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From: metabase:user:322078bc-2aae-11df-837a-5e0a49663a4f
Subject: PASS BioPerl-1.007000_006 v5.10.0 FreeBSD
Date: 2016-09-22T15:11:21Z
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 0.9160. Testers personal comments may appear
at the end of this report.
Thank you for uploading your work to CPAN. Congratulations!
All tests were successful.
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/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/Taxonomy/sqlite.t ............ skipped: The optional module DBI (or dependencies thereof) was not installed
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 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/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-refac.t ......... ok
t/Restriction/Analysis.t ............... ok
t/Restriction/Gel.t .................... ok
t/Restriction/IO.t ..................... ok
t/Root/Exception.t ..................... ok
t/Root/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/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/cross_match.t ............... ok
t/SearchIO/erpin.t ..................... ok
t/SearchIO/exonerate.t ................. ok
t/SearchIO/fasta.t ..................... ok
t/SearchIO/gmap_f9.t ................... ok
t/SearchIO/hmmer.t ..................... ok
t/SearchIO/hmmer_pull.t ................ ok
t/SearchIO/infernal.t .................. ok
t/SearchIO/megablast.t ................. ok
t/SearchIO/psl.t ....................... ok
t/SearchIO/rnamotif.t .................. ok
t/SearchIO/sim4.t ...................... ok
t/SearchIO/waba.t ...................... ok
t/SearchIO/wise.t ...................... ok
t/Seq/DBLink.t ......................... ok
t/Seq/EncodedSeq.t ..................... ok
t/Seq/LargeLocatableSeq.t .............. ok
t/Seq/LargePSeq.t ...................... ok
t/Seq/LocatableSeq.t ................... ok
t/Seq/MetaSeq.t ........................ ok
t/Seq/PrimaryQual.t .................... ok
t/Seq/PrimarySeq.t ..................... ok
t/Seq/PrimedSeq.t ...................... ok
t/Seq/Quality.t ........................ ok
t/Seq/Seq.t ............................ ok
t/Seq/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/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
t/SeqTools/SeqUtils.t .................. ok
t/SeqTools/SeqWords.t .................. ok
t/Species.t ............................ ok
t/Structure/IO.t ....................... ok
t/Structure/Structure.t ................ ok
t/Symbol.t ............................. ok
t/TaxonTree.t .......................... skipped: 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/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::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/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/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 5.012 generated the following error:
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
All tests successful.
Files=325, Tests=18361, 152 wallclock secs ( 2.87 usr 0.71 sys + 106.77 cusr 29.77 csys = 140.12 CPU)
Result: PASS
PREREQUISITES:
Here is a list of prerequisites you specified and versions we
managed to load:
Module Name Have Want
CPAN 1.9205 1.81
Data::Stag 0.14 0.11
ExtUtils::Manifest 1.70 1.52
IO::String 1.08 0
Module::Build 0.4220 0.42
Scalar::Util 1.19 0
Test::Harness 3.36 2.62
Test::Most 0.35 0
URI::Escape 3.31 0
Perl module toolchain versions installed:
Module Name Have
CPANPLUS 0.9160
CPANPLUS::Dist::Build 0.80
Cwd 3.62
ExtUtils::CBuilder 0.280224
ExtUtils::Command 7.24
ExtUtils::Install 2.04
ExtUtils::MakeMaker 7.24
ExtUtils::Manifest 1.70
ExtUtils::ParseXS 3.30
File::Spec 3.62
Module::Build 0.4220
Pod::Parser 1.35
Pod::Simple 3.32
Test2 1.302052
Test::Harness 3.36
Test::More 1.302052
version 0.9917
******************************** 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 0.98.
Powered by minismokebox version 0.58
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
AUTOMATED_TESTING = 1
NONINTERACTIVE_TESTING = 1
PATH = /usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/IcNDUZBQft/BioPerl-1.007000_006/blib/script:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/9YcB1cHOjM/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/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/dlcJiAndMh/IO-String-1.08/blib/lib:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/dlcJiAndMh/IO-String-1.08/blib/arch:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/9YcB1cHOjM/Data-Stag-0.14/blib/lib:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/9YcB1cHOjM/Data-Stag-0.14/blib/arch:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/IqHV4BVB2l/Class-Data-Inheritable-0.08/blib/lib:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/IqHV4BVB2l/Class-Data-Inheritable-0.08/blib/arch:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/5kUDXMHVTL/Devel-StackTrace-2.01/blib/lib:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/5kUDXMHVTL/Devel-StackTrace-2.01/blib/arch:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/s4Y8PfyYYB/Exception-Class-1.40/blib/lib:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/s4Y8PfyYYB/Exception-Class-1.40/blib/arch:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/Zxjh2KnsrP/Test-Deep-1.123/blib/lib:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/Zxjh2KnsrP/Test-Deep-1.123/blib/arch:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/gPHwCsqRp6/Capture-Tiny-0.44/blib/lib:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/gPHwCsqRp6/Capture-Tiny-0.44/blib/arch:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/o6pgTR0Pr3/Data-Dumper-2.161/blib/lib:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/o6pgTR0Pr3/Data-Dumper-2.161/blib/arch:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/_jSCuINtIZ/Algorithm-Diff-1.1903/blib/lib:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/_jSCuINtIZ/Algorithm-Diff-1.1903/blib/arch:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/jtz4qPfGUV/Text-Diff-1.44/blib/lib:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/jtz4qPfGUV/Text-Diff-1.44/blib/arch:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/j075cr0Y0D/Test-Differences-0.64/blib/lib:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/j075cr0Y0D/Test-Differences-0.64/blib/arch:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/eGBSdopQbN/Sub-Uplevel-0.2600/blib/lib:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/eGBSdopQbN/Sub-Uplevel-0.2600/blib/arch:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/ygvVRlPSZ2/Test-Exception-0.43/blib/lib:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/ygvVRlPSZ2/Test-Exception-0.43/blib/arch:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/QkP8tt_tKQ/Carp-1.38/blib/lib:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/QkP8tt_tKQ/Carp-1.38/blib/arch:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/5dzVkXG3Zu/Test-Warn-0.30/blib/lib:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/5dzVkXG3Zu/Test-Warn-0.30/blib/arch:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/5oNgkpsvEW/Test-Most-0.35/blib/lib:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/5oNgkpsvEW/Test-Most-0.35/blib/arch:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/5Q2Ci0HIg0/URI-1.71/blib/lib:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/5Q2Ci0HIg0/URI-1.71/blib/arch:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/IcNDUZBQft/BioPerl-1.007000_006/blib/lib:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/IcNDUZBQft/BioPerl-1.007000_006/blib/arch
PERL5_CPANPLUS_IS_RUNNING = 61043
PERL5_CPANPLUS_IS_VERSION = 0.9160
PERL5_MINISMOKEBOX = 0.58
PERL5_YACSMOKE_BASE = /usr/home/cpan/pit/bare/conf/perl-5.10.0
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/bare/perl-5.10.0/bin/perl
