0s autopkgtest [03:56:38]: starting date and time: 2024-03-24 03:56:38+0000 0s autopkgtest [03:56:38]: git checkout: 4a1cd702 l/adt_testbed: don't blame the testbed for unsolvable build deps 0s autopkgtest [03:56:38]: host juju-7f2275-prod-proposed-migration-environment-2; command line: /home/ubuntu/autopkgtest/runner/autopkgtest --output-dir /tmp/autopkgtest-work.8k8fs579/out --timeout-copy=6000 -a i386 --setup-commands /home/ubuntu/autopkgtest-cloud/worker-config-production/setup-canonical.sh --setup-commands /home/ubuntu/autopkgtest/setup-commands/setup-testbed --apt-pocket=proposed=src:r-base --apt-upgrade roary --timeout-short=300 --timeout-copy=20000 --timeout-build=20000 --env=ADT_TEST_TRIGGERS=r-base/4.3.3-2build1 -- ssh -s /home/ubuntu/autopkgtest/ssh-setup/nova -- --flavor autopkgtest --security-groups autopkgtest-juju-7f2275-prod-proposed-migration-environment-2@lcy02-1.secgroup --name adt-noble-i386-roary-20240324-032302-juju-7f2275-prod-proposed-migration-environment-2 --image adt/ubuntu-noble-amd64-server --keyname testbed-juju-7f2275-prod-proposed-migration-environment-2 --net-id=net_prod-proposed-migration -e TERM=linux -e ''"'"'http_proxy=http://squid.internal:3128'"'"'' -e ''"'"'https_proxy=http://squid.internal:3128'"'"'' -e ''"'"'no_proxy=127.0.0.1,127.0.1.1,login.ubuntu.com,localhost,localdomain,novalocal,internal,archive.ubuntu.com,ports.ubuntu.com,security.ubuntu.com,ddebs.ubuntu.com,changelogs.ubuntu.com,launchpadlibrarian.net,launchpadcontent.net,launchpad.net,10.24.0.0/24,keystone.ps5.canonical.com,objectstorage.prodstack5.canonical.com'"'"'' --mirror=http://ftpmaster.internal/ubuntu/ 932s autopkgtest [04:12:10]: testbed dpkg architecture: amd64 932s autopkgtest [04:12:10]: testbed apt version: 2.7.12 932s autopkgtest [04:12:10]: test architecture: i386 932s autopkgtest [04:12:10]: @@@@@@@@@@@@@@@@@@@@ test bed setup 933s Get:1 http://ftpmaster.internal/ubuntu noble-proposed InRelease [117 kB] 933s Get:2 http://ftpmaster.internal/ubuntu noble-proposed/main Sources [494 kB] 933s Get:3 http://ftpmaster.internal/ubuntu noble-proposed/multiverse Sources [56.9 kB] 933s Get:4 http://ftpmaster.internal/ubuntu noble-proposed/restricted Sources [6540 B] 933s Get:5 http://ftpmaster.internal/ubuntu noble-proposed/universe Sources [3982 kB] 933s Get:6 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 Packages [725 kB] 933s Get:7 http://ftpmaster.internal/ubuntu noble-proposed/main i386 Packages [486 kB] 933s Get:8 http://ftpmaster.internal/ubuntu noble-proposed/main amd64 c-n-f Metadata [3508 B] 933s Get:9 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 Packages [30.5 kB] 933s Get:10 http://ftpmaster.internal/ubuntu noble-proposed/restricted i386 Packages [6700 B] 933s Get:11 http://ftpmaster.internal/ubuntu noble-proposed/restricted amd64 c-n-f Metadata [116 B] 933s Get:12 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 Packages [4422 kB] 933s Get:13 http://ftpmaster.internal/ubuntu noble-proposed/universe i386 Packages [1304 kB] 933s Get:14 http://ftpmaster.internal/ubuntu noble-proposed/universe amd64 c-n-f Metadata [9396 B] 933s Get:15 http://ftpmaster.internal/ubuntu noble-proposed/multiverse i386 Packages [27.1 kB] 933s Get:16 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 Packages [96.1 kB] 933s Get:17 http://ftpmaster.internal/ubuntu noble-proposed/multiverse amd64 c-n-f Metadata [196 B] 937s Fetched 11.8 MB in 1s (7980 kB/s) 937s Reading package lists... 939s Reading package lists... 939s Building dependency tree... 939s Reading state information... 939s Calculating upgrade... 940s The following packages will be upgraded: 940s libc-bin libc6 locales 940s 3 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 940s Need to get 8176 kB of archives. 940s After this operation, 2048 B of additional disk space will be used. 940s Get:1 http://ftpmaster.internal/ubuntu noble/main amd64 libc6 amd64 2.39-0ubuntu6 [3262 kB] 940s Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 libc-bin amd64 2.39-0ubuntu6 [682 kB] 940s Get:3 http://ftpmaster.internal/ubuntu noble/main amd64 locales all 2.39-0ubuntu6 [4232 kB] 940s Preconfiguring packages ... 940s Fetched 8176 kB in 0s (85.0 MB/s) 941s (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 ... 71864 files and directories currently installed.) 941s Preparing to unpack .../libc6_2.39-0ubuntu6_amd64.deb ... 941s Unpacking libc6:amd64 (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 941s Setting up libc6:amd64 (2.39-0ubuntu6) ... 941s (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 ... 71864 files and directories currently installed.) 941s Preparing to unpack .../libc-bin_2.39-0ubuntu6_amd64.deb ... 941s Unpacking libc-bin (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 941s Setting up libc-bin (2.39-0ubuntu6) ... 942s (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 ... 71864 files and directories currently installed.) 942s Preparing to unpack .../locales_2.39-0ubuntu6_all.deb ... 942s Unpacking locales (2.39-0ubuntu6) over (2.39-0ubuntu2) ... 942s Setting up locales (2.39-0ubuntu6) ... 942s Generating locales (this might take a while)... 944s en_US.UTF-8... done 944s Generation complete. 944s Processing triggers for man-db (2.12.0-3) ... 945s Reading package lists... 946s Building dependency tree... 946s Reading state information... 946s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 947s sh: Attempting to set up Debian/Ubuntu apt sources automatically 947s sh: Distribution appears to be Ubuntu 948s Reading package lists... 948s Building dependency tree... 948s Reading state information... 948s eatmydata is already the newest version (131-1). 948s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 948s Reading package lists... 949s Building dependency tree... 949s Reading state information... 949s dbus is already the newest version (1.14.10-4ubuntu1). 949s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 949s Reading package lists... 949s Building dependency tree... 949s Reading state information... 950s rng-tools-debian is already the newest version (2.4). 950s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 950s Reading package lists... 950s Building dependency tree... 950s Reading state information... 950s The following packages will be REMOVED: 950s cloud-init* python3-configobj* python3-debconf* 951s 0 upgraded, 0 newly installed, 3 to remove and 0 not upgraded. 951s After this operation, 3256 kB disk space will be freed. 951s (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 ... 71864 files and directories currently installed.) 951s Removing cloud-init (24.1.2-0ubuntu1) ... 951s Removing python3-configobj (5.0.8-3) ... 951s Removing python3-debconf (1.5.86) ... 951s Processing triggers for man-db (2.12.0-3) ... 952s (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 ... 71475 files and directories currently installed.) 952s Purging configuration files for cloud-init (24.1.2-0ubuntu1) ... 952s dpkg: warning: while removing cloud-init, directory '/etc/cloud/cloud.cfg.d' not empty so not removed 952s Processing triggers for rsyslog (8.2312.0-3ubuntu3) ... 952s invoke-rc.d: policy-rc.d denied execution of try-restart. 953s Reading package lists... 953s Building dependency tree... 953s Reading state information... 953s linux-generic is already the newest version (6.8.0-11.11+1). 953s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 953s Hit:1 http://ftpmaster.internal/ubuntu noble InRelease 953s Hit:2 http://ftpmaster.internal/ubuntu noble-updates InRelease 953s Hit:3 http://ftpmaster.internal/ubuntu noble-security InRelease 956s Reading package lists... 956s Reading package lists... 956s Building dependency tree... 956s Reading state information... 956s Calculating upgrade... 956s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 957s Reading package lists... 957s Building dependency tree... 957s Reading state information... 957s 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. 957s autopkgtest [04:12:35]: rebooting testbed after setup commands that affected boot 987s autopkgtest [04:13:05]: testbed running kernel: Linux 6.8.0-11-generic #11-Ubuntu SMP PREEMPT_DYNAMIC Wed Feb 14 00:29:05 UTC 2024 988s autopkgtest [04:13:06]: @@@@@@@@@@@@@@@@@@@@ apt-source roary 989s Get:1 http://ftpmaster.internal/ubuntu noble/universe roary 3.13.0+dfsg-1 (dsc) [2501 B] 989s Get:2 http://ftpmaster.internal/ubuntu noble/universe roary 3.13.0+dfsg-1 (tar) [207 kB] 989s Get:3 http://ftpmaster.internal/ubuntu noble/universe roary 3.13.0+dfsg-1 (diff) [6612 B] 990s gpgv: Signature made Fri Nov 8 13:51:49 2019 UTC 990s gpgv: using RSA key 5B34BA5AAB5507E903426E85E8D37AE2F09F4872 990s gpgv: Can't check signature: No public key 990s dpkg-source: warning: cannot verify inline signature for ./roary_3.13.0+dfsg-1.dsc: no acceptable signature found 990s autopkgtest [04:13:08]: testing package roary version 3.13.0+dfsg-1 990s autopkgtest [04:13:08]: build not needed 990s autopkgtest [04:13:08]: test test-installed: preparing testbed 996s Note, using file '/tmp/autopkgtest.3U64ZN/1-autopkgtest-satdep.dsc' to get the build dependencies 996s Reading package lists... 