[Bioperl-l] bioperl-1.5.0 RC2

Raoul Jean Pierre Bonnal raoul.bonnal at itb.cnr.it
Fri Jan 21 10:11:11 EST 2005 

This is perl, v5.8.4 built for i386-linux-thread-multi

Debian Unstable/Amd Athlon XP

PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e"
"test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/AAChange...................ok
t/AAReverseMutate............ok
t/AlignIO....................ok
t/AlignStats.................ok
t/AlignUtil..................ok
t/Allele.....................ok
t/Alphabet...................ok
t/Annotation.................ok
t/AnnotationAdaptor..........ok
t/Assembly...................ok
t/Biblio.....................ok
t/Biblio_biofetch............ok
t/Biblio_eutils..............ok
t/BiblioReferences...........ok
t/BioDBGFF...................ok
t/BioFetch_DB................ok
t/BioGraphics................ok
t/BlastIndex.................ok
t/BPbl2seq...................ok
t/BPlite.....................ok
t/BPpsilite..................ok
t/Chain......................ok
t/cigarstring................ok
t/ClusterIO..................ok
t/Coalescent.................ok
t/CodonTable.................ok
t/consed.....................ok
t/CoordinateGraph............ok
t/CoordinateMapper...........ok
t/Correlate..................ok
t/CytoMap....................ok
t/DB.........................ok
t/DBCUTG.....................ok
        22/24 skipped: tests which require remote servers - set env
variable BIOPERLDEBUG to test
t/DBFasta....................ok
t/DNAMutation................ok
t/Domcut.....................ok
        22/25 skipped: tests which require remote servers - set env
variable BIOPERLDEBUG to test
t/ECnumber...................ok
t/ELM........................ok
t/EMBL_DB....................ok
t/EMBOSS_Tools...............ok
t/EncodedSeq.................ok
t/ePCR.......................ok
t/ESEfinder..................error is 0
t/ESEfinder..................ok
        10/12 skipped: tests which require remote servers - set env
variable BIOPERLDEBUG to test
t/est2genome.................ok
t/Exception..................ok
t/Exonerate..................ok
t/flat.......................ok
t/FootPrinter................ok
t/game.......................ok
t/GDB........................ok
t/GeneCoordinateMapper.......ok
t/Geneid.....................ok
t/Genewise...................ok
        2/51 skipped:
t/Genomewise.................ok
t/Genpred....................ok
t/GFF........................ok
t/GOR4.......................ok
        10/13 skipped: tests which require remote servers - set env
variable BIOPERLDEBUG to test
t/GOterm.....................ok
t/GuessSeqFormat.............ok
t/hmmer......................ok
t/HNN........................ok
        10/13 skipped: tests which require remote servers - set env
variable BIOPERLDEBUG to test
t/HtSNP......................ok
t/Index......................ok
t/InstanceSite...............ok
t/InterProParser.............ok
t/IUPAC......................ok
t/largefasta.................ok
t/LargeLocatableSeq..........ok
t/largepseq..................ok
t/LinkageMap.................ok
t/LiveSeq....................ok
t/LocatableSeq...............ok
t/Location...................ok
t/LocationFactory............ok
t/LocusLink..................ok
t/lucy.......................ok
t/Map........................ok
t/MapIO......................ok
t/Matrix.....................ok
t/Measure....................ok
t/MeSH.......................ok
t/MetaSeq....................ok
t/MicrosatelliteMarker.......ok
t/MiniMIMentry...............ok
t/MitoProt...................ok
        5/8 skipped: tests which require remote servers - set env
variable BIOPERLDEBUG to test
t/Molphy.....................ok
t/multiple_fasta.............ok
t/Mutation...................ok
t/Mutator....................ok
t/NetPhos....................ok
t/Node.......................ok
t/OddCodes...................ok
t/OMIMentry..................ok
t/OMIMentryAllelicVariant....ok
t/OMIMparser.................ok
t/Ontology...................ok
t/OntologyEngine.............ok
t/OntologyStore..............ok
t/PAML.......................ok
t/Perl.......................ok
t/phd........................ok
t/Phenotype..................ok
