BioPerl v1.007002 Perl 5 v5.14.3 i686-linux-thread-multi
- Status
- Fail
- From
- Nigel Horne
- Dist
-
BioPerl v1.007002
- Platform
- Perl 5 v5.14.3 i686-linux-thread-multi
- Date
- 2017-11-08 20:17:45
- ID
- e20fed6a-c4c1-11e7-8e07-958d21cd0eb8
This distribution has been tested as part of the CPAN Testers
project, supporting the Perl programming language. See
http://wiki.cpantesters.org/ for more information or email
questions to cpan-testers-discuss@perl.org
--
Dear Christopher Fields,
This is a computer-generated report for BioPerl-1.007002
on perl 5.14.3, created by CPAN-Reporter-1.2017.
Thank you for uploading your work to CPAN. However, there was a problem
testing your distribution.
If you think this report is invalid, please consult the CPAN Testers Wiki
for suggestions on how to avoid getting FAIL reports for missing library
or binary dependencies, unsupported operating systems, and so on:
http://wiki.cpantesters.org/wiki/CPANAuthorNotes
Sections of this report:
* Tester comments
* Program output
* Prerequisites
* Environment and other context
------------------------------
TESTER COMMENTS
------------------------------
Additional comments from tester:
this report is from an automated smoke testing program
and was not reviewed by a human for accuracy
------------------------------
PROGRAM OUTPUT
------------------------------
Output from './Build test':
t/Align/AlignUtil.t .................... ok
t/Align/AlignStats.t ................... ok
t/Align/Graphics.t ..................... skipped: The optional module GD (or dependencies thereof) was not installed
t/Align/TreeBuild.t .................... ok
t/Align/SimpleAlign.t .................. ok
t/Align/Utilities.t .................... ok
t/AlignIO/arp.t ........................ ok
t/AlignIO/AlignIO.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/nexml.t ...................... skipped: The optional module Bio::Phylo (or dependencies thereof) was not installed
t/AlignIO/msf.t ........................ ok
t/AlignIO/pfam.t ....................... ok
t/AlignIO/nexus.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/xmfa.t ....................... ok
t/AlignIO/stockholm.t .................. ok
t/Alphabet.t ........................... ok
t/Annotation/Annotation.t .............. ok
t/Annotation/AnnotationAdaptor.t ....... ok
t/Assembly/IO/bowtie.t ................. skipped: The optional module Bio::DB::Sam (or dependencies thereof) was not installed
t/Assembly/IO/sam.t .................... skipped: The optional module Bio::DB::Sam (or dependencies thereof) was not installed
t/Assembly/ContigSpectrum.t ............ ok
t/Cluster/UniGene.t .................... ok
t/ClusterIO/ClusterIO.t ................ ok
t/ClusterIO/SequenceFamily.t ........... ok
t/ClusterIO/unigene.t .................. ok
t/Draw/Pictogram.t ..................... skipped: The optional module SVG (or dependencies thereof) was not installed
t/LiveSeq/Chain.t ...................... ok
t/LiveSeq/LiveSeq.t .................... ok
t/LiveSeq/Mutation.t ................... ok
t/Assembly/core.t ...................... ok
t/LiveSeq/Mutator.t .................... ok
Subroutine Bio::DB::IndexedBase::_strip_crnl redefined at Bio/DB/IndexedBase.pm line 304.
You are loading a Bio::DB::GFF database with GFF3 formatted data.
While this will likely work fine, the Bio::DB::GFF schema does not
always faithfully capture the complexity represented in GFF3 files.
