BioPerl v1.007002 Perl 5 v5.16.3 x86_64-linux-thread-multi
- Status
- Pass
- From
- Nigel Horne
- Dist
-
BioPerl v1.007002
- Platform
- Perl 5 v5.16.3 x86_64-linux-thread-multi
- Date
- 2018-10-04 12:09:59
- ID
- 6a0d4e5a-c7ce-11e8-a45e-cc933bb958d5
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 5.16.3, 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/SimpleAlign.t .................. ok
t/Align/TreeBuild.t .................... ok
t/Align/Utilities.t .................... ok
t/AlignIO/bl2seq.t ..................... ok
t/AlignIO/AlignIO.t .................... ok
t/AlignIO/arp.t ........................ ok
t/AlignIO/prodom.t ..................... ok
t/AlignIO/clustalw.t ................... ok
t/AlignIO/psi.t ........................ ok
t/AlignIO/emboss.t ..................... ok
t/AlignIO/fasta.t ...................... ok
t/Align/Graphics.t ..................... ok
t/AlignIO/largemultifasta.t ............ ok
t/AlignIO/mase.t ....................... ok
t/AlignIO/maf.t ........................ ok
t/AlignIO/mega.t ....................... ok
t/AlignIO/selex.t ...................... ok
t/AlignIO/meme.t ....................... ok
t/AlignIO/metafasta.t .................. ok
t/AlignIO/stockholm.t .................. ok
t/Assembly/ContigSpectrum.t ............ ok
t/AlignIO/xmfa.t ....................... ok
t/AlignIO/msf.t ........................ ok
t/Assembly/IO/sam.t .................... skipped: The optional module Bio::DB::Sam (or dependencies thereof) was not installed
t/AlignIO/nexus.t ...................... ok
t/AlignIO/pfam.t ....................... ok
t/Annotation/AnnotationAdaptor.t ....... ok
t/AlignIO/phylip.t ..................... ok
t/Annotation/Annotation.t .............. ok
t/AlignIO/po.t ......................... ok
t/Alphabet.t ........................... ok
t/ClusterIO/ClusterIO.t ................ ok
t/Assembly/IO/bowtie.t ................. skipped: The optional module Bio::DB::Sam (or dependencies thereof) was not installed
t/LiveSeq/LiveSeq.t .................... ok
t/Cluster/UniGene.t .................... ok
t/LocalDB/Index/BlastTable.t ........... ok
t/LocalDB/Flat.t ....................... ok
t/ClusterIO/SequenceFamily.t ........... ok
t/Draw/Pictogram.t ..................... skipped: The optional module SVG (or dependencies thereof) was not installed
t/ClusterIO/unigene.t .................. ok
t/Assembly/core.t ...................... ok
t/LocalDB/transfac_pro.t ............... ok
t/LocalDB/Taxonomy/greengenes.t ........ ok
t/LiveSeq/Chain.t ...................... ok
t/Map/MapIO.t .......................... ok
t/Map/Linkage.t ........................ ok
t/LiveSeq/Mutation.t ................... ok
t/Map/Cyto.t ........................... ok
t/LocalDB/Index/Blast.t ................ ok
t/Map/MicrosatelliteMarker.t ........... ok
t/LiveSeq/Mutator.t .................... ok
t/Matrix/Matrix.t ...................... ok
t/Matrix/SiteMatrix.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/Map/Map.t ............................ ok
t/LocalDB/BioDBGFF.t ................... ok
t/Ontology/GOterm.t .................... skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/LocalDB/Index/Index.t ................ ok
t/Matrix/ProtMatrix.t .................. ok
t/Map/Physical.t ....................... ok
t/Matrix/InstanceSite.t ................ ok
t/LocalDB/Taxonomy/silva.t ............. ok
t/Matrix/IO/masta.t .................... ok
t/Ontology/OntologyStore.t ............. skipped: The optional module Graph (or dependencies thereof) was not installed
t/LocalDB/Registry.t ................... ok
t/Ontology/IO/obo.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/Matrix/IO/psm.t ...................... ok
t/Ontology/IO/go.t ..................... skipped: The optional module Graph (or dependencies thereof) was not installed
t/LocalDB/Taxonomy/sqlite.t ............ ok
t/Ontology/Term.t ...................... skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/Matrix/ProtPsm.t ..................... ok
t/Ontology/RelationshipType.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/Phenotype/Correlate.t ................ ok
t/Phenotype/OMIMentryAllelicVariant.t .. ok
t/Ontology/Relationship.t .............. skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
Subroutine new redefined at Bio/DB/IndexedBase.pm line 1159.
