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cpantestlogs/Bio::DB::ESoap_genfailure.log
ryan 4fe8bf59aa Second run of tests
2017-05-02 18:44:36 -07:00

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perl-blead
==========
cpanm (App::cpanminus) 1.7043 on perl 5.026000 built for x86_64-linux
Work directory is /home/ryan/.cpanm/work/1493067340.1215
You have make /usr/bin/make
You have LWP 6.26
You have /bin/tar: tar (GNU tar) 1.29
Copyright (C) 2015 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
Written by John Gilmore and Jay Fenlason.
You have /usr/bin/unzip
Searching Bio::DB::ESoap () on cpanmetadb ...
Unpacking BioPerl-Run-1.007001.tar.gz
--> Working on Bio::DB::ESoap
Fetching http://www.cpan.org/authors/id/C/CJ/CJFIELDS/BioPerl-Run-1.007001.tar.gz ... OK
BioPerl-Run-1.007001
BioPerl-Run-1.007001/.travis.yml
BioPerl-Run-1.007001/AUTHORS
BioPerl-Run-1.007001/Build.PL
BioPerl-Run-1.007001/Changes
BioPerl-Run-1.007001/DEPENDENCIES
BioPerl-Run-1.007001/INSTALL
BioPerl-Run-1.007001/INSTALL.PROGRAMS
BioPerl-Run-1.007001/INSTALL.SKIP
BioPerl-Run-1.007001/LICENSE
BioPerl-Run-1.007001/MANIFEST
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BioPerl-Run-1.007001/t/data/H_pylori_J99.glimmer3.icm
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BioPerl-Run-1.007001/t/data/hmmpfam_protein_input
BioPerl-Run-1.007001/t/data/human.genomic
BioPerl-Run-1.007001/t/data/hyphy1.fasta
BioPerl-Run-1.007001/t/data/hyphy1.tree
BioPerl-Run-1.007001/t/data/lagan_dna.fa
BioPerl-Run-1.007001/t/data/longnames.aln
BioPerl-Run-1.007001/t/data/lvb.fa
BioPerl-Run-1.007001/t/data/lvb_sequential.phy
BioPerl-Run-1.007001/t/data/neighbor.dist
BioPerl-Run-1.007001/t/data/new_dna.fa
BioPerl-Run-1.007001/t/data/new_pep.fa
BioPerl-Run-1.007001/t/data/njtree_aln2.nucl.mfa
BioPerl-Run-1.007001/t/data/NM_002254.gb
BioPerl-Run-1.007001/t/data/NM_002254.tfa
BioPerl-Run-1.007001/t/data/pal2nal.aln
BioPerl-Run-1.007001/t/data/pal2nal.nuc
BioPerl-Run-1.007001/t/data/pfam_sample_R11
BioPerl-Run-1.007001/t/data/Phrap.fa
BioPerl-Run-1.007001/t/data/primate_query.fa
BioPerl-Run-1.007001/t/data/primate_target.fa
BioPerl-Run-1.007001/t/data/Primer3.fa
BioPerl-Run-1.007001/t/data/prints.dat
BioPerl-Run-1.007001/t/data/Prints_prot.FastA
BioPerl-Run-1.007001/t/data/profile_prot.FastA
BioPerl-Run-1.007001/t/data/prosite.dat
BioPerl-Run-1.007001/t/data/protpars.phy
BioPerl-Run-1.007001/t/data/ps1.fa
BioPerl-Run-1.007001/t/data/purine.1.sto
BioPerl-Run-1.007001/t/data/purine.added.fa
BioPerl-Run-1.007001/t/data/purine.all.fa
BioPerl-Run-1.007001/t/data/purine.c.cm
BioPerl-Run-1.007001/t/data/purine.cm
BioPerl-Run-1.007001/t/data/r1.fq
BioPerl-Run-1.007001/t/data/r1bwa.fq
BioPerl-Run-1.007001/t/data/r2.fq
BioPerl-Run-1.007001/t/data/r2bwa.fq
BioPerl-Run-1.007001/t/data/repeatmasker.fa
