Back
From: metabase:user:30ae4450-2aae-11df-837a-5e0a49663a4f
Subject: FAIL BioPerl-1.6.923 v5.16.0
Date: 2013-12-20T16:15:51Z
This distribution has been tested as part of the CPAN Testers
project, supporting the Perl programming language. See
http://wiki.cpantesters.org/ for more information or email
questions to cpan-testers-discuss@perl.org
--
Dear Christopher Fields,
This is a computer-generated report for BioPerl-1.6.923
on perl 5.16.0, created by CPAN-Reporter-1.2010_01.
Thank you for uploading your work to CPAN. However, there was a problem
testing your distribution.
If you think this report is invalid, please consult the CPAN Testers Wiki
for suggestions on how to avoid getting FAIL reports for missing library
or binary dependencies, unsupported operating systems, and so on:
http://wiki.cpantesters.org/wiki/CPANAuthorNotes
Sections of this report:
* Tester comments
* Program output
* Prerequisites
* Environment and other context
------------------------------
TESTER COMMENTS
------------------------------
Additional comments from tester:
this report is from an automated smoke testing program
and was not reviewed by a human for accuracy
------------------------------
PROGRAM OUTPUT
------------------------------
Output from 'C:\strawberry160\perl\bin\perl.exe ./Build test':
t/Align/AlignStats.t ................... ok
t/Align/AlignUtil.t .................... ok
t/Align/Graphics.t ..................... ok
t/Align/SimpleAlign.t .................. ok
t/Align/TreeBuild.t .................... ok
t/Align/Utilities.t .................... ok
t/AlignIO/AlignIO.t .................... ok
t/AlignIO/arp.t ........................ ok
t/AlignIO/bl2seq.t ..................... ok
t/AlignIO/clustalw.t ................... ok
t/AlignIO/emboss.t ..................... ok
t/AlignIO/fasta.t ...................... ok
t/AlignIO/largemultifasta.t ............ ok
t/AlignIO/maf.t ........................ ok
t/AlignIO/mase.t ....................... ok
t/AlignIO/mega.t ....................... ok
t/AlignIO/meme.t ....................... ok
t/AlignIO/metafasta.t .................. ok
t/AlignIO/msf.t ........................ ok
t/AlignIO/nexml.t ...................... skipped: The optional module Bio::Phylo (or dependencies thereof) was not installed
t/AlignIO/nexus.t ...................... ok
t/AlignIO/pfam.t ....................... ok
t/AlignIO/phylip.t ..................... ok
t/AlignIO/po.t ......................... ok
t/AlignIO/prodom.t ..................... ok
t/AlignIO/psi.t ........................ ok
t/AlignIO/selex.t ...................... ok
t/AlignIO/stockholm.t .................. ok
t/AlignIO/xmfa.t ....................... ok
t/Alphabet.t ........................... ok
t/Annotation/Annotation.t .............. ok
t/Annotation/AnnotationAdaptor.t ....... ok
t/Assembly/ContigSpectrum.t ............ ok
t/Assembly/IO/bowtie.t ................. skipped: The optional module Bio::DB::Sam (or dependencies thereof) was not installed
t/Assembly/IO/sam.t .................... skipped: The optional module Bio::DB::Sam (or dependencies thereof) was not installed
Can't do inplace edit without backup at Bio/Root/IO.pm line 570.
# Looks like you planned 890 tests but ran 246.
# Looks like your test exited with 25 just after 246.
t/Assembly/core.t ......................
Dubious, test returned 25 (wstat 6400, 0x1900)
Failed 644/890 subtests
t/Cluster/UniGene.t .................... ok
t/ClusterIO/ClusterIO.t ................ ok
t/ClusterIO/SequenceFamily.t ........... ok
t/ClusterIO/unigene.t .................. ok
t/Coordinate/CoordinateBoundaryTest.t .. ok
t/Coordinate/CoordinateGraph.t ......... ok
t/Coordinate/CoordinateMapper.t ........ ok
t/Coordinate/GeneCoordinateMapper.t .... ok
t/Draw/Pictogram.t ..................... ok
t/LiveSeq/Chain.t ...................... ok
t/LiveSeq/LiveSeq.t .................... ok
t/LiveSeq/Mutation.t ................... ok
t/LiveSeq/Mutator.t .................... ok
You are loading a Bio::DB::GFF database with GFF3 formatted data.