997s Building dependency tree... 997s Reading state information... 997s Starting pkgProblemResolver with broken count: 0 997s Starting 2 pkgProblemResolver with broken count: 0 997s Done 997s The following NEW packages will be installed: 997s bedtools bioperl build-essential cd-hit cpp cpp-13 cpp-13-x86-64-linux-gnu 997s cpp-x86-64-linux-gnu fasttree fontconfig fontconfig-config fonts-dejavu-core 997s fonts-dejavu-mono g++ g++-13 g++-13-x86-64-linux-gnu g++-x86-64-linux-gnu 997s gcc gcc-13 gcc-13-x86-64-linux-gnu gcc-x86-64-linux-gnu libalgorithm-c3-perl 997s libalgorithm-diff-perl libarray-utils-perl libasan8 libatomic1 997s libb-hooks-op-check-perl libbio-perl-perl libblas3 libc-dev-bin libc6-dev 997s libcairo2 libcapture-tiny-perl libcc1-0 libclass-c3-perl 997s libclass-data-inheritable-perl libclass-load-perl libclass-load-xs-perl 997s libclone-perl libcrypt-dev libdata-optlist-perl libdata-stag-perl libdatrie1 997s libdeflate0 libdevel-callchecker-perl libdevel-globaldestruction-perl 997s libdevel-overloadinfo-perl libdevel-stacktrace-perl libdigest-md5-file-perl 997s libdist-checkconflicts-perl libdynaloader-functions-perl 997s libencode-locale-perl libenv-path-perl libeval-closure-perl 997s libexception-class-perl libfile-find-rule-perl libfile-grep-perl 997s libfile-listing-perl libfile-slurper-perl libfile-which-perl 997s libfindbin-libs-perl libfontconfig1 libgcc-13-dev libgfortran5 libgomp1 997s libgraph-perl libgraph-readwrite-perl libgraphite2-3 libharfbuzz0b 997s libheap-perl libhtml-parser-perl libhtml-tagset-perl libhtml-tree-perl 997s libhttp-cookies-perl libhttp-date-perl libhttp-message-perl 997s libhttp-negotiate-perl libhwasan0 libice6 libio-all-perl libio-html-perl 997s libio-socket-ssl-perl libio-string-perl libisl23 libitm1 libjbig0 997s libjpeg-turbo8 libjpeg8 liblapack3 liblerc4 liblog-log4perl-perl liblsan0 997s liblwp-mediatypes-perl liblwp-protocol-https-perl libmbedcrypto7 997s libmbedtls14 libmbedx509-1 libmodule-implementation-perl 997s libmodule-runtime-conflicts-perl libmodule-runtime-perl libmoose-perl 997s libmpc3 libmro-compat-perl libnet-http-perl libnet-ssleay-perl 997s libnumber-compare-perl libpackage-deprecationmanager-perl 997s libpackage-stash-perl libpackage-stash-xs-perl libpango-1.0-0 997s libpangocairo-1.0-0 libpangoft2-1.0-0 libpaper-utils libpaper1 997s libparams-classify-perl libparams-util-perl libparse-yapp-perl 997s libperlio-utf8-strict-perl libpixman-1-0 libquadmath0 libset-object-perl 997s libsharpyuv0 libsm6 libspiffy-perl libstdc++-13-dev libsub-exporter-perl 997s libsub-exporter-progressive-perl libsub-install-perl libsub-uplevel-perl 997s libtcl8.6 libtest-deep-perl libtest-differences-perl libtest-exception-perl 997s libtest-file-perl libtest-files-perl libtest-most-perl libtest-output-perl 997s libtest-warn-perl libtext-csv-perl libtext-diff-perl libtext-glob-perl 997s libthai-data libthai0 libtiff6 libtimedate-perl libtingea0 libtk8.6 997s libtry-tiny-perl libtsan2 libubsan1 liburi-perl libwebp7 libwww-perl 997s libwww-robotrules-perl libxcb-render0 libxcb-shm0 libxft2 libxml-parser-perl 997s libxml-writer-perl libxrender1 libxss1 libxt6 linux-libc-dev mafft mcl 997s ncbi-blast+ ncbi-data parallel perl-openssl-defaults prank r-base-core 997s r-cran-cli r-cran-colorspace r-cran-fansi r-cran-farver r-cran-ggplot2 997s r-cran-glue r-cran-gtable r-cran-isoband r-cran-labeling r-cran-lattice 997s r-cran-lifecycle r-cran-magrittr r-cran-mass r-cran-matrix r-cran-mgcv 997s r-cran-munsell r-cran-nlme r-cran-pillar r-cran-pkgconfig r-cran-r6 997s r-cran-rcolorbrewer r-cran-rlang r-cran-scales r-cran-tibble r-cran-utf8 997s r-cran-vctrs r-cran-viridislite r-cran-withr roary rpcsvc-proto unzip 997s x11-common xdg-utils zip 997s 0 upgraded, 205 newly installed, 0 to remove and 0 not upgraded. 997s Need to get 162 MB of archives. 997s After this operation, 477 MB of additional disk space will be used. 997s Get:1 http://ftpmaster.internal/ubuntu noble/universe amd64 bedtools amd64 2.31.1+dfsg-2 [674 kB] 997s Get:2 http://ftpmaster.internal/ubuntu noble/main amd64 libio-string-perl all 1.08-4 [11.1 kB] 997s Get:3 http://ftpmaster.internal/ubuntu noble/universe amd64 libdata-stag-perl all 0.14-3 [372 kB] 997s Get:4 http://ftpmaster.internal/ubuntu noble/universe amd64 libbio-perl-perl all 1.7.8-1 [2580 kB] 997s Get:5 http://ftpmaster.internal/ubuntu noble/main amd64 libclass-data-inheritable-perl all 0.08-3 [8084 B] 997s Get:6 http://ftpmaster.internal/ubuntu noble/main amd64 libdevel-stacktrace-perl all 2.0500-1 [22.1 kB] 997s Get:7 http://ftpmaster.internal/ubuntu noble/main amd64 libexception-class-perl all 1.45-1 [28.6 kB] 997s Get:8 http://ftpmaster.internal/ubuntu noble/universe amd64 libtest-deep-perl all 1.204-1 [47.1 kB] 997s Get:9 http://ftpmaster.internal/ubuntu noble/main amd64 libcapture-tiny-perl all 0.48-2 [20.2 kB] 997s Get:10 http://ftpmaster.internal/ubuntu noble/main amd64 libalgorithm-diff-perl all 1.201-1 [41.8 kB] 997s Get:11 http://ftpmaster.internal/ubuntu noble/universe amd64 libtext-diff-perl all 1.45-2 [25.6 kB] 997s Get:12 http://ftpmaster.internal/ubuntu noble/universe amd64 libtest-differences-perl all 0.71-1 [15.8 kB] 997s Get:13 http://ftpmaster.internal/ubuntu noble/universe amd64 libsub-uplevel-perl all 0.2800-3 [11.6 kB] 997s Get:14 http://ftpmaster.internal/ubuntu noble/universe amd64 libtest-exception-perl all 0.43-3 [13.4 kB] 997s Get:15 http://ftpmaster.internal/ubuntu noble/universe amd64 libtest-warn-perl all 0.37-2 [12.6 kB] 997s Get:16 http://ftpmaster.internal/ubuntu noble/universe amd64 libtest-most-perl all 0.38-1 [21.5 kB] 997s Get:17 http://ftpmaster.internal/ubuntu noble/universe amd64 bioperl all 1.7.8-1 [216 kB] 997s Get:18 http://ftpmaster.internal/ubuntu noble/main amd64 libc-dev-bin amd64 2.39-0ubuntu6 [20.4 kB] 997s Get:19 http://ftpmaster.internal/ubuntu noble/main amd64 linux-libc-dev amd64 6.8.0-11.11 [1595 kB] 997s Get:20 http://ftpmaster.internal/ubuntu noble/main amd64 libcrypt-dev amd64 1:4.4.36-4 [128 kB] 997s Get:21 http://ftpmaster.internal/ubuntu noble/main amd64 rpcsvc-proto amd64 1.4.2-0ubuntu6 [68.5 kB] 997s Get:22 http://ftpmaster.internal/ubuntu noble/main amd64 libc6-dev amd64 2.39-0ubuntu6 [2126 kB] 997s Get:23 http://ftpmaster.internal/ubuntu noble/main amd64 libisl23 amd64 0.26-3 [741 kB] 998s Get:24 http://ftpmaster.internal/ubuntu noble/main amd64 libmpc3 amd64 1.3.1-1 [54.1 kB] 998s Get:25 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [11.2 MB] 998s Get:26 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-13 amd64 13.2.0-17ubuntu2 [1030 B] 998s Get:27 http://ftpmaster.internal/ubuntu noble/main amd64 cpp-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [5326 B] 998s Get:28 http://ftpmaster.internal/ubuntu noble/main amd64 cpp amd64 4:13.2.0-7ubuntu1 [22.4 kB] 998s Get:29 http://ftpmaster.internal/ubuntu noble/main amd64 libcc1-0 amd64 14-20240303-1ubuntu1 [47.7 kB] 998s Get:30 http://ftpmaster.internal/ubuntu noble/main amd64 libgomp1 amd64 14-20240303-1ubuntu1 [147 kB] 998s Get:31 http://ftpmaster.internal/ubuntu noble/main amd64 libitm1 amd64 14-20240303-1ubuntu1 [29.1 kB] 998s Get:32 http://ftpmaster.internal/ubuntu noble/main amd64 libatomic1 amd64 14-20240303-1ubuntu1 [10.4 kB] 998s Get:33 http://ftpmaster.internal/ubuntu noble/main amd64 libasan8 amd64 14-20240303-1ubuntu1 [3026 kB] 998s Get:34 http://ftpmaster.internal/ubuntu noble/main amd64 liblsan0 amd64 14-20240303-1ubuntu1 [1310 kB] 998s Get:35 http://ftpmaster.internal/ubuntu noble/main amd64 libtsan2 amd64 14-20240303-1ubuntu1 [2732 kB] 998s Get:36 http://ftpmaster.internal/ubuntu noble/main amd64 libubsan1 amd64 14-20240303-1ubuntu1 [1172 kB] 998s Get:37 http://ftpmaster.internal/ubuntu noble/main amd64 libhwasan0 amd64 14-20240303-1ubuntu1 [1629 kB] 998s Get:38 http://ftpmaster.internal/ubuntu noble/main amd64 libquadmath0 amd64 14-20240303-1ubuntu1 [155 kB] 998s Get:39 http://ftpmaster.internal/ubuntu noble/main amd64 libgcc-13-dev amd64 13.2.0-17ubuntu2 [2687 kB] 998s Get:40 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [21.9 MB] 998s Get:41 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-13 amd64 13.2.0-17ubuntu2 [477 kB] 998s Get:42 http://ftpmaster.internal/ubuntu noble/main amd64 