BioPerl v1.007002 Perl 5 v5.26.2 x86_64-linux-thread-multi
- Status
- Pass
- From
- Slaven Rezić (SREZIC)
- Dist
-
BioPerl v1.007002
- Platform
- Perl 5 v5.26.2 x86_64-linux-thread-multi
- Date
- 2018-11-28 14:48:06
- ID
- 9d8cbf6c-f31c-11e8-97d7-ccea552b50bf
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 5.26.2, created by CPAN-Reporter-1.2018.
Thank you for uploading your work to CPAN. Congratulations!
All tests were successful.
Sections of this report:
* Tester comments
* Program output
* Prerequisites
* Environment and other context
------------------------------
TESTER COMMENTS
------------------------------
Additional comments from tester:
none provided
------------------------------
PROGRAM OUTPUT
------------------------------
Output from './Build 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
Possible precedence issue with control flow operator at Bio/DB/IndexedBase.pm line 845, <GEN0> line 20.
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
Possible precedence issue with control flow operator at Bio/DB/IndexedBase.pm line 845.
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
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at Bio/DB/GFF.pm line 2000.
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
Possible precedence issue with control flow operator at Bio/DB/IndexedBase.pm line 845.
Subroutine Bio::DB::IndexedBase::_strip_crnl redefined at Bio/DB/IndexedBase.pm line 304.
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
Possible precedence issue with control flow operator at Bio/DB/IndexedBase.pm line 845.
Subroutine Bio::DB::IndexedBase::_strip_crnl redefined at Bio/DB/IndexedBase.pm line 304.
t/LocalDB/Qual.t ....................... ok
t/LocalDB/Registry.t ................... ok
Possible precedence issue with control flow operator at Bio/DB/IndexedBase.pm line 845.
Subroutine Bio::DB::IndexedBase::_strip_crnl redefined at Bio/DB/IndexedBase.pm line 304.
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 DBD::SQLite (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: Network tests have not been requested
t/RemoteDB/CUTG.t ...................... ok
t/RemoteDB/EMBL.t ...................... skipped: Network tests have not been requested
t/RemoteDB/EntrezGene.t ................ skipped: The optional module Bio::ASN1::EntrezGene (or dependencies thereof) was not installed
t/RemoteDB/GenBank.t ................... skipped: Network tests have not been requested
t/RemoteDB/GenPept.t ................... skipped: Network tests have not been requested
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 CGI (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: Network tests have not been requested
t/RemoteDB/Query/GenBank.t ............. skipped: Network tests have not been requested
t/RemoteDB/RefSeq.t .................... ok
t/RemoteDB/SeqRead_fail.t .............. skipped: Network tests have not been requested
t/RemoteDB/SeqVersion.t ................ skipped: The optional module HTML::TableExtract (or dependencies thereof) was not installed
t/RemoteDB/SwissProt.t ................. skipped: Network tests have not been requested
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 ..................... 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
--------------------- WARNING ---------------------
MSG: find_exe: Multiple paths to 'gzip' found. Using /usr/bin/gzip.
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: find_exe: Multiple paths to 'gzip' found. Using /usr/bin/gzip.
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: find_exe: Multiple paths to 'gunzip' found. Using /usr/bin/gunzip.
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: find_exe: Multiple paths to 'gzip' found. Using /usr/bin/gzip.
---------------------------------------------------
--------------------- WARNING ---------------------
MSG: find_exe: Multiple paths to 'gunzip' found. Using /usr/bin/gunzip.
