BioPerl errors (master) - 6/28/2016

gistfile1.txt

[cjfields@Chriss-MacBook-Air bioperl-live (master)]$ ./Build test
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 ...................... 1/125 # WARNING: NeXML parsing for NeXML v0.9 is currently very experimental support
t/AlignIO/nexml.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/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
t/Assembly/core.t ...................... ok
t/Cluster/UniGene.t .................... ok
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
t/LocalDB/BioDBGFF.t ................... 1/275
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/SeqFeature_BDB.t ............. ok
t/LocalDB/SeqFeature_SQLite.t .......... ok
t/LocalDB/Taxonomy/greengenes.t ........ ok
t/LocalDB/Taxonomy/silva.t ............. ok
t/LocalDB/Taxonomy/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
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 ............. ok
t/Ontology/Relationship.t .............. ok
t/Ontology/RelationshipType.t .......... ok
t/Ontology/Term.t ...................... ok
t/Perl.t ............................... 26/31
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 .................. ok
t/RemoteDB/CUTG.t ...................... ok
t/RemoteDB/EMBL.t ...................... ok
t/RemoteDB/EntrezGene.t ................ Unescaped left brace in regex is deprecated, passed through in regex; marked by <-- HERE in m/\G{ <-- HERE / at /Users/cjfields/perl5/perlbrew/perls/perl-5.22.1/lib/site_perl/5.22.1/Bio/ASN1/EntrezGene.pm line 148.
t/RemoteDB/EntrezGene.t ................ ok
t/RemoteDB/GenBank.t ................... ok
t/RemoteDB/GenPept.t ................... ok
t/RemoteDB/HIV/HIV.t ................... ok
t/RemoteDB/HIV/HIVAnnotProcessor.t ..... ok
t/RemoteDB/HIV/HIVQuery.t .............. 1/41
#   Failed test 'use Bio::DB::Query::HIVQuery;'
#   at t/RemoteDB/HIV/HIVQuery.t line 13.
#     Tried to use 'Bio::DB::Query::HIVQuery'.
#     Error:  Can't locate CGI.pm in @INC (you may need to install the CGI module) (@INC contains: /Users/cjfields/bioperl/bioperl-live/blib/lib /Users/cjfields/bioperl/bioperl-live/blib/arch /Users/cjfields/bioperl/bioperl-live /Users/cjfields/bioperl/Bio-EUtilities/lib /Users/cjfields/bioperl/Bio-Root/lib /Users/cjfields/bioperl/bioperl-live /Users/cjfields/bioperl/Bio-Root/lib /Users/cjfields/bioperl/Bio-EUtilities/lib /Users/cjfields/perl5/perlbrew/perls/perl-5.22.1/lib/site_perl/5.22.1/darwin-thread-multi-2level /Users/cjfields/perl5/perlbrew/perls/perl-5.22.1/lib/site_perl/5.22.1 /Users/cjfields/perl5/perlbrew/perls/perl-5.22.1/lib/5.22.1/darwin-thread-multi-2level /Users/cjfields/perl5/perlbrew/perls/perl-5.22.1/lib/5.22.1 .) at /Users/cjfields/bioperl/bioperl-live/blib/lib/Bio/DB/Query/HIVQuery.pm line 212.
# BEGIN failed--compilation aborted at /Users/cjfields/bioperl/bioperl-live/blib/lib/Bio/DB/Query/HIVQuery.pm line 212.
# Compilation failed in require at t/RemoteDB/HIV/HIVQuery.t line 13.
# BEGIN failed--compilation aborted at t/RemoteDB/HIV/HIVQuery.t line 13.
Can't locate object method "new" via package "Bio::DB::Query::HIVQuery" at t/RemoteDB/HIV/HIVQuery.t line 22.
# Looks like your test exited with 255 just after 6.
t/RemoteDB/HIV/HIVQuery.t .............. Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 36/41 subtests
t/RemoteDB/HIV/HIVQueryHelper.t ........ ok
t/RemoteDB/MeSH.t ...................... ok
t/RemoteDB/Query/GenBank.t ............. ok
t/RemoteDB/RefSeq.t .................... ok
t/RemoteDB/SeqHound.t .................. 1/15
--------------------- WARNING ---------------------
MSG: HTTP::Request error: 500 Can't connect to dogboxonline.unleashedinformatics.com:80

