BioPerl v1.007002 Perl 5 v5.22.0 darwin-thread-multi-2level
- Status
- Fail
- From
- Nigel Horne
- Dist
-
BioPerl v1.007002
- Platform
- Perl 5 v5.22.0 darwin-thread-multi-2level
- Date
- 2018-01-11 05:12:20
- ID
- 004aba3c-f68e-11e7-a892-7c78baf9c033
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-1.007002
on perl 5.22.0, created by CPAN-Reporter-1.2018.
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 './Build test':
t/Align/AlignUtil.t .................... ok
t/Align/Graphics.t ..................... ok
t/Align/AlignStats.t ................... ok
t/Align/Utilities.t .................... ok
t/Align/TreeBuild.t .................... ok
t/Align/SimpleAlign.t .................. ok
t/AlignIO/arp.t ........................ ok
t/AlignIO/bl2seq.t ..................... ok
t/AlignIO/AlignIO.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/nexml.t ...................... skipped: The optional module Bio::Phylo (or dependencies thereof) was not installed
t/AlignIO/msf.t ........................ ok
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/xmfa.t ....................... ok
t/AlignIO/stockholm.t .................. ok
t/Alphabet.t ........................... ok
t/Annotation/AnnotationAdaptor.t ....... ok
t/Annotation/Annotation.t .............. ok
t/Assembly/IO/bowtie.t ................. skipped: The optional module Bio::DB::Sam (or dependencies thereof) was not installed
Possible precedence issue with control flow operator at Bio/DB/IndexedBase.pm line 845, <GEN0> line 20.
t/Assembly/ContigSpectrum.t ............ ok
t/Assembly/IO/sam.t .................... skipped: The optional module Bio::DB::Sam (or dependencies thereof) was not installed
Possible precedence issue with control flow operator at Bio/DB/IndexedBase.pm line 845.
t/Cluster/UniGene.t .................... ok
t/ClusterIO/ClusterIO.t ................ ok
t/ClusterIO/SequenceFamily.t ........... ok
t/ClusterIO/unigene.t .................. ok
t/LiveSeq/Chain.t ...................... ok
t/Draw/Pictogram.t ..................... ok
t/LiveSeq/Mutation.t ................... ok
t/LiveSeq/LiveSeq.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/Assembly/core.t ...................... ok
t/LocalDB/BioDBGFF.t ................... ok
Possible precedence issue with control flow operator at Bio/DB/IndexedBase.pm line 845.
Subroutine Bio::DB::IndexedBase::_strip_crnl redefined at Bio/DB/IndexedBase.pm line 304.
t/LiveSeq/Mutator.t .................... ok
t/LocalDB/Fasta.t ...................... ok
t/LocalDB/Flat.t ....................... ok
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: This index file is from version [1.007002] - You need to rebuild it to use module version [0.2]
STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:447
STACK: Bio::Index::Abstract::_type_and_version Bio/Index/Abstract.pm:493
STACK: Bio::Index::Abstract::open_dbm Bio/Index/Abstract.pm:415
STACK: Bio::Index::Abstract::new Bio/Index/Abstract.pm:162
STACK: Bio::Index::AbstractSeq::new Bio/Index/AbstractSeq.pm:93
STACK: t/LocalDB/Index/Index.t:27
-----------------------------------------------------------
# Looks like your test exited with 255 just after 10.
t/LocalDB/Index/Index.t ................
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 63/73 subtests
t/LocalDB/Index/Blast.t ................ ok
t/LocalDB/Index/BlastTable.t ........... ok
Possible precedence issue with control flow operator at Bio/DB/IndexedBase.pm line 845.
Subroutine Bio::DB::IndexedBase::_strip_crnl redefined at Bio/DB/IndexedBase.pm line 304.
t/LocalDB/Qual.t ....................... ok
Possible precedence issue with control flow operator at Bio/DB/IndexedBase.pm line 845.
Subroutine Bio::DB::IndexedBase::_strip_crnl redefined at Bio/DB/IndexedBase.pm line 304.