---------------------------------------------------
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::Writer (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 ........................ ok
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::Writer (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 ......................... ok
t/SeqIO/tigrxml.t ...................... skipped: The optional module XML::SAX::Writer (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 ............. ok
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: Network tests have not been requested
t/Tools/Analysis/Protein/Domcut.t ...... skipped: Network tests have not been requested
t/Tools/Analysis/Protein/ELM.t ......... skipped: Network tests have not been requested
t/Tools/Analysis/Protein/GOR4.t ........ skipped: Network tests have not been requested
t/Tools/Analysis/Protein/HNN.t ......... skipped: Network tests have not been requested
t/Tools/Analysis/Protein/NetPhos.t ..... skipped: Network tests have not been requested
t/Tools/Analysis/Protein/Scansite.t .... ok
t/Tools/Analysis/Protein/Sopma.t ....... skipped: Network tests have not been requested
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/Phylip/ProtDist.t ........ ok
t/Tools/Primer3.t ...................... ok
t/Tools/Promoterwise.t ................. ok
t/Tools/PrositeScan.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: Network tests have not been requested
t/Tools/Run/RemoteBlast_rpsblast.t ..... skipped: Network tests have not been requested
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 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 ............... ok
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=18308, 83 wallclock secs ( 2.43 usr 0.64 sys + 71.18 cusr 9.33 csys = 83.58 CPU)
Result: PASS
------------------------------
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 5.026002
Scalar::Util 0 1.49
build_requires:
Module Need Have
------------------ ------ --------
CPAN 1.81 2.18
Module::Build 0.42 0.4224
Test::Harness 2.62 3.42
Test::Most 0 0.35
URI::Escape 0 3.31
configure_requires:
Module Need Have
------------------ ------ --------
Module::Build 0.42 0.4224
------------------------------
ENVIRONMENT AND OTHER CONTEXT
------------------------------
Environment variables:
LANG = en_US.UTF-8
PATH = /usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/cpansand/bin/linux-gnu:/home/cpansand/bin/sh:/home/cpansand/bin:/usr/games:/home/cpansand/devel:/home/eserte/src/srezic-misc/scripts
PERL5LIB = /home/cpansand/.cpan/build/2018112815/Test-Most-0.35-0/blib/arch:/home/cpansand/.cpan/build/2018112815/Test-Most-0.35-0/blib/lib:/home/cpansand/.cpan/build/2018112815/Test-Warn-0.36-0/blib/arch:/home/cpansand/.cpan/build/2018112815/Test-Warn-0.36-0/blib/lib:/home/cpansand/.cpan/build/2018112815/Test-Exception-0.43-0/blib/arch:/home/cpansand/.cpan/build/2018112815/Test-Exception-0.43-0/blib/lib:/home/cpansand/.cpan/build/2018112815/Sub-Uplevel-0.2800-0/blib/arch:/home/cpansand/.cpan/build/2018112815/Sub-Uplevel-0.2800-0/blib/lib:/home/cpansand/.cpan/build/2018112815/Test-Differences-0.64-0/blib/arch:/home/cpansand/.cpan/build/2018112815/Test-Differences-0.64-0/blib/lib:/home/cpansand/.cpan/build/2018112815/Test-