UID: $< = 1002
EUID: $> = 1002
GID: $( = 1002 1002
EGID: $) = 1002 1002
-------------------------------
--
Summary of my perl5 (revision 5 version 10 subversion 0) configuration:
Platform:
osname=freebsd, osvers=10.3-release-p2, archname=i386-freebsd
uname='freebsd froggle 10.3-release-p2 freebsd 10.3-release-p2 #0: wed may 4 14:06:02 utc 2016 root@amd64-builder.daemonology.net:usrobjusrsrcsysgeneric i386 '
config_args='-des -Dprefix=/usr/home/cpan/pit/bare/perl-5.10.0'
hint=recommended, useposix=true, d_sigaction=define
useithreads=undef, usemultiplicity=undef
useperlio=define, d_sfio=undef, uselargefiles=define, usesocks=undef
use64bitint=undef, use64bitall=undef, uselongdouble=undef
usemymalloc=n, bincompat5005=undef
Compiler:
cc='cc', ccflags ='-DHAS_FPSETMASK -DHAS_FLOATINGPOINT_H -fno-strict-aliasing -pipe -I/usr/local/include',
optimize='-O',
cppflags='-DHAS_FPSETMASK -DHAS_FLOATINGPOINT_H -fno-strict-aliasing -pipe -I/usr/local/include'
ccversion='', gccversion='4.2.1 Compatible FreeBSD Clang 3.4.1 (tags/RELEASE_34/dot1-final 208032)', 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 ='-Wl,-E -L/usr/local/lib'
libpth=/usr/lib /usr/local/lib
libs=-lgdbm -lm -lcrypt -lutil -lc
perllibs=-lm -lcrypt -lutil -lc
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'
Characteristics of this binary (from libperl):
Compile-time options: PERL_DONT_CREATE_GVSV PERL_MALLOC_WRAP
USE_LARGE_FILES USE_PERLIO
Locally applied patches:
Devel::PatchPerl 1.42
Built under freebsd
Compiled at May 7 2016 19:16:42
%ENV:
PERL5LIB=":/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/dlcJiAndMh/IO-String-1.08/blib/lib:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/dlcJiAndMh/IO-String-1.08/blib/arch:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/9YcB1cHOjM/Data-Stag-0.14/blib/lib:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/9YcB1cHOjM/Data-Stag-0.14/blib/arch:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/IqHV4BVB2l/Class-Data-Inheritable-0.08/blib/lib:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/IqHV4BVB2l/Class-Data-Inheritable-0.08/blib/arch:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/5kUDXMHVTL/Devel-StackTrace-2.01/blib/lib:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/5kUDXMHVTL/Devel-StackTrace-2.01/blib/arch:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/s4Y8PfyYYB/Exception-Class-1.40/blib/lib:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/s4Y8PfyYYB/Exception-Class-1.40/blib/arch:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/Zxjh2KnsrP/Test-Deep-1.123/blib/lib:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/Zxjh2KnsrP/Test-Deep-1.123/blib/arch:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/gPHwCsqRp6/Capture-Tiny-0.44/blib/lib:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/gPHwCsqRp6/Capture-Tiny-0.44/blib/arch:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/o6pgTR0Pr3/Data-Dumper-2.161/blib/lib:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/o6pgTR0Pr3/Data-Dumper-2.161/blib/arch:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/_jSCuINtIZ/Algorithm-Diff-1.1903/blib/lib:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/_jSCuINtIZ/Algorithm-Diff-1.1903/blib/arch:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/jtz4qPfGUV/Text-Diff-1.44/blib/lib:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/jtz4qPfGUV/Text-Diff-1.44/blib/arch:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/j075cr0Y0D/Test-Differences-0.64/blib/lib:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/j075cr0Y0D/Test-Differences-0.64/blib/arch:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/eGBSdopQbN/Sub-Uplevel-0.2600/blib/lib:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/eGBSdopQbN/Sub-Uplevel-0.2600/blib/arch:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/ygvVRlPSZ2/Test-Exception-0.43/blib/lib:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/ygvVRlPSZ2/Test-Exception-0.43/blib/arch:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/QkP8tt_tKQ/Carp-1.38/blib/lib:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/QkP8tt_tKQ/Carp-1.38/blib/arch:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/5dzVkXG3Zu/Test-Warn-0.30/blib/lib:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/5dzVkXG3Zu/Test-Warn-0.30/blib/arch:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/5oNgkpsvEW/Test-Most-0.35/blib/lib:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/5oNgkpsvEW/Test-Most-0.35/blib/arch:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/5Q2Ci0HIg0/URI-1.71/blib/lib:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/5Q2Ci0HIg0/URI-1.71/blib/arch:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/IcNDUZBQft/BioPerl-1.007000_006/blib/lib:/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/IcNDUZBQft/BioPerl-1.007000_006/blib/arch"