/var/folders/pz/pd7y1qjs6s3cbk170cw50fjc000c61/T/SeqFeatureLoadHelper_V3XNEG for /var/folders/pz/pd7y1qjs6s3cbk170cw50fjc000c61/T/SeqFeatureLoadHelper_V3XNEG: No such file or directory at Bio/DB/SeqFeature/Store/LoadHelper.pm line 69.
t/LocalDB/Registry.t ................... ok
t/LocalDB/Taxonomy/greengenes.t ........ ok
t/LocalDB/SeqFeature.t ................. ok
t/LocalDB/Taxonomy/silva.t ............. ok
t/Map/Cyto.t ........................... ok
t/LocalDB/Taxonomy/sqlite.t ............ ok
t/Map/Linkage.t ........................ ok
t/Map/MapIO.t .......................... ok
t/Map/Map.t ............................ ok
t/Map/MicrosatelliteMarker.t ........... ok
t/Map/Physical.t ....................... ok
t/Matrix/IO/masta.t .................... ok
t/Matrix/InstanceSite.t ................ ok
t/Matrix/IO/psm.t ...................... ok
t/Matrix/ProtMatrix.t .................. ok
t/Matrix/Matrix.t ...................... ok
t/Matrix/SiteMatrix.t .................. ok
t/Matrix/ProtPsm.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/LocalDB/transfac_pro.t ............... ok
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/Phenotype/Correlate.t ................ ok
t/Phenotype/MeSH.t ..................... ok
t/Phenotype/Measure.t .................. ok
t/Perl.t ............................... ok
t/Phenotype/MiniMIMentry.t ............. ok
t/Phenotype/OMIMentryAllelicVariant.t .. ok
t/Phenotype/OMIMentry.t ................ ok
t/Phenotype/OMIMparser.t ............... ok
t/Phenotype/Phenotype.t ................ ok
t/PopGen/Coalescent.t .................. ok
t/PopGen/HtSNP.t ....................... ok
t/PopGen/MK.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/PopGen/PopGen.t ...................... ok
t/RemoteDB/EntrezGene.t ................ skipped: The optional module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed
t/RemoteDB/EMBL.t ...................... skipped: Network tests have not been requested
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/HIVAnnotProcessor.t ..... ok
t/RemoteDB/HIV/HIV.t ................... ok
t/RemoteDB/HIV/HIVQueryHelper.t ........ ok
t/RemoteDB/HIV/HIVQuery.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/SeqRead_fail.t .............. skipped: Network tests have not been requested
t/RemoteDB/SeqVersion.t ................ skipped: The optional module HTML::TableExtract (or dependencies thereof) was not installed
t/RemoteDB/SwissProt.t ................. skipped: Network tests have not been requested
t/PodSyntax.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/IO.t ............................ ok
t/Restriction/Analysis-refac.t ......... ok
t/Root/RootI.t ......................... ok
t/Root/Storable.t ...................... ok
t/Root/RootIO.t ........................ skipped: Network tests have not been requested
t/SearchDist.t ......................... skipped: The optional module Bio::Ext::Align (or dependencies thereof) was not installed
--------------------- WARNING ---------------------
MSG: find_exe: Multiple paths to 'gzip' found. Using /usr/bin/gzip.
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: find_exe: Multiple paths to 'gzip' found. Using /usr/bin/gzip.
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: find_exe: Multiple paths to 'gunzip' found. Using /usr/bin/gunzip.
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: find_exe: Multiple paths to 'gzip' found. Using /usr/bin/gzip.
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: find_exe: Multiple paths to 'gunzip' found. Using /usr/bin/gunzip.
