302 lines
16 KiB
Text
302 lines
16 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/1492935327.26001
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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::AutomatedAnnotation () on cpanmetadb ...
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Unpacking Bio-AutomatedAnnotation-1.133090.tar.gz
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--> Working on Bio::AutomatedAnnotation
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Fetching http://www.cpan.org/authors/id/A/AJ/AJPAGE/Bio-AutomatedAnnotation-1.133090.tar.gz ... OK
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Bio-AutomatedAnnotation-1.133090/
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Bio-AutomatedAnnotation-1.133090/bin/
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Bio-AutomatedAnnotation-1.133090/dist.ini
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Bio-AutomatedAnnotation-1.133090/GPL-LICENSE
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Bio-AutomatedAnnotation-1.133090/lib/
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Bio-AutomatedAnnotation-1.133090/LICENSE
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Bio-AutomatedAnnotation-1.133090/Makefile.PL
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Bio-AutomatedAnnotation-1.133090/MANIFEST
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Bio-AutomatedAnnotation-1.133090/META.yml
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Bio-AutomatedAnnotation-1.133090/README
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Bio-AutomatedAnnotation-1.133090/t/
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Bio-AutomatedAnnotation-1.133090/t/bin/
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Bio-AutomatedAnnotation-1.133090/t/Bio/
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Bio-AutomatedAnnotation-1.133090/t/data/
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Bio-AutomatedAnnotation-1.133090/t/lib/
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Bio-AutomatedAnnotation-1.133090/t/requires_external.t
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Bio-AutomatedAnnotation-1.133090/t/lib/TestHelper.pm
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Bio-AutomatedAnnotation-1.133090/t/data/cmscan_output.txt
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Bio-AutomatedAnnotation-1.133090/t/data/copy_of_example_annotation.gff
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Bio-AutomatedAnnotation-1.133090/t/data/different_to_example_annotation.gff
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Bio-AutomatedAnnotation-1.133090/t/data/empty_annotation.gff
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Bio-AutomatedAnnotation-1.133090/t/data/example_annotation.gff
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Bio-AutomatedAnnotation-1.133090/t/data/expected_aa_output.yfnB.fa
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Bio-AutomatedAnnotation-1.133090/t/data/expected_example.csv
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Bio-AutomatedAnnotation-1.133090/t/data/expected_gene_occurances_output_all_files.csv
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Bio-AutomatedAnnotation-1.133090/t/data/expected_gene_occurances_output_one_file.csv
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Bio-AutomatedAnnotation-1.133090/t/data/expected_gene_occurances_output_two_files.csv
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Bio-AutomatedAnnotation-1.133090/t/data/expected_output.16SribosomalRNA.fa
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Bio-AutomatedAnnotation-1.133090/t/data/expected_output.hypothetical.fa
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Bio-AutomatedAnnotation-1.133090/t/data/expected_output.yfnB.fa
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Bio-AutomatedAnnotation-1.133090/t/data/minimal_contigs.fa
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Bio-AutomatedAnnotation-1.133090/t/Bio/AutomatedAnnotation/
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Bio-AutomatedAnnotation-1.133090/t/Bio/AutomatedAnnotation.t
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Bio-AutomatedAnnotation-1.133090/t/Bio/AutomatedAnnotation/CommandLine/
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Bio-AutomatedAnnotation-1.133090/t/Bio/AutomatedAnnotation/External/
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Bio-AutomatedAnnotation-1.133090/t/Bio/AutomatedAnnotation/GeneNameOccurances.t