Deep-1.128-0/blib/arch:/home/cpansand/.cpan/build/2018112815/Test-Deep-1.128-0/blib/lib:/home/cpansand/.cpan/build/2018112815/Exception-Class-1.44-0/blib/arch:/home/cpansand/.cpan/build/2018112815/Exception-Class-1.44-0/blib/lib:/home/cpansand/.cpan/build/2018112815/Devel-StackTrace-2.03-0/blib/arch:/home/cpansand/.cpan/build/2018112815/Devel-StackTrace-2.03-0/blib/lib:/home/cpansand/.cpan/build/2018112815/Class-Data-Inheritable-0.08-0/blib/arch:/home/cpansand/.cpan/build/2018112815/Class-Data-Inheritable-0.08-0/blib/lib:/home/cpansand/.cpan/build/2018112815/Data-Stag-0.14-0/blib/arch:/home/cpansand/.cpan/build/2018112815/Data-Stag-0.14-0/blib/lib:/home/cpansand/.cpan/build/2018112815/IO-String-1.08-0/blib/arch:/home/cpansand/.cpan/build/2018112815/IO-String-1.08-0/blib/lib
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 24150
PERL5_CPAN_IS_RUNNING = 24150
PERL5_CPAN_IS_RUNNING_IN_RECURSION = 23837,24150
PERLDOC = -MPod::Perldoc::ToTextOverstrike
PERL_BATCH = yes
PERL_CANARY_STABILITY_NOPROMPT = 1
PERL_CPAN_REPORTER_CONFIG = /var/tmp/cpansmoker-1023/2018112815/cpanreporter_000_config.ini
PERL_EXTUTILS_AUTOINSTALL = --defaultdeps
PERL_USE_UNSAFE_INC = 1
SHELL = /usr/bin/zsh
TERM = screen
TMPDIR = /var/tmp/cpansmoker-1023/2018112815
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /usr/bin/perl
$UID/$EUID = 1023 / 1023
$GID = 1023 1023
$EGID = 1023 1023
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.18
CPAN::Meta 2.150010
Cwd 3.75
ExtUtils::CBuilder 0.280230
ExtUtils::Command 7.34
ExtUtils::Install 2.14
ExtUtils::MakeMaker 7.34
ExtUtils::Manifest 1.70
ExtUtils::ParseXS 3.35
File::Spec 3.75
JSON n/a
JSON::PP 2.97001
Module::Build 0.4224
Module::Signature n/a
Parse::CPAN::Meta 2.150010
Test::Harness 3.42
Test::More 1.302135
YAML n/a
YAML::Syck 1.30
version 0.9924
--
Summary of my perl5 (revision 5 version 26 subversion 2) configuration:
Platform:
osname=linux
osvers=4.18.10-200.fc28.x86_64
archname=x86_64-linux-thread-multi
uname='linux buildvm-30.phx2.fedoraproject.org 4.18.10-200.fc28.x86_64 #1 smp wed sep 26 09:48:36 utc 2018 x86_64 x86_64 x86_64 gnulinux '
config_args='-des -Doptimize=none -Dccflags=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -Dldflags=-Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -Dccdlflags=-Wl,--enable-new-dtags -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -Dlddlflags=-shared -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -Dshrpdir=/usr/lib64 -DDEBUGGING=-g -Dversion=5.26.2 -Dmyhostname=localhost -Dperladmin=root@localhost -Dcc=gcc -Dcf_by=Red Hat, Inc. -Dprefix=/usr -Dvendorprefix=/usr -Dsiteprefix=/usr/local -Dsitelib=/usr/local/share/perl5 -Dsitearch=/usr/local/lib64/perl5 -Dprivlib=/usr/share/perl5 -Dvendorlib=/usr/share/perl5/vendor_perl -Darchlib=/usr/lib64/perl5 -Dvendorarch=/usr/lib64/perl5/vendor_perl -Darchname=x86_64-linux-thread-multi -Dlibpth=/usr/local/lib64 /lib64 /usr/lib64 -Duseshrplib -Dusethreads -Duseithreads -Dusedtrace=/usr/bin/dtrace -Duselargefiles -Dd_semctl_semun -Di_db -Ui_ndbm -Di_gdbm -Di_shadow -Di_syslog -Dman3ext=3pm -Duseperlio -Dinstallusrbinperl=n -Ubincompat5005 -Uversiononly -Dpager=/usr/bin/less -isr -Dd_gethostent_r_proto -Ud_endhostent_r_proto -Ud_sethostent_r_proto -Ud_endprotoent_r_proto -Ud_setprotoent_r_proto -Ud_endservent_r_proto -Ud_setservent_r_proto -Dscriptdir=/usr/bin -Dusesitecustomize -Duse64bitint'
