Back
From: metabase:user:322078bc-2aae-11df-837a-5e0a49663a4f
Subject: FAIL BioPerl-1.6.923 v5.18.1 FreeBSD
Date: 2013-12-24T09:19:48Z
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 CJFIELDS,
This is a computer-generated error report created automatically by
CPANPLUS, version 0.9144. Testers personal comments may appear
at the end of this report.
Thank you for uploading your work to CPAN. However, it appears that
there were some problems testing your distribution.
TEST RESULTS:
Below is the error stack from stage 'make test':
t/Align/AlignStats.t ................... ok
t/Align/AlignUtil.t .................... ok
t/Align/Graphics.t ..................... skipped: The optional module GD (or dependencies thereof) was not installed
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/nexml.t ...................... skipped: The optional module Bio::Phylo (or dependencies thereof) was not installed
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/ContigSpectrum.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/core.t ...................... ok
t/Cluster/UniGene.t .................... ok
t/ClusterIO/ClusterIO.t ................ ok
t/ClusterIO/SequenceFamily.t ........... ok
t/ClusterIO/unigene.t .................. ok
t/Coordinate/CoordinateBoundaryTest.t .. ok
t/Coordinate/CoordinateGraph.t ......... ok
t/Coordinate/CoordinateMapper.t ........ ok
t/Coordinate/GeneCoordinateMapper.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/LiveSeq/Mutator.t .................... ok
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/Fasta.t ...................... ok
t/LocalDB/Flat.t ....................... ok
t/LocalDB/Index/Blast.t ................ ok
t/LocalDB/Index/BlastTable.t ........... ok
t/LocalDB/Index/Index.t ................ ok
t/LocalDB/Qual.t ....................... ok
t/LocalDB/Registry.t ................... ok
t/LocalDB/SeqFeature.t ................. ok
t/LocalDB/Taxonomy/greengenes.t ........ ok
t/LocalDB/Taxonomy/silva.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 .................... skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/Ontology/GraphAdaptor.t .............. skipped: The optional module Graph (or dependencies thereof) was not installed
t/Ontology/IO/go.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/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 .......................... skipped: Test::Pod 1.00 required for testing POD
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 HTTP::Request::Common (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 XML::Simple (or dependencies thereof) was not installed
t/RemoteDB/HIV/HIVAnnotProcessor.t ..... ok
t/RemoteDB/HIV/HIVQuery.t .............. skipped: The optional module XML::Simple (or dependencies thereof) was not installed
t/RemoteDB/HIV/HIVQueryHelper.t ........ skipped: The optional module XML::Simple (or dependencies thereof) was not installed
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/SeqHound.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 XML::Twig (or dependencies thereof) was not installed
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 ..................... skipped: The optional module Error (or dependencies thereof) was not installed
t/Root/HTTPget.t ....................... skipped: Network tests have not been requested
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/Writer/TextWriter.t ......... ok
t/SearchIO/axt.t ....................... ok
t/SearchIO/blast.t ..................... ok
t/SearchIO/blast_pull.t ................ ok
t/SearchIO/blasttable.t ................ ok
t/SearchIO/blastxml.t .................. skipped: The optional module XML::SAX (or dependencies thereof) was not installed
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
Can't store CODE items at Bio/Root/Root.pm line 223.
# Looks like you planned 73 tests but ran 33.
# Looks like your test exited with 255 just after 33.
t/Seq/Seq.t ............................
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 40/73 subtests
t/Seq/SimulatedRead.t .................. ok
t/Seq/WithQuality.t .................... ok
t/SeqEvolution.t ....................... ok
t/SeqFeature/Amplicon.t ................ ok
t/SeqFeature/Clone.t ................... ok
t/SeqFeature/Collection.t .............. ok
t/SeqFeature/Computation.t ............. ok
t/SeqFeature/FeaturePair.t ............. ok
t/SeqFeature/Gene.t .................... ok
t/SeqFeature/Generic.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/SubSeq.t .................. ok
t/SeqFeature/Unflattener.t ............. ok
t/SeqFeature/Unflattener2.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/SeqIO/swiss.t ........................ ok
t/SeqIO/tab.t .......................... ok
t/SeqIO/table.t ........................ skipped: The optional module IO::Scalar (or dependencies thereof) was not installed
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/GuessSeqFormat.t ............ ok
t/SeqTools/OddCodes.t .................. ok
t/SeqTools/SeqPattern.t ................ ok
t/SeqTools/SeqStats.t .................. ok
Can't store CODE items at Bio/Root/Root.pm line 223.