BioPerl-Run-1.007001/t/data/road.pep
BioPerl-Run-1.007001/t/data/sample_dataset_1.fa
BioPerl-Run-1.007001/t/data/sample_dataset_1.qual
BioPerl-Run-1.007001/t/data/sample_dataset_1_aligned.fa
BioPerl-Run-1.007001/t/data/segmask_data.asn
BioPerl-Run-1.007001/t/data/semphy.seq
BioPerl-Run-1.007001/t/data/semphy.tree
BioPerl-Run-1.007001/t/data/signalp_input_protein
BioPerl-Run-1.007001/t/data/sim4_cdna.fa
BioPerl-Run-1.007001/t/data/sim4_database.fa
BioPerl-Run-1.007001/t/data/sim4_genomic.fa
BioPerl-Run-1.007001/t/data/simprot_tree.nh
BioPerl-Run-1.007001/t/data/species_tree_njtree.nh
BioPerl-Run-1.007001/t/data/test-aln.msf
BioPerl-Run-1.007001/t/data/test-query.fas
BioPerl-Run-1.007001/t/data/test-spa-p.fas
BioPerl-Run-1.007001/t/data/test-spa.fas
BioPerl-Run-1.007001/t/data/test.txt
BioPerl-Run-1.007001/t/data/test_prot.FastA
BioPerl-Run-1.007001/t/data/testaln.phylip
BioPerl-Run-1.007001/t/data/transfac.dat
BioPerl-Run-1.007001/t/data/tree_of_life
BioPerl-Run-1.007001/t/data/treefile.example
BioPerl-Run-1.007001/t/data/TribeMCL.bls
BioPerl-Run-1.007001/t/data/TribeMCL.desc
BioPerl-Run-1.007001/t/data/vista.cls
BioPerl-Run-1.007001/t/data/vista.gff
BioPerl-Run-1.007001/t/data/xprt.gb
BioPerl-Run-1.007001/t/data/bowtie
BioPerl-Run-1.007001/t/data/bowtie/indexes
BioPerl-Run-1.007001/t/data/bowtie/indexes/e_coli.1.ebwt
BioPerl-Run-1.007001/t/data/bowtie/indexes/e_coli.2.ebwt
BioPerl-Run-1.007001/t/data/bowtie/indexes/e_coli.3.ebwt
BioPerl-Run-1.007001/t/data/bowtie/indexes/e_coli.4.ebwt
BioPerl-Run-1.007001/t/data/bowtie/indexes/e_coli.rev.1.ebwt
BioPerl-Run-1.007001/t/data/bowtie/indexes/e_coli.rev.2.ebwt
BioPerl-Run-1.007001/t/data/bowtie/reads
BioPerl-Run-1.007001/t/data/bowtie/reads/e_coli.cb
BioPerl-Run-1.007001/t/data/bowtie/reads/e_coli_1000.fa
BioPerl-Run-1.007001/t/data/bowtie/reads/e_coli_1000.fq
BioPerl-Run-1.007001/t/data/bowtie/reads/e_coli_1000.raw
BioPerl-Run-1.007001/t/data/bowtie/reads/e_coli_10000snp.fa
BioPerl-Run-1.007001/t/data/bowtie/reads/e_coli_10000snp.fq
BioPerl-Run-1.007001/t/data/bowtie/reads/e_coli_1000_1.fa
BioPerl-Run-1.007001/t/data/bowtie/reads/e_coli_1000_1.fq
BioPerl-Run-1.007001/t/data/bowtie/reads/e_coli_1000_2.fa
BioPerl-Run-1.007001/t/data/bowtie/reads/e_coli_1000_2.fq
BioPerl-Run-1.007001/t/data/gerp
BioPerl-Run-1.007001/t/data/gerp/ENr111.gerp.tree
BioPerl-Run-1.007001/t/data/gerp/ENr111.mfa.gz
BioPerl-Run-1.007001/t/data/gumby
BioPerl-Run-1.007001/t/data/gumby/hmrd.mfa
BioPerl-Run-1.007001/t/data/gumby/hmrd.tree
BioPerl-Run-1.007001/t/data/gumby/human.gff
BioPerl-Run-1.007001/t/data/gumby/readme.txt
BioPerl-Run-1.007001/t/data/taxdump
BioPerl-Run-1.007001/t/data/taxdump/names.dmp
BioPerl-Run-1.007001/t/data/taxdump/nodes.dmp
BioPerl-Run-1.007001/t/Tools
BioPerl-Run-1.007001/t/Tools/Run
BioPerl-Run-1.007001/t/Tools/Run/Dummy.pm
