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Setting up autoConTAMPR !

Jit
  • Public
By Jit 1677 days ago Comments (1)
(base) jit@jit-HP-Pro-3335-MT:~/Downloads/testDock$ docker build -t autocontampr . Sending build context to Docker daemon 9.024MB Step 1/16 : FROM ubuntu:14.04 ---> 6e4f1fe62ff1 Step 2/16 : FROM perl:latest ---> de6996f7ef50 Step 3/16 : FROM bioperl/bioperl-deps ---> e890cc223da3 Step 4/16 : MAINTAINER "Jitendra Narayan" <jnarayan81@gmail.com> ---> Using cache ---> c0e65f263890 Step 5/16 : RUN apt-get clean && apt-get update --yes && apt-get install --yes git && apt-get install -y wget ---> Using cache ---> 646453255081 Step 6/16 : RUN apt-get install --yes build-essential gcc-multilib perl ---> Using cache ---> 5c8f91f5e722 Step 7/16 : RUN apt-get -y install r-base ---> Using cache ---> e2f4b21b0c27 Step 8/16 : RUN echo "r <- getOption('repos'); r['CRAN'] <- 'http://cran.us.r-project.org'; options(repos = r);" > ~/.Rprofile ---> Using cache ---> 113232f4f250 Step 9/16 : RUN Rscript -e "install.packages('ggplot2')" ---> Using cache ---> 0953f592efa6 Step 10/16 : RUN wget http://www.zlib.net/zlib-1.2.11.tar.gz && tar -xzf zlib-1.2.11.tar.gz && cd zlib-1.2.11 && ./configure && make && sudo make install && cd .. ---> Using cache ---> 850cb02378d4 Step 11/16 : RUN wget https://sourceforge.net/projects/staden/files/io_lib/1.9.0/io_lib-1.9.0.tar.gz && tar -xzf io_lib-1.9.0.tar.gz && cd io_lib-1.9.0 && export CFLAGS="-fPIC" && ./configure && make && sudo make install && cd .. ---> Using cache ---> 1acadedd1157 Step 12/16 : RUN apt-get install -y bioperl && apt-get install -y libstatistics-distributions-perl && apt-get install -y libterm-progressbar-simple-perl && apt-get install -y libbio-scf-perl ---> Running in 7adc9dbdb955 Reading package lists... Building dependency tree... Reading state information... The following extra packages will be installed: amap-align apache2-bin bedtools bioperl-run blast2 bowtie bwa clustalw dialign emboss emboss-data emboss-lib exonerate ghostscript gsfonts hmmer infernal kalign libace-perl libalgorithm-c3-perl libalgorithm-munkres-perl libapache-dbi-perl libapache2-mod-perl2 libapache2-reload-perl libapr1 libaprutil1 libaprutil1-dbd-sqlite3 libaprutil1-ldap libarray-compare-perl libavahi-client3 libavahi-common-data libavahi-common3 libb-hooks-endofscope-perl libbio-asn1-entrezgene-perl libbio-perl-perl libbio-perl-run-perl libbit-vector-perl libbsd-resource-perl libcache-cache-perl libcarp-clan-perl libclass-c3-perl libclass-c3-xs-perl libclass-inspector-perl libclass-load-perl libclass-load-xs-perl libclass-tiny-perl libclone-perl libconvert-binary-c-perl libconvert-binhex-perl libcrypt-ssleay-perl libcups2 libcupsfilters1 libcupsimage2 libdata-optlist-perl libdata-stag-perl libdate-calc-perl libdate-calc-xs-perl libdate-manip-perl libdevel-caller-perl libdevel-globaldestruction-perl libdevel-lexalias-perl libdevel-partialdump-perl libdevel-symdump-perl libeval-closure-perl libfcgi-perl libfile-slurp-perl libfreezethaw-perl libgd-gd2-perl libgraph-perl libgraphviz-perl libgs9 libgs9-common libheap-perl libhpdf-2.2.1 libhtml-tableextract-perl libijs-0.35 libio-pty-perl libio-sessiondata-perl libio-string-perl libio-stringy-perl libipc-run-perl libipc-sharelite-perl libjbig2dec0 libjcode-pm-perl libmath-derivative-perl libmath-spline-perl libmime-tools-perl libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoose-perl libmro-compat-perl libnamespace-clean-perl libncbi6 libole-storage-lite-perl libossp-uuid-perl libossp-uuid16 libpackage-deprecationmanager-perl libpackage-stash-perl libpackage-stash-xs-perl libpadwalker-perl libparams-classify-perl libparams-util-perl libparse-recdescent-perl libperl5.18 libpostscript-perl libruby1.9.1 libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libstatistics-descriptive-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsvg-graph-perl libsvg-perl libtask-weaken-perl libtie-ixhash-perl libtree-dagnode-perl libtry-tiny-perl libunicode-map-perl libvariable-magic-perl libxml-dom-perl libxml-dom-xpath-perl libxml-filter-buffertext-perl libxml-libxml-perl libxml-libxslt-perl libxml-namespacesupport-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 libxmlrpc-lite-perl libyaml-0-2 libyaml-libyaml-perl libyaml-perl lynx lynx-cur mafft maq muscle ncbi-data perl-doc perl-tk phyml poppler-data primer3 probalign probcons ruby ruby1.9.1 samtools sim4 t-coffee tigr-glimmer tm-align wise wise-data Suggested packages: www-browser apache2-doc apache2-suexec-pristine apache2-suexec-custom filo gmap paml phylip libvibrant6b ncbi-rrna-data ncbi-tools-bin ncbi-tools-x11 bowtie-examples clustalx seaview emboss-doc emboss-test embassy ghostscript-x hpijs hmmer-doc libxml-sax-expatxs-perl cups-common fonts-droid libhtml-element-extended-perl uuid libscalar-number-perl libmime-lite-perl libnet-jabber-perl libunicode-map8-perl libunicode-string-perl xml-twig-tools libyaml-shell-perl groff poppler-utils fonts-japanese-mincho fonts-ipafont-mincho fonts-japanese-gothic fonts-ipafont-gothic fonts-arphic-ukai fonts-arphic-uming fonts-unfonts-core ncbi-epcr probcons-extra ri ruby-dev ruby1.9.1-examples ri1.9.1 ruby1.9.1-dev ruby-switch boxshade t-coffee-examples dialign-tx poa proda pymol rasmol wise-doc Recommended packages: libgd-perl The following NEW packages will be installed: amap-align apache2-bin bedtools bioperl bioperl-run blast2 bowtie bwa clustalw dialign emboss emboss-data emboss-lib exonerate ghostscript gsfonts hmmer infernal kalign libace-perl libalgorithm-c3-perl libalgorithm-munkres-perl libapache-dbi-perl libapache2-mod-perl2 libapache2-reload-perl libapr1 libaprutil1 libaprutil1-dbd-sqlite3 libaprutil1-ldap libarray-compare-perl libavahi-client3 libavahi-common-data libavahi-common3 libb-hooks-endofscope-perl libbio-asn1-entrezgene-perl libbio-perl-perl libbio-perl-run-perl libbit-vector-perl libbsd-resource-perl libcache-cache-perl libcarp-clan-perl libclass-c3-perl libclass-c3-xs-perl libclass-inspector-perl libclass-load-perl libclass-load-xs-perl libclass-tiny-perl libclone-perl libconvert-binary-c-perl libconvert-binhex-perl libcrypt-ssleay-perl libcups2 libcupsfilters1 libcupsimage2 libdata-optlist-perl libdata-stag-perl libdate-calc-perl libdate-calc-xs-perl libdate-manip-perl libdevel-caller-perl libdevel-globaldestruction-perl libdevel-lexalias-perl libdevel-partialdump-perl libdevel-symdump-perl libeval-closure-perl libfcgi-perl libfile-slurp-perl libfreezethaw-perl libgd-gd2-perl libgraph-perl libgraphviz-perl libgs9 libgs9-common libheap-perl libhpdf-2.2.1 libhtml-tableextract-perl libijs-0.35 libio-pty-perl libio-sessiondata-perl libio-string-perl libio-stringy-perl libipc-run-perl libipc-sharelite-perl libjbig2dec0 libjcode-pm-perl libmath-derivative-perl libmath-spline-perl libmime-tools-perl libmldbm-perl libmodule-implementation-perl libmodule-runtime-perl libmoose-perl libmro-compat-perl libnamespace-clean-perl libncbi6 libole-storage-lite-perl libossp-uuid-perl libossp-uuid16 libpackage-deprecationmanager-perl libpackage-stash-perl libpackage-stash-xs-perl libpadwalker-perl libparams-classify-perl libparams-util-perl libparse-recdescent-perl libperl5.18 libpostscript-perl libruby1.9.1 libset-scalar-perl libsoap-lite-perl libsort-naturally-perl libspreadsheet-parseexcel-perl libspreadsheet-writeexcel-perl libstatistics-descriptive-perl libsub-exporter-perl libsub-exporter-progressive-perl libsub-identify-perl libsub-install-perl libsub-name-perl libsvg-graph-perl libsvg-perl libtask-weaken-perl libtie-ixhash-perl libtree-dagnode-perl libtry-tiny-perl libunicode-map-perl libvariable-magic-perl libxml-dom-perl libxml-dom-xpath-perl libxml-filter-buffertext-perl libxml-libxml-perl libxml-libxslt-perl libxml-namespacesupport-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 libxmlrpc-lite-perl libyaml-0-2 libyaml-libyaml-perl libyaml-perl lynx lynx-cur mafft maq muscle ncbi-data perl-doc perl-tk phyml poppler-data primer3 probalign probcons ruby ruby1.9.1 samtools sim4 t-coffee tigr-glimmer tm-align wise wise-data 0 upgraded, 170 newly installed, 0 to remove and 50 not upgraded. Need to get 134 MB of archives. After this operation, 749 MB of additional disk space will be used. Get:1 http://archive.ubuntu.com/ubuntu/ trusty/main libapr1 amd64 1.5.0-1 [85.1 kB] Get:2 http://archive.ubuntu.com/ubuntu/ trusty/main libaprutil1 amd64 1.5.3-1 [76.4 kB] Get:3 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libavahi-common-data amd64 0.6.31-4ubuntu1.3 [21.1 kB] Get:4 