[Bioperl-l] About to tag the last RC...
Dave Messina
David.Messina at sbc.su.se
Tue Jan 13 18:49:03 UTC 2009
Hey Chris,
I just tested RC2 under a vanilla Perl 5.8.8 install on OS X 10.5.6.
When I skip install of optional modules, BioPerl scripts, and network tests,
everything goes fine.
All tests successful, 58 tests and 319 subtests skipped.
Files=320, Tests=14927, 121 wallclock secs (83.92 cusr + 13.91 csys = 97.83
CPU)
However, when I request installation of all optional modules, all BioPerl
scripts, and the network tests, I run into some minor problems. Note that
I'm building and testing on the command line, not via the CPAN shell.
Test output is below (minus the 'copying script' stuff at the beginning).
Dave
t/Align/AlignStats...........................ok
t/Align/AlignUtil............................ok
t/Align/SimpleAlign..........................ok
t/Align/TreeBuild............................ok
t/Align/Utilities............................ok
t/AlignIO/AlignIO............................ok
t/AlignIO/arp................................ok
t/AlignIO/bl2seq.............................ok
t/AlignIO/clustalw...........................ok
t/AlignIO/emboss.............................ok
t/AlignIO/fasta..............................ok
t/AlignIO/largemultifasta....................ok
t/AlignIO/maf................................ok
t/AlignIO/mase...............................ok
t/AlignIO/mega...............................ok
t/AlignIO/meme...............................ok
t/AlignIO/metafasta..........................ok
t/AlignIO/msf................................ok
t/AlignIO/nexus..............................ok
t/AlignIO/pfam...............................ok
t/AlignIO/phylip.............................ok
t/AlignIO/po.................................ok
t/AlignIO/prodom.............................ok
t/AlignIO/psi................................ok
t/AlignIO/selex..............................ok
t/AlignIO/stockholm..........................ok
t/AlignIO/xmfa...............................ok
t/Alphabet...................................ok
t/Annotation/Annotation......................1/155
# Failed (TODO) test 'The object isa Bio::Annotation::Comment'
# in t/Annotation/Annotation.t at line 214.
# The object isn't a 'Bio::Annotation::Comment' it's a
'Bio::Annotation::OntologyTerm'
t/Annotation/Annotation......................ok
t/Annotation/AnnotationAdaptor...............ok
t/Assembly/Assembly..........................2/50
--------------------- WARNING ---------------------
MSG: Adding non-nucleotidic sequence ML4922R
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: Adding non-nucleotidic sequence ML4947F
---------------------------------------------------
t/Assembly/Assembly..........................ok
t/Assembly/ContigSpectrum....................ok
t/Biblio/Biblio..............................ok
t/Biblio/References..........................ok
t/Biblio/biofetch............................ok
t/Biblio/eutils..............................1/4
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Bio/DB/Biblio/eutils.pm: eutils cannot be found or loaded
Exception Can't locate XML/Twig.pm in @INC (@INC contains:
/Users/dave/.cpan/build/BioPerl-1.5.9._2 _build/lib t/lib .
/Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib
/Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/arch
/Users/dave/src/bioperl-live /Users/dave/src/sonnh/dmess
/System/Library/Perl/5.8.8/darwin-thread-multi-2level
/System/Library/Perl/5.8.8 /Library/Perl/5.8.8/darwin-thread-multi-2level
/Library/Perl/5.8.8 /Library/Perl
/Network/Library/Perl/5.8.8/darwin-thread-multi-2level
/Network/Library/Perl/5.8.8 /Network/Library/Perl
/System/Library/Perl/Extras/5.8.8/darwin-thread-multi-2level
/System/Library/Perl/Extras/5.8.8 /Library/Perl/5.8.6 /Library/Perl/5.8.1)
at /Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/DB/Biblio/eutils.pm line
122.
BEGIN failed--compilation aborted at
/Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/DB/Biblio/eutils.pm line 122.