gcc-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [1212 B] 998s Get:43 http://ftpmaster.internal/ubuntu noble/main amd64 gcc amd64 4:13.2.0-7ubuntu1 [5018 B] 998s Get:44 http://ftpmaster.internal/ubuntu noble/main amd64 libstdc++-13-dev amd64 13.2.0-17ubuntu2 [2340 kB] 998s Get:45 http://ftpmaster.internal/ubuntu noble/main amd64 g++-13-x86-64-linux-gnu amd64 13.2.0-17ubuntu2 [12.5 MB] 998s Get:46 http://ftpmaster.internal/ubuntu noble/main amd64 g++-13 amd64 13.2.0-17ubuntu2 [14.5 kB] 998s Get:47 http://ftpmaster.internal/ubuntu noble/main amd64 g++-x86-64-linux-gnu amd64 4:13.2.0-7ubuntu1 [964 B] 998s Get:48 http://ftpmaster.internal/ubuntu noble/main amd64 g++ amd64 4:13.2.0-7ubuntu1 [1100 B] 998s Get:49 http://ftpmaster.internal/ubuntu noble/main amd64 build-essential amd64 12.10ubuntu1 [4928 B] 998s Get:50 http://ftpmaster.internal/ubuntu noble/universe amd64 cd-hit amd64 4.8.1-4 [521 kB] 998s Get:51 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-dejavu-mono all 2.37-8 [502 kB] 998s Get:52 http://ftpmaster.internal/ubuntu noble/main amd64 fonts-dejavu-core all 2.37-8 [835 kB] 998s Get:53 http://ftpmaster.internal/ubuntu noble/main amd64 fontconfig-config amd64 2.15.0-1ubuntu1 [36.9 kB] 998s Get:54 http://ftpmaster.internal/ubuntu noble/main amd64 libfontconfig1 amd64 2.15.0-1ubuntu1 [139 kB] 998s Get:55 http://ftpmaster.internal/ubuntu noble/main amd64 fontconfig amd64 2.15.0-1ubuntu1 [180 kB] 998s Get:56 http://ftpmaster.internal/ubuntu noble/universe amd64 libalgorithm-c3-perl all 0.11-2 [10.2 kB] 998s Get:57 http://ftpmaster.internal/ubuntu noble/universe amd64 libarray-utils-perl all 0.5-3 [5862 B] 998s Get:58 http://ftpmaster.internal/ubuntu noble/main amd64 libb-hooks-op-check-perl amd64 0.22-2build2 [9452 B] 998s Get:59 http://ftpmaster.internal/ubuntu noble/main amd64 libblas3 amd64 3.12.0-3 [238 kB] 998s Get:60 http://ftpmaster.internal/ubuntu noble/main amd64 libpixman-1-0 amd64 0.42.2-1 [268 kB] 998s Get:61 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-render0 amd64 1.15-1 [16.3 kB] 998s Get:62 http://ftpmaster.internal/ubuntu noble/main amd64 libxcb-shm0 amd64 1.15-1 [5740 B] 998s Get:63 http://ftpmaster.internal/ubuntu noble/main amd64 libxrender1 amd64 1:0.9.10-1.1 [20.0 kB] 998s Get:64 http://ftpmaster.internal/ubuntu noble/main amd64 libcairo2 amd64 1.18.0-1 [572 kB] 998s Get:65 http://ftpmaster.internal/ubuntu noble/universe amd64 libclass-c3-perl all 0.35-2 [18.4 kB] 998s Get:66 http://ftpmaster.internal/ubuntu noble/main amd64 libparams-util-perl amd64 1.102-2build1 [21.1 kB] 998s Get:67 http://ftpmaster.internal/ubuntu noble/main amd64 libsub-install-perl all 0.929-1 [9764 B] 998s Get:68 http://ftpmaster.internal/ubuntu noble/main amd64 libdata-optlist-perl all 0.114-1 [9708 B] 998s Get:69 http://ftpmaster.internal/ubuntu noble/main amd64 libdynaloader-functions-perl all 0.003-3 [12.1 kB] 998s Get:70 http://ftpmaster.internal/ubuntu noble/main amd64 libdevel-callchecker-perl amd64 0.008-2build1 [13.9 kB] 998s Get:71 http://ftpmaster.internal/ubuntu noble/main amd64 libparams-classify-perl amd64 0.015-2build3 [20.0 kB] 998s Get:72 http://ftpmaster.internal/ubuntu noble/main amd64 libmodule-runtime-perl all 0.016-2 [16.4 kB] 998s Get:73 http://ftpmaster.internal/ubuntu noble/main amd64 libtry-tiny-perl all 0.31-2 [20.8 kB] 998s Get:74 http://ftpmaster.internal/ubuntu noble/main amd64 libmodule-implementation-perl all 0.09-2 [12.0 kB] 998s Get:75 http://ftpmaster.internal/ubuntu noble/main amd64 libpackage-stash-perl all 0.40-1 [19.5 kB] 998s Get:76 http://ftpmaster.internal/ubuntu noble/universe amd64 libclass-load-perl all 0.25-2 [12.7 kB] 998s Get:77 http://ftpmaster.internal/ubuntu noble/universe amd64 libclass-load-xs-perl amd64 0.10-2build2 [13.5 kB] 998s Get:78 http://ftpmaster.internal/ubuntu noble/main amd64 libclone-perl amd64 0.46-1build1 [10.6 kB] 998s Get:79 http://ftpmaster.internal/ubuntu noble/main amd64 libdatrie1 amd64 0.2.13-3 [20.9 kB] 998s Get:80 http://ftpmaster.internal/ubuntu noble/main amd64 libdeflate0 amd64 1.19-1 [43.7 kB] 998s Get:81 http://ftpmaster.internal/ubuntu noble/main amd64 libsub-exporter-progressive-perl all 0.001013-3 [6718 B] 998s Get:82 http://ftpmaster.internal/ubuntu noble/universe amd64 libdevel-globaldestruction-perl all 0.14-4 [6114 B] 998s Get:83 http://ftpmaster.internal/ubuntu noble/universe amd64 libmro-compat-perl all 0.15-2 [10.1 kB] 998s Get:84 http://ftpmaster.internal/ubuntu noble/universe amd64 libdevel-overloadinfo-perl all 0.007-1 [7422 B] 998s Get:85 http://ftpmaster.internal/ubuntu noble/main amd64 libencode-locale-perl all 1.05-3 [11.6 kB] 998s Get:86 http://ftpmaster.internal/ubuntu noble/main amd64 libtimedate-perl all 2.3300-2 [34.0 kB] 998s Get:87 http://ftpmaster.internal/ubuntu noble/main amd64 libhttp-date-perl all 6.06-1 [10.2 kB] 998s Get:88 http://ftpmaster.internal/ubuntu noble/main amd64 libfile-listing-perl all 6.16-1 [11.3 kB] 998s Get:89 http://ftpmaster.internal/ubuntu noble/main amd64 libhtml-tagset-perl all 3.20-6 [11.3 kB] 998s Get:90 http://ftpmaster.internal/ubuntu noble/main amd64 liburi-perl all 5.27-1 [88.0 kB] 998s Get:91 http://ftpmaster.internal/ubuntu noble/main amd64 libhtml-parser-perl amd64 3.81-1build1 [85.7 kB] 998s Get:92 http://ftpmaster.internal/ubuntu noble/main amd64 libhtml-tree-perl all 5.07-3 [200 kB] 998s Get:93 http://ftpmaster.internal/ubuntu noble/main amd64 libio-html-perl all 1.004-3 [15.9 kB] 998s Get:94 http://ftpmaster.internal/ubuntu noble/main amd64 liblwp-mediatypes-perl all 6.04-2 [20.1 kB] 998s Get:95 http://ftpmaster.internal/ubuntu noble/main amd64 libhttp-message-perl all 6.45-1ubuntu1 [78.2 kB] 998s Get:96 http://ftpmaster.internal/ubuntu noble/main amd64 libhttp-cookies-perl all 6.11-1 [18.2 kB] 998s Get:97 http://ftpmaster.internal/ubuntu noble/main amd64 libhttp-negotiate-perl all 6.01-2 [12.4 kB] 998s Get:98 http://ftpmaster.internal/ubuntu noble/main amd64 perl-openssl-defaults amd64 7 [7536 B] 998s Get:99 http://ftpmaster.internal/ubuntu noble/main amd64 libnet-ssleay-perl amd64 1.94-1 [316 kB] 998s Get:100 http://ftpmaster.internal/ubuntu noble/main amd64 libio-socket-ssl-perl all 2.085-1 [195 kB] 998s Get:101 http://ftpmaster.internal/ubuntu noble/main amd64 libnet-http-perl all 6.23-1 [22.3 kB] 998s Get:102 http://ftpmaster.internal/ubuntu noble/main amd64 liblwp-protocol-https-perl all 6.13-1 [9006 B] 998s Get:103 http://ftpmaster.internal/ubuntu noble/main amd64 libwww-robotrules-perl all 6.02-1 [12.6 kB] 998s Get:104 http://ftpmaster.internal/ubuntu noble/main amd64 libwww-perl all 6.76-1 [138 kB] 998s Get:105 http://ftpmaster.internal/ubuntu noble/universe amd64 libdigest-md5-file-perl all 0.08-1.1 [8968 B] 998s Get:106 http://ftpmaster.internal/ubuntu noble/universe amd64 libdist-checkconflicts-perl all 0.11-2 [9942 B] 998s Get:107 http://ftpmaster.internal/ubuntu noble/universe amd64 libenv-path-perl all 0.19-4 [18.0 kB] 998s Get:108 http://ftpmaster.internal/ubuntu noble/main amd64 libsub-exporter-perl all 0.990-1 [49.0 kB] 998s Get:109 http://ftpmaster.internal/ubuntu noble/universe amd64 libeval-closure-perl all 0.14-3 [10.1 kB] 998s Get:110 http://ftpmaster.internal/ubuntu noble/main amd64 libnumber-compare-perl all 0.03-3 [5974 B] 998s Get:111 http://ftpmaster.internal/ubuntu noble/main amd64 libtext-glob-perl all 0.11-3 [6780 B] 998s Get:112 http://ftpmaster.internal/ubuntu noble/main amd64 libfile-find-rule-perl all 0.34-3 [24.4 kB] 998s Get:113 http://ftpmaster.internal/ubuntu noble/universe amd64 libfile-grep-perl all 0.02-3 [8248 B] 998s Get:114 http://ftpmaster.internal/ubuntu noble/main amd64 libfile-slurper-perl all 0.014-1 [7660 B] 998s Get:115 http://ftpmaster.internal/ubuntu noble/main amd64 libfile-which-perl all 1.27-2 [12.5 kB] 998s Get:116 http://ftpmaster.internal/ubuntu noble/universe amd64 libfindbin-libs-perl all 3.0.2-1 [22.3 kB] 998s Get:117 http://ftpmaster.internal/ubuntu noble/main amd64 libgfortran5 amd64 14-20240303-1ubuntu1 [924 kB] 998s Get:118 http://ftpmaster.internal/ubuntu noble/universe amd64 libheap-perl all 0.80-5 [33.8 kB] 998s Get:119 http://ftpmaster.internal/ubuntu noble/universe amd64 libset-object-perl amd64 1.42-1build3 [33.3 kB] 998s Get:120 http://ftpmaster.internal/ubuntu noble/universe amd64 libgraph-perl all 1:0.9727-1 [100 kB] 998s Get:121 http://ftpmaster.internal/ubuntu noble/universe amd64 libspiffy-perl all 0.46-1 [23.9 kB] 998s Get:122 http://ftpmaster.internal/ubuntu noble/universe amd64 libio-all-perl all 0.87-2 [61.3 kB] 998s Get:123 http://ftpmaster.internal/ubuntu noble/universe amd64 libparse-yapp-perl all 1.21-3 [38.0 kB] 998s Get:124 http://ftpmaster.internal/ubuntu noble/main amd64 libxml-parser-perl amd64 