211 lines
11 KiB
Text
211 lines
11 KiB
Text
perl-blead
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==========
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cpanm (App::cpanminus) 1.7043 on perl 5.026000 built for x86_64-linux
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Work directory is /home/ryan/.cpanm/work/1493530396.5142
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You have make /usr/bin/make
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You have LWP 6.26
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You have /bin/tar: tar (GNU tar) 1.29
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Copyright (C) 2015 Free Software Foundation, Inc.
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License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>.
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This is free software: you are free to change and redistribute it.
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There is NO WARRANTY, to the extent permitted by law.
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Written by John Gilmore and Jay Fenlason.
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You have /usr/bin/unzip
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Searching Bio::GeneDesign::Exceptions () on cpanmetadb ...
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Unpacking Bio-GeneDesign-5.52.tar.gz
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--> Working on Bio::GeneDesign::Exceptions
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Fetching http://www.cpan.org/authors/id/N/NO/NOTDOCTOR/Bio-GeneDesign-5.52.tar.gz ... OK
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Bio-GeneDesign-5.52
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Bio-GeneDesign-5.52/Build.PL
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Bio-GeneDesign-5.52/Changes
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Bio-GeneDesign-5.52/Makefile.PL
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Bio-GeneDesign-5.52/MANIFEST
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Bio-GeneDesign-5.52/META.json
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Bio-GeneDesign-5.52/META.yml
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Bio-GeneDesign-5.52/README
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Bio-GeneDesign-5.52/ToDo
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Bio-GeneDesign-5.52/bin
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Bio-GeneDesign-5.52/bin/GD_Filter_Enzymes.pl
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Bio-GeneDesign-5.52/bin/GD_Generate_RSCU_Table.pl
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Bio-GeneDesign-5.52/bin/GD_Graph_Dotplot.pl
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Bio-GeneDesign-5.52/bin/GD_Graph_RSCU_Values.pl
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Bio-GeneDesign-5.52/bin/GD_Juggle_Codons.pl
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Bio-GeneDesign-5.52/bin/GD_Reverse_Translate.pl
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Bio-GeneDesign-5.52/bin/GD_Sequence_Subtraction.pl
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Bio-GeneDesign-5.52/codon_tables
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Bio-GeneDesign-5.52/codon_tables/arabidopsis_thaliana.rscu
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Bio-GeneDesign-5.52/codon_tables/Bacillus_subtilis.rscu
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Bio-GeneDesign-5.52/codon_tables/Caenorhabditis_elegans.rscu
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Bio-GeneDesign-5.52/codon_tables/Cglut.rscu
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Bio-GeneDesign-5.52/codon_tables/Deinococcus_radiodurans.rscu
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Bio-GeneDesign-5.52/codon_tables/Drosophila_melanogaster.rscu
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Bio-GeneDesign-5.52/codon_tables/Escherichia_coli.rscu
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Bio-GeneDesign-5.52/codon_tables/Flat.rscu
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Bio-GeneDesign-5.52/codon_tables/Homo_sapiens.rscu
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Bio-GeneDesign-5.52/codon_tables/Mycoplasma_genitalium.ct
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Bio-GeneDesign-5.52/codon_tables/Mycoplasma_genitalium.rscu
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Bio-GeneDesign-5.52/codon_tables/oryza_sativa.rscu
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Bio-GeneDesign-5.52/codon_tables/Saccharomyces_cerevisiae.rscu
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Bio-GeneDesign-5.52/codon_tables/Standard.ct
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Bio-GeneDesign-5.52/codon_tables/yeast.rscu
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Bio-GeneDesign-5.52/enzymes
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Bio-GeneDesign-5.52/enzymes/all_enzymes
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Bio-GeneDesign-5.52/enzymes/blunts
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Bio-GeneDesign-5.52/enzymes/IIB
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Bio-GeneDesign-5.52/enzymes/nonpal
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Bio-GeneDesign-5.52/enzymes/nonpal_and_IIB
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Bio-GeneDesign-5.52/enzymes/nonpal_short
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Bio-GeneDesign-5.52/enzymes/outside
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Bio-GeneDesign-5.52/enzymes/standard
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Bio-GeneDesign-5.52/enzymes/standard_and_IIB
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Bio-GeneDesign-5.52/enzymes/test
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Bio-GeneDesign-5.52/lib
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Bio-GeneDesign-5.52/lib/Bio
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Bio-GeneDesign-5.52/lib/Bio/GeneDesign.pm
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Bio-GeneDesign-5.52/lib/Bio/GeneDesign
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Bio-GeneDesign-5.52/lib/Bio/GeneDesign/Basic.pm
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Bio-GeneDesign-5.52/lib/Bio/GeneDesign/CodonJuggle.pm