Unless you have a specific reason for using Bio::DB::GFF, we suggest
that you use a Bio::DB::SeqFeature::Store database and its corresponding
loader, bp_seqfeature_load.pl.
t/LocalDB/BioDBGFF.t ................... ok
t/LocalDB/Flat.t ....................... ok
t/LocalDB/Fasta.t ...................... ok
------------- EXCEPTION -------------
MSG: This index file is type [Bio::Index::Blast] - Can't access it with module for [Bio::Index::BlastTable]
STACK Bio::Index::Abstract::_type_and_version Bio/Index/Abstract.pm:495
STACK Bio::Index::Abstract::open_dbm Bio/Index/Abstract.pm:415
STACK Bio::Index::Abstract::new Bio/Index/Abstract.pm:162
STACK Bio::Index::BlastTable::new Bio/Index/BlastTable.pm:141
STACK toplevel t/LocalDB/Index/BlastTable.t:22
-------------------------------------
# Looks like your test exited with 2 just after 3.
t/LocalDB/Index/BlastTable.t ...........
Dubious, test returned 2 (wstat 512, 0x200)
Failed 24/27 subtests
t/LocalDB/Index/Blast.t ................ ok
Subroutine Bio::DB::IndexedBase::_strip_crnl redefined at Bio/DB/IndexedBase.pm line 304.
t/LocalDB/Qual.t ....................... ok
t/LocalDB/Registry.t ................... ok
Subroutine Bio::DB::IndexedBase::_strip_crnl redefined at Bio/DB/IndexedBase.pm line 304.
t/LocalDB/Index/Index.t ................ ok
t/LocalDB/Taxonomy/greengenes.t ........ ok
t/LocalDB/Taxonomy/silva.t ............. ok
t/LocalDB/SeqFeature.t ................. ok
t/LocalDB/Taxonomy/sqlite.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/LocalDB/transfac_pro.t ............... ok
t/Matrix/ProtPsm.t ..................... ok
t/Ontology/GOterm.t .................... skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/Matrix/SiteMatrix.t .................. ok
t/Ontology/IO/go.t ..................... skipped: The optional module Graph (or dependencies thereof) was not installed
t/Ontology/GraphAdaptor.t .............. skipped: The optional module Graph (or dependencies thereof) was not installed
t/Ontology/IO/interpro.t ............... skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed
t/Ontology/IO/obo.t .................... skipped: The optional module Graph (or dependencies thereof) was not installed
t/Ontology/Ontology.t .................. skipped: The optional module Graph (or dependencies thereof) was not installed
t/Ontology/OntologyEngine.t ............ skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/Ontology/OntologyStore.t ............. skipped: The optional module Graph (or dependencies thereof) was not installed
t/Ontology/Relationship.t .............. skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/Ontology/RelationshipType.t .......... skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/Ontology/Term.t ...................... skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/Phenotype/Correlate.t ................ ok
t/Perl.t ............................... ok
t/Phenotype/MeSH.t ..................... ok
t/Phenotype/Measure.t .................. ok
t/Phenotype/MiniMIMentry.t ............. ok
t/Phenotype/OMIMentryAllelicVariant.t .. ok
t/Phenotype/OMIMentry.t ................ ok
t/Phenotype/OMIMparser.t ............... ok
t/Phenotype/Phenotype.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 .................. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/CUTG.t ...................... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/EMBL.t ...................... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/EntrezGene.t ................ skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/GenBank.t ................... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/GenPept.t ................... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/HIV/HIV.t ................... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/HIV/HIVAnnotProcessor.t ..... ok
t/RemoteDB/HIV/HIVQuery.t .............. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/HIV/HIVQueryHelper.t ........ skipped: The optional module XML::Simple (or dependencies thereof) was not installed
t/PodSyntax.t .......................... ok
t/RemoteDB/MeSH.t ...................... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/Query/GenBank.t ............. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/RefSeq.t .................... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/SeqRead_fail.t .............. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/SeqVersion.t ................ skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/SwissProt.t ................. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/RemoteDB/Taxonomy.t .................. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Restriction/Analysis.t ............... ok
t/Restriction/Gel.t .................... ok
t/Restriction/IO.t ..................... ok