---------------------------------------------------
t/Root/Utilities.t ..................... ok
t/SearchIO/SearchIO.t .................. ok
t/SearchIO/CigarString.t ............... ok
t/SearchIO/SimilarityPair.t ............ ok
t/SearchIO/Writer/GbrowseGFF.t ......... ok
t/SearchIO/Writer/HSPTableWriter.t ..... ok
t/SearchIO/Writer/HTMLWriter.t ......... ok
t/SearchIO/Tiling.t .................... ok
t/SearchIO/Writer/HitTableWriter.t ..... ok
t/SearchIO/Writer/TextWriter.t ......... ok
t/SearchIO/axt.t ....................... ok
t/SearchIO/blast_pull.t ................ ok
t/SearchIO/blasttable.t ................ ok
t/SearchIO/cross_match.t ............... ok
t/SearchIO/erpin.t ..................... ok
t/SearchIO/exonerate.t ................. ok
t/RemoteDB/Taxonomy.t .................. ok
t/SearchIO/blast.t ..................... ok
t/SearchIO/fasta.t ..................... ok
t/SearchIO/hmmer_pull.t ................ ok
t/SearchIO/infernal.t .................. ok
t/SearchIO/megablast.t ................. ok
t/SearchIO/psl.t ....................... ok
t/SearchIO/gmap_f9.t ................... ok
t/SearchIO/rnamotif.t .................. ok
t/SearchIO/sim4.t ...................... ok
t/SearchIO/hmmer.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/SimulatedRead.t .................. ok
t/Seq/Seq.t ............................ ok
t/Seq/WithQuality.t .................... ok
t/SeqEvolution.t ....................... ok
t/Seq/Quality.t ........................ ok
t/SeqFeature/Amplicon.t ................ ok
t/SeqFeature/Clone.t ................... ok
t/SeqFeature/Computation.t ............. ok
t/SeqFeature/FeaturePair.t ............. ok
t/SeqFeature/Collection.t .............. ok
t/SeqFeature/Gene.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/Generic.t ................. ok
t/SeqFeature/SeqAnalysisParser.t ....... ok
t/SeqFeature/SubSeq.t .................. ok
t/SeqIO/MultiFile.t .................... ok
t/SeqIO/Multiple_fasta.t ............... ok
t/SeqIO/SeqBuilder.t ................... ok
t/SeqIO/Handler.t ...................... ok
t/SeqIO/SeqIO.t ........................ ok
t/SeqIO/abi.t .......................... skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqIO/Splicedseq.t ................... ok
t/SeqIO/ace.t .......................... ok
t/SeqIO/agave.t ........................ skipped: The optional module XML::Writer (or dependencies thereof) was not installed
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 ..................... skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed
t/SeqIO/chadoxml.t ..................... skipped: The optional module XML::Writer (or dependencies thereof) was not installed
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/entrezgene.t ................... skipped: The optional module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed
t/SeqIO/embl.t ......................... ok
t/SeqIO/excel.t ........................ ok
t/SeqIO/exp.t .......................... skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqIO/fasta.t ........................ ok
t/SeqIO/flybase_chadoxml.t ............. skipped: The optional module XML::Writer (or dependencies thereof) was not installed
t/SeqIO/game.t ......................... skipped: The optional module XML::Writer (or dependencies thereof) was not installed
t/SeqIO/fastq.t ........................ ok