Subroutine next_seq redefined at Bio/DB/IndexedBase.pm line 1168.
Subroutine TIEHANDLE redefined at Bio/DB/IndexedBase.pm line 1177.
Subroutine READLINE redefined at Bio/DB/IndexedBase.pm line 1182.
Subroutine dl_load_flags redefined at (eval 103) line 8.
Subroutine Bio::DB::IndexedBase::_strip_crnl redefined at (eval 103) line 9.
t/LocalDB/Fasta.t ...................... ok
t/Ontology/IO/interpro.t ............... skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/Ontology/Ontology.t .................. skipped: The optional module Graph (or dependencies thereof) was not installed
t/Phenotype/Phenotype.t ................ ok
t/AlignIO/nexml.t ...................... skipped: The optional module Bio::Phylo (or dependencies thereof) was not installed
t/Phenotype/OMIMparser.t ............... ok
t/Phenotype/Measure.t .................. ok
t/Phenotype/MeSH.t ..................... ok
t/PopGen/TagHaplotype.t ................ ok
t/PopGen/HtSNP.t ....................... ok
t/Phenotype/OMIMentry.t ................ ok
t/PopGen/MK.t .......................... ok
t/PopGen/Coalescent.t .................. ok
t/PopGen/PopGen.t ...................... ok
t/RemoteDB/EMBL.t ...................... skipped: Network tests have not been requested
t/RemoteDB/GenBank.t ................... skipped: Network tests have not been requested
t/PopGen/PopGenSims.t .................. ok
t/Phenotype/MiniMIMentry.t ............. ok
t/PodSyntax.t .......................... ok
t/Restriction/Gel.t .................... ok
t/Restriction/Analysis.t ............... ok
t/RemoteDB/CUTG.t ...................... ok
t/RemoteDB/HIV/HIVAnnotProcessor.t ..... ok
t/Root/IO.t ............................ ok
t/RemoteDB/RefSeq.t .................... ok
t/Root/RootI.t ......................... ok
t/Root/Utilities.t ..................... ok
t/Root/HTTPget.t ....................... skipped: Network tests have not been requested
t/SearchIO/CigarString.t ............... ok
t/Restriction/Analysis-refac.t ......... ok
t/SearchDist.t ......................... skipped: The optional module Bio::Ext::Align (or dependencies thereof) was not installed
t/Root/Storable.t ...................... ok
t/RemoteDB/EntrezGene.t ................ skipped: Network tests have not been requested
t/RemoteDB/MeSH.t ...................... skipped: Network tests have not been requested
t/RemoteDB/SeqRead_fail.t .............. skipped: Network tests have not been requested
t/SearchIO/SearchIO.t .................. ok
t/RemoteDB/SwissProt.t ................. skipped: Network tests have not been requested
t/Root/Exception.t ..................... ok
t/SearchIO/SimilarityPair.t ............ ok
t/RemoteDB/HIV/HIVQueryHelper.t ........ ok
t/RemoteDB/Query/GenBank.t ............. skipped: Network tests have not been requested
t/SearchIO/Writer/GbrowseGFF.t ......... ok
t/SearchIO/Writer/HSPTableWriter.t ..... ok
t/RemoteDB/BioFetch.t .................. skipped: Network tests have not been requested
t/Perl.t ............................... ok
t/SearchIO/Tiling.t .................... ok
t/SearchIO/Writer/HTMLWriter.t ......... ok
t/Root/RootIO.t ........................ skipped: Network tests have not been requested
t/SearchIO/cross_match.t ............... ok
t/RemoteDB/SeqVersion.t ................ ok
t/SearchIO/blast.t ..................... ok
t/SearchIO/axt.t ....................... ok
t/SearchIO/blast_pull.t ................ ok
t/SearchIO/Writer/HitTableWriter.t ..... ok
t/SearchIO/Writer/TextWriter.t ......... ok
t/SearchIO/infernal.t .................. ok
t/SearchIO/fasta.t ..................... ok