BioPerl-Run-1.007001/t/Tools/Run/RemoteBlast.t
BioPerl-Run-1.007001/t/Tools/Run/RemoteBlast_rpsblast.t
BioPerl-Run-1.007001/t/Tools/Run/StandAloneBlast.t
BioPerl-Run-1.007001/t/Tools/Run/WBCommandExts.t
BioPerl-Run-1.007001/t/Tools/Run/WrapperBase.t
BioPerl-Run-1.007001/t/Tools/Run/Dummy
BioPerl-Run-1.007001/t/Tools/Run/Dummy/Config.pm
Entering BioPerl-Run-1.007001
Checking configure dependencies from META.json
Checking if you have Module::Build 0.42 ... Yes (0.4222)
Checking if you have ExtUtils::Install 1.46 ... Yes (2.04)
Running Build.PL
Configuring BioPerl-Run-1.007001 ... Install scripts? y/n [n ]n
Do you want to run tests that require connection to servers across the internet
(likely to cause some failures)? y/n [n ]n
- will not run internet-requiring tests
Created MYMETA.yml and MYMETA.json
Creating new 'Build' script for 'BioPerl-Run' version '1.007001'
Checking dependencies from MYMETA.json ...
Checking if you have Bio::Root::Test 0 ... Yes (undef)
Checking if you have Bio::Root::Root 0 ... Yes (undef)
Checking if you have Bio::Root::Version 1.007000 ... Yes (1.007001)
OK
Building and testing BioPerl-Run-1.007001 ... Building BioPerl-Run
# Required executable for Bio::Tools::Run::Alignment::Amap is not present
t/Amap.t ...................... ok
t/AnalysisFactory_soap.t ...... skipped: Network tests have not been requested
t/Analysis_soap.t ............. skipped: Network tests have not been requested
# Required executable for Bio::Tools::Run::BEDTools is not present
t/BEDTools.t .................. ok
# Required executable for Bio::Tools::Run::BWA is not present
t/BWA.t ....................... ok
# Required executable for Bio::Tools::Run::Alignment::Blat is not present
t/Blat.t ...................... ok
# Required executable for Bio::Tools::Run::Bowtie is not present
t/Bowtie.t .................... ok
# Required executable for Bio::Tools::Run::Cap3 is not present
t/Cap3.t ...................... ok
# Required executable for Bio::Tools::Run::Alignment::Clustalw is not present
t/Clustalw.t .................. ok
# Required executable for Bio::Tools::Run::Coil is not present
t/Coil.t ...................... ok
# Required executable for Bio::Tools::Run::Phylo::Phylip::Consense is not present
t/Consense.t .................. ok
# Required executable for Bio::Tools::Run::Alignment::DBA is not present
t/DBA.t ....................... ok
# Required executable for Bio::Tools::Run::Phylo::Phylip::DrawGram is not present
t/DrawGram.t .................. ok
# Required executable for Bio::Tools::Run::Phylo::Phylip::DrawTree is not present
t/DrawTree.t .................. ok
t/EMBOSS.t .................... ok
t/Ensembl.t ................... skipped: Network tests have not been requested
# Looks like you planned 7 tests but ran 2.
t/Eponine.t ...................