t/SeqIO/gcg.t .......................... ok
t/SeqIO/gbxml.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/genbank.t ...................... ok
t/SeqIO/locuslink.t .................... skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/SeqIO/lasergene.t .................... ok
t/SeqIO/mbsout.t ....................... ok
t/SeqIO/metafasta.t .................... ok
t/SeqIO/nexml.t ........................ skipped: The optional module Bio::Phylo (or dependencies thereof) was not installed
t/SeqIO/msout.t ........................ ok
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/seqxml.t ....................... skipped: The optional module XML::LibXML (or dependencies thereof) was not installed
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/scf.t .......................... ok
t/SeqIO/tigrxml.t ...................... skipped: The optional module XML::SAX::Writer (or dependencies thereof) was not installed
t/SeqIO/tigr.t ......................... ok
t/SeqIO/tinyseq.t ...................... skipped: The optional module XML::Writer (or dependencies thereof) was not installed
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/OddCodes.t .................. ok
t/SeqTools/GuessSeqFormat.t ............ ok
t/SeqTools/SeqPattern.t ................ ok
t/SeqTools/SeqStats.t .................. ok
t/SeqTools/SeqWords.t .................. ok
t/SeqTools/SeqUtils.t .................. ok
t/SeqFeature/Unflattener.t ............. ok
t/Structure/IO.t ....................... ok
t/Species.t ............................ ok
t/Structure/Structure.t ................ ok
t/Symbol.t ............................. ok
t/TaxonTree.t .......................... skipped: These modules are now probably deprecated
t/Tools/Alignment/Consed.t ............. ok
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/NetPhos.t ..... skipped: Network tests have not been requested
t/Tools/Analysis/Protein/Sopma.t ....... skipped: Network tests have not been requested
t/Tools/EMBOSS/Palindrome.t ............ ok
t/Tools/Analysis/Protein/Scansite.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/IUPAC.t ........................ ok
t/Tools/Genpred.t ...................... ok
t/Tools/Lucy.t ......................... ok
t/Tools/Match.t ........................ ok
t/Tools/Phylo/Gerp.t ................... ok
t/Tools/Hmmer.t ........................ ok
t/Tools/Phylo/Molphy.t ................. ok
t/Tools/Phylo/Phylip/ProtDist.t ........ ok
t/Tools/Primer3.t ...................... ok
t/Tools/Promoterwise.t ................. ok
t/Tools/PrositeScan.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/Seg.t .......................... ok
t/Tools/Sigcleave.t .................... ok
t/Tools/Signalp.t ...................... ok
t/Tools/SiRNA.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/tRNAscanSE.t ................... ok
t/Tree/Node.t .......................... ok
t/Tree/Compatible.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/lintree.t ................ ok
t/Tree/TreeIO/nexml.t .................. skipped: The optional module Bio::Phylo (or dependencies thereof) was not installed
t/Tree/TreeIO/newick.t ................. ok
t/Tree/TreeIO.t ........................ ok
t/Tree/TreeIO/phyloxml.t ............... skipped: The optional module XML::LibXML (or dependencies thereof) was not installed
t/Tree/TreeIO/nhx.t .................... ok