t/SearchIO/erpin.t ..................... ok
t/RemoteDB/GenPept.t ................... skipped: Network tests have not been requested
t/SearchIO/rnamotif.t .................. ok
t/SearchIO/megablast.t ................. ok
t/SearchIO/waba.t ...................... ok
t/SearchIO/psl.t ....................... ok
t/SearchIO/exonerate.t ................. ok
t/SearchIO/gmap_f9.t ................... ok
t/Restriction/IO.t ..................... ok
t/Seq/LargePSeq.t ...................... ok
t/Seq/LocatableSeq.t ................... ok
t/SearchIO/blasttable.t ................ ok
t/Seq/PrimarySeq.t ..................... ok
t/Seq/Quality.t ........................ ok
t/Seq/DBLink.t ......................... ok
t/SearchIO/wise.t ...................... ok
t/Seq/MetaSeq.t ........................ ok
t/Seq/LargeLocatableSeq.t .............. ok
t/SearchIO/sim4.t ...................... ok
t/Seq/PrimedSeq.t ...................... ok
t/Seq/EncodedSeq.t ..................... ok
t/SearchIO/hmmer_pull.t ................ ok
t/Seq/WithQuality.t .................... ok
t/SeqFeature/Amplicon.t ................ ok
t/SearchIO/hmmer.t ..................... ok
t/Seq/Seq.t ............................ ok
t/SeqFeature/Clone.t ................... ok
t/SeqFeature/FeaturePair.t ............. ok
t/SeqFeature/Computation.t ............. ok
t/Seq/SimulatedRead.t .................. ok
t/Seq/PrimaryQual.t .................... ok
t/SeqEvolution.t ....................... ok
t/SeqFeature/Range.t ................... ok
t/SeqFeature/SubSeq.t .................. ok
t/SeqFeature/Location.t ................ ok
t/SeqFeature/Gene.t .................... ok
t/SeqIO/SeqBuilder.t ................... ok
t/SeqIO/Multiple_fasta.t ............... ok
t/SeqIO/MultiFile.t .................... ok
t/SeqFeature/LocationFactory.t ......... ok
t/SeqIO/SeqIO.t ........................ ok
t/SeqFeature/RangeI.t .................. ok
t/SeqFeature/Primer.t .................. ok
t/SeqIO/bsml_sax.t ..................... ok
t/SeqIO/alf.t .......................... skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqIO/agave.t ........................ ok
t/SeqFeature/Collection.t .............. ok
t/SeqIO/chadoxml.t ..................... ok
t/SeqIO/ctf.t .......................... skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqFeature/SeqAnalysisParser.t ....... ok
t/SeqIO/asciitree.t .................... ok
t/SeqIO/Handler.t ...................... ok
t/SeqIO/chaos.t ........................ ok
t/SeqIO/bsml.t ......................... ok
t/SeqIO/excel.t ........................ ok
t/SeqIO/ace.t .......................... ok
t/SeqIO/abi.t .......................... skipped: The optional module Bio::SeqIO::staden::read (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/chaosxml.t ..................... ok
t/SeqIO/embl.t ......................... ok
t/SeqIO/fasta.t ........................ ok
t/SeqIO/game.t ......................... ok
t/SeqIO/flybase_chadoxml.t ............. ok
t/SeqIO/largefasta.t ................... ok
t/SeqIO/gcg.t .......................... ok
t/SeqIO/entrezgene.t ................... ok
t/SeqIO/kegg.t ......................... ok
t/SeqIO/interpro.t ..................... ok
t/SeqFeature/Generic.t ................. ok
t/SeqIO/mbsout.t ....................... ok
t/SeqIO/phd.t .......................... ok
t/SeqIO/pln.t .......................... skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/SeqIO/pir.t .......................... ok
t/SeqFeature/Unflattener.t ............. ok
t/SeqIO/metafasta.t .................... ok