While this will likely work fine, the Bio::DB::GFF schema does not
always faithfully capture the complexity represented in GFF3 files.
Unless you have a specific reason for using Bio::DB::GFF, we suggest
that you use a Bio::DB::SeqFeature::Store database and its corresponding
loader, bp_seqfeature_load.pl.
t/LocalDB/BioDBGFF.t ................... ok
t/LocalDB/Fasta.t ...................... ok
t/LocalDB/Flat.t ....................... ok
t/LocalDB/Index/Blast.t ................ ok
t/LocalDB/Index/BlastTable.t ........... ok
t/LocalDB/Index/Index.t ................ ok
t/LocalDB/Qual.t ....................... ok
t/LocalDB/Registry.t ................... ok
t/LocalDB/SeqFeature.t ................. ok
t/LocalDB/Taxonomy/greengenes.t ........ ok
t/LocalDB/Taxonomy/silva.t ............. ok
cannot unlink file for C:\DOCUME~1\a\LOCALS~1\Temp\TObMceTtcF\id2names: Permission denied at C:/strawberry160/perl/lib/File/Temp.pm line 902.
cannot unlink file for C:\DOCUME~1\a\LOCALS~1\Temp\TObMceTtcF\nodes: Permission denied at C:/strawberry160/perl/lib/File/Temp.pm line 902.
cannot remove directory for C:\DOCUME~1\a\LOCALS~1\Temp\TObMceTtcF: Directory not empty at C:/strawberry160/perl/lib/File/Temp.pm line 902.
t/LocalDB/transfac_pro.t ............... ok
t/Map/Cyto.t ........................... ok
t/Map/Linkage.t ........................ ok
t/Map/Map.t ............................ ok
t/Map/MapIO.t .......................... ok
t/Map/MicrosatelliteMarker.t ........... ok
t/Map/Physical.t ....................... ok
t/Matrix/IO/masta.t .................... ok
t/Matrix/IO/psm.t ...................... ok
t/Matrix/InstanceSite.t ................ ok
t/Matrix/Matrix.t ...................... ok
t/Matrix/ProtMatrix.t .................. ok
t/Matrix/ProtPsm.t ..................... ok
t/Matrix/SiteMatrix.t .................. ok
t/Ontology/GOterm.t .................... skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/Ontology/GraphAdaptor.t .............. skipped: The optional module Graph (or dependencies thereof) was not installed
t/Ontology/IO/go.t ..................... skipped: The optional module Graph (or dependencies thereof) was not installed
t/Ontology/IO/interpro.t ............... skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/Ontology/IO/obo.t .................... skipped: The optional module Graph (or dependencies thereof) was not installed
t/Ontology/Ontology.t .................. skipped: The optional module Graph (or dependencies thereof) was not installed
t/Ontology/OntologyEngine.t ............ skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/Ontology/OntologyStore.t ............. skipped: The optional module Graph (or dependencies thereof) was not installed
t/Ontology/Relationship.t .............. skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/Ontology/RelationshipType.t .......... skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/Ontology/Term.t ...................... skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/Perl.t ............................... ok
t/Phenotype/Correlate.t ................ ok
t/Phenotype/MeSH.t ..................... ok
t/Phenotype/Measure.t .................. ok
t/Phenotype/MiniMIMentry.t ............. ok
t/Phenotype/OMIMentry.t ................ ok
t/Phenotype/OMIMentryAllelicVariant.t .. ok
t/Phenotype/OMIMparser.t ............... ok
t/Phenotype/Phenotype.t ................ ok
t/PodSyntax.t .......................... ok
t/PopGen/Coalescent.t .................. ok
t/PopGen/HtSNP.t ....................... ok
t/PopGen/MK.t .......................... ok
t/PopGen/PopGen.t ...................... ok
t/PopGen/PopGenSims.t .................. ok
t/PopGen/TagHaplotype.t ................ ok