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Bio-AutomatedAnnotation-1.133090/t/Bio/AutomatedAnnotation/GeneNamesFromGFF.t
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Bio-AutomatedAnnotation-1.133090/t/Bio/AutomatedAnnotation/ParseGenesFromGFF.t
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Bio-AutomatedAnnotation-1.133090/t/Bio/AutomatedAnnotation/ParseGenesFromGFFs.t
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Bio-AutomatedAnnotation-1.133090/t/Bio/AutomatedAnnotation/Prokka.t
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Bio-AutomatedAnnotation-1.133090/t/Bio/AutomatedAnnotation/SpreadsheetOfGeneOccurances.t
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Bio-AutomatedAnnotation-1.133090/t/Bio/AutomatedAnnotation/External/Cmscan.t
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Bio-AutomatedAnnotation-1.133090/t/Bio/AutomatedAnnotation/CommandLine/GeneNameOccurances.t
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Bio-AutomatedAnnotation-1.133090/t/Bio/AutomatedAnnotation/CommandLine/ParseGenesFromGFFs.t
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Bio-AutomatedAnnotation-1.133090/t/bin/dummy_cmscan
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Bio-AutomatedAnnotation-1.133090/lib/Bio/
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Bio-AutomatedAnnotation-1.133090/lib/Bio/AutomatedAnnotation/
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Bio-AutomatedAnnotation-1.133090/lib/Bio/AutomatedAnnotation.pm
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Bio-AutomatedAnnotation-1.133090/lib/Bio/AutomatedAnnotation/CommandLine/
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Bio-AutomatedAnnotation-1.133090/lib/Bio/AutomatedAnnotation/Exceptions.pm
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Bio-AutomatedAnnotation-1.133090/lib/Bio/AutomatedAnnotation/External/
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Bio-AutomatedAnnotation-1.133090/lib/Bio/AutomatedAnnotation/GeneNameOccurances.pm
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Bio-AutomatedAnnotation-1.133090/lib/Bio/AutomatedAnnotation/GeneNamesFromGFF.pm
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Bio-AutomatedAnnotation-1.133090/lib/Bio/AutomatedAnnotation/notes
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Bio-AutomatedAnnotation-1.133090/lib/Bio/AutomatedAnnotation/ParseGenesFromGFF.pm
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Bio-AutomatedAnnotation-1.133090/lib/Bio/AutomatedAnnotation/ParseGenesFromGFFs.pm
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Bio-AutomatedAnnotation-1.133090/lib/Bio/AutomatedAnnotation/Prokka.pm
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Bio-AutomatedAnnotation-1.133090/lib/Bio/AutomatedAnnotation/SpreadsheetOfGeneOccurances.pm
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Bio-AutomatedAnnotation-1.133090/lib/Bio/AutomatedAnnotation/External/Cmscan.pm
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Bio-AutomatedAnnotation-1.133090/lib/Bio/AutomatedAnnotation/CommandLine/AnnotateBacteria.pm
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Bio-AutomatedAnnotation-1.133090/lib/Bio/AutomatedAnnotation/CommandLine/GeneNameOccurances.pm
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Bio-AutomatedAnnotation-1.133090/lib/Bio/AutomatedAnnotation/CommandLine/ParseGenesFromGFFs.pm
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Bio-AutomatedAnnotation-1.133090/bin/annotate_bacteria
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Bio-AutomatedAnnotation-1.133090/bin/gene_name_occurances
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Bio-AutomatedAnnotation-1.133090/bin/parse_genes_from_gffs
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Entering Bio-AutomatedAnnotation-1.133090
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Checking configure dependencies from META.yml
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Checking if you have ExtUtils::MakeMaker 6.58 ... Yes (7.24)
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Running Makefile.PL
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Configuring Bio-AutomatedAnnotation-1.133090 ... Checking if your kit is complete...
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Looks good
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Generating a Unix-style Makefile
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Writing Makefile for Bio::AutomatedAnnotation
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Writing MYMETA.yml and MYMETA.json
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Checking dependencies from MYMETA.json ...