t/SeqIO/genbank.t ...................... ok
t/SeqIO/lasergene.t .................... ok
t/SeqIO/fastq.t ........................ ok
t/SeqIO/Splicedseq.t ................... ok
t/RemoteDB/Taxonomy.t .................. ok
t/SeqIO/gbxml.t ........................ ok
t/SeqIO/qual.t ......................... ok
t/SeqIO/tab.t .......................... ok
t/SeqIO/msout.t ........................ ok
t/SeqIO/table.t ........................ ok
t/SeqIO/locuslink.t .................... skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/SeqIO/tigr.t ......................... ok
t/SeqIO/tigrxml.t ...................... ok
t/SeqIO/swiss.t ........................ ok
t/SeqIO/strider.t ...................... skipped: The optional module Convert::Binary::C (or dependencies thereof) was not installed
t/SeqIO/nexml.t ........................ skipped: The optional module Bio::Phylo (or dependencies thereof) was not installed
t/SeqIO/raw.t .......................... ok
t/SeqTools/SeqWords.t .................. ok
t/SeqIO/scf.t .......................... ok
t/SeqTools/SeqStats.t .................. ok
t/Structure/Structure.t ................ ok
t/RemoteDB/HIV/HIV.t ................... ok
t/Structure/IO.t ....................... ok
t/SeqIO/tinyseq.t ...................... ok
t/Symbol.t ............................. ok
t/SeqTools/SeqPattern.t ................ ok
t/SeqTools/ECnumber.t .................. ok
t/SeqTools/SeqUtils.t .................. ok
t/Tools/Alignment/Consed.t ............. ok
t/SeqIO/ztr.t .......................... skipped: The optional module Bio::SeqIO::staden::read (or dependencies thereof) was not installed
t/Tools/Analysis/DNA/ESEfinder.t ....... skipped: Network tests have not been requested
t/TaxonTree.t .......................... skipped: These modules are now probably deprecated
t/SeqTools/GuessSeqFormat.t ............ ok
t/SeqIO/seqxml.t ....................... ok
t/Tools/Analysis/Protein/GOR4.t ........ skipped: Network tests have not been requested
t/SeqTools/OddCodes.t .................. ok
t/RemoteDB/HIV/HIVQuery.t .............. ok
t/Tools/AmpliconSearch.t ............... ok
t/SeqTools/CodonTable.t ................ ok
t/Tools/Analysis/Protein/ELM.t ......... skipped: Network tests have not been requested
t/Tools/Genewise.t ..................... ok
t/Tools/EMBOSS/Palindrome.t ............ ok
t/Tools/GFF.t .......................... ok
t/Tools/Analysis/Protein/NetPhos.t ..... skipped: Network tests have not been requested
t/Tools/IUPAC.t ........................ ok
t/Tools/Primer3.t ...................... ok
t/Tools/FootPrinter.t .................. ok
t/Tools/Est2Genome.t ................... ok
t/Tools/Genomewise.t ................... ok
t/Tools/Phylo/Phylip/ProtDist.t ........ ok
t/Tools/Analysis/Protein/Sopma.t ....... skipped: Network tests have not been requested
t/Tools/Hmmer.t ........................ ok
t/Tools/Geneid.t ....................... ok
t/Tools/Promoterwise.t ................. ok
t/Tools/Genpred.t ...................... ok
t/Tools/QRNA.t ......................... ok
t/Tools/RandDistFunctions.t ............ ok
t/Tools/Analysis/Protein/Domcut.t ...... skipped: Network tests have not been requested
t/Tools/Pseudowise.t ................... ok
t/Tools/PrositeScan.t .................. ok
t/Tools/Seg.t .......................... ok
t/Tools/Phylo/Gerp.t ................... ok
t/Tools/SiRNA.t ........................ ok
t/Tools/TandemRepeatsFinder.t .......... ok
t/Tools/Match.t ........................ ok
t/Tools/Spidey/Spidey.t ................ ok
t/Tools/Lucy.t ......................... ok
