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t/Align/AlignStats.t ......................... ok
t/Align/AlignUtil.t .......................... ok
t/Align/Graphics.t ........................... skipped: The optional module GD (or dependencies thereof) was not installed
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 ............................ 1/35 -------------------------- EXCEPTION ----------------------------
Message: Wrong version number, can only handle 0.9: 0.8
An exception of type Bio::Phylo::Util::Exceptions::BadFormat
was thrown.
This kind of error happens when a bad
parse or unparse format was specified.
Refer to the Bio::Phylo::Util::Exceptions documentation for more
information.
------------------------- STACK TRACE ---------------------------
STACK: Bio::Phylo::Parsers::Nexml::_handle_nexml() called at /usr/local/share/perl/5.10.0/Bio/Phylo/Parsers/Nexml.pm line 157
STACK: Bio::Phylo::Parsers::Nexml::__ANON__() called at /usr/share/perl5/XML/Twig.pm line 1926
STACK: XML::Twig::_twig_end() called at /usr/lib/perl5/XML/Parser/Expat.pm line 474
STACK: XML::Parser::Expat::parse() called at /usr/lib/perl5/XML/Parser.pm line 187
STACK: (eval)() called at /usr/lib/perl5/XML/Parser.pm line 186
STACK: XML::Parser::parse() called at /usr/share/perl5/XML/Twig.pm line 658
STACK: (eval)() called at /usr/share/perl5/XML/Twig.pm line 658
STACK: XML::Twig::parse() called at /usr/local/share/perl/5.10.0/Bio/Phylo/Parsers/Nexml.pm line 186
STACK: Bio::Phylo::Parsers::Nexml::_parse() called at /usr/local/share/perl/5.10.0/Bio/Phylo/Parsers/Abstract.pm line 155
STACK: Bio::Phylo::Parsers::Abstract::_process() called at /usr/local/share/perl/5.10.0/Bio/Phylo/IO.pm line 198
STACK: Bio::Phylo::IO::parse() called at /home/drin/bioinformatics/bioperl/bioperl-live/blib/lib/Bio/AlignIO/nexml.pm line 140
STACK: Bio::AlignIO::nexml::_parse() called at /home/drin/bioinformatics/bioperl/bioperl-live/blib/lib/Bio/AlignIO/nexml.pm line 92
STACK: Bio::AlignIO::nexml::next_aln() called at t/AlignIO/nexml.t line 16
-----------------------------------------------------------------
# Looks like you planned 35 tests but ran 2.
# Looks like your test exited with 9 just after 2.
t/AlignIO/nexml.t ............................ Dubious, test returned 9 (wstat 2304, 0x900)
Failed 33/35 subtests
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::Tools::Run::Samtools (or dependencies thereof) was not installed
t/Assembly/IO/sam.t .......................... skipped: The optional module Bio::DB::Sam (or dependencies thereof) was not installed
t/Assembly/core.t ............................ 1/890
--------------------- WARNING ---------------------
MSG: Setting end to equal start[1]
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Adding non-nucleotidic sequence ML4922R
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Setting end to equal start[1]
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Adding non-nucleotidic sequence ML4947F
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Setting end to equal start[1]
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Setting end to equal start[1]
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Adding non-nucleotidic sequence ML4922R
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Setting end to equal start[1]
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Adding non-nucleotidic sequence ML4947F
---------------------------------------------------
t/Assembly/core.t ............................ ok
t/Biblio/Biblio.t ............................ ok
t/Biblio/References.t ........................ ok
t/Biblio/biofetch.t .......................... skipped: Network tests have not been requested
t/Biblio/eutils.t ............................ skipped: Network tests have not been requested
t/ClusterIO/ClusterIO.t ...................... ok
t/ClusterIO/SequenceFamily.t ................. ok
t/ClusterIO/unigene.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
t/LocalDB/BioDBGFF.t ......................... ok
t/LocalDB/DBFasta.t .......................... ok
t/LocalDB/DBQual.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/Registry.t ......................... ok
t/LocalDB/SeqFeature.t ....................... ok
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 .......................... ok
t/Ontology/GraphAdaptor.t .................... ok
t/Ontology/IO/go.t ........................... ok
t/Ontology/IO/interpro.t ..................... ok
t/Ontology/IO/obo.t .......................... ok
t/Ontology/Ontology.t ........................ ok
t/Ontology/OntologyEngine.t .................. ok
t/Ontology/OntologyStore.t ................... skipped: Network tests have not been requested
t/Ontology/Relationship.t .................... ok
t/Ontology/RelationshipType.t ................ ok
t/Ontology/Term.t ............................ ok
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/EUtilities.t ...................... skipped: Valid email not provided; required for tests
t/RemoteDB/EntrezGene.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/HIV.t ......................... ok
t/RemoteDB/HIV/HIVAnnotProcessor.t ........... ok
t/RemoteDB/HIV/HIVQuery.t .................... 1/41 Use of uninitialized value $rest[0] in join or string at (eval 69) line 15.