t/RemoteDB/BioFetch.t .................. skipped: Network tests have not been requested
t/RemoteDB/CUTG.t ...................... ok
t/RemoteDB/EMBL.t ...................... skipped: Network tests have not been requested
t/RemoteDB/EntrezGene.t ................ skipped: The optional module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed
t/RemoteDB/GenBank.t ................... skipped: Network tests have not been requested
t/RemoteDB/GenPept.t ................... skipped: Network tests have not been requested
t/RemoteDB/HIV/HIV.t ................... ok
t/RemoteDB/HIV/HIVAnnotProcessor.t ..... ok
t/RemoteDB/HIV/HIVQuery.t .............. ok
t/RemoteDB/HIV/HIVQueryHelper.t ........ ok
t/RemoteDB/MeSH.t ...................... skipped: Network tests have not been requested
t/RemoteDB/Query/GenBank.t ............. skipped: Network tests have not been requested
t/RemoteDB/RefSeq.t .................... ok
t/RemoteDB/SeqHound.t .................. skipped: Network tests have not been requested
t/RemoteDB/SeqRead_fail.t .............. skipped: Network tests have not been requested
t/RemoteDB/SeqVersion.t ................ ok
t/RemoteDB/SwissProt.t ................. skipped: Network tests have not been requested
t/RemoteDB/Taxonomy.t .................. ok
t/Restriction/Analysis-refac.t ......... ok
t/Restriction/Analysis.t ............... ok
t/Restriction/Gel.t .................... ok
t/Restriction/IO.t ..................... ok
t/Root/Exception.t ..................... ok
t/Root/HTTPget.t ....................... skipped: Network tests have not been requested
t/Root/RootI.t ......................... ok
# Failed test 'executable file'
# at t/Root/RootIO.t line 59.
Can't do inplace edit without backup at Bio/Root/IO.pm line 570.
Error removing C:\DOCUME~1\a\LOCALS~1\Temp\iqM6NLvOrB at C:/strawberry160/perl/lib/File/Temp.pm line 890.
# Looks like you planned 77 tests but ran 45.
# Looks like you failed 1 test of 45 run.
# Looks like your test exited with 25 just after 45.
t/Root/RootIO.t ........................
Dubious, test returned 25 (wstat 6400, 0x1900)
Failed 33/77 subtests
t/Root/Storable.t ...................... ok
t/Root/Tempfile.t ...................... ok
t/Root/Utilities.t ..................... ok
t/SearchDist.t ......................... skipped: The optional module Bio::Ext::Align (or dependencies thereof) was not installed
t/SearchIO/CigarString.t ............... ok
t/SearchIO/SearchIO.t .................. ok
t/SearchIO/SimilarityPair.t ............ ok
t/SearchIO/Tiling.t .................... ok
t/SearchIO/Writer/GbrowseGFF.t ......... ok
t/SearchIO/Writer/HSPTableWriter.t ..... ok
t/SearchIO/Writer/HTMLWriter.t ......... ok
t/SearchIO/Writer/HitTableWriter.t ..... ok
t/SearchIO/Writer/TextWriter.t ......... ok
t/SearchIO/axt.t ....................... ok
t/SearchIO/blast.t ..................... ok
t/SearchIO/blast_pull.t ................ ok
t/SearchIO/blasttable.t ................ ok
t/SearchIO/blastxml.t .................. ok
t/SearchIO/cross_match.t ............... ok
t/SearchIO/erpin.t ..................... ok
t/SearchIO/exonerate.t ................. ok
t/SearchIO/fasta.t ..................... ok
t/SearchIO/gmap_f9.t ................... ok
'cat' is not recognized as an internal or external command,
operable program or batch file.
# Failed test 'Check for the correct result reference type'
# at t/SearchIO/hmmer.t line 637.
# got: ''
# expected: 'Bio::Search::Result::HMMERResult'
Can't call method "num_hits" on an undefined value at t/SearchIO/hmmer.t line 641.
# Looks like you planned 327 tests but ran 298.
# Looks like you failed 1 test of 298 run.
# Looks like your test exited with 256 just after 298.
t/SearchIO/hmmer.t .....................
