Date: Wed, 28 May 2014 19:24:25 +0600 (BDT) From: Muhammad Moinur Rahman <5u623l20@gmail.com> To: FreeBSD-gnats-submit@FreeBSD.org Cc: wen@FreeBSD.org Subject: ports/190342: [PATCH] biology/p5-bioperl: update to 1.6.923, Add STAGE support Message-ID: <201405281324.s4SDOP7T058025@bofh.1asiacom.net> Resent-Message-ID: <201405281330.s4SDU02P025265@freefall.freebsd.org>
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>Number: 190342 >Category: ports >Synopsis: [PATCH] biology/p5-bioperl: update to 1.6.923, Add STAGE support >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: update >Submitter-Id: current-users >Arrival-Date: Wed May 28 13:30:00 UTC 2014 >Closed-Date: >Last-Modified: >Originator: Muhammad Moinur Rahman >Release: FreeBSD 11.0-CURRENT amd64 >Organization: >Environment: System: FreeBSD bofh.1asiacom.net 11.0-CURRENT FreeBSD 11.0-CURRENT #2 r265972: Wed May 14 02:05:04 BDT >Description: - Update to 1.6.923 - Add STAGE support - Fix BROKEN For Committer's reference: http://pdr.s.ubze.ro/bulk/latest-per-pkg/p5-bioperl/1.6.923/ Fails to build in 11.0 due to failure of a dependency graphics/libglapi Port maintainer (wen@FreeBSD.org) is cc'd. Generated with FreeBSD Port Tools 1.02 (mode: update, diff: ports) >How-To-Repeat: >Fix: --- p5-bioperl-1.6.923.patch begins here --- diff -ruN /usr/ports//biology/p5-bioperl/Makefile ./Makefile --- /usr/ports//biology/p5-bioperl/Makefile 2014-04-09 15:49:02.000000000 +0600 +++ ./Makefile 2014-05-28 18:39:33.004379957 +0600 @@ -2,18 +2,19 @@ # $FreeBSD: head/biology/p5-bioperl/Makefile 350675 2014-04-09 09:49:02Z bapt $ PORTNAME= bioperl -PORTVERSION= 1.6.1 -PORTREVISION= 4 +PORTVERSION= 1.6.923 CATEGORIES= biology perl5 -MASTER_SITES= http://bioperl.org/DIST/ \ - CPAN +MASTER_SITES= CPAN +MASTER_SITE_SUBDIR= CPAN:CJFIELDS PKGNAMEPREFIX= p5- DISTNAME= BioPerl-${PORTVERSION} MAINTAINER= wen@FreeBSD.org COMMENT= A collection of Perl modules for bioinformatics -BROKEN= not staged +LICENSE= ART10 GPLv1 +LICENSE_COMB= dual + BUILD_DEPENDS= p5-Text-Tabs+Wrap>=0:${PORTSDIR}/textproc/p5-Text-Tabs+Wrap \ p5-Bio-ASN1-EntrezGene>=0:${PORTSDIR}/biology/p5-Bio-ASN1-EntrezGene \ p5-Class-AutoClass>=0:${PORTSDIR}/devel/p5-Class-AutoClass \ @@ -38,7 +39,6 @@ p5-XML-SAX-Writer>=0:${PORTSDIR}/textproc/p5-XML-SAX-Writer \ p5-XML-Twig>=0:${PORTSDIR}/textproc/p5-XML-Twig \ p5-XML-Writer>=0:${PORTSDIR}/textproc/p5-XML-Writer \ - p5-AcePerl>=0:${PORTSDIR}/biology/p5-AcePerl \ p5-Clone>=0:${PORTSDIR}/devel/p5-Clone \ p5-DBD-mysql>=0:${PORTSDIR}/databases/p5-DBD-mysql \ p5-GD>=0:${PORTSDIR}/graphics/p5-GD \ @@ -53,954 +53,40 @@ p5-Math-Random>=0:${PORTSDIR}/math/p5-Math-Random \ p5-PostScript>=0:${PORTSDIR}/print/p5-PostScript \ p5-Set-Scalar>=0:${PORTSDIR}/devel/p5-Set-Scalar \ - p5-URI>=0:${PORTSDIR}/net/p5-URI + p5-URI>=0:${PORTSDIR}/net/p5-URI \ + p5-Test-Most>=0:${PORTSDIR}/devel/p5-Test-Most \ + p5-HTML-TableExtract>=2:${PORTSDIR}/www/p5-HTML-TableExtract \ + p5-Sort-Naturally>=1:${PORTSDIR}/textproc/p5-Sort-Naturally \ + p5-XML-Simple>=2:${PORTSDIR}/textproc/p5-XML-Simple \ + p5-YAML>=0:${PORTSDIR}/textproc/p5-YAML \ + p5-Error>=0:${PORTSDIR}/lang/p5-Error RUN_DEPENDS:= ${BUILD_DEPENDS} -#CONFLICTS= p5-bioperl-1.[13579]* - USES= perl5 USE_PERL5= modbuild -MAN1= bp_aacomp.pl.1 \ - bp_biblio.pl.1 \ - bp_biofetch_genbank_proxy.pl.1 \ - bp_bioflat_index.pl.1 \ - bp_biogetseq.pl.1 \ - bp_blast2tree.pl.1 \ - bp_bulk_load_gff.pl.1 \ - bp_chaos_plot.pl.1 \ - bp_classify_hits_kingdom.pl.1 \ - bp_composite_LD.pl.1 \ - bp_dbsplit.pl.1 \ - bp_download_query_genbank.pl.1 \ - bp_einfo.pl.1 \ - bp_extract_feature_seq.pl.1 \ - bp_fast_load_gff.pl.1 \ - bp_fastam9_to_table.pl.1 \ - bp_fetch.pl.1 \ - bp_filter_search.pl.1 \ - bp_flanks.pl.1 \ - bp_gccalc.pl.1 \ - bp_genbank2gff.pl.1 \ - bp_genbank2gff3.pl.1 \ - bp_generate_histogram.pl.1 \ - bp_heterogeneity_test.pl.1 \ - bp_hivq.pl.1 \ - bp_hmmer_to_table.pl.1 \ - bp_index.pl.1 \ - bp_load_gff.pl.1 \ - bp_local_taxonomydb_query.pl.1 \ - bp_make_mrna_protein.pl.1 \ - bp_mask_by_search.pl.1 \ - bp_meta_gff.pl.1 \ - bp_mrtrans.pl.1 \ - bp_mutate.pl.1 \ - bp_nexus2nh.pl.1 \ - bp_nrdb.pl.1 \ - bp_oligo_count.pl.1 \ - bp_pairwise_kaks.pl.1 \ - bp_parse_hmmsearch.pl.1 \ - bp_process_gadfly.pl.1 \ - bp_process_sgd.pl.1 \ - bp_process_wormbase.pl.1 \ - bp_query_entrez_taxa.pl.1 \ - bp_remote_blast.pl.1 \ - bp_revtrans-motif.pl.1 \ - bp_search2BSML.pl.1 \ - bp_search2alnblocks.pl.1 \ - 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Bio::OntologyIO::InterProParser.3 \ - Bio::OntologyIO::dagflat.3 \ - Bio::OntologyIO::goflat.3 \ - Bio::OntologyIO::obo.3 \ - Bio::OntologyIO::simplehierarchy.3 \ - Bio::OntologyIO::soflat.3 \ - Bio::ParameterBaseI.3 \ - Bio::Perl.3 \ - Bio::Phenotype::Correlate.3 \ - Bio::Phenotype::MeSH::Term.3 \ - Bio::Phenotype::MeSH::Twig.3 \ - Bio::Phenotype::Measure.3 \ - Bio::Phenotype::OMIM::MiniMIMentry.3 \ - Bio::Phenotype::OMIM::OMIMentry.3 \ - Bio::Phenotype::OMIM::OMIMentryAllelicVariant.3 \ - Bio::Phenotype::OMIM::OMIMparser.3 \ - Bio::Phenotype::Phenotype.3 \ - Bio::Phenotype::PhenotypeI.3 \ - Bio::PhyloNetwork.3 \ - Bio::PhyloNetwork::Factory.3 \ - Bio::PhyloNetwork::FactoryX.3 \ - Bio::PhyloNetwork::GraphViz.3 \ - Bio::PhyloNetwork::RandomFactory.3 \ - Bio::PhyloNetwork::TreeFactory.3 \ - Bio::PhyloNetwork::TreeFactoryMulti.3 \ - Bio::PhyloNetwork::TreeFactoryX.3 \ - Bio::PhyloNetwork::muVector.3 \ - Bio::PopGen::Genotype.3 \ - Bio::PopGen::GenotypeI.3 \ - Bio::PopGen::HtSNP.3 \ - Bio::PopGen::IO.3 \ - Bio::PopGen::IO::csv.3 \ - Bio::PopGen::IO::hapmap.3 \ - Bio::PopGen::IO::phase.3 \ - Bio::PopGen::IO::prettybase.3 \ - Bio::PopGen::Individual.3 \ - Bio::PopGen::IndividualI.3 \ - Bio::PopGen::Marker.3 \ - Bio::PopGen::MarkerI.3 \ - Bio::PopGen::PopStats.3 \ - Bio::PopGen::Population.3 \ - Bio::PopGen::PopulationI.3 \ - Bio::PopGen::Simulation::Coalescent.3 \ - Bio::PopGen::Simulation::GeneticDrift.3 \ - Bio::PopGen::Statistics.3 \ - Bio::PopGen::TagHaplotype.3 \ - Bio::PopGen::Utilities.3 \ - Bio::PrimarySeq.3 \ - Bio::PrimarySeqI.3 \ - Bio::PullParserI.3 \ - Bio::Range.3 \ - Bio::RangeI.3 \ - Bio::Restriction::Analysis.3 \ - Bio::Restriction::Enzyme.3 \ - Bio::Restriction::Enzyme::MultiCut.3 \ - Bio::Restriction::Enzyme::MultiSite.3 \ - Bio::Restriction::EnzymeCollection.3 \ - Bio::Restriction::EnzymeI.3 \ - Bio::Restriction::IO.3 \ - Bio::Restriction::IO::bairoch.3 \ - Bio::Restriction::IO::base.3 \ - Bio::Restriction::IO::itype2.3 \ - Bio::Restriction::IO::prototype.3 \ - Bio::Restriction::IO::withrefm.3 \ - Bio::Root::Build.3 \ - Bio::Root::Exception.3 \ - Bio::Root::HTTPget.3 \ - Bio::Root::IO.3 \ - Bio::Root::Root.3 \ - Bio::Root::RootI.3 \ - Bio::Root::Storable.3 \ - Bio::Root::Test.3 \ - Bio::Root::Test::Warn.3 \ - Bio::Root::Utilities.3 \ - Bio::Root::Version.3 \ - Bio::Search::BlastStatistics.3 \ - Bio::Search::BlastUtils.3 \ - Bio::Search::DatabaseI.3 \ - Bio::Search::GenericDatabase.3 \ - Bio::Search::GenericStatistics.3 \ - Bio::Search::HSP::BlastHSP.3 \ - Bio::Search::HSP::BlastPullHSP.3 \ - Bio::Search::HSP::FastaHSP.3 \ - Bio::Search::HSP::GenericHSP.3 \ - Bio::Search::HSP::HMMERHSP.3 \ - Bio::Search::HSP::HSPFactory.3 \ - Bio::Search::HSP::HSPI.3 \ - Bio::Search::HSP::HmmpfamHSP.3 \ - Bio::Search::HSP::ModelHSP.3 \ - Bio::Search::HSP::PSLHSP.3 \ - Bio::Search::HSP::PsiBlastHSP.3 \ - Bio::Search::HSP::PullHSPI.3 \ - Bio::Search::HSP::WABAHSP.3 \ - Bio::Search::Hit::BlastHit.3 \ - Bio::Search::Hit::BlastPullHit.3 \ - Bio::Search::Hit::Fasta.3 \ - Bio::Search::Hit::GenericHit.3 \ - Bio::Search::Hit::HMMERHit.3 \ - Bio::Search::Hit::HitFactory.3 \ - Bio::Search::Hit::HitI.3 \ - Bio::Search::Hit::HmmpfamHit.3 \ - Bio::Search::Hit::ModelHit.3 \ - Bio::Search::Hit::PsiBlastHit.3 \ - Bio::Search::Hit::PullHitI.3 \ - Bio::Search::Iteration::GenericIteration.3 \ - Bio::Search::Iteration::IterationI.3 \ - Bio::Search::Processor.3 \ - Bio::Search::Result::BlastPullResult.3 \ - Bio::Search::Result::BlastResult.3 \ - Bio::Search::Result::CrossMatchResult.3 \ - Bio::Search::Result::GenericResult.3 \ - Bio::Search::Result::HMMERResult.3 \ - Bio::Search::Result::HmmpfamResult.3 \ - Bio::Search::Result::PullResultI.3 \ - Bio::Search::Result::ResultFactory.3 \ - Bio::Search::Result::ResultI.3 \ - Bio::Search::Result::WABAResult.3 \ - Bio::Search::SearchUtils.3 \ - Bio::Search::StatisticsI.3 \ - Bio::Search::Tiling::MapTileUtils.3 \ - Bio::Search::Tiling::MapTiling.3 \ - Bio::Search::Tiling::TilingI.3 \ - Bio::SearchDist.3 \ - Bio::SearchIO.3 \ - Bio::SearchIO::EventHandlerI.3 \ - Bio::SearchIO::FastHitEventBuilder.3 \ - Bio::SearchIO::IteratedSearchResultEventBuilder.3 \ - Bio::SearchIO::SearchResultEventBuilder.3 \ - Bio::SearchIO::SearchWriterI.3 \ - Bio::SearchIO::Writer::BSMLResultWriter.3 \ - Bio::SearchIO::Writer::GbrowseGFF.3 \ - Bio::SearchIO::Writer::HSPTableWriter.3 \ - Bio::SearchIO::Writer::HTMLResultWriter.3 \ - Bio::SearchIO::Writer::HitTableWriter.3 \ - Bio::SearchIO::Writer::ResultTableWriter.3 \ - Bio::SearchIO::Writer::TextResultWriter.3 \ - Bio::SearchIO::XML::BlastHandler.3 \ - Bio::SearchIO::XML::PsiBlastHandler.3 \ - Bio::SearchIO::axt.3 \ - Bio::SearchIO::blast.3 \ - Bio::SearchIO::blast_pull.3 \ - Bio::SearchIO::blasttable.3 \ - Bio::SearchIO::blastxml.3 \ - Bio::SearchIO::cross_match.3 \ - Bio::SearchIO::erpin.3 \ - Bio::SearchIO::exonerate.3 \ - Bio::SearchIO::fasta.3 \ - Bio::SearchIO::hmmer.3 \ - Bio::SearchIO::hmmer_pull.3 \ - Bio::SearchIO::infernal.3 \ - Bio::SearchIO::gmap_f9.3 \ - Bio::SearchIO::megablast.3 \ - Bio::SearchIO::psl.3 \ - Bio::SearchIO::rnamotif.3 \ - Bio::SearchIO::sim4.3 \ - Bio::SearchIO::waba.3 \ - Bio::SearchIO::wise.3 \ - Bio::Seq.3 \ - Bio::Seq::BaseSeqProcessor.3 \ - Bio::Seq::EncodedSeq.3 \ - Bio::Seq::LargeLocatableSeq.3 \ - Bio::Seq::LargePrimarySeq.3 \ - Bio::Seq::LargeSeq.3 \ - Bio::Seq::LargeSeqI.3 \ - Bio::Seq::Meta.3 \ - Bio::Seq::Meta::Array.3 \ - Bio::Seq::MetaI.3 \ - Bio::Seq::PrimaryQual.3 \ - Bio::Seq::PrimedSeq.3 \ - Bio::Seq::QualI.3 \ - Bio::Seq::Quality.3 \ - Bio::Seq::RichSeq.3 \ - Bio::Seq::RichSeqI.3 \ - Bio::Seq::SeqBuilder.3 \ - Bio::Seq::SeqFactory.3 \ - Bio::Seq::SeqFastaSpeedFactory.3 \ - Bio::Seq::SeqWithQuality.3 \ - Bio::Seq::SequenceTrace.3 \ - Bio::Seq::TraceI.3 \ - Bio::SeqAnalysisParserI.3 \ - Bio::SeqEvolution::DNAPoint.3 \ - Bio::SeqEvolution::EvolutionI.3 \ - Bio::SeqEvolution::Factory.3 \ - Bio::SeqFeature::Annotated.3 \ - Bio::SeqFeature::AnnotationAdaptor.3 \ - Bio::SeqFeature::Collection.3 \ - Bio::SeqFeature::CollectionI.3 \ - Bio::SeqFeature::Computation.3 \ - Bio::SeqFeature::FeaturePair.3 \ - Bio::SeqFeature::Gene::Exon.3 \ - Bio::SeqFeature::Gene::ExonI.3 \ - Bio::SeqFeature::Gene::GeneStructure.3 \ - Bio::SeqFeature::Gene::GeneStructureI.3 \ - Bio::SeqFeature::Gene::Intron.3 \ - Bio::SeqFeature::Gene::NC_Feature.3 \ - Bio::SeqFeature::Gene::Poly_A_site.3 \ - Bio::SeqFeature::Gene::Promoter.3 \ - Bio::SeqFeature::Gene::Transcript.3 \ - Bio::SeqFeature::Gene::TranscriptI.3 \ - Bio::SeqFeature::Gene::UTR.3 \ - Bio::SeqFeature::Generic.3 \ - Bio::SeqFeature::Lite.3 \ - Bio::SeqFeature::PositionProxy.3 \ - Bio::SeqFeature::Primer.3 \ - Bio::SeqFeature::SiRNA::Oligo.3 \ - Bio::SeqFeature::SiRNA::Pair.3 \ - Bio::SeqFeature::Similarity.3 \ - Bio::SeqFeature::SimilarityPair.3 \ - Bio::SeqFeature::Tools::FeatureNamer.3 \ - Bio::SeqFeature::Tools::IDHandler.3 \ - Bio::SeqFeature::Tools::TypeMapper.3 \ - Bio::SeqFeature::Tools::Unflattener.3 \ - Bio::SeqFeature::TypedSeqFeatureI.3 \ - Bio::SeqFeatureI.3 \ - Bio::SeqI.3 \ - Bio::SeqIO.3 \ - Bio::SeqIO::FTHelper.3 \ - Bio::SeqIO::Handler::GenericRichSeqHandler.3 \ - Bio::SeqIO::MultiFile.3 \ - Bio::SeqIO::abi.3 \ - Bio::SeqIO::ace.3 \ - Bio::SeqIO::agave.3 \ - Bio::SeqIO::alf.3 \ - Bio::SeqIO::asciitree.3 \ - Bio::SeqIO::bsml.3 \ - Bio::SeqIO::bsml_sax.3 \ - Bio::SeqIO::chadoxml.3 \ - Bio::SeqIO::chaos.3 \ - Bio::SeqIO::chaosxml.3 \ - Bio::SeqIO::ctf.3 \ - Bio::SeqIO::embl.3 \ - Bio::SeqIO::embldriver.3 \ - Bio::SeqIO::entrezgene.3 \ - Bio::SeqIO::excel.3 \ - Bio::SeqIO::exp.3 \ - Bio::SeqIO::fasta.3 \ - Bio::SeqIO::fastq.3 \ - Bio::SeqIO::flybase_chadoxml.3 \ - Bio::SeqIO::game.3 \ - Bio::SeqIO::game::featHandler.3 \ - Bio::SeqIO::game::gameHandler.3 \ - Bio::SeqIO::game::gameSubs.3 \ - Bio::SeqIO::game::gameWriter.3 \ - Bio::SeqIO::game::seqHandler.3 \ - Bio::SeqIO::gbdriver.3 \ - Bio::SeqIO::gcg.3 \ - Bio::SeqIO::genbank.3 \ - Bio::SeqIO::interpro.3 \ - Bio::SeqIO::kegg.3 \ - Bio::SeqIO::largefasta.3 \ - Bio::SeqIO::lasergene.3 \ - Bio::SeqIO::locuslink.3 \ - Bio::SeqIO::metafasta.3 \ - Bio::SeqIO::phd.3 \ - Bio::SeqIO::pir.3 \ - Bio::SeqIO::pln.3 \ - Bio::SeqIO::qual.3 \ - Bio::SeqIO::raw.3 \ - Bio::SeqIO::scf.3 \ - Bio::SeqIO::strider.3 \ - Bio::SeqIO::swiss.3 \ - Bio::SeqIO::swissdriver.3 \ - Bio::SeqIO::tab.3 \ - Bio::SeqIO::table.3 \ - Bio::SeqIO::tigr.3 \ - Bio::SeqIO::tigrxml.3 \ - Bio::SeqIO::tinyseq.3 \ - Bio::SeqIO::tinyseq::tinyseqHandler.3 \ - Bio::SeqIO::ztr.3 \ - Bio::SeqUtils.3 \ - Bio::SimpleAlign.3 \ - Bio::SimpleAnalysisI.3 \ - Bio::Species.3 \ - Bio::Structure::Atom.3 \ - Bio::Structure::Chain.3 \ - Bio::Structure::Entry.3 \ - Bio::Structure::IO.3 \ - Bio::Structure::IO::pdb.3 \ - Bio::Structure::Model.3 \ - Bio::Structure::Residue.3 \ - Bio::Structure::SecStr::DSSP::Res.3 \ - Bio::Structure::SecStr::STRIDE::Res.3 \ - Bio::Structure::StructureI.3 \ - Bio::Symbol::Alphabet.3 \ - Bio::Symbol::AlphabetI.3 \ - Bio::Symbol::DNAAlphabet.3 \ - Bio::Symbol::ProteinAlphabet.3 \ - Bio::Symbol::Symbol.3 \ - Bio::Symbol::SymbolI.3 \ - Bio::Taxon.3 \ - Bio::Taxonomy.3 \ - Bio::Taxonomy::FactoryI.3 \ - Bio::Taxonomy::Node.3 \ - Bio::Taxonomy::Taxon.3 \ - Bio::Taxonomy::Tree.3 \ - Bio::Tools::AlignFactory.3 \ - Bio::Tools::Alignment::Consed.3 \ - Bio::Tools::Alignment::Trim.3 \ - Bio::Tools::Analysis::DNA::ESEfinder.3 \ - Bio::Tools::Analysis::Protein::Domcut.3 \ - Bio::Tools::Analysis::Protein::ELM.3 \ - Bio::Tools::Analysis::Protein::GOR4.3 \ - Bio::Tools::Analysis::Protein::HNN.3 \ - Bio::Tools::Analysis::Protein::Mitoprot.3 \ - Bio::Tools::Analysis::Protein::NetPhos.3 \ - Bio::Tools::Analysis::Protein::Scansite.3 \ - Bio::Tools::Analysis::Protein::Sopma.3 \ - Bio::Tools::Analysis::SimpleAnalysisBase.3 \ - Bio::Tools::AnalysisResult.3 \ - Bio::Tools::Blat.3 \ - Bio::Tools::CodonTable.3 \ - Bio::Tools::Coil.3 \ - Bio::Tools::ECnumber.3 \ - Bio::Tools::EMBOSS::Palindrome.3 \ - Bio::Tools::EPCR.3 \ - Bio::Tools::ERPIN.3 \ - Bio::Tools::ESTScan.3 \ - Bio::Tools::EUtilities.3 \ - Bio::Tools::EUtilities::Cookie.3 \ - Bio::Tools::EUtilities::EUtilDataI.3 \ - Bio::Tools::EUtilities::EUtilParameters.3 \ - Bio::Tools::EUtilities::History.3 \ - Bio::Tools::EUtilities::HistoryI.3 \ - Bio::Tools::EUtilities::Info.3 \ - Bio::Tools::EUtilities::Info::FieldInfo.3 \ - Bio::Tools::EUtilities::Info::LinkInfo.3 \ - Bio::Tools::EUtilities::Link.3 \ - Bio::Tools::EUtilities::Link::LinkSet.3 \ - Bio::Tools::EUtilities::Link::UrlLink.3 \ - Bio::Tools::EUtilities::Query.3 \ - Bio::Tools::EUtilities::Query::GlobalQuery.3 \ - Bio::Tools::EUtilities::Summary.3 \ - Bio::Tools::EUtilities::Summary::DocSum.3 \ - Bio::Tools::EUtilities::Summary::Item.3 \ - Bio::Tools::EUtilities::Summary::ItemContainerI.3 \ - Bio::Tools::Eponine.3 \ - Bio::Tools::Est2Genome.3 \ - Bio::Tools::Fgenesh.3 \ - Bio::Tools::FootPrinter.3 \ - Bio::Tools::GFF.3 \ - Bio::Tools::Gel.3 \ - Bio::Tools::Geneid.3 \ - Bio::Tools::Genemark.3 \ - Bio::Tools::Genewise.3 \ - Bio::Tools::Genomewise.3 \ - Bio::Tools::Genscan.3 \ - Bio::Tools::Glimmer.3 \ - Bio::Tools::Grail.3 \ - Bio::Tools::GuessSeqFormat.3 \ - Bio::Tools::HMMER::Domain.3 \ - Bio::Tools::HMMER::Results.3 \ - Bio::Tools::HMMER::Set.3 \ - Bio::Tools::Hmmpfam.3 \ - Bio::Tools::IUPAC.3 \ - Bio::Tools::Infernal.3 \ - Bio::Tools::Lucy.3 \ - Bio::Tools::MZEF.3 \ - Bio::Tools::Match.3 \ - Bio::Tools::OddCodes.3 \ - Bio::Tools::Phylo::Gerp.3 \ - Bio::Tools::Phylo::Gumby.3 \ - Bio::Tools::Phylo::Molphy.3 \ - Bio::Tools::Phylo::Molphy::Result.3 \ - Bio::Tools::Phylo::PAML.3 \ - Bio::Tools::Phylo::PAML::ModelResult.3 \ - Bio::Tools::Phylo::PAML::Result.3 \ - Bio::Tools::Phylo::Phylip::ProtDist.3 \ - Bio::Tools::Prediction::Exon.3 \ - Bio::Tools::Prediction::Gene.3 \ - Bio::Tools::Primer3.3 \ - Bio::Tools::Primer::Assessor::Base.3 \ - Bio::Tools::Primer::AssessorI.3 \ - Bio::Tools::Primer::Feature.3 \ - Bio::Tools::Primer::Pair.3 \ - Bio::Tools::Prints.3 \ - Bio::Tools::Profile.3 \ - Bio::Tools::Promoterwise.3 \ - Bio::Tools::PrositeScan.3 \ - Bio::Tools::Protparam.3 \ - Bio::Tools::Pseudowise.3 \ - Bio::Tools::QRNA.3 \ - Bio::Tools::RNAMotif.3 \ - Bio::Tools::RandomDistFunctions.3 \ - Bio::Tools::RepeatMasker.3 \ - Bio::Tools::Run::GenericParameters.3 \ - Bio::Tools::Run::ParametersI.3 \ - Bio::Tools::Run::RemoteBlast.3 \ - Bio::Tools::Run::StandAloneBlast.3 \ - Bio::Tools::Run::StandAloneNCBIBlast.3 \ - Bio::Tools::Run::StandAloneWUBlast.3 \ - Bio::Tools::Run::WrapperBase.3 \ - Bio::Tools::Seg.3 \ - Bio::Tools::SeqPattern::Backtranslate.3 \ - Bio::Tools::SeqPattern.3 \ - Bio::Tools::SeqStats.3 \ - Bio::Tools::SeqWords.3 \ - Bio::Tools::SiRNA.3 \ - Bio::Tools::SiRNA::Ruleset::saigo.3 \ - Bio::Tools::SiRNA::Ruleset::tuschl.3 \ - Bio::Tools::Sigcleave.3 \ - Bio::Tools::Signalp.3 \ - Bio::Tools::Signalp::ExtendedSignalp.3 \ - Bio::Tools::Sim4::Exon.3 \ - Bio::Tools::Sim4::Results.3 \ - Bio::Tools::Spidey::Exon.3 \ - Bio::Tools::Spidey::Results.3 \ - Bio::Tools::TandemRepeatsFinder.3 \ - Bio::Tools::TargetP.3 \ - Bio::Tools::Tmhmm.3 \ - Bio::Tools::dpAlign.3 \ - Bio::Tools::ipcress.3 \ - Bio::Tools::isPcr.3 \ - Bio::Tools::pICalculator.3 \ - Bio::Tools::pSW.3 \ - Bio::Tools::tRNAscanSE.3 \ - Bio::Tree::AlleleNode.3 \ - Bio::Tree::AnnotatableNode.3 \ - Bio::Tree::Compatible.3 \ - Bio::Tree::DistanceFactory.3 \ - Bio::Tree::Draw::Cladogram.3 \ - Bio::Tree::Node.3 \ - Bio::Tree::NodeI.3 \ - Bio::Tree::NodeNHX.3 \ - Bio::Tree::RandomFactory.3 \ - Bio::Tree::Statistics.3 \ - Bio::Tree::Tree.3 \ - Bio::Tree::TreeFunctionsI.3 \ - Bio::Tree::TreeI.3 \ - Bio::TreeIO.3 \ - Bio::TreeIO::TreeEventBuilder.3 \ - Bio::TreeIO::cluster.3 \ - Bio::TreeIO::lintree.3 \ - Bio::TreeIO::newick.3 \ - Bio::TreeIO::nexus.3 \ - Bio::TreeIO::nhx.3 \ - Bio::TreeIO::pag.3 \ - Bio::TreeIO::phyloxml.3 \ - Bio::TreeIO::svggraph.3 \ - Bio::TreeIO::tabtree.3 \ - Bio::UpdateableSeqI.3 \ - Bio::Variation::AAChange.3 \ - Bio::Variation::AAReverseMutate.3 \ - Bio::Variation::Allele.3 \ - Bio::Variation::DNAMutation.3 \ - Bio::Variation::IO.3 \ - Bio::Variation::IO::flat.3 \ - Bio::Variation::IO::xml.3 \ - Bio::Variation::RNAChange.3 \ - Bio::Variation::SNP.3 \ - Bio::Variation::SeqDiff.3 \ - Bio::Variation::VariantI.3 \ - Bio::WebAgent.3 - -# now install all extra stuff (docs, examples, scripts, models) -NO_STAGE= yes - -OPTIONS_DEFINE= DOCS +OPTIONS_DEFINE= DOCS PGTEST SQLITETEST +PGTEST_DESC= Test PostGreSQL +SQLITETEST_DESC= Test SQLite +PGTEST_RUN_DEPENDS= p5-DBD-Pg>=3:${PORTSDIR}/databases/p5-DBD-Pg +PGTEST_BUILD_DEPENDS= p5-DBD-Pg>=3:${PORTSDIR}/databases/p5-DBD-Pg +SQLITETEST_RUN_DEPENDS= p5-DBD-SQLite>=1:${PORTSDIR}/databases/p5-DBD-SQLite +SQLITETEST_BUILD_DEPENDS= p5-DBD-SQLite>=1:${PORTSDIR}/databases/p5-DBD-SQLite .include <bsd.port.options.mk> post-install: - ${MKDIR} ${DATADIR} - ${CP} -R ${WRKSRC}/scripts ${WRKSRC}/models ${DATADIR} - ${MKDIR} ${EXAMPLESDIR} - ${CP} -R ${WRKSRC}/examples/* ${EXAMPLESDIR} + ${MKDIR} ${STAGEDIR}${DATADIR} + ${CP} -R ${WRKSRC}/scripts ${WRKSRC}/models ${STAGEDIR}${DATADIR} + ${MKDIR} ${STAGEDIR}${EXAMPLESDIR} + ${CP} -R ${WRKSRC}/examples/* ${STAGEDIR}${EXAMPLESDIR} .if ${PORT_OPTIONS:MDOCS} - ${MKDIR} ${DOCSDIR} + ${MKDIR} ${STAGEDIR}${DOCSDIR} .for doc in AUTHORS BUGS Changes DEPENDENCIES DEPRECATED INSTALL LICENSE MANIFEST README - ${INSTALL_MAN} ${WRKSRC}/${doc} ${DOCSDIR} + ${INSTALL_MAN} ${WRKSRC}/${doc} ${STAGEDIR}${DOCSDIR} .endfor - ${CP} -R ${WRKSRC}/doc ${DOCSDIR} + ${CP} -R ${WRKSRC}/doc ${STAGEDIR}${DOCSDIR} .endif .include <bsd.port.mk> diff -ruN /usr/ports//biology/p5-bioperl/distinfo ./distinfo --- /usr/ports//biology/p5-bioperl/distinfo 2014-01-22 21:30:13.000000000 +0600 +++ ./distinfo 2014-05-28 15:19:33.131207174 +0600 @@ -1,2 +1,2 @@ -SHA256 (BioPerl-1.6.1.tar.gz) = ac36dace2b4dd973567b02cce29158beac05fd672872ca8769e02bbddddc95a3 -SIZE (BioPerl-1.6.1.tar.gz) = 10462526 +SHA256 (BioPerl-1.6.923.tar.gz) = 6f6ada4ebd51ad223662e4b1ddcccc37a4fb8c47f3ecbbf060e6844d361730cd +SIZE (BioPerl-1.6.923.tar.gz) = 12562520 diff -ruN /usr/ports//biology/p5-bioperl/files/patch-Bio-Root-Build.pm ./files/patch-Bio-Root-Build.pm --- /usr/ports//biology/p5-bioperl/files/patch-Bio-Root-Build.pm 2014-01-22 23:40:44.000000000 +0600 +++ ./files/patch-Bio-Root-Build.pm 2014-05-28 15:51:47.688073934 +0600 @@ -1,31 +1,33 @@ --- Bio/Root/Build.pm.orig 2009-09-30 00:33:53.000000000 +0800 +++ Bio/Root/Build.pm 2009-12-01 10:31:39.000000000 +0800 -@@ -124,48 +124,8 @@ +@@ -127,49 +127,9 @@ } } closedir($scripts_dir); -- my $question = $int_ok ? "Install [a]ll BioPerl scripts, [n]one, or choose groups [i]nteractively?" : "Install [a]ll BioPerl scripts or [n]one?"; -- +- my $question = $int_ok ? "Install [a]ll BioPerl scripts, [n]one, ". +- "or choose groups [i]nteractively?" : "Install [a]ll BioPerl scripts ". +- "or [n]one?"; +- - my $prompt = $accept ? 'a' : $self->prompt($question, 'a'); -- +- - if ($prompt =~ /^[aA]/) { - $self->log_info(" - will install all scripts\n"); - $self->notes(chosen_scripts => 'all'); - } - elsif ($prompt =~ /^[iI]/) { - $self->log_info(" - will install interactively:\n"); -- +- - my @chosen_scripts; - foreach my $group_dir (@group_dirs) { - my $group = File::Basename::basename($group_dir); - print " * group '$group' has:\n"; -- +- - my @script_files = @{$self->rscan_dir($group_dir, qr/\.PLS$|\.pl$/)}; - foreach my $script_file (@script_files) { - my $script = File::Basename::basename($script_file); - print " $script\n"; - } -- +- - my $result = $self->prompt(" Install scripts for group '$group'? [y]es [n]o [q]uit", 'n'); - die if $result =~ /^[qQ]/; - if ($result =~ /^[yY]/) { @@ -36,30 +38,34 @@ - $self->log_info(" - will not install group '$group'\n"); - } - } -- + - my $chosen_scripts = @chosen_scripts ? join("|", @chosen_scripts) : 'none'; -- +- - $self->notes(chosen_scripts => $chosen_scripts); - } - else { - $self->log_info(" - won't install any scripts\n"); - $self->notes(chosen_scripts => 'none'); - } -- -+ $self->log_info(" - will install all scripts\n"); -+ $self->notes(chosen_scripts => 'all'); ++ $self->log_info(" - willt install all scripts\n"); ++ $self->notes(chosen_scripts => 'all'); + print "\n"; } - -@@ -1205,16 +1165,9 @@ +@@ -1136,21 +1096,9 @@ sub prompt_for_network { my ($self, $accept) = @_; - my $proceed = $accept ? 0 : $self->y_n("Do you want to run tests that require connection to servers across the internet\n(likely to cause some failures)? y/n", 'n'); -- +- - if ($proceed) { -- $self->notes(network => 1); +- $self->notes('network' => 1); - $self->log_info(" - will run internet-requiring tests\n"); +- my $use_email = $self->y_n("Do you want to run tests requiring a valid email address? y/n",'n'); +- if ($use_email) { +- my $address = $self->prompt("Enter email address:"); +- $self->notes(email => $address); +- } - } - else { - $self->notes(network => 0); @@ -70,4 +76,4 @@ + $self->log_info(" - will not run internet-requiring tests\n"); } - 1; + # override the build script warnings flag diff -ruN /usr/ports//biology/p5-bioperl/files/patch-Build.PL ./files/patch-Build.PL --- /usr/ports//biology/p5-bioperl/files/patch-Build.PL 2014-01-22 23:40:44.000000000 +0600 +++ ./files/patch-Build.PL 2014-05-28 15:52:02.303073270 +0600 @@ -1,22 +1,21 @@ --- Build.PL.orig 2009-09-30 00:33:45.000000000 +0800 +++ Build.PL 2009-12-01 10:25:51.000000000 +0800 -@@ -37,7 +37,7 @@ - 'Test::More' => 0, +@@ -187,7 +187,6 @@ + }, + + build_requires => { +- 'CPAN' => 1.81, 'Module::Build' => 0.2805, 'Test::Harness' => 2.62, -- 'CPAN' => 1.81 -+ #'CPAN' => 1.81 - }, - recommends => { # does what you would expect of recommends, except more informative output and generates optional_features in META.yml - 'Ace' => '0/access of ACeDB database/Bio::DB::Ace,Bio::DB::GFF::Adaptor::ace', -@@ -234,86 +234,9 @@ + 'Test::Most' => 0, +@@ -376,86 +375,8 @@ sub prompt_for_biodb { my $accept = shift; - my $proceed = $accept ? 0 : $build->y_n("Do you want to run the Bio::DB::GFF or ". - "Bio::DB::SeqFeature::Store live database tests? ". - "y/n", 'n'); -- +- - if ($proceed) { - my @driver_choices; - foreach my $poss ('SQLite', 'mysql', 'Pg', 'Oracle') { @@ -26,7 +25,7 @@ - push(@driver_choices, $choice); - } - } -- +- - my $driver; - if (@driver_choices > 1) { - my ($default) = $driver_choices[0] =~ /\[(.)/; @@ -47,19 +46,19 @@ - elsif ($driver =~ /^[sS]/) { - $driver = 'SQLite'; - } -- +- - my $test_db = $build->prompt("Which database should I use for testing the $driver driver?