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
t/Root/RootIO.t .............................. ok
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
t/SearchIO/hmmer.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/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/WithQuality.t .......................... ok
t/SeqEvolution.t ............................. ok
t/SeqFeature/Clone.t ......................... ok
t/SeqFeature/FeatureIO.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/SeqFeatAnnotated.t .............. skipped: Network tests have not been requested
t/SeqFeature/SeqFeatCollection.t ............. ok
t/SeqFeature/SeqFeature.t .................... ok
t/SeqFeature/SeqFeaturePrimer.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 ......................... 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/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 ........................... ok
t/SeqIO/kegg.t ............................... ok
t/SeqIO/largefasta.t ......................... ok
t/SeqIO/lasergene.t .......................... ok
t/SeqIO/locuslink.t .......................... ok
t/SeqIO/mbsout.t ............................. ok
t/SeqIO/metafasta.t .......................... ok
t/SeqIO/msout.t .............................. ok
t/SeqIO/nexml.t .............................. 1/44 -------------------------- EXCEPTION ----------------------------
Message: Wrong version number, can only handle 0.9: 0.8
An exception of type Bio::Phylo::Util::Exceptions::BadFormat
was thrown.
This kind of error happens when a bad
parse or unparse format was specified.
Refer to the Bio::Phylo::Util::Exceptions documentation for more
information.
------------------------- STACK TRACE ---------------------------
STACK: Bio::Phylo::Parsers::Nexml::_handle_nexml() called at /usr/local/share/perl/5.10.0/Bio/Phylo/Parsers/Nexml.pm line 157
STACK: Bio::Phylo::Parsers::Nexml::__ANON__() called at /usr/share/perl5/XML/Twig.pm line 1926
STACK: XML::Twig::_twig_end() called at /usr/lib/perl5/XML/Parser/Expat.pm line 474
STACK: XML::Parser::Expat::parse() called at /usr/lib/perl5/XML/Parser.pm line 187
STACK: (eval)() called at /usr/lib/perl5/XML/Parser.pm line 186
STACK: XML::Parser::parse() called at /usr/share/perl5/XML/Twig.pm line 658
STACK: (eval)() called at /usr/share/perl5/XML/Twig.pm line 658
STACK: XML::Twig::parse() called at /usr/local/share/perl/5.10.0/Bio/Phylo/Parsers/Nexml.pm line 186
STACK: Bio::Phylo::Parsers::Nexml::_parse() called at /usr/local/share/perl/5.10.0/Bio/Phylo/Parsers/Abstract.pm line 155
STACK: Bio::Phylo::Parsers::Abstract::_process() called at /usr/local/share/perl/5.10.0/Bio/Phylo/IO.pm line 198
STACK: Bio::Phylo::IO::parse() called at /home/drin/bioinformatics/bioperl/bioperl-live/blib/lib/Bio/SeqIO/nexml.pm line 154
STACK: Bio::SeqIO::nexml::_parse() called at /home/drin/bioinformatics/bioperl/bioperl-live/blib/lib/Bio/SeqIO/nexml.pm line 106