Failed 30/327 subtests
t/SearchIO/hmmer_pull.t ................ ok
t/SearchIO/infernal.t .................. ok
t/SearchIO/megablast.t ................. ok
t/SearchIO/psl.t ....................... ok
t/SearchIO/rnamotif.t .................. ok
t/SearchIO/sim4.t ...................... ok
t/SearchIO/waba.t ...................... ok
t/SearchIO/wise.t ...................... ok
t/Seq/DBLink.t ......................... ok
t/Seq/EncodedSeq.t ..................... ok
t/Seq/LargeLocatableSeq.t .............. ok
t/Seq/LargePSeq.t ...................... ok
t/Seq/LocatableSeq.t ................... ok
t/Seq/MetaSeq.t ........................ ok
t/Seq/PrimaryQual.t .................... ok
t/Seq/PrimarySeq.t ..................... ok
t/Seq/PrimedSeq.t ...................... ok
t/Seq/Quality.t ........................ ok
t/Seq/Seq.t ............................ ok
t/Seq/SimulatedRead.t .................. ok
t/Seq/WithQuality.t .................... ok
t/SeqEvolution.t ....................... ok
t/SeqFeature/Amplicon.t ................ ok
t/SeqFeature/Clone.t ................... ok
t/SeqFeature/Collection.t .............. ok
t/SeqFeature/Computation.t ............. ok
t/SeqFeature/FeaturePair.t ............. ok
t/SeqFeature/Gene.t .................... ok
t/SeqFeature/Generic.t ................. ok
t/SeqFeature/Location.t ................ ok
t/SeqFeature/LocationFactory.t ......... ok
t/SeqFeature/Primer.t .................. ok
t/SeqFeature/Range.t ................... ok
t/SeqFeature/RangeI.t .................. ok
t/SeqFeature/SeqAnalysisParser.t ....... ok
t/SeqFeature/SubSeq.t .................. ok
t/SeqFeature/Unflattener.t ............. ok
t/SeqFeature/Unflattener2.t ............ ok
t/SeqIO/Handler.t ...................... ok
t/SeqIO/MultiFile.t .................... ok
t/SeqIO/Multiple_fasta.t ............... ok
t/SeqIO/SeqBuilder.t ................... ok
t/SeqIO/SeqIO.t ........................ ok
t/SeqIO/Splicedseq.t ................... ok
t/SeqIO/abi.t .......................... skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqIO/ace.t .......................... ok
t/SeqIO/agave.t ........................ ok
t/SeqIO/alf.t .......................... skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqIO/asciitree.t .................... ok
t/SeqIO/bsml.t ......................... ok
t/SeqIO/bsml_sax.t ..................... ok
t/SeqIO/chadoxml.t ..................... ok
t/SeqIO/chaos.t ........................ ok
t/SeqIO/chaosxml.t ..................... ok
t/SeqIO/ctf.t .......................... skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqIO/embl.t ......................... ok
t/SeqIO/entrezgene.t ................... skipped: The optional module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed
t/SeqIO/excel.t ........................ ok
t/SeqIO/exp.t .......................... skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
Subroutine _initialize redefined at Bio\SeqIO\fasta.pm line 85.
Subroutine next_seq redefined at Bio\SeqIO\fasta.pm line 119.
Subroutine write_seq redefined at Bio\SeqIO\fasta.pm line 199.
Subroutine width redefined at Bio\SeqIO\fasta.pm line 289.
Subroutine block redefined at Bio\SeqIO\fasta.pm line 310.
Subroutine preferred_id_type redefined at Bio\SeqIO\fasta.pm line 335.