# Looks like you planned 133 tests but ran 43.
# Looks like your test exited with 255 just after 43.
t/SeqTools/SeqUtils.t ..................
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 90/133 subtests
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/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/Mitoprot.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/GuessSeqFormat.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 .............. skipped: The optional module LWP (or dependencies thereof) was not installed
t/Tools/Run/RemoteBlast_rpsblast.t ..... skipped: The optional module LWP (or dependencies thereof) was not installed
t/Tools/Run/StandAloneBlast.t .......... ok
t/Tools/Run/WBCommandExts.t ............ skipped: The optional module Bio::Tools::Run::WrapperBase::CommandExts (or dependencies thereof) was not installed
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 .................... skipped: The optional module Set::Scalar (or dependencies thereof) was not installed
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.t ........................ ok
t/Tree/TreeIO/lintree.t ................ ok
t/Tree/TreeIO/newick.t ................. ok
t/Tree/TreeIO/nexml.t .................. skipped: The optional module Bio::Phylo (or dependencies thereof) was not installed
t/Tree/TreeIO/nexus.t .................. ok
t/Tree/TreeIO/nhx.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/Map/Physical.t (Wstat: 0 Tests: 40 Failed: 0)
TODO passed: 40
t/Seq/Seq.t (Wstat: 65280 Tests: 33 Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 73 tests but ran 33.
t/SeqTools/SeqUtils.t (Wstat: 65280 Tests: 43 Failed: 0)
Non-zero exit status: 255
Parse errors: Bad plan. You planned 133 tests but ran 43.
Files=337, Tests=17884, 271 wallclock secs ( 3.86 usr 4.52 sys + 199.86 cusr 56.34 csys = 264.58 CPU)
Result: FAIL
Failed 2/337 test programs. 0/17884 subtests failed.
BEGIN failed--compilation aborted at -e line 1.
PREREQUISITES:
Here is a list of prerequisites you specified and versions we
managed to load:
Module Name Have Want
CPAN 2.00 1.81
DB_File 1.827 0
Data::Stag 0.14 0.11
ExtUtils::Manifest 1.63 1.52
IO::String 1.08 0
Module::Build 0.4203 0.2805
Scalar::Util 1.35 0
Test::Harness 3.30 2.62
Test::Most 0.31 0
URI::Escape 3.31 0
Perl module toolchain versions installed:
Module Name Have
CPANPLUS 0.9144
CPANPLUS::Dist::Build 0.74
Cwd 3.40
ExtUtils::CBuilder 0.280212
ExtUtils::Command 1.17
ExtUtils::Install 1.59
ExtUtils::MakeMaker 6.84
ExtUtils::Manifest 1.63
ExtUtils::ParseXS 3.22
File::Spec 3.40
Module::Build 0.4203
Pod::Parser 1.60
Pod::Simple 3.28
Test::Harness 3.30
Test::More 1.001002
version 0.9904
******************************** NOTE ********************************
The comments above are created mechanically, possibly without manual
checking by the sender. As there are many people performing automatic
tests on each upload to CPAN, it is likely that you will receive
identical messages about the same problem.
If you believe that the message is mistaken, please reply to the first
one with correction and/or additional informations, and do not take
it personally. We appreciate your patience. :)
**********************************************************************
Additional comments:
This report was machine-generated by CPANPLUS::Dist::YACSmoke 0.90.