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 5/7 subtests
# Required executable for Bio::Tools::Run::Alignment::Exonerate is not present
t/Exonerate.t ................. ok
# Required executable for Bio::Tools::Run::Phylo::FastTree is not present
t/FastTree.t .................. ok
# Required executable for Bio::Tools::Run::FootPrinter is not present
t/FootPrinter.t ............... ok
# Required environment variable $GENEMARK_MODELS is not set
t/Genemark.hmm.prokaryotic.t .. ok
# Required executable for Bio::Tools::Run::Genewise is not present
t/Genewise.t .................. ok
# Required environment variable $GENSCANDIR is not set
t/Genscan.t ................... ok
# Required executable for Bio::Tools::Run::Phylo::Gerp is not present
t/Gerp.t ...................... ok
# Required executable for Bio::Tools::Run::Glimmer is not present
t/Glimmer2.t .................. ok
# Required executable for Bio::Tools::Run::Glimmer is not present
t/Glimmer3.t .................. ok
# Failed test 'use Bio::Tools::Run::Phylo::Gumby;'
# at t/Gumby.t line 10.
# Tried to use 'Bio::Tools::Run::Phylo::Gumby'.
# Error: Can't locate Bio/SeqFeature/Annotated.pm in @INC (you may need to install the Bio::SeqFeature::Annotated module) (@INC contains: /home/ryan/.cpanm/work/1493067340.1215/BioPerl-Run-1.007001/blib/lib /home/ryan/.cpanm/work/1493067340.1215/BioPerl-Run-1.007001/blib/arch /home/ryan/.cpanm/work/1493067340.1215/BioPerl-Run-1.007001/_build/lib /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/x86_64-linux /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0 /home/ryan/perl5/perlbrew/perls/perl-blead/lib/5.26.0/x86_64-linux /home/ryan/perl5/perlbrew/perls/perl-blead/lib/5.26.0 .) at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Bio/Tools/Phylo/Gumby.pm line 83.
# BEGIN failed--compilation aborted at /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/Bio/Tools/Phylo/Gumby.pm line 83.
# Compilation failed in require at /home/ryan/.cpanm/work/1493067340.1215/BioPerl-Run-1.007001/blib/lib/Bio/Tools/Run/Phylo/Gumby.pm line 142.
# BEGIN failed--compilation aborted at /home/ryan/.cpanm/work/1493067340.1215/BioPerl-Run-1.007001/blib/lib/Bio/Tools/Run/Phylo/Gumby.pm line 142.
# Compilation failed in require at t/Gumby.t line 10.
# BEGIN failed--compilation aborted at t/Gumby.t line 10.
Can't locate object method "new" via package "Bio::Tools::Run::Phylo::Gumby" at t/Gumby.t line 25.
# Looks like your test exited with 255 just after 8.
t/Gumby.t .....................
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 117/124 subtests
# Required executable for Bio::Tools::Run::Hmmer is not present
t/Hmmer.t ..................... ok
# Required executable for Bio::Tools::Run::Phylo::Hyphy::REL is not present
t/Hyphy.t ..................... ok
# Required executable for Bio::Tools::Run::Infernal is not present
t/Infernal.t .................. ok
# Required executable for Bio::Tools::Run::Alignment::Kalign is not present
t/Kalign.t .................... ok
# Required executable for Bio::Tools::Run::Phylo::LVB is not present
t/LVB.t ....................... ok
# Required executable for Bio::Tools::Run::Alignment::Lagan is not present
t/Lagan.t ..................... ok
# Required executable for Bio::Tools::Run::Alignment::MAFFT is not present
t/MAFFT.t ..................... ok
# Failed test 'use Bio::Tools::Run::MCS;'
# at t/MCS.t line 9.
# Tried to use 'Bio::Tools::Run::MCS'.
# Error: Can't locate Bio/FeatureIO.pm in @INC (you may need to install the Bio::FeatureIO module) (@INC contains: /home/ryan/.cpanm/work/1493067340.1215/BioPerl-Run-1.007001/blib/lib /home/ryan/.cpanm/work/1493067340.1215/BioPerl-Run-1.007001/blib/arch /home/ryan/.cpanm/work/1493067340.1215/BioPerl-Run-1.007001/_build/lib /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/x86_64-linux /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0 /home/ryan/perl5/perlbrew/perls/perl-blead/lib/5.26.0/x86_64-linux /home/ryan/perl5/perlbrew/perls/perl-blead/lib/5.26.0 .) at /home/ryan/.cpanm/work/1493067340.1215/BioPerl-Run-1.007001/blib/lib/Bio/Tools/Run/MCS.pm line 131.
