301 lines
14 KiB
Text
301 lines
14 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/1493520529.5514
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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::ViennaNGS () on cpanmetadb ...
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Unpacking Bio-ViennaNGS-v0.16.tar.gz
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--> Working on Bio::ViennaNGS
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Fetching http://www.cpan.org/authors/id/M/MT/MTW/Bio-ViennaNGS-v0.16.tar.gz ... OK
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Bio-ViennaNGS-v0.16/
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Bio-ViennaNGS-v0.16/inc/
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Bio-ViennaNGS-v0.16/inc/File/
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Bio-ViennaNGS-v0.16/inc/File/ShareDir/
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Bio-ViennaNGS-v0.16/inc/File/ShareDir/Install.pm
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Bio-ViennaNGS-v0.16/scripts/
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Bio-ViennaNGS-v0.16/scripts/Tutorial_pipeline01.pl
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Bio-ViennaNGS-v0.16/scripts/sj_visualizer.pl
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Bio-ViennaNGS-v0.16/scripts/extend_bed.pl
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Bio-ViennaNGS-v0.16/scripts/Tutorial_pipeline03.pl
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Bio-ViennaNGS-v0.16/scripts/trim_fastq.pl
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Bio-ViennaNGS-v0.16/scripts/newUCSCdb.pl
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Bio-ViennaNGS-v0.16/scripts/kmer_analysis.pl
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Bio-ViennaNGS-v0.16/scripts/bam_uniq.pl
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Bio-ViennaNGS-v0.16/scripts/Tutorial_pipeline02.pl
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Bio-ViennaNGS-v0.16/scripts/splice_site_summary.pl
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Bio-ViennaNGS-v0.16/scripts/track_hub_constructor.pl
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Bio-ViennaNGS-v0.16/scripts/bed2bedGraph.pl
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Bio-ViennaNGS-v0.16/scripts/bam_split.pl
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Bio-ViennaNGS-v0.16/scripts/assembly_hub_constructor.pl
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Bio-ViennaNGS-v0.16/scripts/MEME_xml_motif_extractor.pl
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Bio-ViennaNGS-v0.16/scripts/bam_to_bigwig.pl
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Bio-ViennaNGS-v0.16/scripts/normalize_multicov.pl
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Bio-ViennaNGS-v0.16/scripts/Tutorial_pipeline00.pl
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Bio-ViennaNGS-v0.16/scripts/bam_quality_stat.pl
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Bio-ViennaNGS-v0.16/scripts/rnaseq_peakfinder.pl
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Bio-ViennaNGS-v0.16/scripts/gff2bed.pl
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Bio-ViennaNGS-v0.16/scripts/bed2nt2aa.pl
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Bio-ViennaNGS-v0.16/Changes
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Bio-ViennaNGS-v0.16/MANIFEST
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Bio-ViennaNGS-v0.16/META.yml
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Bio-ViennaNGS-v0.16/share/
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Bio-ViennaNGS-v0.16/share/data2/
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Bio-ViennaNGS-v0.16/share/data2/MIOS_sj.bed
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Bio-ViennaNGS-v0.16/share/data2/MIOS.bed12
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Bio-ViennaNGS-v0.16/share/data1/
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Bio-ViennaNGS-v0.16/share/data1/SRR794848.8k.bam
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Bio-ViennaNGS-v0.16/share/data1/NC_000913.CDS.bed
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Bio-ViennaNGS-v0.16/share/data1/NC_000913.3.30k.fa
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Bio-ViennaNGS-v0.16/share/data1/NC_000913.3.chrom.sizes
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Bio-ViennaNGS-v0.16/share/data1/NC_000913.3.30k.gff
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Bio-ViennaNGS-v0.16/share/template-TrackHub/
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Bio-ViennaNGS-v0.16/share/template-TrackHub/trackDb.txt
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Bio-ViennaNGS-v0.16/share/template-TrackHub/genome.txt
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Bio-ViennaNGS-v0.16/share/template-TrackHub/description.html
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Bio-ViennaNGS-v0.16/share/template-TrackHub/hub.txt
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Bio-ViennaNGS-v0.16/share/template-AssemblyHub/
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Bio-ViennaNGS-v0.16/share/template-AssemblyHub/trackDb.txt
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Bio-ViennaNGS-v0.16/share/template-AssemblyHub/genome.txt
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Bio-ViennaNGS-v0.16/share/template-AssemblyHub/groups.txt
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Bio-ViennaNGS-v0.16/share/template-AssemblyHub/description.html
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Bio-ViennaNGS-v0.16/share/template-AssemblyHub/hub.txt
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Bio-ViennaNGS-v0.16/META.json
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Bio-ViennaNGS-v0.16/Makefile.PL
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Bio-ViennaNGS-v0.16/lib/
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Bio-ViennaNGS-v0.16/lib/Bio/
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Bio-ViennaNGS-v0.16/lib/Bio/ViennaNGS/
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Bio-ViennaNGS-v0.16/lib/Bio/ViennaNGS/Tutorial.pm
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Bio-ViennaNGS-v0.16/lib/Bio/ViennaNGS/AnnoC.pm
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Bio-ViennaNGS-v0.16/lib/Bio/ViennaNGS/Fasta.pm
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Bio-ViennaNGS-v0.16/lib/Bio/ViennaNGS/MinimalFeature.pm