Powered by minismokebox version 0.58
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
NONINTERACTIVE_TESTING = 1
PATH = /usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/BioPerl-1.6.923/blib/script:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Data-Stag-0.14/blib/script:/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/home/cpan/bin
PERL5LIB = :/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/IO-String-1.08/blib/lib:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/IO-String-1.08/blib/arch:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Data-Stag-0.14/blib/lib:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Data-Stag-0.14/blib/arch:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Class-Data-Inheritable-0.08/blib/lib:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Class-Data-Inheritable-0.08/blib/arch:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Devel-StackTrace-1.30/blib/lib:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Devel-StackTrace-1.30/blib/arch:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Exception-Class-1.37/blib/lib:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Exception-Class-1.37/blib/arch:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Test-Tester-0.109/blib/lib:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Test-Tester-0.109/blib/arch:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Test-NoWarnings-1.04/blib/lib:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Test-NoWarnings-1.04/blib/arch:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Test-Deep-0.112/blib/lib:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Test-Deep-0.112/blib/arch:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Algorithm-Diff-1.1902/blib/lib:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Algorithm-Diff-1.1902/blib/arch:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Text-Diff-1.41/blib/lib:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Text-Diff-1.41/blib/arch:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Test-Differences-0.61/blib/lib:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Test-Differences-0.61/blib/arch:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Sub-Uplevel-0.24/blib/lib:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Sub-Uplevel-0.24/blib/arch:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Test-Exception-0.32/blib/lib:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Test-Exception-0.32/blib/arch:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/File-Slurp-9999.19/blib/lib:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/File-Slurp-9999.19/blib/arch:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Tree-DAG_Node-1.18/blib/lib:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Tree-DAG_Node-1.18/blib/arch:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Test-Warn-0.24/blib/lib:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Test-Warn-0.24/blib/arch:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Test-Most-0.31/blib/lib:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Test-Most-0.31/blib/arch:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/URI-1.60/blib/lib:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/URI-1.60/blib/arch:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/BioPerl-1.6.923/blib/lib:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/BioPerl-1.6.923/blib/arch
PERL5_CPANPLUS_IS_RUNNING = 8307
PERL5_CPANPLUS_IS_VERSION = 0.9144
PERL5_MINISMOKEBOX = 0.58
PERL5_YACSMOKE_BASE = /usr/home/cpan/pit/thr/conf/perl-5.18.1
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_MM_USE_DEFAULT = 1
SHELL = /usr/local/bin/bash
TERM = screen
Perl special variables (and OS-specific diagnostics, for MSWin32):
Perl: $^X = /usr/home/cpan/pit/thr/perl-5.18.1/bin/perl
UID: $< = 1002
EUID: $> = 1002
GID: $( = 1002 1002
EGID: $) = 1002 1002
-------------------------------
--
Summary of my perl5 (revision 5 version 18 subversion 1) configuration:
Platform:
osname=freebsd, osvers=9.2-release, archname=amd64-freebsd-thread-multi
uname='freebsd fforc 9.2-release freebsd 9.2-release #0 r255898: thu sep 26 22:50:31 utc 2013 root@bake.isc.freebsd.org:usrobjusrsrcsysgeneric amd64 '
config_args='-des -Dprefix=/usr/home/cpan/pit/thr/perl-5.18.1 -Dusethreads -Dcc=clang'
hint=recommended, useposix=true, d_sigaction=define
useithreads=define, usemultiplicity=define
useperlio=define, d_sfio=undef, uselargefiles=define, usesocks=undef
use64bitint=define, use64bitall=define, uselongdouble=undef
usemymalloc=n, bincompat5005=undef
Compiler:
cc='clang', ccflags ='-DHAS_FPSETMASK -DHAS_FLOATINGPOINT_H -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include',
optimize='-O',
cppflags='-DHAS_FPSETMASK -DHAS_FLOATINGPOINT_H -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include'
ccversion='', gccversion='4.2.1 Compatible FreeBSD Clang 3.3 (tags/RELEASE_33/final 183502)', gccosandvers=''
intsize=4, longsize=8, ptrsize=8, doublesize=8, byteorder=12345678
d_longlong=define, longlongsize=8, d_longdbl=define, longdblsize=16
ivtype='long', ivsize=8, nvtype='double', nvsize=8, Off_t='off_t', lseeksize=8
alignbytes=8, prototype=define
Linker and Libraries:
ld='clang', ldflags ='-pthread -Wl,-E -fstack-protector -L/usr/local/lib'
libpth=/usr/lib /usr/local/lib
libs=-lgdbm -lm -lcrypt
perllibs=-lm -lcrypt
libc=, so=so, useshrplib=false, libperl=libperl.a
gnulibc_version=''
Dynamic Linking:
dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags=' '
cccdlflags='-DPIC -fPIC', lddlflags='-shared -L/usr/local/lib -fstack-protector'
Characteristics of this binary (from libperl):
Compile-time options: HAS_TIMES MULTIPLICITY PERLIO_LAYERS
PERL_DONT_CREATE_GVSV
PERL_HASH_FUNC_ONE_AT_A_TIME_HARD
PERL_IMPLICIT_CONTEXT PERL_MALLOC_WRAP
PERL_PRESERVE_IVUV PERL_SAWAMPERSAND USE_64_BIT_ALL
USE_64_BIT_INT USE_ITHREADS USE_LARGE_FILES
USE_LOCALE USE_LOCALE_COLLATE USE_LOCALE_CTYPE
USE_LOCALE_NUMERIC USE_PERLIO USE_PERL_ATOF
USE_REENTRANT_API
Built under freebsd
Compiled at Oct 3 2013 21:20:50
%ENV:
PERL5LIB=":/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/IO-String-1.08/blib/lib:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/IO-String-1.08/blib/arch:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Data-Stag-0.14/blib/lib:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Data-Stag-0.14/blib/arch:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Class-Data-Inheritable-0.08/blib/lib:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Class-Data-Inheritable-0.08/blib/arch:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Devel-StackTrace-1.30/blib/lib:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Devel-StackTrace-1.30/blib/arch:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Exception-Class-1.37/blib/lib:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Exception-Class-1.37/blib/arch:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Test-Tester-0.109/blib/lib:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Test-Tester-0.109/blib/arch:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Test-NoWarnings-1.04/blib/lib:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Test-NoWarnings-1.04/blib/arch:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Test-Deep-0.112/blib/lib:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Test-Deep-0.112/blib/arch:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Algorithm-Diff-1.1902/blib/lib:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Algorithm-Diff-1.1902/blib/arch:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Text-Diff-1.41/blib/lib:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Text-Diff-1.41/blib/arch:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Test-Differences-0.61/blib/lib:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Test-Differences-0.61/blib/arch:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Sub-Uplevel-0.24/blib/lib:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Sub-Uplevel-0.24/blib/arch:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Test-Exception-0.32/blib/lib:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Test-Exception-0.32/blib/arch:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/File-Slurp-9999.19/blib/lib:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/File-Slurp-9999.19/blib/arch:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Tree-DAG_Node-1.18/blib/lib:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Tree-DAG_Node-1.18/blib/arch:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Test-Warn-0.24/blib/lib:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Test-Warn-0.24/blib/arch:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Test-Most-0.31/blib/lib:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Test-Most-0.31/blib/arch:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/URI-1.60/blib/lib:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/URI-1.60/blib/arch:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/BioPerl-1.6.923/blib/lib:/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/BioPerl-1.6.923/blib/arch"
PERL5_CPANPLUS_IS_RUNNING="8307"
PERL5_CPANPLUS_IS_VERSION="0.9144"
PERL5_MINISMOKEBOX="0.58"
PERL5_YACSMOKE_BASE="/usr/home/cpan/pit/thr/conf/perl-5.18.1"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_MM_USE_DEFAULT="1"
@INC:
/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/IO-String-1.08/blib/lib
/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/IO-String-1.08/blib/arch
/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Data-Stag-0.14/blib/lib
/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Data-Stag-0.14/blib/arch
/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Class-Data-Inheritable-0.08/blib/lib
/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Class-Data-Inheritable-0.08/blib/arch
/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Devel-StackTrace-1.30/blib/lib
/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Devel-StackTrace-1.30/blib/arch
/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Exception-Class-1.37/blib/lib
/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Exception-Class-1.37/blib/arch
/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Test-Tester-0.109/blib/lib
/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Test-Tester-0.109/blib/arch
/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Test-NoWarnings-1.04/blib/lib
/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Test-NoWarnings-1.04/blib/arch
/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Test-Deep-0.112/blib/lib
/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Test-Deep-0.112/blib/arch
/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Algorithm-Diff-1.1902/blib/lib
/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Algorithm-Diff-1.1902/blib/arch
/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Text-Diff-1.41/blib/lib
/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Text-Diff-1.41/blib/arch
/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Test-Differences-0.61/blib/lib
/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Test-Differences-0.61/blib/arch
/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Sub-Uplevel-0.24/blib/lib
/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Sub-Uplevel-0.24/blib/arch
/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Test-Exception-0.32/blib/lib
/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Test-Exception-0.32/blib/arch
/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/File-Slurp-9999.19/blib/lib
/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/File-Slurp-9999.19/blib/arch
/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Tree-DAG_Node-1.18/blib/lib
/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Tree-DAG_Node-1.18/blib/arch
/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Test-Warn-0.24/blib/lib
/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Test-Warn-0.24/blib/arch
/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Test-Most-0.31/blib/lib
/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/Test-Most-0.31/blib/arch
/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/URI-1.60/blib/lib
/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/URI-1.60/blib/arch
/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/BioPerl-1.6.923/blib/lib
/usr/home/cpan/pit/thr/conf/perl-5.18.1/.cpanplus/5.18.1/build/BioPerl-1.6.923/blib/arch
/usr/home/cpan/pit/thr/perl-5.18.1/lib/site_perl/5.18.1/amd64-freebsd-thread-multi
/usr/home/cpan/pit/thr/perl-5.18.1/lib/site_perl/5.18.1
/usr/home/cpan/pit/thr/perl-5.18.1/lib/5.18.1/amd64-freebsd-thread-multi
/usr/home/cpan/pit/thr/perl-5.18.1/lib/5.18.1
.