# BEGIN failed--compilation aborted at /home/ryan/.cpanm/work/1493067340.1215/BioPerl-Run-1.007001/blib/lib/Bio/Tools/Run/MCS.pm line 131.
# Compilation failed in require at t/MCS.t line 9.
# BEGIN failed--compilation aborted at t/MCS.t line 9.
# Failed test 'use Bio::SeqFeature::Annotated;'
# at t/MCS.t line 10.
# Tried to use 'Bio::SeqFeature::Annotated'.
# Error: Can't locate Bio/SeqFeature/Annotated.pm in @INC (you may need to install the Bio::SeqFeature::Annotated module) (@INC contains: /home/ryan/.cpanm/work/1493067340.1215/BioPerl-Run-1.007001/blib/lib /home/ryan/.cpanm/work/1493067340.1215/BioPerl-Run-1.007001/blib/arch /home/ryan/.cpanm/work/1493067340.1215/BioPerl-Run-1.007001/_build/lib /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/x86_64-linux /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0 /home/ryan/perl5/perlbrew/perls/perl-blead/lib/5.26.0/x86_64-linux /home/ryan/perl5/perlbrew/perls/perl-blead/lib/5.26.0 .) at t/MCS.t line 10.
# BEGIN failed--compilation aborted at t/MCS.t line 10.
Can't locate object method "new" via package "Bio::Tools::Run::MCS" at t/MCS.t line 18.
# Looks like your test exited with 255 just after 4.
t/MCS.t .......................
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 22/24 subtests
# Required executable for Bio::Tools::Run::Alignment::MSAProbs is not present
t/MSAProbs.t .................. ok
# Required executable for Bio::Tools::Run::Maq is not present
t/Maq.t ....................... ok
# Failed test 'use Bio::Tools::Run::Match;'
# at t/Match.t line 10.
# Tried to use 'Bio::Tools::Run::Match'.
# Error: Can't locate Bio/FeatureIO.pm in @INC (you may need to install the Bio::FeatureIO module) (@INC contains: /home/ryan/.cpanm/work/1493067340.1215/BioPerl-Run-1.007001/blib/lib /home/ryan/.cpanm/work/1493067340.1215/BioPerl-Run-1.007001/blib/arch /home/ryan/.cpanm/work/1493067340.1215/BioPerl-Run-1.007001/_build/lib /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/x86_64-linux /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0 /home/ryan/perl5/perlbrew/perls/perl-blead/lib/5.26.0/x86_64-linux /home/ryan/perl5/perlbrew/perls/perl-blead/lib/5.26.0 .) at /home/ryan/.cpanm/work/1493067340.1215/BioPerl-Run-1.007001/blib/lib/Bio/Tools/Run/Match.pm line 116.
# BEGIN failed--compilation aborted at /home/ryan/.cpanm/work/1493067340.1215/BioPerl-Run-1.007001/blib/lib/Bio/Tools/Run/Match.pm line 116.
# Compilation failed in require at t/Match.t line 10.
# BEGIN failed--compilation aborted at t/Match.t line 10.
Can't locate object method "new" via package "Bio::Tools::Run::Match" at t/Match.t line 17.
# Looks like your test exited with 255 just after 1.
t/Match.t .....................