Compilation failed in require at
/Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/Biblio.pm line 315.
For more information about the Biblio system please see the Bio::Biblio
docs.
STACK: Error::throw
STACK: Bio::Root::Root::throw
/Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/Root/Root.pm:357
STACK: Bio::Biblio::_load_access_module
/Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/Biblio.pm:319
STACK: Bio::Biblio::new
/Users/dave/.cpan/build/BioPerl-1.5.9._2/Bio/Biblio.pm:280
STACK: t/Biblio/eutils.t:22
-----------------------------------------------------------
# Looks like you planned 4 tests but only ran 1.
t/Biblio/eutils.............................. Dubious, test returned 255
(wstat 65280, 0xff00)
Failed 3/4 subtests
t/ClusterIO/ClusterIO........................ok
t/ClusterIO/SequenceFamily...................ok
t/ClusterIO/unigene..........................ok
t/Coordinate/CoordinateGraph.................ok
t/Coordinate/CoordinateMapper................ok
t/Coordinate/GeneCoordinateMapper............ok
t/LiveSeq/Chain..............................ok
t/LiveSeq/LiveSeq............................ok
t/LiveSeq/Mutation...........................ok
t/LiveSeq/Mutator............................ok
t/LocalDB/BioDBGFF...........................ok
t/LocalDB/BlastIndex.........................ok
t/LocalDB/DBFasta............................ok
t/LocalDB/DBQual.............................ok
t/LocalDB/Flat...............................ok
t/LocalDB/Index..............................ok
t/LocalDB/Registry...........................ok
t/LocalDB/SeqFeature.........................ok
t/LocalDB/SeqFeature_BDB.....................ok
t/LocalDB/transfac_pro.......................ok
t/Map/Cyto...................................ok
t/Map/Linkage................................ok
t/Map/Map....................................ok
t/Map/MapIO..................................ok
t/Map/MicrosatelliteMarker...................ok
t/Map/Physical...............................ok
t/Matrix/IO/masta............................ok
t/Matrix/IO/psm..............................ok
t/Matrix/InstanceSite........................ok
t/Matrix/Matrix..............................ok
t/Matrix/ProtMatrix..........................ok
t/Matrix/ProtPsm.............................ok
t/Matrix/SiteMatrix..........................ok
t/Ontology/GOterm............................skipped: The optional module
Graph::Directed (or dependencies thereof) was not installed
t/Ontology/GraphAdaptor......................skipped: The optional module
Graph (or dependencies thereof) was not installed
t/Ontology/IO/go.............................skipped: The optional module
Graph (or dependencies thereof) was not installed
t/Ontology/IO/interpro.......................skipped: The optional module
XML::Parser::PerlSAX (or dependencies thereof) was not installed
t/Ontology/IO/obo............................skipped: The optional module
Graph (or dependencies thereof) was not installed
t/Ontology/Ontology..........................skipped: The optional module
Graph (or dependencies thereof) was not installed
t/Ontology/OntologyEngine....................skipped: The optional module
Graph::Directed (or dependencies thereof) was not installed
t/Ontology/OntologyStore.....................skipped: The optional module
Graph (or dependencies thereof) was not installed
t/Ontology/Relationship......................skipped: The optional module
Graph::Directed (or dependencies thereof) was not installed
t/Ontology/RelationshipType..................skipped: The optional module
Graph::Directed (or dependencies thereof) was not installed
t/Ontology/Term..............................skipped: The optional module