t/SeqIO/fasta.t ........................ ok
t/SeqIO/fastq.t ........................ ok
t/SeqIO/flybase_chadoxml.t ............. ok
t/SeqIO/game.t ......................... ok
t/SeqIO/gbxml.t ........................ ok
t/SeqIO/gcg.t .......................... ok
t/SeqIO/genbank.t ...................... ok
t/SeqIO/interpro.t ..................... skipped: The optional module XML::DOM::XPath (or dependencies thereof) was not installed
t/SeqIO/kegg.t ......................... ok
t/SeqIO/largefasta.t ................... ok
t/SeqIO/lasergene.t .................... ok
t/SeqIO/locuslink.t .................... skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/SeqIO/mbsout.t ....................... ok
t/SeqIO/metafasta.t .................... ok
t/SeqIO/msout.t ........................ ok
t/SeqIO/nexml.t ........................ skipped: The optional module Bio::Phylo (or dependencies thereof) was not installed
t/SeqIO/phd.t .......................... ok
t/SeqIO/pir.t .......................... ok
t/SeqIO/pln.t .......................... skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqIO/qual.t ......................... ok
t/SeqIO/raw.t .......................... ok
t/SeqIO/scf.t .......................... ok
t/SeqIO/seqxml.t ....................... ok
t/SeqIO/strider.t ...................... skipped: The optional module Convert::Binary::C (or dependencies thereof) was not installed
t/SeqIO/swiss.t ........................ ok
t/SeqIO/tab.t .......................... ok
t/SeqIO/table.t ........................ ok
t/SeqIO/tigr.t ......................... ok
t/SeqIO/tigrxml.t ...................... ok
t/SeqIO/tinyseq.t ...................... ok
t/SeqIO/ztr.t .......................... skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqTools/Backtranslate.t ............. ok
t/SeqTools/CodonTable.t ................ ok
t/SeqTools/ECnumber.t .................. ok
t/SeqTools/GuessSeqFormat.t ............ ok
t/SeqTools/OddCodes.t .................. ok
t/SeqTools/SeqPattern.t ................ ok
t/SeqTools/SeqStats.t .................. ok
t/SeqTools/SeqUtils.t .................. ok
t/SeqTools/SeqWords.t .................. ok
t/Species.t ............................ ok
t/Structure/IO.t ....................... ok
t/Structure/Structure.t ................ ok
t/Symbol.t ............................. ok
t/TaxonTree.t .......................... skipped: All tests are being skipped, probably because the module(s) being tested here are now deprecated
t/Tools/Alignment/Consed.t ............. skipped: Not compatible with your Operating System
t/Tools/AmpliconSearch.t ............... ok
t/Tools/Analysis/DNA/ESEfinder.t ....... skipped: Network tests have not been requested
t/Tools/Analysis/Protein/Domcut.t ...... skipped: Network tests have not been requested
t/Tools/Analysis/Protein/ELM.t ......... skipped: Network tests have not been requested
t/Tools/Analysis/Protein/GOR4.t ........ skipped: Network tests have not been requested
t/Tools/Analysis/Protein/HNN.t ......... skipped: Network tests have not been requested
t/Tools/Analysis/Protein/Mitoprot.t .... skipped: Network tests have not been requested
t/Tools/Analysis/Protein/NetPhos.t ..... skipped: Network tests have not been requested
t/Tools/Analysis/Protein/Scansite.t .... ok
t/Tools/Analysis/Protein/Sopma.t ....... ok
t/Tools/EMBOSS/Palindrome.t ............ ok
t/Tools/Est2Genome.t ................... ok
t/Tools/FootPrinter.t .................. ok
t/Tools/GFF.t .......................... ok
t/Tools/Geneid.t ....................... ok
t/Tools/Genewise.t ..................... ok
t/Tools/Genomewise.t ................... ok
t/Tools/Genpred.t ...................... ok
t/Tools/GuessSeqFormat.t ............... ok
t/Tools/Hmmer.t ........................ ok
t/Tools/IUPAC.t ........................ ok
t/Tools/Lucy.t ......................... ok
t/Tools/Match.t ........................ ok
t/Tools/Phylo/Gerp.t ................... ok
t/Tools/Phylo/Molphy.t ................. ok
t/Tools/Phylo/PAML.t ................... ok
t/Tools/Phylo/Phylip/ProtDist.t ........ ok
t/Tools/Primer3.t ...................... ok
t/Tools/Promoterwise.t ................. ok
t/Tools/Pseudowise.t ................... ok
t/Tools/QRNA.t ......................... ok
t/Tools/RandDistFunctions.t ............ ok
t/Tools/RepeatMasker.t ................. ok
t/Tools/Run/RemoteBlast.t .............. skipped: Network tests have not been requested
t/Tools/Run/RemoteBlast_rpsblast.t ..... skipped: Network tests have not been requested
t/Tools/Run/StandAloneBlast.t .......... ok
# Failed test 'find in syspath'
# at t/Tools/Run/WBCommandExts.t line 64.
# Looks like you failed 1 test of 25.
t/Tools/Run/WBCommandExts.t ............
Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/25 subtests
(1 TODO test unexpectedly succeeded)
t/Tools/Run/WrapperBase.t .............. ok
t/Tools/Seg.t .......................... ok
t/Tools/SiRNA.t ........................ ok
t/Tools/Sigcleave.t .................... ok
t/Tools/Signalp.t ...................... ok
t/Tools/Signalp/ExtendedSignalp.t ...... ok
t/Tools/Sim4.t ......................... ok
t/Tools/Spidey/Spidey.t ................ ok
t/Tools/TandemRepeatsFinder.t .......... ok
t/Tools/TargetP.t ...................... ok
t/Tools/Tmhmm.t ........................ ok
t/Tools/ePCR.t ......................... ok
t/Tools/pICalculator.t ................. ok
t/Tools/rnamotif.t ..................... skipped: All tests are being skipped, probably because the module(s) being tested here are now deprecated
t/Tools/tRNAscanSE.t ................... ok
t/Tree/Compatible.t .................... ok
t/Tree/Node.t .......................... ok
t/Tree/PhyloNetwork/Factory.t .......... skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed
t/Tree/PhyloNetwork/GraphViz.t ......... skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed
t/Tree/PhyloNetwork/MuVector.t ......... ok
t/Tree/PhyloNetwork/PhyloNetwork.t ..... skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/Tree/PhyloNetwork/RandomFactory.t .... skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed
t/Tree/PhyloNetwork/TreeFactory.t ...... skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed
t/Tree/RandomTreeFactory.t ............. ok
t/Tree/Tree.t .......................... ok
t/Tree/TreeIO.t ........................ ok
t/Tree/TreeIO/lintree.t ................ ok
t/Tree/TreeIO/newick.t ................. ok
t/Tree/TreeIO/nexml.t .................. skipped: The optional module Bio::Phylo (or dependencies thereof) was not installed
t/Tree/TreeIO/nexus.t .................. ok
t/Tree/TreeIO/nhx.t .................... ok
t/Tree/TreeIO/phyloxml.t ............... ok
t/Tree/TreeIO/svggraph.t ............... ok
t/Tree/TreeIO/tabtree.t ................ ok
t/Tree/TreeStatistics.t ................ ok
t/Variation/AAChange.t ................. ok
t/Variation/AAReverseMutate.t .......... ok
t/Variation/Allele.t ................... ok
t/Variation/DNAMutation.t .............. ok
t/Variation/RNAChange.t ................ ok
t/Variation/SNP.t ...................... ok
t/Variation/SeqDiff.t .................. ok
t/Variation/Variation_IO.t ............. ok
t/nexml.t .............................. skipped: The optional module Bio::Phylo (or dependencies thereof) was not installed
Test Summary Report
-------------------
t/Assembly/core.t (Wstat: 6400 Tests: 246 Failed: 0)
Non-zero exit status: 25
Parse errors: Bad plan. You planned 890 tests but ran 246.
t/Map/Physical.t (Wstat: 0 Tests: 40 Failed: 0)
TODO passed: 40
t/Root/RootIO.t (Wstat: 6400 Tests: 45 Failed: 1)
Failed test: 13
Non-zero exit status: 25
Parse errors: Bad plan. You planned 77 tests but ran 45.
t/SearchIO/hmmer.t (Wstat: 0 Tests: 298 Failed: 1)
Failed test: 298
Parse errors: Bad plan. You planned 327 tests but ran 298.
t/Tools/Run/WBCommandExts.t (Wstat: 256 Tests: 25 Failed: 1)
Failed test: 25
TODO passed: 14
Non-zero exit status: 1
Files=337, Tests=19931, 392 wallclock secs ( 1.74 usr + 3.86 sys = 5.60 CPU)
Result: FAIL
Failed 4/337 test programs. 3/19931 subtests failed.