2.47-1build1 [204 kB] 998s Get:125 http://ftpmaster.internal/ubuntu noble/universe amd64 libxml-writer-perl all 0.900-2 [24.0 kB] 998s Get:126 http://ftpmaster.internal/ubuntu noble/universe amd64 libgraph-readwrite-perl all 2.10-1 [44.0 kB] 998s Get:127 http://ftpmaster.internal/ubuntu noble/main amd64 libgraphite2-3 amd64 1.3.14-2 [83.1 kB] 998s Get:128 http://ftpmaster.internal/ubuntu noble/main amd64 libharfbuzz0b amd64 8.3.0-2 [469 kB] 998s Get:129 http://ftpmaster.internal/ubuntu noble/main amd64 x11-common all 1:7.7+23ubuntu2 [23.4 kB] 998s Get:130 http://ftpmaster.internal/ubuntu noble/main amd64 libice6 amd64 2:1.0.10-1build2 [42.6 kB] 998s Get:131 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg-turbo8 amd64 2.1.5-2ubuntu1 [147 kB] 998s Get:132 http://ftpmaster.internal/ubuntu noble/main amd64 libjpeg8 amd64 8c-2ubuntu11 [2148 B] 998s Get:133 http://ftpmaster.internal/ubuntu noble/main amd64 liblapack3 amd64 3.12.0-3 [2649 kB] 998s Get:134 http://ftpmaster.internal/ubuntu noble/main amd64 liblerc4 amd64 4.0.0+ds-4ubuntu1 [184 kB] 998s Get:135 http://ftpmaster.internal/ubuntu noble/universe amd64 liblog-log4perl-perl all 1.57-1 [345 kB] 998s Get:136 http://ftpmaster.internal/ubuntu noble/universe amd64 libmbedcrypto7 amd64 2.28.7-1ubuntu1 [206 kB] 998s Get:137 http://ftpmaster.internal/ubuntu noble/universe amd64 libmbedx509-1 amd64 2.28.7-1ubuntu1 [46.4 kB] 998s Get:138 http://ftpmaster.internal/ubuntu noble/universe amd64 libmbedtls14 amd64 2.28.7-1ubuntu1 [82.1 kB] 998s Get:139 http://ftpmaster.internal/ubuntu noble/universe amd64 libmodule-runtime-conflicts-perl all 0.003-2 [6956 B] 998s Get:140 http://ftpmaster.internal/ubuntu noble/universe amd64 libpackage-deprecationmanager-perl all 0.18-1 [16.7 kB] 998s Get:141 http://ftpmaster.internal/ubuntu noble/main amd64 libpackage-stash-xs-perl amd64 0.30-1build2 [18.8 kB] 998s Get:142 http://ftpmaster.internal/ubuntu noble/universe amd64 libmoose-perl amd64 2.2207-1 [717 kB] 998s Get:143 http://ftpmaster.internal/ubuntu noble/main amd64 libthai-data all 0.1.29-2 [158 kB] 998s Get:144 http://ftpmaster.internal/ubuntu noble/main amd64 libthai0 amd64 0.1.29-2 [18.8 kB] 998s Get:145 http://ftpmaster.internal/ubuntu noble/main amd64 libpango-1.0-0 amd64 1.51.0+ds-4 [228 kB] 998s Get:146 http://ftpmaster.internal/ubuntu noble/main amd64 libpangoft2-1.0-0 amd64 1.51.0+ds-4 [42.1 kB] 998s Get:147 http://ftpmaster.internal/ubuntu noble/main amd64 libpangocairo-1.0-0 amd64 1.51.0+ds-4 [29.0 kB] 998s Get:148 http://ftpmaster.internal/ubuntu noble/main amd64 libpaper1 amd64 1.1.29 [13.4 kB] 998s Get:149 http://ftpmaster.internal/ubuntu noble/main amd64 libpaper-utils amd64 1.1.29 [8658 B] 998s Get:150 http://ftpmaster.internal/ubuntu noble/main amd64 libperlio-utf8-strict-perl amd64 0.010-1build1 [11.0 kB] 998s Get:151 http://ftpmaster.internal/ubuntu noble/main amd64 libsharpyuv0 amd64 1.3.2-0.4 [15.6 kB] 998s Get:152 http://ftpmaster.internal/ubuntu noble/main amd64 libsm6 amd64 2:1.2.3-1build2 [16.7 kB] 998s Get:153 http://ftpmaster.internal/ubuntu noble/main amd64 libtcl8.6 amd64 8.6.13+dfsg-2 [984 kB] 998s Get:154 http://ftpmaster.internal/ubuntu noble/universe amd64 libtest-file-perl all 1.993-1 [20.7 kB] 998s Get:155 http://ftpmaster.internal/ubuntu noble/universe amd64 libtest-files-perl all 0.15-1 [9744 B] 998s Get:156 http://ftpmaster.internal/ubuntu noble/universe amd64 libtest-output-perl all 1.034-1 [14.2 kB] 998s Get:157 http://ftpmaster.internal/ubuntu noble/universe amd64 libtext-csv-perl all 2.04-1 [109 kB] 998s Get:158 http://ftpmaster.internal/ubuntu noble/main amd64 libjbig0 amd64 2.1-6.1ubuntu1 [29.3 kB] 998s Get:159 http://ftpmaster.internal/ubuntu noble/main amd64 libwebp7 amd64 1.3.2-0.4 [230 kB] 998s Get:160 http://ftpmaster.internal/ubuntu noble/main amd64 libtiff6 amd64 4.5.1+git230720-3ubuntu1 [232 kB] 998s Get:161 http://ftpmaster.internal/ubuntu noble/universe amd64 libtingea0 amd64 21-361-2 [54.4 kB] 998s Get:162 http://ftpmaster.internal/ubuntu noble/main amd64 libxft2 amd64 2.3.6-1 [44.5 kB] 998s Get:163 http://ftpmaster.internal/ubuntu noble/main amd64 libxss1 amd64 1:1.2.3-1build2 [8476 B] 998s Get:164 http://ftpmaster.internal/ubuntu noble/main amd64 libtk8.6 amd64 8.6.14-1 [779 kB] 998s Get:165 http://ftpmaster.internal/ubuntu noble/main amd64 libxt6 amd64 1:1.2.1-1.1 [173 kB] 998s Get:166 http://ftpmaster.internal/ubuntu noble/universe amd64 mafft amd64 7.505-1 [795 kB] 998s Get:167 http://ftpmaster.internal/ubuntu noble/universe amd64 ncbi-data all 6.1.20170106+dfsg1-10 [4395 kB] 999s Get:168 http://ftpmaster.internal/ubuntu noble/universe amd64 ncbi-blast+ amd64 2.12.0+ds-4 [12.6 MB] 999s Get:169 http://ftpmaster.internal/ubuntu noble/universe amd64 prank amd64 0.0.170427+dfsg-3 [396 kB] 999s Get:170 http://ftpmaster.internal/ubuntu noble/main amd64 zip amd64 3.0-13 [176 kB] 999s Get:171 http://ftpmaster.internal/ubuntu noble/main amd64 unzip amd64 6.0-28ubuntu3 [174 kB] 999s Get:172 http://ftpmaster.internal/ubuntu noble/main amd64 xdg-utils all 1.1.3-4.1ubuntu3 [62.0 kB] 999s Get:173 http://ftpmaster.internal/ubuntu noble/universe amd64 r-base-core amd64 4.3.2-1build1 [27.0 MB] 999s Get:174 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-cli amd64 3.6.2-1 [1380 kB] 999s Get:175 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-colorspace amd64 2.1-0+dfsg-1 [1541 kB] 999s Get:176 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-fansi amd64 1.0.5-1 [619 kB] 999s Get:177 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-farver amd64 2.1.1-1 [1353 kB] 999s Get:178 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-glue amd64 1.7.0-1 [154 kB] 999s Get:179 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rlang amd64 1.1.3-1 [1663 kB] 999s Get:180 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-lifecycle all 1.0.4+dfsg-1 [110 kB] 999s Get:181 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-gtable all 0.3.4+dfsg-1 [191 kB] 999s Get:182 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-isoband amd64 0.2.7-1 [1481 kB] 999s Get:183 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-mass amd64 7.3-60.0.1-1 [1119 kB] 999s Get:184 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-lattice amd64 0.22-5-1 [1342 kB] 999s Get:185 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-nlme amd64 3.1.164-1 [2260 kB] 999s Get:186 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-matrix amd64 1.6-5-1 [3830 kB] 999s Get:187 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-mgcv amd64 1.9-1-1 [3252 kB] 999s Get:188 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-labeling all 0.4.3-1 [62.1 kB] 999s Get:189 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-munsell all 0.5.0-2build1 [208 kB] 999s Get:190 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-r6 all 2.5.1-1 [99.0 kB] 999s Get:191 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-rcolorbrewer all 1.1-3-1build1 [55.4 kB] 999s Get:192 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-viridislite all 0.4.2-2 [1088 kB] 999s Get:193 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-scales all 1.3.0-1 [603 kB] 999s Get:194 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-magrittr amd64 2.0.3-1 [154 kB] 999s Get:195 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-utf8 amd64 1.2.4-1 [140 kB] 999s Get:196 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-vctrs amd64 0.6.5-1 [1335 kB] 999s Get:197 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-pillar all 1.9.0+dfsg-1 [464 kB] 999s Get:198 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-pkgconfig all 2.0.3-2build1 [19.7 kB] 999s Get:199 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-tibble amd64 3.2.1+dfsg-2 [415 kB] 999s Get:200 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-withr all 2.5.0-1 [225 kB] 999s Get:201 http://ftpmaster.internal/ubuntu noble/universe amd64 r-cran-ggplot2 all 3.4.4+dfsg-1 [3411 kB] 999s Get:202 http://ftpmaster.internal/ubuntu noble/universe amd64 fasttree amd64 2.1.11-2 [174 kB] 999s Get:203 http://ftpmaster.internal/ubuntu noble/universe amd64 mcl amd64 1:22-282+ds-2 [550 kB] 999s Get:204 http://ftpmaster.internal/ubuntu noble/universe amd64 parallel all 20231122+ds-1 [1944 kB] 1000s Get:205 http://ftpmaster.internal/ubuntu noble/universe amd64 roary all 3.13.0+dfsg-1 [172 kB] 1000s Preconfiguring packages ... 1000s Fetched 162 MB in 2s (75.8 MB/s) 1000s Selecting previously unselected package bedtools. 1000s (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 ... 71420 files and directories currently installed.) 1000s Preparing to unpack .../000-bedtools_2.31.1+dfsg-2_amd64.deb ... 1000s Unpacking bedtools (2.31.1+dfsg-2) ... 