Graph::Directed (or dependencies thereof) was not installed
t/Perl.......................................ok
t/Phenotype/Correlate........................ok
t/Phenotype/MeSH.............................ok
t/Phenotype/Measure..........................ok
t/Phenotype/MiniMIMentry.....................ok
t/Phenotype/OMIMentry........................ok
t/Phenotype/OMIMentryAllelicVariant..........ok
t/Phenotype/OMIMparser.......................ok
t/Phenotype/Phenotype........................ok
t/PodSyntax..................................skipped: Test::Pod 1.00
required for testing POD
t/PopGen/Coalescent..........................ok
t/PopGen/HtSNP...............................ok
t/PopGen/MK..................................ok
t/PopGen/PopGen..............................ok
t/PopGen/PopGenSims..........................ok
t/PopGen/TagHaplotype........................ok
t/RemoteDB/BioFetch..........................ok
t/RemoteDB/CUTG..............................ok
t/RemoteDB/DB................................104/116
# Failed test in t/RemoteDB/DB.t at line 352.
# got: 'unknown'
# expected: 'GDB:188393'
t/RemoteDB/DB................................114/116 # Looks like you failed
1 test of 116.
t/RemoteDB/DB................................ Dubious, test returned 1
(wstat 256, 0x100)
Failed 1/116 subtests
(less 8 skipped subtests: 107 okay)
t/RemoteDB/EMBL..............................ok
t/RemoteDB/EUtilities........................ok
t/RemoteDB/GDB...............................2/12
# Failed test 'info was unknown'
# in t/RemoteDB/GDB.t at line 40.
# got: 'unknown'
# expected: 'GDB:188296'
# Failed test 'info was notfound'
# in t/RemoteDB/GDB.t at line 41.
# got: 'notfound'
# expected: 'GCCCAGGAGGTTGAGG'
# Failed test 'info was notfound'
# in t/RemoteDB/GDB.t at line 42.
# got: 'notfound'
# expected: 'AAGGCAGGCTTGAATTACAG'
Use of uninitialized value in concatenation (.) or string at
t/RemoteDB/GDB.t line 43.
# Failed test 'info was '
# in t/RemoteDB/GDB.t at line 43.
# got: undef
# expected: '226'
t/RemoteDB/GDB...............................8/12
# Failed test 'info was unknown'
# in t/RemoteDB/GDB.t at line 55.
# got: 'unknown'
# expected: 'GDB:198271'
# Failed test 'info was notfound'
# in t/RemoteDB/GDB.t at line 56.
# got: 'notfound'
# expected: 'GGGTGACAGAACAAGACCT'
# Failed test 'info was notfound'
# in t/RemoteDB/GDB.t at line 57.
# got: 'notfound'
# expected: 'ACCCATTAGCCTTGAACTGA'
Use of uninitialized value in concatenation (.) or string at
t/RemoteDB/GDB.t line 58.
# Failed test 'info was '
# in t/RemoteDB/GDB.t at line 58.
# got: undef
# expected: '155'
# Looks like you failed 8 tests of 12.
t/RemoteDB/GDB............................... Dubious, test returned 8
(wstat 2048, 0x800)
Failed 8/12 subtests
t/RemoteDB/HIV/HIV...........................21/29 # Error:
# ------------- EXCEPTION: Bio::WebError::Exception -------------
# MSG: Unparsed failure at
/Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/DB/HIV.pm line 275.
#
# VALUE: An empty string ("")
# STACK: Error::throw
# STACK: Bio::Root::Root::throw
/Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/Root/Root.pm:357
# STACK: Bio::DB::HIV::get_request
/Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/DB/HIV.pm:277
# STACK: Bio::DB::HIV::get_seq_stream
/Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/DB/HIV.pm:396
# STACK: Bio::DB::HIV::get_Stream_by_acc
/Users/dave/.cpan/build/BioPerl-1.5.9._2/blib/lib/Bio/DB/HIV.pm:491
# STACK: t/RemoteDB/HIV/HIV.t:78
# ---------------------------------------------------------------
t/RemoteDB/HIV/HIV...........................22/29 # Looks like you planned
29 tests but ran 1 extra.