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Checking if you have Time::Seconds 0 ... Yes (1.31)
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Checking if you have Bio::Tools::GFF 0 ... Yes (undef)
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Checking if you have XML::Simple 0 ... Yes (2.22)
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Checking if you have Moose::Role 0 ... Yes (2.2004)
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Checking if you have Text::CSV 0 ... Yes (1.94)
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Checking if you have Getopt::Long 0 ... Yes (2.49)
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Checking if you have Bio::PrimarySeq 0 ... Yes (undef)
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Checking if you have Cwd 0 ... Yes (3.62)
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Checking if you have POSIX 0 ... Yes (1.76)
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Checking if you have Env::Path 0 ... Yes (0.19)
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Checking if you have Bio::SeqIO 0 ... Yes (undef)
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Checking if you have Scalar::Util 0 ... Yes (1.47)
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Checking if you have File::Copy 0 ... Yes (2.32)
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Checking if you have List::Util 0 ... Yes (1.47)
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Checking if you have File::Basename 0 ... Yes (2.85)
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Checking if you have Bio::Perl 0 ... Yes (undef)
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Checking if you have strict 0 ... Yes (1.11)
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Checking if you have Exception::Class 0 ... Yes (1.42)
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Checking if you have File::Find 0 ... Yes (1.34)
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Checking if you have File::Slurp 0 ... Yes (9999.19)
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Checking if you have Time::Piece 0 ... Yes (1.31)
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Checking if you have FindBin 0 ... Yes (1.51)
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Checking if you have File::Temp 0 ... Yes (0.2304)
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Checking if you have Bio::Seq 0 ... Yes (undef)
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Checking if you have warnings 0 ... Yes (1.37)
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Checking if you have Bio::SearchIO 0 ... Yes (undef)
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Checking if you have Bio::SeqFeature::Generic 0 ... Yes (undef)
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Checking if you have Test::Most 0 ... Yes (0.35)
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Checking if you have Data::Dumper 0 ... Yes (2.161)
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Checking if you have Moose 0 ... Yes (2.2004)
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OK
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Building and testing Bio-AutomatedAnnotation-1.133090 ... cp lib/Bio/AutomatedAnnotation/CommandLine/AnnotateBacteria.pm blib/lib/Bio/AutomatedAnnotation/CommandLine/AnnotateBacteria.pm
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cp lib/Bio/AutomatedAnnotation/CommandLine/GeneNameOccurances.pm blib/lib/Bio/AutomatedAnnotation/CommandLine/GeneNameOccurances.pm
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cp lib/Bio/AutomatedAnnotation/External/Cmscan.pm blib/lib/Bio/AutomatedAnnotation/External/Cmscan.pm
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cp lib/Bio/AutomatedAnnotation/ParseGenesFromGFFs.pm blib/lib/Bio/AutomatedAnnotation/ParseGenesFromGFFs.pm
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cp lib/Bio/AutomatedAnnotation/Exceptions.pm blib/lib/Bio/AutomatedAnnotation/Exceptions.pm
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cp lib/Bio/AutomatedAnnotation/ParseGenesFromGFF.pm blib/lib/Bio/AutomatedAnnotation/ParseGenesFromGFF.pm
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cp lib/Bio/AutomatedAnnotation/GeneNameOccurances.pm blib/lib/Bio/AutomatedAnnotation/GeneNameOccurances.pm
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cp lib/Bio/AutomatedAnnotation.pm blib/lib/Bio/AutomatedAnnotation.pm
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cp lib/Bio/AutomatedAnnotation/SpreadsheetOfGeneOccurances.pm blib/lib/Bio/AutomatedAnnotation/SpreadsheetOfGeneOccurances.pm
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cp lib/Bio/AutomatedAnnotation/Prokka.pm blib/lib/Bio/AutomatedAnnotation/Prokka.pm
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cp lib/Bio/AutomatedAnnotation/GeneNamesFromGFF.pm blib/lib/Bio/AutomatedAnnotation/GeneNamesFromGFF.pm
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cp lib/Bio/AutomatedAnnotation/CommandLine/ParseGenesFromGFFs.pm blib/lib/Bio/AutomatedAnnotation/CommandLine/ParseGenesFromGFFs.pm
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cp lib/Bio/AutomatedAnnotation/notes blib/lib/Bio/AutomatedAnnotation/notes
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cp bin/annotate_bacteria blib/script/annotate_bacteria
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"/home/ryan/perl5/perlbrew/perls/perl-blead/bin/perl5.26.0" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/annotate_bacteria
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cp bin/gene_name_occurances blib/script/gene_name_occurances
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"/home/ryan/perl5/perlbrew/perls/perl-blead/bin/perl5.26.0" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/gene_name_occurances
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cp bin/parse_genes_from_gffs blib/script/parse_genes_from_gffs
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"/home/ryan/perl5/perlbrew/perls/perl-blead/bin/perl5.26.0" -MExtUtils::MY -e 'MY->fixin(shift)' -- blib/script/parse_genes_from_gffs
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Manifying 3 pod documents
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Manifying 12 pod documents
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PERL_DL_NONLAZY=1 "/home/ryan/perl5/perlbrew/perls/perl-blead/bin/perl5.26.0" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t t/Bio/*.t t/Bio/AutomatedAnnotation/*.t t/Bio/AutomatedAnnotation/CommandLine/*.t t/Bio/AutomatedAnnotation/External/*.t
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t/Bio/AutomatedAnnotation.t ................................. ok
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# Failed test 'Actual and expected output match for '-o different_output_filename t/data/example_annotation.gff''
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# at t/lib/TestHelper.pm line 29.