t/Tree/TreeIO/nexus.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/SNP.t ...................... ok
t/Variation/RNAChange.t ................ ok
t/Variation/SeqDiff.t .................. ok
t/Variation/Variation_IO.t ............. skipped: The optional module XML::Writer (or dependencies thereof) was not installed
t/nexml.t .............................. skipped: The optional module Bio::Phylo (or dependencies thereof) was not installed
Test Summary Report
-------------------
t/LocalDB/Index/Index.t (Wstat: 65280 Tests: 10 Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 73 tests but ran 10.
t/Root/IO.t (Wstat: 0 Tests: 154 Failed: 0)
TODO passed: 109, 112, 115, 118
Files=325, Tests=20002, 30 wallclock secs ( 2.07 usr 1.10 sys + 69.03 cusr 20.40 csys = 92.60 CPU)
Result: FAIL
Failed 1/325 test programs. 0/20002 subtests failed.
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
------------------ ------ --------
Data::Stag 0.11 0.14
ExtUtils::Manifest 1.52 1.70
IO::String 0 1.08
perl v5.6.1 5.022000
Scalar::Util 0 1.42
build_requires:
Module Need Have
------------------ ------ --------
CPAN 1.81 2.16
Module::Build 0.42 0.4214
Test::Harness 2.62 3.36
Test::Most 0 0.35
URI::Escape 0 3.31
configure_requires:
Module Need Have
------------------ ------ --------
Module::Build 0.42 0.4214
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
HARNESS_OPTIONS = c:j3
LANG = en_US.UTF-8
LC_ALL = POSIX
PATH = /Users/hornenj/perl5/perlbrew/bin:/Users/hornenj/perl5/perlbrew/perls/perl-5.22.0/bin:src/njh/smoker/bin:/Users/hornenj/bin:/usr/bin:/bin:/usr/X11R6/bin:/sw/bin
PERL5LIB = /Users/hornenj/.cpan/build/Data-Stag-0.14-30/blib/arch:/Users/hornenj/.cpan/build/Data-Stag-0.14-30/blib/lib:/Users/hornenj/.cpan/build/Array-Utils-0.5-22/blib/arch:/Users/hornenj/.cpan/build/Array-Utils-0.5-22/blib/lib:/Users/hornenj/.cpan/build/Net-Async-Ping-0.003001-22/blib/arch:/Users/hornenj/.cpan/build/Net-Async-Ping-0.003001-22/blib/lib:/Users/hornenj/.cpan/build/Socket-2.025-21/blib/arch:/Users/hornenj/.cpan/build/Socket-2.025-21/blib/lib:/Users/hornenj/.cpan/build/Net-Frame-Simple-1.09-21/blib/arch:/Users/hornenj/.cpan/build/Net-Frame-Simple-1.09-21/blib/lib:/Users/hornenj/.cpan/build/Net-Frame-Layer-IPv6-1.08-21/blib/arch:/Users/hornenj/.cpan/build/Net-Frame-Layer-IPv6-1.08-21/blib/lib:/Users/hornenj/.cpan/build/Net-Frame-Layer-ICMPv6-1.10-21/blib/arch:/Users/hornenj/.cpan/build/Net-Frame-Layer-ICMPv6-1.10-21/blib/lib:/Users/hornenj/.cpan/build/Net-Frame-1.17-21/blib/arch:/Users/hornenj/.cpan/build/Net-Frame-1.17-21/blib/lib:/Users/hornenj/.cpan/build/Net-IPv6Addr-0.91-21/blib/arch:/Users/hornenj/.cpan/build/Net-IPv6Addr-0.91-21/blib/lib:/Users/hornenj/.cpan/build/Net-IPv4Addr-0.10-21/blib/arch:/Users/hornenj/.cpan/build/Net-IPv4Addr-0.10-21/blib/lib:/Users/hornenj/.cpan/build/Math-Base85-0.4-21/blib/arch:/Users/hornenj/.cpan/build/Math-Base85-0.4-21/blib/lib:/Users/hornenj/.cpan/build/Class-Gomor-1.03-21/blib/arch:/Users/hornenj/.cpan/build/Class-Gomor-1.03-21/blib/lib:/Users/hornenj/.cpan/build/IO-Async-0.71-21/blib/arch:/Users/hornenj/.cpan/build/IO-Async-0.71-21/blib/lib:/Users/hornenj/.cpan/build/Struct-Dumb-0.09-21/blib/arch:/Users/hornenj/.cpan/build/Struct-Dumb-0.09-21/blib/lib:/Users/hornenj/.cpan/build/Future-0.38-21/blib/arch:/Users/hornenj/.cpan/build/Future-0.38-21/blib/lib:/Users/hornenj/.cpan/build/Test-Refcount-0.08-21/blib/arch:/Users/hornenj/.cpan/build/Test-Refcount-0.08-21/blib/lib:/Users/hornenj/.cpan/build/Test-Identity-0.01-21/blib/arch:/Users/hornenj/.cpan/build/Test-Identity-0.01-21/blib/lib