t/RemoteDB/HIV/HIV........................... Dubious, test returned 255
(wstat 65280, 0xff00)
All 29 subtests passed
(less 9 skipped subtests: 20 okay)
t/RemoteDB/HIV/HIVAnnotProcessor.............ok
t/RemoteDB/HIV/HIVQuery......................ok
t/RemoteDB/HIV/HIVQueryHelper................ok
t/RemoteDB/RefSeq............................ok
t/RemoteDB/SeqHound..........................ok
t/RemoteDB/SeqRead_fail......................ok
t/RemoteDB/SeqVersion........................ok
t/RemoteDB/Taxonomy..........................skipped: The optional module
XML::Twig (or dependencies thereof) was not installed
t/Restriction/Analysis.......................ok
t/Restriction/Gel............................ok
t/Restriction/IO.............................1/18
# Failed (TODO) test in t/Restriction/IO.t at line 31.
t/Restriction/IO.............................ok
t/Root/Exception.............................ok
t/Root/RootI.................................ok
t/Root/RootIO................................30/31
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: request failed: HTTP/1.0 400 Bad Request
STACK: Error::throw
STACK: Bio::Root::Root::throw Bio/Root/Root.pm:357
STACK: Bio::Root::HTTPget::getFH Bio/Root/HTTPget.pm:234
STACK: Bio::Root::IO::_initialize_io Bio/Root/IO.pm:279
STACK: Bio::Root::IO::new Bio/Root/IO.pm:223
STACK: t/Root/RootIO.t:107
-----------------------------------------------------------
# Looks like you planned 31 tests but only ran 30.
t/Root/RootIO................................ Dubious, test returned 255
(wstat 65280, 0xff00)