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Bio-ViennaNGS-v0.16/lib/Bio/ViennaNGS/FeatureIO.pm
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Bio-ViennaNGS-v0.16/lib/Bio/ViennaNGS/BamStat.pm
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Bio-ViennaNGS-v0.16/lib/Bio/ViennaNGS/Peak.pm
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Bio-ViennaNGS-v0.16/lib/Bio/ViennaNGS/FeatureLine.pm
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Bio-ViennaNGS-v0.16/lib/Bio/ViennaNGS/ExtFeature.pm
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Bio-ViennaNGS-v0.16/lib/Bio/ViennaNGS/Bed.pm
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Bio-ViennaNGS-v0.16/lib/Bio/ViennaNGS/Util.pm
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Bio-ViennaNGS-v0.16/lib/Bio/ViennaNGS/BamStatSummary.pm
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Bio-ViennaNGS-v0.16/lib/Bio/ViennaNGS/SpliceJunc.pm
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Bio-ViennaNGS-v0.16/lib/Bio/ViennaNGS/Expression.pm
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Bio-ViennaNGS-v0.16/lib/Bio/ViennaNGS/UCSC.pm
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Bio-ViennaNGS-v0.16/lib/Bio/ViennaNGS/Bam.pm
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Bio-ViennaNGS-v0.16/lib/Bio/ViennaNGS/FeatureChain.pm
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Bio-ViennaNGS-v0.16/lib/Bio/ViennaNGS/BedGraphEntry.pm
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Bio-ViennaNGS-v0.16/lib/Bio/ViennaNGS/Feature.pm
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Bio-ViennaNGS-v0.16/lib/Bio/ViennaNGS/FeatureInterval.pm
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Bio-ViennaNGS-v0.16/lib/Bio/ViennaNGS.pm
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Bio-ViennaNGS-v0.16/Doxyfile
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Bio-ViennaNGS-v0.16/README
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Bio-ViennaNGS-v0.16/AUTHORS
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Bio-ViennaNGS-v0.16/t/
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Bio-ViennaNGS-v0.16/t/06-SpliceJunc.t
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Bio-ViennaNGS-v0.16/t/01-basics.t
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Bio-ViennaNGS-v0.16/t/02-thirdparty.t
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Bio-ViennaNGS-v0.16/t/04-UCSC-TrackHub.t
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Bio-ViennaNGS-v0.16/t/05-UCSC-AssemblyHub.t
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Entering Bio-ViennaNGS-v0.16
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Checking configure dependencies from META.json
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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-ViennaNGS-v0.16.0 ... Warning: prerequisite Statistics::R 0 not found.
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Warning: prerequisite Tie::Hash::Indexed 0 not found.
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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::ViennaNGS
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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 Bio::DB::Sam 1.37 ... Yes (1.43)
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Checking if you have namespace::autoclean 0 ... Yes (0.28)
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Checking if you have Bio::Root::Version 1.00690001 ... Yes (1.007001)
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Checking if you have Carp 0 ... Yes (1.38)
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Checking if you have Bio::Tools::GFF 0 ... Yes (undef)
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Checking if you have PerlIO::gzip 0 ... Yes (0.19)
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Checking if you have Math::Round 0 ... Yes (0.07)
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Checking if you have Pod::Usage 0 ... Yes (1.69)
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Checking if you have IPC::Cmd 0 ... Yes (0.96)
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Checking if you have Test::More 0 ... Yes (1.302083)
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Checking if you have Bio::DB::Fasta 0 ... Yes (undef)
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Checking if you have File::Slurp 0 ... Yes (9999.19)
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Checking if you have File::Share 0 ... Yes (0.25)
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Checking if you have Getopt::Long 2.0 ... Yes (2.49)
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Checking if you have Test::File::Contents 0 ... Yes (0.23)
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Checking if you have Test::Deep 0 ... Yes (1.126)
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Checking if you have MooseX::Clone 0 ... Yes (0.06)
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Checking if you have Test::Files 0 ... Yes (0.14)
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Checking if you have Moose 0 ... Yes (2.2004)
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Checking if you have File::Temp 0 ... Yes (0.2304)
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Checking if you have MooseX::InstanceTracking 0 ... Yes (0.06)
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Checking if you have Tie::Hash::Indexed 0 ... No
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Checking if you have List::Util 0 ... Yes (1.47)
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Checking if you have Data::Dumper 0 ... Yes (2.161)
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Checking if you have Moose::Util::TypeConstraints 0 ... Yes (2.2004)
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Checking if you have Template 0 ... Yes (2.27)
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Checking if you have Statistics::R 0 ... No
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Checking if you have Path::Class 0 ... Yes (0.37)
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Checking if you have POSIX 0 ... Yes (1.76)
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Checking if you have File::Basename 0 ... Yes (2.85)
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Searching Tie::Hash::Indexed (0) on cpanmetadb ...