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# got: '"File","hly","yfnB","speH","arcC1","argF"
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# "t/data/example_annotation.gff","1","1","1","1","1"
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# "% Total","1","1","1","1","1"
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# '
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# expected: '"File","speH","hly","arcC1","yfnB","argF"
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# "t/data/example_annotation.gff","1","1","1","1","1"
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# "% Total","1","1","1","1","1"
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# '
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# Failed test 'Actual and expected output match for 't/data/example_annotation.gff''
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# at t/lib/TestHelper.pm line 29.
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# got: '"File","argF","arcC1","speH","yfnB","hly"
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# "t/data/example_annotation.gff","1","1","1","1","1"
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# "% Total","1","1","1","1","1"
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# '
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# expected: '"File","speH","hly","arcC1","yfnB","argF"
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# "t/data/example_annotation.gff","1","1","1","1","1"
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# "% Total","1","1","1","1","1"
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# '
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# Failed test 'Actual and expected output match for 't/data/example_annotation.gff t/data/copy_of_example_annotation.gff t/data/empty_annotation.gff t/data/different_to_example_annotation.gff''
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# at t/lib/TestHelper.pm line 29.
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# got: '"File","yfnB","speH","hly","arcC1","argF","another_yfnB","another_hly","another_arcC1","another_speH","another_argF"
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# "t/data/empty_annotation.gff","0","0","0","0","0","0","0","0","0","0"
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# "t/data/different_to_example_annotation.gff","0","0","0","0","0","1","1","1","1","1"
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# "t/data/example_annotation.gff","1","1","1","1","1","0","0","0","0","0"
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# "t/data/copy_of_example_annotation.gff","1","1","1","1","1","0","0","0","0","0"
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# "% Total","0.5","0.5","0.5","0.5","0.5","0.25","0.25","0.25","0.25","0.25"
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# '
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# expected: '"File","speH","hly","arcC1","yfnB","argF","another_argF","another_hly","another_yfnB","another_arcC1","another_speH"
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# "t/data/example_annotation.gff","1","1","1","1","1","0","0","0","0","0"
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# "t/data/empty_annotation.gff","0","0","0","0","0","0","0","0","0","0"
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# "t/data/copy_of_example_annotation.gff","1","1","1","1","1","0","0","0","0","0"
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# "t/data/different_to_example_annotation.gff","0","0","0","0","0","1","1","1","1","1"
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# "% Total","0.5","0.5","0.5","0.5","0.5","0.25","0.25","0.25","0.25","0.25"
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# '
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# Failed test 'Actual and expected output match for 't/data/example_annotation.gff t/data/empty_annotation.gff''
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# at t/lib/TestHelper.pm line 29.
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# got: '"File","hly","speH","yfnB","arcC1","argF"
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# "t/data/example_annotation.gff","1","1","1","1","1"
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# "t/data/empty_annotation.gff","0","0","0","0","0"
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# "% Total","0.5","0.5","0.5","0.5","0.5"
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# '
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# expected: '"File","speH","hly","arcC1","yfnB","argF"
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# "t/data/example_annotation.gff","1","1","1","1","1"
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# "t/data/empty_annotation.gff","0","0","0","0","0"
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# "% Total","0.5","0.5","0.5","0.5","0.5"
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# '
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# Looks like you failed 4 tests of 9.
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t/Bio/AutomatedAnnotation/CommandLine/GeneNameOccurances.t ..
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Dubious, test returned 4 (wstat 1024, 0x400)
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Failed 4/9 subtests
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t/Bio/AutomatedAnnotation/CommandLine/ParseGenesFromGFFs.t .. ok
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t/Bio/AutomatedAnnotation/External/Cmscan.t ................. ok
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# Failed test 'gene names sorted by value desc'
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# at t/Bio/AutomatedAnnotation/GeneNameOccurances.t line 150.
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# Structures begin differing at:
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# $got->[1] = 'yfnB'
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# $expected->[1] = 'hly'
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# Looks like you failed 1 test of 14.
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t/Bio/AutomatedAnnotation/GeneNameOccurances.t ..............
