164 lines
6.4 KiB
Text
164 lines
6.4 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/1493530381.5047
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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::BuildingBlock () on cpanmetadb ...
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Unpacking Bio-GeneDesign-3.05.tar.gz
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--> Working on Bio::GeneDesign::BuildingBlock
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Fetching http://www.cpan.org/authors/id/N/NO/NOTDOCTOR/Bio-GeneDesign-3.05.tar.gz ... OK
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Bio-GeneDesign-3.05
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Bio-GeneDesign-3.05/Build.PL
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Bio-GeneDesign-3.05/Changes
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Bio-GeneDesign-3.05/ignore.txt
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Bio-GeneDesign-3.05/Makefile.PL
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Bio-GeneDesign-3.05/MANIFEST
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Bio-GeneDesign-3.05/META.json
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Bio-GeneDesign-3.05/META.yml
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Bio-GeneDesign-3.05/README
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Bio-GeneDesign-3.05/lib
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Bio-GeneDesign-3.05/lib/Bio
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Bio-GeneDesign-3.05/lib/Bio/GeneDesign
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Bio-GeneDesign-3.05/lib/Bio/GeneDesign/Basic.pm
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Bio-GeneDesign-3.05/lib/Bio/GeneDesign/BuildingBlock.pm
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Bio-GeneDesign-3.05/lib/Bio/GeneDesign/Codons.pm
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Bio-GeneDesign-3.05/lib/Bio/GeneDesign/HTML.pm
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Bio-GeneDesign-3.05/lib/Bio/GeneDesign/Oligo.pm
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Bio-GeneDesign-3.05/lib/Bio/GeneDesign/Random.pm
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Bio-GeneDesign-3.05/lib/Bio/GeneDesign/RestrictionEnzyme.pm
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Bio-GeneDesign-3.05/lib/Bio/GeneDesign/RestrictionEnzymes.pm
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Bio-GeneDesign-3.05/lib/Bio/GeneDesign/SufTree.pm
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Bio-GeneDesign-3.05/t
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Bio-GeneDesign-3.05/t/00-load.t
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Bio-GeneDesign-3.05/t/01-basic.t
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Bio-GeneDesign-3.05/t/02-codons.t
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Bio-GeneDesign-3.05/t/03-enzymes.t
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Bio-GeneDesign-3.05/t/boilerplate.t
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Bio-GeneDesign-3.05/t/GeneDesign.conf
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Bio-GeneDesign-3.05/t/manifest.t
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Bio-GeneDesign-3.05/t/pod-coverage.t
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Bio-GeneDesign-3.05/t/pod.t
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Bio-GeneDesign-3.05/t/codon_tables
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Bio-GeneDesign-3.05/t/codon_tables/Saccharomyces_cerevisiae.rscu
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Bio-GeneDesign-3.05/t/codon_tables/Standard.ct
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Bio-GeneDesign-3.05/t/enzymes
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Bio-GeneDesign-3.05/t/enzymes/test
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Entering Bio-GeneDesign-3.05
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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-3.05 ... Created MYMETA.yml and MYMETA.json
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Creating new 'Build' script for 'Bio-GeneDesign' version '3.05'
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Checking dependencies from MYMETA.json ...
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Checking if you have Text::Wrap 2009.0305 ... Yes (2013.0523)
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Checking if you have Bio::Root::Root 0 ... Yes (undef)
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Checking if you have Test::More 0 ... Yes (1.302083)
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Checking if you have List::Util 0 ... Yes (1.47)
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Checking if you have Perl6::Slurp 0.03 ... Yes (0.051005)
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OK
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Building and testing Bio-GeneDesign-3.05 ... Building Bio-GeneDesign
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# Testing Bio::GeneDesign::Basic 3.05, Perl 5.026000, /home/ryan/perl5/perlbrew/perls/perl-blead/bin/perl5.26.0
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t/00-load.t ....... ok
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# Testing Bio::GeneDesign::Basic 3.05, Perl 5.026000, /home/ryan/perl5/perlbrew/perls/perl-blead/bin/perl5.26.0
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# Failed test 'nearest neighbor thermodynamics Tm'
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# at t/01-basic.t line 88.
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# got: '67.3152820409048'
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# expected: '67.3152820409049'
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# Looks like you failed 1 test of 4.
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# Failed test 'melt'
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# at t/01-basic.t line 89.
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# Looks like you failed 1 test of 7.
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t/01-basic.t ......
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Dubious, test returned 1 (wstat 256, 0x100)
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Failed 1/7 subtests
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# Testing Bio::GeneDesign::Codons 3.05, Perl 5.026000, /home/ryan/perl5/perlbrew/perls/perl-blead/bin/perl5.26.0
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# Failed test 'define reverse codon table'
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# at t/02-codons.t line 64.
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# Structures begin differing at:
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# $got->{A}[0] = 'GCG'
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# $expected->{A}[0] = 'GCC'
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# Failed test 'ambiguous transcription, no peptide'
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# at t/02-codons.t line 156.
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# Structures begin differing at:
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# $got->[0] = 'ATGCGT'
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# $expected->[0] = 'AGGCTT'
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# Looks like you failed 1 test of 2.
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# Failed test 'ambiguous nucleotide transcription'
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# at t/02-codons.t line 162.
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# Failed test 'ambiguous translate WCY'
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# at t/02-codons.t line 176.
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# Structures begin differing at:
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# $got->[0] = 'T'
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# $expected->[0] = 'S'
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# Looks like you failed 1 test of 25.
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# Failed test 'ambiguous codon translation'
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# at t/02-codons.t line 178.
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# Failed test 'least different codon replacement'
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# at t/02-codons.t line 388.
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# got: 'ATGGATAGATCCTGGAAGCAGAAGCTTAACCGG'
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# expected: 'ATGGATAGATCCTGGAAGCAGAAGCTTAACCGA'
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# Looks like you failed 1 test of 5.
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# Failed test 'change codons'
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# at t/02-codons.t line 389.
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# Looks like you failed 4 tests of 22.
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t/02-codons.t .....
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Dubious, test returned 4 (wstat 1024, 0x400)
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Failed 4/22 subtests
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# Testing Bio::GeneDesign::RestrictionEnzymes 3.05, Perl 5.026000, /home/ryan/perl5/perlbrew/perls/perl-blead/bin/perl5.26.0
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t/03-enzymes.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/01-basic.t (Wstat: 256 Tests: 7 Failed: 1)
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Failed test: 4
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Non-zero exit status: 1
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t/02-codons.t (Wstat: 1024 Tests: 22 Failed: 4)
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Failed tests: 4, 8-9, 20
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Non-zero exit status: 4
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t/boilerplate.t (Wstat: 0 Tests: 8 Failed: 0)
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TODO passed: 2-8
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Files=8, Tests=64, 1 wallclock secs ( 0.07 usr 0.01 sys + 0.68 cusr 0.10 csys = 0.86 CPU)
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Result: FAIL
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Failed 2/8 test programs. 5/64 subtests failed.
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! Installing Bio::GeneDesign::BuildingBlock failed. See /home/ryan/.cpanm/work/1493530381.5047/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::BuildingBlock] 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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