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Unpacking Tie-Hash-Indexed-0.05.tar.gz
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OK
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==> Found dependencies: Tie::Hash::Indexed, Statistics::R
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--> Working on Tie::Hash::Indexed
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Fetching http://www.cpan.org/authors/id/M/MH/MHX/Tie-Hash-Indexed-0.05.tar.gz ... OK
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Tie-Hash-Indexed-0.05/
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Tie-Hash-Indexed-0.05/t/
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Tie-Hash-Indexed-0.05/t/103_bugs.t
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Tie-Hash-Indexed-0.05/t/102_storable.t
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Tie-Hash-Indexed-0.05/t/101_basic.t
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Tie-Hash-Indexed-0.05/lib/
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Tie-Hash-Indexed-0.05/lib/Tie/
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Tie-Hash-Indexed-0.05/lib/Tie/Hash/
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Tie-Hash-Indexed-0.05/lib/Tie/Hash/Indexed.pm
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Tie-Hash-Indexed-0.05/TODO
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Tie-Hash-Indexed-0.05/README
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Tie-Hash-Indexed-0.05/Changes
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Tie-Hash-Indexed-0.05/Indexed.xs
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Tie-Hash-Indexed-0.05/Makefile.PL
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Tie-Hash-Indexed-0.05/ppport.h
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Tie-Hash-Indexed-0.05/META.yml
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Tie-Hash-Indexed-0.05/typemap
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Tie-Hash-Indexed-0.05/MANIFEST
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Entering Tie-Hash-Indexed-0.05
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Checking configure dependencies from META.yml
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Running Makefile.PL
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Configuring Tie-Hash-Indexed-0.05 ... Setting license tag...
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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 Tie::Hash::Indexed
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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 ExtUtils::MakeMaker 0 ... Yes (7.24)
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Checking if you have Test 0 ... Yes (1.26)
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OK
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Building and testing Tie-Hash-Indexed-0.05 ... cp lib/Tie/Hash/Indexed.pm blib/lib/Tie/Hash/Indexed.pm
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Running Mkbootstrap for Indexed ()
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chmod 644 "Indexed.bs"
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"/home/ryan/perl5/perlbrew/perls/perl-blead/bin/perl5.26.0" -MExtUtils::Command::MM -e 'cp_nonempty' -- Indexed.bs blib/arch/auto/Tie/Hash/Indexed/Indexed.bs 644
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"/home/ryan/perl5/perlbrew/perls/perl-blead/bin/perl5.26.0" "/home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/ExtUtils/xsubpp" -typemap '/home/ryan/perl5/perlbrew/perls/perl-blead/lib/5.26.0/ExtUtils/typemap' -typemap '/home/ryan/.cpanm/work/1493520529.5514/Tie-Hash-Indexed-0.05/typemap' Indexed.xs > Indexed.xsc
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mv Indexed.xsc Indexed.c
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cc -c -I. -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2 -DVERSION=\"0.05\" -DXS_VERSION=\"0.05\" -fPIC "-I/home/ryan/perl5/perlbrew/perls/perl-blead/lib/5.26.0/x86_64-linux/CORE" -DNDEBUG Indexed.c
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rm -f blib/arch/auto/Tie/Hash/Indexed/Indexed.so
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cc -shared -O2 -L/usr/local/lib -fstack-protector-strong Indexed.o -o blib/arch/auto/Tie/Hash/Indexed/Indexed.so \
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\
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chmod 755 blib/arch/auto/Tie/Hash/Indexed/Indexed.so
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Manifying 1 pod document
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"/home/ryan/perl5/perlbrew/perls/perl-blead/bin/perl5.26.0" -MExtUtils::Command::MM -e 'cp_nonempty' -- Indexed.bs blib/arch/auto/Tie/Hash/Indexed/Indexed.bs 644
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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
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# Failed test 8 in t/101_basic.t at line 43
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# t/101_basic.t line 43 is: skip($scalar, $s =~ /^(\d+)\/\d+$/ && $1 == scalar keys %h);
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# Failed test 11 in t/101_basic.t at line 49
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# t/101_basic.t line 49 is: skip($scalar, $s =~ /^(\d+)\/\d+$/ && $1 == scalar keys %h);
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# Failed test 14 in t/101_basic.t at line 55
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# t/101_basic.t line 55 is: skip($scalar, $s =~ /^(\d+)\/\d+$/ && $1 == scalar keys %h);
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t/101_basic.t .....