t/PhylipDist.................ok
t/pICalculator...............ok
t/Pictogram..................SVG not installed, skipping tests at
t/Pictogram.t line 29.
t/Pictogram..................ok
t/PopGen.....................ok
t/PopGenSims.................ok
t/primaryqual................ok
t/PrimarySeq.................ok
t/primedseq..................ok
t/Primer.....................ok
t/primer3....................ok
t/Promoterwise...............ok
t/ProtDist...................ok
t/protgraph..................Class::AutoClass or Clone not installed.
This means that the module is not usable. Skipping tests at
t/protgraph.t line 23.
t/protgraph..................ok
t/ProtMatrix.................ok
t/ProtPsm....................ok
t/psm........................ok
t/QRNA.......................ok
t/qual.......................ok
t/RandDistFunctions..........ok
t/RandomTreeFactory..........ok
t/Range......................ok
t/RangeI.....................ok
t/RefSeq.....................ok
        10/13 skipped: tests which require remote servers - set env
variable BIOPERLDEBUG to test
t/Registry...................ok
t/Relationship...............ok
t/RelationshipType...........ok
t/RemoteBlast................ok
        4/6 skipped: to avoid timeout
t/RepeatMasker...............ok
t/RestrictionAnalysis........ok
t/RestrictionEnzyme..........ok
t/RestrictionIO..............ok
t/RNAChange..................ok
t/RootI......................ok
t/RootIO.....................ok
t/RootStorable...............ok
t/Scansite...................ok
t/scf........................ok
t/SearchDist.................ok
t/SearchIO...................ok
t/Seq........................ok
t/SeqAnalysisParser..........ok
t/SeqBuilder.................ok
t/SeqDiff....................ok
t/SeqFeatCollection..........ok
t/SeqFeature.................ok
t/seqfeaturePrimer...........ok
t/SeqIO......................XML::DOM::XPath not found - skipping
interpro tests
XML::SAX::Base or XML::SAX or XML::SAX::Writer not found - skipping
BSML_SAX tests
t/SeqIO......................ok
t/SeqPattern.................ok
t/seqread_fail...............ok
t/SeqStats...................ok
t/SequenceFamily.............ok
t/sequencetrace..............ok
t/SeqUtils...................ok
t/seqwithquality.............ok
t/SeqWords...................ok
t/Sigcleave..................ok
t/Sim4.......................ok
t/SimilarityPair.............ok
t/SimpleAlign................ok
t/simpleGOparser.............ok 88/101Use of uninitialized value in hash
element
at /home/febo/DownLoad/bioperl-1.5.0-RC2/blib/lib/Bio/Ontology/OntologyStore.pm line 263, <GEN3> line 11.
t/simpleGOparser.............ok
t/singlet....................ok
t/sirna......................ok
t/SiteMatrix.................ok
t/SNP........................ok
t/Sopma......................ok
        12/15 skipped: tests which require remote servers - set env
variable BIOPERLDEBUG to test
t/Species....................ok
t/splicedseq.................ok
t/StandAloneBlast............ok
t/StructIO...................ok
t/Structure..................ok
t/Swiss......................ok
t/Symbol.....................ok
t/TagHaplotype...............ok
t/Taxonomy...................ok
        7/8 skipped: to avoid blocking
t/Tempfile...................ok
t/Term.......................ok
t/tinyseq....................ok
t/Tools......................ok
t/Tree.......................ok
t/TreeBuild..................ok
t/TreeIO.....................ok
        2/50 skipped: SVG::Graph output, SVG::Graph not installed
t/trim.......................ok
t/tRNAscanSE.................ok
t/tutorial...................ok 18/21Use of uninitialized value in print
at /home/febo/DownLoad/bioperl-1.5.0-RC2/blib/lib/bptutorial.pl line
4039, <GEN21>line 934.
t/tutorial...................ok
t/UCSCParsers................ok
t/Unflattener................ok
t/Unflattener2...............ok
t/UniGene....................ok
t/Variation_IO...............ok
t/WABA.......................ok
t/XEMBL_DB...................ok
All tests successful, 116 subtests skipped.
Files=193, Tests=8942, 298 wallclock secs (114.66 cusr +  6.80 csys =
121.46 CPU)



by RJP

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