reorg test run

gistfile1.txt

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
[fai_load] build FASTA index.
t/Assembly/IO/bowtie.t ....................... ok
t/Assembly/IO/sam.t .......................... ok

--------------------- WARNING ---------------------
MSG: Setting end to equal start[1]
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Setting end to equal start[1]
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Setting end to equal start[1]
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Setting end to equal start[1]
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Setting end to equal start[1]
---------------------------------------------------
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/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/DBFasta.t .......................... ok
t/LocalDB/DBQual.t ........................... ok
t/LocalDB/Flat.t ............................. ok
Use of uninitialized value $args[1] in join or string at Bio/Index/Abstract.pm line 777.
t/LocalDB/Index/Blast.t ...................... ok
Use of uninitialized value $args[1] in join or string at Bio/Index/Abstract.pm line 777.
t/LocalDB/Index/BlastTable.t ................. ok
Use of uninitialized value $args[1] in join or string at Bio/Index/Abstract.pm line 777, <$fh> line 40.
t/LocalDB/Index/Index.t ...................... ok
t/LocalDB/Registry.t ......................... ok
t/LocalDB/SeqFeature.t ....................... ok
t/LocalDB/SeqFeature_BDB.t ................... ok
t/LocalDB/SeqFeature_SQLite.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
Subroutine num redefined at t/Ontology/IO/go.t line 246.
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: 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
Use of uninitialized value $rest[0] in join or string at (eval 77) 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/HTTPget.t ............................. skipped: Network tests have not been requested
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

#   Failed test at t/SearchIO/blast.t line 1926.
#          got: ''
#     expected: '2.2.15 [Oct-15-2006]'
# Looks like you failed 1 test of 1354.
t/SearchIO/blast.t ........................... 
Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/1354 subtests 
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

--------------------- WARNING ---------------------
MSG: Positions of substitutions and deletions have to be strictly positive but got 0. Skipping substitution or deletion at this position

---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Position 13 is beyond end of read (12 residues). Skipping errors specified at this position.

---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Positions of substitutions and deletions have to be strictly positive but got 0. Skipping substitution or deletion at this position

---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Position 13 is beyond end of read (12 residues). Skipping errors specified at this position.

---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Position 13 is beyond end of read (12 residues). Skipping errors specified at this position.

---------------------------------------------------
t/Seq/SimulatedRead.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 ............................... skipped: The optional module XML::DOM (or dependencies thereof) was not installed
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 .............................. skipped: The optional module Spreadsheet::ParseExcel (or dependencies thereof) was not installed
t/SeqIO/exp.t ................................ skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqIO/fasta.t .............................. ok
Useless use of a constant (edge case; single 0 in quality fails) in void context at t/SeqIO/fastq.t line 432.
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 .......................... ok
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 ............................... skipped: The optional module Error (or dependencies thereof) was not installed
t/SeqIO/tigrxml.t ............................ ok
Use of uninitialized value $Bio::SeqIO::tinyseq::VERSION in concatenation (.) or string at Bio/SeqIO/tinyseq.pm line 360.
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/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
t/Tools/Run/WBCommandExts.t .................. ok
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 .......................... skipped: The optional module Set::Scalar (or dependencies thereof) was not installed
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 Array::Compare (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/SearchIO/blast.t                         (Wstat: 256 Tests: 1354 Failed: 1)
  Failed test:  1182
  Non-zero exit status: 1
Files=342, Tests=21931, 111 wallclock secs ( 3.74 usr  0.58 sys + 100.09 cusr  9.24 csys = 113.65 CPU)
Result: FAIL
Failed 1/342 test programs. 1/21931 subtests failed.