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 26361
PERL5_CPAN_IS_RUNNING = 26361
PERLBREW_BASHRC_VERSION = 0.80
PERLBREW_HOME = /Users/hornenj/.perlbrew
PERLBREW_MANPATH = /Users/hornenj/perl5/perlbrew/perls/perl-5.22.0/man
PERLBREW_PATH = /Users/hornenj/perl5/perlbrew/bin:/Users/hornenj/perl5/perlbrew/perls/perl-5.22.0/bin
PERLBREW_PERL = perl-5.22.0
PERLBREW_ROOT = /Users/hornenj/perl5/perlbrew
PERLBREW_VERSION = 0.80
SHELL = /bin/bash
TERM = xterm-256color
TMPDIR = /var/folders/pz/pd7y1qjs6s3cbk170cw50fjc000c61/T/
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /Users/hornenj/perl5/perlbrew/perls/perl-5.22.0/bin/perl
$UID/$EUID = 12481 / 12481
$GID = 14 14 5344 37191 527 12 62 204 399 206 37223 241 223
$EGID = 14 14 5344 37191 527 12 62 204 399 206 37223 241 223
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.16
CPAN::Meta 2.150005
Cwd 3.56
ExtUtils::CBuilder 0.280223
ExtUtils::Command 7.30
ExtUtils::Install 2.06
ExtUtils::MakeMaker 7.30
ExtUtils::Manifest 1.70
ExtUtils::ParseXS 3.30
File::Spec 3.56
JSON 2.93
JSON::PP 2.27400
Module::Build 0.4214
Module::Signature n/a
Parse::CPAN::Meta 1.4422
Test::Harness 3.36
Test::More 1.302106
YAML 1.24
YAML::Syck 1.30
version 0.9912
--
Summary of my perl5 (revision 5 version 22 subversion 0) configuration:
Platform:
osname=darwin, osvers=14.3.0, archname=darwin-thread-multi-2level
uname='darwin ncbimac2027.ncbi.nlm.nih.gov 14.3.0 darwin kernel version 14.3.0: mon mar 23 11:59:05 pdt 2015; root:xnu-2782.20.48~5release_x86_64 x86_64 '
config_args='-de -Dprefix=/Users/hornenj/perl5/perlbrew/perls/perl-5.22.0 -Duseithreads -Dusemultiplicity -Dusedevel -Accflags=-O2 -W -Wformat=2 -Wswitch -Wshadow -Wwrite-strings -Wuninitialized -Wall -pipe -mtune=native -march=native -fomit-frame-pointer -msse2 -msse -mmmx -pedantic -D_FORTIFY_SOURCE=2 -Wpointer-arith -Wstrict-prototypes -fstack-protector -Wstack-protector -Wextra -Wbad-function-cast -Wcast-align -Wcast-qual -Wdisabled-optimization -Wendif-labels -Wfloat-equal -Wformat-nonliteral -Winline -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wpointer-arith -Wundef -Wformat-security -fassociative-math -Acc=cc -Aeval:scriptdir=/Users/hornenj/perl5/perlbrew/perls/perl-5.22.0/bin'
hint=recommended, useposix=true, d_sigaction=define
useithreads=define, usemultiplicity=define
use64bitint=define, use64bitall=define, uselongdouble=undef
usemymalloc=n, bincompat5005=undef
Compiler:
cc=' cc', ccflags ='-fno-common -DPERL_DARWIN -O2 -W -Wformat=2 -Wswitch -Wshadow -Wwrite-strings -Wuninitialized -Wall -pipe -mtune=native -march=native -fomit-frame-pointer -msse2 -msse -mmmx -pedantic -D_FORTIFY_SOURCE=2 -Wpointer-arith -Wstrict-prototypes -fstack-protector -Wstack-protector -Wextra -Wbad-function-cast -Wcast-align -Wcast-qual -Wdisabled-optimization -Wendif-labels -Wfloat-equal -Wformat-nonliteral -Winline -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wpointer-arith -Wundef -Wformat-security -fassociative-math -fno-strict-aliasing -I/usr/local/include',
optimize='-O3',