t/Tools/Sigcleave.t .................... ok
t/Tools/Tmhmm.t ........................ ok
t/Tools/RepeatMasker.t ................. ok
t/Tools/pICalculator.t ................. ok
t/Tools/Analysis/Protein/Scansite.t .... ok
t/Tools/ePCR.t ......................... ok
t/Tools/Phylo/Molphy.t ................. ok
t/Tools/Signalp/ExtendedSignalp.t ...... ok
t/Tree/Node.t .......................... ok
t/Tools/TargetP.t ...................... ok
t/Tree/PhyloNetwork/GraphViz.t ......... skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed
t/SeqTools/Backtranslate.t ............. ok
t/Tree/Compatible.t .................... ok
t/Tools/Sim4.t ......................... ok
t/Tree/PhyloNetwork/RandomFactory.t .... skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed
t/Species.t ............................ ok
t/Tools/Signalp.t ...................... ok
t/Tree/PhyloNetwork/PhyloNetwork.t ..... skipped: The optional module Graph::Directed (or dependencies thereof) was not installed
t/Tree/RandomTreeFactory.t ............. ok
t/Tools/tRNAscanSE.t ................... ok
t/Tree/TreeIO/nexml.t .................. skipped: The optional module Bio::Phylo (or dependencies thereof) was not installed
t/Tree/TreeIO/nhx.t .................... ok
t/Tree/TreeIO.t ........................ ok
t/Tools/Analysis/Protein/HNN.t ......... skipped: Network tests have not been requested
t/Tree/PhyloNetwork/TreeFactory.t ...... skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed
t/Tree/TreeIO/newick.t ................. ok
t/Tree/TreeIO/svggraph.t ............... ok
t/Tools/Run/RemoteBlast_rpsblast.t ..... skipped: Network tests have not been requested
t/Tree/Tree.t .......................... ok
t/Tree/TreeStatistics.t ................ ok
t/Tree/TreeIO/nexus.t .................. ok
t/Variation/DNAMutation.t .............. ok
t/Variation/SNP.t ...................... ok
t/Tree/PhyloNetwork/Factory.t .......... skipped: The optional module Bio::PhyloNetwork (or dependencies thereof) was not installed
t/Tree/PhyloNetwork/MuVector.t ......... ok
t/Variation/SeqDiff.t .................. ok
t/Variation/Allele.t ................... ok
t/Tools/Run/RemoteBlast.t .............. skipped: Network tests have not been requested
t/Tree/TreeIO/phyloxml.t ............... ok
t/Tree/TreeIO/tabtree.t ................ ok
t/Tree/TreeIO/lintree.t ................ ok
t/Variation/RNAChange.t ................ ok
t/Variation/AAReverseMutate.t .......... ok
t/Variation/Variation_IO.t ............. ok
t/Variation/AAChange.t ................. ok
t/nexml.t .............................. skipped: The optional module Bio::Phylo (or dependencies thereof) was not installed
t/LocalDB/Qual.t ....................... ok
t/LocalDB/SeqFeature.t ................. ok
All tests successful.
Files=325, Tests=21829, 121 wallclock secs ( 3.20 usr 0.81 sys + 112.81 cusr 73.20 csys = 190.02 CPU)
Result: PASS
------------------------------
PREREQUISITES
------------------------------
Prerequisite modules loaded:
requires:
Module Need Have
------------------ ------ --------
Data::Stag 0.11 0.14
ExtUtils::Manifest 1.52 1.71
IO::String 0 1.08
perl v5.6.1 5.016003
Scalar::Util 0 1.50
build_requires:
Module Need Have
------------------ ------ --------
CPAN 1.81 2.16
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:
HARNESS_OPTIONS = c:j24
LANG = en_US.UTF-8
LC_ALL = POSIX