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
------------------ ------ --------
Data::Stag 0.11 0.14
DB_File 0 1.826
ExtUtils::Manifest 1.52 1.61
IO::String 0 1.08
perl v5.6.1 5.016000
Scalar::Util 0 1.35
build_requires:
Module Need Have
------------------ ------ --------
CPAN 1.81 2.00
Module::Build 0.2805 0.4203
Test::Harness 2.62 3.30
Test::Most 0 0.31
URI::Escape 0 3.31
configure_requires:
Module Need Have
------------------ ------ --------
Module::Build 0.42 0.4203
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
COMSPEC = C:\WINDOWS\system32\cmd.exe
NUMBER_OF_PROCESSORS = 1
PATH = C:\Program Files\Far Manager\;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\strawberry160\c\bin;C:\strawberry160\perl\site\bin;C:\strawberry160\perl\bin
PERL5LIB = C:\strawberry160\cpan\build\Number-FormatEng-0.01-mKttIq/blib/arch;C:\strawberry160\cpan\build\Number-FormatEng-0.01-mKttIq/blib/lib;C:\strawberry160\cpan\build\Statistics-Zed-0.072-zdQ5U1/blib/arch;C:\strawberry160\cpan\build\Statistics-Zed-0.072-zdQ5U1/blib/lib;C:\strawberry160\cpan\build\Math-Cephes-0.5303-KdRHUb/blib/arch;C:\strawberry160\cpan\build\Math-Cephes-0.5303-KdRHUb/blib/lib;C:\strawberry160\cpan\build\Statistics-Distributions-1.02-C6Q7ZT/blib/arch;C:\strawberry160\cpan\build\Statistics-Distributions-1.02-C6Q7ZT/blib/lib;C:\strawberry160\cpan\build\Statistics-Lite-3.2-VSgHUw/blib/arch;C:\strawberry160\cpan\build\Statistics-Lite-3.2-VSgHUw/blib/lib
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 31284
PERL5_CPAN_IS_RUNNING = 31284
PERL5_CPAN_IS_RUNNING_IN_RECURSION = 1028,31284
PERL_CR_SMOKER_CURRENT = Mecom-1.15
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_JSON_BACKEND = JSON::XS
PERL_MM_USE_DEFAULT = 1
PERL_YAML_BACKEND = YAML
PROCESSOR_IDENTIFIER = x86 Family 16 Model 5 Stepping 3, AuthenticAMD
TEMP = C:\DOCUME~1\a\LOCALS~1\Temp
TERM = dumb
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = C:\strawberry160\perl\bin\perl.exe
$UID/$EUID = 0 / 0
$GID = 0
$EGID = 0
Win32::GetOSName = WinXP/.Net
Win32::GetOSVersion = Service Pack 3, 5, 1, 2600, 2, 3, 0, 256, 1
Win32::FsType = NTFS
Win32::IsAdminUser = 1
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.00
CPAN::Meta 2.133380
Cwd 3.40
ExtUtils::CBuilder 0.280206
ExtUtils::Command 1.17
ExtUtils::Install 1.58
ExtUtils::MakeMaker 6.84
ExtUtils::Manifest 1.61
ExtUtils::ParseXS 3.22
File::Spec 3.40
JSON 2.53
JSON::PP 2.27203
Module::Build 0.4203
Module::Signature 0.68
Parse::CPAN::Meta 1.4405
Test::Harness 3.30
Test::More 1.001002
YAML 0.88
YAML::Syck 1.27
version 0.9904
--
Summary of my perl5 (revision 5 version 16 subversion 0) configuration:
Platform:
osname=MSWin32, osvers=4.0, archname=MSWin32-x86-multi-thread
uname='Win32 strawberry-perl 5.16.0.1 #1 Mon May 21 22:07:30 2012 i386'
config_args='undef'
hint=recommended, useposix=true, d_sigaction=undef
useithreads=define, usemultiplicity=define
useperlio=define, d_sfio=undef, uselargefiles=define, usesocks=undef
use64bitint=undef, use64bitall=undef, uselongdouble=undef
usemymalloc=n, bincompat5005=undef
Compiler:
cc='gcc', ccflags =' -s -O2 -DWIN32 -DPERL_TEXTMODE_SCRIPTS -DPERL_IMPLICIT_CONTEXT -DPERL_IMPLICIT_SYS -fno-strict-aliasing -mms-bitfields',
optimize='-s -O2',
cppflags='-DWIN32'
