Package: bioperl Version: 1.6.0-2 Severity: serious User: [email protected] Usertags: qa-ftbfs-20090620 qa-ftbfs Justification: FTBFS on amd64
Hi, During a rebuild of all packages in sid, your package failed to build on amd64. Relevant part: > 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......................ok > t/Annotation/AnnotationAdaptor...............ok > > # Failed (TODO) test at t/Assembly/Assembly.t line 35. > t/Assembly/Assembly..........................ok > t/Assembly/ContigSpectrum....................ok > t/Biblio/Biblio..............................ok > t/Biblio/References..........................ok > t/Biblio/biofetch............................skipped > all skipped: Network tests have not been requested > t/Biblio/eutils..............................skipped > all skipped: Network tests have not been requested > 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 > 11/279 skipped: various reasons > t/LocalDB/BlastIndex.........................ok > t/LocalDB/DBFasta............................ok > t/LocalDB/DBQual.............................ok > t/LocalDB/Flat...............................ok > t/LocalDB/Index..............................ok > t/LocalDB/Registry...........................ok > 11/14 skipped: various reasons > t/LocalDB/SeqFeature.........................ok > t/LocalDB/transfac_pro.......................ok > t/Map/Cyto...................................ok > t/Map/Linkage................................ok > t/Map/Map....................................ok > 19/267 skipped: various reasons > 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 > 10/14 skipped: various reasons > t/Matrix/SiteMatrix..........................ok > t/Ontology/GOterm............................ok > t/Ontology/GraphAdaptor......................ok > t/Ontology/IO/go.............................ok > t/Ontology/IO/interpro.......................ok > t/Ontology/IO/obo............................ok > t/Ontology/Ontology..........................ok > t/Ontology/OntologyEngine....................ok > t/Ontology/OntologyStore.....................skipped > all skipped: Network tests have not been requested > t/Ontology/Relationship......................ok > t/Ontology/RelationshipType..................ok > t/Ontology/Term..............................ok > t/Perl.......................................ok > 10/29 skipped: various reasons > 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 > all skipped: Test::Pod 1.00 required for testing POD > t/PopGen/Coalescent..........................ok > t/PopGen/HtSNP...............................ok > t/PopGen/MK..................................ok > 4/46 skipped: various reasons > t/PopGen/PopGen..............................ok > t/PopGen/PopGenSims..........................ok > t/PopGen/TagHaplotype........................ok > t/RemoteDB/BioFetch..........................skipped > all skipped: Network tests have not been requested > t/RemoteDB/CUTG..............................ok > 14/37 skipped: various reasons > t/RemoteDB/DB................................skipped > all skipped: Network tests have not been requested > t/RemoteDB/EMBL..............................skipped > all skipped: Network tests have not been requested > t/RemoteDB/EUtilities........................skipped > all skipped: The optional module XML::Simple (or dependencies > thereof) was not installed > t/RemoteDB/HIV/HIV...........................skipped > all skipped: The optional module XML::Simple (or dependencies > thereof) was not installed > t/RemoteDB/HIV/HIVAnnotProcessor.............ok > t/RemoteDB/HIV/HIVQuery......................skipped > all skipped: The optional module XML::Simple (or dependencies > thereof) was not installed > t/RemoteDB/HIV/HIVQueryHelper................skipped > all skipped: The optional module XML::Simple (or dependencies > thereof) was not installed > t/RemoteDB/RefSeq............................ok > 10/16 skipped: various reasons > t/RemoteDB/SeqHound..........................skipped > all skipped: Network tests have not been requested > t/RemoteDB/SeqRead_fail......................skipped > all skipped: Network tests have not been requested > t/RemoteDB/SeqVersion........................ok > 8/10 skipped: various reasons > t/RemoteDB/Taxonomy..........................ok > 44/103 skipped: various reasons > t/Restriction/Analysis.......................ok > t/Restriction/Gel............................ok > > # Failed (TODO) test at t/Restriction/IO.t line 31. > t/Restriction/IO.............................ok > 3/18 skipped: various reasons > t/Root/Exception.............................ok > t/Root/RootI.................................ok > t/Root/RootIO................................ok > 2/31 skipped: various reasons > t/Root/Storable..............................ok > t/Root/Tempfile..............................ok > t/Root/Utilities.............................ok > t/SearchDist.................................skipped > all 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 > > # Failed (TODO) test at t/SearchIO/blast.t line 527. > # '0.852' > # > > # '0.9' > > # Failed (TODO) test at t/SearchIO/blast.t line 528. > # '1.599' > # <= > # '1' > t/SearchIO/blast.............................ok > > # Failed (TODO) test at t/SearchIO/blast_pull.t line 260. > # got: '0.946' > # expected: '0.943' > t/SearchIO/blast_pull........................ok > t/SearchIO/blasttable........................ok > > --------------------- WARNING --------------------- > MSG: error in parsing a report: > http error : Operation in progress > > --------------------------------------------------- > > # Failed test at t/SearchIO/blastxml.t line 243. > # got: '0' > # expected: '1' > Can't call method "database_name" on an undefined value at > t/SearchIO/blastxml.t line 244. > # Looks like you planned 298 tests but only ran 148. > # Looks like you failed 1 test of 148 run. > # Looks like your test died just after 148. > t/SearchIO/blastxml..........................dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 148-298 > Failed 151/298 tests, 49.33% okay > t/SearchIO/cross_match.......................ok > t/SearchIO/erpin.............................ok > t/SearchIO/exonerate.........................ok > 4/45 skipped: various reasons > 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 > > # Failed (TODO) test at t/Seq/LocatableSeq.t line 45. > # got: 'Bio::Location::Simple=HASH(0x306cf90)' > # expected: undef > > # Failed (TODO) test at t/Seq/LocatableSeq.t line 284. > # got: '\-\.=~' > # expected: '-\?' > > # Failed (TODO) test at t/Seq/LocatableSeq.t 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.......................ok > 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 > all skipped: Network tests have not been requested > t/SeqFeature/SeqFeatCollection...............ok > t/SeqFeature/SeqFeature......................ok > 7/214 skipped: various reasons > t/SeqFeature/SeqFeaturePrimer................ok > t/SeqFeature/Unflattener.....................ok > t/SeqFeature/Unflattener2....................ok > t/SeqIO......................................ok > 6/41 skipped: various reasons > 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 > all 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..................................skipped > all skipped: The optional module Bio::SeqIO::staden::read (or > dependencies thereof) was not installed > t/SeqIO/asciitree............................ok > t/SeqIO/bsml.................................ok > http error : Operation in progress > # Looks like you planned 15 tests but only ran 1. > # Looks like your test died just after 1. > t/SeqIO/bsml_sax.............................dubious > Test returned status 255 (wstat 65280, 0xff00) > DIED. FAILED tests 2-15 > Failed 14/15 tests, 6.67% okay > t/SeqIO/chadoxml.............................ok > t/SeqIO/chaos................................ok > t/SeqIO/chaosxml.............................ok > t/SeqIO/ctf..................................skipped > all skipped: The optional module Bio::SeqIO::staden::read (or > dependencies thereof) was not installed > t/SeqIO/embl.................................ok > t/SeqIO/entrezgene...........................ok > t/SeqIO/excel................................ok > t/SeqIO/exp..................................skipped > all skipped: The optional module Bio::SeqIO::staden::read (or > dependencies thereof) was not installed > t/SeqIO/fasta................................ok > 4/18 skipped: various reasons > t/SeqIO/fastq................................ok > t/SeqIO/flybase_chadoxml.....................ok > t/SeqIO/game.................................ok > > # Failed (TODO) test 'primary_id' > # at t/SeqIO/gcg.t line 54. > # got: 'Bio::PrimarySeq=HASH(0x2c4d170)' > # expected: 'roa1_drome' > t/SeqIO/gcg..................................ok > 4/17 skipped: various reasons > t/SeqIO/genbank..............................ok > t/SeqIO/interpro.............................ok > t/SeqIO/kegg.................................ok > t/SeqIO/largefasta...........................ok > t/SeqIO/lasergene............................ok > t/SeqIO/locuslink............................ok > t/SeqIO/metafasta............................ok > t/SeqIO/phd..................................ok > t/SeqIO/pir..................................ok > t/SeqIO/pln..................................skipped > all skipped: The optional module Bio::SeqIO::staden::read (or > dependencies thereof) was not installed > t/SeqIO/qual.................................ok > t/SeqIO/raw..................................ok > 4/14 skipped: various reasons > > # Failed (TODO) test 'accuracies' > # at t/SeqIO/scf.t line 78. > # got: 'ARRAY(0x1971e68)' > # expected: '482' > t/SeqIO/scf..................................ok > t/SeqIO/strider..............................ok > t/SeqIO/swiss................................ok > t/SeqIO/tab..................................ok > t/SeqIO/table................................ok > t/SeqIO/tigr.................................ok > t/SeqIO/tigrxml..............................ok > t/SeqIO/tinyseq..............................ok > t/SeqIO/ztr..................................skipped > all 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 > 5/21 skipped: various reasons > t/Structure/IO...............................ok > t/Structure/Structure........................ok > t/Symbol.....................................ok > t/TaxonTree..................................skipped > all 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...............skipped > all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/Domcut..............skipped > all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/ELM.................skipped > all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/GOR4................skipped > all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/HNN.................skipped > all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/Mitoprot............skipped > all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/NetPhos.............skipped > all skipped: Network tests have not been requested > t/Tools/Analysis/Protein/Scansite............ok > 6/14 skipped: various reasons > t/Tools/Analysis/Protein/Sopma...............ok > 12/16 skipped: various reasons > t/Tools/EMBOSS/Palindrome....................ok > t/Tools/EUtilities/EUtilParameters...........ok > t/Tools/EUtilities/egquery...................skipped > all skipped: The optional module XML::Simple (or dependencies > thereof) was not installed > t/Tools/EUtilities/einfo.....................skipped > all skipped: The optional module XML::Simple (or dependencies > thereof) was not installed > t/Tools/EUtilities/elink_acheck..............skipped > all skipped: The optional module XML::Simple (or dependencies > thereof) was not installed > t/Tools/EUtilities/elink_lcheck..............skipped > all skipped: The optional module XML::Simple (or dependencies > thereof) was not installed > t/Tools/EUtilities/elink_llinks..............skipped > all skipped: The optional module XML::Simple (or dependencies > thereof) was not installed > t/Tools/EUtilities/elink_ncheck..............skipped > all skipped: The optional module XML::Simple (or dependencies > thereof) was not installed > t/Tools/EUtilities/elink_neighbor............skipped > all skipped: The optional module XML::Simple (or dependencies > thereof) was not installed > t/Tools/EUtilities/elink_neighbor_history....skipped > all skipped: The optional module XML::Simple (or dependencies > thereof) was not installed > t/Tools/EUtilities/elink_scores..............skipped > all skipped: The optional module XML::Simple (or dependencies > thereof) was not installed > t/Tools/EUtilities/epost.....................skipped > all skipped: The optional module XML::Simple (or dependencies > thereof) was not installed > t/Tools/EUtilities/esearch...................skipped > all skipped: The optional module XML::Simple (or dependencies > thereof) was not installed > t/Tools/EUtilities/espell....................skipped > all skipped: The optional module XML::Simple (or dependencies > thereof) was not installed > t/Tools/EUtilities/esummary..................skipped > all skipped: The optional module XML::Simple (or dependencies > thereof) was not installed > 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..............................ok > t/Tools/Promoterwise.........................ok > t/Tools/Pseudowise...........................ok > t/Tools/QRNA.................................ok > t/Tools/RandDistFunctions....................ok > t/Tools/RepeatMasker.........................ok > t/Tools/Run/RemoteBlast......................skipped > all skipped: Network tests have not been requested > t/Tools/Run/StandAloneBlast..................ok > 12/45 skipped: various reasons > 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 skipped: All tests are being skipped, probably because the > module(s) being tested here are now deprecated > t/Tools/tRNAscanSE...........................ok > t/Tree/Compatible............................ok > t/Tree/Node..................................ok > t/Tree/PhyloNetwork/Factory..................ok > t/Tree/PhyloNetwork/GraphViz.................ok > t/Tree/PhyloNetwork/MuVector.................ok > t/Tree/PhyloNetwork/PhyloNetwork.............ok > t/Tree/PhyloNetwork/RandomFactory............skipped > all skipped: The optional module Math::Random (or dependencies > thereof) was not installed > t/Tree/PhyloNetwork/TreeFactory..............ok > 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.......................ok > 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.......................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 > Failed 2/318 test programs. 165/16485 subtests failed. > t/Variation/Variation_IO.....................ok > Failed Test Stat Wstat Total Fail List of Failed > ------------------------------------------------------------------------------- > t/SearchIO/blastxml.t 255 65280 298 301 148-298 > t/SeqIO/bsml_sax.t 255 65280 15 28 2-15 > 45 tests and 210 subtests skipped. > Failed 2/318 test scripts. 165/16485 subtests failed. > Files=318, Tests=16485, 172 wallclock secs (81.32 cusr + 6.65 csys = 87.97 > CPU) > make: *** [build-stamp] Error 255 The full build log is available from: http://people.debian.org/~lucas/logs/2009/06/20/bioperl_1.6.0-2_lsid64.buildlog A list of current common problems and possible solutions is available at http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute! About the archive rebuild: The rebuild was done on about 50 AMD64 nodes of the Grid'5000 platform, using a clean chroot. Internet was not accessible from the build systems. -- | Lucas Nussbaum | [email protected] http://www.lucas-nussbaum.net/ | | jabber: [email protected] GPG: 1024D/023B3F4F | -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". Trouble? Contact [email protected]