1000s Selecting previously unselected package libio-string-perl. 1000s Preparing to unpack .../001-libio-string-perl_1.08-4_all.deb ... 1000s Unpacking libio-string-perl (1.08-4) ... 1000s Selecting previously unselected package libdata-stag-perl. 1000s Preparing to unpack .../002-libdata-stag-perl_0.14-3_all.deb ... 1000s Unpacking libdata-stag-perl (0.14-3) ... 1000s Selecting previously unselected package libbio-perl-perl. 1000s Preparing to unpack .../003-libbio-perl-perl_1.7.8-1_all.deb ... 1000s Unpacking libbio-perl-perl (1.7.8-1) ... 1001s Selecting previously unselected package libclass-data-inheritable-perl. 1001s Preparing to unpack .../004-libclass-data-inheritable-perl_0.08-3_all.deb ... 1001s Unpacking libclass-data-inheritable-perl (0.08-3) ... 1001s Selecting previously unselected package libdevel-stacktrace-perl. 1001s Preparing to unpack .../005-libdevel-stacktrace-perl_2.0500-1_all.deb ... 1001s Unpacking libdevel-stacktrace-perl (2.0500-1) ... 1001s Selecting previously unselected package libexception-class-perl. 1001s Preparing to unpack .../006-libexception-class-perl_1.45-1_all.deb ... 1001s Unpacking libexception-class-perl (1.45-1) ... 1001s Selecting previously unselected package libtest-deep-perl. 1001s Preparing to unpack .../007-libtest-deep-perl_1.204-1_all.deb ... 1001s Unpacking libtest-deep-perl (1.204-1) ... 1001s Selecting previously unselected package libcapture-tiny-perl. 1001s Preparing to unpack .../008-libcapture-tiny-perl_0.48-2_all.deb ... 1001s Unpacking libcapture-tiny-perl (0.48-2) ... 1001s Selecting previously unselected package libalgorithm-diff-perl. 1001s Preparing to unpack .../009-libalgorithm-diff-perl_1.201-1_all.deb ... 1001s Unpacking libalgorithm-diff-perl (1.201-1) ... 1001s Selecting previously unselected package libtext-diff-perl. 1001s Preparing to unpack .../010-libtext-diff-perl_1.45-2_all.deb ... 1001s Unpacking libtext-diff-perl (1.45-2) ... 1001s Selecting previously unselected package libtest-differences-perl. 1001s Preparing to unpack .../011-libtest-differences-perl_0.71-1_all.deb ... 1001s Unpacking libtest-differences-perl (0.71-1) ... 1001s Selecting previously unselected package libsub-uplevel-perl. 1001s Preparing to unpack .../012-libsub-uplevel-perl_0.2800-3_all.deb ... 1001s Unpacking libsub-uplevel-perl (0.2800-3) ... 1001s Selecting previously unselected package libtest-exception-perl. 1001s Preparing to unpack .../013-libtest-exception-perl_0.43-3_all.deb ... 1001s Unpacking libtest-exception-perl (0.43-3) ... 1001s Selecting previously unselected package libtest-warn-perl. 1001s Preparing to unpack .../014-libtest-warn-perl_0.37-2_all.deb ... 1001s Unpacking libtest-warn-perl (0.37-2) ... 1001s Selecting previously unselected package libtest-most-perl. 1001s Preparing to unpack .../015-libtest-most-perl_0.38-1_all.deb ... 1001s Unpacking libtest-most-perl (0.38-1) ... 1001s Selecting previously unselected package bioperl. 1001s Preparing to unpack .../016-bioperl_1.7.8-1_all.deb ... 1001s Unpacking bioperl (1.7.8-1) ... 1001s Selecting previously unselected package libc-dev-bin. 1001s Preparing to unpack .../017-libc-dev-bin_2.39-0ubuntu6_amd64.deb ... 1001s Unpacking libc-dev-bin (2.39-0ubuntu6) 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unpack .../043-libstdc++-13-dev_13.2.0-17ubuntu2_amd64.deb ... 1003s Unpacking libstdc++-13-dev:amd64 (13.2.0-17ubuntu2) ... 1003s Selecting previously unselected package g++-13-x86-64-linux-gnu. 1003s Preparing to unpack .../044-g++-13-x86-64-linux-gnu_13.2.0-17ubuntu2_amd64.deb ... 1003s Unpacking g++-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 1003s Selecting previously unselected package g++-13. 1003s Preparing to unpack .../045-g++-13_13.2.0-17ubuntu2_amd64.deb ... 1003s Unpacking g++-13 (13.2.0-17ubuntu2) ... 1003s Selecting previously unselected package g++-x86-64-linux-gnu. 1003s Preparing to unpack .../046-g++-x86-64-linux-gnu_4%3a13.2.0-7ubuntu1_amd64.deb ... 1003s Unpacking g++-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 1003s Selecting previously unselected package g++. 1003s Preparing to unpack .../047-g++_4%3a13.2.0-7ubuntu1_amd64.deb ... 1003s Unpacking g++ (4:13.2.0-7ubuntu1) ... 1003s Selecting previously unselected package build-essential. 1003s Preparing to unpack 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libfontconfig1:amd64 (2.15.0-1ubuntu1) ... 1004s Selecting previously unselected package fontconfig. 1004s Preparing to unpack .../054-fontconfig_2.15.0-1ubuntu1_amd64.deb ... 1004s Unpacking fontconfig (2.15.0-1ubuntu1) ... 1004s Selecting previously unselected package libalgorithm-c3-perl. 1004s Preparing to unpack .../055-libalgorithm-c3-perl_0.11-2_all.deb ... 1004s Unpacking libalgorithm-c3-perl (0.11-2) ... 1004s Selecting previously unselected package libarray-utils-perl. 1004s Preparing to unpack .../056-libarray-utils-perl_0.5-3_all.deb ... 1004s Unpacking libarray-utils-perl (0.5-3) ... 1004s Selecting previously unselected package libb-hooks-op-check-perl:amd64. 1004s Preparing to unpack .../057-libb-hooks-op-check-perl_0.22-2build2_amd64.deb ... 1004s Unpacking libb-hooks-op-check-perl:amd64 (0.22-2build2) ... 1004s Selecting previously unselected package libblas3:amd64. 1004s Preparing to unpack .../058-libblas3_3.12.0-3_amd64.deb ... 1004s Unpacking libblas3:amd64 (3.12.0-3) ... 1004s Selecting previously unselected package libpixman-1-0:amd64. 1004s Preparing to unpack .../059-libpixman-1-0_0.42.2-1_amd64.deb ... 1004s Unpacking libpixman-1-0:amd64 (0.42.2-1) ... 1004s Selecting previously unselected package libxcb-render0:amd64. 1004s Preparing to unpack .../060-libxcb-render0_1.15-1_amd64.deb ... 1004s Unpacking libxcb-render0:amd64 (1.15-1) ... 1004s Selecting previously unselected package libxcb-shm0:amd64. 1004s Preparing to unpack .../061-libxcb-shm0_1.15-1_amd64.deb ... 1004s Unpacking libxcb-shm0:amd64 (1.15-1) ... 1004s Selecting previously unselected package libxrender1:amd64. 1004s Preparing to unpack .../062-libxrender1_1%3a0.9.10-1.1_amd64.deb ... 1004s Unpacking libxrender1:amd64 (1:0.9.10-1.1) ... 1004s Selecting previously unselected package libcairo2:amd64. 1004s Preparing to unpack .../063-libcairo2_1.18.0-1_amd64.deb ... 1004s Unpacking libcairo2:amd64 (1.18.0-1) ... 1004s Selecting previously unselected package libclass-c3-perl. 1004s Preparing to unpack .../064-libclass-c3-perl_0.35-2_all.deb ... 1004s Unpacking libclass-c3-perl (0.35-2) ... 1004s Selecting previously unselected package libparams-util-perl. 1004s Preparing to unpack .../065-libparams-util-perl_1.102-2build1_amd64.deb ... 1004s Unpacking libparams-util-perl (1.102-2build1) ... 1004s Selecting previously unselected package libsub-install-perl. 1004s Preparing to unpack .../066-libsub-install-perl_0.929-1_all.deb ... 1004s Unpacking libsub-install-perl (0.929-1) ... 1004s Selecting previously unselected package libdata-optlist-perl. 1004s Preparing to unpack .../067-libdata-optlist-perl_0.114-1_all.deb ... 1004s Unpacking libdata-optlist-perl (0.114-1) ... 1004s Selecting previously unselected package libdynaloader-functions-perl. 1004s Preparing to unpack .../068-libdynaloader-functions-perl_0.003-3_all.deb ... 1004s Unpacking libdynaloader-functions-perl (0.003-3) ... 1004s Selecting previously unselected package libdevel-callchecker-perl:amd64. 1004s Preparing to unpack .../069-libdevel-callchecker-perl_0.008-2build1_amd64.deb ... 1004s Unpacking libdevel-callchecker-perl:amd64 (0.008-2build1) ... 1004s Selecting previously unselected package libparams-classify-perl:amd64. 1004s Preparing to unpack .../070-libparams-classify-perl_0.015-2build3_amd64.deb ... 1004s Unpacking libparams-classify-perl:amd64 (0.015-2build3) ... 1004s Selecting previously unselected package libmodule-runtime-perl. 1004s Preparing to unpack .../071-libmodule-runtime-perl_0.016-2_all.deb ... 1004s Unpacking libmodule-runtime-perl (0.016-2) ... 1004s Selecting previously unselected package libtry-tiny-perl. 1004s Preparing to unpack .../072-libtry-tiny-perl_0.31-2_all.deb ... 1004s Unpacking libtry-tiny-perl (0.31-2) ... 1004s Selecting previously unselected package libmodule-implementation-perl. 1004s Preparing to unpack .../073-libmodule-implementation-perl_0.09-2_all.deb ... 1004s Unpacking libmodule-implementation-perl (0.09-2) ... 1004s Selecting previously unselected package libpackage-stash-perl. 1004s Preparing to unpack .../074-libpackage-stash-perl_0.40-1_all.deb ... 1004s Unpacking libpackage-stash-perl (0.40-1) ... 1004s Selecting previously unselected package libclass-load-perl. 1004s Preparing to unpack .../075-libclass-load-perl_0.25-2_all.deb ... 1004s Unpacking libclass-load-perl (0.25-2) ... 