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Bio-GeneDesign-5.52/lib/Bio/GeneDesign/Codons.pm
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Bio-GeneDesign-5.52/lib/Bio/GeneDesign/Exceptions.pm
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Bio-GeneDesign-5.52/lib/Bio/GeneDesign/Graph.pm
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Bio-GeneDesign-5.52/lib/Bio/GeneDesign/Oligo.pm
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Bio-GeneDesign-5.52/lib/Bio/GeneDesign/PrefixTree.pm
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Bio-GeneDesign-5.52/lib/Bio/GeneDesign/Random.pm
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Bio-GeneDesign-5.52/lib/Bio/GeneDesign/RestrictionEnzyme.pm
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Bio-GeneDesign-5.52/lib/Bio/GeneDesign/RestrictionEnzymes.pm
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Bio-GeneDesign-5.52/lib/Bio/GeneDesign/ReverseTranslate.pm
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Bio-GeneDesign-5.52/t
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Bio-GeneDesign-5.52/t/00-load.t
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Bio-GeneDesign-5.52/t/10-basic.t
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Bio-GeneDesign-5.52/t/12-io.t
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Bio-GeneDesign-5.52/t/15-codons.t
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Bio-GeneDesign-5.52/t/20-reverse_translate.t
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Bio-GeneDesign-5.52/t/25-codon_juggle.t
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Bio-GeneDesign-5.52/t/30-enzymes.t
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Bio-GeneDesign-5.52/t/35-subtract_sequence.t
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Bio-GeneDesign-5.52/t/40-graph.t
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Bio-GeneDesign-5.52/t/60-prefix.t
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Bio-GeneDesign-5.52/t/65-random.t
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Bio-GeneDesign-5.52/t/boilerplate.t
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Bio-GeneDesign-5.52/t/manifest.t
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Bio-GeneDesign-5.52/t/pod-coverage.t
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Bio-GeneDesign-5.52/t/pod.t
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Bio-GeneDesign-5.52/t/testagene.fasta
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Bio-GeneDesign-5.52/t/testr_GRV_yeast.gif
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Entering Bio-GeneDesign-5.52
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Checking configure dependencies from META.json
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Checking if you have Module::Build 0.38 ... Yes (0.4222)
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Checking if you have ExtUtils::Install 1.46 ... Yes (2.04)
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Running Build.PL
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Configuring Bio-GeneDesign-5.52 ...
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Where should configuration files be installed? [/etc/GeneDesign/ ]/etc/GeneDesign/
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Where should scripts be installed? [/usr/local/bin ]/usr/local/bin
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Where should GeneDesign write tmp files? [/tmp ]/tmp
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Enable GD::Graphics support? [Y ]Y
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Configuration files will be in /etc/GeneDesign/
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Scripts will be in /usr/local/bin
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Temporary files will be written to /tmp
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Created MYMETA.yml and MYMETA.json
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Creating new 'Build' script for 'Bio-GeneDesign' version '5.52'
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Checking dependencies from MYMETA.json ...
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Checking if you have Bio::Root::Root 0 ... Yes (undef)
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Checking if you have Math::Combinatorics 0.09 ... Yes (0.09)
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Checking if you have Test::Deep 0.1 ... Yes (1.126)
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Checking if you have Exception::Class 0 ... Yes (1.42)
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Checking if you have Test::More 0.8 ... Yes (1.302083)
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Checking if you have List::Util 1.22 ... Yes (1.47)
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Checking if you have Text::Wrap 2009.0305 ... Yes (2013.0523)
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OK
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Building and testing Bio-GeneDesign-5.52 ... Building Bio-GeneDesign
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t/00-load.t ............... ok
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t/10-basic.t .............. ok
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t/12-io.t ................. ok
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# Failed test 'reverse codon table'
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# at t/15-codons.t line 70.
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# Structures begin differing at:
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# $got->{F}[0] = 'TTC'
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# $expected->{F}[0] = 'TTT'
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# Looks like you failed 1 test of 9.
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t/15-codons.t .............
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Dubious, test returned 1 (wstat 256, 0x100)
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Failed 1/9 subtests
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t/20-reverse_translate.t .. ok
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# Failed test 'codon juggle most different sequence'
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# at t/25-codon_juggle.t line 68.
