diff options
| author | Martin Wilke <miwi@FreeBSD.org> | 2009-06-05 20:38:36 +0000 |
|---|---|---|
| committer | Martin Wilke <miwi@FreeBSD.org> | 2009-06-05 20:38:36 +0000 |
| commit | f128ddfb8e824bce7cd0ef1addba5b707e8adc66 (patch) | |
| tree | 3f59163d342879f3073e32d5466a9463002dd536 | |
| parent | Reinstate PKGNAMESUFFIX which was lost in rev. 1.6. (diff) | |
2009-05-31 biology/p5-bioperl-devel: no longer under development
2009-05-31 biology/p5-bioperl-run-devel: no longer under development
2009-06-01 net-p2p/deluge05: use net-p2p/deluge instead
2009-06-03 textproc/gmat: failed to build for a long time, no maintainer and apparently no users either
Notes
Notes:
svn path=/head/; revision=235227
30 files changed, 4 insertions, 5174 deletions
@@ -3970,3 +3970,7 @@ japanese/mplusfonts|japanese/font-mplus|2009-05-30|Renamed japanese/vlgothic|japanese/font-vlgothic|2009-05-30|Renamed japanese/shinonome|japanese/font-shinonome|2009-05-30|Renamed net/tftp-hpa|ftp/tftp-hpa|2009-05-31|Duplicate port +biology/p5-bioperl-devel||2009-06-05|Has expired: no longer under development +biology/p5-bioperl-run-devel||2009-06-05|Has expired: no longer under development +net-p2p/deluge05||2009-06-05|Has expired: use net-p2p/deluge instead +textproc/gmat||2009-06-05|Has expired: failed to build for a long time, no maintainer and apparently no users either diff --git a/biology/Makefile b/biology/Makefile index 892e117aa36c..8f120d02a7b3 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -62,9 +62,7 @@ SUBDIR += p5-Bio-Graphics SUBDIR += p5-Bio-Phylo SUBDIR += p5-bioperl - SUBDIR += p5-bioperl-devel SUBDIR += p5-bioperl-run - SUBDIR += p5-bioperl-run-devel SUBDIR += paml SUBDIR += phd2fasta SUBDIR += phrap diff --git a/biology/p5-bioperl-devel/Makefile b/biology/p5-bioperl-devel/Makefile deleted file mode 100644 index 9371a7171c6d..000000000000 --- a/biology/p5-bioperl-devel/Makefile +++ /dev/null @@ -1,1008 +0,0 @@ -# New ports collection makefile for: biology/p5-bioperl-devel -# Date created: 21 November 2005 -# Whom: Mauricio Herrera Cuadra <mauricio@arareko.net> -# -# $FreeBSD$ -# - -PORTNAME= bioperl -PORTVERSION= 1.5.2 -CATEGORIES= biology perl5 -MASTER_SITES= http://bioperl.org/DIST/ -PKGNAMEPREFIX= p5- -DISTNAME= ${PORTNAME}-${PORTVERSION}_102 - -MAINTAINER= mauricio@arareko.net -COMMENT= A collection of Perl modules for bioinformatics (developer release) - -BUILD_DEPENDS= ${LOCALBASE}/lib/perl5/${PERL_VERSION}/Text/Wrap.pm:${PORTSDIR}/lang/${PERL_PORT} \ - ${LOCALBASE}/lib/perl5/${PERL_VERSION}/${PERL_ARCH}/DB_File.pm:${PORTSDIR}/lang/${PERL_PORT} \ - ${SITE_PERL}/Bio/ASN1/EntrezGene.pm:${PORTSDIR}/biology/p5-Bio-ASN1-EntrezGene \ - ${SITE_PERL}/Class/AutoClass.pm:${PORTSDIR}/devel/p5-Class-AutoClass \ - ${SITE_PERL}/Data/Stag/ITextWriter.pm:${PORTSDIR}/devel/p5-Data-Stag \ - ${SITE_PERL}/Data/Stag/SxprWriter.pm:${PORTSDIR}/devel/p5-Data-Stag \ - ${SITE_PERL}/Data/Stag/XMLWriter.pm:${PORTSDIR}/devel/p5-Data-Stag \ - ${SITE_PERL}/GD/SVG.pm:${PORTSDIR}/graphics/p5-GD-SVG \ - ${SITE_PERL}/Graph/Directed.pm:${PORTSDIR}/math/p5-Graph \ - ${SITE_PERL}/HTTP/Request/Common.pm:${PORTSDIR}/www/p5-libwww \ - ${SITE_PERL}/IO/Scalar.pm:${PORTSDIR}/devel/p5-IO-stringy \ - ${SITE_PERL}/IO/String.pm:${PORTSDIR}/devel/p5-IO-String \ - ${SITE_PERL}/LWP/UserAgent.pm:${PORTSDIR}/www/p5-libwww \ - ${SITE_PERL}/Set/Scalar.pm:${PORTSDIR}/devel/p5-Set-Scalar \ - ${SITE_PERL}/SOAP/Lite.pm:${PORTSDIR}/net/p5-SOAP-Lite \ - ${SITE_PERL}/Spreadsheet/ParseExcel.pm:${PORTSDIR}/textproc/p5-Spreadsheet-ParseExcel \ - ${SITE_PERL}/SVG.pm:${PORTSDIR}/textproc/p5-SVG \ - ${SITE_PERL}/SVG/Graph.pm:${PORTSDIR}/graphics/p5-SVG-Graph \ - ${SITE_PERL}/Test/Harness.pm:${PORTSDIR}/devel/p5-Test-Harness \ - ${SITE_PERL}/Text/Shellwords.pm:${PORTSDIR}/textproc/p5-Text-Shellwords \ - ${SITE_PERL}/XML/DOM.pm:${PORTSDIR}/textproc/p5-XML-DOM \ - ${SITE_PERL}/XML/DOM/XPath.pm:${PORTSDIR}/textproc/p5-XML-DOM-XPath \ - ${SITE_PERL}/XML/Parser/PerlSAX.pm:${PORTSDIR}/textproc/p5-libxml \ - ${SITE_PERL}/XML/SAX.pm:${PORTSDIR}/textproc/p5-XML-SAX \ - ${SITE_PERL}/XML/SAX/Base.pm:${PORTSDIR}/textproc/p5-XML-SAX \ - ${SITE_PERL}/XML/SAX/Writer.pm:${PORTSDIR}/textproc/p5-XML-SAX-Writer \ - ${SITE_PERL}/XML/Twig.pm:${PORTSDIR}/textproc/p5-XML-Twig \ - ${SITE_PERL}/XML/Writer.pm:${PORTSDIR}/textproc/p5-XML-Writer \ - ${SITE_PERL}/${PERL_ARCH}/Ace.pm:${PORTSDIR}/biology/p5-AcePerl \ - ${SITE_PERL}/${PERL_ARCH}/Clone.pm:${PORTSDIR}/devel/p5-Clone \ - ${SITE_PERL}/${PERL_ARCH}/Convert/Binary/C.pm:${PORTSDIR}/converters/p5-Convert-Binary-C \ - ${SITE_PERL}/${PERL_ARCH}/DBD/mysql.pm:${PORTSDIR}/databases/p5-DBD-mysql \ - ${SITE_PERL}/${PERL_ARCH}/GD.pm:${PORTSDIR}/graphics/p5-GD \ - ${SITE_PERL}/${PERL_ARCH}/HTML/Entities.pm:${PORTSDIR}/www/p5-HTML-Parser \ - ${SITE_PERL}/${PERL_ARCH}/HTML/Parser.pm:${PORTSDIR}/www/p5-HTML-Parser \ - ${SITE_PERL}/${PERL_ARCH}/Storable.pm:${PORTSDIR}/devel/p5-Storable \ - ${SITE_PERL}/${PERL_ARCH}/XML/Parser.pm:${PORTSDIR}/textproc/p5-XML-Parser -RUN_DEPENDS= ${BUILD_DEPENDS} - -CONFLICTS= p5-bioperl-1.[02468]* - -LATEST_LINK= p5-bioperl-devel - -DEPRECATED= no longer under development -EXPIRATION_DATE= 2009-05-31 - -PERL_MODBUILD= YES - -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_contig_draw.pl.1 \ - bp_dbsplit.pl.1 \ - bp_embl2picture.pl.1 \ - bp_extract_feature_seq.pl.1 \ - bp_fast_load_gff.pl.1 \ - bp_fastam9_to_table.pl.1 \ - bp_feature_draw.pl.1 \ - bp_fetch.pl.1 \ - bp_filter_search.pl.1 \ - bp_flanks.pl.1 \ - bp_frend.pl.1 \ - bp_gccalc.pl.1 \ - bp_genbank2gff.pl.1 \ - bp_genbank2gff3.pl.1 \ - bp_generate_histogram.pl.1 \ - bp_glyphs1-demo.pl.1 \ - bp_glyphs2-demo.pl.1 \ - bp_heterogeneity_test.