1004s Selecting previously unselected package libclass-load-xs-perl. 1004s Preparing to unpack .../076-libclass-load-xs-perl_0.10-2build2_amd64.deb ... 1004s Unpacking libclass-load-xs-perl (0.10-2build2) ... 1004s Selecting previously unselected package libclone-perl:amd64. 1004s Preparing to unpack .../077-libclone-perl_0.46-1build1_amd64.deb ... 1004s Unpacking libclone-perl:amd64 (0.46-1build1) ... 1004s Selecting previously unselected package libdatrie1:amd64. 1004s Preparing to unpack .../078-libdatrie1_0.2.13-3_amd64.deb ... 1004s Unpacking libdatrie1:amd64 (0.2.13-3) ... 1004s Selecting previously unselected package libdeflate0:amd64. 1004s Preparing to unpack .../079-libdeflate0_1.19-1_amd64.deb ... 1004s Unpacking libdeflate0:amd64 (1.19-1) ... 1004s Selecting previously unselected package libsub-exporter-progressive-perl. 1004s Preparing to unpack .../080-libsub-exporter-progressive-perl_0.001013-3_all.deb ... 1004s Unpacking libsub-exporter-progressive-perl (0.001013-3) ... 1005s Selecting previously unselected package libdevel-globaldestruction-perl. 1005s Preparing to unpack .../081-libdevel-globaldestruction-perl_0.14-4_all.deb ... 1005s Unpacking libdevel-globaldestruction-perl (0.14-4) ... 1005s Selecting previously unselected package libmro-compat-perl. 1005s Preparing to unpack .../082-libmro-compat-perl_0.15-2_all.deb ... 1005s Unpacking libmro-compat-perl (0.15-2) ... 1005s Selecting previously unselected package libdevel-overloadinfo-perl. 1005s Preparing to unpack .../083-libdevel-overloadinfo-perl_0.007-1_all.deb ... 1005s Unpacking libdevel-overloadinfo-perl (0.007-1) ... 1005s Selecting previously unselected package libencode-locale-perl. 1005s Preparing to unpack .../084-libencode-locale-perl_1.05-3_all.deb ... 1005s Unpacking libencode-locale-perl (1.05-3) ... 1005s Selecting previously unselected package libtimedate-perl. 1005s Preparing to unpack .../085-libtimedate-perl_2.3300-2_all.deb ... 1005s Unpacking libtimedate-perl (2.3300-2) ... 1005s Selecting previously unselected package libhttp-date-perl. 1005s Preparing to unpack .../086-libhttp-date-perl_6.06-1_all.deb ... 1005s Unpacking libhttp-date-perl (6.06-1) ... 1005s Selecting previously unselected package libfile-listing-perl. 1005s Preparing to unpack .../087-libfile-listing-perl_6.16-1_all.deb ... 1005s Unpacking libfile-listing-perl (6.16-1) ... 1005s Selecting previously unselected package libhtml-tagset-perl. 1005s Preparing to unpack .../088-libhtml-tagset-perl_3.20-6_all.deb ... 1005s Unpacking libhtml-tagset-perl (3.20-6) ... 1005s Selecting previously unselected package liburi-perl. 1005s Preparing to unpack .../089-liburi-perl_5.27-1_all.deb ... 1005s Unpacking liburi-perl (5.27-1) ... 1005s Selecting previously unselected package libhtml-parser-perl:amd64. 1005s Preparing to unpack .../090-libhtml-parser-perl_3.81-1build1_amd64.deb ... 1005s Unpacking libhtml-parser-perl:amd64 (3.81-1build1) ... 1005s Selecting previously unselected package libhtml-tree-perl. 1005s Preparing to unpack .../091-libhtml-tree-perl_5.07-3_all.deb ... 1005s Unpacking libhtml-tree-perl (5.07-3) ... 1005s Selecting previously unselected package libio-html-perl. 1005s Preparing to unpack .../092-libio-html-perl_1.004-3_all.deb ... 1005s Unpacking libio-html-perl (1.004-3) ... 1005s Selecting previously unselected package liblwp-mediatypes-perl. 1005s Preparing to unpack .../093-liblwp-mediatypes-perl_6.04-2_all.deb ... 1005s Unpacking liblwp-mediatypes-perl (6.04-2) ... 1005s Selecting previously unselected package libhttp-message-perl. 1005s Preparing to unpack .../094-libhttp-message-perl_6.45-1ubuntu1_all.deb ... 1005s Unpacking libhttp-message-perl (6.45-1ubuntu1) ... 1005s Selecting previously unselected package libhttp-cookies-perl. 1005s Preparing to unpack .../095-libhttp-cookies-perl_6.11-1_all.deb ... 1005s Unpacking libhttp-cookies-perl (6.11-1) ... 1005s Selecting previously unselected package libhttp-negotiate-perl. 1005s Preparing to unpack .../096-libhttp-negotiate-perl_6.01-2_all.deb ... 1005s Unpacking libhttp-negotiate-perl (6.01-2) ... 1005s Selecting previously unselected package perl-openssl-defaults:amd64. 1005s Preparing to unpack .../097-perl-openssl-defaults_7_amd64.deb ... 1005s Unpacking perl-openssl-defaults:amd64 (7) ... 1005s Selecting previously unselected package libnet-ssleay-perl:amd64. 1005s Preparing to unpack .../098-libnet-ssleay-perl_1.94-1_amd64.deb ... 1005s Unpacking libnet-ssleay-perl:amd64 (1.94-1) ... 1005s Selecting previously unselected package libio-socket-ssl-perl. 1005s Preparing to unpack .../099-libio-socket-ssl-perl_2.085-1_all.deb ... 1005s Unpacking libio-socket-ssl-perl (2.085-1) ... 1005s Selecting previously unselected package libnet-http-perl. 1005s Preparing to unpack .../100-libnet-http-perl_6.23-1_all.deb ... 1005s Unpacking libnet-http-perl (6.23-1) ... 1005s Selecting previously unselected package liblwp-protocol-https-perl. 1005s Preparing to unpack .../101-liblwp-protocol-https-perl_6.13-1_all.deb ... 1005s Unpacking liblwp-protocol-https-perl (6.13-1) ... 1005s Selecting previously unselected package libwww-robotrules-perl. 1005s Preparing to unpack .../102-libwww-robotrules-perl_6.02-1_all.deb ... 1005s Unpacking libwww-robotrules-perl (6.02-1) ... 1005s Selecting previously unselected package libwww-perl. 1005s Preparing to unpack .../103-libwww-perl_6.76-1_all.deb ... 1005s Unpacking libwww-perl (6.76-1) ... 1005s Selecting previously unselected package libdigest-md5-file-perl. 1005s Preparing to unpack .../104-libdigest-md5-file-perl_0.08-1.1_all.deb ... 1005s Unpacking libdigest-md5-file-perl (0.08-1.1) ... 1005s Selecting previously unselected package libdist-checkconflicts-perl. 1005s Preparing to unpack .../105-libdist-checkconflicts-perl_0.11-2_all.deb ... 1005s Unpacking libdist-checkconflicts-perl (0.11-2) ... 1005s Selecting previously unselected package libenv-path-perl. 1005s Preparing to unpack .../106-libenv-path-perl_0.19-4_all.deb ... 1005s Unpacking libenv-path-perl (0.19-4) ... 1005s Selecting previously unselected package libsub-exporter-perl. 1005s Preparing to unpack .../107-libsub-exporter-perl_0.990-1_all.deb ... 1005s Unpacking libsub-exporter-perl (0.990-1) ... 1005s Selecting previously unselected package libeval-closure-perl. 1005s Preparing to unpack .../108-libeval-closure-perl_0.14-3_all.deb ... 1005s Unpacking libeval-closure-perl (0.14-3) ... 1005s Selecting previously unselected package libnumber-compare-perl. 1005s Preparing to unpack .../109-libnumber-compare-perl_0.03-3_all.deb ... 1005s Unpacking libnumber-compare-perl (0.03-3) ... 1005s Selecting previously unselected package libtext-glob-perl. 1005s Preparing to unpack .../110-libtext-glob-perl_0.11-3_all.deb ... 1005s Unpacking libtext-glob-perl (0.11-3) ... 1005s Selecting previously unselected package libfile-find-rule-perl. 1005s Preparing to unpack .../111-libfile-find-rule-perl_0.34-3_all.deb ... 1005s Unpacking libfile-find-rule-perl (0.34-3) ... 1005s Selecting previously unselected package libfile-grep-perl. 1005s Preparing to unpack .../112-libfile-grep-perl_0.02-3_all.deb ... 1005s Unpacking libfile-grep-perl (0.02-3) ... 1005s Selecting previously unselected package libfile-slurper-perl. 1005s Preparing to unpack .../113-libfile-slurper-perl_0.014-1_all.deb ... 1005s Unpacking libfile-slurper-perl (0.014-1) ... 1006s Selecting previously unselected package libfile-which-perl. 1006s Preparing to unpack .../114-libfile-which-perl_1.27-2_all.deb ... 1006s Unpacking libfile-which-perl (1.27-2) ... 1006s Selecting previously unselected package libfindbin-libs-perl. 1006s Preparing to unpack .../115-libfindbin-libs-perl_3.0.2-1_all.deb ... 1006s Unpacking libfindbin-libs-perl (3.0.2-1) ... 1006s Selecting previously unselected package libgfortran5:amd64. 1006s Preparing to unpack .../116-libgfortran5_14-20240303-1ubuntu1_amd64.deb ... 1006s Unpacking libgfortran5:amd64 (14-20240303-1ubuntu1) ... 1006s Selecting previously unselected package libheap-perl. 1006s Preparing to unpack .../117-libheap-perl_0.80-5_all.deb ... 1006s Unpacking libheap-perl (0.80-5) ... 1006s Selecting previously unselected package libset-object-perl. 1006s Preparing to unpack .../118-libset-object-perl_1.42-1build3_amd64.deb ... 1006s Unpacking libset-object-perl (1.42-1build3) ... 1006s Selecting previously unselected package libgraph-perl. 1006s Preparing to unpack .../119-libgraph-perl_1%3a0.9727-1_all.deb ... 1006s Unpacking libgraph-perl (1:0.9727-1) ... 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to unpack .../150-libsharpyuv0_1.3.2-0.4_amd64.deb ... 1007s Unpacking libsharpyuv0:amd64 (1.3.2-0.4) ... 