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libavahi-common3 amd64 0.6.31-4ubuntu1.3 [21.7 kB] Get:5 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libavahi-client3 amd64 0.6.31-4ubuntu1.3 [25.2 kB] Get:6 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libcups2 amd64 1.7.2-0ubuntu1.11 [178 kB] Get:7 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libcupsfilters1 amd64 1.0.52-0ubuntu1.8 [73.7 kB] Get:8 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libcupsimage2 amd64 1.7.2-0ubuntu1.11 [15.4 kB] Get:9 http://archive.ubuntu.com/ubuntu/ trusty/universe ncbi-data all 6.1.20120620-7 [5863 kB] Get:10 http://archive.ubuntu.com/ubuntu/ trusty/universe libncbi6 amd64 6.1.20120620-7 [4725 kB] Get:11 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libyaml-0-2 amd64 0.1.4-3ubuntu3.1 [48.1 kB] Get:12 http://archive.ubuntu.com/ubuntu/ trusty/main poppler-data all 0.4.6-4 [1479 kB] Get:13 http://archive.ubuntu.com/ubuntu/ trusty/universe wise-data all 2.4.1-14 [33.9 kB] Get:14 http://archive.ubuntu.com/ubuntu/ trusty/universe wise amd64 2.4.1-14 [951 kB] Get:15 http://archive.ubuntu.com/ubuntu/ trusty/universe amap-align amd64 2.2-4 [158 kB] Get:16 http://archive.ubuntu.com/ubuntu/ trusty/main libaprutil1-dbd-sqlite3 amd64 1.5.3-1 [10.5 kB] Get:17 http://archive.ubuntu.com/ubuntu/ trusty/main libaprutil1-ldap amd64 1.5.3-1 [8634 B] Get:18 http://archive.ubuntu.com/ubuntu/ trusty-updates/main apache2-bin amd64 2.4.7-1ubuntu4.22 [845 kB] Get:19 http://archive.ubuntu.com/ubuntu/ trusty/universe bedtools amd64 2.17.0-1 [431 kB] Get:20 http://archive.ubuntu.com/ubuntu/ trusty/main libio-string-perl all 1.08-3 [11.1 kB] Get:21 http://archive.ubuntu.com/ubuntu/ trusty/universe libdata-stag-perl all 0.13-1 [429 kB] Get:22 http://archive.ubuntu.com/ubuntu/ trusty/universe libbio-perl-perl all 1.6.923-1 [4732 kB] Get:23 http://archive.ubuntu.com/ubuntu/ trusty/universe bioperl all 1.6.923-1 [386 kB] Get:24 http://archive.ubuntu.com/ubuntu/ trusty/universe libbio-perl-run-perl all 1.6.9-2 [897 kB] Get:25 http://archive.ubuntu.com/ubuntu/ trusty/universe bioperl-run all 1.6.9-2 [42.0 kB] Get:26 http://archive.ubuntu.com/ubuntu/ trusty/universe blast2 amd64 1:2.2.26.20120620-7 [640 kB] Get:27 http://archive.ubuntu.com/ubuntu/ trusty/universe bwa amd64 0.7.5a-2 [170 kB] Get:28 http://archive.ubuntu.com/ubuntu/ trusty/multiverse clustalw amd64 2.1+lgpl-4 [270 kB] Get:29 http://archive.ubuntu.com/ubuntu/ trusty/universe dialign amd64 2.2.1-6 [204 kB] Get:30 http://archive.ubuntu.com/ubuntu/ trusty/universe libhpdf-2.2.1 amd64 2.2.1-1ubuntu2 [334 kB] Get:31 http://archive.ubuntu.com/ubuntu/ trusty/universe emboss-lib amd64 6.6.0-1 [3082 kB] Get:32 http://archive.ubuntu.com/ubuntu/ trusty/universe emboss-data all 6.6.0-1 [60.8 MB] Get:33 http://archive.ubuntu.com/ubuntu/ trusty/universe emboss amd64 6.6.0-1 [953 kB] Get:34 http://archive.ubuntu.com/ubuntu/ trusty/universe exonerate amd64 2.2.0-6 [3107 kB] Get:35 http://archive.ubuntu.com/ubuntu/ trusty/main libijs-0.35 amd64 0.35-8build1 [16.8 kB] Get:36 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libjbig2dec0 amd64 0.11+20120125-1ubuntu1.1 [43.0 kB] Get:37 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libgs9-common all 9.26~dfsg+0-0ubuntu0.14.04.8 [5098 kB] Get:38 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libgs9 amd64 9.26~dfsg+0-0ubuntu0.14.04.8 [2355 kB] Get:39 http://archive.ubuntu.com/ubuntu/ trusty/main gsfonts all 1:8.11+urwcyr1.0.7~pre44-4.2ubuntu1 [3374 kB] Get:40 http://archive.ubuntu.com/ubuntu/ trusty-updates/main ghostscript amd64 9.26~dfsg+0-0ubuntu0.14.04.8 [47.1 kB] Get:41 http://archive.ubuntu.com/ubuntu/ trusty/universe infernal amd64 1.1~rc4-2 [1800 kB] Get:42 http://archive.ubuntu.com/ubuntu/ trusty/universe kalign amd64 1:2.03+20110620-2 [102 kB] Get:43 http://archive.ubuntu.com/ubuntu/ trusty/main libipc-sharelite-perl amd64 0.17-3build1 [25.5 kB] Get:44 http://archive.ubuntu.com/ubuntu/ trusty/universe libcache-cache-perl all 1.06-2 [75.8 kB] Get:45 http://archive.ubuntu.com/ubuntu/ trusty/universe libace-perl amd64 1.92-3 [352 kB] Get:46 http://archive.ubuntu.com/ubuntu/ trusty/main libalgorithm-c3-perl all 0.08-1 [11.8 kB] Get:47 http://archive.ubuntu.com/ubuntu/ trusty/universe libalgorithm-munkres-perl all 0.08-2 [12.4 kB] Get:48 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libperl5.18 amd64 5.18.2-2ubuntu1.7 [1330 B] Get:49 http://archive.ubuntu.com/ubuntu/ trusty/main libdevel-symdump-perl all 2.11-2 [13.4 kB] Get:50 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libapache2-mod-perl2 amd64 2.0.8+httpd24-r1449661-6ubuntu2.1 [848 kB] Get:51 http://archive.ubuntu.com/ubuntu/ trusty/universe libapache-dbi-perl all 1.12-1 [47.0 kB] Get:52 http://archive.ubuntu.com/ubuntu/ trusty/main libapache2-reload-perl all 0.12-2 [17.3 kB] Get:53 http://archive.ubuntu.com/ubuntu/ trusty/main libparams-util-perl amd64 1.07-1build1 [22.4 kB] Get:54 http://archive.ubuntu.com/ubuntu/ trusty/main libsub-install-perl all 0.927-1 [10.6 kB] Get:55 http://archive.ubuntu.com/ubuntu/ trusty/main libdata-optlist-perl all 0.109-1 [9920 B] Get:56 http://archive.ubuntu.com/ubuntu/ trusty/main libparams-classify-perl amd64 0.013-4build2 [23.0 kB] Get:57 http://archive.ubuntu.com/ubuntu/ trusty/main libmodule-runtime-perl all 0.013-1 [15.8 kB] Get:58 http://archive.ubuntu.com/ubuntu/ trusty/main libtry-tiny-perl all 0.19-1 [17.6 kB] Get:59 http://archive.ubuntu.com/ubuntu/ trusty/main libmodule-implementation-perl all 0.07-1 [12.8 kB] Get:60 http://archive.ubuntu.com/ubuntu/ trusty/main libpackage-stash-perl all 0.36-1 [21.7 kB] Get:61 http://archive.ubuntu.com/ubuntu/ trusty/main libclass-load-perl all 0.20-1 [11.6 kB] Get:62 http://archive.ubuntu.com/ubuntu/ trusty/main libclass-load-xs-perl amd64 0.06-1build1 [13.9 kB] Get:63 http://archive.ubuntu.com/ubuntu/ trusty/main libsub-exporter-progressive-perl all 0.001011-1 [7064 B] Get:64 http://archive.ubuntu.com/ubuntu/ trusty/main libdevel-globaldestruction-perl all 0.12-1 [7858 B] Get:65 http://archive.ubuntu.com/ubuntu/ trusty/main libsub-exporter-perl all 0.986-1 [50.6 kB] Get:66 http://archive.ubuntu.com/ubuntu/ trusty/main libeval-closure-perl all 0.11-1 [11.3 kB] Get:67 http://archive.ubuntu.com/ubuntu/ trusty/main libclass-c3-perl all 0.25-1 [21.5 kB] Get:68 http://archive.ubuntu.com/ubuntu/ trusty/main libmro-compat-perl all 0.12-1 [12.2 kB] Get:69 http://archive.ubuntu.com/ubuntu/ trusty/main libpackage-deprecationmanager-perl all 0.13-1 [12.9 kB] Get:70 http://archive.ubuntu.com/ubuntu/ trusty/main libpackage-stash-xs-perl amd64 0.28-1 [18.7 kB] Get:71 http://archive.ubuntu.com/ubuntu/ trusty/main libsub-name-perl amd64 0.05-1build4 [9774 B] Get:72 http://archive.ubuntu.com/ubuntu/ trusty/main libtask-weaken-perl all 1.04-1 [7628 B] Get:73 http://archive.ubuntu.com/ubuntu/ trusty/main libmoose-perl amd64 2.1005-1 [849 kB] Get:74 http://archive.ubuntu.com/ubuntu/ trusty/universe libarray-compare-perl all 2.02-1 [13.4 kB] Get:75 http://archive.ubuntu.com/ubuntu/ trusty/main libvariable-magic-perl amd64 0.53-1 [36.2 kB] Get:76 http://archive.ubuntu.com/ubuntu/ trusty/main libb-hooks-endofscope-perl all 0.13-1 [14.4 kB] Get:77 http://archive.ubuntu.com/ubuntu/ trusty/universe libbio-asn1-entrezgene-perl all 1.700-1 [41.8 kB] Get:78 http://archive.ubuntu.com/ubuntu/ trusty/main libcarp-clan-perl all 6.04-1 [14.1 kB] Get:79 http://archive.ubuntu.com/ubuntu/ trusty/main libbit-vector-perl amd64 7.3-1build1 [160 kB] Get:80 http://archive.ubuntu.com/ubuntu/ trusty/main libclass-c3-xs-perl amd64 0.13-1build4 [15.1 kB] Get:81 http://archive.ubuntu.com/ubuntu/ trusty/main libclass-inspector-perl all 1.28-1 [18.7 kB] Get:82 http://archive.ubuntu.com/ubuntu/ trusty/main libclass-tiny-perl all 0.012-1 [14.9 kB] Get:83 http://archive.ubuntu.com/ubuntu/ trusty/main libclone-perl amd64 0.36-1 [11.0 kB] Get:84 http://archive.ubuntu.com/ubuntu/ trusty/universe libconvert-binary-c-perl amd64 0.76-3build1 [299 kB] Get:85 http://archive.ubuntu.com/ubuntu/ trusty/main libconvert-binhex-perl all 1.123-1 [32.2 kB] Get:86 http://archive.ubuntu.com/ubuntu/ trusty/universe libcrypt-ssleay-perl amd64 0.58-1build1 [40.4 kB] Get:87 http://archive.ubuntu.com/ubuntu/ trusty/universe libdate-calc-perl all 6.3-1 [209 kB] Get:88 http://archive.ubuntu.com/ubuntu/ trusty/universe libdate-calc-xs-perl amd64 6.3-1build1 [56.0 kB] Get:89 http://archive.ubuntu.com/ubuntu/ trusty/main libdate-manip-perl all 6.42-1 [913 kB] Get:90 http://archive.ubuntu.com/ubuntu/ trusty/main libpadwalker-perl amd64 1.98-1 [17.1 