[Debian-med-packaging] Bug#533976: bioperl: FTBFS: test failures
Lucas Nussbaum
lucas at lucas-nussbaum.net
Sun Jun 21 14:22:38 UTC 2009
Package: bioperl
Version: 1.6.0-2
Severity: serious
User: debian-qa at lists.debian.org
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
| lucas at lucas-nussbaum.net http://www.lucas-nussbaum.net/ |
| jabber: lucas at nussbaum.fr GPG: 1024D/023B3F4F |
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