1007s Selecting previously unselected package libsm6:amd64. 1007s Preparing to unpack .../151-libsm6_2%3a1.2.3-1build2_amd64.deb ... 1007s Unpacking libsm6:amd64 (2:1.2.3-1build2) ... 1007s Selecting previously unselected package libtcl8.6:amd64. 1007s Preparing to unpack .../152-libtcl8.6_8.6.13+dfsg-2_amd64.deb ... 1007s Unpacking libtcl8.6:amd64 (8.6.13+dfsg-2) ... 1007s Selecting previously unselected package libtest-file-perl. 1007s Preparing to unpack .../153-libtest-file-perl_1.993-1_all.deb ... 1007s Unpacking libtest-file-perl (1.993-1) ... 1007s Selecting previously unselected package libtest-files-perl. 1007s Preparing to unpack .../154-libtest-files-perl_0.15-1_all.deb ... 1007s Unpacking libtest-files-perl (0.15-1) ... 1007s Selecting previously unselected package libtest-output-perl. 1007s Preparing to unpack .../155-libtest-output-perl_1.034-1_all.deb ... 1007s 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unselected package libxft2:amd64. 1007s Preparing to unpack .../161-libxft2_2.3.6-1_amd64.deb ... 1007s Unpacking libxft2:amd64 (2.3.6-1) ... 1007s Selecting previously unselected package libxss1:amd64. 1007s Preparing to unpack .../162-libxss1_1%3a1.2.3-1build2_amd64.deb ... 1007s Unpacking libxss1:amd64 (1:1.2.3-1build2) ... 1007s Selecting previously unselected package libtk8.6:amd64. 1007s Preparing to unpack .../163-libtk8.6_8.6.14-1_amd64.deb ... 1007s Unpacking libtk8.6:amd64 (8.6.14-1) ... 1007s Selecting previously unselected package libxt6:amd64. 1007s Preparing to unpack .../164-libxt6_1%3a1.2.1-1.1_amd64.deb ... 1007s Unpacking libxt6:amd64 (1:1.2.1-1.1) ... 1007s Selecting previously unselected package mafft. 1007s Preparing to unpack .../165-mafft_7.505-1_amd64.deb ... 1007s Unpacking mafft (7.505-1) ... 1007s Selecting previously unselected package ncbi-data. 1007s Preparing to unpack .../166-ncbi-data_6.1.20170106+dfsg1-10_all.deb ... 1007s Unpacking ncbi-data 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unpack .../178-r-cran-rlang_1.1.3-1_amd64.deb ... 1009s Unpacking r-cran-rlang (1.1.3-1) ... 1009s Selecting previously unselected package r-cran-lifecycle. 1009s Preparing to unpack .../179-r-cran-lifecycle_1.0.4+dfsg-1_all.deb ... 1009s Unpacking r-cran-lifecycle (1.0.4+dfsg-1) ... 1009s Selecting previously unselected package r-cran-gtable. 1009s Preparing to unpack .../180-r-cran-gtable_0.3.4+dfsg-1_all.deb ... 1009s Unpacking r-cran-gtable (0.3.4+dfsg-1) ... 1009s Selecting previously unselected package r-cran-isoband. 1009s Preparing to unpack .../181-r-cran-isoband_0.2.7-1_amd64.deb ... 1009s Unpacking r-cran-isoband (0.2.7-1) ... 1009s Selecting previously unselected package r-cran-mass. 1009s Preparing to unpack .../182-r-cran-mass_7.3-60.0.1-1_amd64.deb ... 1009s Unpacking r-cran-mass (7.3-60.0.1-1) ... 1009s Selecting previously unselected package r-cran-lattice. 1009s Preparing to unpack .../183-r-cran-lattice_0.22-5-1_amd64.deb ... 1009s Unpacking r-cran-lattice (0.22-5-1) 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Selecting previously unselected package r-cran-vctrs. 1009s Preparing to unpack .../195-r-cran-vctrs_0.6.5-1_amd64.deb ... 1009s Unpacking r-cran-vctrs (0.6.5-1) ... 1009s Selecting previously unselected package r-cran-pillar. 1009s Preparing to unpack .../196-r-cran-pillar_1.9.0+dfsg-1_all.deb ... 1009s Unpacking r-cran-pillar (1.9.0+dfsg-1) ... 1009s Selecting previously unselected package r-cran-pkgconfig. 1009s Preparing to unpack .../197-r-cran-pkgconfig_2.0.3-2build1_all.deb ... 1009s Unpacking r-cran-pkgconfig (2.0.3-2build1) ... 1009s Selecting previously unselected package r-cran-tibble. 1009s Preparing to unpack .../198-r-cran-tibble_3.2.1+dfsg-2_amd64.deb ... 1009s Unpacking r-cran-tibble (3.2.1+dfsg-2) ... 1010s Selecting previously unselected package r-cran-withr. 1010s Preparing to unpack .../199-r-cran-withr_2.5.0-1_all.deb ... 1010s Unpacking r-cran-withr (2.5.0-1) ... 1010s Selecting previously unselected package r-cran-ggplot2. 1010s Preparing to unpack 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(0.5-3) ... 1010s Setting up libgraphite2-3:amd64 (1.3.14-2) ... 1010s Setting up ncbi-data (6.1.20170106+dfsg1-10) ... 1010s Setting up libpixman-1-0:amd64 (0.42.2-1) ... 1010s Setting up libsharpyuv0:amd64 (1.3.2-0.4) ... 1010s Setting up libpaper1:amd64 (1.1.29) ... 1010s 1010s Creating config file /etc/papersize with new version 1010s Setting up libfile-slurper-perl (0.014-1) ... 1010s Setting up libfile-which-perl (1.27-2) ... 1010s Setting up liblerc4:amd64 (4.0.0+ds-4ubuntu1) ... 1010s Setting up libparse-yapp-perl (1.21-3) ... 1010s Setting up libxrender1:amd64 (1:0.9.10-1.1) ... 1010s Setting up libdynaloader-functions-perl (0.003-3) ... 1010s Setting up libdatrie1:amd64 (0.2.13-3) ... 1010s Setting up libtext-glob-perl (0.11-3) ... 1010s Setting up libtest-deep-perl (1.204-1) ... 1010s Setting up libxcb-render0:amd64 (1.15-1) ... 1010s Setting up mafft (7.505-1) ... 1010s Setting up libclone-perl:amd64 (0.46-1build1) ... 1010s Setting up libalgorithm-diff-perl (1.201-1) ... 1010s Setting up libhtml-tagset-perl (3.20-6) ... 1010s Setting up libtest-file-perl (1.993-1) ... 1010s Setting up unzip (6.0-28ubuntu3) ... 1010s Setting up libheap-perl (0.80-5) ... 1010s Setting up liblwp-mediatypes-perl (6.04-2) ... 1010s Setting up x11-common (1:7.7+23ubuntu2) ... 1011s Setting up libtry-tiny-perl (0.31-2) ... 1011s Setting up libdeflate0:amd64 (1.19-1) ... 1011s Setting up perl-openssl-defaults:amd64 (7) ... 1011s Setting up linux-libc-dev:amd64 (6.8.0-11.11) ... 1011s Setting up libencode-locale-perl (1.05-3) ... 1011s Setting up libxcb-shm0:amd64 (1.15-1) ... 1011s Setting up libfindbin-libs-perl (3.0.2-1) ... 1011s Setting up libpaper-utils (1.1.29) ... 1011s Setting up libgomp1:amd64 (14-20240303-1ubuntu1) ... 1011s Setting up libjbig0:amd64 (2.1-6.1ubuntu1) ... 1011s Setting up libsub-install-perl (0.929-1) ... 1011s Setting up libnumber-compare-perl (0.03-3) ... 1011s Setting up libio-string-perl (1.08-4) ... 1011s Setting up zip (3.0-13) ... 1011s Setting up libpackage-stash-xs-perl:amd64 (0.30-1build2) ... 1011s Setting up libblas3:amd64 (3.12.0-3) ... 1011s update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/x86_64-linux-gnu/libblas.so.3 (libblas.so.3-x86_64-linux-gnu) in auto mode 1011s Setting up libclass-data-inheritable-perl (0.08-3) ... 1011s Setting up libalgorithm-c3-perl (0.11-2) ... 1011s Setting up rpcsvc-proto (1.4.2-0ubuntu6) ... 1011s Setting up libset-object-perl (1.42-1build3) ... 1011s Setting up liblog-log4perl-perl (1.57-1) ... 1011s Setting up libmbedcrypto7:amd64 (2.28.7-1ubuntu1) ... 1011s Setting up libtext-diff-perl (1.45-2) ... 1011s Setting up libfile-find-rule-perl (0.34-3) ... 1011s Setting up libperlio-utf8-strict-perl (0.010-1build1) ... 1011s Setting up libxml-writer-perl (0.900-2) ... 1011s Setting up libenv-path-perl (0.19-4) ... 1011s Setting up libquadmath0:amd64 (14-20240303-1ubuntu1) ... 1011s Setting up fonts-dejavu-mono (2.37-8) ... 1011s Setting up libmpc3:amd64 (1.3.1-1) ... 1011s Setting up libatomic1:amd64 (14-20240303-1ubuntu1) ... 1011s Setting up libio-html-perl (1.004-3) ... 1011s Setting up libtcl8.6:amd64 (8.6.13+dfsg-2) ... 1011s Setting up libb-hooks-op-check-perl:amd64 (0.22-2build2) ... 1011s Setting up libfile-grep-perl (0.02-3) ... 1011s Setting up fonts-dejavu-core (2.37-8) ... 1011s Setting up libjpeg-turbo8:amd64 (2.1.5-2ubuntu1) ... 1011s Setting up libparams-util-perl (1.102-2build1) ... 1011s Setting up parallel (20231122+ds-1) ... 1011s Setting up libspiffy-perl (0.46-1) ... 1011s Setting up libgfortran5:amd64 (14-20240303-1ubuntu1) ... 1011s Setting up libsub-exporter-progressive-perl (0.001013-3) ... 1011s Setting up libwebp7:amd64 (1.3.2-0.4) ... 1011s Setting up libcapture-tiny-perl (0.48-2) ... 1011s Setting up libtimedate-perl (2.3300-2) ... 1011s Setting up libubsan1:amd64 (14-20240303-1ubuntu1) ... 1011s Setting up libdata-stag-perl (0.14-3) ... 1011s Setting up libhwasan0:amd64 (14-20240303-1ubuntu1) ... 1011s Setting up libcrypt-dev:amd64 (1:4.4.36-4) ... 1011s Setting up libasan8:amd64 (14-20240303-1ubuntu1) ... 1011s Setting up libtingea0:amd64 (21-361-2) ... 1011s Setting up libsub-uplevel-perl (0.2800-3) ... 1011s Setting up libharfbuzz0b:amd64 (8.3.0-2) ... 1011s Setting up libthai-data (0.1.29-2) ... 1011s Setting up libdevel-globaldestruction-perl (0.14-4) ... 1011s Setting up fasttree (2.1.11-2) ... 1011s Setting up libdevel-stacktrace-perl (2.0500-1) ... 1011s Setting up libbio-perl-perl (1.7.8-1) ... 1011s Setting up libxss1:amd64 (1:1.2.3-1build2) ... 1011s Setting up libtsan2:amd64 (14-20240303-1ubuntu1) ... 1011s Setting up libisl23:amd64 (0.26-3) ... 