STACK: Bio::SeqIO::nexml::next_seq() called at t/SeqIO/nexml.t line 17
-----------------------------------------------------------------
# Looks like you planned 44 tests but ran 3.
# Looks like your test exited with 9 just after 3.
t/SeqIO/nexml.t .............................. Dubious, test returned 9 (wstat 2304, 0x900)
Failed 41/44 subtests
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 ............................. skipped: The optional module XML::LibXML (or dependencies thereof) was not installed
t/SeqIO/strider.t ............................ ok
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 ................... 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/EUtilities/EUtilParameters.t ......... ok
t/Tools/EUtilities/egquery.t ................. ok
t/Tools/EUtilities/einfo.t ................... ok
t/Tools/EUtilities/elink_acheck.t ............ ok
t/Tools/EUtilities/elink_lcheck.t ............ ok
t/Tools/EUtilities/elink_llinks.t ............ ok
t/Tools/EUtilities/elink_ncheck.t ............ ok
t/Tools/EUtilities/elink_neighbor.t .......... ok
t/Tools/EUtilities/elink_neighbor_history.t .. ok
t/Tools/EUtilities/elink_scores.t ............ ok
t/Tools/EUtilities/epost.t ................... ok
t/Tools/EUtilities/esearch.t ................. ok
t/Tools/EUtilities/espell.t .................. ok
t/Tools/EUtilities/esummary.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/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
t/Tools/Run/WBCommandExts.t .................. skipped: The optional module Bio::Tools::Run::WrapperBase::CommandExts (or dependencies thereof) was not installed
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 ................ ok
t/Tree/PhyloNetwork/GraphViz.t ............... skipped: The optional module GraphViz (or dependencies thereof) was not installed
t/Tree/PhyloNetwork/MuVector.t ............... ok
t/Tree/PhyloNetwork/PhyloNetwork.t ........... ok
t/Tree/PhyloNetwork/RandomFactory.t .......... skipped: The optional module Math::Random (or dependencies thereof) was not installed
t/Tree/PhyloNetwork/TreeFactory.t ............ ok
t/Tree/RandomTreeFactory.t ................... ok
t/Tree/Tree.t ................................ ok
t/Tree/TreeIO.t .............................. 1/78 Use of uninitialized value $txt[0] in join or string at /usr/local/share/perl/5.10.0/SVG/Element.pm line 1202.
Use of uninitialized value $txt[0] in join or string at /usr/local/share/perl/5.10.0/SVG/Element.pm line 1202.
Use of uninitialized value $txt[0] in join or string at /usr/local/share/perl/5.10.0/SVG/Element.pm line 1202.
Use of uninitialized value $txt[0] in join or string at /usr/local/share/perl/5.10.0/SVG/Element.pm line 1202.
Use of uninitialized value $txt[0] in join or string at /usr/local/share/perl/5.10.0/SVG/Element.pm line 1202.
Use of uninitialized value $txt[0] in join or string at /usr/local/share/perl/5.10.0/SVG/Element.pm line 1202.
t/Tree/TreeIO.t .............................. ok
t/Tree/TreeIO/lintree.t ...................... ok
t/Tree/TreeIO/newick.t ....................... ok
t/Tree/TreeIO/nexml.t ........................ 1/46 -------------------------- EXCEPTION ----------------------------
Message: Wrong version number, can only handle 0.9: 0.8
An exception of type Bio::Phylo::Util::Exceptions::BadFormat
was thrown.
This kind of error happens when a bad
parse or unparse format was specified.
Refer to the Bio::Phylo::Util::Exceptions documentation for more
information.
------------------------- STACK TRACE ---------------------------
STACK: Bio::Phylo::Parsers::Nexml::_handle_nexml() called at /usr/local/share/perl/5.10.0/Bio/Phylo/Parsers/Nexml.pm line 157
STACK: Bio::Phylo::Parsers::Nexml::__ANON__() called at /usr/share/perl5/XML/Twig.pm line 1926
STACK: XML::Twig::_twig_end() called at /usr/lib/perl5/XML/Parser/Expat.pm line 474
STACK: XML::Parser::Expat::parse() called at /usr/lib/perl5/XML/Parser.pm line 187
STACK: (eval)() called at /usr/lib/perl5/XML/Parser.pm line 186
STACK: XML::Parser::parse() called at /usr/share/perl5/XML/Twig.pm line 658
STACK: (eval)() called at /usr/share/perl5/XML/Twig.pm line 658
STACK: XML::Twig::parse() called at /usr/local/share/perl/5.10.0/Bio/Phylo/Parsers/Nexml.pm line 186
STACK: Bio::Phylo::Parsers::Nexml::_parse() called at /usr/local/share/perl/5.10.0/Bio/Phylo/Parsers/Abstract.pm line 155
STACK: Bio::Phylo::Parsers::Abstract::_process() called at /usr/local/share/perl/5.10.0/Bio/Phylo/IO.pm line 198
STACK: Bio::Phylo::IO::parse() called at /home/drin/bioinformatics/bioperl/bioperl-live/blib/lib/Bio/TreeIO/nexml.pm line 153
STACK: Bio::TreeIO::nexml::_parse() called at /home/drin/bioinformatics/bioperl/bioperl-live/blib/lib/Bio/TreeIO/nexml.pm line 105