cppflags='-fno-common -DPERL_DARWIN -O2 -W -Wformat=2 -Wswitch -Wshadow -Wwrite-strings -Wuninitialized -Wall -pipe -mtune=native -march=native -fomit-frame-pointer -msse2 -msse -mmmx -pedantic -D_FORTIFY_SOURCE=2 -Wpointer-arith -Wstrict-prototypes -fstack-protector -Wstack-protector -Wextra -Wbad-function-cast -Wcast-align -Wcast-qual -Wdisabled-optimization -Wendif-labels -Wfloat-equal -Wformat-nonliteral -Winline -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wpointer-arith -Wundef -Wformat-security -fassociative-math -fno-strict-aliasing -I/usr/local/include'
ccversion='', gccversion='4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.56)', gccosandvers=''
intsize=4, longsize=8, ptrsize=8, doublesize=8, byteorder=12345678, doublekind=3
d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=16, longdblkind=3
ivtype='long', ivsize=8, nvtype='double', nvsize=8, Off_t='off_t', lseeksize=8
alignbytes=8, prototype=define
Linker and Libraries:
ld='env MACOSX_DEPLOYMENT_TARGET=10.3 cc', ldflags =' -fstack-protector -L/usr/local/lib'
libpth=/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/6.0/lib /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/lib /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/lib /usr/local/lib /usr/lib
libs=-lpthread -ldbm -ldl -lm -lutil -lc
perllibs=-lpthread -ldl -lm -lutil -lc
libc=, so=dylib, useshrplib=false, libperl=libperl.a
gnulibc_version=''
Dynamic Linking:
dlsrc=dl_dlopen.xs, dlext=bundle, d_dlsymun=undef, ccdlflags=' '
cccdlflags=' ', lddlflags=' -bundle -undefined dynamic_lookup -L/usr/local/lib -fstack-protector'
Characteristics of this binary (from libperl):
Compile-time options: HAS_TIMES MULTIPLICITY PERLIO_LAYERS
PERL_DONT_CREATE_GVSV
PERL_HASH_FUNC_ONE_AT_A_TIME_HARD
PERL_IMPLICIT_CONTEXT PERL_MALLOC_WRAP
PERL_NEW_COPY_ON_WRITE PERL_PRESERVE_IVUV
PERL_USE_DEVEL USE_64_BIT_ALL USE_64_BIT_INT
USE_ITHREADS USE_LARGE_FILES USE_LOCALE
USE_LOCALE_COLLATE USE_LOCALE_CTYPE
USE_LOCALE_NUMERIC USE_LOCALE_TIME USE_PERLIO
USE_PERL_ATOF USE_REENTRANT_API
Locally applied patches:
Devel::PatchPerl 1.30
Built under darwin
Compiled at Jun 2 2015 11:16:32
%ENV:
PERL5LIB="/Users/hornenj/.cpan/build/Data-Stag-0.14-30/blib/arch:/Users/hornenj/.cpan/build/Data-Stag-0.14-30/blib/lib:/Users/hornenj/.cpan/build/Array-Utils-0.5-22/blib/arch:/Users/hornenj/.cpan/build/Array-Utils-0.5-22/blib/lib:/Users/hornenj/.cpan/build/Net-Async-Ping-0.003001-22/blib/arch:/Users/hornenj/.cpan/build/Net-Async-Ping-0.003001-22/blib/lib:/Users/hornenj/.cpan/build/Socket-2.025-21/blib/arch:/Users/hornenj/.cpan/build/Socket-2.025-21/blib/lib:/Users/hornenj/.cpan/build/Net-Frame-Simple-1.09-21/blib/arch:/Users/hornenj/.cpan/build/Net-Frame-Simple-1.09-21/blib/lib:/Users/hornenj/.cpan/build/Net-Frame-Layer-IPv6-1.08-21/blib/arch:/Users/hornenj/.cpan/build/Net-Frame-Layer-IPv6-1.08-21/blib/lib:/Users/hornenj/.cpan/build/Net-Frame-Layer-ICMPv6-1.10-21/blib/arch:/Users/hornenj/.cpan/build/Net-Frame-Layer-ICMPv6-1.10-21/blib/lib:/Users/hornenj/.cpan/build/Net-Frame-1.17-21/blib/arch:/Users/hornenj/.cpan/build/Net-Frame-1.17-21/blib/lib:/Users/hornenj/.cpan/build/Net-IPv6Addr-0.91-21/blib/arch:/Users/hornenj/.cpan/build/Net-IPv6Addr-0.91-21/blib/lib:/Users/hornenj/.cpan/build/Net-IPv4Addr-0.10-21/blib/arch:/Users/hornenj/.cpan/build/Net-IPv4Addr-0.10-21/blib/lib:/Users/hornenj/.cpan/build/Math-Base85-0.4-21/blib/arch:/Users/hornenj/.cpan/build/Math-Base85-0.4-21/blib/lib:/Users/hornenj/.cpan/build