1011s Setting up libc-dev-bin (2.39-0ubuntu6) ... 1011s Setting up xdg-utils (1.1.3-4.1ubuntu3) ... 1011s update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode 1011s Setting up bedtools (2.31.1+dfsg-2) ... 1011s Setting up libcc1-0:amd64 (14-20240303-1ubuntu1) ... 1011s Setting up liburi-perl (5.27-1) ... 1011s Setting up liblsan0:amd64 (14-20240303-1ubuntu1) ... 1011s Setting up libitm1:amd64 (14-20240303-1ubuntu1) ... 1011s Setting up prank (0.0.170427+dfsg-3) ... 1011s Setting up libtext-csv-perl (2.04-1) ... 1011s Setting up libnet-ssleay-perl:amd64 (1.94-1) ... 1011s Setting up cd-hit (4.8.1-4) ... 1011s Setting up libjpeg8:amd64 (8c-2ubuntu11) ... 1011s Setting up libice6:amd64 (2:1.0.10-1build2) ... 1011s Setting up libhttp-date-perl (6.06-1) ... 1011s Setting up liblapack3:amd64 (3.12.0-3) ... 1011s update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode 1011s Setting up libfile-listing-perl (6.16-1) ... 1011s Setting up libmbedx509-1:amd64 (2.28.7-1ubuntu1) ... 1011s Setting up libmbedtls14:amd64 (2.28.7-1ubuntu1) ... 1011s Setting up cpp-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 1011s Setting up fontconfig-config (2.15.0-1ubuntu1) ... 1011s Setting up libtest-warn-perl (0.37-2) ... 1011s Setting up libtest-differences-perl (0.71-1) ... 1011s Setting up libnet-http-perl (6.23-1) ... 1011s Setting up libexception-class-perl (1.45-1) ... 1011s Setting up libio-all-perl (0.87-2) ... 1011s Setting up libclass-c3-perl (0.35-2) ... 1011s Setting up libgraph-perl (1:0.9727-1) ... 1011s Setting up libdevel-callchecker-perl:amd64 (0.008-2build1) ... 1011s Setting up libtest-files-perl (0.15-1) ... 1011s Setting up ncbi-blast+ (2.12.0+ds-4) ... 1011s Setting up libthai0:amd64 (0.1.29-2) ... 1011s Setting up libtest-exception-perl (0.43-3) ... 1011s Setting up mcl (1:22-282+ds-2) ... 1011s Setting up libdata-optlist-perl (0.114-1) ... 1011s Setting up libtest-output-perl (1.034-1) ... 1011s Setting up libwww-robotrules-perl (6.02-1) ... 1011s Setting up libgcc-13-dev:amd64 (13.2.0-17ubuntu2) ... 1011s Setting up libtiff6:amd64 (4.5.1+git230720-3ubuntu1) ... 1011s Setting up libhtml-parser-perl:amd64 (3.81-1build1) ... 1011s Setting up libc6-dev:amd64 (2.39-0ubuntu6) ... 1011s Setting up libfontconfig1:amd64 (2.15.0-1ubuntu1) ... 1011s Setting up libmro-compat-perl (0.15-2) ... 1011s Setting up libsm6:amd64 (2:1.2.3-1build2) ... 1011s Setting up libio-socket-ssl-perl (2.085-1) ... 1011s Setting up libstdc++-13-dev:amd64 (13.2.0-17ubuntu2) ... 1011s Setting up libsub-exporter-perl (0.990-1) ... 1011s Setting up libhttp-message-perl (6.45-1ubuntu1) ... 1011s Setting up libeval-closure-perl (0.14-3) ... 1011s Setting up cpp-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 1011s Setting up libhttp-negotiate-perl (6.01-2) ... 1011s Setting up fontconfig (2.15.0-1ubuntu1) ... 1013s Regenerating fonts cache... done. 1013s Setting up libxft2:amd64 (2.3.6-1) ... 1013s Setting up cpp-13 (13.2.0-17ubuntu2) ... 1013s Setting up libhttp-cookies-perl (6.11-1) ... 1013s Setting up libtest-most-perl (0.38-1) ... 1013s Setting up gcc-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 1013s Setting up libhtml-tree-perl (5.07-3) ... 1013s Setting up libtk8.6:amd64 (8.6.14-1) ... 1013s Setting up libparams-classify-perl:amd64 (0.015-2build3) ... 1013s Setting up libpango-1.0-0:amd64 (1.51.0+ds-4) ... 1013s Setting up libcairo2:amd64 (1.18.0-1) ... 1013s Setting up libmodule-runtime-perl (0.016-2) ... 1013s Setting up gcc-13 (13.2.0-17ubuntu2) ... 1013s Setting up libdist-checkconflicts-perl (0.11-2) ... 1013s Setting up libxt6:amd64 (1:1.2.1-1.1) ... 1013s Setting up cpp (4:13.2.0-7ubuntu1) ... 1013s Setting up libpangoft2-1.0-0:amd64 (1.51.0+ds-4) ... 1013s Setting up libpangocairo-1.0-0:amd64 (1.51.0+ds-4) ... 1013s Setting up bioperl (1.7.8-1) ... 1013s Setting up g++-13-x86-64-linux-gnu (13.2.0-17ubuntu2) ... 1013s Setting up gcc-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 1013s Setting up libmodule-implementation-perl (0.09-2) ... 1013s Setting up libpackage-stash-perl (0.40-1) ... 1013s Setting up libmodule-runtime-conflicts-perl (0.003-2) ... 1013s Setting up libclass-load-perl (0.25-2) ... 1013s Setting up gcc (4:13.2.0-7ubuntu1) ... 1013s Setting up r-base-core (4.3.2-1build1) ... 1013s 1013s Creating config file /etc/R/Renviron with new version 1013s Setting up r-cran-labeling (0.4.3-1) ... 1013s Setting up r-cran-lattice (0.22-5-1) ... 1013s Setting up r-cran-nlme (3.1.164-1) ... 1013s Setting up r-cran-farver (2.1.1-1) ... 1013s Setting up libpackage-deprecationmanager-perl (0.18-1) ... 1013s Setting up r-cran-viridislite (0.4.2-2) ... 1013s Setting up g++-x86-64-linux-gnu (4:13.2.0-7ubuntu1) ... 1013s Setting up libdevel-overloadinfo-perl (0.007-1) ... 1013s Setting up libclass-load-xs-perl (0.10-2build2) ... 1013s Setting up r-cran-r6 (2.5.1-1) ... 1013s Setting up r-cran-magrittr (2.0.3-1) ... 1013s Setting up g++-13 (13.2.0-17ubuntu2) ... 1013s Setting up r-cran-rlang (1.1.3-1) ... 1013s Setting up r-cran-withr (2.5.0-1) ... 1013s Setting up libmoose-perl:amd64 (2.2207-1) ... 1013s Setting up r-cran-fansi (1.0.5-1) ... 1013s Setting up r-cran-mass (7.3-60.0.1-1) ... 1013s Setting up r-cran-glue (1.7.0-1) ... 1013s Setting up r-cran-cli (3.6.2-1) ... 1013s Setting up r-cran-lifecycle (1.0.4+dfsg-1) ... 1013s Setting up r-cran-pkgconfig (2.0.3-2build1) ... 1013s Setting up r-cran-utf8 (1.2.4-1) ... 1013s Setting up r-cran-colorspace (2.1-0+dfsg-1) ... 1013s Setting up r-cran-rcolorbrewer (1.1-3-1build1) ... 1013s Setting up r-cran-isoband (0.2.7-1) ... 1013s Setting up r-cran-gtable (0.3.4+dfsg-1) ... 1013s Setting up r-cran-matrix (1.6-5-1) ... 1013s Setting up r-cran-mgcv (1.9-1-1) ... 1013s Setting up g++ (4:13.2.0-7ubuntu1) ... 1013s update-alternatives: using /usr/bin/g++ to provide /usr/bin/c++ (c++) in auto mode 1013s Setting up build-essential (12.10ubuntu1) ... 1013s Setting up r-cran-vctrs (0.6.5-1) ... 1013s Setting up r-cran-pillar (1.9.0+dfsg-1) ... 1013s Setting up r-cran-munsell (0.5.0-2build1) ... 1013s Setting up r-cran-tibble (3.2.1+dfsg-2) ... 1013s Setting up r-cran-scales (1.3.0-1) ... 1013s Setting up r-cran-ggplot2 (3.4.4+dfsg-1) ... 1013s Setting up liblwp-protocol-https-perl (6.13-1) ... 1013s Setting up libwww-perl (6.76-1) ... 1013s Setting up libdigest-md5-file-perl (0.08-1.1) ... 1013s Setting up libxml-parser-perl (2.47-1build1) ... 1013s Setting up libgraph-readwrite-perl (2.10-1) ... 1013s Setting up roary (3.13.0+dfsg-1) ... 1013s Processing triggers for install-info (7.1-3) ... 1013s Processing triggers for libc-bin (2.39-0ubuntu6) ... 1013s Processing triggers for man-db (2.12.0-3) ... 1019s Reading package lists... 1019s Building dependency tree... 1019s Reading state information... 1020s Starting pkgProblemResolver with broken count: 0 1020s Starting 2 pkgProblemResolver with broken count: 0 1020s Done 1021s The following NEW packages will be installed: 1021s autopkgtest-satdep 1021s 0 upgraded, 1 newly installed, 0 to remove and 0 not upgraded. 1021s Need to get 0 B/696 B of archives. 1021s After this operation, 0 B of additional disk space will be used. 1021s Get:1 /tmp/autopkgtest.3U64ZN/2-autopkgtest-satdep.deb autopkgtest-satdep amd64 0 [696 B] 1021s Selecting previously unselected package autopkgtest-satdep. 1021s (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 ... 83425 files and directories currently installed.) 1021s Preparing to unpack .../2-autopkgtest-satdep.deb ... 1021s Unpacking autopkgtest-satdep (0) ... 1021s Setting up autopkgtest-satdep (0) ... 1023s (Reading database ... 83425 files and directories currently installed.) 1023s Removing autopkgtest-satdep (0) ... 1023s autopkgtest [04:13:41]: test test-installed: [----------------------- 1024s 1024s Please cite Roary if you use any of the results it produces: 1024s Andrew J. Page, Carla A. Cummins, Martin Hunt, Vanessa K. Wong, Sandra Reuter, Matthew T. G. Holden, Maria Fookes, Daniel Falush, Jacqueline A. Keane, Julian Parkhill, 1024s "Roary: Rapid large-scale prokaryote pan genome analysis", Bioinformatics, 2015 Nov 15;31(22):3691-3693 1024s doi: http://doi.org/10.1093/bioinformatics/btv421 1024s Pubmed: 26198102 1024s 1027s autopkgtest [04:13:45]: test test-installed: -----------------------] 1027s autopkgtest [04:13:45]: test test-installed: - - - - - - - - - - results - - - - - - - - - - 1027s test-installed PASS 1030s autopkgtest [04:13:48]: @@@@@@@@@@@@@@@@@@@@ summary 1030s test-installed PASS 1048s Creating nova instance adt-noble-i386-roary-20240324-032302-juju-7f2275-prod-proposed-migration-environment-2 from image adt/ubuntu-noble-amd64-server-20240323.img (UUID 5df8a563-0957-4fdd-8453-862df650aaf8)...