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 7/7 subtests
# Required executable for Bio::Tools::Run::Mdust is not present
t/Mdust.t ..................... ok
# Required executable for Bio::Tools::Run::Meme is not present
t/Meme.t ...................... ok
# Required executable for Bio::Tools::Run::Minimo is not present
t/Minimo.t .................... ok
# Required executable for Bio::Tools::Run::Phylo::Molphy::ProtML is not present
t/Molphy.t .................... ok
# Required executable for Bio::Tools::Run::Alignment::Muscle is not present
t/Muscle.t .................... ok
# Required executable for Bio::Tools::Run::Phylo::Phylip::Neighbor is not present
t/Neighbor.t .................. ok
# Required executable for Bio::Tools::Run::Newbler is not present
t/Newbler.t ................... ok
# Required executable for Bio::Tools::Run::Phylo::Njtree::Best is not present
t/Njtree.t .................... ok
# Required executable for Bio::Tools::Run::Phylo::PAML::Codeml is not present
t/PAML.t ...................... ok
# Required executable for Bio::Tools::Run::Alignment::Pal2Nal is not present
t/Pal2Nal.t ................... ok
# Failed test 'use Bio::Tools::Run::Phylo::Phast::PhastCons;'
# at t/PhastCons.t line 10.
# Tried to use 'Bio::Tools::Run::Phylo::Phast::PhastCons'.
# Error: Can't locate Bio/FeatureIO.pm in @INC (you may need to install the Bio::FeatureIO module) (@INC contains: /home/ryan/.cpanm/work/1493067340.1215/BioPerl-Run-1.007001/blib/lib /home/ryan/.cpanm/work/1493067340.1215/BioPerl-Run-1.007001/blib/arch /home/ryan/.cpanm/work/1493067340.1215/BioPerl-Run-1.007001/_build/lib /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0/x86_64-linux /home/ryan/perl5/perlbrew/perls/perl-blead/lib/site_perl/5.26.0 /home/ryan/perl5/perlbrew/perls/perl-blead/lib/5.26.0/x86_64-linux /home/ryan/perl5/perlbrew/perls/perl-blead/lib/5.26.0 .) at /home/ryan/.cpanm/work/1493067340.1215/BioPerl-Run-1.007001/blib/lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm line 140.
# BEGIN failed--compilation aborted at /home/ryan/.cpanm/work/1493067340.1215/BioPerl-Run-1.007001/blib/lib/Bio/Tools/Run/Phylo/Phast/PhastCons.pm line 140.
# Compilation failed in require at t/PhastCons.t line 10.
# BEGIN failed--compilation aborted at t/PhastCons.t line 10.
Can't locate object method "new" via package "Bio::Tools::Run::Phylo::Phast::PhastCons" at t/PhastCons.t line 23.
# Looks like your test exited with 255 just after 6.
t/PhastCons.t .................
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 176/181 subtests
# Required executable for Bio::Tools::Run::Phrap is not present
t/Phrap.t ..................... ok
# Required executable for Bio::Tools::Run::Phylo::Phyml is not present
t/Phyml.t ..................... ok
# Required executable for Bio::Tools::Run::Primate is not present
t/Primate.t ................... ok
# Required executable for Bio::Tools::Run::Primer3 is not present
t/Primer3.t ................... ok
# Required executable for Bio::Tools::Run::Prints is not present
t/Prints.t .................... ok
# Required executable for Bio::Tools::Run::Alignment::Probalign is not present
t/Probalign.t ................. ok
# Required executable for Bio::Tools::Run::Alignment::Probcons is not present
t/Probcons.t .................. ok
# Required executable for Bio::Tools::Run::Profile is not present
t/Profile.t ................... ok
# Required executable for Bio::Tools::Run::Promoterwise is not present
t/Promoterwise.t .............. ok
# Required executable for Bio::Tools::Run::Phylo::Phylip::ProtDist is not present
t/ProtDist.t .................. ok
# Required executable for Bio::Tools::Run::Phylo::Phylip::ProtPars is not present
t/ProtPars.t .................. ok
# Required executable for Bio::Tools::Run::Pseudowise is not present
t/Pseudowise.t ................ ok
# Required executable for Bio::Tools::Run::Phylo::QuickTree is not present
t/QuickTree.t ................. ok
# Required executable for Bio::Tools::Run::Phylo::Raxml is not present
t/Raxml.t ..................... ok
# Required executable for Bio::Tools::Run::RepeatMasker is not present
t/RepeatMasker.t .............. ok
# Required executable for Bio::Tools::Run::BlastPlus is not present
# Looks like you planned 73 tests but ran 69.
t/SABlastPlus.t ...............
