[Bioperl-l] BioPerl 1.6.0 alpha 6 released (?!?)
Chris Fields
cjfields at illinois.edu
Mon Sep 28 17:00:09 UTC 2009
Charles (and everyone else),
This bug was a bit sneaky. The tests skipped on pretty much every
system b/c of a requirement for both DB_File and BerkeleyDB (e.g. if
both weren't installed, the tests were skipped). I committed a fix
for it; unfortunately that means I need to set up another alpha for
testing, so...
The final final alpha has just been uploaded to CPAN and is now
available here:
http://bioperl.org/DIST/RC/BioPerl-1.6.0_6.tar.gz
The final 1.6.1 release should still be in the next day or two, just
awaiting some test reports via CPAN...
chris
On Sep 28, 2009, at 1:30 AM, Charles Plessy wrote:
> Le Sun, Sep 27, 2009 at 11:34:01PM -0500, Chris Fields a écrit :
>>
>> http://bioperl.org/DIST/RC/BioPerl-1.6.0_5.tar.gz
>>
>
> Hi Chris,
>
> I have the following errors when building bioperl with perl 5.10.1
> on Debian:
>
> Test Summary Report
> -------------------
> t/LocalDB/Registry.t (Wstat: 2304 Tests: 13
> Failed: 1)
> Failed test: 13
> Non-zero exit status: 9
> Parse errors: Bad plan. You planned 14 tests but ran 13.
> t/RemoteDB/EUtilities.t (Wstat: 256 Tests: 309
> Failed: 1)
> Failed test: 309
> Non-zero exit status: 1
> t/Tools/Run/RemoteBlast.t (Wstat: 65280 Tests: 13
> Failed: 0)
> Non-zero exit status: 255
> Parse errors: Bad plan. You planned 16 tests but ran 13.
> Files=329, Tests=20766, 434 wallclock secs ( 2.64 usr 0.51 sys +
> 100.55 cusr 6.24 csys = 109.94 CPU)
> Result: FAIL
>
>
> t/Align/AlignStats.t ......................... ok
> t/Align/AlignUtil.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/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/Assembly.t ........................ ok
> t/Assembly/ContigSpectrum.t .................. ok
> t/Biblio/Biblio.t ............................ ok
> t/Biblio/References.t ........................ ok
> t/Biblio/biofetch.t .......................... ok
> t/Biblio/eutils.t ............................ ok
> 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/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/BlastIndex.t ....................... ok
> t/LocalDB/DBFasta.t .......................... ok
> t/LocalDB/DBQual.t ........................... ok
> t/LocalDB/Flat.t ............................. ok
> t/LocalDB/Index.t ............................ ok
> t/LocalDB/Registry.t ......................... 1/14
> --------------------- WARNING ---------------------
> MSG:
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: The sequence does not appear to be FASTA format (lacks a
> descriptor line '>')
> STACK: Error::throw
> STACK: Bio::Root::Root::throw Bio/Root/Root.pm:368
> STACK: Bio::SeqIO::fasta::next_seq Bio/SeqIO/fasta.pm:127
> STACK: Bio::DB::Flat::BDB::get_Seq_by_id Bio/DB/Flat/BDB.pm:143
> STACK: Bio::DB::Failover::get_Seq_by_id Bio/DB/Failover.pm:122
> STACK: t/LocalDB/Registry.t:69
> -----------------------------------------------------------
>
> ---------------------------------------------------
>
> --------------------- WARNING ---------------------
> MSG: No sequence retrieved by database Bio::DB::Flat::BDB::fasta
> ---------------------------------------------------
>
> # Failed test at t/LocalDB/Registry.t line 70.
> Can't call method "seq" on an undefined value at t/LocalDB/
> Registry.t line 71, <GEN17> line 1.
> # Looks like you planned 14 tests but ran 13.
> # Looks like you failed 1 test of 13 run.
> # Looks like your test exited with 9 just after 13.
> t/LocalDB/Registry.t ......................... Dubious, test
> returned 9 (wstat 2304, 0x900)
> Failed 2/14 subtests
> 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 ................... ok
> 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 ........................ ok
> t/RemoteDB/CUTG.t ............................ ok
> t/RemoteDB/EMBL.t ............................ ok
> t/RemoteDB/EUtilities.t ...................... 309/309
> # Failed test 'EPost to EFetch'
> # at t/RemoteDB/EUtilities.t line 159.
> # got: '0'
> # expected: '5'
> # Looks like you failed 1 test of 309.
> t/RemoteDB/EUtilities.t ...................... Dubious, test
> returned 1 (wstat 256, 0x100)
> Failed 1/309 subtests
> 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 .................... 22/41 Use of
> uninitialized value $rest[0] in join or string at (eval 68) line 15.
> t/RemoteDB/HIV/HIVQuery.t .................... ok
> 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 ........................ ok
> t/RemoteDB/SeqRead_fail.t .................... ok
> t/RemoteDB/SeqVersion.t ...................... ok
> t/RemoteDB/SwissProt.t ....................... ok
> 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/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/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/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 .............. ok
> 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.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/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/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/metafasta.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/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 ............. ok
> t/Tools/Analysis/Protein/Domcut.t ............ ok
> t/Tools/Analysis/Protein/ELM.t ............... ok
> t/Tools/Analysis/Protein/GOR4.t .............. ok
> t/Tools/Analysis/Protein/HNN.t ............... ok
> t/Tools/Analysis/Protein/Mitoprot.t .......... ok
> t/Tools/Analysis/Protein/NetPhos.t ........... ok
> 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 .................... 13/16
> --------------------- WARNING ---------------------
> MSG: Server failed to return any data
> ---------------------------------------------------
> # Looks like you planned 16 tests but ran 13.
> t/Tools/Run/RemoteBlast.t .................... Dubious, test
> returned 255 (wstat 65280, 0xff00)
> Failed 3/16 subtests
> t/Tools/Run/RemoteBlast_rpsblast.t ........... ok
> t/Tools/Run/StandAloneBlast.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 .......................... 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 .......... 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 .............................. ok
> t/Tree/TreeIO/lintree.t ...................... ok
> t/Tree/TreeIO/newick.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 ..................... 1/4 Use of
> uninitialized value $txt[0] in join or string at /usr/share/perl5/
> SVG/Element.pm line 1195, <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
>
>
> Cheers,
>
> --
> Charles Plessy
> Debian Med packaging team,
> http://www.debian.org/devel/debian-med
> Tsurumi, Kanagawa, Japan
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