PERL5_CPANPLUS_IS_RUNNING="61043"
PERL5_CPANPLUS_IS_VERSION="0.9160"
PERL5_MINISMOKEBOX="0.58"
PERL5_YACSMOKE_BASE="/usr/home/cpan/pit/bare/conf/perl-5.10.0"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_MM_USE_DEFAULT="1"
@INC:
/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/dlcJiAndMh/IO-String-1.08/blib/lib
/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/dlcJiAndMh/IO-String-1.08/blib/arch
/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/9YcB1cHOjM/Data-Stag-0.14/blib/lib
/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/9YcB1cHOjM/Data-Stag-0.14/blib/arch
/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/IqHV4BVB2l/Class-Data-Inheritable-0.08/blib/lib
/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/IqHV4BVB2l/Class-Data-Inheritable-0.08/blib/arch
/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/5kUDXMHVTL/Devel-StackTrace-2.01/blib/lib
/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/5kUDXMHVTL/Devel-StackTrace-2.01/blib/arch
/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/s4Y8PfyYYB/Exception-Class-1.40/blib/lib
/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/s4Y8PfyYYB/Exception-Class-1.40/blib/arch
/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/Zxjh2KnsrP/Test-Deep-1.123/blib/lib
/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/Zxjh2KnsrP/Test-Deep-1.123/blib/arch
/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/gPHwCsqRp6/Capture-Tiny-0.44/blib/lib
/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/gPHwCsqRp6/Capture-Tiny-0.44/blib/arch
/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/o6pgTR0Pr3/Data-Dumper-2.161/blib/lib
/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/o6pgTR0Pr3/Data-Dumper-2.161/blib/arch
/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/_jSCuINtIZ/Algorithm-Diff-1.1903/blib/lib
/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/_jSCuINtIZ/Algorithm-Diff-1.1903/blib/arch
/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/jtz4qPfGUV/Text-Diff-1.44/blib/lib
/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/jtz4qPfGUV/Text-Diff-1.44/blib/arch
/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/j075cr0Y0D/Test-Differences-0.64/blib/lib
/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/j075cr0Y0D/Test-Differences-0.64/blib/arch
/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/eGBSdopQbN/Sub-Uplevel-0.2600/blib/lib
/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/eGBSdopQbN/Sub-Uplevel-0.2600/blib/arch
/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/ygvVRlPSZ2/Test-Exception-0.43/blib/lib
/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/ygvVRlPSZ2/Test-Exception-0.43/blib/arch
/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/QkP8tt_tKQ/Carp-1.38/blib/lib
/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/QkP8tt_tKQ/Carp-1.38/blib/arch
/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/5dzVkXG3Zu/Test-Warn-0.30/blib/lib
/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/5dzVkXG3Zu/Test-Warn-0.30/blib/arch
/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/5oNgkpsvEW/Test-Most-0.35/blib/lib
/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/5oNgkpsvEW/Test-Most-0.35/blib/arch
/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/5Q2Ci0HIg0/URI-1.71/blib/lib
/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/5Q2Ci0HIg0/URI-1.71/blib/arch
/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/IcNDUZBQft/BioPerl-1.007000_006/blib/lib
/usr/home/cpan/pit/bare/conf/perl-5.10.0/.cpanplus/5.10.0/build/IcNDUZBQft/BioPerl-1.007000_006/blib/arch
/usr/home/cpan/pit/bare/perl-5.10.0/lib/5.10.0/i386-freebsd
/usr/home/cpan/pit/bare/perl-5.10.0/lib/5.10.0
/usr/home/cpan/pit/bare/perl-5.10.0/lib/site_perl/5.10.0/i386-freebsd
/usr/home/cpan/pit/bare/perl-5.10.0/lib/site_perl/5.10.0
.