/Class-Gomor-1.03-21/blib/arch:/Users/hornenj/.cpan/build/Class-Gomor-1.03-21/blib/lib:/Users/hornenj/.cpan/build/IO-Async-0.71-21/blib/arch:/Users/hornenj/.cpan/build/IO-Async-0.71-21/blib/lib:/Users/hornenj/.cpan/build/Struct-Dumb-0.09-21/blib/arch:/Users/hornenj/.cpan/build/Struct-Dumb-0.09-21/blib/lib:/Users/hornenj/.cpan/build/Future-0.38-21/blib/arch:/Users/hornenj/.cpan/build/Future-0.38-21/blib/lib:/Users/hornenj/.cpan/build/Test-Refcount-0.08-21/blib/arch:/Users/hornenj/.cpan/build/Test-Refcount-0.08-21/blib/lib:/Users/hornenj/.cpan/build/Test-Identity-0.01-21/blib/arch:/Users/hornenj/.cpan/build/Test-Identity-0.01-21/blib/lib"
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="26361"
PERL5_CPAN_IS_RUNNING="26361"
PERLBREW_BASHRC_VERSION="0.80"
PERLBREW_HOME="/Users/hornenj/.perlbrew"
PERLBREW_MANPATH="/Users/hornenj/perl5/perlbrew/perls/perl-5.22.0/man"
PERLBREW_PATH="/Users/hornenj/perl5/perlbrew/bin:/Users/hornenj/perl5/perlbrew/perls/perl-5.22.0/bin"
PERLBREW_PERL="perl-5.22.0"
PERLBREW_ROOT="/Users/hornenj/perl5/perlbrew"
PERLBREW_VERSION="0.80"
@INC:
/Users/hornenj/.cpan/build/Data-Stag-0.14-30/blib/arch
/Users/hornenj/.cpan/build/Data-Stag-0.14-30/blib/lib
/Users/hornenj/.cpan/build/Array-Utils-0.5-22/blib/arch
/Users/hornenj/.cpan/build/Array-Utils-0.5-22/blib/lib
/Users/hornenj/.cpan/build/Net-Async-Ping-0.003001-22/blib/arch
/Users/hornenj/.cpan/build/Net-Async-Ping-0.003001-22/blib/lib
/Users/hornenj/.cpan/build/Socket-2.025-21/blib/arch
/Users/hornenj/.cpan/build/Socket-2.025-21/blib/lib
/Users/hornenj/.cpan/build/Net-Frame-Simple-1.09-21/blib/arch
/Users/hornenj/.cpan/build/Net-Frame-Simple-1.09-21/blib/lib
/Users/hornenj/.cpan/build/Net-Frame-Layer-IPv6-1.08-21/blib/arch
/Users/hornenj/.cpan/build/Net-Frame-Layer-IPv6-1.08-21/blib/lib
/Users/hornenj/.cpan/build/Net-Frame-Layer-ICMPv6-1.10-21/blib/arch
/Users/hornenj/.cpan/build/Net-Frame-Layer-ICMPv6-1.10-21/blib/lib
/Users/hornenj/.cpan/build/Net-Frame-1.17-21/blib/arch
/Users/hornenj/.cpan/build/Net-Frame-1.17-21/blib/lib
/Users/hornenj/.cpan/build/Net-IPv6Addr-0.91-21/blib/arch
/Users/hornenj/.cpan/build/Net-IPv6Addr-0.91-21/blib/lib
/Users/hornenj/.cpan/build/Net-IPv4Addr-0.10-21/blib/arch
/Users/hornenj/.cpan/build/Net-IPv4Addr-0.10-21/blib/lib
/Users/hornenj/.cpan/build/Math-Base85-0.4-21/blib/arch
/Users/hornenj/.cpan/build/Math-Base85-0.4-21/blib/lib
/Users/hornenj/.cpan/build/Class-Gomor-1.03-21/blib/arch
/Users/hornenj/.cpan/build/Class-Gomor-1.03-21/blib/lib
/Users/hornenj/.cpan/build/IO-Async-0.71-21/blib/arch
/Users/hornenj/.cpan/build/IO-Async-0.71-21/blib/lib
/Users/hornenj/.cpan/build/Struct-Dumb-0.09-21/blib/arch
/Users/hornenj/.cpan/build/Struct-Dumb-0.09-21/blib/lib
/Users/hornenj/.cpan/build/Future-0.38-21/blib/arch
/Users/hornenj/.cpan/build/Future-0.38-21/blib/lib
/Users/hornenj/.cpan/build/Test-Refcount-0.08-21/blib/arch
/Users/hornenj/.cpan/build/Test-Refcount-0.08-21/blib/lib
/Users/hornenj/.cpan/build/Test-Identity-0.01-21/blib/arch
/Users/hornenj/.cpan/build/Test-Identity-0.01-21/blib/lib
/Users/hornenj/perl5/perlbrew/perls/perl-5.22.0/lib/site_perl/5.22.0/darwin-thread-multi-2level
/Users/hornenj/perl5/perlbrew/perls/perl-5.22.0/lib/site_perl/5.22.0
/Users/hornenj/perl5/perlbrew/perls/perl-5.22.0/lib/5.22.0/darwin-thread-multi-2level
/Users/hornenj/perl5/perlbrew/perls/perl-5.22.0/lib/5.22.0
.