kB] Get:91 http://archive.ubuntu.com/ubuntu/ trusty/main libdevel-caller-perl amd64 2.06-1build1 [12.1 kB] Get:92 http://archive.ubuntu.com/ubuntu/ trusty/main libdevel-lexalias-perl amd64 0.05-1build1 [9962 B] Get:93 http://archive.ubuntu.com/ubuntu/ trusty/main libsub-identify-perl amd64 0.04-1build3 [9254 B] Get:94 http://archive.ubuntu.com/ubuntu/ trusty/main libnamespace-clean-perl all 0.24-1 [13.0 kB] Get:95 http://archive.ubuntu.com/ubuntu/ trusty/main libdevel-partialdump-perl all 0.17-1 [13.6 kB] Get:96 http://archive.ubuntu.com/ubuntu/ trusty/universe libfcgi-perl amd64 0.74-1build2 [36.8 kB] Get:97 http://archive.ubuntu.com/ubuntu/ trusty/universe libfreezethaw-perl all 0.5001-1 [18.2 kB] Get:98 http://archive.ubuntu.com/ubuntu/ trusty/universe libheap-perl all 0.80-2 [40.4 kB] Get:99 http://archive.ubuntu.com/ubuntu/ trusty/universe libgraph-perl all 1:0.96-1.1 [127 kB] Get:100 http://archive.ubuntu.com/ubuntu/ trusty/main libio-pty-perl amd64 1:1.08-1build4 [36.9 kB] Get:101 http://archive.ubuntu.com/ubuntu/ trusty/main libipc-run-perl all 0.92-1 [101 kB] Get:102 http://archive.ubuntu.com/ubuntu/ trusty/universe libxml-twig-perl all 1:3.44-1 [154 kB] Get:103 http://archive.ubuntu.com/ubuntu/ trusty/universe libxml-xpath-perl all 1.13-7 [80.7 kB] Get:104 http://archive.ubuntu.com/ubuntu/ trusty/main libparse-recdescent-perl all 1.967009+dfsg-1 [158 kB] Get:105 http://archive.ubuntu.com/ubuntu/ trusty/universe libgraphviz-perl all 2.14-1 [111 kB] Get:106 http://archive.ubuntu.com/ubuntu/ trusty/universe libhtml-tableextract-perl all 2.11-1 [29.8 kB] Get:107 http://archive.ubuntu.com/ubuntu/ trusty/universe libio-sessiondata-perl all 1.03-1 [5606 B] Get:108 http://archive.ubuntu.com/ubuntu/ trusty/main libio-stringy-perl all 2.110-5 [93.5 kB] Get:109 http://archive.ubuntu.com/ubuntu/ trusty/universe libjcode-pm-perl amd64 2.06-1 [31.0 kB] Get:110 http://archive.ubuntu.com/ubuntu/ trusty/universe libmath-derivative-perl all 0.01-6 [6260 B] Get:111 http://archive.ubuntu.com/ubuntu/ trusty/universe libmath-spline-perl all 0.02-1 [7966 B] Get:112 http://archive.ubuntu.com/ubuntu/ trusty/main libmime-tools-perl all 5.505-1 [206 kB] Get:113 http://archive.ubuntu.com/ubuntu/ trusty/universe libmldbm-perl all 2.05-1 [18.3 kB] Get:114 http://archive.ubuntu.com/ubuntu/ trusty/universe libole-storage-lite-perl all 0.19-1 [26.1 kB] Get:115 http://archive.ubuntu.com/ubuntu/ trusty/main libossp-uuid16 amd64 1.6.2-1.3ubuntu1 [29.6 kB] Get:116 http://archive.ubuntu.com/ubuntu/ trusty/universe libossp-uuid-perl amd64 1.6.2-1.3ubuntu1 [19.8 kB] Get:117 http://archive.ubuntu.com/ubuntu/ trusty/universe libpostscript-perl all 0.06-2 [31.2 kB] Get:118 http://archive.ubuntu.com/ubuntu/ trusty/main ruby all 1:1.9.3.4 [5334 B] Get:119 http://archive.ubuntu.com/ubuntu/ trusty-updates/main ruby1.9.1 amd64 1.9.3.484-2ubuntu1.14 [35.6 kB] Get:120 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libruby1.9.1 amd64 1.9.3.484-2ubuntu1.14 [2648 kB] Get:121 http://archive.ubuntu.com/ubuntu/ trusty/universe libsoap-lite-perl all 1.09-1 [253 kB] Get:122 http://archive.ubuntu.com/ubuntu/ trusty/universe libsort-naturally-perl all 1.02-1 [14.4 kB] Get:123 http://archive.ubuntu.com/ubuntu/ trusty/universe libspreadsheet-writeexcel-perl all 2.40-1 [628 kB] Get:124 http://archive.ubuntu.com/ubuntu/ trusty/universe libunicode-map-perl amd64 0.112-11 [143 kB] Get:125 http://archive.ubuntu.com/ubuntu/ trusty/universe libspreadsheet-parseexcel-perl all 0.5800-1 [160 kB] Get:126 http://archive.ubuntu.com/ubuntu/ trusty/universe libstatistics-descriptive-perl all 3.0605-1 [38.7 kB] Get:127 http://archive.ubuntu.com/ubuntu/ trusty/universe libsvg-perl all 2.59-1 [79.0 kB] Get:128 http://archive.ubuntu.com/ubuntu/ trusty/main libfile-slurp-perl all 9999.19-4 [41.3 kB] Get:129 http://archive.ubuntu.com/ubuntu/ trusty/main libtree-dagnode-perl all 1.17-1 [59.6 kB] Get:130 http://archive.ubuntu.com/ubuntu/ trusty/universe libsvg-graph-perl all 0.02-2 [128 kB] Get:131 http://archive.ubuntu.com/ubuntu/ trusty/main libtie-ixhash-perl all 1.23-1 [11.7 kB] Get:132 http://archive.ubuntu.com/ubuntu/ trusty/main libxml-perl all 0.08-2 [113 kB] Get:133 http://archive.ubuntu.com/ubuntu/ trusty/main libxml-regexp-perl all 0.04-1 [8072 B] Get:134 http://archive.ubuntu.com/ubuntu/ trusty/main libxml-dom-perl all 1.44-1 [185 kB] Get:135 http://archive.ubuntu.com/ubuntu/ trusty/universe libxml-xpathengine-perl all 0.13-1 [37.1 kB] Get:136 http://archive.ubuntu.com/ubuntu/ trusty/universe libxml-dom-xpath-perl all 0.14-1 [9722 B] Get:137 http://archive.ubuntu.com/ubuntu/ trusty/main libxml-namespacesupport-perl all 1.11-1 [13.2 kB] Get:138 http://archive.ubuntu.com/ubuntu/ trusty/main libxml-sax-base-perl all 1.07-1 [21.5 kB] Get:139 http://archive.ubuntu.com/ubuntu/ trusty/main libxml-sax-perl all 0.99+dfsg-2ubuntu1 [64.6 kB] Get:140 http://archive.ubuntu.com/ubuntu/ trusty/main libxml-filter-buffertext-perl all 1.01-5 [7374 B] Get:141 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libxml-libxml-perl amd64 2.0108+dfsg-1ubuntu0.2 [336 kB] Get:142 http://archive.ubuntu.com/ubuntu/ trusty/main libxml-libxslt-perl amd64 1.84-1 [42.3 kB] Get:143 http://archive.ubuntu.com/ubuntu/ trusty/main libxml-sax-expat-perl all 0.40-2 [11.5 kB] Get:144 http://archive.ubuntu.com/ubuntu/ trusty/main libxml-sax-writer-perl all 0.53-1 [22.3 kB] Get:145 http://archive.ubuntu.com/ubuntu/ trusty/main libxml-simple-perl all 2.20-1 [68.3 kB] Get:146 http://archive.ubuntu.com/ubuntu/ trusty/universe libxml-writer-perl all 0.623-1 [27.2 kB] Get:147 http://archive.ubuntu.com/ubuntu/ trusty/universe libxmlrpc-lite-perl all 0.717-1 [26.0 kB] Get:148 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libyaml-libyaml-perl amd64 0.41-5ubuntu0.14.04.1 [63.8 kB] Get:149 http://archive.ubuntu.com/ubuntu/ trusty/main libyaml-perl all 0.84-1 [68.3 kB] Get:150 http://archive.ubuntu.com/ubuntu/ trusty/universe mafft amd64 7.123-1 [776 kB] Get:151 http://archive.ubuntu.com/ubuntu/ trusty/universe maq amd64 0.7.1-5 [298 kB] Get:152 http://archive.ubuntu.com/ubuntu/ trusty/universe muscle amd64 1:3.8.31-1 [169 kB] Get:153 http://archive.ubuntu.com/ubuntu/ trusty-updates/main perl-doc all 5.18.2-2ubuntu1.7 [7264 kB] Get:154 http://archive.ubuntu.com/ubuntu/ trusty/universe perl-tk amd64 1:804.031-1build1 [2619 kB] Get:155 http://archive.ubuntu.com/ubuntu/ trusty/universe phyml amd64 2:20120412-2 [1562 kB] Get:156 http://archive.ubuntu.com/ubuntu/ trusty/universe primer3 amd64 2.3.6-1 [169 kB] Get:157 http://archive.ubuntu.com/ubuntu/ trusty/universe probalign amd64 1.4-3 [81.4 kB] Get:158 http://archive.ubuntu.com/ubuntu/ trusty/universe probcons amd64 1.12-9 [228 kB] Get:159 http://archive.ubuntu.com/ubuntu/ trusty/universe samtools amd64 0.1.19-1 [560 kB] Get:160 http://archive.ubuntu.com/ubuntu/ trusty/universe sim4 amd64 0.0.20121010-1 [55.8 kB] Get:161 http://archive.ubuntu.com/ubuntu/ trusty/universe t-coffee amd64 10.00.r1613-1 [873 kB] Get:162 http://archive.ubuntu.com/ubuntu/ trusty/universe tigr-glimmer amd64 3.02-3 [446 kB] Get:163 http://archive.ubuntu.com/ubuntu/ trusty/universe tm-align amd64 20130511+dfsg-1 [66.4 kB] Get:164 http://archive.ubuntu.com/ubuntu/ trusty/universe bowtie amd64 1.0.0-5 [1276 kB] Get:165 http://archive.ubuntu.com/ubuntu/ trusty/universe hmmer amd64 3.1b1-3 [1022 kB] Get:166 http://archive.ubuntu.com/ubuntu/ trusty/main libbsd-resource-perl amd64 1.2907-1build1 [31.8 kB] Get:167 http://archive.ubuntu.com/ubuntu/ trusty/main libgd-gd2-perl amd64 1:2.46-3.1build1 [181 kB] Get:168 http://archive.ubuntu.com/ubuntu/ trusty/universe libset-scalar-perl all 1.27-1 [33.4 kB] Get:169 http://archive.ubuntu.com/ubuntu/ trusty/main lynx-cur amd64 2.8.8pre4-1 [956 kB] Get:170 http://archive.ubuntu.com/ubuntu/ trusty/main lynx all 2.8.8pre4-1 [4184 B] debconf: unable to initialize frontend: Dialog debconf: (TERM is not set, so the dialog frontend is not usable.) debconf: falling back to frontend: Readline debconf: unable to initialize frontend: Readline debconf: (This frontend requires a controlling tty.) debconf: falling back to frontend: Teletype dpkg-preconfigure: unable to re-open stdin: Fetched 134 MB in 40min 11s (55.5 kB/s) Selecting previously unselected package libapr1:amd64. (Reading database ... 