LD_LIBRARY_PATH = /opt/ghostscript/lib64:/opt/qt4/lib64:/netopt/ncbi_tools64/boost-1.52.0-ncbi1/lib:/usr/local/intel/Compiler/17.0/compilers_and_libraries_2017.4.196/linux/compiler/lib/intel64:/usr/local/intel/Compiler/17.0/compilers_and_libraries_2017.4.196/linux/compiler/lib/intel64_lin:/usr/local/intel/Compiler/17.0/compilers_and_libraries_2017.4.196/linux/ipp/lib/intel64:/usr/local/intel/Compiler/17.0/compilers_and_libraries_2017.4.196/linux/compiler/lib/intel64_lin:/usr/local/intel/Compiler/17.0/compilers_and_libraries_2017.4.196/linux/mkl/lib/intel64_lin:/usr/local/intel/Compiler/17.0/compilers_and_libraries_2017.4.196/linux/tbb/lib/intel64/gcc4.7:/usr/local/intel/Compiler/17.0/debugger_2017/iga/lib:/usr/local/intel/Compiler/17.0/debugger_2017/libipt/intel64/lib:/usr/local/intel/Compiler/17.0/compilers_and_libraries_2017.4.196/linux/daal/lib/intel64_lin:/usr/local/intel/Compiler/17.0/compilers_and_libraries_2017.4.196/linux/daal/../tbb/lib/intel64_lin/gcc4.4:/usr/local/R/3.5.1/lib64/R/lib/:/usr/local/gsl/1.12/lib
PATH = /home/hornenj/perl5/bin:/home/hornenj/bin:/opt/python-all/bin:/opt/perl/5.16.3/bin:/opt/fcron/bin:/usr/local/rstudio/0.99.903/bin:/usr/local/intel/Compiler/17.0/compilers_and_libraries_2017.4.196/linux/bin/intel64:/usr/local/intel/Compiler/17.0/debugger_2017/gdb/intel64_mic/bin:/usr/local/intel/Compiler/17.0/bin:/usr/local/R/3.5.1/bin:/usr/local/netcdf/4.3.3/bin:/usr/local/gsl/1.12/bin:/usr/local/purify/7.0.1.0-006/releases/PurifyPlus.7.0.1.0-006/i386_linux2/bin:/usr/local/purify/7.0.1.0-006/bin:/netmnt/gridengine/current/bin/lx-amd64:/opt/ruby/2.0/bin:/usr/local/subversion/1.7.22/bin:/usr/local/svnmucc/1.5.7/bin:/usr/local/ninja/1.7.2/bin:/usr/local/nedit/5.5/bin:/netopt/ncbi_tools64/bin:/am/ncbiapdata/bin:/usr/local/joe/3.7/bin:/usr/local/git/latest/bin:/opt/ncbi/gcc/4.9.3/bin:/usr/local/ddd/3.3.12/bin:/usr/local/ctags/5.8/bin:/usr/local/cmake/3.1.0/bin:/usr/lib64/ccache:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/sbin:/sbin:/usr/local/sbin:/opt/sybase/clients/current/bin:/opt/sybase/utils/bin:/opt/dell/srvadmin/bin
PERL5LIB = /home/hornenj/perl5/lib/perl5:
PERL5OPT =
PERL5_CPANPLUS_IS_RUNNING = 118801
PERL5_CPAN_IS_RUNNING = 118801
PERL_LOCAL_LIB_ROOT = :/home/hornenj/perl5
PERL_MB_OPT = --install_base /home/hornenj/perl5
PERL_MM_OPT = INSTALL_BASE=/home/hornenj/perl5
SHELL = /bin/bash
TERM = xterm-256color
Perl special variables (and OS-specific diagnostics, for MSWin32):
$^X = /usr/bin/perl
$UID/$EUID = 12481 / 12481
$GID = 14 14 241 527 5344 37191 37223
$EGID = 14 14 241 527 5344 37191 37223
Perl module toolchain versions installed:
Module Have
------------------- --------
CPAN 2.16
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 1.71
ExtUtils::ParseXS 3.35
File::Spec 3.75
JSON 2.97001
JSON::PP 2.97001
Module::Build 0.4224
Module::Signature 0.81
Parse::CPAN::Meta 2.150010
Test::Harness 3.42
Test::More 1.302140
YAML 1.26
YAML::Syck 1.30
version 0.9924
--
Summary of my perl5 (revision 5 version 16 subversion 3) configuration:
Platform:
osname=linux, osvers=3.10.0-514.16.1.el7.x86_64, archname=x86_64-linux-thread-multi
uname='linux c1bm.rdu2.centos.org 3.10.0-514.16.1.el7.x86_64 #1 smp wed apr 12 15:04:24 utc 2017 x86_64 x86_64 x86_64 gnulinux '
config_args='-des -Doptimize=-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -Dccdlflags=-Wl,--enable-new-dtags -Dlddlflags=-shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -Wl,-z,relro -DDEBUGGING=-g -Dversion=5.16.3 -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'
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='gcc', ccflags ='-D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64',
optimize='-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic',
