboss-data all 6.6.0+dfsg-6 [61.1 MB] Get:120 http://deb.debian.org/debian stretch/main amd64 emboss amd64 6.6.0+dfsg-6 [1058 kB] Get:121 http://deb.debian.org/debian stretch/main amd64 libglib2.0-0 amd64 2.50.3-2+deb9u2 [2692 kB] Get:122 http://deb.debian.org/debian stretch/main amd64 exonerate amd64 2.4.0-2 [1476 kB] Get:123 http://deb.debian.org/debian stretch/main amd64 fonts-noto-mono all 20161116-1 [79.2 kB] Get:124 http://deb.debian.org/debian stretch/main amd64 mummer amd64 3.23+dfsg-2 [809 kB] Get:125 http://deb.debian.org/debian stretch/main amd64 fsa amd64 1.15.9+dfsg-3 [753 kB] Get:126 http://deb.debian.org/debian stretch/main amd64 libgd-perl amd64 2.53-3 [177 kB] Get:127 http://deb.debian.org/debian stretch/main amd64 libbio-graphics-perl all 2.40-1 [611 kB] Get:128 http://deb.debian.org/debian stretch/main amd64 libbio-coordinate-perl all 1.7.1-1 [56.0 kB] Get:129 http://deb.debian.org/debian stretch/main amd64 libhtml-tagset-perl all 3.20-3 [12.7 kB] Get:130 http://deb.debian.org/debian stretch/main amd64 liburi-perl all 1.71-1 [88.6 kB] Get:131 http://deb.debian.org/debian stretch/main amd64 libhtml-parser-perl amd64 3.72-3 [104 kB] Get:132 http://deb.debian.org/debian stretch/main amd64 libcgi-pm-perl all 4.35-1 [222 kB] Get:133 http://deb.debian.org/debian stretch/main amd64 libcgi-session-perl all 4.48-3 [119 kB] Get:134 http://deb.debian.org/debian stretch/main amd64 libjson-perl all 2.90-1 [86.0 kB] Get:135 http://deb.debian.org/debian stretch/main amd64 libexporter-tiny-perl all 0.042-1 [32.4 kB] Get:136 http://deb.debian.org/debian stretch/main amd64 liblist-moreutils-perl amd64 0.416-1+b1 [63.0 kB] Get:137 http://deb.debian.org/debian stretch/main amd64 libstatistics-descriptive-perl all 3.0612-1 [41.9 kB] Get:138 http://deb.debian.org/debian stretch/main amd64 libencode-locale-perl all 1.05-1 [13.7 kB] Get:139 http://deb.debian.org/debian stretch/main amd64 libtimedate-perl all 2.3000-2+deb9u1 [37.9 kB] Get:140 http://deb.debian.org/debian stretch/main amd64 libhttp-date-perl all 6.02-1 [10.7 kB] Get:141 http://deb.debian.org/debian stretch/main amd64 libfile-listing-perl all 6.04-1 [10.3 kB] Get:142 http://deb.debian.org/debian stretch/main amd64 libhtml-tree-perl all 5.03-2 [210 kB] Get:143 http://deb.debian.org/debian stretch/main amd64 libio-html-perl all 1.001-1 [17.6 kB] Get:144 http://deb.debian.org/debian stretch/main amd64 liblwp-mediatypes-perl all 6.02-1 [22.1 kB] Get:145 http://deb.debian.org/debian stretch/main amd64 libhttp-message-perl all 6.11-1 [75.9 kB] Get:146 http://deb.debian.org/debian stretch/main amd64 libhttp-cookies-perl all 6.01-1 [17.4 kB] Get:147 http://deb.debian.org/debian stretch/main amd64 libhttp-negotiate-perl all 6.00-2 [13.6 kB] Get:148 http://deb.debian.org/debian stretch/main amd64 perl-openssl-defaults amd64 3 [6782 B] Get:149 http://deb.debian.org/debian stretch/main amd64 libnet-ssleay-perl amd64 1.80-1 [285 kB] Get:150 http://deb.debian.org/debian stretch/main amd64 libio-socket-ssl-perl all 2.044-1 [195 kB] Get:151 http://deb.debian.org/debian stretch/main amd64 libnet-http-perl all 6.12-1 [23.8 kB] Get:152 http://deb.debian.org/debian stretch/main amd64 liblwp-protocol-https-perl all 6.06-2 [9582 B] Get:153 http://deb.debian.org/debian stretch/main amd64 libwww-robotrules-perl all 6.01-1 [14.3 kB] Get:154 http://deb.debian.org/debian stretch/main amd64 libwww-perl all 6.15-1 [195 kB] Get:155 http://deb.debian.org/debian stretch/main amd64 libhttp-daemon-perl all 6.01-1 [17.3 kB] Get:156 http://deb.debian.org/debian stretch/main amd64 libterm-readkey-perl amd64 2.37-1 [27.2 kB] Get:157 http://deb.debian.org/debian stretch/main amd64 sqlite3 amd64 3.16.2-5+deb9u1 [784 kB] Get:158 http://deb.debian.org/debian stretch/main amd64 libdbi-perl amd64 1.636-1+b1 [766 kB] Get:159 http://deb.debian.org/debian stretch/main amd64 libdbd-sqlite3-perl amd64 1.54-1 [164 kB] Get:160 http://deb.debian.org/debian stretch/main amd64 libjs-prototype all 1.7.1-3 [44.3 kB] Get:161 http://deb.debian.org/debian stretch/main amd64 libjs-scriptaculous all 1.9.0-2 [129 kB] Get:162 http://deb.debian.org/debian stretch/main amd64 libanyevent-perl amd64 7.130-2 [391 kB] Get:163 http://deb.debian.org/debian stretch/main amd64 libanyevent-cachedns-perl all 0.08-2 [7150 B] Get:164 http://deb.debian.org/debian stretch/main amd64 libcommon-sense-perl amd64 3.74-2 [23.6 kB] Get:165 http://deb.debian.org/debian stretch/main amd64 libanyevent-http-perl all 2.23-1 [34.6 kB] Get:166 http://deb.debian.org/debian stretch/main amd64 libstring-approx-perl amd64 3.27-1+b4 [40.0 kB] Get:167 http://deb.debian.org/debian stretch/main amd64 libxml-namespacesupport-perl all 1.11-1 [14.8 kB] Get:168 http://deb.debian.org/debian stretch/main amd64 libxml-sax-base-perl all 1.07-1 [23.1 kB] Get:169 http://deb.debian.org/debian stretch/main amd64 libxml-sax-perl all 0.99+dfsg-2 [68.3 kB] Get:170 http://deb.debian.org/debian stretch/main amd64 libxml-libxml-perl amd64 2.0128+dfsg-1+deb9u1 [338 kB] Get:171 http://deb.debian.org/debian stretch/main amd64 libxml-parser-perl amd64 2.44-2+b1 [212 kB] Get:172 http://deb.debian.org/debian stretch/main amd64 libxml-sax-expat-perl all 0.40-2 [12.9 kB] Get:173 http://deb.debian.org/debian stretch/main amd64 libxml-simple-perl all 2.22-1 [71.8 kB] Get:174 http://deb.debian.org/debian stretch/main amd64 libvm-ec2-perl all 1.28-2 [768 kB] Get:175 http://deb.debian.org/debian stretch/main amd64 gbrowse all 2.56+dfsg-2 [2373 kB] Get:176 http://deb.debian.org/debian stretch/main amd64 libavahi-common-data amd64 0.6.32-2 [118 kB] Get:177 http://deb.debian.org/debian stretch/main amd64 libavahi-common3 amd64 0.6.32-2 [52.0 kB] Get:178 http://deb.debian.org/debian stretch/main amd64 libavahi-client3 amd64 0.6.32-2 [55.3 kB] Get:179 http://deb.debian.org/debian stretch/main amd64 libcups2 amd64 2.2.1-8+deb9u6 [307 kB] Get:180 http://deb.debian.org/debian stretch/main amd64 libcupsimage2 amd64 2.2.1-8+deb9u6 [122 kB] Get:181 http://deb.debian.org/debian stretch/main amd64 libijs-0.35 amd64 0.35-12 [18.4 kB] Get:182 http://deb.debian.org/debian stretch/main amd64 libjbig2dec0 amd64 0.13-4.1 [60.1 kB] Get:183 http://deb.debian.org/debian stretch/main amd64 liblcms2-2 amd64 2.8-4+deb9u1 [143 kB] Get:184 http://deb.debian.org/debian stretch/main amd64 libopenjp2-7 amd64 2.1.2-1.1+deb9u4 [122 kB] Get:185 http://deb.debian.org/debian stretch/main amd64 libpaper1 amd64 1.1.24+nmu5 [21.6 kB] Get:186 http://deb.debian.org/debian stretch/main amd64 libgs9-common all 9.26a~dfsg-0+deb9u6 [5143 kB] Get:187 http://deb.debian.org/debian stretch/main amd64 libgs9 amd64 9.26a~dfsg-0+deb9u6 [2213 kB] Get:188 http://deb.debian.org/debian stretch/main amd64 ghostscript amd64 9.26a~dfsg-0+deb9u6 [99.2 kB] Get:189 http://deb.debian.org/debian stretch/main amd64 libann0 amd64 1.1.2+doc-6 [24.9 kB] Get:190 http://deb.debian.org/debian stretch/main amd64 libcdt5 amd64 2.38.0-17 [59.6 kB] Get:191 http://deb.debian.org/debian stretch/main amd64 libcgraph6 amd64 2.38.0-17 [82.2 kB] Get:192 http://deb.debian.org/debian stretch/main amd64 libgts-0.7-5 amd64 0.7.6+darcs121130-4 [158 kB] Get:193 http://deb.debian.org/debian stretch/main amd64 libpixman-1-0 amd64 0.34.0-1 [530 kB] Get:194 http://deb.debian.org/debian stretch/main amd64 libxcb-render0 amd64 1.12-1 [105 kB] Get:195 http://deb.debian.org/debian stretch/main amd64 libxcb-shm0 amd64 1.12-1 [95.9 kB] Get:196 http://deb.debian.org/debian stretch/main amd64 libxext6 amd64 2:1.3.3-1+b2 [52.5 kB] Get:197 http://deb.debian.org/debian stretch/main amd64 libxrender1 amd64 1:0.9.10-1 [33.0 kB] Get:198 http://deb.debian.org/debian stretch/main amd64 libcairo2 amd64 1.14.8-1 [771 kB] Get:199 http://deb.debian.org/debian stretch/main amd64 libltdl7 amd64 2.4.6-2 [389 kB] Get:200 http://deb.debian.org/debian stretch/main amd64 libthai-data all 0.1.26-1 [166 kB] Get:201 http://deb.debian.org/debian stretch/main amd64 libdatrie1 amd64 0.2.10-4+b1 [36.4 kB] Get:202 http://deb.debian.org/debian stretch/main amd64 libthai0 amd64 0.1.26-1 [52.1 kB] Get:203 http://deb.debian.org/debian stretch/main amd64 libpango-1.0-0 amd64 1.40.5-1 [320 kB] Get:204 http://deb.debian.org/debian stretch/main amd64 libgraphite2-3 amd64 1.3.10-1 [84.2 kB] Get:205 http://deb.debian.org/debian stretch/main amd64 libharfbuzz0b amd64 1.4.2-1 [671 kB] Get:206 http://deb.debian.org/debian stretch/main amd64 libpangoft2-1.0-0 amd64 1.40.5-1 [205 kB] Get:207 http://deb.debian.org/debian stretch/main amd64 libpangocairo-1.0-0 amd64 1.40.5-1 [193 kB] Get:208 http://deb.debian.org/debian stretch/main amd64 libpathplan4 amd64 2.38.0-17 [62.8 kB] Get:209 http://deb.debian.org/debian stretch/main amd64 libxdot4 amd64 2.38.0-17 [55.6 kB] Get:210 http://deb.debian.org/debian stretch/main amd64 libgvc6 amd64 2.38.0-17 [639 kB] Get:211 http://deb.debian.org/debian stretch/main amd64 libgvpr2 amd64 2.38.0-17 [211 kB] Get:212 http://deb.debian.org/debian stretch/main amd64 x11-common all 1:7.7+19 [251 kB] Get:213 http://deb.debian.org/debian stretch/main amd64 libice6 amd64 2:1.0.9-2 [58.7 kB] Get:214 http://deb.debian.org/debian stretch/main amd64 libsm6 amd64 2:1.2.2-1+b3 [33.3 kB] Get:215 http://deb.debian.org/debian stretch/main amd64 libxt6 amd64 1:1.1.5-1 [188 kB] Get:216 http://deb.debian.org/debian stretch/main amd64 libxmu6 amd64 2:1.1.2-2 [60.3 kB] Get:217 http://deb.debian.org/debian stretch/main amd64 libxaw7 amd64 2:1.0.13-1+b2 [201 kB] Get:218 http://deb.debian.org/debian stretch/main amd64 graphviz amd64 2.38.0-17 [802 kB] Get:219 http://deb.debian.org/debian stretch/main amd64 gsfonts all 1:8.11+urwcyr1.0.7~pre44-4.3 [3126 kB] Get:220 http://deb.debian.org/debian stretch/main amd64 libdivsufsort3 amd64 2.0.1-2 [46.3 kB] Get:221 http://deb.debian.org/debian stretch/main amd64 hmmer amd64 3.1b2+dfsg-5 [1122 kB] Get:222 http://deb.debian.org/debian stretch/main amd64 hyphy-common all 2.2.7+dfsg-1 [619 kB] Get:223 http://deb.debian.org/debian stretch/main amd64 libunistring0 amd64 0.9.6+really0.9.3-0.1 [279 kB] Get:224 http://deb.debian.org/debian stretch/main amd64 libidn2-0 amd64 0.16-1+deb9u1 [60.7 kB] Get:225 http://deb.debian.org/debian stretch/main amd64 libpsl5 amd64 0.17.0-3 [41.8 kB] Get:226 http://deb.debian.org/debian stretch/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-1+b1 [60.4 kB] Get:227 http://deb.debian.org/debian stretch/main amd64 libssh2-1 amd64 1.7.0-1+deb9u1 [139 kB] Get:228 http://deb.debian.org/debian stretch/main amd64 libcurl3-gnutls amd64 7.52.1-5+deb9u10 [290 kB] Get:229 http://deb.debian.org/debian stretch/main amd64 libnl-3-200 amd64 3.2.27-2 [61.5 kB] Get:230 http://deb.debian.org/debian stretch/main amd64 libnl-route-3-200 amd64 3.2.27-2 [136 kB] Get:231 http://deb.debian.org/debian stretch/main amd64 libibverbs1 amd64 1.2.1-2 [39.3 kB] Get:232 http://deb.debian.org/debian stretch/main amd64 libpsm-infinipath1 amd64 3.3+19.g67c0807.open-3 [169 kB] Get:233 http://deb.debian.org/debian stretch/main amd64 librdmacm1 amd64 1.1.0-2 [49.4 kB] Get:234 http://deb.debian.org/debian stretch/main amd64 libfabric1 amd64 1.4.0-1 [259 kB] Get:235 http://deb.debian.org/debian stretch/main amd64 libquadmath0 amd64 6.3.0-18+deb9u1 [131 kB] Get:236 http://deb.debian.org/debian stretch/main amd64 libgfortran3 amd64 6.3.0-18+deb9u1 [265 kB] Get:237 http://deb.debian.org/debian stretch/main amd64 libnuma1 amd64 2.0.11-2.1 [33.3 kB] Get:238 http://deb.debian.org/debian stretch/main amd64 libhwloc5 amd64 1.11.5-1 [105 kB] Get:239 http://deb.debian.org/debian stretch/main amd64 libpciaccess0 amd64 0.13.4-1+b2 [50.0 kB] Get:240 http://deb.debian.org/debian stretch/main amd64 ocl-icd-libopencl1 amd64 2.2.11-1 [36.8 kB] Get:241 http://deb.debian.org/debian stretch/main amd64 libhwloc-plugins amd64 1.11.5-1 [16.1 kB] Get:242 http://deb.debian.org/debian stretch/main amd64 libopenmpi2 amd64 2.0.2-2 [2008 kB] Get:243 http://deb.debian.org/debian stretch/main amd64 hyphy-mpi amd64 2.2.7+dfsg-1+b2 [920 kB] Get:244 http://deb.debian.org/debian stretch/main amd64 infernal amd64 1.1.2-1 [22.0 MB] Get:245 http://deb.debian.org/debian stretch/main amd64 javascript-common all 11 [6120 B] Get:246 http://deb.debian.org/debian stretch/main amd64 kalign amd64 1:2.03+20110620-3 [99.7 kB] Get:247 http://deb.debian.org/debian stretch/main amd64 liberror-perl all 0.17024-1 [26.9 kB] Get:248 http://deb.debian.org/debian stretch/main amd64 libipc-sharelite-perl amd64 0.17-4 [24.0 kB] Get:249 http://deb.debian.org/debian stretch/main amd64 libcache-cache-perl all 1.08-2 [76.6 kB] Get:250 http://deb.debian.org/debian stretch/main amd64 libace-perl amd64 1.92-4+b1 [286 kB] Get:251 http://deb.debian.org/debian stretch/main amd64 libalgorithm-diff-perl all 1.19.03-1 [48.7 kB] Get:252 http://deb.debian.org/debian stretch/main amd64 libalgorithm-diff-xs-perl amd64 0.04-4+b2 [11.6 kB] Get:253 http://deb.debian.org/debian stretch/main amd64 libalgorithm-munkres-perl all 0.08-3 [12.1 kB] Get:254 http://deb.debian.org/debian stretch/main amd64 libdevel-symdump-perl all 2.17-1 [17.0 kB] Get:255 http://deb.debian.org/debian stretch/main amd64 libapache2-mod-perl2 amd64 2.0.10-2+deb9u1 [886 kB] Get:256 http://deb.debian.org/debian stretch/main amd64 libapache-dbi-perl all 1.12-1 [54.6 kB] Get:257 http://deb.debian.org/debian stretch/main amd64 libapache2-reload-perl all 0.13-1 [17.4 kB] Get:258 http://deb.debian.org/debian stretch/main amd64 libclass-method-modifiers-perl all 2.12-1 [18.6 kB] Get:259 http://deb.debian.org/debian stretch/main amd64 libsub-exporter-progressive-perl all 0.001013-1 [7588 B] Get:260 http://deb.debian.org/debian stretch/main amd64 libdevel-globaldestruction-perl all 0.14-1 [8084 B] Get:261 http://deb.debian.org/debian stretch/main amd64 libparams-classify-perl amd64 0.013-6+b1 [24.4 kB] Get:262 http://deb.debian.org/debian stretch/main amd64 libmodule-runtime-perl all 0.014-2 [18.0 kB] Get:263 http://deb.debian.org/debian stretch/main amd64 libimport-into-perl all 1.002005-1 [11.6 kB] Get:264 http://deb.debian.org/debian stretch/main amd64 librole-tiny-perl all 2.000005-1 [19.0 kB] Get:265 http://deb.debian.org/debian stretch/main amd64 libstrictures-perl all 2.000003-1 [18.1 kB] Get:266 http://deb.debian.org/debian stretch/main amd64 libmoo-perl all 2.002005-1 [67.0 kB] Get:267 http://deb.debian.org/debian stretch/main amd64 libtype-tiny-perl all 1.000005-1 [271 kB] Get:268 http://deb.debian.org/debian stretch/main amd64 libarray-compare-perl all 3.0.0-1 [14.0 kB] Get:269 http://deb.debian.org/debian stretch/main amd64 libasync-interrupt-perl amd64 1.21-1+b2 [33.9 kB] Get:270 http://deb.debian.org/debian stretch/main amd64 libauthen-sasl-perl all 2.1600-1 [50.8 kB] Get:271 http://deb.debian.org/debian stretch/main amd64 libbio-asn1-entrezgene-perl all 1.720-1 [38.5 kB] Get:272 http://deb.debian.org/debian stretch/main amd64 libstaden-read11 amd64 1.14.8-2 [311 kB] Get:273 http://deb.debian.org/debian stretch/main amd64 libbio-scf-perl amd64 1.03-3 [20.3 kB] Get:274 http://deb.debian.org/debian stretch/main amd64 libcarp-clan-perl all 6.06-1 [12.9 kB] Get:275 http://deb.debian.org/debian stretch/main amd64 libbit-vector-perl amd64 7.4-1+b2 [146 kB] Get:276 http://deb.debian.org/debian