hint=recommended
useposix=true
d_sigaction=define
useithreads=define
usemultiplicity=define
use64bitint=define
use64bitall=define
uselongdouble=undef
usemymalloc=n
default_inc_excludes_dot=define
bincompat5005=undef
Compiler:
cc='gcc'
ccflags ='-D_REENTRANT -D_GNU_SOURCE -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fwrapv -fno-strict-aliasing -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64'
optimize=' -g'
cppflags='-D_REENTRANT -D_GNU_SOURCE -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fwrapv -fno-strict-aliasing -I/usr/local/include'
ccversion=''
gccversion='8.2.1 20181011 (Red Hat 8.2.1-4)'
gccosandvers=''
intsize=4
longsize=8
ptrsize=8
doublesize=8
byteorder=12345678
doublekind=3
d_longlong=define
longlongsize=8
d_longdbl=define
longdblsize=16
longdblkind=3
ivtype='long'
ivsize=8
nvtype='double'
nvsize=8
Off_t='off_t'
lseeksize=8
alignbytes=8
prototype=define
Linker and Libraries:
ld='gcc'
ldflags ='-Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -fstack-protector-strong -L/usr/local/lib'
libpth=/usr/local/lib64 /lib64 /usr/lib64 /usr/local/lib /usr/lib /lib/../lib64 /usr/lib/../lib64 /lib
libs=-lpthread -lresolv -lgdbm -ldb -ldl -lm -lcrypt -lutil -lc -lgdbm_compat
perllibs=-lpthread -lresolv -ldl -lm -lcrypt -lutil -lc
libc=libc-2.27.so
so=so
useshrplib=true
libperl=libperl.so
gnulibc_version='2.27'
Dynamic Linking:
dlsrc=dl_dlopen.xs
dlext=so
d_dlsymun=undef
ccdlflags='-Wl,--enable-new-dtags -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld'
cccdlflags='-fPIC'
lddlflags='-lpthread -shared -Wl,-z,relro -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -L/usr/local/lib -fstack-protector-strong'
Characteristics of this binary (from libperl):
Compile-time options:
HAS_TIMES
MULTIPLICITY
PERLIO_LAYERS
PERL_COPY_ON_WRITE
PERL_DONT_CREATE_GVSV
PERL_IMPLICIT_CONTEXT
PERL_MALLOC_WRAP
PERL_OP_PARENT
PERL_PRESERVE_IVUV
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_LOCALE_TIME
USE_PERLIO
USE_PERL_ATOF
USE_REENTRANT_API
USE_SITECUSTOMIZE
Locally applied patches:
Fedora Patch1: Removes date check, Fedora/RHEL specific
Fedora Patch3: support for libdir64
Fedora Patch4: use libresolv instead of libbind
Fedora Patch5: USE_MM_LD_RUN_PATH
Fedora Patch6: Provide MM::maybe_command independently (bug #1129443)
Fedora Patch7: Dont run one io test due to random builder failures
Fedora Patch15: Define SONAME for libperl.so
Fedora Patch16: Install libperl.so to -Dshrpdir value
Fedora Patch22: Document Math::BigInt::CalcEmu requires Math::BigInt (CPAN RT#85015)
Fedora Patch26: Make *DBM_File desctructors thread-safe (RT#61912)
Fedora Patch27: Make PadlistNAMES() lvalue again (CPAN RT#101063)
Fedora Patch30: Replace EU::MakeMaker dependency with EU::MM::Utils in IPC::Cmd (bug #1129443)
Fedora Patch31: Make File::Glob more resistant against degenerative matching (RT#131211)
Fedora Patch36: Fix glob UTF-8 flag on a glob reassignment (RT#131263)
Fedora Patch38: Fix handling backslashes in PATH environment variable when executing "perl -S" (RT#129183)
Fedora Patch45: Fix File::Glob rt131211.t test random failures
Fedora Patch46: Fix t/op/hash.t test random failures