30278 files and directories currently installed.) Preparing to unpack .../libapr1_1.5.0-1_amd64.deb ... Unpacking libapr1:amd64 (1.5.0-1) ... Selecting previously unselected package libaprutil1:amd64. Preparing to unpack .../libaprutil1_1.5.3-1_amd64.deb ... Unpacking libaprutil1:amd64 (1.5.3-1) ... Selecting previously unselected package libavahi-common-data:amd64. Preparing to unpack .../libavahi-common-data_0.6.31-4ubuntu1.3_amd64.deb ... Unpacking libavahi-common-data:amd64 (0.6.31-4ubuntu1.3) ... Selecting previously unselected package libavahi-common3:amd64. Preparing to unpack .../libavahi-common3_0.6.31-4ubuntu1.3_amd64.deb ... Unpacking libavahi-common3:amd64 (0.6.31-4ubuntu1.3) ... Selecting previously unselected package libavahi-client3:amd64. Preparing to unpack .../libavahi-client3_0.6.31-4ubuntu1.3_amd64.deb ... Unpacking libavahi-client3:amd64 (0.6.31-4ubuntu1.3) ... Selecting previously unselected package libcups2:amd64. Preparing to unpack .../libcups2_1.7.2-0ubuntu1.11_amd64.deb ... Unpacking libcups2:amd64 (1.7.2-0ubuntu1.11) ... Selecting previously unselected package libcupsfilters1:amd64. Preparing to unpack .../libcupsfilters1_1.0.52-0ubuntu1.8_amd64.deb ... Unpacking libcupsfilters1:amd64 (1.0.52-0ubuntu1.8) ... Selecting previously unselected package libcupsimage2:amd64. Preparing to unpack .../libcupsimage2_1.7.2-0ubuntu1.11_amd64.deb ... Unpacking libcupsimage2:amd64 (1.7.2-0ubuntu1.11) ... Selecting previously unselected package ncbi-data. Preparing to unpack .../ncbi-data_6.1.20120620-7_all.deb ... Unpacking ncbi-data (6.1.20120620-7) ... Selecting previously unselected package libncbi6:amd64. Preparing to unpack .../libncbi6_6.1.20120620-7_amd64.deb ... Unpacking libncbi6:amd64 (6.1.20120620-7) ... Selecting previously unselected package libyaml-0-2:amd64. Preparing to unpack .../libyaml-0-2_0.1.4-3ubuntu3.1_amd64.deb ... Unpacking libyaml-0-2:amd64 (0.1.4-3ubuntu3.1) ... Selecting previously unselected package poppler-data. Preparing to unpack .../poppler-data_0.4.6-4_all.deb ... Unpacking poppler-data (0.4.6-4) ... Selecting previously unselected package wise-data. Preparing to unpack .../wise-data_2.4.1-14_all.deb ... Unpacking wise-data (2.4.1-14) ... Selecting previously unselected package wise. Preparing to unpack .../wise_2.4.1-14_amd64.deb ... Unpacking wise (2.4.1-14) ... Selecting previously unselected package amap-align. Preparing to unpack .../amap-align_2.2-4_amd64.deb ... Unpacking amap-align (2.2-4) ... Selecting previously unselected package libaprutil1-dbd-sqlite3:amd64. Preparing to unpack .../libaprutil1-dbd-sqlite3_1.5.3-1_amd64.deb ... Unpacking libaprutil1-dbd-sqlite3:amd64 (1.5.3-1) ... Selecting previously unselected package libaprutil1-ldap:amd64. Preparing to unpack .../libaprutil1-ldap_1.5.3-1_amd64.deb ... Unpacking libaprutil1-ldap:amd64 (1.5.3-1) ... Selecting previously unselected package apache2-bin. Preparing to unpack .../apache2-bin_2.4.7-1ubuntu4.22_amd64.deb ... Unpacking apache2-bin (2.4.7-1ubuntu4.22) ... Selecting previously unselected package bedtools. Preparing to unpack .../bedtools_2.17.0-1_amd64.deb ... Unpacking bedtools (2.17.0-1) ... Selecting previously unselected package libio-string-perl. Preparing to unpack .../libio-string-perl_1.08-3_all.deb ... Unpacking libio-string-perl (1.08-3) ... Selecting previously unselected package libdata-stag-perl. Preparing to unpack .../libdata-stag-perl_0.13-1_all.deb ... Unpacking libdata-stag-perl (0.13-1) ... Selecting previously unselected package libbio-perl-perl. Preparing to unpack .../libbio-perl-perl_1.6.923-1_all.deb ... Unpacking libbio-perl-perl (1.6.923-1) ... Selecting previously unselected package bioperl. Preparing to unpack .../bioperl_1.6.923-1_all.deb ... Unpacking bioperl (1.6.923-1) ... Selecting previously unselected package libbio-perl-run-perl. Preparing to unpack .../libbio-perl-run-perl_1.6.9-2_all.deb ... Unpacking libbio-perl-run-perl (1.6.9-2) ... Selecting previously unselected package bioperl-run. Preparing to unpack .../bioperl-run_1.6.9-2_all.deb ... Unpacking bioperl-run (1.6.9-2) ... Selecting previously unselected package blast2. Preparing to unpack .../blast2_1%3a2.2.26.20120620-7_amd64.deb ... Unpacking blast2 (1:2.2.26.20120620-7) ... Selecting previously unselected package bwa. Preparing to unpack .../bwa_0.7.5a-2_amd64.deb ... Unpacking bwa (0.7.5a-2) ... Selecting previously unselected package clustalw. Preparing to unpack .../clustalw_2.1+lgpl-4_amd64.deb ... Unpacking clustalw (2.1+lgpl-4) ... Selecting previously unselected package dialign. Preparing to unpack .../dialign_2.2.1-6_amd64.deb ... Unpacking dialign (2.2.1-6) ... Selecting previously unselected package libhpdf-2.2.1. Preparing to unpack .../libhpdf-2.2.1_2.2.1-1ubuntu2_amd64.deb ... Unpacking libhpdf-2.2.1 (2.2.1-1ubuntu2) ... Selecting previously unselected package emboss-lib. Preparing to unpack .../emboss-lib_6.6.0-1_amd64.deb ... Unpacking emboss-lib (6.6.0-1) ... Selecting previously unselected package emboss-data. Preparing to unpack .../emboss-data_6.6.0-1_all.deb ... Unpacking emboss-data (6.6.0-1) ... Selecting previously unselected package emboss. Preparing to unpack .../emboss_6.6.0-1_amd64.deb ... Unpacking emboss (6.6.0-1) ... Selecting previously unselected package exonerate. Preparing to unpack .../exonerate_2.2.0-6_amd64.deb ... Unpacking exonerate (2.2.0-6) ... Selecting previously unselected package libijs-0.35. Preparing to unpack .../libijs-0.35_0.35-8build1_amd64.deb ... Unpacking libijs-0.35 (0.35-8build1) ... Selecting previously unselected package libjbig2dec0. Preparing to unpack .../libjbig2dec0_0.11+20120125-1ubuntu1.1_amd64.deb ... Unpacking libjbig2dec0 (0.11+20120125-1ubuntu1.1) ... Selecting previously unselected package libgs9-common. Preparing to unpack .../libgs9-common_9.26~dfsg+0-0ubuntu0.14.04.8_all.deb ... Unpacking libgs9-common (9.26~dfsg+0-0ubuntu0.14.04.8) ... Selecting previously unselected package libgs9. Preparing to unpack .../libgs9_9.26~dfsg+0-0ubuntu0.14.04.8_amd64.deb ... Unpacking libgs9 (9.26~dfsg+0-0ubuntu0.14.04.8) ... Selecting previously unselected package gsfonts. Preparing to unpack .../gsfonts_1%3a8.11+urwcyr1.0.7~pre44-4.2ubuntu1_all.deb ... Unpacking gsfonts (1:8.11+urwcyr1.0.7~pre44-4.2ubuntu1) ... Selecting previously unselected package ghostscript. Preparing to unpack .../ghostscript_9.26~dfsg+0-0ubuntu0.14.04.8_amd64.deb ... Unpacking ghostscript (9.26~dfsg+0-0ubuntu0.14.04.8) ... Selecting previously unselected package infernal. Preparing to unpack .../infernal_1.1~rc4-2_amd64.deb ... Unpacking infernal (1.1~rc4-2) ... Selecting previously unselected package kalign. Preparing to unpack .../kalign_1%3a2.03+20110620-2_amd64.deb ... Unpacking kalign (1:2.03+20110620-2) ... Selecting previously unselected package libipc-sharelite-perl. Preparing to unpack .../libipc-sharelite-perl_0.17-3build1_amd64.deb ... Unpacking libipc-sharelite-perl (0.17-3build1) ... Selecting previously unselected package libcache-cache-perl. Preparing to unpack .../libcache-cache-perl_1.06-2_all.deb ... Unpacking libcache-cache-perl (1.06-2) ... Selecting previously unselected package libace-perl. Preparing to unpack .../libace-perl_1.92-3_amd64.deb ... Unpacking libace-perl (1.92-3) ... Selecting previously unselected package libalgorithm-c3-perl. Preparing to unpack .../libalgorithm-c3-perl_0.08-1_all.deb ... Unpacking libalgorithm-c3-perl (0.08-1) ... Selecting previously unselected package libalgorithm-munkres-perl. Preparing to unpack .../libalgorithm-munkres-perl_0.08-2_all.deb ... Unpacking libalgorithm-munkres-perl (0.08-2) ... Selecting previously unselected package libperl5.18. Preparing to unpack .../libperl5.18_5.18.2-2ubuntu1.7_amd64.deb ... Unpacking libperl5.18 (5.18.2-2ubuntu1.7) ... Selecting previously unselected package libdevel-symdump-perl. Preparing to unpack .../libdevel-symdump-perl_2.11-2_all.deb ... Unpacking libdevel-symdump-perl (2.11-2) ... Selecting previously unselected package libapache2-mod-perl2. Preparing to unpack .../libapache2-mod-perl2_2.0.8+httpd24-r1449661-6ubuntu2.1_amd64.deb ... Unpacking libapache2-mod-perl2 (2.0.8+httpd24-r1449661-6ubuntu2.1) ... Selecting previously unselected package libapache-dbi-perl. Preparing to unpack .../libapache-dbi-perl_1.12-1_all.deb ... Unpacking libapache-dbi-perl (1.12-1) ... Selecting previously unselected package libapache2-reload-perl. Preparing to unpack .../libapache2-reload-perl_0.12-2_all.deb ... Unpacking libapache2-reload-perl (0.12-2) ... Selecting previously unselected package libparams-util-perl. Preparing to unpack .../libparams-util-perl_1.07-1build1_amd64.deb ... Unpacking libparams-util-perl (1.07-1build1) ... Selecting previously unselected package libsub-install-perl. Preparing to unpack .../libsub-install-perl_0.927-1_all.deb ... Unpacking libsub-install-perl (0.927-1) ... Selecting previously unselected package libdata-optlist-perl. Preparing to unpack .../libdata-optlist-perl_0.109-1_all.deb ... Unpacking libdata-optlist-perl (0.109-1) ... Selecting previously unselected package libparams-classify-perl. Preparing to unpack .../libparams-classify-perl_0.013-4build2_amd64.deb ... Unpacking libparams-classify-perl (0.013-4build2) ... Selecting previously unselected package libmodule-runtime-perl. Preparing to unpack .../libmodule-runtime-perl_0.013-1_all.deb ... Unpacking libmodule-runtime-perl (0.013-1) ... Selecting previously unselected package libtry-tiny-perl. Preparing to unpack .../libtry-tiny-perl_0.19-1_all.deb ... Unpacking libtry-tiny-perl (0.19-1) ... Selecting previously unselected package libmodule-implementation-perl. Preparing to unpack .../libmodule-implementation-perl_0.07-1_all.deb ... Unpacking libmodule-implementation-perl (0.07-1) ... Selecting previously unselected package libpackage-stash-perl. Preparing to unpack .../libpackage-stash-perl_0.36-1_all.deb ... Unpacking libpackage-stash-perl (0.36-1) ... Selecting previously unselected package libclass-load-perl. Preparing to unpack .../libclass-load-perl_0.20-1_all.deb ... Unpacking libclass-load-perl (0.20-1) ... Selecting previously unselected package libclass-load-xs-perl. Preparing to unpack .../libclass-load-xs-perl_0.06-1build1_amd64.deb ... Unpacking libclass-load-xs-perl (0.06-1build1) ... Selecting previously unselected package libsub-exporter-progressive-perl. Preparing to unpack .../libsub-exporter-progressive-perl_0.001011-1_all.deb ... Unpacking libsub-exporter-progressive-perl (0.001011-1) ... Selecting previously unselected package libdevel-globaldestruction-perl. Preparing to unpack .../libdevel-globaldestruction-perl_0.12-1_all.deb ... Unpacking libdevel-globaldestruction-perl (0.12-1) ... Selecting previously unselected package libsub-exporter-perl. Preparing to unpack .../libsub-exporter-perl_0.986-1_all.deb ... Unpacking libsub-exporter-perl (0.986-1) ... Selecting previously unselected package libeval-closure-perl. Preparing to unpack .../libeval-closure-perl_0.11-1_all.deb ... Unpacking libeval-closure-perl (0.11-1) ... Selecting previously unselected package libclass-c3-perl. Preparing to unpack .../libclass-c3-perl_0.25-1_all.deb ... Unpacking libclass-c3-perl (0.25-1) ... Selecting previously unselected package libmro-compat-perl. Preparing to unpack .../libmro-compat-perl_0.12-1_all.deb ... Unpacking libmro-compat-perl (0.12-1) ... Selecting previously unselected package libpackage-deprecationmanager-perl. Preparing to unpack .../libpackage-deprecationmanager-perl_0.13-1_all.deb ... Unpacking libpackage-deprecationmanager-perl (0.13-1) ... Selecting previously unselected package libpackage-stash-xs-perl. Preparing to unpack .../libpackage-stash-xs-perl_0.28-1_amd64.deb ... Unpacking libpackage-stash-xs-perl (0.28-1) ... Selecting previously unselected package libsub-name-perl. Preparing to unpack .../libsub-name-perl_0.05-1build4_amd64.deb ... Unpacking libsub-name-perl (0.05-1build4) ... Selecting previously unselected package libtask-weaken-perl. Preparing to unpack .../libtask-weaken-perl_1.04-1_all.deb ... Unpacking libtask-weaken-perl (1.04-1) ... Selecting previously unselected package libmoose-perl. Preparing to unpack .../libmoose-perl_2.1005-1_amd64.deb ... Unpacking libmoose-perl (2.1005-1) ... Selecting previously unselected package libarray-compare-perl. Preparing to unpack .../libarray-compare-perl_2.02-1_all.deb ... Unpacking libarray-compare-perl (2.02-1) ... Selecting previously unselected package libvariable-magic-perl. Preparing to unpack .../libvariable-magic-perl_0.53-1_amd64.deb ... Unpacking libvariable-magic-perl (0.53-1) ... Selecting previously unselected package libb-hooks-endofscope-perl. Preparing to unpack .../libb-hooks-endofscope-perl_0.13-1_all.deb ... Unpacking libb-hooks-endofscope-perl (0.13-1) ... Selecting previously unselected package libbio-asn1-entrezgene-perl. Preparing to unpack .../libbio-asn1-entrezgene-perl_1.700-1_all.deb ... Unpacking libbio-asn1-entrezgene-perl (1.700-1) ... Selecting previously unselected package libcarp-clan-perl. Preparing to unpack .../libcarp-clan-perl_6.04-1_all.deb ... Unpacking libcarp-clan-perl (6.04-1) ... Selecting previously unselected package libbit-vector-perl. Preparing to unpack .../libbit-vector-perl_7.3-1build1_amd64.deb ... Unpacking libbit-vector-perl (7.3-1build1) ... Selecting previously unselected package libclass-c3-xs-perl. Preparing to unpack .../libclass-c3-xs-perl_0.13-1build4_amd64.deb ... Unpacking libclass-c3-xs-perl (0.13-1build4) ... Selecting previously unselected package libclass-inspector-perl. Preparing to unpack .../libclass-inspector-perl_1.28-1_all.deb ... Unpacking libclass-inspector-perl (1.28-1) ... Selecting previously unselected package libclass-tiny-perl. Preparing to unpack .../libclass-tiny-perl_0.012-1_all.deb ... Unpacking libclass-tiny-perl (0.012-1) ... Selecting previously unselected package libclone-perl. Preparing to unpack .../libclone-perl_0.36-1_amd64.deb ... Unpacking libclone-perl (0.36-1) ... Selecting previously unselected package libconvert-binary-c-perl. Preparing to unpack .../libconvert-binary-c-perl_0.76-3build1_amd64.deb ... Unpacking libconvert-binary-c-perl (0.76-3build1) ... Selecting previously unselected package libconvert-binhex-perl. Preparing to unpack .../libconvert-binhex-perl_1.123-1_all.deb ... Unpacking libconvert-binhex-perl (1.123-1) ... Selecting previously unselected package libcrypt-ssleay-perl. 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Setting up libcupsimage2:amd64 (1.7.2-0ubuntu1.11) ... Setting up ncbi-data (6.1.20120620-7) ... Setting up libncbi6:amd64 (6.1.20120620-7) ... Setting up libyaml-0-2:amd64 (0.1.4-3ubuntu3.1) ... Setting up poppler-data (0.4.6-4) ... Setting up wise-data (2.4.1-14) ... Setting up wise (2.4.1-14) ... Setting up amap-align (2.2-4) ... Setting up libaprutil1-dbd-sqlite3:amd64 (1.5.3-1) ... Setting up libaprutil1-ldap:amd64 (1.5.3-1) ... Setting up apache2-bin (2.4.7-1ubuntu4.22) ... Setting up bedtools (2.17.0-1) ... Setting up libio-string-perl (1.08-3) ... Setting up libdata-stag-perl (0.13-1) ... Setting up libbio-perl-perl (1.6.923-1) ... Setting up bioperl (1.6.923-1) ... Setting up libbio-perl-run-perl (1.6.9-2) ... Setting up bioperl-run (1.6.9-2) ... Setting up blast2 (1:2.2.26.20120620-7) ... Setting up bwa (0.7.5a-2) ... Setting up clustalw (2.1+lgpl-4) ... Setting up dialign (2.2.1-6) ... Setting up libhpdf-2.2.1 (2.2.1-1ubuntu2) ... Setting up emboss-lib (6.6.0-1) ... Setting up emboss-data (6.6.0-1) ... Setting up emboss (6.6.0-1) ... Setting up exonerate (2.2.0-6) ... Setting up libijs-0.35 (0.35-8build1) ... Setting up libjbig2dec0 (0.11+20120125-1ubuntu1.1) ... Setting up libgs9-common (9.26~dfsg+0-0ubuntu0.14.04.8) ... update-alternatives: using /usr/share/ghostscript/9.26 to provide /usr/share/ghostscript/current (ghostscript-current) in auto mode Setting up libgs9 (9.26~dfsg+0-0ubuntu0.14.04.8) ... Setting up gsfonts (1:8.11+urwcyr1.0.7~pre44-4.2ubuntu1) ... Setting up ghostscript (9.26~dfsg+0-0ubuntu0.14.04.8) ... Setting up infernal (1.1~rc4-2) ... Setting up kalign (1:2.03+20110620-2) ... Setting up libipc-sharelite-perl (0.17-3build1) ... Setting up libcache-cache-perl (1.06-2) ... Setting up libace-perl (1.92-3) ... Setting up libalgorithm-c3-perl (0.08-1) ... Setting up libalgorithm-munkres-perl (0.08-2) ... Setting up libperl5.18 (5.18.2-2ubuntu1.7) ... Setting up libdevel-symdump-perl (2.11-2) ... Setting up libapache2-mod-perl2 (2.0.8+httpd24-r1449661-6ubuntu2.1) ... Setting up libapache-dbi-perl (1.12-1) ... Setting up libapache2-reload-perl (0.12-2) ... Setting up libparams-util-perl (1.07-1build1) ... Setting up libsub-install-perl (0.927-1) ... Setting up libdata-optlist-perl (0.109-1) ... Setting up libparams-classify-perl (0.013-4build2) ... Setting up libmodule-runtime-perl (0.013-1) ... Setting up libtry-tiny-perl (0.19-1) ... Setting up libmodule-implementation-perl (0.07-1) ... Setting up libpackage-stash-perl (0.36-1) ... Setting up libclass-load-perl (0.20-1) ... Setting up libclass-load-xs-perl (0.06-1build1) ... Setting up libsub-exporter-progressive-perl (0.001011-1) ... Setting up libdevel-globaldestruction-perl (0.12-1) ... Setting up libsub-exporter-perl (0.986-1) ... Setting up libeval-closure-perl (0.11-1) ... Setting up libclass-c3-perl (0.25-1) ... Setting up