STACK: Bio::TreeIO::nexml::next_tree() called at t/Tree/TreeIO/nexml.t line 18
-----------------------------------------------------------------
# Looks like you planned 46 tests but ran 4.
# Looks like your test exited with 9 just after 4.
t/Tree/TreeIO/nexml.t ........................ Dubious, test returned 9 (wstat 2304, 0x900)
Failed 42/46 subtests
t/Tree/TreeIO/nexus.t ........................ ok
t/Tree/TreeIO/nhx.t .......................... ok
t/Tree/TreeIO/phyloxml.t ..................... skipped: The optional module XML::LibXML (or dependencies thereof) was not installed
t/Tree/TreeIO/svggraph.t ..................... 1/4 Use of uninitialized value $txt[0] in join or string at /usr/local/share/perl/5.10.0/SVG/Element.pm line 1202, <GEN0> line 1.
Use of uninitialized value $txt[0] in join or string at /usr/local/share/perl/5.10.0/SVG/Element.pm line 1202, <GEN0> line 1.
Use of uninitialized value $txt[0] in join or string at /usr/local/share/perl/5.10.0/SVG/Element.pm line 1202, <GEN0> line 1.
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 .................................... 1/125 -------------------------- EXCEPTION ----------------------------
Message: Wrong version number, can only handle 0.9: 0.8
An exception of type Bio::Phylo::Util::Exceptions::BadFormat
was thrown.
This kind of error happens when a bad
parse or unparse format was specified.
Refer to the Bio::Phylo::Util::Exceptions documentation for more
information.
------------------------- STACK TRACE ---------------------------
STACK: Bio::Phylo::Parsers::Nexml::_handle_nexml() called at /usr/local/share/perl/5.10.0/Bio/Phylo/Parsers/Nexml.pm line 157
STACK: Bio::Phylo::Parsers::Nexml::__ANON__() called at /usr/share/perl5/XML/Twig.pm line 1926
STACK: XML::Twig::_twig_end() called at /usr/lib/perl5/XML/Parser/Expat.pm line 474
STACK: XML::Parser::Expat::parse() called at /usr/lib/perl5/XML/Parser.pm line 187
STACK: (eval)() called at /usr/lib/perl5/XML/Parser.pm line 186
STACK: XML::Parser::parse() called at /usr/share/perl5/XML/Twig.pm line 658
STACK: (eval)() called at /usr/share/perl5/XML/Twig.pm line 658
STACK: XML::Twig::parse() called at /usr/local/share/perl/5.10.0/Bio/Phylo/Parsers/Nexml.pm line 186
STACK: Bio::Phylo::Parsers::Nexml::_parse() called at /usr/local/share/perl/5.10.0/Bio/Phylo/Parsers/Abstract.pm line 155
STACK: Bio::Phylo::Parsers::Abstract::_process() called at /usr/local/share/perl/5.10.0/Bio/Phylo/IO.pm line 198
STACK: Bio::Phylo::IO::parse() called at /home/drin/bioinformatics/bioperl/bioperl-live/blib/lib/Bio/NexmlIO.pm line 148
STACK: Bio::NexmlIO::new() called at t/nexml.t line 16
-----------------------------------------------------------------
# Looks like you planned 125 tests but ran 1.
# Looks like your test exited with 255 just after 1.
t/nexml.t .................................... Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 124/125 subtests
Test Summary Report
-------------------
t/AlignIO/nexml.t (Wstat: 2304 Tests: 2 Failed: 0)
Non-zero exit status: 9
Parse errors: Bad plan. You planned 35 tests but ran 2.
t/SeqIO/nexml.t (Wstat: 2304 Tests: 3 Failed: 0)
Non-zero exit status: 9
Parse errors: Bad plan. You planned 44 tests but ran 3.
t/Tree/TreeIO/nexml.t (Wstat: 2304 Tests: 4 Failed: 0)
Non-zero exit status: 9
Parse errors: Bad plan. You planned 46 tests but ran 4.
t/nexml.t (Wstat: 65280 Tests: 1 Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 125 tests but ran 1.
Files=347, Tests=22174, 181 wallclock secs ( 4.31 usr 0.88 sys + 162.28 cusr 8.86 csys = 176.33 CPU)
Result: FAIL
Failed 4/347 test programs. 0/22174 subtests failed.
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