ccversion='', gccversion='4.6.3', gccosandvers=''
intsize=4, longsize=4, ptrsize=4, doublesize=8, byteorder=1234
d_longlong=undef, longlongsize=8, d_longdbl=define, longdblsize=12
ivtype='long', ivsize=4, nvtype='double', nvsize=8, Off_t='long long', lseeksize=8
alignbytes=8, prototype=define
Linker and Libraries:
ld='g++', ldflags ='-s -L"C:\strawberry160\perl\lib\CORE" -L"C:\strawberry160\c\lib"'
libpth=C:\strawberry160\c\lib C:\strawberry160\c\i686-w64-mingw32\lib
libs=-lmoldname -lkernel32 -luser32 -lgdi32 -lwinspool -lcomdlg32 -ladvapi32 -lshell32 -lole32 -loleaut32 -lnetapi32 -luuid -lws2_32 -lmpr -lwinmm -lversion -lodbc32 -lodbccp32 -lcomctl32
perllibs=-lmoldname -lkernel32 -luser32 -lgdi32 -lwinspool -lcomdlg32 -ladvapi32 -lshell32 -lole32 -loleaut32 -lnetapi32 -luuid -lws2_32 -lmpr -lwinmm -lversion -lodbc32 -lodbccp32 -lcomctl32
libc=, so=dll, useshrplib=true, libperl=libperl516.a
gnulibc_version=''
Dynamic Linking:
dlsrc=dl_win32.xs, dlext=dll, d_dlsymun=undef, ccdlflags=' '
cccdlflags=' ', lddlflags='-mdll -s -L"C:\strawberry160\perl\lib\CORE" -L"C:\strawberry160\c\lib"'
Characteristics of this binary (from libperl):
Compile-time options: HAS_TIMES HAVE_INTERP_INTERN MULTIPLICITY
PERLIO_LAYERS PERL_DONT_CREATE_GVSV
PERL_IMPLICIT_CONTEXT PERL_IMPLICIT_SYS
PERL_MALLOC_WRAP PERL_PRESERVE_IVUV PL_OP_SLAB_ALLOC
USE_ITHREADS USE_LARGE_FILES USE_LOCALE
USE_LOCALE_COLLATE USE_LOCALE_CTYPE
USE_LOCALE_NUMERIC USE_PERLIO USE_PERL_ATOF
Built under MSWin32
Compiled at May 21 2012 22:15:38
%ENV:
PERL5LIB="C:\strawberry160\cpan\build\Number-FormatEng-0.01-mKttIq/blib/arch;C:\strawberry160\cpan\build\Number-FormatEng-0.01-mKttIq/blib/lib;C:\strawberry160\cpan\build\Statistics-Zed-0.072-zdQ5U1/blib/arch;C:\strawberry160\cpan\build\Statistics-Zed-0.072-zdQ5U1/blib/lib;C:\strawberry160\cpan\build\Math-Cephes-0.5303-KdRHUb/blib/arch;C:\strawberry160\cpan\build\Math-Cephes-0.5303-KdRHUb/blib/lib;C:\strawberry160\cpan\build\Statistics-Distributions-1.02-C6Q7ZT/blib/arch;C:\strawberry160\cpan\build\Statistics-Distributions-1.02-C6Q7ZT/blib/lib;C:\strawberry160\cpan\build\Statistics-Lite-3.2-VSgHUw/blib/arch;C:\strawberry160\cpan\build\Statistics-Lite-3.2-VSgHUw/blib/lib"
PERL5_CPANPLUS_IS_RUNNING="31284"
PERL5_CPAN_IS_RUNNING="31284"
PERL5_CPAN_IS_RUNNING_IN_RECURSION="1028,31284"
PERL_CR_SMOKER_CURRENT="Mecom-1.15"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_JSON_BACKEND="JSON::XS"
PERL_MM_USE_DEFAULT="1"
PERL_YAML_BACKEND="YAML"
@INC:
C:\strawberry160\cpan\build\Number-FormatEng-0.01-mKttIq/blib/arch
C:\strawberry160\cpan\build\Number-FormatEng-0.01-mKttIq/blib/lib
C:\strawberry160\cpan\build\Statistics-Zed-0.072-zdQ5U1/blib/arch
C:\strawberry160\cpan\build\Statistics-Zed-0.072-zdQ5U1/blib/lib
C:\strawberry160\cpan\build\Math-Cephes-0.5303-KdRHUb/blib/arch
C:\strawberry160\cpan\build\Math-Cephes-0.5303-KdRHUb/blib/lib
C:\strawberry160\cpan\build\Statistics-Distributions-1.02-C6Q7ZT/blib/arch
C:\strawberry160\cpan\build\Statistics-Distributions-1.02-C6Q7ZT/blib/lib
C:\strawberry160\cpan\build\Statistics-Lite-3.2-VSgHUw/blib/arch
C:\strawberry160\cpan\build\Statistics-Lite-3.2-VSgHUw/blib/lib
C:/strawberry160/perl/site/lib
C:/strawberry160/perl/vendor/lib
C:/strawberry160/perl/lib
.