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# got: 'ATGGATCGCAGCTGGAAACAAAAATTAAATAGAGATACGGTCAAATTAACGGAAGTCATGACGTGGCGCCGCCCAGCGGCAAAGTGGTTCTACACGCTTATAAACGCAAACTACCTTCCTCCTTGTCCTCCAGATCATCAGGACCATAGACAACAGCAGTTGCCAGAACCAGACCAACCAGAGCACCAGAGACCAGAGCAACCACACCAGGCCGCCCCTCCAGATAGGTTAGCAGCCCAGGCCGGCCCACATTTGTTACTTCCACCTGGCGATCCTCCAGCCAGGGAGGGCCCTGCCTTGCCAGCCGGGGAGGGCTTAGAGGATCACTTGAGTGGGCAGAGACCAGAGGAGGCCGGGTGGAGGGGGCACCCAGACCAAAGGCAGGACAGGTTGCCTGCGCAGGGGGACCAGGAGGGCCAGGGCGGCCCTTTGCACCCAGACCAGGGCCAGGACCCAGCCGGCGGCGCAGAACACAGCGAGCACTTGAGACCACAGAGACCTAGAAGACATTTGCACCAGGGCCATCCAAGGGAGGCAGAGGGGCCTCACAGAAGTCCTCATCACCACAGGAGAAGGCCAGAGCATCCACCAGAACAA'
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# expected: 'ATGGATCGCAGCTGGAAACAAAAATTAAATAGAGATACGGTCAAATTAACGGAAGTCATGACGTGGCGCCGCCCAGCGGCAAAGTGGTTCTACACGCTTATAAACGCAAACTACCTTCCTCCTTGTCCTCCAGATCATCAGGACCATAGACAACAGCAGTTGCCAGAACCAGACCAACCAGAGCACCAGAGACCAGAGCAACCACACCAGGCCGCCCCTCCAGATAGGTTAGCAGCCCAGGCCGGCCCACATTTGTTACTTCCACCTGGCGATCCTCCAGCCAGGGAGGGCCCTGCCTTGCCAGCCGGGGAGGGCTTAGAGGATCACTTGAGTGGGCAGAGACCAGAGGAGGCCGGGTGGAGAGGGCACCCAGACCAAAGGCAGGACAGGTTGCCTGCGCAGGGGGACCAGGAGGGCCAGGGCGGCCCTTTGCACCCAGACCAGGGCCAGGACCCAGCCGGCGGCGCAGAACACAGCGAGCACTTGAGACCACAGAGACCTAGAAGACATTTGCACCAGGGCCATCCAAGAGAGGCAGAGGGGCCTCACAGAAGTCCTCATCACCACAGAAGAAGGCCAGAGCATCCACCAGAACAA'
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# Failed test 'codon juggle least different rscu'
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# at t/25-codon_juggle.t line 87.
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# got: 'ATGGATAGGTCCTGGAAGCAGAAGCTGAACCGCGATACTGTCAAGCTGACTGAGGTCATGACTTGGAGGAGGCCTGCGGCAAAATGGTTTTATACCTTGATAAATGCAAATTATTTACCTCCTTGTCCTCCTGATCACCAAGACCACAGGCAGCAACAATTACCCGAGCCCGACCAGCCCGAACATCAAAGGCCCGAACAGCCTCATCAAGCAGCGCCGCCCGATAGGCTGGCAGCGCAAGCGGGGCCTCACCTCCTGTTACCCCCTGGGGATCCTCCCGCAAGGGAAGGGCCGGCGTTACCCGCAGGCGAAGGACTGGAAGATCATCTCTCGGGTCAAAGGCCCGAAGAAGCGGGTTGGCGTGGTCATCCCGACCAGAGGCAAGACAGGCTCCCTGCGCAAGGCGACCAAGAAGGGCAAGGGGGACCTCTCCATCCCGACCAAGGACAAGACCCCGCGGGGGGGGCAGAGCATTCCGAACATTTACGCCCTCAACGCCCGCGCCGCCACCTCCATCAAGGGCACCCCCGTGAAGCAGAAGGTCCTCATCGCTCTCCTCACCATCATCGTAGGAGGCCCGAACACCCTCCCGAGCAG'
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# expected: 'ATGGATCGATCCTGGAAGCAGAAGCTGAACCGCGATACTGTCAAGCTGACTGAGGTCATGACTTGGCGACGACCTGCGGCAAAATGGTTTTATACCTTGATAAATGCAAATTATTTACCTCCTTGTCCTCCTGATCACCAAGACCACCGACAGCAACAATTACCCGAGCCCGACCAGCCCGAACATCAACGACCCGAACAGCCTCATCAAGCAGCGCCGCCCGATAGACTGGCAGCGCAAGCGGGGCCTCACCTCCTGTTACCCCCTGGGGATCCTCCCGCAAGAGAAGGGCCGGCGTTACCCGCAGGCGAAGGACTGGAAGATCATCTCTCGGGTCAACGACCCGAAGAAGCGGGTTGGCGTGGTCATCCCGACCAGAGACAAGACAGACTCCCTGCGCAAGGCGACCAAGAAGGGCAAGGGGGACCTCTCCATCCCGACCAAGGACAAGACCCCGCGGGGGGGGCAGAGCATTCCGAACATTTACGCCCTCAACGCCCGCGCCGCCACCTCCATCAAGGGCACCCCCGTGAAGCAGAAGGTCCTCATCGCTCTCCTCACCATCATCGTCGAAGACCCGAACACCCTCCCGAGCAG'
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# Looks like you failed 2 tests of 5.