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

--------------------- WARNING ---------------------
MSG: HTTP::Request error: 500 Can't connect to dogboxonline.unleashedinformatics.com:80

---------------------------------------------------
t/RemoteDB/SeqHound.t .................. ok
t/RemoteDB/SeqRead_fail.t .............. ok
t/RemoteDB/SeqVersion.t ................ 10/?
#   Failed test at t/RemoteDB/SeqVersion.t line 41.
#          got: 'suppressed'
#     expected: 'dead'

#   Failed test at t/RemoteDB/SeqVersion.t line 47.
#          got: 'suppressed'
#     expected: 'dead'
# Looks like you failed 2 tests of 15.
t/RemoteDB/SeqVersion.t ................ Dubious, test returned 2 (wstat 512, 0x200)
Failed 2/15 subtests
t/RemoteDB/SwissProt.t ................. ok
t/RemoteDB/Taxonomy.t .................. 61/202
#   Failed test at t/RemoteDB/Taxonomy.t line 178.
#     '2'
#         >=
#     '8'
t/RemoteDB/Taxonomy.t .................. 65/202
#   Failed test at t/RemoteDB/Taxonomy.t line 180.
#          got: '0'
#     expected: '1'

#   Failed test at t/RemoteDB/Taxonomy.t line 181.
#          got: undef
#     expected: '231509'
t/RemoteDB/Taxonomy.t .................. 149/202 # Looks like you failed 3 tests of 202.
t/RemoteDB/Taxonomy.t .................. Dubious, test returned 3 (wstat 768, 0x300)
Failed 3/202 subtests
t/Restriction/Analysis-refac.t ......... ok
t/Restriction/Analysis.t ............... ok
t/Restriction/Gel.t .................... ok
t/Restriction/IO.t ..................... 15/17
--------------------- WARNING ---------------------
MSG: The enzyme name Hpy99XIV-mut1 was changed to Hpy99XIV-mutI
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: The enzyme name HpyAXVI-mut1 was changed to HpyAXVI-mutI
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: The enzyme name HpyUM032XIII-mut1 was changed to HpyUM032XIII-mutI
---------------------------------------------------

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Unrecognized characters in site: [GTGGNAG,TNGGNAG]
STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:444
STACK: Bio::Restriction::Enzyme::site Bio/Restriction/Enzyme.pm:534
STACK: Bio::Restriction::Enzyme::new Bio/Restriction/Enzyme.pm:381
STACK: Bio::Restriction::IO::prototype::read /Users/cjfields/bioperl/bioperl-live/Bio/Restriction/IO/prototype.pm:129
STACK: t/Restriction/IO.t:79
-----------------------------------------------------------
# Looks like your test exited with 25 just after 15.
t/Restriction/IO.t ..................... Dubious, test returned 25 (wstat 6400, 0x1900)
Failed 2/17 subtests
t/Root/Exception.t ..................... ok
t/Root/HTTPget.t ....................... ok
t/Root/IO.t ............................ ok
t/Root/RootI.t ......................... ok
t/Root/RootIO-url.t .................... Can't locate object method "new" via package "Bio::Root::IO" (perhaps you forgot to load "Bio::Root::IO"?) at t/Root/RootIO-url.t line 19.
t/Root/RootIO-url.t .................... Dubious, test returned 255 (wstat 65280, 0xff00)
No subtests run
t/Root/RootIO.t ........................ ok
t/Root/Storable.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/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 ..................... 1/312
--------------------- WARNING ---------------------
MSG: Translating partial ORF ATGAATGTAAAT from end of nucleotide sequence
---------------------------------------------------