stretch/main amd64 libbsd-resource-perl amd64 1.2910-1+b1 [33.7 kB] Get:277 http://deb.debian.org/debian stretch/main amd64 libfcgi-perl amd64 0.78-2 [38.2 kB] Get:278 http://deb.debian.org/debian stretch/main amd64 libcgi-fast-perl all 1:2.12-1 [11.2 kB] Get:279 http://deb.debian.org/debian stretch/main amd64 libclass-inspector-perl all 1.31-1 [18.7 kB] Get:280 http://deb.debian.org/debian stretch/main amd64 libclass-xsaccessor-perl amd64 1.19-2+b7 [36.7 kB] Get:281 http://deb.debian.org/debian stretch/main amd64 libclone-perl amd64 0.38-2+b1 [13.6 kB] Get:282 http://deb.debian.org/debian stretch/main amd64 libconvert-binary-c-perl amd64 0.78-1+b1 [271 kB] Get:283 http://deb.debian.org/debian stretch/main amd64 libconvert-binhex-perl all 1.125-1 [30.5 kB] Get:284 http://deb.debian.org/debian stretch/main amd64 libcrypt-rc4-perl all 2.02-2 [8150 B] Get:285 http://deb.debian.org/debian stretch/main amd64 libcupsfilters1 amd64 1.11.6-3+deb9u1 [129 kB] Get:286 http://deb.debian.org/debian stretch/main amd64 libdate-calc-perl all 6.4-1 [194 kB] Get:287 http://deb.debian.org/debian stretch/main amd64 libdate-calc-xs-perl amd64 6.4-1+b2 [54.3 kB] Get:288 http://deb.debian.org/debian stretch/main amd64 libdate-manip-perl all 6.57-1 [911 kB] Get:289 http://deb.debian.org/debian stretch/main amd64 libdbd-mysql-perl amd64 4.041-2 [114 kB] Get:290 http://deb.debian.org/debian stretch/main amd64 libdbd-pg-perl amd64 3.5.3-1+b2 [203 kB] Get:291 http://deb.debian.org/debian stretch/main amd64 libpadwalker-perl amd64 2.2-2+b1 [19.7 kB] Get:292 http://deb.debian.org/debian stretch/main amd64 libdevel-caller-perl amd64 2.06-1+b4 [11.8 kB] Get:293 http://deb.debian.org/debian stretch/main amd64 libdevel-lexalias-perl amd64 0.05-1+b4 [8752 B] Get:294 http://deb.debian.org/debian stretch/main amd64 libdigest-perl-md5-perl all 1.9-1 [11.7 kB] Get:295 http://deb.debian.org/debian stretch/main amd64 libdrm2 amd64 2.4.74-1 [36.2 kB] Get:296 http://deb.debian.org/debian stretch/main amd64 libdrm-intel1 amd64 2.4.74-1 [68.7 kB] Get:297 http://deb.debian.org/debian stretch/main amd64 libfile-slurp-tiny-perl all 0.003-1 [6852 B] Get:298 http://deb.debian.org/debian stretch/main amd64 libfont-afm-perl all 1.20-2 [13.6 kB] Get:299 http://deb.debian.org/debian stretch/main amd64 libfreezethaw-perl all 0.5001-1 [18.2 kB] Get:300 http://deb.debian.org/debian stretch/main amd64 libsvg-perl all 2.64-1 [69.8 kB] Get:301 http://deb.debian.org/debian stretch/main amd64 libgd-svg-perl all 0.33-1 [64.8 kB] Get:302 http://deb.debian.org/debian stretch/main amd64 libglib2.0-data all 2.50.3-2+deb9u2 [2517 kB] Get:303 http://deb.debian.org/debian stretch/main amd64 libgraph-perl all 1:0.96-2 [126 kB] Get:304 http://deb.debian.org/debian stretch/main amd64 libio-pty-perl amd64 1:1.08-1.1+b2 [33.6 kB] Get:305 http://deb.debian.org/debian stretch/main amd64 libipc-run-perl all 0.94-1+deb9u1 [99.1 kB] Get:306 http://deb.debian.org/debian stretch/main amd64 libparse-recdescent-perl all 1.967013+dfsg-1 [159 kB] Get:307 http://deb.debian.org/debian stretch/main amd64 libxml-twig-perl all 1:3.50-1 [179 kB] Get:308 http://deb.debian.org/debian stretch/main amd64 libxml-xpath-perl all 1.40-1 [69.2 kB] Get:309 http://deb.debian.org/debian stretch/main amd64 libgraphviz-perl all 2.22-1 [107 kB] Get:310 http://deb.debian.org/debian stretch/main amd64 libgts-bin amd64 0.7.6+darcs121130-4 [50.8 kB] Get:311 http://deb.debian.org/debian stretch/main amd64 libguard-perl amd64 1.023-1+b2 [15.8 kB] Get:312 http://deb.debian.org/debian stretch/main amd64 libxfixes3 amd64 1:5.0.3-1 [21.9 kB] Get:313 http://deb.debian.org/debian stretch/main amd64 beignet-opencl-icd amd64 1.3.0-4 [12.8 MB] Get:314 http://deb.debian.org/debian stretch/main amd64 libhmsbeagle1v5 amd64 2.1.2+20160831-5 [116 kB] Get:315 http://deb.debian.org/debian stretch/main amd64 libhtml-form-perl all 6.03-1 [23.9 kB] Get:316 http://deb.debian.org/debian stretch/main amd64 libhtml-format-perl all 2.12-1 [43.5 kB] Get:317 http://deb.debian.org/debian stretch/main amd64 libhtml-tableextract-perl all 2.13-1 [30.7 kB] Get:318 http://deb.debian.org/debian stretch/main amd64 libhts1 amd64 1.3.2-2 [257 kB] Get:319 http://deb.debian.org/debian stretch/main amd64 libio-sessiondata-perl all 1.03-1 [5782 B] Get:320 http://deb.debian.org/debian stretch/main amd64 libio-stringy-perl all 2.111-2 [61.2 kB] Get:321 http://deb.debian.org/debian stretch/main amd64 libjcode-pm-perl amd64 2.06-1 [30.9 kB] Get:322 http://deb.debian.org/debian stretch/main amd64 libjs-jquery all 3.1.1-2+deb9u1 [154 kB] Get:323 http://deb.debian.org/debian stretch/main amd64 libtypes-serialiser-perl all 1.0-1 [12.7 kB] Get:324 http://deb.debian.org/debian stretch/main amd64 libjson-xs-perl amd64 3.030-1 [91.6 kB] Get:325 http://deb.debian.org/debian stretch/main amd64 libnet-smtp-ssl-perl all 1.04-1 [6184 B] Get:326 http://deb.debian.org/debian stretch/main amd64 libmailtools-perl all 2.18-1 [88.5 kB] Get:327 http://deb.debian.org/debian stretch/main amd64 libmath-derivative-perl all 0.04-2 [7208 B] Get:328 http://deb.debian.org/debian stretch/main amd64 libmath-spline-perl all 0.02-1 [7992 B] Get:329 http://deb.debian.org/debian stretch/main amd64 libmime-tools-perl all 5.508-1 [212 kB] Get:330 http://deb.debian.org/debian stretch/main amd64 libmldbm-perl all 2.05-2 [18.4 kB] Get:331 http://deb.debian.org/debian stretch/main amd64 libole-storage-lite-perl all 0.19-1+deb9u1 [23.4 kB] Get:332 http://deb.debian.org/debian stretch/main amd64 libossp-uuid16 amd64 1.6.2-1.5+b4 [38.3 kB] Get:333 http://deb.debian.org/debian stretch/main amd64 libossp-uuid-perl amd64 1.6.2-1.5+b4 [28.7 kB] Get:334 http://deb.debian.org/debian stretch/main amd64 libpaper-utils amd64 1.1.24+nmu5 [17.6 kB] Get:335 http://deb.debian.org/debian stretch/main amd64 libpostscript-perl all 0.06-2 [31.4 kB] Get:336 http://deb.debian.org/debian stretch/main amd64 libsasl2-modules amd64 2.1.27~101-g0780600+dfsg-3+deb9u1 [102 kB] Get:337 http://deb.debian.org/debian stretch/main amd64 libtask-weaken-perl all 1.04-1 [7990 B] Get:338 http://deb.debian.org/debian stretch/main amd64 libsoap-lite-perl all 1.20-1 [259 kB] Get:339 http://deb.debian.org/debian stretch/main amd64 libsort-naturally-perl all 1.03-1 [13.9 kB] Get:340 http://deb.debian.org/debian stretch/main amd64 libspreadsheet-writeexcel-perl all 2.40-1 [550 kB] Get:341 http://deb.debian.org/debian stretch/main amd64 libunicode-map-perl amd64 0.112-11+b3 [145 kB] Get:342 http://deb.debian.org/debian stretch/main amd64 libspreadsheet-parseexcel-perl all 0.6500-1 [159 kB] Get:343 http://deb.debian.org/debian stretch/main amd64 libsub-name-perl amd64 0.21-1 [13.1 kB] Get:344 http://deb.debian.org/debian stretch/main amd64 libtree-dagnode-perl all 1.29-1 [60.6 kB] Get:345 http://deb.debian.org/debian stretch/main amd64 libsvg-graph-perl all 0.02-2 [130 kB] Get:346 http://deb.debian.org/debian stretch/main amd64 libtext-iconv-perl amd64 1.7-5+b4 [15.3 kB] Get:347 http://deb.debian.org/debian stretch/main amd64 libtie-ixhash-perl all 1.23-2 [11.7 kB] Get:348 http://deb.debian.org/debian stretch/main amd64 libtype-tiny-xs-perl amd64 0.012-1+b2 [26.8 kB] Get:349 http://deb.debian.org/debian stretch/main amd64 libxft2 amd64 2.3.2-1+b2 [56.5 kB] Get:350 http://deb.debian.org/debian stretch/main amd64 libxml-perl all 0.08-2 [113 kB] Get:351 http://deb.debian.org/debian stretch/main amd64 libxml-regexp-perl all 0.04-1 [8370 B] Get:352 http://deb.debian.org/debian stretch/main amd64 libxml-dom-perl all 1.44-2 [179 kB] Get:353 http://deb.debian.org/debian stretch/main amd64 libxml-xpathengine-perl all 0.13-1 [39.1 kB] Get:354 http://deb.debian.org/debian stretch/main amd64 libxml-dom-xpath-perl all 0.14-2 [9622 B] Get:355 http://deb.debian.org/debian stretch/main amd64 libxml-filter-buffertext-perl all 1.01-5 [7354 B] Get:356 http://deb.debian.org/debian stretch/main amd64 libxslt1.1 amd64 1.1.29-2.1+deb9u2 [233 kB] Get:357 http://deb.debian.org/debian stretch/main amd64 libxml-libxslt-perl amd64 1.95-1+b1 [46.8 kB] Get:358 http://deb.debian.org/debian stretch/main amd64 libxml-sax-writer-perl all 0.56-1 [23.7 kB] Get:359 http://deb.debian.org/debian stretch/main amd64 libxml-writer-perl all 0.625-1 [29.7 kB] Get:360 http://deb.debian.org/debian stretch/main amd64 libxmlrpc-lite-perl all 0.717-1 [26.1 kB] Get:361 http://deb.debian.org/debian stretch/main amd64 libyaml-0-2 amd64 0.1.7-2 [47.6 kB] Get:362 http://deb.debian.org/debian stretch/main amd64 libyaml-libyaml-perl amd64 0.63-2 [68.8 kB] Get:363 http://deb.debian.org/debian stretch/main amd64 libyaml-perl all 1.21-1 [64.8 kB] Get:364 http://deb.debian.org/debian stretch/main amd64 lynx-common all 2.8.9dev11-1 [1098 kB] Get:365 http://deb.debian.org/debian stretch/main amd64 mafft amd64 7.307-1 [889 kB] Get:366 http://deb.debian.org/debian stretch/main amd64 maq amd64 0.7.1-7 [311 kB] Get:367 http://deb.debian.org/debian stretch/main amd64 muscle amd64 1:3.8.31+dfsg-2 [151 kB] Get:368 http://deb.debian.org/debian stretch/main amd64 mustang amd64 3.2.3-1 [113 kB] Get:369 http://deb.debian.org/debian stretch/main amd64 perl-doc all 5.24.1-3+deb9u7 [7145 kB] Get:370 http://deb.debian.org/debian stretch/main amd64 perl-tk amd64 1:804.033-1+b3 [1943 kB] Get:371 http://deb.debian.org/debian stretch/main amd64 phylip amd64 1:3.696+dfsg-5 [942 kB] Get:372 http://deb.debian.org/debian stretch/main amd64 openmpi-common all 2.0.2-2 [149 kB] Get:373 http://deb.debian.org/debian stretch/main amd64 openmpi-bin amd64 2.0.2-2 [186 kB] Get:374 http://deb.debian.org/debian stretch/main amd64 phyml amd64 3:3.2.0+dfsg-7+b1 [1298 kB] Get:375 http://deb.debian.org/debian stretch/main amd64 poa amd64 2.0+20060928-4+b1 [45.4 kB] Get:376 http://deb.debian.org/debian stretch/main amd64 prank amd64 0.0.150803-2 [374 kB] Get:377 http://deb.debian.org/debian stretch/main amd64 primer3 amd64 2.3.7-3 [173 kB] Get:378 http://deb.debian.org/debian stretch/main amd64 probalign amd64 1.4-5 [65.4 kB] Get:379 http://deb.debian.org/debian stretch/main amd64 probcons amd64 1.12-11 [107 kB] Get:380 http://deb.debian.org/debian stretch/main amd64 proda amd64 1.0-10 [60.1 kB] Get:381 http://deb.debian.org/debian stretch/main amd64 psmisc amd64 22.21-2.1+b2 [123 kB] Get:382 http://deb.debian.org/debian stretch/main amd64 rubygems-integration all 1.11 [4994 B] Get:383 http://deb.debian.org/debian stretch/main amd64 ruby-did-you-mean all 1.0.0-2 [11.2 kB] Get:384 http://deb.debian.org/debian stretch/main amd64 ruby-minitest all 5.9.0-1 [51.1 kB] Get:385 http://deb.debian.org/debian stretch/main amd64 ruby-net-telnet all 0.1.1-2 [12.5 kB] Get:386 http://deb.debian.org/debian stretch/main amd64 ruby-power-assert all 0.3.0-1 [7902 B] Get:387 http://deb.debian.org/debian stretch/main amd64 ruby-test-unit all 3.1.7-2 [69.6 kB] Get:388 http://deb.debian.org/debian stretch/main amd64 libruby2.3 amd64 2.3.3-1+deb9u8 [3108 kB] Get:389 http://deb.debian.org/debian stretch/main amd64 ruby2.3 amd64 2.3.3-1+deb9u8 [189 kB] Get:390 http://deb.debian.org/debian stretch/main amd64 ruby amd64 1:2.3.3 [10.8 kB] Get:391 http://deb.debian.org/debian stretch/main amd64 rake all 10.5.0-2+deb9u1 [49.7 kB] Get:392 http://deb.debian.org/debian stretch/main amd64 raxml amd64 8.2.9+dfsg-1+b1 [1278 kB] Get:393 http://deb.debian.org/debian stretch/main amd64 rename all 0.20-4 [12.5 kB] Get:394 http://deb.debian.org/debian stretch/main amd64 samtools amd64 1.3.1-3 [254 kB] Get:395 http://deb.debian.org/debian stretch/main amd64 shared-mime-info amd64 1.8-1+deb9u1 [731 kB] Get:396 http://deb.debian.org/debian stretch/main amd64 sim4 amd64 0.0.20121010-4 [396 kB] Get:397 http://deb.debian.org/debian stretch/main amd64 ssl-cert all 1.0.39 [20.8 kB] Get:398 http://deb.debian.org/debian stretch/main amd64 t-coffee amd64 11.00.8cbe486-5 [1918 kB] Get:399 http://deb.debian.org/debian stretch/main amd64 tigr-glimmer amd64 3.02b-1 [283 kB] Get:400 http://deb.debian.org/debian stretch/main amd64 tm-align amd64 20160521+dfsg-2 [868 kB] Get:401 http://deb.debian.org/debian stretch/main amd64 unzip amd64 6.0-21+deb9u2 [172 kB] Get:402 http://deb.debian.org/debian stretch/main amd64 wise-data all 2.4.1-19 [108 kB] Get:403 http://deb.debian.org/debian stretch/main amd64 wise amd64 2.4.1-19 [993 kB] Get:404 http://deb.debian.org/debian stretch/main amd64 xdg-user-dirs amd64 0.15-2+b1 [52.2 kB] Get:405 http://deb.debian.org/debian stretch/main amd64 xml-core all 0.17 [23.2 kB] Get:406 http://deb.debian.org/debian stretch/main amd64 zip amd64 3.0-11+b1 [234 kB] Get:407 http://deb.debian.org/debian stretch/main amd64 bowtie amd64 1.1.2-6 [1618 kB] Get:408 http://deb.debian.org/debian stretch/main amd64 libev-perl amd64 4.22-1+b1 [240 kB] Get:409 http://deb.debian.org/debian stretch/main amd64 libset-scalar-perl all 1.29-2 [31.4 kB] Get:410 http://deb.debian.org/debian stretch/main amd64 lynx amd64 2.8.9dev11-1 [632 kB] Get:411 http://deb.debian.org/debian stretch/main amd64 med-config all 3.0.1 [17.1 kB] Get:412 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 248 MB in 2s (108 MB/s) Selecting previously unselected package perl-modules-5.24. (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-perl-modules-5.24_5.24.1-3+deb9u7_all.deb ... Unpacking perl-modules-5.24 (5.24.1-3+deb9u7) ... Selecting previously unselected package libgdbm3:amd64. Preparing to unpack .../01-libgdbm3_1.8.3-14_amd64.deb ... Unpacking libgdbm3:amd64 (1.8.3-14) ... Selecting previously unselected package libperl5.24:amd64. Preparing to unpack .../02-libperl5.24_5.24.1-3+deb9u7_amd64.deb ... Unpacking libperl5.24:amd64 (5.24.1-3+deb9u7) ... Selecting previously unselected package perl. Preparing to unpack .../03-perl_5.24.1-3+deb9u7_amd64.deb ... Unpacking perl (5.24.1-3+deb9u7) ... Selecting previously unselected package libpython2.7-minimal:amd64. Preparing to unpack .../04-libpython2.7-minimal_2.7.13-2+deb9u3_amd64.deb ... Unpacking libpython2.7-minimal:amd64 (2.7.13-2+deb9u3) ... Selecting previously unselected package python2.7-minimal. Preparing to unpack .../05-python2.7-minimal_2.7.13-2+deb9u3_amd64.deb ... Unpacking python2.7-minimal (2.7.13-2+deb9u3) ... Selecting previously unselected package python-minimal. Preparing to unpack .../06-python-minimal_2.7.13-2_amd64.deb ... Unpacking python-minimal (2.7.13-2) ... Selecting previously unselected package mime-support. Preparing to unpack .../07-mime-support_3.60_all.deb ... Unpacking mime-support (3.60) ... 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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 bwa (0.7.15-2+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 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 libnuma1:amd64 (2.0.11-2.1) ... 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 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 dialign (2.2.1-8) ... Setting up libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Setting up menu (2.1.47+b1) ... Setting up apache2-data (2.4.25-3+deb9u9) ... Setting up libdatrie1:amd64 (0.2.10-4+b1) ... Setting up libtiff5:amd64 (4.0.8-2+deb9u5) ... Setting up libmariadbclient18:amd64 (10.1.45-0+deb9u1) ... 