libmro-compat-perl (0.12-1) ... Setting up libpackage-deprecationmanager-perl (0.13-1) ... Setting up libpackage-stash-xs-perl (0.28-1) ... Setting up libsub-name-perl (0.05-1build4) ... Setting up libtask-weaken-perl (1.04-1) ... Setting up libmoose-perl (2.1005-1) ... Setting up libarray-compare-perl (2.02-1) ... Setting up libvariable-magic-perl (0.53-1) ... Setting up libb-hooks-endofscope-perl (0.13-1) ... Setting up libbio-asn1-entrezgene-perl (1.700-1) ... Setting up libcarp-clan-perl (6.04-1) ... Setting up libbit-vector-perl (7.3-1build1) ... Setting up libclass-c3-xs-perl (0.13-1build4) ... Setting up libclass-inspector-perl (1.28-1) ... Setting up libclass-tiny-perl (0.012-1) ... Setting up libclone-perl (0.36-1) ... Setting up libconvert-binary-c-perl (0.76-3build1) ... Setting up libconvert-binhex-perl (1.123-1) ... Setting up libcrypt-ssleay-perl (0.58-1build1) ... Setting up libdate-calc-perl (6.3-1) ... Setting up libdate-calc-xs-perl (6.3-1build1) ... Setting up libdate-manip-perl (6.42-1) ... Setting up libpadwalker-perl (1.98-1) ... Setting up libdevel-caller-perl (2.06-1build1) ... Setting up libdevel-lexalias-perl (0.05-1build1) ... Setting up libsub-identify-perl (0.04-1build3) ... Setting up libnamespace-clean-perl (0.24-1) ... Setting up libdevel-partialdump-perl (0.17-1) ... Setting up libfcgi-perl (0.74-1build2) ... Setting up libfreezethaw-perl (0.5001-1) ... Setting up libheap-perl (0.80-2) ... Setting up libgraph-perl (1:0.96-1.1) ... Setting up libio-pty-perl (1:1.08-1build4) ... Setting up libipc-run-perl (0.92-1) ... Setting up libxml-twig-perl (1:3.44-1) ... Setting up libxml-xpath-perl (1.13-7) ... Setting up libparse-recdescent-perl (1.967009+dfsg-1) ... Setting up libgraphviz-perl (2.14-1) ... Setting up libhtml-tableextract-perl (2.11-1) ... Setting up libio-sessiondata-perl (1.03-1) ... Setting up libio-stringy-perl (2.110-5) ... Setting up libjcode-pm-perl (2.06-1) ... Setting up libmath-derivative-perl (0.01-6) ... Setting up libmath-spline-perl (0.02-1) ... Setting up libmime-tools-perl (5.505-1) ... Setting up libmldbm-perl (2.05-1) ... Setting up libole-storage-lite-perl (0.19-1) ... Setting up libossp-uuid16 (1.6.2-1.3ubuntu1) ... Setting up libossp-uuid-perl (1.6.2-1.3ubuntu1) ... Setting up libpostscript-perl (0.06-2) ... Setting up libsoap-lite-perl (1.09-1) ... Setting up libsort-naturally-perl (1.02-1) ... Setting up libspreadsheet-writeexcel-perl (2.40-1) ... Setting up libunicode-map-perl (0.112-11) ... Setting up libspreadsheet-parseexcel-perl (0.5800-1) ... Setting up libstatistics-descriptive-perl (3.0605-1) ... Setting up libsvg-perl (2.59-1) ... Setting up libfile-slurp-perl (9999.19-4) ... Setting up libtree-dagnode-perl (1.17-1) ... Setting up libsvg-graph-perl (0.02-2) ... Setting up libtie-ixhash-perl (1.23-1) ... Setting up libxml-perl (0.08-2) ... Setting up libxml-regexp-perl (0.04-1) ... Setting up libxml-dom-perl (1.44-1) ... Setting up libxml-xpathengine-perl (0.13-1) ... Setting up libxml-dom-xpath-perl (0.14-1) ... Setting up libxml-namespacesupport-perl (1.11-1) ... Setting up libxml-sax-base-perl (1.07-1) ... Setting up libxml-sax-perl (0.99+dfsg-2ubuntu1) ... update-perl-sax-parsers: Non-vendor version of XML::SAX is installed. update-perl-sax-parsers: Automatic registration of SAX parsers might not work. update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::PurePerl with priority 10... update-perl-sax-parsers: Non-vendor version of XML::SAX is installed. update-perl-sax-parsers: Automatic registration of SAX parsers might not work. update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... debconf: unable to initialize frontend: Dialog debconf: (TERM is not set, so the dialog frontend is not usable.) debconf: falling back to frontend: Readline debconf: unable to initialize frontend: Readline debconf: (This frontend requires a controlling tty.) debconf: falling back to frontend: Teletype Creating config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libxml-filter-buffertext-perl (1.01-5) ... Setting up libxml-libxml-perl (2.0108+dfsg-1ubuntu0.2) ... update-perl-sax-parsers: Non-vendor version of XML::SAX is installed. update-perl-sax-parsers: Automatic registration of SAX parsers might not work. update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX::Parser with priority 50... update-perl-sax-parsers: Non-vendor version of XML::SAX is installed. update-perl-sax-parsers: Automatic registration of SAX parsers might not work. update-perl-sax-parsers: Registering Perl SAX parser XML::LibXML::SAX with priority 50... update-perl-sax-parsers: Non-vendor version of XML::SAX is installed. update-perl-sax-parsers: Automatic registration of SAX parsers might not work. update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... debconf: unable to initialize frontend: Dialog debconf: (TERM is not set, so the dialog frontend is not usable.) debconf: falling back to frontend: Readline debconf: unable to initialize frontend: Readline debconf: (This frontend requires a controlling tty.) debconf: falling back to frontend: Teletype Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libxml-libxslt-perl (1.84-1) ... Setting up libxml-sax-expat-perl (0.40-2) ... update-perl-sax-parsers: Non-vendor version of XML::SAX is installed. update-perl-sax-parsers: Automatic registration of SAX parsers might not work. update-perl-sax-parsers: Registering Perl SAX parser XML::SAX::Expat with priority 50... update-perl-sax-parsers: Non-vendor version of XML::SAX is installed. update-perl-sax-parsers: Automatic registration of SAX parsers might not work. update-perl-sax-parsers: Updating overall Perl SAX parser modules info file... debconf: unable to initialize frontend: Dialog debconf: (TERM is not set, so the dialog frontend is not usable.) debconf: falling back to frontend: Readline debconf: unable to initialize frontend: Readline debconf: (This frontend requires a controlling tty.) debconf: falling back to frontend: Teletype Replacing config file /etc/perl/XML/SAX/ParserDetails.ini with new version Setting up libxml-sax-writer-perl (0.53-1) ... Setting up libxml-simple-perl (2.20-1) ... Setting up libxml-writer-perl (0.623-1) ... Setting up libxmlrpc-lite-perl (0.717-1) ... Setting up libyaml-libyaml-perl (0.41-5ubuntu0.14.04.1) ... Setting up libyaml-perl (0.84-1) ... Setting up mafft (7.123-1) ...

Comments

  • Jit
    Jit 1677 days ago


    Setting up mafft (7.123-1) ...
    Setting up maq (0.7.1-5) ...
    Setting up muscle (1:3.8.31-1) ...
    Setting up perl-doc (5.18.2-2ubuntu1.7) ...
    Setting up perl-tk (1:804.031-1build1) ...
    Setting up phyml (2:20120412-2) ...
    Setting up primer3 (2.3.6-1) ...
    Setting up probalign (1.4-3) ...
    Setting up probcons (1.12-9) ...
    Setting up samtools (0.1.19-1) ...
    Setting up sim4 (0.0.20121010-1) ...
    Setting up t-coffee (10.00.r1613-1) ...
    Setting up tigr-glimmer (3.02-3) ...
    Setting up tm-align (20130511+dfsg-1) ...
    Setting up bowtie (1.0.0-5) ...
    Setting up hmmer (3.1b1-3) ...
    Setting up libbsd-resource-perl (1.2907-1build1) ...
    Setting up libgd-gd2-perl (1:2.46-3.1build1) ...
    Setting up libset-scalar-perl (1.27-1) ...
    Setting up lynx-cur (2.8.8pre4-1) ...
    update-alternatives: using /usr/bin/lynx to provide /usr/bin/www-browser (www-browser) in auto mode
    Setting up lynx (2.8.8pre4-1) ...
    Setting up ruby (1:1.9.3.4) ...
    Setting up ruby1.9.1 (1.9.3.484-2ubuntu1.14) ...
    Setting up libruby1.9.1 (1.9.3.484-2ubuntu1.14) ...
    Processing triggers for libc-bin (2.19-0ubuntu6.14) ...
    Reading package lists...
    Building dependency tree...
    Reading state information...
    The following NEW packages will be installed:
      libstatistics-distributions-perl
    0 upgraded, 1 newly installed, 0 to remove and 50 not upgraded.
    Need to get 9994 B of archives.
    After this operation, 70.7 kB of additional disk space will be used.
    Get:1 http://archive.ubuntu.com/ubuntu/ trusty/universe libstatistics-distributions-perl all 1.02-1 [9994 B]
    debconf: unable to initialize frontend: Dialog
    debconf: (TERM is not set, so the dialog frontend is not usable.)
    debconf: falling back to frontend: Readline
    debconf: unable to initialize frontend: Readline
    debconf: (This frontend requires a controlling tty.)
    debconf: falling back to frontend: Teletype
    dpkg-preconfigure: unable to re-open stdin:
    Fetched 9994 B in 1s (8676 B/s)
    Selecting previously unselected package libstatistics-distributions-perl.