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Dubious, test returned 1 (wstat 256, 0x100)
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Failed 1/14 subtests
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t/Bio/AutomatedAnnotation/GeneNamesFromGFF.t ................ ok
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t/Bio/AutomatedAnnotation/ParseGenesFromGFF.t ............... ok
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--------------------- WARNING ---------------------
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MSG: Got a sequence without letters. Could not guess alphabet
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---------------------------------------------------
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t/Bio/AutomatedAnnotation/ParseGenesFromGFFs.t .............. ok
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t/Bio/AutomatedAnnotation/Prokka.t .......................... ok
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# Failed test 'Spredsheet data as expected'
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# at t/Bio/AutomatedAnnotation/SpreadsheetOfGeneOccurances.t line 30.
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# got: '"File","speH","argF","hly","arcC1","yfnB","another_speH","another_yfnB","another_argF","another_hly","another_arcC1"
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# "t/data/copy_of_example_annotation.gff","1","1","1","1","1","0","0","0","0","0"
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# "t/data/example_annotation.gff","1","1","1","1","1","0","0","0","0","0"
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# "t/data/different_to_example_annotation.gff","0","0","0","0","0","1","1","1","1","1"
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# "t/data/empty_annotation.gff","0","0","0","0","0","0","0","0","0","0"
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# "% Total","0.5","0.5","0.5","0.5","0.5","0.25","0.25","0.25","0.25","0.25"
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# '
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# expected: '"File","speH","hly","arcC1","yfnB","argF","another_argF","another_hly","another_yfnB","another_arcC1","another_speH"
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# "t/data/example_annotation.gff","1","1","1","1","1","0","0","0","0","0"
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# "t/data/empty_annotation.gff","0","0","0","0","0","0","0","0","0","0"
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# "t/data/copy_of_example_annotation.gff","1","1","1","1","1","0","0","0","0","0"
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# "t/data/different_to_example_annotation.gff","0","0","0","0","0","1","1","1","1","1"
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# "% Total","0.5","0.5","0.5","0.5","0.5","0.25","0.25","0.25","0.25","0.25"
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# '
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# Looks like you failed 1 test of 5.
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t/Bio/AutomatedAnnotation/SpreadsheetOfGeneOccurances.t .....
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Dubious, test returned 1 (wstat 256, 0x100)
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Failed 1/5 subtests
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# Failed test 'makeblastdb in PATH'
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# at t/requires_external.t line 8.
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# Failed test 'blastp in PATH'
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# at t/requires_external.t line 8.
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# Failed test 'prodigal in PATH'
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# at t/requires_external.t line 8.
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# Failed test 'parallel in PATH'
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# at t/requires_external.t line 8.
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# Failed test 'hmmscan in PATH'
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# at t/requires_external.t line 8.
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# Looks like you failed 5 tests of 11.
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t/requires_external.t .......................................
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Dubious, test returned 5 (wstat 1280, 0x500)
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Failed 5/11 subtests
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Test Summary Report
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-------------------
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t/Bio/AutomatedAnnotation/CommandLine/GeneNameOccurances.t (Wstat: 1024 Tests: 9 Failed: 4)
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Failed tests: 3, 5, 7, 9
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Non-zero exit status: 4
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t/Bio/AutomatedAnnotation/GeneNameOccurances.t (Wstat: 256 Tests: 14 Failed: 1)
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Failed test: 14
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Non-zero exit status: 1
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t/Bio/AutomatedAnnotation/SpreadsheetOfGeneOccurances.t (Wstat: 256 Tests: 5 Failed: 1)
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Failed test: 5
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Non-zero exit status: 1
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t/requires_external.t (Wstat: 1280 Tests: 11 Failed: 5)
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Failed tests: 7-11
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Non-zero exit status: 5
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Files=11, Tests=118, 3 wallclock secs ( 0.03 usr 0.00 sys + 1.96 cusr 0.15 csys = 2.14 CPU)
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Result: FAIL
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Failed 4/11 test programs. 11/118 subtests failed.
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Makefile:983: recipe for target 'test_dynamic' failed
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make: *** [test_dynamic] Error 5
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! Installing Bio::AutomatedAnnotation failed. See /home/ryan/.cpanm/work/1492935327.26001/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::AutomatedAnnotation] 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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