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t/25-codon_juggle.t .......
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Dubious, test returned 2 (wstat 512, 0x200)
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Failed 2/5 subtests
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t/30-enzymes.t ............ ok
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t/35-subtract_sequence.t .. ok
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can't write test filehandle, Permission denied at t/40-graph.t line 54.
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# Looks like your test exited with 13 before it could output anything.
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t/40-graph.t ..............
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Dubious, test returned 13 (wstat 3328, 0xd00)
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Failed 1/1 subtests
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# Failed test 'search_prefix_tree pep'
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# at t/60-prefix.t line 1996.
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# Structures begin differing at:
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# $got->[0][0] = 'TaqI'
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# $expected->[0][0] = 'AciI'
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# Looks like you failed 1 test of 6.
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t/60-prefix.t .............
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Dubious, test returned 1 (wstat 256, 0x100)
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Failed 1/6 subtests
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t/65-random.t ............. ok
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t/boilerplate.t ........... ok
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t/manifest.t .............. skipped: Author tests not required for installation
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t/pod-coverage.t .......... ok
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t/pod.t ................... ok
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Test Summary Report
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-------------------
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t/15-codons.t (Wstat: 256 Tests: 9 Failed: 1)
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Failed test: 2
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Non-zero exit status: 1
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t/25-codon_juggle.t (Wstat: 512 Tests: 5 Failed: 2)
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Failed tests: 2-3
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Non-zero exit status: 2
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t/40-graph.t (Wstat: 3328 Tests: 0 Failed: 0)
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Non-zero exit status: 13
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Parse errors: Bad plan. You planned 1 tests but ran 0.
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t/60-prefix.t (Wstat: 256 Tests: 6 Failed: 1)
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Failed test: 2
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Non-zero exit status: 1
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t/boilerplate.t (Wstat: 0 Tests: 14 Failed: 0)
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TODO passed: 1-14
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Files=15, Tests=100, 6 wallclock secs ( 0.14 usr 0.02 sys + 5.31 cusr 0.11 csys = 5.58 CPU)
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Result: FAIL
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Failed 4/15 test programs. 4/100 subtests failed.
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! Installing Bio::GeneDesign::Exceptions failed. See /home/ryan/.cpanm/work/1493530396.5142/build.log for details. Retry with --force to force install it.
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FAIL
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Command [cpanm --reinstall --verbose Bio::GeneDesign::Exceptions] terminated with exit code 1 ($? = 256) under the following perl environment:
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Command terminated with non-zero status.
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Current perl:
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Name: perl-blead
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Path: /home/ryan/perl5/perlbrew/perls/perl-blead/bin/perl
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Config: -de -Dprefix=/home/ryan/perl5/perlbrew/perls/perl-blead -Dusedevel -Aeval:scriptdir=/home/ryan/perl5/perlbrew/perls/perl-blead/bin
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Compiled at: Mar 30 2017 03:10:09
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perlbrew:
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version: 0.78
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ENV:
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PERLBREW_ROOT: /home/ryan/perl5/perlbrew
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PERLBREW_HOME: /home/ryan/.perlbrew
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PERLBREW_PATH: /home/ryan/perl5/perlbrew/bin:/home/ryan/perl5/perlbrew/perls/perl-blead/bin
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PERLBREW_MANPATH: /home/ryan/perl5/perlbrew/perls/perl-blead/man
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