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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 libssl1.0.2:amd64 (1.0.2u-1~deb9u1) ... Setting up libxml-sax-base-perl (1.07-1) ... 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 libyaml-0-2:amd64 (0.1.7-2) ... 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 libssh2-1:amd64 (1.7.0-1+deb9u1) ... 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 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 libunistring0:amd64 (0.9.6+really0.9.3-0.1) ... 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 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 libijs-0.35:amd64 (0.35-12) ... Setting up libsqlite3-0:amd64 (3.16.2-5+deb9u1) ... Setting up libann0 (1.1.2+doc-6) ... 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 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 libxml-xpathengine-perl (0.13-1) ... Setting up libnet-http-perl (6.12-1) ... 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 libffi6:amd64 (3.2.1-6) ... Setting up liblua5.2-0:amd64 (5.2.4-1.1+b2) ... Setting up libconvert-binary-c-perl (0.78-1+b1) ... Setting up libthai-data (0.1.26-1) ... Setting up libxdmcp6:amd64 (1:1.1.2-3) ... Setting up xml-core (0.17) ... Setting up javascript-common (11) ... Package apache2 is not configured yet. Will defer actions by package javascript-common. Setting up ocl-icd-libopencl1:amd64 (2.2.11-1) ... Setting up libkeyutils1:amd64 (1.5.9-9) ... Setting up libsasl2-modules:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Setting up libconvert-binhex-perl (1.125-1) ... Setting up libstring-approx-perl (3.27-1+b4) ... Setting up libio-sessiondata-perl (1.03-1) ... Setting up libjson-perl (2.90-1) ... Setting up libnl-3-200:amd64 (3.2.27-2) ... Setting up libpadwalker-perl (2.2-2+b1) ... Setting up ruby-minitest (5.9.0-1) ... Setting up libjs-prototype (1.7.1-3) ... 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 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 libalgorithm-munkres-perl (0.08-3) ... Setting up libyaml-libyaml-perl (0.63-2) ... Setting up libpostscript-perl (0.06-2) ... Setting up libparams-classify-perl (0.013-6+b1) ... 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 libguard-perl (1.023-1+b2) ... 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 libidn11:amd64 (1.33-1+deb9u1) ... Setting up libdbus-1-3:amd64 (1.10.32-0+deb9u1) ... Setting up hyphy-common (2.2.7+dfsg-1) ... Setting up libclass-inspector-perl (1.31-1) ... 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 libtask-weaken-perl (1.04-1) ... Setting up netbase (5.4) ... Setting up libwebp6:amd64 (0.5.2-1) ... Setting up libhtml-tagset-perl (3.20-3) ... Setting up libpaper1:amd64 (1.1.24+nmu5) ... Creating config file /etc/papersize with new version Setting up libdevel-symdump-perl (2.17-1) ... Setting up mafft (7.307-1) ... Setting up libio-stringy-perl (2.111-2) ... Setting up libcommon-sense-perl (3.74-2) ... Setting up libhpdf-2.2.1 (2.2.1-1.1+b1) ... Setting up libipc-sharelite-perl (0.17-4) ... Setting up libsub-exporter-progressive-perl (0.001013-1) ... 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 fontconfig-config (2.11.0-6.7) ... Setting up libidn2-0:amd64 (0.16-1+deb9u1) ... 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 libanyevent-perl (7.130-2) ... Setting up libio-pty-perl (1:1.08-1.1+b2) ... Setting up libencode-locale-perl (1.05-1) ... 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 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 libbio-asn1-entrezgene-perl (1.720-1) ... Setting up perl-openssl-defaults:amd64 (3) ... Setting up libfreezethaw-perl (0.5001-1) ... Setting up apache2-utils (2.4.25-3+deb9u9) ... 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 mummer (3.23+dfsg-2) ... Setting up libasync-interrupt-perl (1.21-1+b2) ... 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 libio-html-perl (1.001-1) ... Setting up libexporter-tiny-perl (0.042-1) ... Setting up libossp-uuid-perl (1.6.2-1.5+b4) ... Setting up libtie-ixhash-perl (1.23-2) ... Setting up libev-perl (4.22-1+b1) ... Setting up exonerate (2.4.0-2) ... Setting up libcarp-clan-perl (6.06-1) ... 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 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 libnl-route-3-200:amd64 (3.2.27-2) ... Setting up ssl-cert (1.0.39) ... Setting up libthai0:amd64 (0.1.26-1) ... Setting up libtype-tiny-xs-perl (0.012-1+b2) ... Setting up libjs-scriptaculous (1.9.0-2) ... Setting up libjcode-pm-perl (2.06-1) ... Setting up file (1:5.30-1+deb9u3) ... Setting up libtypes-serialiser-perl (1.0-1) ... 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 sqlite3 (3.16.2-5+deb9u1) ... Setting up libterm-readkey-perl (2.37-1) ... Setting up fsa (1.15.9+dfsg-3) ... Setting up libpython-stdlib:amd64 (2.7.13-2) ... Setting up libhwloc-plugins (1.11.5-1) ... Setting up libdrm-intel1:amd64 (2.4.74-1) ... Setting up libalgorithm-diff-xs-perl (0.04-4+b2) ... Setting up libanyevent-http-perl (2.23-1) ... Setting up wise (2.4.1-19) ... Setting up libp11-kit0:amd64 (0.23.3-2) ... Setting up libhtml-parser-perl (3.72-3) ... 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 libavahi-common3:amd64 (0.6.32-2) ... 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 libdbd-mysql-perl (4.041-2) ... Setting up libbio-perl-run-perl (1.7.1-3) ... 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 libanyevent-cachedns-perl (0.08-2) ... 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 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 libsm6:amd64 (2:1.2.2-1+b3) ... Setting up libk5crypto3:amd64 (1.15-1+deb9u1) ... Setting up libhttp-date-perl (6.02-1) ... Setting up libcgi-session-perl (4.48-3) ... 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 libimport-into-perl (1.002005-1) ... Setting up libcache-cache-perl (1.08-2) ... Setting up libnet-ssleay-perl (1.80-1) ... Setting up libtype-tiny-perl (1.000005-1) ... Setting up libgnutls30:amd64 (3.5.8-5+deb9u5) ... Setting up libx11-6:amd64 (2:1.6.4-3+deb9u1) ... Setting up libjson-xs-perl (3.030-1) ... Setting up librtmp1:amd64 (2.4+20151223.gitfa8646d.1-1+b1) ... Setting up librdmacm1 (1.1.0-2) ... Setting up libio-socket-ssl-perl (2.044-1) ... Setting up libcgi-fast-perl (1:2.12-1) ... Setting up libhtml-tree-perl (5.03-2) ... Setting up libbio-coordinate-perl (1.7.1-1) ... 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 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 libxrender1:amd64 (1:0.9.10-1) ... Setting up libmoo-perl (2.002005-1) ... Setting up libhttp-message-perl (6.11-1) ... Setting up libavahi-client3:amd64 (0.6.32-2) ... Setting up libkrb5-3:amd64 (1.15-1+deb9u1) ... Setting up libgts-bin (0.7.6+darcs121130-4) ... 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 fontconfig (2.11.0-6.7+b1) ... Regenerating fonts cache... done. Setting up libhttp-negotiate-perl (6.00-2) ... 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 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 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 libgd-perl (2.53-3) ... Setting up libxmu6:amd64 (2:1.1.2-2) ... Setting up libgssapi-krb5-2:amd64 (1.15-1+deb9u1) ... Setting up libxml-simple-perl (2.22-1) ... Setting up libgd-svg-perl (0.33-1) ... Setting up libpq5:amd64 (9.6.17-0+deb9u1) ... Setting up libxml-libxslt-perl (1.95-1+b1) ... 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 libhtml-form-perl (6.03-1) ... Setting up libopenmpi2:amd64 (2.0.2-2) ... Setting up beignet-opencl-icd:amd64 (1.3.0-4) ... Setting up libcups2:amd64 (2.2.1-8+deb9u6) ... Setting up libxaw7:amd64 (2:1.0.13-1+b2) ... Setting up ncbi-blast+-legacy (2.6.0-1) ... Setting up libcairo2:amd64 (1.14.8-1) ... Setting up libmailtools-perl (2.18-1) ... Setting up apache2 (2.4.25-3+deb9u9) ... Enabling module mpm_event. Enabling module authz_core. Enabling module authz_host. Enabling module authn_core. Enabling module auth_basic. Enabling module access_compat. Enabling module authn_file. Enabling module authz_user. Enabling module alias. Enabling module dir. Enabling module autoindex. Enabling module env. Enabling module mime. Enabling module negotiation. Enabling module setenvif. Enabling module filter. Enabling module deflate. Enabling module status. Enabling module reqtimeout. Enabling conf charset. Enabling conf localized-error-pages. Enabling conf other-vhosts-access-log. Enabling conf security. Enabling conf serve-cgi-bin. Enabling site 000-default. info: Executing deferred 'a2enconf javascript-common' for package javascript-common Enabling conf javascript-common. invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up libbio-graphics-perl (2.40-1) ... Setting up libcurl3-gnutls:amd64 (7.52.1-5+deb9u10) ... Setting up blast2 (1:2.6.0-1) ... Setting up libhmsbeagle1v5 (2.1.2+20160831-5) ... Setting up libdbd-pg-perl (3.5.3-1+b2) ... 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 libpangoft2-1.0-0:amd64 (1.40.5-1) ... Setting up libcupsimage2:amd64 (2.2.1-8+deb9u6) ... Setting up emboss (6.6.0+dfsg-6) ... 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 libstaden-read11:amd64 (1.14.8-2) ... Setting up hyphy-mpi (2.2.7+dfsg-1+b2) ... 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 libbio-scf-perl (1.03-3) ... Setting up libgvc6 (2.38.0-17) ... Setting up graphviz (2.38.0-17) ... 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 153) ... 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) ... apache2_invoke: Enable module perl invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of restart. Setting up libvm-ec2-perl (1.28-2) ... Setting up rake (10.5.0-2+deb9u1) ... Setting up gbrowse (2.56+dfsg-2) ... apache2_invoke: Enable configuration gbrowse invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of reload. Setting up libxml-parser-perl (2.44-2+b1) ... Setting up libapache2-reload-perl (0.13-1) ... 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 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. 0m53.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'apt-get', '-y', 'install', 'gbrowse=2.56+dfsg-2'] 0m53.9s INFO: Running scripts post_install 0m53.9s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/post_install_exceptions'] 0m53.9s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/post_install_exceptions'] 0m54.0s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppkudj_pn'] 0m55.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppkudj_pn'] 0m59.0s ERROR: WARN: Broken symlinks: /usr/share/gbrowse/htdocs/i -> debian/gbrowse/var/cache/gbrowse/images (gbrowse) 1m0.4s DEBUG: Starting command: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', '-ac', '--ignore-obsolete'] 1m4.5s DEBUG: Command ok: ['debsums', '--root', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', '-ac', '--ignore-obsolete'] 1m4.5s DEBUG: Starting command: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m4.5s DUMP: 0.15.6 1m4.5s DEBUG: Command ok: ['dpkg-query', '-f', '${Version}\n', '-W', 'adequate'] 1m4.5s INFO: Running adequate version 0.15.6 now. 1m4.5s DEBUG: Starting command: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'gbrowse'] 1m4.7s DUMP: gbrowse: broken-symlink /usr/share/gbrowse/htdocs/i -> debian/gbrowse/var/cache/gbrowse/images 1m4.7s DEBUG: Command ok: ['adequate', '--root', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'gbrowse'] 1m4.7s ERROR: WARN: Inadequate results from running adequate! gbrowse: broken-symlink /usr/share/gbrowse/htdocs/i -> debian/gbrowse/var/cache/gbrowse/images 1m4.7s ERROR: WARN: Running adequate resulted in less interesting tags found: broken-symlink 1m4.7s INFO: Running scripts pre_remove 1m4.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/pre_remove_40_find_missing_md5sums'] 1m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m4.8s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/pre_remove_40_find_obsolete_conffiles'] 1m4.8s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m11.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/pre_remove_40_find_unowned_lib_links'] 1m11.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m11.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/pre_remove_50_find_bad_permissions'] 1m11.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m11.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/pre_remove_50_find_missing_copyright'] 1m11.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/pre_remove_exceptions'] 1m11.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/pre_remove_exceptions'] 1m11.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m11.7s DUMP: install ok installed adduser adduser 3.115 install ok installed amap-align amap-align 2.2-6 install ok installed apache2 apache2 2.4.25-3+deb9u9 install ok installed apache2-bin apache2-bin 2.4.25-3+deb9u9 install ok installed apache2-data apache2-data 2.4.25-3+deb9u9 install ok installed apache2-utils apache2-utils 2.4.25-3+deb9u9 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 bedtools bedtools 2.26.0+dfsg-3 install ok installed beignet-opencl-icd:amd64 beignet-opencl-icd 1.3.0-4 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 bwa bwa 0.7.15-2+deb9u1 install ok installed bzip2 bzip2 1.0.6-8.1 install ok installed ca-certificates ca-certificates 20200601~deb9u1 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 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 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 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 exonerate exonerate 2.4.0-2 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 gawk gawk 1:4.1.4+dfsg-1 install ok installed gbrowse gbrowse 2.56+dfsg-2 install ok installed gcc-6-base:amd64 gcc-6-base 6.3.0-18+deb9u1 install ok installed ghostscript ghostscript 9.26a~dfsg-0+deb9u6 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 gzip gzip 1.6-5+b1 install ok installed hmmer hmmer 3.1b2+dfsg-5 install ok installed hostname hostname 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libanyevent-perl 7.130-2 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 libasync-interrupt-perl libasync-interrupt-perl 1.21-1+b2 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 libbio-asn1-entrezgene-perl libbio-asn1-entrezgene-perl 1.720-1 install ok installed libbio-coordinate-perl libbio-coordinate-perl 1.7.1-1 install ok installed libbio-graphics-perl libbio-graphics-perl 2.40-1 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 libbio-scf-perl libbio-scf-perl 1.03-3 install ok installed libbit-vector-perl libbit-vector-perl 7.4-1+b2 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 libc-bin libc-bin 2.24-11+deb9u4 install ok installed libc6:amd64 libc6 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 libcarp-clan-perl libcarp-clan-perl 6.06-1 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 libcgi-session-perl libcgi-session-perl 4.48-3 install ok installed libcgraph6 libcgraph6 2.38.0-17 install ok installed libclass-inspector-perl libclass-inspector-perl 1.31-1 install ok installed libclass-method-modifiers-perl libclass-method-modifiers-perl 2.12-1 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 libcommon-sense-perl libcommon-sense-perl 3.74-2 