t/Root/Exception.t ..................... ok
t/Root/HTTPget.t ....................... skipped: Network tests have not been requested
t/Root/IO.t ............................ ok
t/Root/RootI.t ......................... ok
t/Root/RootIO.t ........................ skipped: Network tests have not been requested
t/Root/Storable.t ...................... ok
t/Root/Utilities.t ..................... ok
t/SearchDist.t ......................... skipped: The optional module Bio::Ext::Align (or dependencies thereof) was not installed
t/Restriction/Analysis-refac.t ......... ok
t/SearchIO/CigarString.t ............... ok
t/SearchIO/SearchIO.t .................. ok
t/SearchIO/SimilarityPair.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/Writer/TextWriter.t ......... ok
t/SearchIO/Tiling.t .................... ok
t/SearchIO/axt.t ....................... ok
t/SearchIO/blast_pull.t ................ ok
t/SearchIO/blasttable.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/blast.t ..................... ok
t/SearchIO/gmap_f9.t ................... ok
t/SearchIO/hmmer_pull.t ................ ok
t/SearchIO/infernal.t .................. ok
t/SearchIO/megablast.t ................. ok
t/SearchIO/hmmer.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/PrimedSeq.t ...................... ok
t/Seq/PrimarySeq.t ..................... ok
t/Seq/Seq.t ............................ ok
t/Seq/SimulatedRead.t .................. ok
t/Seq/Quality.t ........................ ok
t/Seq/WithQuality.t .................... ok
t/SeqEvolution.t ....................... ok
t/SeqFeature/Amplicon.t ................ ok
t/SeqFeature/Clone.t ................... ok
t/SeqFeature/Computation.t ............. ok
t/SeqFeature/FeaturePair.t ............. ok
t/SeqFeature/Collection.t .............. ok
t/SeqFeature/Gene.t .................... ok
t/SeqFeature/Location.t ................ ok
t/SeqFeature/LocationFactory.t ......... ok
t/SeqFeature/Generic.t ................. ok
t/SeqFeature/Primer.t .................. ok
t/SeqFeature/Range.t ................... ok
t/SeqFeature/RangeI.t .................. ok
t/SeqFeature/SeqAnalysisParser.t ....... ok
t/SeqFeature/SubSeq.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/SeqIO.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 ........................ skipped: The optional module XML::Writer (or dependencies thereof) was not installed
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 ......................... skipped: The optional module XML::DOM (or dependencies thereof) was not installed
t/SeqIO/bsml_sax.t ..................... skipped: The optional module XML::SAX (or dependencies thereof) was not installed
t/SeqIO/chadoxml.t ..................... skipped: The optional module XML::Writer (or dependencies thereof) was not installed
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 ................... skipped: The optional module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed
t/SeqIO/excel.t ........................ skipped: The optional module Spreadsheet::ParseExcel (or dependencies thereof) was not installed
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 ............. skipped: The optional module XML::Writer (or dependencies thereof) was not installed
t/SeqIO/game.t ......................... skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed
t/SeqIO/gbxml.t ........................ skipped: The optional module XML::SAX (or dependencies thereof) was not installed
t/SeqIO/gcg.t .......................... ok
t/SeqIO/genbank.t ...................... ok
t/SeqIO/interpro.t ..................... skipped: The optional module XML::DOM::XPath (or dependencies thereof) was not installed
t/SeqIO/kegg.t ......................... ok
t/SeqIO/largefasta.t ................... ok
t/SeqIO/lasergene.t .................... ok
t/SeqIO/locuslink.t .................... skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/SeqIO/mbsout.t ....................... ok
t/SeqIO/metafasta.t .................... ok
t/SeqIO/msout.t ........................ ok
t/SeqIO/nexml.t ........................ skipped: The optional module Bio::Phylo (or dependencies thereof) was not installed
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/seqxml.t ....................... skipped: The optional module XML::LibXML (or dependencies thereof) was not installed
t/SeqIO/strider.t ...................... skipped: The optional module Convert::Binary::C (or dependencies thereof) was not installed
t/SeqFeature/Unflattener.t ............. ok
t/SeqIO/swiss.t ........................ ok
t/SeqIO/table.t ........................ skipped: The optional module IO::Scalar (or dependencies thereof) was not installed
t/SeqIO/tab.t .......................... ok
t/SeqIO/tigr.t ......................... skipped: The optional module Error (or dependencies thereof) was not installed