    (Reading database ... 43981 files and directories currently installed.)
    Preparing to unpack .../libstatistics-distributions-perl_1.02-1_all.deb ...
    Unpacking libstatistics-distributions-perl (1.02-1) ...
    Processing triggers for man-db (2.6.7.1-1ubuntu1) ...
    Setting up libstatistics-distributions-perl (1.02-1) ...
    Reading package lists...
    Building dependency tree...
    Reading state information...
    The following extra packages will be installed:
      libclass-methodmaker-perl libio-interactive-perl libsub-uplevel-perl
      libterm-progressbar-perl libterm-progressbar-quiet-perl libterm-readkey-perl
      libtest-exception-perl libtest-mockobject-perl libtest-warn-perl
      libuniversal-can-perl libuniversal-isa-perl
    The following NEW packages will be installed:
      libclass-methodmaker-perl libio-interactive-perl libsub-uplevel-perl
      libterm-progressbar-perl libterm-progressbar-quiet-perl
      libterm-progressbar-simple-perl libterm-readkey-perl libtest-exception-perl
      libtest-mockobject-perl libtest-warn-perl libuniversal-can-perl
      libuniversal-isa-perl
    0 upgraded, 12 newly installed, 0 to remove and 50 not upgraded.
    Need to get 365 kB of archives.
    After this operation, 22.3 MB of additional disk space will be used.
    Get:1 http://archive.ubuntu.com/ubuntu/ trusty/universe libclass-methodmaker-perl amd64 2.19-1 [201 kB]
    Get:2 http://archive.ubuntu.com/ubuntu/ trusty/universe libio-interactive-perl all 0.0.6-1 [10.6 kB]
    Get:3 http://archive.ubuntu.com/ubuntu/ trusty/main libsub-uplevel-perl all 0.2400-1 [13.8 kB]
    Get:4 http://archive.ubuntu.com/ubuntu/ trusty/main libterm-readkey-perl amd64 2.31-1 [27.4 kB]
    Get:5 http://archive.ubuntu.com/ubuntu/ trusty/universe libterm-progressbar-perl all 2.14-1 [21.4 kB]
    Get:6 http://archive.ubuntu.com/ubuntu/ trusty/main libtest-exception-perl all 0.32-1 [16.0 kB]
    Get:7 http://archive.ubuntu.com/ubuntu/ trusty/main libtest-warn-perl all 0.24-1 [14.8 kB]
    Get:8 http://archive.ubuntu.com/ubuntu/ trusty/universe libuniversal-isa-perl all 1.20120726-1 [8714 B]
    Get:9 http://archive.ubuntu.com/ubuntu/ trusty/universe libuniversal-can-perl all 1.20140124-1 [11.8 kB]
    Get:10 http://archive.ubuntu.com/ubuntu/ trusty/universe libtest-mockobject-perl all 1.20120301-1 [26.9 kB]
    Get:11 http://archive.ubuntu.com/ubuntu/ trusty/universe libterm-progressbar-quiet-perl all 0.31-1 [4994 B]
    Get:12 http://archive.ubuntu.com/ubuntu/ trusty/universe libterm-progressbar-simple-perl all 0.03-1 [7654 B]
    debconf: unable to initialize frontend: Dialog
    debconf: (TERM is not set, so the dialog frontend is not usable.)
    debconf: falling back to frontend: Readline
    debconf: unable to initialize frontend: Readline
    debconf: (This frontend requires a controlling tty.)
    debconf: falling back to frontend: Teletype
    dpkg-preconfigure: unable to re-open stdin:
    Fetched 365 kB in 16s (21.5 kB/s)
    Selecting previously unselected package libclass-methodmaker-perl.
    (Reading database ... 43989 files and directories currently installed.)
    Preparing to unpack .../libclass-methodmaker-perl_2.19-1_amd64.deb ...
    Unpacking libclass-methodmaker-perl (2.19-1) ...
    Selecting previously unselected package libio-interactive-perl.
    Preparing to unpack .../libio-interactive-perl_0.0.6-1_all.deb ...
    Unpacking libio-interactive-perl (0.0.6-1) ...
    Selecting previously unselected package libsub-uplevel-perl.
    Preparing to unpack .../libsub-uplevel-perl_0.2400-1_all.deb ...
    Unpacking libsub-uplevel-perl (0.2400-1) ...
    Selecting previously unselected package libterm-readkey-perl.
    Preparing to unpack .../libterm-readkey-perl_2.31-1_amd64.deb ...
    Unpacking libterm-readkey-perl (2.31-1) ...
    Selecting previously unselected package libterm-progressbar-perl.
    Preparing to unpack .../libterm-progressbar-perl_2.14-1_all.deb ...
    Unpacking libterm-progressbar-perl (2.14-1) ...
    Selecting previously unselected package libtest-exception-perl.
    Preparing to unpack .../libtest-exception-perl_0.32-1_all.deb ...
    Unpacking libtest-exception-perl (0.32-1) ...
    Selecting previously unselected package libtest-warn-perl.
    Preparing to unpack .../libtest-warn-perl_0.24-1_all.deb ...
    Unpacking libtest-warn-perl (0.24-1) ...
    Selecting previously unselected package libuniversal-isa-perl.
    Preparing to unpack .../libuniversal-isa-perl_1.20120726-1_all.deb ...
    Unpacking libuniversal-isa-perl (1.20120726-1) ...
    Selecting previously unselected package libuniversal-can-perl.
    Preparing to unpack .../libuniversal-can-perl_1.20140124-1_all.deb ...
    Unpacking libuniversal-can-perl (1.20140124-1) ...
    Selecting previously unselected package libtest-mockobject-perl.
    Preparing to unpack .../libtest-mockobject-perl_1.20120301-1_all.deb ...
    Unpacking libtest-mockobject-perl (1.20120301-1) ...
    Selecting previously unselected package libterm-progressbar-quiet-perl.
    Preparing to unpack .../libterm-progressbar-quiet-perl_0.31-1_all.deb ...
    Unpacking libterm-progressbar-quiet-perl (0.31-1) ...
    Selecting previously unselected package libterm-progressbar-simple-perl.
    Preparing to unpack .../libterm-progressbar-simple-perl_0.03-1_all.deb ...
    Unpacking libterm-progressbar-simple-perl (0.03-1) ...
    Processing triggers for man-db (2.6.7.1-1ubuntu1) ...
    Setting up libclass-methodmaker-perl (2.19-1) ...
    Setting up libio-interactive-perl (0.0.6-1) ...
    Setting up libsub-uplevel-perl (0.2400-1) ...
    Setting up libterm-readkey-perl (2.31-1) ...
    Setting up libterm-progressbar-perl (2.14-1) ...
    Setting up libtest-exception-perl (0.32-1) ...
    Setting up libtest-warn-perl (0.24-1) ...
    Setting up libuniversal-isa-perl (1.20120726-1) ...
    Setting up libuniversal-can-perl (1.20140124-1) ...
    Setting up libtest-mockobject-perl (1.20120301-1) ...
    Setting up libterm-progressbar-quiet-perl (0.31-1) ...
    Setting up libterm-progressbar-simple-perl (0.03-1) ...
    Reading package lists...
    Building dependency tree...
    Reading state information...
    The following extra packages will be installed:
      libstaden-read1
    The following NEW packages will be installed:
      libbio-scf-perl libstaden-read1
    0 upgraded, 2 newly installed, 0 to remove and 50 not upgraded.
    Need to get 205 kB of archives.
    After this operation, 620 kB of additional disk space will be used.
    Get:1 http://archive.ubuntu.com/ubuntu/ trusty/universe libstaden-read1 amd64 1.13.5-1.1 [182 kB]
    Get:2 http://archive.ubuntu.com/ubuntu/ trusty/universe libbio-scf-perl amd64 1.03-1build4 [23.3 kB]
    debconf: unable to initialize frontend: Dialog
    debconf: (TERM is not set, so the dialog frontend is not usable.)
    debconf: falling back to frontend: Readline
    debconf: unable to initialize frontend: Readline
    debconf: (This frontend requires a controlling tty.)
    debconf: falling back to frontend: Teletype
    dpkg-preconfigure: unable to re-open stdin:
    Fetched 205 kB in 6s (33.0 kB/s)
    Selecting previously unselected package libstaden-read1.
    (Reading database ... 44971 files and directories currently installed.)
    Preparing to unpack .../libstaden-read1_1.13.5-1.1_amd64.deb ...
    Unpacking libstaden-read1 (1.13.5-1.1) ...
    Selecting previously unselected package libbio-scf-perl.
    Preparing to unpack .../libbio-scf-perl_1.03-1build4_amd64.deb ...
    Unpacking libbio-scf-perl (1.03-1build4) ...
    Processing triggers for man-db (2.6.7.1-1ubuntu1) ...
    Setting up libstaden-read1 (1.13.5-1.1) ...
    Setting up libbio-scf-perl (1.03-1build4) ...
    Processing triggers for libc-bin (2.19-0ubuntu6.14) ...
    Removing intermediate container 7adc9dbdb955
     ---> 1ca0a9d66656
    Step 13/16 : RUN apt-get install -y curl &&     cpan install App::cpanminus
     ---> Running in aabe5835266c
    Reading package lists...
    Building dependency tree...
    Reading state information...
    The following extra packages will be installed:
      libcurl3
    The following packages will be upgraded:
      curl libcurl3
    2 upgraded, 0 newly installed, 0 to remove and 48 not upgraded.
    Need to get 297 kB of archives.
    After this operation, 0 B of additional disk space will be used.
    Get:1 http://archive.ubuntu.com/ubuntu/ trusty-updates/main curl amd64 7.35.0-1ubuntu2.20 [123 kB]
    Get:2 http://archive.ubuntu.com/ubuntu/ trusty-updates/main libcurl3 amd64 7.35.0-1ubuntu2.20 [173 kB]
    debconf: unable to initialize frontend: Dialog
    debconf: (TERM is not set, so the dialog frontend is not usable.)
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    debconf: unable to initialize frontend: Readline
    debconf: (This frontend requires a controlling tty.)
    debconf: falling back to frontend: Teletype
    dpkg-preconfigure: unable to re-open stdin:
    Fetched 297 kB in 11s (26.2 kB/s)
    (Reading database ... 44993 files and directories currently installed.)
    Preparing to unpack .../curl_7.35.0-1ubuntu2.20_amd64.deb ...
    Unpacking curl (7.35.0-1ubuntu2.20) over (7.35.0-1ubuntu2.17) ...
    Preparing to unpack .../libcurl3_7.35.0-1ubuntu2.20_amd64.deb ...