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-gnutls:amd64 libcurl3-gnutls 7.52.1-5+deb9u10 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-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 libdivsufsort3:amd64 libdivsufsort3 2.0.1-2 install ok installed libdrm-intel1:amd64 libdrm-intel1 2.4.74-1 install ok installed libdrm2:amd64 libdrm2 2.4.74-1 install ok installed libencode-locale-perl libencode-locale-perl 1.05-1 install ok installed liberror-perl liberror-perl 0.17024-1 install ok installed libev-perl libev-perl 4.22-1+b1 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 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-listing-perl libfile-listing-perl 6.04-1 install ok installed libfile-slurp-tiny-perl libfile-slurp-tiny-perl 0.003-1 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 libfreetype6:amd64 libfreetype6 2.6.3-3.2+deb9u1 install ok installed libfreezethaw-perl libfreezethaw-perl 0.5001-1 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 libgd-svg-perl libgd-svg-perl 0.33-1 install ok installed libgd3:amd64 libgd3 2.2.4-2+deb9u5 install ok installed libgdbm3:amd64 libgdbm3 1.8.3-14 install ok installed libgfortran3:amd64 libgfortran3 6.3.0-18+deb9u1 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 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 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 libguard-perl libguard-perl 1.023-1+b2 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 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-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-sharelite-perl libipc-sharelite-perl 0.17-4 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 libjpeg62-turbo:amd64 libjpeg62-turbo 1:1.5.1-2 install ok installed libjs-jquery libjs-jquery 3.1.1-2+deb9u1 install ok installed libjs-prototype libjs-prototype 1.7.1-3 install ok installed libjs-scriptaculous libjs-scriptaculous 1.9.0-2 install ok installed libjson-perl libjson-perl 2.90-1 install ok installed libjson-xs-perl libjson-xs-perl 3.030-1 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 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 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 liblzma5:amd64 liblzma5 5.2.2-1.2+b1 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 libmailtools-perl libmailtools-perl 2.18-1 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-tools-perl libmime-tools-perl 5.508-1 install ok installed libmldbm-perl libmldbm-perl 2.05-2 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 libmount1:amd64 libmount1 2.29.2-1+deb9u1 install ok installed libmpfr4:amd64 libmpfr4 3.1.5-1 install ok installed libncurses5:amd64 libncurses5 6.0+20161126-1+deb9u2 install ok installed libncursesw5:amd64 libncursesw5 6.0+20161126-1+deb9u2 install ok installed 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 libnuma1:amd64 libnuma1 2.0.11-2.1 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 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 libparse-recdescent-perl libparse-recdescent-perl 1.967013+dfsg-1 install ok installed libpathplan4 libpathplan4 2.38.0-17 install ok installed libpciaccess0:amd64 libpciaccess0 0.13.4-1+b2 install ok installed libpcre3:amd64 libpcre3 2:8.39-3 install ok installed libperl5.24:amd64 libperl5.24 5.24.1-3+deb9u7 install ok installed libpixman-1-0:amd64 libpixman-1-0 0.34.0-1 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-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 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 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 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 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 libstaden-read11:amd64 libstaden-read11 1.14.8-2 install ok installed libstatistics-descriptive-perl libstatistics-descriptive-perl 3.0612-1 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 libstring-approx-perl libstring-approx-perl 3.27-1+b4 install ok installed libsub-exporter-progressive-perl libsub-exporter-progressive-perl 0.001013-1 install ok installed libsub-name-perl libsub-name-perl 0.21-1 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 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 libterm-readkey-perl libterm-readkey-perl 2.37-1 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 libtinfo5:amd64 libtinfo5 6.0+20161126-1+deb9u2 install ok installed libtree-dagnode-perl libtree-dagnode-perl 1.29-1 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 libtypes-serialiser-perl libtypes-serialiser-perl 1.0-1 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 libvm-ec2-perl libvm-ec2-perl 1.28-2 install ok installed libwebp6:amd64 libwebp6 0.5.2-1 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 libxau6:amd64 libxau6 1:1.0.8-1 install ok installed libxaw7:amd64 libxaw7 2:1.0.13-1+b2 install ok installed libxcb-render0:amd64 libxcb-render0 1.12-1 install ok installed libxcb-shm0:amd64 libxcb-shm0 1.12-1 install ok installed libxcb1:amd64 libxcb1 1.12-1 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 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 libxpm4:amd64 libxpm4 1:3.5.12-1 install ok installed libxrender1:amd64 libxrender1 1:0.9.10-1 install ok installed libxslt1.1:amd64 libxslt1.1 1.1.29-2.1+deb9u2 install ok installed libxt6:amd64 libxt6 1:1.1.5-1 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 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 maq maq 0.7.1-7 install ok installed mawk mawk 1.3.3-17+b3 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 passwd passwd 1:4.4-4.1 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 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 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 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 sqlite3 sqlite3 3.16.2-5+deb9u1 install ok installed ssl-cert ssl-cert 1.0.39 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 tigr-glimmer tigr-glimmer 3.02b-1 install ok installed tm-align tm-align 20160521+dfsg-2 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 xdg-user-dirs xdg-user-dirs 0.15-2+b1 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 1m11.7s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'dpkg-query', '-W', '-f', '${Status}\\t${binary:Package}\\t${Package}\\t${Version}\\n'] 1m11.7s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'apt-get', 'remove', 'amap-align', 'apache2', 'apache2-bin', 'apache2-data', 'apache2-utils', 'bedtools', 'beignet-opencl-icd:amd64', 'bioperl', 'bioperl-run', 'blast2', 'blends-common', 'bowtie', 'bwa', 'bzip2', 'ca-certificates', 'clustalo', 'clustalw', 'dbus', 'dialign', 'dialign-tx', 'dialign-tx-data', 'emboss', 'emboss-data', 'emboss-lib', 'exonerate', 'file', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-droid-fallback', 'fonts-lato', 'fonts-liberation', 'fonts-noto-mono', 'fsa', 'gawk', 'ghostscript', 'graphviz', 'gsfonts', 'hmmer', 'hyphy-common', 'hyphy-mpi', 'infernal', 'javascript-common', 'kalign', 'krb5-locales', 'libace-perl', 'libalgorithm-diff-perl', 'libalgorithm-diff-xs-perl', 'libalgorithm-munkres-perl', 'libann0', 'libanyevent-cachedns-perl', 'libanyevent-http-perl', 'libanyevent-perl', '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', 'libasync-interrupt-perl', 'libauthen-sasl-perl', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbio-asn1-entrezgene-perl', 'libbio-coordinate-perl', 'libbio-graphics-perl', 'libbio-perl-perl', 'libbio-perl-run-perl', 'libbio-scf-perl', 'libbit-vector-perl', 'libbsd-resource-perl', 'libbsd0:amd64', 'libcache-cache-perl', 'libcairo2:amd64', 'libcarp-clan-perl', 'libcdt5', 'libcgi-fast-perl', 'libcgi-pm-perl', 'libcgi-session-perl', 'libcgraph6', 'libclass-inspector-perl', 'libclass-method-modifiers-perl', 'libclass-xsaccessor-perl', 'libclone-perl', 'libcommon-sense-perl', 'libconvert-binary-c-perl', 'libconvert-binhex-perl', 'libcrypt-rc4-perl', 'libcups2:amd64', 'libcupsfilters1:amd64', 'libcupsimage2:amd64', 'libcurl3-gnutls:amd64', '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-symdump-perl', 'libdigest-perl-md5-perl', 'libdivsufsort3:amd64', 'libdrm-intel1:amd64', 'libdrm2:amd64', 'libencode-locale-perl', 'liberror-perl', 'libev-perl', 'libexpat1:amd64', 'libexporter-tiny-perl', 'libfabric1', 'libfcgi-perl', 'libffi6:amd64', 'libfile-listing-perl', 'libfile-slurp-tiny-perl', 'libfont-afm-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfreezethaw-perl', 'libgd-perl', 'libgd-svg-perl', 'libgd3:amd64', 'libgdbm3:amd64', 'libgfortran3:amd64', 'libglib2.0-0:amd64', 'libglib2.0-data', 'libgmp10:amd64', 'libgnutls30:amd64', 'libgomp1:amd64', 'libgpm2:amd64', 'libgraph-perl', 'libgraphite2-3:amd64', 'libgraphviz-perl', 'libgs9:amd64', 'libgs9-common', 'libgssapi-krb5-2:amd64', 'libgts-0.7-5:amd64', 'libgts-bin', 'libguard-perl', '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', 'libicu57:amd64', 'libidn11:amd64', 'libidn2-0:amd64', 'libijs-0.35:amd64', 'libimport-into-perl', 'libio-html-perl', 'libio-pty-perl', 'libio-sessiondata-perl', 'libio-socket-ssl-perl', 'libio-string-perl', 'libio-stringy-perl', 'libipc-run-perl', 'libipc-sharelite-perl', 'libjbig0:amd64', 'libjbig2dec0:amd64', 'libjcode-pm-perl', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-prototype', 'libjs-scriptaculous', 'libjson-perl', 'libjson-xs-perl', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'liblist-moreutils-perl', 'libltdl7:amd64', 'liblua5.2-0:amd64', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'libmagic-mgc', 'libmagic1:amd64', 'libmailtools-perl', 'libmariadbclient18:amd64', 'libmath-derivative-perl', 'libmath-spline-perl', 'libmime-tools-perl', 'libmldbm-perl', 'libmodule-runtime-perl', 'libmoo-perl', 'libmpfr4:amd64', 'libncurses5:amd64', 'libnet-http-perl', 'libnet-smtp-ssl-perl', 'libnet-ssleay-perl', 'libnettle6:amd64', 'libnghttp2-14:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnuma1:amd64', 'libole-storage-lite-perl', 'libopenjp2-7:amd64', 'libopenmpi2:amd64', 'libossp-uuid-perl', 'libossp-uuid16:amd64', 'libp11-kit0:amd64', 'libpadwalker-perl', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libparams-classify-perl', 'libparse-recdescent-perl', 'libpathplan4', 'libpciaccess0:amd64', 'libperl5.24:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libpostscript-perl', 'libpq5:amd64', 'libprocps6:amd64', 'libpsl5:amd64', 'libpsm-infinipath1', 'libpython-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'librdmacm1', 'libreadline7:amd64', 'librole-tiny-perl', 'librtmp1:amd64', 'libruby2.3:amd64', 'libsasl2-2:amd64', 'libsasl2-modules:amd64', 'libsasl2-modules-db:amd64', 'libset-scalar-perl', 'libsigsegv2:amd64', 'libsm6:amd64', 'libsoap-lite-perl', 'libsort-naturally-perl', 'libspreadsheet-parseexcel-perl', 'libspreadsheet-writeexcel-perl', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.0.2:amd64', 'libssl1.1:amd64', 'libstaden-read11:amd64', 'libstatistics-descriptive-perl', 'libstrictures-perl', 'libstring-approx-perl', 'libsub-exporter-progressive-perl', 'libsub-name-perl', 'libsvg-graph-perl', 'libsvg-perl', 'libtask-weaken-perl', 'libtasn1-6:amd64', 'libterm-readkey-perl', 'libtext-iconv-perl', 'libthai-data', 'libthai0:amd64', 'libtie-ixhash-perl', 'libtiff5:amd64', 'libtimedate-perl', 'libtree-dagnode-perl', 'libtype-tiny-perl', 'libtype-tiny-xs-perl', 'libtypes-serialiser-perl', 'libunicode-map-perl', 'libunistring0:amd64', 'liburi-perl', 'libvm-ec2-perl', 'libwebp6:amd64', 'libwww-perl', 'libwww-robotrules-perl', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxaw7:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxdot4', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2: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', 'libxpm4:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxt6:amd64', 'libyaml-0-2:amd64', 'libyaml-libyaml-perl', 'libyaml-perl', 'lsb-base', 'lynx', 'lynx-common', 'mafft', 'maq', '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', 'perl', 'perl-doc', 'perl-modules-5.24', 'perl-openssl-defaults:amd64', 'perl-tk', 'phylip', 'phyml', 'poa', 'poppler-data', 'prank', 'primer3', 'probalign', 'probcons', 'procps', 'proda', 'psmisc', 'publicsuffix', 'python', 'python-minimal', 'python2.7', 'python2.7-minimal', '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', 'sqlite3', 'ssl-cert', 't-coffee', 'tigr-glimmer', 'tm-align', 'ucf', 'unzip', 'wise', 'wise-data', 'x11-common', 'xdg-user-dirs', 'xml-core', 'xz-utils', 'zip', 'gbrowse'] 1m15.3s DUMP: Reading package lists... Building dependency tree... Reading state information... The following packages will be REMOVED: amap-align apache2 apache2-bin apache2-data apache2-utils bedtools beignet-opencl-icd bioperl bioperl-run blast2 blends-common bowtie bwa bzip2 ca-certificates clustalo clustalw dbus dialign dialign-tx dialign-tx-data emboss emboss-data emboss-lib exonerate file fontconfig fontconfig-config fonts-dejavu-core fonts-droid-fallback fonts-lato fonts-liberation fonts-noto-mono fsa gawk gbrowse ghostscript graphviz gsfonts hmmer hyphy-common hyphy-mpi infernal javascript-common kalign krb5-locales libace-perl libalgorithm-diff-perl libalgorithm-diff-xs-perl libalgorithm-munkres-perl libann0 libanyevent-cachedns-perl libanyevent-http-perl libanyevent-perl libapache-dbi-perl libapache2-mod-perl2 libapache2-reload-perl libapparmor1 libapr1 libaprutil1 libaprutil1-dbd-sqlite3 libaprutil1-ldap libargtable2-0 libarray-compare-perl libasync-interrupt-perl libauthen-sasl-perl libavahi-client3 libavahi-common-data libavahi-common3 libbio-asn1-entrezgene-perl libbio-coordinate-perl libbio-graphics-perl libbio-perl-perl libbio-perl-run-perl libbio-scf-perl libbit-vector-perl libbsd-resource-perl libbsd0 libcache-cache-perl libcairo2 libcarp-clan-perl libcdt5 libcgi-fast-perl libcgi-pm-perl libcgi-session-perl libcgraph6 libclass-inspector-perl libclass-method-modifiers-perl libclass-xsaccessor-perl libclone-perl libcommon-sense-perl libconvert-binary-c-perl libconvert-binhex-perl libcrypt-rc4-perl libcups2 libcupsfilters1 libcupsimage2 libcurl3-gnutls 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-symdump-perl libdigest-perl-md5-perl libdivsufsort3 libdrm-intel1 libdrm2 libencode-locale-perl liberror-perl libev-perl libexpat1 libexporter-tiny-perl libfabric1 libfcgi-perl libffi6 libfile-listing-perl libfile-slurp-tiny-perl libfont-afm-perl libfontconfig1 libfreetype6 libfreezethaw-perl libgd-perl libgd-svg-perl libgd3 libgdbm3 libgfortran3 libglib2.0-0 libglib2.0-data libgmp10 libgnutls30 libgomp1 libgpm2 libgraph-perl libgraphite2-3 libgraphviz-perl libgs9 libgs9-common libgssapi-krb5-2 libgts-0.7-5 libgts-bin libguard-perl 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 libicu57 libidn11 libidn2-0 libijs-0.35 libimport-into-perl libio-html-perl libio-pty-perl libio-sessiondata-perl libio-socket-ssl-perl libio-string-perl libio-stringy-perl libipc-run-perl libipc-sharelite-perl libjbig0 libjbig2dec0 libjcode-pm-perl libjpeg62-turbo libjs-jquery libjs-prototype libjs-scriptaculous libjson-perl libjson-xs-perl libk5crypto3 libkeyutils1 libkrb5-3 libkrb5support0 liblcms2-2 libldap-2.4-2 libldap-common liblist-moreutils-perl libltdl7 liblua5.2-0 liblwp-mediatypes-perl