--------------------- WARNING ---------------------
MSG: Translating partial ORF ATGAATGTAAAT from end of nucleotide sequence
---------------------------------------------------
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/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 ................... Unescaped left brace in regex is deprecated, passed through in regex; marked by <-- HERE in m/\G{ <-- HERE / at /Users/cjfields/perl5/perlbrew/perls/perl-5.22.1/lib/site_perl/5.22.1/Bio/ASN1/EntrezGene.pm line 148.
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 ........................ 1/126 # WARNING: NeXML parsing for NeXML v0.9 is currently very experimental support
t/SeqIO/nexml.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/scf.t .......................... ok
t/SeqIO/seqxml.t ....................... ok
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: These modules are now probably deprecated
t/Tools/Alignment/Consed.t ............. ok
t/Tools/AmpliconSearch.t ............... ok
t/Tools/Analysis/DNA/ESEfinder.t ....... ok
t/Tools/Analysis/Protein/Domcut.t ...... ok
t/Tools/Analysis/Protein/ELM.t ......... ok
t/Tools/Analysis/Protein/GOR4.t ........ skipped: These modules are now probably deprecated
t/Tools/Analysis/Protein/HNN.t ......... skipped: These modules are now probably deprecated
t/Tools/Analysis/Protein/Mitoprot.t .... 6/10
#   Failed test at t/Tools/Analysis/Protein/Mitoprot.t line 35.
#          got: undef
#     expected: '-13'
# Looks like you failed 1 test of 10.
t/Tools/Analysis/Protein/Mitoprot.t .... Dubious, test returned 1 (wstat 256, 0x100)
Failed 1/10 subtests
t/Tools/Analysis/Protein/NetPhos.t ..... ok
t/Tools/Analysis/Protein/Scansite.t .... ok
t/Tools/Analysis/Protein/Sopma.t ....... skipped: These modules are now probably deprecated
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/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 .............. ok
t/Tools/Run/RemoteBlast_rpsblast.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: These modules are now probably 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 ......... ok
t/Tree/PhyloNetwork/MuVector.t ......... ok
t/Tree/PhyloNetwork/PhyloNetwork.t ..... ok
t/Tree/PhyloNetwork/RandomFactory.t .... ok
t/Tree/PhyloNetwork/TreeFactory.t ...... ok
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 .................. 1/46 # WARNING: NeXML parsing for NeXML v0.9 is currently very experimental support
# Begin tests for writing tree files
t/Tree/TreeIO/nexml.t .................. ok
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 .............................. 1/125 # WARNING: NeXML parsing for NeXML v0.9 is currently very experimental support
t/nexml.t .............................. ok

Test Summary Report
-------------------
t/RemoteDB/HIV/HIVQuery.t            (Wstat: 65280 Tests: 6 Failed: 1)
  Failed test:  1
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 41 tests but ran 6.
t/RemoteDB/SeqVersion.t              (Wstat: 512 Tests: 15 Failed: 2)
  Failed tests:  11, 15
  Non-zero exit status: 2
t/RemoteDB/Taxonomy.t                (Wstat: 768 Tests: 202 Failed: 3)
  Failed tests:  64-66
  Non-zero exit status: 3
t/Restriction/IO.t                   (Wstat: 6400 Tests: 15 Failed: 0)
  Non-zero exit status: 25
  Parse errors: Bad plan.  You planned 17 tests but ran 15.
t/Root/RootIO-url.t                  (Wstat: 65280 Tests: 0 Failed: 0)
  Non-zero exit status: 255
  Parse errors: No plan found in TAP output
t/Tools/Analysis/Protein/Mitoprot.t  (Wstat: 256 Tests: 10 Failed: 1)
  Failed test:  9
  Non-zero exit status: 1
Files=331, Tests=23735, 422 wallclock secs ( 3.38 usr  1.07 sys + 112.16 cusr 16.76 csys = 133.37 CPU)
Result: FAIL
Failed 6/331 test programs. 7/23735 subtests failed.