    Unpacking libcurl3:amd64 (7.35.0-1ubuntu2.20) over (7.35.0-1ubuntu2.17) ...
    Processing triggers for man-db (2.6.7.1-1ubuntu1) ...
    Setting up libcurl3:amd64 (7.35.0-1ubuntu2.20) ...
    Setting up curl (7.35.0-1ubuntu2.20) ...
    Processing triggers for libc-bin (2.19-0ubuntu6.14) ...

    CPAN.pm requires configuration, but most of it can be done automatically.
    If you answer 'no' below, you will enter an interactive dialog for each
    configuration option instead.

    Would you like to configure as much as possible automatically? [yes] yes

    Would you like me to automatically choose some CPAN mirror
    sites for you? (This means connecting to the Internet) [yes] yes
    Fetching with LWP:
    http://espejito.fder.edu.uy/cpan/authors/01mailrc.txt.gz
    Reading '/root/.cpan/sources/authors/01mailrc.txt.gz'
    ............................................................................DONE
    Fetching with LWP:
    http://espejito.fder.edu.uy/cpan/modules/02packages.details.txt.gz
    Reading '/root/.cpan/sources/modules/02packages.details.txt.gz'
      Database was generated on Sun, 24 May 2020 12:41:03 GMT
    .............
      New CPAN.pm version (v2.27) available.
      [Currently running version is v2.00]
      You might want to try
        install CPAN
        reload cpan
      to both upgrade CPAN.pm and run the new version without leaving
      the current session.


    ...............................................................DONE
    Fetching with LWP:
    http://espejito.fder.edu.uy/cpan/modules/03modlist.data.gz
    Reading '/root/.cpan/sources/modules/03modlist.data.gz'
    DONE
    Writing /root/.cpan/Metadata
    Running install for module 'App::cpanminus'
    Running make for M/MI/MIYAGAWA/App-cpanminus-1.7044.tar.gz
    Fetching with LWP:
    http://espejito.fder.edu.uy/cpan/authors/id/M/MI/MIYAGAWA/App-cpanminus-1.7044.tar.gz
    Fetching with LWP:
    http://espejito.fder.edu.uy/cpan/authors/id/M/MI/MIYAGAWA/CHECKSUMS
    Checksum for /root/.cpan/sources/authors/id/M/MI/MIYAGAWA/App-cpanminus-1.7044.tar.gz ok

      CPAN.pm: Building M/MI/MIYAGAWA/App-cpanminus-1.7044.tar.gz

    Checking if your kit is complete...
    Looks good
    Generating a Unix-style Makefile
    Writing Makefile for App::cpanminus
    Writing MYMETA.yml and MYMETA.json
    cp lib/App/cpanminus.pm blib/lib/App/cpanminus.pm
    cp lib/App/cpanminus/fatscript.pm blib/lib/App/cpanminus/fatscript.pm
    cp bin/cpanm blib/script/cpanm
    "/usr/bin/perl" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/cpanm
    Manifying 1 pod document
    Manifying 2 pod documents
      MIYAGAWA/App-cpanminus-1.7044.tar.gz
      /usr/bin/make -- OK
    Running make test
    PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
    # App::cpanminus/1.7044
    t/happy_cpantesters.t .. ok
    All tests successful.
    Files=1, Tests=1,  1 wallclock secs ( 0.02 usr  0.01 sys +  0.08 cusr  0.01 csys =  0.12 CPU)
    Result: PASS
      MIYAGAWA/App-cpanminus-1.7044.tar.gz
      /usr/bin/make test -- OK
    Running make install
    Manifying 1 pod document
    Manifying 2 pod documents
    Installing /usr/local/share/perl/5.18.2/App/cpanminus.pm
    Installing /usr/local/share/perl/5.18.2/App/cpanminus/fatscript.pm
    Installing /usr/local/man/man1/cpanm.1p
    Installing /usr/local/man/man3/App::cpanminus.3pm
    Installing /usr/local/man/man3/App::cpanminus::fatscript.3pm
    Installing /usr/local/bin/cpanm
    Appending installation info to /usr/lib/perl/5.18/perllocal.pod
      MIYAGAWA/App-cpanminus-1.7044.tar.gz
      /usr/bin/make install  -- OK
    Removing intermediate container aabe5835266c
     ---> 2efe9777690b
    Step 14/16 : RUN cpanm install File::chdir &&     cpanm install lib::abs &&     cpanm install File::Remove &&     cpanm install Spreadsheet::Read &&     cpanm install Statistics::ChiSquare &&     cpan install Text::CSV
     ---> Running in 89e48c724c49
    --> Working on install
    Fetching http://www.cpan.org/authors/id/D/DA/DAGOLDEN/install-0.01.tar.gz ... OK
    Configuring install-0.01 ... OK
    Building and testing install-0.01 ... OK
    Successfully installed install-0.01
    --> Working on File::chdir
    Fetching http://www.cpan.org/authors/id/D/DA/DAGOLDEN/File-chdir-0.1010.tar.gz ... OK
    Configuring File-chdir-0.1010 ... OK
    Building and testing File-chdir-0.1010 ... OK
    Successfully installed File-chdir-0.1010
    2 distributions installed
    install is up to date. (0.01)
    --> Working on lib::abs
    Fetching http://www.cpan.org/authors/id/M/MO/MONS/lib-abs-0.95.tar.gz ... OK
    Configuring lib-abs-0.95 ... OK
    Building and testing lib-abs-0.95 ... OK
    Successfully installed lib-abs-0.95
    1 distribution installed
    install is up to date. (0.01)
    --> Working on File::Remove
    Fetching http://www.cpan.org/authors/id/S/SH/SHLOMIF/File-Remove-1.58.tar.gz ... OK
    Configuring File-Remove-1.58 ... OK
    Building and testing File-Remove-1.58 ... OK
    Successfully installed File-Remove-1.58
    1 distribution installed
    install is up to date. (0.01)
    --> Working on Spreadsheet::Read
    Fetching http://www.cpan.org/authors/id/H/HM/HMBRAND/Spreadsheet-Read-0.81.tgz ... OK
    Configuring Spreadsheet-Read-0.81 ... OK
    Building and testing Spreadsheet-Read-0.81 ... OK
    Successfully installed Spreadsheet-Read-0.81
    1 distribution installed
    install is up to date. (0.01)
    --> Working on Statistics::ChiSquare
    Fetching http://www.cpan.org/authors/id/D/DC/DCANTRELL/Statistics-ChiSquare-1.0000.tar.gz ... OK
    Configuring Statistics-ChiSquare-1.0000 ... OK
    Building and testing Statistics-ChiSquare-1.0000 ... OK
    Successfully installed Statistics-ChiSquare-1.0000
    1 distribution installed
    Reading '/root/.cpan/Metadata'
      Database was generated on Sun, 24 May 2020 12:41:03 GMT
    Running install for module 'Text::CSV'
    Running make for I/IS/ISHIGAKI/Text-CSV-2.00.tar.gz
    Fetching with LWP:
    http://espejito.fder.edu.uy/cpan/authors/id/I/IS/ISHIGAKI/Text-CSV-2.00.tar.gz
    Fetching with LWP:
    http://espejito.fder.edu.uy/cpan/authors/id/I/IS/ISHIGAKI/CHECKSUMS
    Checksum for /root/.cpan/sources/authors/id/I/IS/ISHIGAKI/Text-CSV-2.00.tar.gz ok

      CPAN.pm: Building I/IS/ISHIGAKI/Text-CSV-2.00.tar.gz

    Welcome to Text::CSV (v.2.00)
    =============================
    If you install Text::CSV_XS v.1.02, it makes Text::CSV faster.

    Checking if your kit is complete...
    Looks good
    Generating a Unix-style Makefile
    Writing Makefile for Text::CSV
    Writing MYMETA.yml and MYMETA.json
    cp lib/Text/CSV_PP.pm blib/lib/Text/CSV_PP.pm
    cp lib/Text/CSV.pm blib/lib/Text/CSV.pm
    Manifying 2 pod documents
      ISHIGAKI/Text-CSV-2.00.tar.gz
      /usr/bin/make -- OK
    Running make test
    PERL_DL_NONLAZY=1 "/usr/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
    # PERL_TEXT_CSV: undef
    t/00_pod.t ............... ok
    t/01_is_pp.t ............. ok
    t/10_base.t .............. ok
    t/12_acc.t ............... ok
    t/15_flags.t ............. ok
    t/20_file.t .............. ok
    t/21_lexicalio.t ......... ok
    t/22_scalario.t .......... ok
    t/30_types.t ............. ok
    t/40_misc.t .............. ok
    t/41_null.t .............. ok
    t/45_eol.t ............... ok
    t/46_eol_si.t ............ ok
    t/50_utf8.t .............. ok
    t/51_utf8.t .............. ok
    t/55_combi.t ............. ok
    t/60_samples.t ........... ok
    t/65_allow.t ............. ok
    t/66_formula.t ........... ok
    t/70_rt.t ................ ok
    t/71_pp.t ................ ok
    t/75_hashref.t ........... ok
    t/76_magic.t ............. ok
    t/77_getall.t ............ ok
    t/78_fragment.t .......... ok
    t/79_callbacks.t ......... ok
    t/80_diag.t .............. ok
    t/81_subclass.t .......... ok
    t/85_util.t .............. ok
    t/90_csv.t ............... ok
    t/91_csv_cb.t ............ ok
    t/fields_containing_0.t .. ok
    t/rt99774.t .............. ok
    All tests successful.
    Files=33, Tests=52231, 55 wallclock secs ( 6.84 usr  0.67 sys + 52.86 cusr  0.66 csys = 61.03 CPU)
    Result: PASS
      ISHIGAKI/Text-CSV-2.00.tar.gz
      /usr/bin/make test -- OK
    Running make install
    Manifying 2 pod documents
    Installing /usr/local/share/perl/5.18.2/Text/CSV_PP.pm
    Installing /usr/local/share/perl/5.18.2/Text/CSV.pm
    Installing /usr/local/man/man3/Text::CSV_PP.3pm
    Installing /usr/local/man/man3/Text::CSV.3pm
    Appending installation info to /usr/lib/perl/5.18/perllocal.pod
      ISHIGAKI/Text-CSV-2.00.tar.gz
      /usr/bin/make install  -- OK
    Removing intermediate container 89e48c724c49
     ---> d2beb40936da
    Step 15/16 : WORKDIR home/
     ---> Running in 1e23f559d32f
    Removing intermediate container 1e23f559d32f
     ---> 7917546826a5
    Step 16/16 : COPY autoConTAMPR home/autoConTAMPR
     ---> ddbd36883355
    Successfully built ddbd36883355
    Successfully tagged autocontampr:latest

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