Failed 1/31 subtests
t/Root/Storable..............................ok
t/Root/Tempfile..............................ok
t/Root/Utilities.............................ok
t/SearchDist.................................skipped: The optional module
Bio::Ext::Align (or dependencies thereof) was not installed
t/SearchIO/CigarString.......................ok
t/SearchIO/GbrowseGFF........................ok
t/SearchIO/SearchIO..........................ok
t/SearchIO/SimilarityPair....................ok
t/SearchIO/Writer/HTMLWriter.................ok
t/SearchIO/Writer/HitTableWriter.............ok
t/SearchIO/blast.............................2/1091
# Failed (TODO) test in t/SearchIO/blast.t at line 527.
# '0.852'
# >
# '0.9'
# Failed (TODO) test in t/SearchIO/blast.t at line 528.
# '1.599'
# <=
# '1'
t/SearchIO/blast.............................ok
t/SearchIO/blast_pull........................10/289
# Failed (TODO) test in t/SearchIO/blast_pull.t at line 260.
# got: '0.946'
# expected: '0.943'
t/SearchIO/blast_pull........................ok
t/SearchIO/blasttable........................ok
t/SearchIO/blastxml..........................1/298
# Failed (TODO) test in t/SearchIO/blastxml.t at line 254.
# got: undef
# expected: '31984247'
# Failed (TODO) test in t/SearchIO/blastxml.t at line 255.
# got: undef
# expected: '88780'
# Failed (TODO) test in t/SearchIO/blastxml.t at line 256.
# got: undef
# expected: '49'
t/SearchIO/blastxml..........................ok
t/SearchIO/cross_match.......................ok
t/SearchIO/erpin.............................ok
t/SearchIO/exonerate.........................ok
t/SearchIO/fasta.............................ok
t/SearchIO/hmmer.............................ok
t/SearchIO/hmmer_pull........................ok
t/SearchIO/infernal..........................ok
t/SearchIO/megablast.........................ok
t/SearchIO/psl...............................ok
t/SearchIO/rnamotif..........................ok
t/SearchIO/sim4..............................ok
t/SearchIO/waba..............................ok
t/SearchIO/wise..............................ok
t/Seq/DBLink.................................ok
t/Seq/EncodedSeq.............................ok
t/Seq/LargeLocatableSeq......................ok
t/Seq/LargePSeq..............................ok
t/Seq/LocatableSeq...........................1/116
# Failed (TODO) test in t/Seq/LocatableSeq.t at line 45.
# got: 'Bio::Location::Simple=HASH(0x812a74)'
# expected: undef
# Failed (TODO) test in t/Seq/LocatableSeq.t at line 284.
# got: '\-\.=~'
# expected: '-\?'
# Failed (TODO) test in t/Seq/LocatableSeq.t at line 286.
# '19'
# ne
# '19'
t/Seq/LocatableSeq...........................ok
t/Seq/MetaSeq................................ok
t/Seq/PrimaryQual............................ok
t/Seq/PrimarySeq.............................ok
t/Seq/PrimedSeq..............................ok
t/Seq/Quality................................ok
t/Seq/Seq....................................ok
t/Seq/WithQuality............................ok
t/SeqEvolution...............................ok
t/SeqFeature/FeatureIO.......................skipped: The optional module
Graph (or dependencies thereof) was not installed
t/SeqFeature/Location........................ok
t/SeqFeature/LocationFactory.................ok
t/SeqFeature/Primer..........................ok
t/SeqFeature/Range...........................ok
t/SeqFeature/RangeI..........................ok
t/SeqFeature/SeqAnalysisParser...............ok
t/SeqFeature/SeqFeatAnnotated................skipped: The optional module
Graph::Directed (or dependencies thereof) was not installed
t/SeqFeature/SeqFeatCollection...............ok
t/SeqFeature/SeqFeature......................ok
t/SeqFeature/SeqFeaturePrimer................ok
t/SeqFeature/Unflattener.....................ok
t/SeqFeature/Unflattener2....................ok
t/SeqIO......................................ok
t/SeqIO/Handler..............................ok
t/SeqIO/MultiFile............................ok
t/SeqIO/Multiple_fasta.......................ok
t/SeqIO/SeqBuilder...........................ok
t/SeqIO/Splicedseq...........................ok
t/SeqIO/abi..................................skipped: The optional module
Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqIO/ace..................................ok
t/SeqIO/agave................................ok
t/SeqIO/alf..................................ok
t/SeqIO/asciitree............................ok
t/SeqIO/bsml.................................skipped: The optional module
XML::DOM (or dependencies thereof) was not installed
t/SeqIO/bsml_sax.............................skipped: The optional module
XML::SAX::Writer (or dependencies thereof) was not installed
t/SeqIO/chadoxml.............................ok
t/SeqIO/chaos................................ok
t/SeqIO/chaosxml.............................ok
t/SeqIO/ctf..................................skipped: The optional module
Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqIO/embl.................................ok
t/SeqIO/entrezgene...........................skipped: The optional module
Bio::ASN1::EntrezGene (or dependencies thereof) was not installed
t/SeqIO/excel................................skipped: The optional module
Spreadsheet::ParseExcel (or dependencies thereof) was not installed
t/SeqIO/exp..................................skipped: The optional module
Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqIO/fasta................................ok
t/SeqIO/fastq................................ok
t/SeqIO/flybase_chadoxml.....................ok
t/SeqIO/game.................................skipped: The optional module
XML::Parser::PerlSAX (or dependencies thereof) was not installed
t/SeqIO/gcg..................................1/17
# Failed (TODO) test 'primary_id'
# in t/SeqIO/gcg.t at line 54.
# got: 'Bio::PrimarySeq=HASH(0x9374bc)'
# expected: 'roa1_drome'
t/SeqIO/gcg..................................ok
t/SeqIO/genbank..............................ok
t/SeqIO/interpro.............................skipped: The optional module
XML::DOM::XPath (or dependencies thereof) was not installed
t/SeqIO/kegg.................................ok
t/SeqIO/largefasta...........................ok
t/SeqIO/lasergene............................ok
t/SeqIO/locuslink............................skipped: The optional module
Graph::Directed (or dependencies thereof) was not installed
t/SeqIO/metafasta............................ok
t/SeqIO/phd..................................ok
t/SeqIO/pir..................................ok
t/SeqIO/pln..................................skipped: The optional module
Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqIO/qual.................................ok