liblwp-protocol-https-perl libmagic-mgc libmagic1 libmailtools-perl libmariadbclient18 libmath-derivative-perl libmath-spline-perl libmime-tools-perl libmldbm-perl libmodule-runtime-perl libmoo-perl libmpfr4 libncurses5 libnet-http-perl libnet-smtp-ssl-perl libnet-ssleay-perl libnettle6 libnghttp2-14 libnl-3-200 libnl-route-3-200 libnuma1 libole-storage-lite-perl libopenjp2-7 libopenmpi2 libossp-uuid-perl libossp-uuid16 libp11-kit0 libpadwalker-perl libpango-1.0-0 libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 libparams-classify-perl libparse-recdescent-perl libpathplan4 libpciaccess0 libperl5.24 libpixman-1-0 libpng16-16 libpostscript-perl libpq5 libprocps6 libpsl5 libpsm-infinipath1 libpython-stdlib libpython2.7-minimal libpython2.7-stdlib libquadmath0 librdmacm1 libreadline7 librole-tiny-perl librtmp1 libruby2.3 libsasl2-2 libsasl2-modules libsasl2-modules-db libset-scalar-perl libsigsegv2 libsm6 libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libsqlite3-0 libssh2-1 libssl1.0.2 libssl1.1 libstaden-read11 libstatistics-descriptive-perl libstrictures-perl libstring-approx-perl libsub-exporter-progressive-perl libsub-name-perl libsvg-graph-perl libsvg-perl libtask-weaken-perl libtasn1-6 libterm-readkey-perl libtext-iconv-perl libthai-data libthai0 libtie-ixhash-perl libtiff5 libtimedate-perl libtree-dagnode-perl libtype-tiny-perl libtype-tiny-xs-perl libtypes-serialiser-perl libunicode-map-perl libunistring0 liburi-perl libvm-ec2-perl libwebp6 libwww-perl libwww-robotrules-perl libx11-6 libx11-data libxau6 libxaw7 libxcb-render0 libxcb-shm0 libxcb1 libxdmcp6 libxdot4 libxext6 libxfixes3 libxft2 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 libxpm4 libxrender1 libxslt1.1 libxt6 libyaml-0-2 libyaml-libyaml-perl libyaml-perl lsb-base lynx lynx-common mafft maq 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 perl perl-doc perl-modules-5.24 perl-openssl-defaults perl-tk phylip phyml poa poppler-data prank primer3 probalign probcons procps proda psmisc publicsuffix python python-minimal python2.7 python2.7-minimal 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 sqlite3 ssl-cert t-coffee tigr-glimmer tm-align ucf unzip wise wise-data x11-common xdg-user-dirs xml-core xz-utils zip 0 upgraded, 0 newly installed, 412 to remove and 0 not upgraded. After this operation, 1154 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 ... 29057 files and directories currently installed.) Removing amap-align (2.2-6) ... Removing gbrowse (2.56+dfsg-2) ... Conf gbrowse disabled. apache2_invoke prerm: Disable configuration gbrowse invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of reload. Removing apache2 (2.4.25-3+deb9u9) ... invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of stop. 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) ... dpkg: warning: while removing apache2-bin, directory '/var/lib/apache2' not empty so not removed Removing apache2-data (2.4.25-3+deb9u9) ... Removing apache2-utils (2.4.25-3+deb9u9) ... 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 libbio-coordinate-perl (1.7.1-1) ... Removing libbio-graphics-perl (2.40-1) ... Removing bioperl-run (1.7.1-3) ... 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 libvm-ec2-perl (1.28-2) ... 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 clustalo (1.2.4-1) ... Removing clustalw (2.1+lgpl-5) ... 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 emboss (6.6.0+dfsg-6) ... Removing emboss-data (6.6.0+dfsg-6) ... Removing emboss-lib (6.6.0+dfsg-6) ... Removing fsa (1.15.9+dfsg-3) ... Removing exonerate (2.4.0-2) ... 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 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 perl-tk (1:804.033-1+b3) ... Removing libxft2:amd64 (2.3.2-1+b2) ... Removing libgd-svg-perl (0.33-1) ... Removing libgd-perl (2.53-3) ... Removing libgd3:amd64 (2.2.4-2+deb9u5) ... 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 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 ghostscript (9.26a~dfsg-0+deb9u6) ... Removing gsfonts (1:8.11+urwcyr1.0.7~pre44-4.3) ... Removing hmmer (3.1b2+dfsg-5) ... Removing hyphy-mpi (2.2.7+dfsg-1+b2) ... Removing hyphy-common (2.2.7+dfsg-1) ... 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 libalgorithm-diff-xs-perl (0.04-4+b2) ... Removing libalgorithm-diff-perl (1.19.03-1) ... Removing libalgorithm-munkres-perl (0.08-3) ... Removing libann0 (1.1.2+doc-6) ... Removing libanyevent-cachedns-perl (0.08-2) ... Removing libanyevent-http-perl (2.23-1) ... Removing libanyevent-perl (7.130-2) ... 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 libasync-interrupt-perl (1.21-1+b2) ... Removing libauthen-sasl-perl (2.1600-1) ... Removing libgs9:amd64 (9.26a~dfsg-0+deb9u6) ... Removing libcupsfilters1:amd64 (1.11.6-3+deb9u1) ... Removing libbio-asn1-entrezgene-perl (1.720-1) ... Removing libbio-perl-run-perl (1.7.1-3) ... Removing libbio-scf-perl (1.03-3) ... 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 libbsd-resource-perl (1.2910-1+b1) ... Removing lynx (2.8.9dev11-1) ... Removing libxaw7:amd64 (2:1.0.13-1+b2) ... Removing libxmu6:amd64 (2:1.1.2-2) ... Removing libxt6:amd64 (1:1.1.5-1) ... Removing libcache-cache-perl (1.08-2) ... Removing libcairo2:amd64 (1.14.8-1) ... 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-session-perl (4.48-3) ... Removing libcgi-pm-perl (4.35-1) ... Removing libxmlrpc-lite-perl (0.717-1) ... Removing libsoap-lite-perl (1.20-1) ... Removing libclass-inspector-perl (1.31-1) ... Removing libmoo-perl (2.002005-1) ... Removing librole-tiny-perl (2.000005-1) ... Removing libclass-method-modifiers-perl (2.12-1) ... Removing libclass-xsaccessor-perl (1.19-2+b7) ... Removing libclone-perl (0.38-2+b1) ... Removing libjson-xs-perl (3.030-1) ... Removing libtypes-serialiser-perl (1.0-1) ... Removing libev-perl (4.22-1+b1) ... Removing libcommon-sense-perl (3.74-2) ... 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 libstaden-read11:amd64 (1.14.8-2) ... Removing samtools (1.3.1-3) ... Removing libhts1:amd64 (1.3.2-2) ... Removing libcurl3-gnutls:amd64 (7.52.1-5+deb9u10) ... Removing libdate-manip-perl (6.57-1) ... Removing libthai0:amd64 (0.1.26-1) ... Removing libdatrie1:amd64 (0.2.10-4+b1) ... 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 libdevel-lexalias-perl (0.05-1+b4) ... Removing libdevel-caller-perl (2.06-1+b4) ... Removing libdevel-globaldestruction-perl (0.14-1) ... Removing libdevel-symdump-perl (2.17-1) ... Removing libdigest-perl-md5-perl (1.9-1) ... Removing libdivsufsort3:amd64 (2.0.1-2) ... Removing libdrm-intel1:amd64 (2.4.74-1) ... Removing libdrm2:amd64 (2.4.74-1) ... 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 libpython-stdlib:amd64 (2.7.13-2) ... Removing libpython2.7-stdlib: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 libfcgi-perl (0.78-2) ... Removing librtmp1:amd64 (2.4+20151223.gitfa8646d.1-1+b1) ... Removing libpq5:amd64 (9.6.17-0+deb9u1) ... Removing libldap-2.4-2:amd64 (2.4.44+dfsg-5+deb9u4) ... Removing wise (2.4.1-19) ... Removing libtree-dagnode-perl (1.29-1) ... Removing libfile-slurp-tiny-perl (0.003-1) ... Removing libhtml-format-perl (2.12-1) ... Removing libfont-afm-perl (1.20-2) ... Removing libharfbuzz0b:amd64 (1.4.2-1) ... Removing libfreezethaw-perl (0.5001-1) ... Removing rename (0.20-4) ... update-alternatives: using /usr/bin/prename to provide /usr/bin/rename (rename) in auto mode Removing mafft (7.307-1) ... Removing perl-doc (5.24.1-3+deb9u7) ... Removing 'diversion of /usr/bin/perldoc to /usr/bin/perldoc.stub by perl-doc' Removing tm-align (20160521+dfsg-2) ... Removing libgfortran3:amd64 (6.3.0-18+deb9u1) ... Removing libglib2.0-data (2.50.3-2+deb9u2) ... Removing libmpfr4:amd64 (3.1.5-1) ... Removing libgomp1:amd64 (6.3.0-18+deb9u1) ... Removing libgpm2:amd64 (1.20.4-6.2+b1) ... Removing libgraph-perl (1:0.96-2) ... Removing libgraphite2-3:amd64 (1.3.10-1) ... Removing libgs9-common (9.26a~dfsg-0+deb9u6) ... Removing libgts-bin (0.7.6+darcs121130-4) ... Removing libgts-0.7-5:amd64 (0.7.6+darcs121130-4) ... Removing libguard-perl (1.023-1+b2) ... Removing libhpdf-2.2.1 (2.2.1-1.1+b1) ... Removing libhtml-form-perl (6.03-1) ... Removing libhtml-tableextract-perl (2.13-1) ... Removing libhttp-daemon-perl (6.01-1) ... Removing libhwloc-plugins (1.11.5-1) ... Removing libhwloc5:amd64 (1.11.5-1) ... Removing librdmacm1 (1.1.0-2) ... Removing libibverbs1 (1.2.1-2) ... Removing libsm6:amd64 (2:1.2.2-1+b3) ... Removing libice6:amd64 (2:1.0.9-2) ... Removing shared-mime-info (1.8-1+deb9u1) ... Removing libxml-libxslt-perl (1.95-1+b1) ... Removing libxslt1.1:amd64 (1.1.29-2.1+deb9u2) ... Removing libpsl5:amd64 (0.17.0-3) ... Removing libidn2-0:amd64 (0.16-1+deb9u1) ... Removing libijs-0.35:amd64 (0.35-12) ... Removing libimport-into-perl (1.002005-1) ... Removing libipc-run-perl (0.94-1+deb9u1) ... Removing libio-pty-perl (1:1.08-1.1+b2) ... Removing libio-sessiondata-perl (1.03-1) ... Removing libmailtools-perl (2.18-1) ... Removing libnet-smtp-ssl-perl (1.04-1) ... Removing libole-storage-lite-perl (0.19-1+deb9u1) ... Removing libio-stringy-perl (2.111-2) ... Removing libipc-sharelite-perl (0.17-4) ... Removing libtiff5:amd64 (4.0.8-2+deb9u5) ... Removing libjbig0:amd64 (2.1-3.1+b2) ... Removing libjbig2dec0:amd64 (0.13-4.1) ... Removing libjcode-pm-perl (2.06-1) ... Removing libjpeg62-turbo:amd64 (1:1.5.1-2) ... Removing libjs-jquery (3.1.1-2+deb9u1) ... Removing libjs-scriptaculous (1.9.0-2) ... Removing libjs-prototype (1.7.1-3) ... Removing libjson-perl (2.90-1) ... Removing liblcms2-2:amd64 (2.8-4+deb9u1) ... Removing libldap-common (2.4.44+dfsg-5+deb9u4) ... Removing libltdl7:amd64 (2.4.6-2) ... Removing liblua5.2-0:amd64 (5.2.4-1.1+b2) ... Removing libmagic1:amd64 (1:5.30-1+deb9u3) ... Removing libmagic-mgc (1:5.30-1+deb9u3) ... Removing libmariadbclient18:amd64 (10.1.45-0+deb9u1) ... Removing libmath-spline-perl (0.02-1) ... Removing libmath-derivative-perl (0.04-2) ... Removing libmldbm-perl (2.05-2) ... Removing libmodule-runtime-perl (0.014-2) ... Removing procps (2:3.3.12-3+deb9u1) ... Removing libnghttp2-14:amd64 (1.18.1-1+deb9u1) ... Removing libnl-route-3-200:amd64 (3.2.27-2) ... Removing libnl-3-200:amd64 (3.2.27-2) ... Removing libnuma1:amd64 (2.0.11-2.1) ... Removing libopenjp2-7:amd64 (2.1.2-1.1+deb9u4) ... Removing libossp-uuid-perl (1.6.2-1.5+b4) ... Removing libossp-uuid16:amd64 (1.6.2-1.5+b4) ... Removing libpadwalker-perl (2.2-2+b1) ... Removing libpaper-utils (1.1.24+nmu5) ... Removing libpaper1:amd64 (1.1.24+nmu5) ... Removing libparams-classify-perl (0.013-6+b1) ... Removing libspreadsheet-writeexcel-perl (2.40-1) ... Removing libparse-recdescent-perl (1.967013+dfsg-1) ... Removing libpathplan4 (2.38.0-17) ... Removing libpciaccess0:amd64 (0.13.4-1+b2) ... Removing libpixman-1-0:amd64 (0.34.0-1) ... Removing libpostscript-perl (0.06-2) ... Removing libprocps6:amd64 (2:3.3.12-3+deb9u1) ... Removing libpsm-infinipath1 (3.3+19.g67c0807.open-3) ... Removing python-minimal (2.7.13-2) ... Removing python2.7-minimal (2.7.13-2+deb9u3) ... Removing libpython2.7-minimal:amd64 (2.7.13-2+deb9u3) ... Removing libquadmath0:amd64 (6.3.0-18+deb9u1) ... Removing sqlite3 (3.16.2-5+deb9u1) ... Removing libsasl2-2:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Removing libsasl2-modules:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Removing libsasl2-modules-db:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u1) ... Removing libset-scalar-perl (1.29-2) ... Removing libsigsegv2:amd64 (2.10-5) ... Removing libsort-naturally-perl (1.03-1) ... Removing libsqlite3-0:amd64 (3.16.2-5+deb9u1) ... Removing libssh2-1:amd64 (1.7.0-1+deb9u1) ... Removing ssl-cert (1.0.39) ... Removing libstrictures-perl (2.000003-1) ... Removing libstring-approx-perl (3.27-1+b4) ... Removing libsub-exporter-progressive-perl (0.001013-1) ... Removing libsub-name-perl (0.21-1) ... Removing libsvg-perl (2.64-1) ... Removing libtask-weaken-perl (1.04-1) ... Removing libterm-readkey-perl (2.37-1) ... Removing libtext-iconv-perl (1.7-5+b4) ... Removing libthai-data (0.1.26-1) ... Removing libtie-ixhash-perl (1.23-2) ... Removing libtype-tiny-xs-perl (0.012-1+b2) ... Removing libunicode-map-perl (0.112-11+b3) ... Removing libunistring0:amd64 (0.9.6+really0.9.3-0.1) ... Removing libwebp6:amd64 (0.5.2-1) ... Removing libxrender1:amd64 (1:0.9.10-1) ... Removing libxcb-shm0:amd64 (1.12-1) ... Removing libxcb-render0:amd64 (1.12-1) ... Removing libxdot4 (2.38.0-17) ... Removing libxext6:amd64 (2:1.3.3-1+b2) ... Removing libxfixes3:amd64 (1:5.0.3-1) ... Removing libxml-dom-xpath-perl (0.14-2) ... Removing libxml-dom-perl (1.44-2) ... Removing libxml-sax-writer-perl (0.56-1) ... Removing libxml-filter-buffertext-perl (1.01-5) ... Removing libxml-libxml-perl (2.0128+dfsg-1+deb9u1) ... update-perl-sax-parsers: Unregistering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Unregistering 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 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-xpath-perl (1.40-1) ... Removing libxml-xpathengine-perl (0.13-1) ... Removing libxpm4:amd64 (1:3.5.12-1) ... Removing libyaml-libyaml-perl (0.63-2) ... Removing libyaml-perl (1.21-1) ... 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 lynx-common (2.8.9dev11-1) ... Removing maq (0.7.1-7) ... Removing menu (2.1.47+b1) ... Removing mime-support (3.60) ... Removing muscle (1:3.8.31+dfsg-2) ... Removing mustang (3.2.3-1) ... Removing mysql-common (5.8+1.0.2) ... Removing ncbi-data (6.1.20170106+dfsg1-0+deb9u1) ... Removing ocl-icd-libopencl1:amd64 (2.2.11-1) ... Removing openmpi-common (2.0.2-2) ... Removing phylip (1:3.696+dfsg-5) ... Removing poa (2.0+20060928-4+b1) ... Removing poppler-data (0.4.7-8) ... Removing prank (0.0.150803-2) ... Removing primer3 (2.3.7-3) ... Removing probalign (1.4-5) ... Removing probcons (1.12-11) ... Removing proda (1.0-10) ... Removing psmisc (22.21-2.1+b2) ... Removing publicsuffix (20190415.1030-0+deb9u1) ... Removing raxml (8.2.9+dfsg-1+b1) ... Removing xml-core (0.17) ... Removing sgml-base (1.29) ... Removing sim4 (0.0.20121010-4) ... Removing t-coffee (11.00.8cbe486-5) ... Removing tigr-glimmer (3.02b-1) ... Removing unzip (6.0-21+deb9u2) ... Removing wise-data (2.4.1-19) ... Removing xdg-user-dirs (0.15-2+b1) ... Removing xz-utils (5.2.2-1.2+b1) ... Removing zip (3.0-11+b1) ... Removing bioperl (1.7.1-2) ... Removing libxml-parser-perl (2.44-2+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 libcups2:amd64 (2.2.1-8+deb9u6) ... Removing libavahi-client3:amd64 (0.6.32-2) ... Removing libavahi-common3:amd64 (0.6.32-2) ... Removing libavahi-common-data:amd64 (0.6.32-2) ... Removing libbio-perl-perl (1.7.1-2) ... 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 libdata-stag-perl (0.14-2) ... Removing libdbus-1-3:amd64 (1.10.32-0+deb9u1) ... Removing libexpat1:amd64 (2.2.0-2+deb9u3) ... Removing libgnutls30:amd64 (3.5.8-5+deb9u5) ... Removing libp11-kit0:amd64 (0.23.3-2) ... Removing libglib2.0-0:amd64 (2.50.3-2+deb9u2) ... Removing libfreetype6:amd64 (2.6.3-3.2+deb9u1) ... Removing libhogweed4:amd64 (3.3-1+b2) ... Removing libgssapi-krb5-2:amd64 (1.15-1+deb9u1) ... Removing libxml2:amd64 (2.9.4+dfsg1-2.2+deb9u2) ... Removing libicu57:amd64 (57.1-6+deb9u4) ... Removing libidn11:amd64 (1.33-1+deb9u1) ... Removing libio-string-perl (1.08-3) ... 