\n". - "This database should already be present but doesn't have to ". - "be preloaded for any schema", 'test'); - my $test_host = $build->prompt("On which host is database '$test_db' running (hostname, ip address or host:port)", 'localhost'); - my $test_user = $build->prompt("User name for connecting to database '$test_db'?", 'undef'); - my $test_pass = $build->prompt("Password for connecting to database '$test_db'?", 'undef'); -- +- - my $use_host = 1; - if ($test_host eq 'undef' || $test_host eq 'localhost') { - $use_host = 0; - } -- +- - my $test_dsn; - if ($driver eq 'Pg' || $driver eq 'SQLite') { - $test_dsn = "dbi:$driver:dbname=$test_db"; @@ -72,14 +71,14 @@ - if ($use_host) { - $test_dsn .= ";host=$test_host"; - } -- +- - $build->notes(dbd_driver => $driver); - $build->notes(test_db => $test_db); - $build->notes(test_host => $test_host); - $build->notes(test_user => $test_user eq 'undef' ? undef : $test_user); - $build->notes(test_pass => $test_pass eq 'undef' ? undef : $test_pass); - $build->notes(test_dsn => $test_dsn); -- +- - $build->log_info(" - will run tests with database driver '$driver' and these settings:\n", - " Database $test_db\n", - " Host $test_host\n", @@ -92,7 +91,7 @@ - else { - $build->log_info(" - will not run the BioDBGFF or BioDBSeqFeature live database tests\n"); - } - +- + my $proceed = 0; + $build->log_info(" - will not run the BioDBGFF or BioDBSeqFeature live database tests\n"); $build->log_info("\n"); diff -ruN /usr/ports//biology/p5-bioperl/pkg-plist ./pkg-plist --- /usr/ports//biology/p5-bioperl/pkg-plist 2014-01-22 21:16:56.000000000 +0600 +++ ./pkg-plist 2014-05-28 16:43:39.173858543 +0600 @@ -1,196 +1,891 @@ -%%DATADIR%%/models/README -%%DATADIR%%/models/biblio.dia -%%DATADIR%%/models/bio_liveseq_variation.dia -%%DATADIR%%/models/bio_map.dia -%%DATADIR%%/models/bioperl.dia -%%DATADIR%%/models/bio_restriction.dia -%%DATADIR%%/models/coordinatemapper.dia -%%DATADIR%%/models/map_proposal.txt -%%DATADIR%%/models/maps_and_markers.dia -%%DATADIR%%/models/popgen.dia -%%DATADIR%%/models/population_proposal.txt -%%DATADIR%%/scripts/Bio-DB-EUtilities/einfo.PLS -%%DATADIR%%/scripts/Bio-DB-GFF/README -%%DATADIR%%/scripts/Bio-DB-GFF/bulk_load_gff.PLS -%%DATADIR%%/scripts/Bio-DB-GFF/fast_load_gff.PLS -%%DATADIR%%/scripts/Bio-DB-GFF/genbank2gff3.PLS -%%DATADIR%%/scripts/Bio-DB-GFF/genbank2gff.PLS -%%DATADIR%%/scripts/Bio-DB-GFF/generate_histogram.PLS -%%DATADIR%%/scripts/Bio-DB-GFF/load_gff.PLS -%%DATADIR%%/scripts/Bio-DB-GFF/meta_gff.PLS 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%%SITE_PERL%%/Bio/Das/FeatureTypeI.pm -%%SITE_PERL%%/Bio/DasI.pm %%SITE_PERL%%/Bio/Das/SegmentI.pm +%%SITE_PERL%%/Bio/DasI.pm %%SITE_PERL%%/Bio/DescribableI.pm +%%SITE_PERL%%/Bio/Draw/Pictogram.pm %%SITE_PERL%%/Bio/Event/EventGeneratorI.pm %%SITE_PERL%%/Bio/Event/EventHandlerI.pm -%%SITE_PERL%%/Bio/Expression/Contact.pm -%%SITE_PERL%%/Bio/Expression/DataSet.pm -%%SITE_PERL%%/Bio/Expression/FeatureGroup/FeatureGroupMas50.pm -%%SITE_PERL%%/Bio/Expression/FeatureGroup.pm -%%SITE_PERL%%/Bio/Expression/FeatureI.pm -%%SITE_PERL%%/Bio/Expression/FeatureSet/FeatureSetMas50.pm -%%SITE_PERL%%/Bio/Expression/Platform.pm -%%SITE_PERL%%/Bio/Expression/ProbeI.pm -%%SITE_PERL%%/Bio/Expression/Sample.pm %%SITE_PERL%%/Bio/Factory/AnalysisI.pm %%SITE_PERL%%/Bio/Factory/ApplicationFactoryI.pm %%SITE_PERL%%/Bio/Factory/DriverFactory.pm @@ -448,29 +1102,22 @@ %%SITE_PERL%%/Bio/Factory/LocationFactoryI.pm %%SITE_PERL%%/Bio/Factory/MapFactoryI.pm %%SITE_PERL%%/Bio/Factory/ObjectBuilderI.pm 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%%SITE_PERL%%/Bio/PhyloNetwork/Factory.pm +%%SITE_PERL%%/Bio/PhyloNetwork/FactoryX.pm %%SITE_PERL%%/Bio/PhyloNetwork/GraphViz.pm %%SITE_PERL%%/Bio/PhyloNetwork/RandomFactory.pm +%%SITE_PERL%%/Bio/PhyloNetwork/TreeFactory.pm %%SITE_PERL%%/Bio/PhyloNetwork/TreeFactoryMulti.pm %%SITE_PERL%%/Bio/PhyloNetwork/TreeFactoryX.pm -%%SITE_PERL%%/Bio/PhyloNetwork/TreeFactory.pm %%SITE_PERL%%/Bio/PhyloNetwork/muVector.pm -%%SITE_PERL%%/Bio/PhyloNetwork.pm -%%SITE_PERL%%/Bio/PopGen/GenotypeI.pm %%SITE_PERL%%/Bio/PopGen/Genotype.pm +%%SITE_PERL%%/Bio/PopGen/GenotypeI.pm %%SITE_PERL%%/Bio/PopGen/HtSNP.pm +%%SITE_PERL%%/Bio/PopGen/IO.pm %%SITE_PERL%%/Bio/PopGen/IO/csv.pm %%SITE_PERL%%/Bio/PopGen/IO/hapmap.pm %%SITE_PERL%%/Bio/PopGen/IO/phase.pm -%%SITE_PERL%%/Bio/PopGen/IO.pm %%SITE_PERL%%/Bio/PopGen/IO/prettybase.pm -%%SITE_PERL%%/Bio/PopGen/IndividualI.pm %%SITE_PERL%%/Bio/PopGen/Individual.pm -%%SITE_PERL%%/Bio/PopGen/MarkerI.pm +%%SITE_PERL%%/Bio/PopGen/IndividualI.pm 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%%SITE_PERL%%/Bio/Search/GenericStatistics.pm %%SITE_PERL%%/Bio/Search/HSP/BlastHSP.pm @@ -701,6 +1347,28 @@ %%SITE_PERL%%/Bio/Search/Hit/ModelHit.pm %%SITE_PERL%%/Bio/Search/Hit/PsiBlastHit.pm %%SITE_PERL%%/Bio/Search/Hit/PullHitI.pm +%%SITE_PERL%%/Bio/Search/Hit/hmmer3Hit.pm +%%SITE_PERL%%/Bio/Search/Iteration/GenericIteration.pm +%%SITE_PERL%%/Bio/Search/Iteration/IterationI.pm +%%SITE_PERL%%/Bio/Search/Processor.pm +%%SITE_PERL%%/Bio/Search/Result/BlastPullResult.pm +%%SITE_PERL%%/Bio/Search/Result/BlastResult.pm +%%SITE_PERL%%/Bio/Search/Result/CrossMatchResult.pm +%%SITE_PERL%%/Bio/Search/Result/GenericResult.pm +%%SITE_PERL%%/Bio/Search/Result/HMMERResult.pm +%%SITE_PERL%%/Bio/Search/Result/HmmpfamResult.pm +%%SITE_PERL%%/Bio/Search/Result/PullResultI.pm +%%SITE_PERL%%/Bio/Search/Result/ResultFactory.pm +%%SITE_PERL%%/Bio/Search/Result/ResultI.pm +%%SITE_PERL%%/Bio/Search/Result/WABAResult.pm +%%SITE_PERL%%/Bio/Search/Result/hmmer3Result.pm +%%SITE_PERL%%/Bio/Search/SearchUtils.pm +%%SITE_PERL%%/Bio/Search/StatisticsI.pm +%%SITE_PERL%%/Bio/Search/Tiling/MapTileUtils.pm +%%SITE_PERL%%/Bio/Search/Tiling/MapTiling.pm +%%SITE_PERL%%/Bio/Search/Tiling/TilingI.pm +%%SITE_PERL%%/Bio/SearchDist.pm +%%SITE_PERL%%/Bio/SearchIO.pm %%SITE_PERL%%/Bio/SearchIO/EventHandlerI.pm %%SITE_PERL%%/Bio/SearchIO/FastHitEventBuilder.pm %%SITE_PERL%%/Bio/SearchIO/IteratedSearchResultEventBuilder.pm @@ -726,70 +1394,77 @@ %%SITE_PERL%%/Bio/SearchIO/fasta.pm %%SITE_PERL%%/Bio/SearchIO/gmap_f9.pm %%SITE_PERL%%/Bio/SearchIO/hmmer.pm +%%SITE_PERL%%/Bio/SearchIO/hmmer2.pm +%%SITE_PERL%%/Bio/SearchIO/hmmer3.pm %%SITE_PERL%%/Bio/SearchIO/hmmer_pull.pm %%SITE_PERL%%/Bio/SearchIO/infernal.pm %%SITE_PERL%%/Bio/SearchIO/megablast.pm -%%SITE_PERL%%/Bio/SearchIO.pm %%SITE_PERL%%/Bio/SearchIO/psl.pm %%SITE_PERL%%/Bio/SearchIO/rnamotif.pm %%SITE_PERL%%/Bio/SearchIO/sim4.pm %%SITE_PERL%%/Bio/SearchIO/waba.pm %%SITE_PERL%%/Bio/SearchIO/wise.pm 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+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/liveseq/change_gene.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/longorf.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/make_primers.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/popgen/parse_calc_stats.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/quality/svgtrace.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/rev_and_trans.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/revcom_dir.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/README +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/exceptions1.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/exceptions2.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/exceptions3.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/exceptions4.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/lib/TestInterface.pm +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/root/lib/TestObject.pm +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/blast_example.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/custom_writer.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/hitwriter.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/hspwriter.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/htmlwriter.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/psiblast_features.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/psiblast_iterations.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/rawwriter.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/resultwriter.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/waba2gff.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/searchio/waba2gff3.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sirna/TAG +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sirna/rnai_finder.cgi +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/structure/structure-io.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/subsequence.cgi +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tk/gsequence.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tk/hitdisplay.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/extract_genes.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/gb_to_gff.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/gff2ps.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/parse_codeml.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/psw.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/reverse-translate.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/run_genscan.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/run_primer3.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/seq_pattern.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tools/standaloneblast.pl +%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tree/paup2phylip.pl @dirrm %%SITE_PERL%%/Bio/Align @dirrm %%SITE_PERL%%/Bio/AlignIO/Handler @dirrm %%SITE_PERL%%/Bio/AlignIO @@ -1157,14 +1944,11 @@ @dirrm %%SITE_PERL%%/Bio/Assembly/IO @dirrm %%SITE_PERL%%/Bio/Assembly/Tools @dirrm %%SITE_PERL%%/Bio/Assembly -@dirrm %%SITE_PERL%%/Bio/Biblio/IO -@dirrm %%SITE_PERL%%/Bio/Biblio @dirrm %%SITE_PERL%%/Bio/Cluster @dirrm %%SITE_PERL%%/Bio/ClusterIO @dirrm %%SITE_PERL%%/Bio/CodonUsage @dirrm %%SITE_PERL%%/Bio/Coordinate/Result @dirrm %%SITE_PERL%%/Bio/Coordinate -@dirrm %%SITE_PERL%%/Bio/DB/Biblio @dirrm %%SITE_PERL%%/Bio/DB/Expression @dirrm %%SITE_PERL%%/Bio/DB/Flat/BDB @dirrm %%SITE_PERL%%/Bio/DB/Flat @@ -1185,12 +1969,9 @@ @dirrm %%SITE_PERL%%/Bio/DB/Taxonomy @dirrm %%SITE_PERL%%/Bio/DB @dirrm %%SITE_PERL%%/Bio/Das +@dirrm %%SITE_PERL%%/Bio/Draw @dirrm %%SITE_PERL%%/Bio/Event -@dirrm %%SITE_PERL%%/Bio/Expression/FeatureGroup -@dirrm %%SITE_PERL%%/Bio/Expression/FeatureSet -@dirrm %%SITE_PERL%%/Bio/Expression @dirrm %%SITE_PERL%%/Bio/Factory -@dirrm %%SITE_PERL%%/Bio/FeatureIO @dirrm %%SITE_PERL%%/Bio/Index @dirrm %%SITE_PERL%%/Bio/LiveSeq/IO @dirrm %%SITE_PERL%%/Bio/LiveSeq @@ -1202,10 +1983,11 @@ @dirrm %%SITE_PERL%%/Bio/Matrix/PSM @dirrm %%SITE_PERL%%/Bio/Matrix @dirrm %%SITE_PERL%%/Bio/MolEvol -@dirrm %%SITE_PERL%%/Bio/OntologyIO/Handlers -@dirrm %%SITE_PERL%%/Bio/OntologyIO +@dirrm %%SITE_PERL%%/Bio/Nexml @dirrm %%SITE_PERL%%/Bio/Ontology/SimpleGOEngine @dirrm %%SITE_PERL%%/Bio/Ontology +@dirrm %%SITE_PERL%%/Bio/OntologyIO/Handlers +@dirrm %%SITE_PERL%%/Bio/OntologyIO @dirrm %%SITE_PERL%%/Bio/Phenotype/MeSH @dirrm %%SITE_PERL%%/Bio/Phenotype/OMIM @dirrm %%SITE_PERL%%/Bio/Phenotype @@ -1216,17 +1998,18 @@ @dirrm %%SITE_PERL%%/Bio/Restriction/Enzyme @dirrm %%SITE_PERL%%/Bio/Restriction/IO @dirrm %%SITE_PERL%%/Bio/Restriction -@dirrm %%SITE_PERL%%/Bio/Root/Test @dirrm %%SITE_PERL%%/Bio/Root @dirrm %%SITE_PERL%%/Bio/Search/HSP @dirrm %%SITE_PERL%%/Bio/Search/Hit -@dirrm %%SITE_PERL%%/Bio/SearchIO/Writer -@dirrm %%SITE_PERL%%/Bio/SearchIO/XML -@dirrm %%SITE_PERL%%/Bio/SearchIO @dirrm %%SITE_PERL%%/Bio/Search/Iteration @dirrm %%SITE_PERL%%/Bio/Search/Result @dirrm %%SITE_PERL%%/Bio/Search/Tiling @dirrm %%SITE_PERL%%/Bio/Search +@dirrm %%SITE_PERL%%/Bio/SearchIO/Writer +@dirrm %%SITE_PERL%%/Bio/SearchIO/XML +@dirrm %%SITE_PERL%%/Bio/SearchIO +@dirrm %%SITE_PERL%%/Bio/Seq/Meta +@dirrm %%SITE_PERL%%/Bio/Seq @dirrm %%SITE_PERL%%/Bio/SeqEvolution @dirrm %%SITE_PERL%%/Bio/SeqFeature/Gene @dirrm %%SITE_PERL%%/Bio/SeqFeature/SiRNA @@ -1236,8 +2019,6 @@ @dirrm %%SITE_PERL%%/Bio/SeqIO/game @dirrm %%SITE_PERL%%/Bio/SeqIO/tinyseq @dirrm %%SITE_PERL%%/Bio/SeqIO -@dirrm %%SITE_PERL%%/Bio/Seq/Meta -@dirrm %%SITE_PERL%%/Bio/Seq @dirrm %%SITE_PERL%%/Bio/Structure/IO @dirrm %%SITE_PERL%%/Bio/Structure/SecStr/DSSP @dirrm %%SITE_PERL%%/Bio/Structure/SecStr/STRIDE @@ -1250,11 +2031,6 @@ @dirrm %%SITE_PERL%%/Bio/Tools/Analysis/Protein @dirrm %%SITE_PERL%%/Bio/Tools/Analysis @dirrm %%SITE_PERL%%/Bio/Tools/EMBOSS -@dirrm %%SITE_PERL%%/Bio/Tools/EUtilities/Info -@dirrm %%SITE_PERL%%/Bio/Tools/EUtilities/Link -@dirrm %%SITE_PERL%%/Bio/Tools/EUtilities/Query -@dirrm %%SITE_PERL%%/Bio/Tools/EUtilities/Summary -@dirrm %%SITE_PERL%%/Bio/Tools/EUtilities @dirrm %%SITE_PERL%%/Bio/Tools/HMMER @dirrm %%SITE_PERL%%/Bio/Tools/Phylo/Molphy @dirrm %%SITE_PERL%%/Bio/Tools/Phylo/PAML @@ -1263,6 +2039,7 @@ @dirrm %%SITE_PERL%%/Bio/Tools/Prediction @dirrm %%SITE_PERL%%/Bio/Tools/Primer/Assessor @dirrm %%SITE_PERL%%/Bio/Tools/Primer +@dirrm %%SITE_PERL%%/Bio/Tools/Run/WrapperBase @dirrm %%SITE_PERL%%/Bio/Tools/Run @dirrm %%SITE_PERL%%/Bio/Tools/SeqPattern @dirrm %%SITE_PERL%%/Bio/Tools/SiRNA/Ruleset @@ -1276,3 +2053,43 @@ @dirrm %%SITE_PERL%%/Bio/TreeIO @dirrm %%SITE_PERL%%/Bio/Variation/IO @dirrm %%SITE_PERL%%/Bio/Variation +@dirrm %%DATADIR%%/models +@dirrm %%DATADIR%%/scripts/Bio-DB-GFF +@dirrm %%DATADIR%%/scripts/Bio-DB-SeqFeature-Store +@dirrm %%DATADIR%%/scripts/DB +@dirrm %%DATADIR%%/scripts/DB-HIV +@dirrm %%DATADIR%%/scripts/das +@dirrm %%DATADIR%%/scripts/index +@dirrm %%DATADIR%%/scripts/popgen +@dirrm %%DATADIR%%/scripts/searchio +@dirrm %%DATADIR%%/scripts/seq +@dirrm %%DATADIR%%/scripts/seqstats +@dirrm %%DATADIR%%/scripts/taxa +@dirrm %%DATADIR%%/scripts/tree +@dirrm %%DATADIR%%/scripts/utilities +@dirrm %%DATADIR%%/scripts +@dirrm %%DATADIR%% +%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator/bin +%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator/cgi-bin +%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator/lib +%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator/t +%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc/Deobfuscator +%%PORTDOCS%%@dirrm %%DOCSDIR%%/doc +%%PORTDOCS%%@dirrm %%DOCSDIR%% +%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/Bio-DB-GFF +%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/align +%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/cluster +%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/contributed +%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/db +%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/liveseq +%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/popgen +%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/quality +%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/root/lib +%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/root +%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/searchio +%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/sirna +%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/structure +%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/tk +%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/tools +%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%/tree +%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%% --- p5-bioperl-1.6.923.patch ends here --- >Release-Note: >Audit-Trail: >Unformatted:
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