t/SeqIO/raw..................................ok
t/SeqIO/scf..................................1/59
# Failed (TODO) test 'accuracies'
# in t/SeqIO/scf.t at line 78.
# got: 'ARRAY(0x989ba0)'
# expected: '482'
t/SeqIO/scf..................................ok
t/SeqIO/strider..............................skipped: The optional module
Convert::Binary::C (or dependencies thereof) was not installed
t/SeqIO/swiss................................ok
t/SeqIO/tab..................................ok
t/SeqIO/table................................ok
t/SeqIO/tigr.................................ok
t/SeqIO/tigrxml..............................skipped: The optional module
XML::SAX::Writer (or dependencies thereof) was not installed
t/SeqIO/tinyseq..............................skipped: The optional module
XML::Parser::PerlSAX (or dependencies thereof) was not installed
t/SeqIO/ztr..................................skipped: The optional module
Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqTools/CodonTable........................ok
t/SeqTools/ECnumber..........................ok
t/SeqTools/GuessSeqFormat....................ok
t/SeqTools/OddCodes..........................ok
t/SeqTools/SeqPattern........................ok
t/SeqTools/SeqStats..........................ok
t/SeqTools/SeqUtils..........................ok
t/SeqTools/SeqWords..........................ok
t/Species....................................ok
t/Structure/IO...............................ok
t/Structure/Structure........................ok
t/Symbol.....................................ok
t/TaxonTree..................................skipped: All tests are being
skipped, probably because the module(s) being tested here are now deprecated
t/Tools/Alignment/Consed.....................ok
t/Tools/Analysis/DNA/ESEfinder...............ok
t/Tools/Analysis/Protein/Domcut..............ok
t/Tools/Analysis/Protein/ELM.................ok
t/Tools/Analysis/Protein/GOR4................ok
t/Tools/Analysis/Protein/HNN.................ok
t/Tools/Analysis/Protein/Mitoprot............ok
t/Tools/Analysis/Protein/NetPhos.............ok
t/Tools/Analysis/Protein/Scansite............ok
t/Tools/Analysis/Protein/Sopma...............ok
t/Tools/EMBOSS/Palindrome....................ok
t/Tools/EUtilities/EUtilParameters...........ok
t/Tools/EUtilities/egquery...................ok
t/Tools/EUtilities/einfo.....................ok
t/Tools/EUtilities/elink_acheck..............ok
t/Tools/EUtilities/elink_lcheck..............ok
t/Tools/EUtilities/elink_llinks..............ok
t/Tools/EUtilities/elink_ncheck..............ok
t/Tools/EUtilities/elink_neighbor............ok
t/Tools/EUtilities/elink_neighbor_history....ok
t/Tools/EUtilities/elink_scores..............ok
t/Tools/EUtilities/epost.....................ok
t/Tools/EUtilities/esearch...................ok
t/Tools/EUtilities/espell....................ok
t/Tools/EUtilities/esummary..................ok
t/Tools/Est2Genome...........................ok
t/Tools/FootPrinter..........................ok
t/Tools/GFF..................................ok
t/Tools/Geneid...............................ok
t/Tools/Genewise.............................ok
t/Tools/Genomewise...........................ok
t/Tools/Genpred..............................ok
t/Tools/Hmmer................................ok
t/Tools/IUPAC................................ok
t/Tools/Lucy.................................ok
t/Tools/Match................................ok
t/Tools/Phylo/Gerp...........................ok
t/Tools/Phylo/Molphy.........................ok
t/Tools/Phylo/PAML...........................ok
t/Tools/Phylo/Phylip/ProtDist................ok
t/Tools/Primer3..............................skipped: The optional module
Clone (or dependencies thereof) was not installed
t/Tools/Promoterwise.........................ok
t/Tools/Pseudowise...........................ok