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 libnettle6:amd64 (3.3-1+b2) ... Removing libpng16-16:amd64 (1.6.28-1+deb9u1) ... Removing libtasn1-6:amd64 (4.10-1.1+deb9u1) ... Removing libx11-data (2:1.6.4-3+deb9u1) ... Removing libxau6:amd64 (1:1.0.8-1) ... Removing ucf (3.0036) ... 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 rake (10.5.0-2+deb9u1) ... 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) ... 1m15.3s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'apt-get', 'remove', 'amap-align', 'apache2', 'apache2-bin', 'apache2-data', 'apache2-utils', 'bedtools', 'beignet-opencl-icd:amd64', 'bioperl', 'bioperl-run', 'blast2', 'blends-common', 'bowtie', 'bwa', 'bzip2', 'ca-certificates', 'clustalo', 'clustalw', 'dbus', 'dialign', 'dialign-tx', 'dialign-tx-data', 'emboss', 'emboss-data', 'emboss-lib', 'exonerate', 'file', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-droid-fallback', 'fonts-lato', 'fonts-liberation', 'fonts-noto-mono', 'fsa', 'gawk', 'ghostscript', 'graphviz', 'gsfonts', 'hmmer', 'hyphy-common', 'hyphy-mpi', 'infernal', 'javascript-common', 'kalign', 'krb5-locales', 'libace-perl', 'libalgorithm-diff-perl', 'libalgorithm-diff-xs-perl', 'libalgorithm-munkres-perl', 'libann0', 'libanyevent-cachedns-perl', 'libanyevent-http-perl', 'libanyevent-perl', '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', 'libasync-interrupt-perl', 'libauthen-sasl-perl', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbio-asn1-entrezgene-perl', 'libbio-coordinate-perl', 'libbio-graphics-perl', 'libbio-perl-perl', 'libbio-perl-run-perl', 'libbio-scf-perl', 'libbit-vector-perl', 'libbsd-resource-perl', 'libbsd0:amd64', 'libcache-cache-perl', 'libcairo2:amd64', 'libcarp-clan-perl', 'libcdt5', 'libcgi-fast-perl', 'libcgi-pm-perl', 'libcgi-session-perl', 'libcgraph6', 'libclass-inspector-perl', 'libclass-method-modifiers-perl', 'libclass-xsaccessor-perl', 'libclone-perl', 'libcommon-sense-perl', 'libconvert-binary-c-perl', 'libconvert-binhex-perl', 'libcrypt-rc4-perl', 'libcups2:amd64', 'libcupsfilters1:amd64', 'libcupsimage2:amd64', 'libcurl3-gnutls:amd64', '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-symdump-perl', 'libdigest-perl-md5-perl', 'libdivsufsort3:amd64', 'libdrm-intel1:amd64', 'libdrm2:amd64', 'libencode-locale-perl', 'liberror-perl', 'libev-perl', 'libexpat1:amd64', 'libexporter-tiny-perl', 'libfabric1', 'libfcgi-perl', 'libffi6:amd64', 'libfile-listing-perl', 'libfile-slurp-tiny-perl', 'libfont-afm-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfreezethaw-perl', 'libgd-perl', 'libgd-svg-perl', 'libgd3:amd64', 'libgdbm3:amd64', 'libgfortran3:amd64', 'libglib2.0-0:amd64', 'libglib2.0-data', 'libgmp10:amd64', 'libgnutls30:amd64', 'libgomp1:amd64', 'libgpm2:amd64', 'libgraph-perl', 'libgraphite2-3:amd64', 'libgraphviz-perl', 'libgs9:amd64', 'libgs9-common', 'libgssapi-krb5-2:amd64', 'libgts-0.7-5:amd64', 'libgts-bin', 'libguard-perl', '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', 'libicu57:amd64', 'libidn11:amd64', 'libidn2-0:amd64', 'libijs-0.35:amd64', 'libimport-into-perl', 'libio-html-perl', 'libio-pty-perl', 'libio-sessiondata-perl', 'libio-socket-ssl-perl', 'libio-string-perl', 'libio-stringy-perl', 'libipc-run-perl', 'libipc-sharelite-perl', 'libjbig0:amd64', 'libjbig2dec0:amd64', 'libjcode-pm-perl', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-prototype', 'libjs-scriptaculous', 'libjson-perl', 'libjson-xs-perl', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'liblist-moreutils-perl', 'libltdl7:amd64', 'liblua5.2-0:amd64', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'libmagic-mgc', 'libmagic1:amd64', 'libmailtools-perl', 'libmariadbclient18:amd64', 'libmath-derivative-perl', 'libmath-spline-perl', 'libmime-tools-perl', 'libmldbm-perl', 'libmodule-runtime-perl', 'libmoo-perl', 'libmpfr4:amd64', 'libncurses5:amd64', 'libnet-http-perl', 'libnet-smtp-ssl-perl', 'libnet-ssleay-perl', 'libnettle6:amd64', 'libnghttp2-14:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnuma1:amd64', 'libole-storage-lite-perl', 'libopenjp2-7:amd64', 'libopenmpi2:amd64', 'libossp-uuid-perl', 'libossp-uuid16:amd64', 'libp11-kit0:amd64', 'libpadwalker-perl', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libparams-classify-perl', 'libparse-recdescent-perl', 'libpathplan4', 'libpciaccess0:amd64', 'libperl5.24:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libpostscript-perl', 'libpq5:amd64', 'libprocps6:amd64', 'libpsl5:amd64', 'libpsm-infinipath1', 'libpython-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'librdmacm1', 'libreadline7:amd64', 'librole-tiny-perl', 'librtmp1:amd64', 'libruby2.3:amd64', 'libsasl2-2:amd64', 'libsasl2-modules:amd64', 'libsasl2-modules-db:amd64', 'libset-scalar-perl', 'libsigsegv2:amd64', 'libsm6:amd64', 'libsoap-lite-perl', 'libsort-naturally-perl', 'libspreadsheet-parseexcel-perl', 'libspreadsheet-writeexcel-perl', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.0.2:amd64', 'libssl1.1:amd64', 'libstaden-read11:amd64', 'libstatistics-descriptive-perl', 'libstrictures-perl', 'libstring-approx-perl', 'libsub-exporter-progressive-perl', 'libsub-name-perl', 'libsvg-graph-perl', 'libsvg-perl', 'libtask-weaken-perl', 'libtasn1-6:amd64', 'libterm-readkey-perl', 'libtext-iconv-perl', 'libthai-data', 'libthai0:amd64', 'libtie-ixhash-perl', 'libtiff5:amd64', 'libtimedate-perl', 'libtree-dagnode-perl', 'libtype-tiny-perl', 'libtype-tiny-xs-perl', 'libtypes-serialiser-perl', 'libunicode-map-perl', 'libunistring0:amd64', 'liburi-perl', 'libvm-ec2-perl', 'libwebp6:amd64', 'libwww-perl', 'libwww-robotrules-perl', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxaw7:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxdot4', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2: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', 'libxpm4:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxt6:amd64', 'libyaml-0-2:amd64', 'libyaml-libyaml-perl', 'libyaml-perl', 'lsb-base', 'lynx', 'lynx-common', 'mafft', 'maq', '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', 'perl', 'perl-doc', 'perl-modules-5.24', 'perl-openssl-defaults:amd64', 'perl-tk', 'phylip', 'phyml', 'poa', 'poppler-data', 'prank', 'primer3', 'probalign', 'probcons', 'procps', 'proda', 'psmisc', 'publicsuffix', 'python', 'python-minimal', 'python2.7', 'python2.7-minimal', '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', 'sqlite3', 'ssl-cert', 't-coffee', 'tigr-glimmer', 'tm-align', 'ucf', 'unzip', 'wise', 'wise-data', 'x11-common', 'xdg-user-dirs', 'xml-core', 'xz-utils', 'zip', 'gbrowse'] 1m15.3s INFO: Running scripts post_remove 1m15.3s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/post_remove_exceptions'] 1m15.4s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/post_remove_exceptions'] 1m15.4s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'dpkg', '--purge', 'amap-align', 'apache2', 'apache2-bin', 'apache2-data', 'apache2-utils', 'bedtools', 'beignet-opencl-icd:amd64', 'bioperl', 'bioperl-run', 'blast2', 'blends-common', 'bowtie', 'bwa', 'bzip2', 'ca-certificates', 'clustalo', 'clustalw', 'dbus', 'dialign', 'dialign-tx', 'dialign-tx-data', 'emboss', 'emboss-data', 'emboss-lib', 'exonerate', 'file', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-droid-fallback', 'fonts-lato', 'fonts-liberation', 'fonts-noto-mono', 'fsa', 'gawk', 'ghostscript', 'graphviz', 'gsfonts', 'hmmer', 'hyphy-common', 'hyphy-mpi', 'infernal', 'javascript-common', 'kalign', 'krb5-locales', 'libace-perl', 'libalgorithm-diff-perl', 'libalgorithm-diff-xs-perl', 'libalgorithm-munkres-perl', 'libann0', 'libanyevent-cachedns-perl', 'libanyevent-http-perl', 'libanyevent-perl', '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', 'libasync-interrupt-perl', 'libauthen-sasl-perl', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbio-asn1-entrezgene-perl', 'libbio-coordinate-perl', 'libbio-graphics-perl', 'libbio-perl-perl', 'libbio-perl-run-perl', 'libbio-scf-perl', 'libbit-vector-perl', 'libbsd-resource-perl', 'libbsd0:amd64', 'libcache-cache-perl', 'libcairo2:amd64', 'libcarp-clan-perl', 'libcdt5', 'libcgi-fast-perl', 'libcgi-pm-perl', 'libcgi-session-perl', 'libcgraph6', 'libclass-inspector-perl', 'libclass-method-modifiers-perl', 'libclass-xsaccessor-perl', 'libclone-perl', 'libcommon-sense-perl', 'libconvert-binary-c-perl', 'libconvert-binhex-perl', 'libcrypt-rc4-perl', 'libcups2:amd64', 'libcupsfilters1:amd64', 'libcupsimage2:amd64', 'libcurl3-gnutls:amd64', '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-symdump-perl', 'libdigest-perl-md5-perl', 'libdivsufsort3:amd64', 'libdrm-intel1:amd64', 'libdrm2:amd64', 'libencode-locale-perl', 'liberror-perl', 'libev-perl', 'libexpat1:amd64', 'libexporter-tiny-perl', 'libfabric1', 'libfcgi-perl', 'libffi6:amd64', 'libfile-listing-perl', 'libfile-slurp-tiny-perl', 'libfont-afm-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfreezethaw-perl', 'libgd-perl', 'libgd-svg-perl', 'libgd3:amd64', 'libgdbm3:amd64', 'libgfortran3:amd64', 'libglib2.0-0:amd64', 'libglib2.0-data', 'libgmp10:amd64', 'libgnutls30:amd64', 'libgomp1:amd64', 'libgpm2:amd64', 'libgraph-perl', 'libgraphite2-3:amd64', 'libgraphviz-perl', 'libgs9:amd64', 'libgs9-common', 'libgssapi-krb5-2:amd64', 'libgts-0.7-5:amd64', 'libgts-bin', 'libguard-perl', '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', 'libicu57:amd64', 'libidn11:amd64', 'libidn2-0:amd64', 'libijs-0.35:amd64', 'libimport-into-perl', 'libio-html-perl', 'libio-pty-perl', 'libio-sessiondata-perl', 'libio-socket-ssl-perl', 'libio-string-perl', 'libio-stringy-perl', 'libipc-run-perl', 'libipc-sharelite-perl', 'libjbig0:amd64', 'libjbig2dec0:amd64', 'libjcode-pm-perl', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-prototype', 'libjs-scriptaculous', 'libjson-perl', 'libjson-xs-perl', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'liblist-moreutils-perl', 'libltdl7:amd64', 'liblua5.2-0:amd64', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'libmagic-mgc', 'libmagic1:amd64', 'libmailtools-perl', 'libmariadbclient18:amd64', 'libmath-derivative-perl', 'libmath-spline-perl', 'libmime-tools-perl', 'libmldbm-perl', 'libmodule-runtime-perl', 'libmoo-perl', 'libmpfr4:amd64', 'libncurses5:amd64', 'libnet-http-perl', 'libnet-smtp-ssl-perl', 'libnet-ssleay-perl', 'libnettle6:amd64', 'libnghttp2-14:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnuma1:amd64', 'libole-storage-lite-perl', 'libopenjp2-7:amd64', 'libopenmpi2:amd64', 'libossp-uuid-perl', 'libossp-uuid16:amd64', 'libp11-kit0:amd64', 'libpadwalker-perl', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libparams-classify-perl', 'libparse-recdescent-perl', 'libpathplan4', 'libpciaccess0:amd64', 'libperl5.24:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libpostscript-perl', 'libpq5:amd64', 'libprocps6:amd64', 'libpsl5:amd64', 'libpsm-infinipath1', 'libpython-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'librdmacm1', 'libreadline7:amd64', 'librole-tiny-perl', 'librtmp1:amd64', 'libruby2.3:amd64', 'libsasl2-2:amd64', 'libsasl2-modules:amd64', 'libsasl2-modules-db:amd64', 'libset-scalar-perl', 'libsigsegv2:amd64', 'libsm6:amd64', 'libsoap-lite-perl', 'libsort-naturally-perl', 'libspreadsheet-parseexcel-perl', 'libspreadsheet-writeexcel-perl', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.0.2:amd64', 'libssl1.1:amd64', 'libstaden-read11:amd64', 'libstatistics-descriptive-perl', 'libstrictures-perl', 'libstring-approx-perl', 'libsub-exporter-progressive-perl', 'libsub-name-perl', 'libsvg-graph-perl', 'libsvg-perl', 'libtask-weaken-perl', 'libtasn1-6:amd64', 'libterm-readkey-perl', 'libtext-iconv-perl', 'libthai-data', 'libthai0:amd64', 'libtie-ixhash-perl', 'libtiff5:amd64', 'libtimedate-perl', 'libtree-dagnode-perl', 'libtype-tiny-perl', 'libtype-tiny-xs-perl', 'libtypes-serialiser-perl', 'libunicode-map-perl', 'libunistring0:amd64', 'liburi-perl', 'libvm-ec2-perl', 'libwebp6:amd64', 'libwww-perl', 'libwww-robotrules-perl', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxaw7:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxdot4', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2: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', 'libxpm4:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxt6:amd64', 'libyaml-0-2:amd64', 'libyaml-libyaml-perl', 'libyaml-perl', 'lsb-base', 'lynx', 'lynx-common', 'mafft', 'maq', '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', 'perl', 'perl-doc', 'perl-modules-5.24', 'perl-openssl-defaults:amd64', 'perl-tk', 'phylip', 'phyml', 'poa', 'poppler-data', 'prank', 'primer3', 'probalign', 'probcons', 'procps', 'proda', 'psmisc', 'publicsuffix', 'python', 'python-minimal', 'python2.7', 'python2.7-minimal', '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', 'sqlite3', 'ssl-cert', 't-coffee', 'tigr-glimmer', 'tm-align', 'ucf', 'unzip', 'wise', 'wise-data', 'x11-common', 'xdg-user-dirs', 'xml-core', 'xz-utils', 'zip'] 1m16.5s DUMP: dpkg: warning: ignoring request to remove amap-align which isn't installed (Reading database ... 4821 files and directories currently installed.) Purging configuration files for apache2 (2.4.25-3+deb9u9) ... dpkg: warning: ignoring request to remove apache2-bin which isn't installed dpkg: warning: ignoring request to remove apache2-data which isn't installed dpkg: warning: ignoring request to remove apache2-utils which isn't installed dpkg: warning: ignoring request to remove bedtools which isn't installed Purging configuration files for beignet-opencl-icd:amd64 (1.3.0-4) ... 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 bwa which isn't installed dpkg: warning: ignoring request to remove bzip2 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 clustalo which isn't installed Purging configuration files for clustalw (2.1+lgpl-5) ... 