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 4/73 subtests
(less 65 skipped subtests: 4 okay)
# Required executable for Bio::Tools::Run::Phylo::SLR is not present
t/SLR.t ....................... ok
# Required executable for Bio::Tools::Run::Samtools is not present
t/Samtools.t .................. ok
# Required executable for Bio::Tools::Run::Seg is not present
t/Seg.t ....................... ok
# Required executable for Bio::Tools::Run::Phylo::Semphy is not present
t/Semphy.t .................... ok
# Required executable for Bio::Tools::Run::Phylo::Phylip::SeqBoot is not present
t/SeqBoot.t ................... ok
# Required executable for Bio::Tools::Run::Signalp is not present
t/Signalp.t ................... ok
# Required executable for Bio::Tools::Run::Alignment::Sim4 is not present
t/Sim4.t ...................... ok
# Required executable for Bio::Tools::Run::Simprot is not present
t/Simprot.t ................... ok
t/SoapEU-function.t ........... skipped: Valid email not provided; required for tests
# NCBI SOAP EUtilities API no longer supported as of 2015, modules are deprecated and will be removed in a future release
t/SoapEU-unit.t ............... ok
# Required executable for Bio::Tools::Run::Alignment::StandAloneFasta is not present
t/StandAloneFasta.t ........... ok
# Required executable for Bio::Tools::Run::Alignment::TCoffee is not present
t/TCoffee.t ................... ok
# Required executable for Bio::Tools::Run::TigrAssembler is not present
# Required executable for Bio::Tools::Run::TigrAssembler is not present
t/TigrAssembler.t ............. ok
# Required executable for Bio::Tools::Run::Tmhmm is not present
t/Tmhmm.t ..................... ok
t/TribeMCL.t .................. ok
t/Vista.t ..................... ok
# Required executable for Bio::Tools::Run::Alignment::Gmap is not present
t/gmap-run.t .................. ok
# Required executable for Bio::Tools::Run::tRNAscanSE is not present
t/tRNAscanSE.t ................ ok
Test Summary Report
-------------------
t/Eponine.t (Wstat: 65280 Tests: 2 Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 7 tests but ran 2.
t/Gumby.t (Wstat: 65280 Tests: 8 Failed: 1)
Failed test: 1
Non-zero exit status: 255
Parse errors: Bad plan. You planned 124 tests but ran 8.
t/MCS.t (Wstat: 65280 Tests: 4 Failed: 2)
Failed tests: 1-2
Non-zero exit status: 255
Parse errors: Bad plan. You planned 24 tests but ran 4.
t/Match.t (Wstat: 65280 Tests: 1 Failed: 1)
Failed test: 1
Non-zero exit status: 255
Parse errors: Bad plan. You planned 7 tests but ran 1.
t/PhastCons.t (Wstat: 65280 Tests: 6 Failed: 1)
Failed test: 1
Non-zero exit status: 255
Parse errors: Bad plan. You planned 181 tests but ran 6.
t/SABlastPlus.t (Wstat: 65280 Tests: 69 Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 73 tests but ran 69.
Files=83, Tests=2767, 22 wallclock secs ( 0.26 usr 0.04 sys + 6.94 cusr 0.62 csys = 7.86 CPU)
Result: FAIL
Failed 6/83 test programs. 5/2767 subtests failed.
! Installing Bio::DB::ESoap failed. See /home/ryan/.cpanm/work/1493067340.1215/build.log for details. Retry with --force to force install it.
FAIL
Command [cpanm --reinstall --verbose Bio::DB::ESoap] terminated with exit code 1 ($? = 256) under the following perl environment:
Command terminated with non-zero status.
Current perl:
Name: perl-blead
Path: /home/ryan/perl5/perlbrew/perls/perl-blead/bin/perl
Config: -de -Dprefix=/home/ryan/perl5/perlbrew/perls/perl-blead -Dusedevel -Aeval:scriptdir=/home/ryan/perl5/perlbrew/perls/perl-blead/bin
Compiled at: Mar 30 2017 03:10:09
perlbrew:
version: 0.78
ENV:
PERLBREW_ROOT: /home/ryan/perl5/perlbrew
PERLBREW_HOME: /home/ryan/.perlbrew
PERLBREW_PATH: /home/ryan/perl5/perlbrew/bin:/home/ryan/perl5/perlbrew/perls/perl-blead/bin
PERLBREW_MANPATH: /home/ryan/perl5/perlbrew/perls/perl-blead/man
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