t/Tools/QRNA.................................ok
t/Tools/RandDistFunctions....................ok
t/Tools/RepeatMasker.........................ok
t/Tools/Run/RemoteBlast......................ok
t/Tools/Run/StandAloneBlast..................ok
t/Tools/Run/WrapperBase......................ok
t/Tools/Seg..................................ok
t/Tools/SiRNA................................ok
t/Tools/Sigcleave............................ok
t/Tools/Signalp..............................ok
t/Tools/Signalp/ExtendedSignalp..............ok
t/Tools/Sim4.................................ok
t/Tools/Spidey/Spidey........................ok
t/Tools/TandemRepeatsFinder..................ok
t/Tools/TargetP..............................ok
t/Tools/Tmhmm................................ok
t/Tools/ePCR.................................ok
t/Tools/pICalculator.........................ok
t/Tools/rnamotif.............................skipped: All tests are being
skipped, probably because the module(s) being tested here are now deprecated
t/Tools/tRNAscanSE...........................ok
t/Tree/Compatible............................skipped: The optional module
Set::Scalar (or dependencies thereof) was not installed
t/Tree/Node..................................ok
t/Tree/PhyloNetwork/Factory..................skipped: The optional module
Bio::PhyloNetwork (or dependencies thereof) was not installed
t/Tree/PhyloNetwork/GraphViz.................skipped: The optional module
Bio::PhyloNetwork (or dependencies thereof) was not installed
t/Tree/PhyloNetwork/MuVector.................ok
t/Tree/PhyloNetwork/PhyloNetwork.............skipped: The optional module
Graph::Directed (or dependencies thereof) was not installed
t/Tree/PhyloNetwork/RandomFactory............skipped: The optional module
Bio::PhyloNetwork (or dependencies thereof) was not installed
t/Tree/PhyloNetwork/TreeFactory..............skipped: The optional module
Bio::PhyloNetwork (or dependencies thereof) was not installed
t/Tree/RandomTreeFactory.....................ok
t/Tree/Tree..................................ok
t/Tree/TreeIO................................ok
t/Tree/TreeIO/lintree........................ok
t/Tree/TreeIO/newick.........................ok
t/Tree/TreeIO/nexus..........................ok
t/Tree/TreeIO/nhx............................ok
t/Tree/TreeIO/phyloxml.......................skipped: The optional module
XML::LibXML::Reader (or dependencies thereof) was not installed
t/Tree/TreeIO/svggraph.......................ok
t/Tree/TreeIO/tabtree........................ok
t/Tree/TreeStatistics........................ok
t/Variation/AAChange.........................ok
t/Variation/AAReverseMutate..................ok
t/Variation/Allele...........................ok
t/Variation/DNAMutation......................ok
t/Variation/RNAChange........................ok
t/Variation/SNP..............................ok
t/Variation/SeqDiff..........................ok
t/Variation/Variation_IO.....................ok
Test Summary Report
-------------------
t/Biblio/eutils (Wstat: 65280 Tests: 1 Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 4 tests but ran 1.
t/RemoteDB/DB (Wstat: 256 Tests: 116 Failed: 1)
Failed test: 104
Non-zero exit status: 1
t/RemoteDB/GDB (Wstat: 2048 Tests: 12 Failed: 8)
Failed tests: 4-7, 9-12
Non-zero exit status: 8
t/RemoteDB/HIV/HIV (Wstat: 65280 Tests: 30 Failed: 1)
Failed test: 30
Non-zero exit status: 255
Parse errors: Bad plan. You planned 29 tests but ran 30.
t/Root/RootIO (Wstat: 65280 Tests: 30 Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 31 tests but ran 30.
Files=320, Tests=15582, 408 wallclock secs ( 3.22 usr 1.69 sys + 87.89 cusr
14.18 csys = 106.98 CPU)
Result: FAIL
Failed 5/320 test programs. 10/15582 subtests failed.
91.424u 16.019s 6:48.97 26.2% 0+0k 1+716io 0pf+0w
Exit 255
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