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 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 dpkg: warning: ignoring request to remove exonerate 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 gawk which isn't installed dpkg: warning: ignoring request to remove ghostscript 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 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 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-diff-perl which isn't installed dpkg: warning: ignoring request to remove libalgorithm-diff-xs-perl which isn't installed dpkg: warning: ignoring request to remove libalgorithm-munkres-perl which isn't installed dpkg: warning: ignoring request to remove libann0 which isn't installed dpkg: warning: ignoring request to remove libanyevent-cachedns-perl which isn't installed dpkg: warning: ignoring request to remove libanyevent-http-perl which isn't installed dpkg: warning: ignoring request to remove libanyevent-perl which isn't installed dpkg: warning: ignoring request to remove libapache-dbi-perl which isn't installed Purging configuration files for libapache2-mod-perl2 (2.0.10-2+deb9u1) ... dpkg: warning: ignoring request to remove libapache2-reload-perl which isn't installed dpkg: warning: ignoring request to remove libapparmor1 which isn't installed dpkg: warning: ignoring request to remove libapr1 which isn't installed dpkg: warning: ignoring request to remove libaprutil1 which isn't installed dpkg: warning: ignoring request to remove libaprutil1-dbd-sqlite3 which isn't installed dpkg: warning: ignoring request to remove libaprutil1-ldap which isn't installed dpkg: warning: ignoring request to remove libargtable2-0 which isn't installed dpkg: warning: ignoring request to remove libarray-compare-perl which isn't installed dpkg: warning: ignoring request to remove libasync-interrupt-perl which isn't installed dpkg: warning: ignoring request to remove libauthen-sasl-perl which isn't installed dpkg: warning: ignoring request to remove libavahi-client3 which isn't installed dpkg: warning: ignoring request to remove libavahi-common-data which isn't installed dpkg: warning: ignoring request to remove libavahi-common3 which isn't installed dpkg: warning: ignoring request to remove libbio-asn1-entrezgene-perl which isn't installed dpkg: warning: ignoring request to remove libbio-coordinate-perl which isn't installed dpkg: warning: ignoring request to remove libbio-graphics-perl which isn't installed dpkg: warning: ignoring request to remove libbio-perl-perl which isn't installed dpkg: warning: ignoring request to remove libbio-perl-run-perl which isn't installed dpkg: warning: ignoring request to remove libbio-scf-perl which isn't installed dpkg: warning: ignoring request to remove libbit-vector-perl which isn't installed dpkg: warning: ignoring request to remove libbsd-resource-perl which isn't installed dpkg: warning: ignoring request to remove libbsd0 which isn't installed dpkg: warning: ignoring request to remove libcache-cache-perl which isn't installed dpkg: warning: ignoring request to remove libcairo2 which isn't installed dpkg: warning: ignoring request to remove libcarp-clan-perl which isn't installed dpkg: warning: ignoring request to remove libcdt5 which isn't installed dpkg: warning: ignoring request to remove libcgi-fast-perl which isn't installed dpkg: warning: ignoring request to remove libcgi-pm-perl which isn't installed dpkg: warning: ignoring request to remove libcgi-session-perl which isn't installed dpkg: warning: ignoring request to remove libcgraph6 which isn't installed dpkg: warning: ignoring request to remove libclass-inspector-perl which isn't installed dpkg: warning: ignoring request to remove libclass-method-modifiers-perl which isn't installed dpkg: warning: ignoring request to remove libclass-xsaccessor-perl which isn't installed dpkg: warning: ignoring request to remove libclone-perl which isn't installed dpkg: warning: ignoring request to remove libcommon-sense-perl which isn't installed dpkg: warning: ignoring request to remove libconvert-binary-c-perl which isn't installed dpkg: warning: ignoring request to remove libconvert-binhex-perl which isn't installed dpkg: warning: ignoring request to remove libcrypt-rc4-perl which isn't installed dpkg: warning: ignoring request to remove libcups2 which isn't installed dpkg: warning: ignoring request to remove libcupsfilters1 which isn't installed dpkg: warning: ignoring request to remove libcupsimage2 which isn't installed dpkg: warning: ignoring request to remove libcurl3-gnutls which isn't installed dpkg: warning: ignoring request to remove libdata-stag-perl which isn't installed dpkg: warning: ignoring request to remove libdate-calc-perl which isn't installed dpkg: warning: ignoring request to remove libdate-calc-xs-perl which isn't installed dpkg: warning: ignoring request to remove libdate-manip-perl which isn't installed dpkg: warning: ignoring request to remove libdatrie1 which isn't installed dpkg: warning: ignoring request to remove libdbd-mysql-perl which isn't installed dpkg: warning: ignoring request to remove libdbd-pg-perl which isn't installed dpkg: warning: ignoring request to remove libdbd-sqlite3-perl which isn't installed dpkg: warning: ignoring request to remove libdbi-perl which isn't installed dpkg: warning: ignoring request to remove libdbus-1-3 which isn't installed dpkg: warning: ignoring request to remove libdevel-caller-perl which isn't installed dpkg: warning: ignoring request to remove libdevel-globaldestruction-perl which isn't installed dpkg: warning: ignoring request to remove libdevel-lexalias-perl which isn't installed dpkg: warning: ignoring request to remove libdevel-symdump-perl which isn't installed dpkg: warning: ignoring request to remove libdigest-perl-md5-perl which isn't installed Purging configuration files for libdivsufsort3:amd64 (2.0.1-2) ... dpkg: warning: ignoring request to remove libdrm-intel1 which isn't installed dpkg: warning: ignoring request to remove libdrm2 which isn't installed dpkg: warning: ignoring request to remove libencode-locale-perl which isn't installed dpkg: warning: ignoring request to remove liberror-perl which isn't installed dpkg: warning: ignoring request to remove libev-perl which isn't installed dpkg: warning: ignoring request to remove libexpat1 which isn't installed dpkg: warning: ignoring request to remove libexporter-tiny-perl which isn't installed dpkg: warning: ignoring request to remove libfabric1 which isn't installed dpkg: warning: ignoring request to remove libfcgi-perl which isn't installed dpkg: warning: ignoring request to remove libffi6 which isn't installed dpkg: warning: ignoring request to remove libfile-listing-perl which isn't installed dpkg: warning: ignoring request to remove libfile-slurp-tiny-perl which isn't installed dpkg: warning: ignoring request to remove libfont-afm-perl which isn't installed dpkg: warning: ignoring request to remove libfontconfig1 which isn't installed dpkg: warning: ignoring request to remove libfreetype6 which isn't installed dpkg: warning: ignoring request to remove libfreezethaw-perl which isn't installed dpkg: warning: ignoring request to remove libgd-perl which isn't installed dpkg: warning: ignoring request to remove libgd-svg-perl which isn't installed dpkg: warning: ignoring request to remove libgd3 which isn't installed dpkg: warning: ignoring request to remove libgdbm3 which isn't installed dpkg: warning: ignoring request to remove libgfortran3 which isn't installed Purging configuration files for libglib2.0-0:amd64 (2.50.3-2+deb9u2) ... dpkg: warning: ignoring request to remove libglib2.0-data which isn't installed dpkg: warning: ignoring request to remove libgmp10 which isn't installed dpkg: warning: ignoring request to remove libgnutls30 which isn't installed dpkg: warning: ignoring request to remove libgomp1 which isn't installed dpkg: warning: ignoring request to remove libgpm2 which isn't installed dpkg: warning: ignoring request to remove libgraph-perl which isn't installed dpkg: warning: ignoring request to remove libgraphite2-3 which isn't installed dpkg: warning: ignoring request to remove libgraphviz-perl which isn't installed dpkg: warning: ignoring request to remove libgs9 which isn't installed dpkg: warning: ignoring request to remove libgs9-common which isn't installed Purging configuration files for libgssapi-krb5-2:amd64 (1.15-1+deb9u1) ... dpkg: warning: ignoring request to remove libgts-0.7-5 which isn't installed dpkg: warning: ignoring request to remove libgts-bin which isn't installed dpkg: warning: ignoring request to remove libguard-perl which isn't installed Purging configuration files for libgvc6 (2.38.0-17) ... dpkg: warning: ignoring request to remove libgvpr2 which isn't installed dpkg: warning: ignoring request to remove libharfbuzz0b which isn't installed dpkg: warning: ignoring request to remove libhmsbeagle1v5 which isn't installed dpkg: warning: ignoring request to remove libhogweed4 which isn't installed dpkg: warning: ignoring request to remove libhpdf-2.2.1 which isn't installed dpkg: warning: ignoring request to remove libhtml-form-perl which isn't installed dpkg: warning: ignoring request to remove libhtml-format-perl which isn't installed dpkg: warning: ignoring request to remove libhtml-parser-perl which isn't installed dpkg: warning: ignoring request to remove libhtml-tableextract-perl which isn't installed dpkg: warning: ignoring request to remove libhtml-tagset-perl which isn't installed dpkg: warning: ignoring request to remove libhtml-tree-perl which isn't installed dpkg: warning: ignoring request to remove libhts1 which isn't installed dpkg: warning: ignoring request to remove libhttp-cookies-perl which isn't installed dpkg: warning: ignoring request to remove libhttp-daemon-perl which isn't installed dpkg: warning: ignoring request to remove libhttp-date-perl which isn't installed dpkg: warning: ignoring request to remove libhttp-message-perl which isn't installed dpkg: warning: ignoring request to remove libhttp-negotiate-perl which isn't installed dpkg: warning: ignoring request to remove libhwloc-plugins which isn't installed dpkg: warning: ignoring request to remove libhwloc5 which isn't installed dpkg: warning: ignoring request to remove libibverbs1 which isn't installed dpkg: warning: ignoring request to remove libice6 which isn't installed dpkg: warning: ignoring request to remove libicu57 which isn't installed dpkg: warning: ignoring request to remove libidn11 which isn't installed dpkg: warning: ignoring request to remove libidn2-0 which isn't installed dpkg: warning: ignoring request to remove libijs-0.35 which isn't installed dpkg: warning: ignoring request to remove libimport-into-perl which isn't installed dpkg: warning: ignoring request to remove libio-html-perl which isn't installed dpkg: warning: ignoring request to remove libio-pty-perl which isn't installed dpkg: warning: ignoring request to remove libio-sessiondata-perl which isn't installed dpkg: warning: ignoring request to remove libio-socket-ssl-perl which isn't installed dpkg: warning: ignoring request to remove libio-string-perl which isn't installed dpkg: warning: ignoring request to remove libio-stringy-perl which isn't installed dpkg: warning: ignoring request to remove libipc-run-perl which isn't installed dpkg: warning: ignoring request to remove libipc-sharelite-perl which isn't installed dpkg: warning: ignoring request to remove libjbig0 which isn't installed dpkg: warning: ignoring request to remove libjbig2dec0 which isn't installed dpkg: warning: ignoring request to remove libjcode-pm-perl which isn't installed dpkg: warning: ignoring request to remove libjpeg62-turbo which isn't installed dpkg: warning: ignoring request to remove libjs-jquery which isn't installed dpkg: warning: ignoring request to remove libjs-prototype which isn't installed dpkg: warning: ignoring request to remove libjs-scriptaculous which isn't installed dpkg: warning: ignoring request to remove libjson-perl which isn't installed dpkg: warning: ignoring request to remove libjson-xs-perl which isn't installed dpkg: warning: ignoring request to remove libk5crypto3 which isn't installed dpkg: warning: ignoring request to remove libkeyutils1 which isn't installed dpkg: warning: ignoring request to remove libkrb5-3 which isn't installed dpkg: warning: ignoring request to remove libkrb5support0 which isn't installed dpkg: warning: ignoring request to remove liblcms2-2 which isn't installed dpkg: warning: ignoring request to remove libldap-2.4-2 which isn't installed Purging configuration files for libldap-common (2.4.44+dfsg-5+deb9u4) ... dpkg: warning: ignoring request to remove liblist-moreutils-perl which isn't installed dpkg: warning: ignoring request to remove libltdl7 which isn't installed dpkg: warning: ignoring request to remove liblua5.2-0 which isn't installed dpkg: warning: ignoring request to remove liblwp-mediatypes-perl which isn't installed dpkg: warning: ignoring request to remove liblwp-protocol-https-perl which isn't installed dpkg: warning: ignoring request to remove libmagic-mgc which isn't installed Purging configuration files for libmagic1:amd64 (1:5.30-1+deb9u3) ... dpkg: warning: ignoring request to remove libmailtools-perl which isn't installed dpkg: warning: ignoring request to remove libmariadbclient18 which isn't installed dpkg: warning: ignoring request to remove libmath-derivative-perl which isn't installed dpkg: warning: ignoring request to remove libmath-spline-perl which isn't installed dpkg: warning: ignoring request to remove libmime-tools-perl which isn't installed dpkg: warning: ignoring request to remove libmldbm-perl which isn't installed dpkg: warning: ignoring request to remove libmodule-runtime-perl which isn't installed dpkg: warning: ignoring request to remove libmoo-perl which isn't installed dpkg: warning: ignoring request to remove libmpfr4 which isn't installed dpkg: warning: ignoring request to remove libncurses5 which isn't installed dpkg: warning: ignoring request to remove libnet-http-perl which isn't installed dpkg: warning: ignoring request to remove libnet-smtp-ssl-perl which isn't installed dpkg: warning: ignoring request to remove libnet-ssleay-perl which isn't installed dpkg: warning: ignoring request to remove libnettle6 which isn't installed dpkg: warning: ignoring request to remove libnghttp2-14 which isn't installed Purging configuration files for libnl-3-200:amd64 (3.2.27-2) ... dpkg: warning: ignoring request to remove libnl-route-3-200 which isn't installed dpkg: warning: ignoring request to remove libnuma1 which isn't installed dpkg: warning: ignoring request to remove libole-storage-lite-perl which isn't installed dpkg: warning: ignoring request to remove libopenjp2-7 which isn't installed dpkg: warning: ignoring request to remove libopenmpi2 which isn't installed dpkg: warning: ignoring request to remove libossp-uuid-perl which isn't installed dpkg: warning: ignoring request to remove libossp-uuid16 which isn't installed dpkg: warning: ignoring request to remove libp11-kit0 which isn't installed dpkg: warning: ignoring request to remove libpadwalker-perl which isn't installed dpkg: warning: ignoring request to remove libpango-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpangocairo-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpangoft2-1.0-0 which isn't installed dpkg: warning: ignoring request to remove libpaper-utils which isn't installed Purging configuration files for libpaper1:amd64 (1.1.24+nmu5) ... dpkg: warning: ignoring request to remove libparams-classify-perl which isn't installed dpkg: warning: ignoring request to remove libparse-recdescent-perl which isn't installed dpkg: warning: ignoring request to remove libpathplan4 which isn't installed dpkg: warning: ignoring request to remove libpciaccess0 which isn't installed dpkg: warning: ignoring request to remove libperl5.24 which isn't installed dpkg: warning: ignoring request to remove libpixman-1-0 which isn't installed dpkg: warning: ignoring request to remove libpng16-16 which isn't installed dpkg: warning: ignoring request to remove libpostscript-perl which isn't installed dpkg: warning: ignoring request to remove libpq5 which isn't installed dpkg: warning: ignoring request to remove libprocps6 which isn't installed