Fedora Patch47: Parse caret variables with subscripts as normal variables inside ${...} escaping (RT#131664)
Fedora Patch49: Do not display too many bytes when reporting malformed UTF-8 character
Fedora Patch51: Fix error message for "our sub foo::bar" (RT#131679)
Fedora Patch52: Fix executing arybase::_tie_it() in Safe compartement (RT#131588)
Fedora Patch54: Fix splitting non-ASCII strings if unicode_strings feature is enabled (RT#130907)
Fedora Patch55: Fix compiler warnings in code generated by ExtUtils::Constant (CPAN RT#63832)
Fedora Patch56: Fix compiler warnings in code generated by ExtUtils::Constant (CPAN RT#101487)
Fedora Patch58: Fix unreliable Time-HiRes tests (CPAN RT#122819)
Fedora Patch61: Fix Term::ReadLine not to create spurious &STDERR files (RT#132008)
Fedora Patch64: Fix an overflow when parsing a character range with no preceding character (RT#132245)
Fedora Patch65: Fix walking symbol table for ISA in Carp
Fedora Patch66: Fix handling file names with null bytes in stat and lstat functions (RT#131895)
Fedora Patch67: Fix a crash when untying an object witout a stash
Fedora Patch68: Fix deparsing of transliterations with unprintable characters (RT#132405)
Fedora Patch69: Fix error reporting on do() on a directory (RT#125774)
Fedora Patch70: Fix stack manipulation when a lexical subroutine is defined in a do block in a member of an iteration list (RT#132442)
Fedora Patch71: Fix setting $! when statting a closed filehandle (RT#108288)
Fedora Patch72: Fix tainting of s/// with overloaded replacement (RT#115266)
Fedora Patch73: Expand system() arguments before a fork (RT#121105)
Fedora Patch76: Avoid undefined behavior when copying memory in Glob and pp_caller (RT#131746)
Fedora Patch78: Fix compatibility with libxcrypt (RT#133184)
Fedora Patch79: Link XS modules to pthread library to fix linking with -z defs
Fedora Patch80: Fix parsing braced subscript after parentheses (RT#8045)
Fedora Patch81: Do not clobber file bytes in :encoding layer (RT#132833)
Fedora Patch82: Fix line numbers in multi-line s/// (RT#131930)
Fedora Patch83: Fix parsing extended bracketed character classes (RT#132167)
Fedora Patch84: Fix a possibly unitialized memory read in the Perl parser (RT#133074)
Fedora Patch85: Fix an infinite loop in the regular expression compiler (RT#133185)
Fedora Patch86: Adjust tests to gdbm-1.15 (RT#133295)
Fedora Patch87: Fix an integer wrap when allocating memory for an environment variable (RT#133204)
Fedora Patch88: Fix printing a warning about a wide character when matching a regular expression while ISO-8859-1 locale is in effect
Fedora Patch89: Fix invoking a check for wide characters while ISO-8859-1 locale is in effect
Fedora Patch90: Pass the correct CFLAGS to dtrace
Fedora Patch200: Link XS modules to libperl.so with EU::CBuilder on Linux
Fedora Patch201: Link XS modules to libperl.so with EU::MM on Linux
Built under linux
Compiled at Oct 25 2018 13:52:29
%ENV:
PERL5LIB="/home/cpansand/.cpan/build/2018112815/Test-Most-0.35-0/blib/arch:/home/cpansand/.cpan/build/2018112815/Test-Most-0.35-0/blib/lib:/home/cpansand/.cpan/build/2018112815/Test-Warn-0.36-0/blib/arch:/home/cpansand/.cpan/build/2018112815/Test-Warn-0.36-0/blib/lib:/home/cpansand/.cpan/build/2018112815/Test-Exception-0.43-0/blib/arch:/home/cpansand/.cpan/build/2018112815/Test-Exception-0.43-0/blib/lib:/home/cpansand/.cpan/build/2018112815/Sub-Uplevel-0.2800-0/blib/arch:/home/cpansand/.cpan/build/2018112815/Sub-Uplevel-0.2800-0/blib/lib:/home/cpansand/.cpan/build/2018112815/Test-Differences-0.64-0/blib/arch:/home/cpansand/.cpan/build/2018112815/Test-Differences-0.64-0/blib/lib:/home/cpansand/.cpan/build/2018112815/Test-Deep-1.128-0/blib/arch:/home/cpansand/.cpan/build/2018112815/Test-Deep-1.128-0/blib/lib:/home/cpansand/.cpan/build/2018112815/Exception-Class-1.44-0/blib/arch:/home/cpansand/.cpan/build/2018112815/Exception-Class-1.44-0/blib/lib:/home/cpansand/.cpan/build/2018112815/Devel-StackTrace-2.03-0/blib/arch:/home/cpansand/.cpan/build/2018112815/Devel-StackTrace-2.03-0/blib/lib:/home/cpansand/.cpan/build/2018112815/Class-Data-Inheritable-0.08-0/blib/arch:/home/cpansand/.cpan/build/2018112815/Class-Data-Inheritable-0.08-0/blib/lib:/home/cpansand/.cpan/build/2018112815/Data-Stag-0.14-0/blib/arch:/home/cpansand/.cpan/build/2018112815/Data-Stag-0.14-0/blib/lib:/home/cpansand/.cpan/build/2018112815/IO-String-1.08-0/blib/arch:/home/cpansand/.cpan/build/2018112815/IO-String-1.08-0/blib/lib"
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="24150"
PERL5_CPAN_IS_RUNNING="24150"
PERL5_CPAN_IS_RUNNING_IN_RECURSION="23837,24150"
PERLDOC="-MPod::Perldoc::ToTextOverstrike"
PERL_BATCH="yes"
PERL_CANARY_STABILITY_NOPROMPT="1"
PERL_CPAN_REPORTER_CONFIG="/var/tmp/cpansmoker-1023/2018112815/cpanreporter_000_config.ini"
PERL_EXTUTILS_AUTOINSTALL="--defaultdeps"
PERL_USE_UNSAFE_INC="1"
@INC:
/home/cpansand/.cpan/build/2018112815/Test-Most-0.35-0/blib/arch
/home/cpansand/.cpan/build/2018112815/Test-Most-0.35-0/blib/lib
/home/cpansand/.cpan/build/2018112815/Test-Warn-0.36-0/blib/arch
/home/cpansand/.cpan/build/2018112815/Test-Warn-0.36-0/blib/lib
/home/cpansand/.cpan/build/2018112815/Test-Exception-0.43-0/blib/arch
/home/cpansand/.cpan/build/2018112815/Test-Exception-0.43-0/blib/lib
/home/cpansand/.cpan/build/2018112815/Sub-Uplevel-0.2800-0/blib/arch
/home/cpansand/.cpan/build/2018112815/Sub-Uplevel-0.2800-0/blib/lib
/home/cpansand/.cpan/build/2018112815/Test-Differences-0.64-0/blib/arch
/home/cpansand/.cpan/build/2018112815/Test-Differences-0.64-0/blib/lib
/home/cpansand/.cpan/build/2018112815/Test-Deep-1.128-0/blib/arch
/home/cpansand/.cpan/build/2018112815/Test-Deep-1.128-0/blib/lib
/home/cpansand/.cpan/build/2018112815/Exception-Class-1.44-0/blib/arch
/home/cpansand/.cpan/build/2018112815/Exception-Class-1.44-0/blib/lib
/home/cpansand/.cpan/build/2018112815/Devel-StackTrace-2.03-0/blib/arch
/home/cpansand/.cpan/build/2018112815/Devel-StackTrace-2.03-0/blib/lib
/home/cpansand/.cpan/build/2018112815/Class-Data-Inheritable-0.08-0/blib/arch
/home/cpansand/.cpan/build/2018112815/Class-Data-Inheritable-0.08-0/blib/lib
/home/cpansand/.cpan/build/2018112815/Data-Stag-0.14-0/blib/arch
/home/cpansand/.cpan/build/2018112815/Data-Stag-0.14-0/blib/lib
/home/cpansand/.cpan/build/2018112815/IO-String-1.08-0/blib/arch
/home/cpansand/.cpan/build/2018112815/IO-String-1.08-0/blib/lib
/usr/local/lib64/perl5
/usr/local/share/perl5
/usr/lib64/perl5/vendor_perl
/usr/share/perl5/vendor_perl
/usr/lib64/perl5
/usr/share/perl5
.