t/SeqIO/tigrxml.t ...................... skipped: The optional module XML::SAX (or dependencies thereof) was not installed
t/SeqIO/tinyseq.t ...................... skipped: The optional module XML::Parser::PerlSAX (or dependencies thereof) was not installed
t/SeqIO/ztr.t .......................... skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqTools/Backtranslate.t ............. skipped: The optional module List::MoreUtils (or dependencies thereof) was not installed
t/SeqTools/CodonTable.t ................ ok
t/SeqTools/ECnumber.t .................. ok
t/SeqTools/OddCodes.t .................. ok
t/SeqTools/GuessSeqFormat.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/Structure.t ................ ok
t/Structure/IO.t ....................... ok
t/Symbol.t ............................. ok
t/TaxonTree.t .......................... skipped: These modules are now probably deprecated
t/Tools/Alignment/Consed.t ............. ok
t/Tools/AmpliconSearch.t ............... ok
t/Tools/Analysis/DNA/ESEfinder.t ....... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/Analysis/Protein/Domcut.t ...... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/Analysis/Protein/ELM.t ......... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/Analysis/Protein/GOR4.t ........ skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/Analysis/Protein/HNN.t ......... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/Analysis/Protein/NetPhos.t ..... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/Analysis/Protein/Scansite.t .... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/Analysis/Protein/Sopma.t ....... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/EMBOSS/Palindrome.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/IUPAC.t ........................ ok
t/Tools/Lucy.t ......................... ok
t/Tools/Match.t ........................ ok
t/Tools/Hmmer.t ........................ ok
t/Tools/Phylo/Gerp.t ................... ok
t/Tools/Phylo/Phylip/ProtDist.t ........ ok
t/Tools/Phylo/Molphy.t ................. ok
t/Tools/Promoterwise.t ................. ok
t/Tools/Primer3.t ...................... ok
t/Tools/PrositeScan.t .................. ok
t/Tools/Pseudowise.t ................... ok
t/Tools/RandDistFunctions.t ............ ok
t/Tools/QRNA.t ......................... ok
t/Tools/RepeatMasker.t ................. ok
t/Tools/Run/RemoteBlast.t .............. skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/Run/RemoteBlast_rpsblast.t ..... skipped: The optional module LWP::UserAgent (or dependencies thereof) was not installed
t/Tools/Seg.t .......................... ok
t/Tools/Sigcleave.t .................... ok
t/Tools/SiRNA.t ........................ ok
t/Tools/Signalp.t ...................... ok
t/Tools/Sim4.t ......................... ok
t/Tools/Signalp/ExtendedSignalp.t ...... ok
t/Tools/Spidey/Spidey.t ................ ok
t/Tools/TandemRepeatsFinder.t .......... ok
t/Tools/Tmhmm.t ........................ ok
t/Tools/TargetP.t ...................... ok
t/Tools/pICalculator.t ................. ok
t/Tools/ePCR.t ......................... ok
t/Tree/Compatible.t .................... skipped: The optional module Set::Scalar (or dependencies thereof) was not installed
t/Tools/tRNAscanSE.t ................... ok
t/Tree/Node.t .......................... ok
t/Tree/PhyloNetwork/Factory.t .......... skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed
t/Tree/PhyloNetwork/GraphViz.t ......... skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed
t/Tree/PhyloNetwork/MuVector.t ......... ok
t/Tree/PhyloNetwork/PhyloNetwork.t ..... skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/Tree/PhyloNetwork/RandomFactory.t .... skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed
t/Tree/PhyloNetwork/TreeFactory.t ...... skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed
t/Tree/RandomTreeFactory.t ............. ok
t/Tree/Tree.t .......................... ok
t/Tree/TreeIO/lintree.t ................ ok
t/Tree/TreeIO/newick.t ................. ok
t/Tree/TreeIO.t ........................ ok
t/Tree/TreeIO/nexml.t .................. skipped: The optional module Bio::Phylo (or dependencies thereof) was not installed
t/Tree/TreeIO/nhx.t .................... ok
t/Tree/TreeIO/nexus.t .................. ok
t/Tree/TreeIO/phyloxml.t ............... skipped: The optional module XML::LibXML (or dependencies thereof) was not installed
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 ............. skipped: The optional module XML::Writer (or dependencies thereof) was not installed
t/nexml.t .............................. skipped: The optional module Bio::Phylo (or dependencies thereof) was not installed
Test Summary Report
-------------------
t/LocalDB/Index/BlastTable.t (Wstat: 512 Tests: 3 Failed: 0)
Non-zero exit status: 2
Parse errors: Bad plan. You planned 27 tests but ran 3.