dpkg: warning: ignoring request to remove libpsl5 which isn't installed dpkg: warning: ignoring request to remove libpsm-infinipath1 which isn't installed dpkg: warning: ignoring request to remove libpython-stdlib which isn't installed Purging configuration files for libpython2.7-minimal:amd64 (2.7.13-2+deb9u3) ... dpkg: warning: ignoring request to remove libpython2.7-stdlib which isn't installed dpkg: warning: ignoring request to remove libquadmath0 which isn't installed dpkg: warning: ignoring request to remove librdmacm1 which isn't installed dpkg: warning: ignoring request to remove libreadline7 which isn't installed dpkg: warning: ignoring request to remove librole-tiny-perl which isn't installed dpkg: warning: ignoring request to remove librtmp1 which isn't installed dpkg: warning: ignoring request to remove libruby2.3 which isn't installed dpkg: warning: ignoring request to remove libsasl2-2 which isn't installed Purging configuration files for libsasl2-modules:amd64 (2.1.27~101-g0780600+dfsg-3+deb9u1) ... dpkg: warning: ignoring request to remove libsasl2-modules-db which isn't installed dpkg: warning: ignoring request to remove libset-scalar-perl which isn't installed dpkg: warning: ignoring request to remove libsigsegv2 which isn't installed dpkg: warning: ignoring request to remove libsm6 which isn't installed dpkg: warning: ignoring request to remove libsoap-lite-perl which isn't installed dpkg: warning: ignoring request to remove libsort-naturally-perl which isn't installed dpkg: warning: ignoring request to remove libspreadsheet-parseexcel-perl which isn't installed dpkg: warning: ignoring request to remove libspreadsheet-writeexcel-perl which isn't installed dpkg: warning: ignoring request to remove libsqlite3-0 which isn't installed dpkg: warning: ignoring request to remove libssh2-1 which isn't installed Purging configuration files for libssl1.0.2:amd64 (1.0.2u-1~deb9u1) ... Purging configuration files for libssl1.1:amd64 (1.1.0l-1~deb9u1) ... dpkg: warning: ignoring request to remove libstaden-read11 which isn't installed dpkg: warning: ignoring request to remove libstatistics-descriptive-perl which isn't installed dpkg: warning: ignoring request to remove libstrictures-perl which isn't installed dpkg: warning: ignoring request to remove libstring-approx-perl which isn't installed dpkg: warning: ignoring request to remove libsub-exporter-progressive-perl which isn't installed dpkg: warning: ignoring request to remove libsub-name-perl which isn't installed dpkg: warning: ignoring request to remove libsvg-graph-perl which isn't installed dpkg: warning: ignoring request to remove libsvg-perl which isn't installed dpkg: warning: ignoring request to remove libtask-weaken-perl which isn't installed dpkg: warning: ignoring request to remove libtasn1-6 which isn't installed dpkg: warning: ignoring request to remove libterm-readkey-perl which isn't installed dpkg: warning: ignoring request to remove libtext-iconv-perl which isn't installed dpkg: warning: ignoring request to remove libthai-data which isn't installed dpkg: warning: ignoring request to remove libthai0 which isn't installed dpkg: warning: ignoring request to remove libtie-ixhash-perl which isn't installed dpkg: warning: ignoring request to remove libtiff5 which isn't installed dpkg: warning: ignoring request to remove libtimedate-perl which isn't installed dpkg: warning: ignoring request to remove libtree-dagnode-perl 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 libtypes-serialiser-perl 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 libvm-ec2-perl which isn't installed dpkg: warning: ignoring request to remove libwebp6 which isn't installed dpkg: warning: ignoring request to remove libwww-perl which isn't installed dpkg: warning: ignoring request to remove libwww-robotrules-perl which isn't installed dpkg: warning: ignoring request to remove libx11-6 which isn't installed dpkg: warning: ignoring request to remove libx11-data which isn't installed 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-render0 which isn't installed dpkg: warning: ignoring request to remove libxcb-shm0 which isn't installed dpkg: warning: ignoring request to remove libxcb1 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 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 libxpm4 which isn't installed dpkg: warning: ignoring request to remove libxrender1 which isn't installed dpkg: warning: ignoring request to remove libxslt1.1 which isn't installed dpkg: warning: ignoring request to remove libxt6 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 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 maq 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) ... dpkg: warning: while removing openssl, directory '/etc/ssl/private' not empty so not removed dpkg: warning: while removing openssl, directory '/etc/ssl/certs' not empty so not removed 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 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) ... 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 dpkg: warning: ignoring request to remove sqlite3 which isn't installed Purging configuration files for ssl-cert (1.0.39) ... dpkg: warning: ignoring request to remove t-coffee 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 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 xdg-user-dirs (0.15-2+b1) ... 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 1m16.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'dpkg', '--purge', 'amap-align', 'apache2', 'apache2-bin', 'apache2-data', 'apache2-utils', 'bedtools', 'beignet-opencl-icd:amd64', 'bioperl', 'bioperl-run', 'blast2', 'blends-common', 'bowtie', 'bwa', 'bzip2', 'ca-certificates', 'clustalo', 'clustalw', 'dbus', 'dialign', 'dialign-tx', 'dialign-tx-data', 'emboss', 'emboss-data', 'emboss-lib', 'exonerate', 'file', 'fontconfig', 'fontconfig-config', 'fonts-dejavu-core', 'fonts-droid-fallback', 'fonts-lato', 'fonts-liberation', 'fonts-noto-mono', 'fsa', 'gawk', 'ghostscript', 'graphviz', 'gsfonts', 'hmmer', 'hyphy-common', 'hyphy-mpi', 'infernal', 'javascript-common', 'kalign', 'krb5-locales', 'libace-perl', 'libalgorithm-diff-perl', 'libalgorithm-diff-xs-perl', 'libalgorithm-munkres-perl', 'libann0', 'libanyevent-cachedns-perl', 'libanyevent-http-perl', 'libanyevent-perl', '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', 'libasync-interrupt-perl', 'libauthen-sasl-perl', 'libavahi-client3:amd64', 'libavahi-common-data:amd64', 'libavahi-common3:amd64', 'libbio-asn1-entrezgene-perl', 'libbio-coordinate-perl', 'libbio-graphics-perl', 'libbio-perl-perl', 'libbio-perl-run-perl', 'libbio-scf-perl', 'libbit-vector-perl', 'libbsd-resource-perl', 'libbsd0:amd64', 'libcache-cache-perl', 'libcairo2:amd64', 'libcarp-clan-perl', 'libcdt5', 'libcgi-fast-perl', 'libcgi-pm-perl', 'libcgi-session-perl', 'libcgraph6', 'libclass-inspector-perl', 'libclass-method-modifiers-perl', 'libclass-xsaccessor-perl', 'libclone-perl', 'libcommon-sense-perl', 'libconvert-binary-c-perl', 'libconvert-binhex-perl', 'libcrypt-rc4-perl', 'libcups2:amd64', 'libcupsfilters1:amd64', 'libcupsimage2:amd64', 'libcurl3-gnutls:amd64', '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-symdump-perl', 'libdigest-perl-md5-perl', 'libdivsufsort3:amd64', 'libdrm-intel1:amd64', 'libdrm2:amd64', 'libencode-locale-perl', 'liberror-perl', 'libev-perl', 'libexpat1:amd64', 'libexporter-tiny-perl', 'libfabric1', 'libfcgi-perl', 'libffi6:amd64', 'libfile-listing-perl', 'libfile-slurp-tiny-perl', 'libfont-afm-perl', 'libfontconfig1:amd64', 'libfreetype6:amd64', 'libfreezethaw-perl', 'libgd-perl', 'libgd-svg-perl', 'libgd3:amd64', 'libgdbm3:amd64', 'libgfortran3:amd64', 'libglib2.0-0:amd64', 'libglib2.0-data', 'libgmp10:amd64', 'libgnutls30:amd64', 'libgomp1:amd64', 'libgpm2:amd64', 'libgraph-perl', 'libgraphite2-3:amd64', 'libgraphviz-perl', 'libgs9:amd64', 'libgs9-common', 'libgssapi-krb5-2:amd64', 'libgts-0.7-5:amd64', 'libgts-bin', 'libguard-perl', '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', 'libicu57:amd64', 'libidn11:amd64', 'libidn2-0:amd64', 'libijs-0.35:amd64', 'libimport-into-perl', 'libio-html-perl', 'libio-pty-perl', 'libio-sessiondata-perl', 'libio-socket-ssl-perl', 'libio-string-perl', 'libio-stringy-perl', 'libipc-run-perl', 'libipc-sharelite-perl', 'libjbig0:amd64', 'libjbig2dec0:amd64', 'libjcode-pm-perl', 'libjpeg62-turbo:amd64', 'libjs-jquery', 'libjs-prototype', 'libjs-scriptaculous', 'libjson-perl', 'libjson-xs-perl', 'libk5crypto3:amd64', 'libkeyutils1:amd64', 'libkrb5-3:amd64', 'libkrb5support0:amd64', 'liblcms2-2:amd64', 'libldap-2.4-2:amd64', 'libldap-common', 'liblist-moreutils-perl', 'libltdl7:amd64', 'liblua5.2-0:amd64', 'liblwp-mediatypes-perl', 'liblwp-protocol-https-perl', 'libmagic-mgc', 'libmagic1:amd64', 'libmailtools-perl', 'libmariadbclient18:amd64', 'libmath-derivative-perl', 'libmath-spline-perl', 'libmime-tools-perl', 'libmldbm-perl', 'libmodule-runtime-perl', 'libmoo-perl', 'libmpfr4:amd64', 'libncurses5:amd64', 'libnet-http-perl', 'libnet-smtp-ssl-perl', 'libnet-ssleay-perl', 'libnettle6:amd64', 'libnghttp2-14:amd64', 'libnl-3-200:amd64', 'libnl-route-3-200:amd64', 'libnuma1:amd64', 'libole-storage-lite-perl', 'libopenjp2-7:amd64', 'libopenmpi2:amd64', 'libossp-uuid-perl', 'libossp-uuid16:amd64', 'libp11-kit0:amd64', 'libpadwalker-perl', 'libpango-1.0-0:amd64', 'libpangocairo-1.0-0:amd64', 'libpangoft2-1.0-0:amd64', 'libpaper-utils', 'libpaper1:amd64', 'libparams-classify-perl', 'libparse-recdescent-perl', 'libpathplan4', 'libpciaccess0:amd64', 'libperl5.24:amd64', 'libpixman-1-0:amd64', 'libpng16-16:amd64', 'libpostscript-perl', 'libpq5:amd64', 'libprocps6:amd64', 'libpsl5:amd64', 'libpsm-infinipath1', 'libpython-stdlib:amd64', 'libpython2.7-minimal:amd64', 'libpython2.7-stdlib:amd64', 'libquadmath0:amd64', 'librdmacm1', 'libreadline7:amd64', 'librole-tiny-perl', 'librtmp1:amd64', 'libruby2.3:amd64', 'libsasl2-2:amd64', 'libsasl2-modules:amd64', 'libsasl2-modules-db:amd64', 'libset-scalar-perl', 'libsigsegv2:amd64', 'libsm6:amd64', 'libsoap-lite-perl', 'libsort-naturally-perl', 'libspreadsheet-parseexcel-perl', 'libspreadsheet-writeexcel-perl', 'libsqlite3-0:amd64', 'libssh2-1:amd64', 'libssl1.0.2:amd64', 'libssl1.1:amd64', 'libstaden-read11:amd64', 'libstatistics-descriptive-perl', 'libstrictures-perl', 'libstring-approx-perl', 'libsub-exporter-progressive-perl', 'libsub-name-perl', 'libsvg-graph-perl', 'libsvg-perl', 'libtask-weaken-perl', 'libtasn1-6:amd64', 'libterm-readkey-perl', 'libtext-iconv-perl', 'libthai-data', 'libthai0:amd64', 'libtie-ixhash-perl', 'libtiff5:amd64', 'libtimedate-perl', 'libtree-dagnode-perl', 'libtype-tiny-perl', 'libtype-tiny-xs-perl', 'libtypes-serialiser-perl', 'libunicode-map-perl', 'libunistring0:amd64', 'liburi-perl', 'libvm-ec2-perl', 'libwebp6:amd64', 'libwww-perl', 'libwww-robotrules-perl', 'libx11-6:amd64', 'libx11-data', 'libxau6:amd64', 'libxaw7:amd64', 'libxcb-render0:amd64', 'libxcb-shm0:amd64', 'libxcb1:amd64', 'libxdmcp6:amd64', 'libxdot4', 'libxext6:amd64', 'libxfixes3:amd64', 'libxft2: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', 'libxpm4:amd64', 'libxrender1:amd64', 'libxslt1.1:amd64', 'libxt6:amd64', 'libyaml-0-2:amd64', 'libyaml-libyaml-perl', 'libyaml-perl', 'lsb-base', 'lynx', 'lynx-common', 'mafft', 'maq', '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', 'perl', 'perl-doc', 'perl-modules-5.24', 'perl-openssl-defaults:amd64', 'perl-tk', 'phylip', 'phyml', 'poa', 'poppler-data', 'prank', 'primer3', 'probalign', 'probcons', 'procps', 'proda', 'psmisc', 'publicsuffix', 'python', 'python-minimal', 'python2.7', 'python2.7-minimal', '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', 'sqlite3', 'ssl-cert', 't-coffee', 'tigr-glimmer', 'tm-align', 'ucf', 'unzip', 'wise', 'wise-data', 'x11-common', 'xdg-user-dirs', 'xml-core', 'xz-utils', 'zip'] 1m16.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'dpkg', '--purge', 'gbrowse'] 1m16.5s DUMP: (Reading database ... 4496 files and directories currently installed.) Purging configuration files for gbrowse (2.56+dfsg-2) ... 1m16.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'dpkg', '--purge', 'gbrowse'] 1m16.5s INFO: Running scripts post_purge 1m16.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/post_purge_exceptions'] 1m16.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/post_purge_exceptions'] 1m16.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'dpkg', '--purge', '--pending'] 1m16.5s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'dpkg', '--purge', '--pending'] 1m16.5s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'dpkg', '--remove', '--pending'] 1m16.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'dpkg', '--remove', '--pending'] 1m16.6s INFO: Running scripts post_test 1m16.6s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/post_test_exceptions'] 1m16.6s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'tmp/scripts/post_test_exceptions'] 1m16.6s DEBUG: Starting command: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppkudj_pn'] 1m16.8s DEBUG: Command failed (status=1), but ignoring error: ['lsof', '-w', '+D', '/srv/piuparts.debian.org/tmp/tmppkudj_pn'] 1m17.2s DEBUG: No broken symlinks as far as we can find. 1m17.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'dpkg-divert', '--list'] 1m17.2s DUMP: local diversion of /bin/sync to /bin/sync.distrib diversion of /usr/share/man/man1/sh.1.gz to /usr/share/man/man1/sh.distrib.1.gz by dash local diversion of /home to /home.distrib diversion of /bin/sh to /bin/sh.distrib by dash 1m17.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'dpkg-divert', '--list'] 1m17.2s DEBUG: Starting command: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'apt-get', 'clean'] 1m17.2s DEBUG: Command ok: ['chroot', '/srv/piuparts.debian.org/tmp/tmppkudj_pn', 'apt-get', 'clean'] 1m17.2s DEBUG: Recording chroot state 1m17.5s INFO: PASS: Installation and purging test. 1m17.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmppkudj_pn/dev/shm'] 1m17.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmppkudj_pn/dev/shm'] 1m17.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmppkudj_pn/dev/console'] 1m17.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmppkudj_pn/dev/console'] 1m17.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmppkudj_pn/dev/ptmx'] 1m17.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmppkudj_pn/dev/ptmx'] 1m17.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmppkudj_pn/dev/pts'] 1m17.8s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmppkudj_pn/dev/pts'] 1m17.8s DEBUG: Starting command: ['umount', '/srv/piuparts.debian.org/tmp/tmppkudj_pn/proc'] 1m17.9s DEBUG: Command ok: ['umount', '/srv/piuparts.debian.org/tmp/tmppkudj_pn/proc'] 1m17.9s DEBUG: Starting command: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmppkudj_pn'] 1m17.9s DEBUG: Command ok: ['rm', '-rf', '--one-file-system', '/srv/piuparts.debian.org/tmp/tmppkudj_pn'] 1m17.9s DEBUG: Removed directory tree at /srv/piuparts.debian.org/tmp/tmppkudj_pn 1m17.9s INFO: PASS: All tests. 1m17.9s INFO: piuparts run ends. ret=0 End: 2023-01-31 19:46:16 GMT