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Failed 3/32 subtests
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t/102_storable.t .. ok
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t/103_bugs.t ...... ok
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Test Summary Report
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-------------------
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t/101_basic.t (Wstat: 0 Tests: 32 Failed: 3)
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Failed tests: 8, 11, 14
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Files=3, Tests=69, 0 wallclock secs ( 0.01 usr 0.00 sys + 0.01 cusr 0.00 csys = 0.02 CPU)
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Result: FAIL
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Failed 1/3 test programs. 3/69 subtests failed.
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Makefile:1023: recipe for target 'test_dynamic' failed
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make: *** [test_dynamic] Error 255
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! Installing Tie::Hash::Indexed failed. See /home/ryan/.cpanm/work/1493520529.5514/build.log for details. Retry with --force to force install it.
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Searching Statistics::R (0) on cpanmetadb ...
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Unpacking Statistics-R-0.34.tar.gz
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FAIL
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--> Working on Statistics::R
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Fetching http://www.cpan.org/authors/id/F/FA/FANGLY/Statistics-R-0.34.tar.gz ... OK
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Statistics-R-0.34/
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Statistics-R-0.34/MYMETA.yml
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Statistics-R-0.34/inc/
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Statistics-R-0.34/inc/Module/
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Statistics-R-0.34/inc/Module/Install/
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Statistics-R-0.34/inc/Module/Install/WriteAll.pm
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Statistics-R-0.34/inc/Module/Install/Makefile.pm
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Statistics-R-0.34/inc/Module/Install/Fetch.pm
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Statistics-R-0.34/inc/Module/Install/Metadata.pm
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Statistics-R-0.34/inc/Module/Install/Base.pm
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Statistics-R-0.34/inc/Module/Install/Can.pm
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Statistics-R-0.34/inc/Module/Install/Win32.pm
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Statistics-R-0.34/inc/Module/Install/External.pm
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Statistics-R-0.34/inc/Module/Install.pm
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Statistics-R-0.34/Makefile.PL
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Statistics-R-0.34/Changes
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Statistics-R-0.34/lib/
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Statistics-R-0.34/lib/Statistics/
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Statistics-R-0.34/lib/Statistics/R.pm
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Statistics-R-0.34/lib/Statistics/R/
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Statistics-R-0.34/lib/Statistics/R/Legacy.pm
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Statistics-R-0.34/lib/Statistics/R/Win32.pm
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Statistics-R-0.34/MANIFEST
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Statistics-R-0.34/MYMETA.json
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Statistics-R-0.34/t/
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Statistics-R-0.34/t/02-legacy.t
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Statistics-R-0.34/t/data/
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Statistics-R-0.34/t/data/script.R
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Statistics-R-0.34/t/07-robust.t
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Statistics-R-0.34/t/01-pod.t
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Statistics-R-0.34/t/00-load.t
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Statistics-R-0.34/t/05-shared.t
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Statistics-R-0.34/t/03-run.t
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Statistics-R-0.34/t/08-errors.t
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Statistics-R-0.34/t/06-get-set.t
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Statistics-R-0.34/t/FlawedStatisticsR.pm
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Statistics-R-0.34/t/04-start-stop.t
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Statistics-R-0.34/META.yml
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Statistics-R-0.34/README
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Entering Statistics-R-0.34
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Checking configure dependencies from META.yml
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Checking if you have ExtUtils::MakeMaker 6.59 ... Yes (7.24)
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Running Makefile.PL
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Configuring Statistics-R-0.34 ... NA: Unable to build distribution on this platform.
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Locating bin:R... missing.
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Unresolvable missing external dependency.
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Please install 'R' seperately and try again.
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Checking dependencies from MYMETA.json ...
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Checking if you have Text::Wrap 0 ... Yes (2013.0523)
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Checking if you have Regexp::Common 0 ... Yes (2017040401)
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Checking if you have Text::Balanced 1.97 ... Yes (2.03)
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Checking if you have ExtUtils::MakeMaker 0 ... Yes (7.24)
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Checking if you have Test::More 0.47 ... Yes (1.302083)
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Checking if you have IPC::Run 0.1 ... Yes (0.94)
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Checking if you have version 0.77 ... Yes (0.9918)
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! Configure failed for Statistics-R-0.33. See /home/ryan/.cpanm/work/1493520529.5514/build.log for details.
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! Installing the dependencies failed: Module 'Statistics::R' is not installed, Module 'Tie::Hash::Indexed' is not installed
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! Bailing out the installation for Bio-ViennaNGS-v0.16.0.
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N/A
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Command [cpanm --reinstall --verbose Bio::ViennaNGS] 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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