Files=325, Tests=19078, 71 wallclock secs ( 2.47 usr 0.90 sys + 113.34 cusr 5.69 csys = 122.40 CPU)
Result: FAIL
Failed 1/325 test programs. 0/19078 subtests failed.
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
------------------ ------ --------
Data::Stag 0.11 0.14
ExtUtils::Manifest 1.52 1.70
IO::String 0 1.08
perl v5.6.1 5.014003
Scalar::Util 0 1.42
build_requires:
Module Need Have
------------------ ------ --------
CPAN 1.81 2.16
Module::Build 0.42 0.4214
Test::Harness 2.62 3.35
Test::Most 0 0.35
URI::Escape 0 3.31
configure_requires:
Module Need Have
------------------ ------ --------
Module::Build 0.42 0.4214
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
HARNESS_OPTIONS = j2
LANG = en_US.UTF-8
PATH = /home/njh/perl5/perlbrew/bin:/home/njh/perl5/perlbrew/perls/perl-5.14.3/bin:/home/njh/perl5/perlbrew/bin:/usr/bin:/bin
PERL5LIB = /home/njh/.cpan/build/Test-Most-0.35-6/blib/arch:/home/njh/.cpan/build/Test-Most-0.35-6/blib/lib:/home/njh/.cpan/build/Test-Simple-1.302106-12/blib/arch:/home/njh/.cpan/build/Test-Simple-1.302106-12/blib/lib:/home/njh/.cpan/build/Test-Exception-0.43-7/blib/arch:/home/njh/.cpan/build/Test-Exception-0.43-7/blib/lib:/home/njh/.cpan/build/Test-Differences-0.64-6/blib/arch:/home/njh/.cpan/build/Test-Differences-0.64-6/blib/lib:/home/njh/.cpan/build/Exception-Class-1.43-8/blib/arch:/home/njh/.cpan/build/Exception-Class-1.43-8/blib/lib:/home/njh/.cpan/build/Devel-StackTrace-2.02-8/blib/arch:/home/njh/.cpan/build/Devel-StackTrace-2.02-8/blib/lib:/home/njh/.cpan/build/Class-Data-Inheritable-0.08-14/blib/arch:/home/njh/.cpan/build/Class-Data-Inheritable-0.08-14/blib/lib:/home/njh/.cpan/build/Data-Stag-0.14-6/blib/arch:/home/njh/.cpan/build/Data-Stag-0.14-6/blib/lib:/home/njh/.cpan/build/IO-String-1.08-9/blib/arch:/home/njh/.cpan/build/IO-String-1.08-9/blib/lib
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 23969
PERL5_CPAN_IS_RUNNING = 23969
PERLBREW_BASHRC_VERSION = 0.73
PERLBREW_HOME = /home/njh/.perlbrew
PERLBREW_LIB =
PERLBREW_MANPATH = /home/njh/perl5/perlbrew/perls/perl-5.14.3/man
PERLBREW_PATH = /home/njh/perl5/perlbrew/bin:/home/njh/perl5/perlbrew/perls/perl-5.14.3/bin
PERLBREW_PERL = perl-5.14.3
PERLBREW_ROOT = /home/njh/perl5/perlbrew
PERLBREW_VERSION = 0.73
PERL_LOCAL_LIB_ROOT =
SHELL = /bin/sh
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /home/njh/perl5/perlbrew/perls/perl-5.14.3/bin/perl
$UID/$EUID = 1000 / 1000
$GID = 1000 4 24 25 29 30 44 46 108 1000
$EGID = 1000 4 24 25 29 30 44 46 108 1000
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.16