cppflags='-D_REENTRANT -D_GNU_SOURCE -fno-strict-aliasing -pipe -fstack-protector -I/usr/local/include'
ccversion='', gccversion='4.8.5 20150623 (Red Hat 4.8.5-16)', 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='gcc', ldflags =' -fstack-protector'
libpth=/usr/local/lib64 /lib64 /usr/lib64
libs=-lresolv -lnsl -lgdbm -ldb -ldl -lm -lcrypt -lutil -lpthread -lc -lgdbm_compat
perllibs=-lresolv -lnsl -ldl -lm -lcrypt -lutil -lpthread -lc
libc=, so=so, useshrplib=true, libperl=libperl.so
gnulibc_version='2.17'
Dynamic Linking:
dlsrc=dl_dlopen.xs, dlext=so, d_dlsymun=undef, ccdlflags='-Wl,--enable-new-dtags -Wl,-rpath,/usr/lib64/perl5/CORE'
cccdlflags='-fPIC', lddlflags='-shared -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -Wl,-z,relro '
Characteristics of this binary (from libperl):
Compile-time options: HAS_TIMES MULTIPLICITY PERLIO_LAYERS
PERL_DONT_CREATE_GVSV PERL_IMPLICIT_CONTEXT
PERL_MALLOC_WRAP 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_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: Skip hostname tests, due to builders not being network capable
Fedora Patch7: Dont run one io test due to random builder failures
Fedora Patch9: Fix find2perl to translate ? glob properly (RT#113054)
Fedora Patch10: Fix broken atof (RT#109318)
Fedora Patch13: Clear $@ before "do" I/O error (RT#113730)
Fedora Patch14: Do not truncate syscall() return value to 32 bits (RT#113980)
Fedora Patch15: Override the Pod::Simple::parse_file (CPANRT#77530)
Fedora Patch16: Do not leak with attribute on my variable (RT#114764)
Fedora Patch17: Allow operator after numeric keyword argument (RT#105924)
Fedora Patch18: Extend stack in File::Glob::glob, (RT#114984)
Fedora Patch19: Do not crash when vivifying $|
Fedora Patch20: Fix misparsing of maketext strings (CVE-2012-6329)
Fedora Patch21: Add NAME headings to CPAN modules (CPANRT#73396)
Fedora Patch22: Fix leaking tied hashes (RT#107000) [1]
Fedora Patch23: Fix leaking tied hashes (RT#107000) [2]
Fedora Patch24: Fix leaking tied hashes (RT#107000) [3]
Fedora Patch25: Fix dead lock in PerlIO after fork from thread (RT#106212)
Fedora Patch26: Make regexp safe in a signal handler (RT#114878)
Fedora Patch27: Update h2ph(1) documentation (RT#117647)
Fedora Patch28: Update pod2html(1) documentation (RT#117623)
Fedora Patch29: Document Math::BigInt::CalcEmu requires Math::BigInt (CPAN RT#85015)
RHEL Patch30: Use stronger algorithm needed for FIPS in t/op/crypt.t (RT#121591)
RHEL Patch31: Make *DBM_File desctructors thread-safe (RT#61912)
RHEL Patch32: Use stronger algorithm needed for FIPS in t/op/taint.t (RT#123338)
RHEL Patch33: Remove CPU-speed-sensitive test in Benchmark test
RHEL Patch34: Make File::Glob work with threads again
RHEL Patch35: Fix CRLF conversion in ASCII FTP upload (CPAN RT#41642)
RHEL Patch36: Do not leak the temp utf8 copy of namepv (CPAN RT#123786)
RHEL Patch37: Fix duplicating PerlIO::encoding when spawning threads (RT#31923)
Built under linux
Compiled at Aug 2 2017 17:45:03
%ENV:
PERL5LIB="/home/hornenj/perl5/lib/perl5:"
PERL5OPT=""
PERL5_CPANPLUS_IS_RUNNING="118801"
PERL5_CPAN_IS_RUNNING="118801"
PERL_LOCAL_LIB_ROOT=":/home/hornenj/perl5"
PERL_MB_OPT="--install_base /home/hornenj/perl5"
PERL_MM_OPT="INSTALL_BASE=/home/hornenj/perl5"
@INC:
/home/hornenj/perl5/lib/perl5/5.16.3/x86_64-linux-thread-multi
/home/hornenj/perl5/lib/perl5/5.16.3
/home/hornenj/perl5/lib/perl5/x86_64-linux-thread-multi
/home/hornenj/perl5/lib/perl5
/usr/local/lib64/perl5
/usr/local/share/perl5
/usr/lib64/perl5/vendor_perl
/usr/share/perl5/vendor_perl
/usr/lib64/perl5
/usr/share/perl5
.