CPAN::Meta 2.150005
Cwd 3.60
ExtUtils::CBuilder 0.280224
ExtUtils::Command 7.18
ExtUtils::Install 2.04
ExtUtils::MakeMaker 7.18
ExtUtils::Manifest 1.70
ExtUtils::ParseXS 3.30
File::Spec 3.60
JSON n/a
JSON::PP 2.27300
Module::Build 0.4214
Module::Signature n/a
Parse::CPAN::Meta 1.4417
Test::Harness 3.35
Test::More 1.302106
YAML 1.23
YAML::Syck 1.30
version 0.9912
--
Summary of my perl5 (revision 5 version 14 subversion 3) configuration:
Platform:
osname=linux, osvers=4.2.0-1-686-pae, archname=i686-linux-thread-multi
uname='linux zack 4.2.0-1-686-pae #1 smp debian 4.2.6-1 (2015-11-10) i686 gnulinux '
config_args='-de -Dprefix=/home/njh/perl5/perlbrew/perls/perl-5.14.3 -Duseithreads -Dusemultiplicity -Dusedevel -Accflags= -Aeval:scriptdir=/home/njh/perl5/perlbrew/perls/perl-5.14.3/bin'
hint=recommended, useposix=true, d_sigaction=define
useithreads=define, usemultiplicity=define
useperlio=define, d_sfio=undef, uselargefiles=define, usesocks=undef
use64bitint=undef, use64bitall=undef, uselongdouble=undef
usemymalloc=n, bincompat5005=undef
Compiler:
cc='cc', ccflags ='-D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64',
optimize='-O2',
cppflags='-D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include'
ccversion='', gccversion='5.2.1 20151121', gccosandvers=''
intsize=4, longsize=4, ptrsize=4, doublesize=8, byteorder=1234
d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=12
ivtype='long', ivsize=4, nvtype='double', nvsize=8, Off_t='off_t', lseeksize=8
alignbytes=4, prototype=define
Linker and Libraries:
ld='cc', ldflags =' -fstack-protector -L/usr/local/lib'
libpth=/usr/local/lib /lib/i386-linux-gnu /lib/../lib /usr/lib/i386-linux-gnu /usr/lib/../lib /lib /usr/lib
libs=-lnsl -lgdbm -ldb -ldl -lm -lcrypt -lutil -lpthread -lc -lgdbm_compat
perllibs=-lnsl -ldl -lm -lcrypt -lutil -lpthread -lc
libc=libc-2.19.so, so=so, useshrplib=false, libperl=libperl.a
gnulibc_version='2.19'
Dynamic Linking:
dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-Wl,-E'
cccdlflags='-fPIC', lddlflags='-shared -O2 -L/usr/local/lib -fstack-protector'
Characteristics of this binary (from libperl):
Compile-time options: MULTIPLICITY PERL_DONT_CREATE_GVSV
PERL_IMPLICIT_CONTEXT PERL_MALLOC_WRAP
PERL_PRESERVE_IVUV PERL_USE_DEVEL USE_ITHREADS
USE_LARGE_FILES USE_PERLIO USE_PERL_ATOF
USE_REENTRANT_API
Locally applied patches:
Devel::PatchPerl 1.38
Built under linux
Compiled at Nov 24 2015 06:17:24
%ENV:
PERL5LIB="/home/njh/.cpan/build/Test-Most-0.35-6/blib/arch:/home/njh/.cpan/build/Test-Most-0.35-6/blib/lib:/home/njh/.cpan/build/Test-Simple-1.302106-12/blib/arch:/home/njh/.cpan/build/Test-Simple-1.302106-12/blib/lib:/home/njh/.cpan/build/Test-Exception-0.43-7/blib/arch:/home/njh/.cpan/build/Test-Exception-0.43-7/blib/lib:/home/njh/.cpan/build/Test-Differences-0.64-6/blib/arch:/home/njh/.cpan/build/Test-Differences-0.64-6/blib/lib:/home/njh/.cpan/build/Exception-Class-1.43-8/blib/arch:/home/njh/.cpan/build/Exception-Class-1.43-8/blib/lib:/home/njh/.cpan/build/Devel-StackTrace-2.02-8/blib/arch:/home/njh/.cpan/build/Devel-StackTrace-2.02-8/blib/lib:/home/njh/.cpan/build/Class-Data-Inheritable-0.08-14/blib/arch:/home/njh/.cpan/build/Class-Data-Inheritable-0.08-14/blib/lib:/home/njh/.cpan/build/Data-Stag-0.14-6/blib/arch:/home/njh/.cpan/build/Data-Stag-0.14-6/blib/lib:/home/njh/.cpan/build/IO-String-1.08-9/blib/arch:/home/njh/.cpan/build/IO-String-1.08-9/blib/lib"
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="23969"
PERL5_CPAN_IS_RUNNING="23969"
PERLBREW_BASHRC_VERSION="0.73"
PERLBREW_HOME="/home/njh/.perlbrew"
PERLBREW_LIB=""
PERLBREW_MANPATH="/home/njh/perl5/perlbrew/perls/perl-5.14.3/man"
PERLBREW_PATH="/home/njh/perl5/perlbrew/bin:/home/njh/perl5/perlbrew/perls/perl-5.14.3/bin"
PERLBREW_PERL="perl-5.14.3"
PERLBREW_ROOT="/home/njh/perl5/perlbrew"
PERLBREW_VERSION="0.73"
PERL_LOCAL_LIB_ROOT=""
@INC:
/home/njh/.cpan/build/Test-Most-0.35-6/blib/arch
/home/njh/.cpan/build/Test-Most-0.35-6/blib/lib
/home/njh/.cpan/build/Test-Simple-1.302106-12/blib/arch
/home/njh/.cpan/build/Test-Simple-1.302106-12/blib/lib
/home/njh/.cpan/build/Test-Exception-0.43-7/blib/arch
/home/njh/.cpan/build/Test-Exception-0.43-7/blib/lib
/home/njh/.cpan/build/Test-Differences-0.64-6/blib/arch
/home/njh/.cpan/build/Test-Differences-0.64-6/blib/lib
/home/njh/.cpan/build/Exception-Class-1.43-8/blib/arch
/home/njh/.cpan/build/Exception-Class-1.43-8/blib/lib
/home/njh/.cpan/build/Devel-StackTrace-2.02-8/blib/arch
/home/njh/.cpan/build/Devel-StackTrace-2.02-8/blib/lib
/home/njh/.cpan/build/Class-Data-Inheritable-0.08-14/blib/arch
/home/njh/.cpan/build/Class-Data-Inheritable-0.08-14/blib/lib
/home/njh/.cpan/build/Data-Stag-0.14-6/blib/arch
/home/njh/.cpan/build/Data-Stag-0.14-6/blib/lib
/home/njh/.cpan/build/IO-String-1.08-9/blib/arch
/home/njh/.cpan/build/IO-String-1.08-9/blib/lib
/home/njh/perl5/perlbrew/perls/perl-5.14.3/lib/site_perl/5.14.3/i686-linux-thread-multi
/home/njh/perl5/perlbrew/perls/perl-5.14.3/lib/site_perl/5.14.3
/home/njh/perl5/perlbrew/perls/perl-5.14.3/lib/5.14.3/i686-linux-thread-multi
/home/njh/perl5/perlbrew/perls/perl-5.14.3/lib/5.14.3
.