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_search_overview.pl.1 \ - bp_search2alnblocks.pl.1 \ - bp_search2BSML.pl.1 \ - bp_search2gff.pl.1 \ - bp_search2table.pl.1 \ - bp_search2tribe.pl.1 \ - bp_seq_length.pl.1 \ - bp_seqconvert.pl.1 \ - bp_seqret.pl.1 \ - bp_split_seq.pl.1 \ - bp_sreformat.pl.1 \ - bp_taxid4species.pl.1 \ - bp_taxonomy2tree.pl.1 \ - bp_translate_seq.pl.1 \ - bp_tree2pag.pl.1 \ - bp_unflatten_seq.pl.1 - -MAN3= Bio::Align::AlignI.3 \ - Bio::Align::DNAStatistics.3 \ - Bio::Align::PairwiseStatistics.3 \ - Bio::Align::ProteinStatistics.3 \ - Bio::Align::StatisticsI.3 \ - Bio::Align::Utilities.3 \ - Bio::AlignIO.3 \ - Bio::AlignIO::bl2seq.3 \ - Bio::AlignIO::clustalw.3 \ - Bio::AlignIO::emboss.3 \ - Bio::AlignIO::fasta.3 \ - Bio::AlignIO::largemultifasta.3 \ - Bio::AlignIO::maf.3 \ - Bio::AlignIO::mase.3 \ - Bio::AlignIO::mega.3 \ - Bio::AlignIO::meme.3 \ - Bio::AlignIO::metafasta.3 \ - Bio::AlignIO::msf.3 \ - Bio::AlignIO::nexus.3 \ - Bio::AlignIO::pfam.3 \ - Bio::AlignIO::phylip.3 \ - Bio::AlignIO::po.3 \ - Bio::AlignIO::prodom.3 \ - Bio::AlignIO::psi.3 \ - Bio::AlignIO::selex.3 \ - Bio::AlignIO::stockholm.3 \ - Bio::AnalysisI.3 \ - Bio::AnalysisParserI.3 \ - Bio::AnalysisResultI.3 \ - Bio::AnnotatableI.3 \ - Bio::Annotation::AnnotationFactory.3 \ - Bio::Annotation::Collection.3 \ - Bio::Annotation::Comment.3 \ - Bio::Annotation::DBLink.3 \ - Bio::Annotation::OntologyTerm.3 \ - Bio::Annotation::Reference.3 \ - Bio::Annotation::SimpleValue.3 \ - Bio::Annotation::StructuredValue.3 \ - Bio::Annotation::Target.3 \ - Bio::Annotation::TypeManager.3 \ - Bio::AnnotationCollectionI.3 \ - Bio::AnnotationI.3 \ - Bio::Assembly::Contig.3 \ - Bio::Assembly::ContigAnalysis.3 \ - Bio::Assembly::IO.3 \ - Bio::Assembly::IO::ace.3 \ - Bio::Assembly::IO::phrap.3 \ - Bio::Assembly::Scaffold.3 \ - Bio::Assembly::ScaffoldI.3 \ - Bio::Assembly::Singlet.3 \ - Bio::Biblio.3 \ - Bio::Biblio::Article.3 \ - Bio::Biblio::BiblioBase.3 \ - Bio::Biblio::Book.3 \ - Bio::Biblio::BookArticle.3 \ - Bio::Biblio::IO.3 \ - Bio::Biblio::IO::medline2ref.3 \ - Bio::Biblio::IO::medlinexml.3 \ - Bio::Biblio::IO::pubmed2ref.3 \ - Bio::Biblio::IO::pubmedxml.3 \ - Bio::Biblio::Journal.3 \ - Bio::Biblio::JournalArticle.3 \ - Bio::Biblio::MedlineArticle.3 \ - Bio::Biblio::MedlineBook.3 \ - Bio::Biblio::MedlineBookArticle.3 \ - Bio::Biblio::MedlineJournal.3 \ - Bio::Biblio::MedlineJournalArticle.3 \ - Bio::Biblio::Organisation.3 \ - Bio::Biblio::Patent.3 \ - Bio::Biblio::Person.3 \ - Bio::Biblio::Proceeding.3 \ - Bio::Biblio::Provider.3 \ - Bio::Biblio::PubmedArticle.3 \ - Bio::Biblio::PubmedBookArticle.3 \ - Bio::Biblio::PubmedJournalArticle.3 \ - Bio::Biblio::Ref.3 \ - Bio::Biblio::Service.3 \ - Bio::Biblio::TechReport.3 \ - Bio::Biblio::Thesis.3 \ - Bio::Biblio::WebResource.3 \ - Bio::Cluster::ClusterFactory.3 \ - Bio::Cluster::FamilyI.3 \ - Bio::Cluster::SequenceFamily.3 \ - Bio::Cluster::UniGene.3 \ - Bio::Cluster::UniGeneI.3 \ - Bio::ClusterI.3 \ - Bio::ClusterIO.3 \ - Bio::ClusterIO::dbsnp.3 \ - Bio::ClusterIO::unigene.3 \ - Bio::CodonUsage::IO.3 \ - Bio::CodonUsage::Table.3 \ - Bio::ConfigData.3 \ - Bio::Coordinate::Chain.3 \ - Bio::Coordinate::Collection.3 \ - Bio::Coordinate::ExtrapolatingPair.3 \ - Bio::Coordinate::GeneMapper.3 \ - Bio::Coordinate::Graph.3 \ - Bio::Coordinate::MapperI.3 \ - Bio::Coordinate::Pair.3 \ - Bio::Coordinate::Result.3 \ - Bio::Coordinate::Result::Gap.3 \ - Bio::Coordinate::Result::Match.3 \ - Bio::Coordinate::ResultI.3 \ - Bio::Coordinate::Utils.3 \ - Bio::DB::Ace.3 \ - Bio::DB::Biblio::biofetch.3 \ - Bio::DB::Biblio::eutils.3 \ - Bio::DB::Biblio::pdf.3 \ - Bio::DB::Biblio::soap.3 \ - Bio::DB::BiblioI.3 \ - Bio::DB::BioFetch.3 \ - Bio::DB::CUTG.3 \ - Bio::DB::DBFetch.3 \ - Bio::DB::EMBL.3 \ - Bio::DB::EUtilities.3 \ - Bio::DB::EUtilities::Cookie.3 \ - Bio::DB::EUtilities::ElinkData.3 \ - Bio::DB::EUtilities::efetch.3 \ - Bio::DB::EUtilities::egquery.3 \ - Bio::DB::EUtilities::einfo.3 \ - Bio::DB::EUtilities::elink.3 \ - Bio::DB::EUtilities::epost.3 \ - Bio::DB::EUtilities::esearch.3 \ - Bio::DB::EUtilities::esummary.3 \ - Bio::DB::EntrezGene.3 \ - Bio::DB::Expression.3 \ - Bio::DB::Expression::geo.3 \ - Bio::DB::Failover.3 \ - Bio::DB::Fasta.3 \ - Bio::DB::FileCache.3 \ - Bio::DB::Flat.3 \ - Bio::DB::Flat::BDB.3 \ - Bio::DB::Flat::BDB::embl.3 \ - Bio::DB::Flat::BDB::fasta.3 \ - Bio::DB::Flat::BDB::genbank.3 \ - Bio::DB::Flat::BDB::swiss.3 \ - Bio::DB::Flat::BDB::swissprot.3 \ - Bio::DB::Flat::BinarySearch.3 \ - Bio::DB::GDB.3 \ - Bio::DB::GenericWebDBI.3 \ - Bio::DB::GFF.3 \ - Bio::DB::GFF::Adaptor::ace.3 \ - Bio::DB::GFF::Adaptor::berkeleydb.3 \ - Bio::DB::GFF::Adaptor::berkeleydb::iterator.3 \ - Bio::DB::GFF::Adaptor::biofetch.3 \ - Bio::DB::GFF::Adaptor::biofetch_oracle.3 \ - Bio::DB::GFF::Adaptor::dbi.3 \ - Bio::DB::GFF::Adaptor::dbi::caching_handle.3 \ - Bio::DB::GFF::Adaptor::dbi::iterator.3 \ - Bio::DB::GFF::Adaptor::dbi::mysql.3 \ - Bio::DB::GFF::Adaptor::dbi::mysqlace.3 \ - Bio::DB::GFF::Adaptor::dbi::mysqlcmap.3 \ - Bio::DB::GFF::Adaptor::dbi::mysqlopt.3 \ - Bio::DB::GFF::Adaptor::dbi::oracle.3 \ - Bio::DB::GFF::Adaptor::dbi::oracleace.3 \ - Bio::DB::GFF::Adaptor::dbi::pg.3 \ - Bio::DB::GFF::Adaptor::dbi::pg_fts.3 \ - Bio::DB::GFF::Adaptor::memory.3 \ - Bio::DB::GFF::Adaptor::memory::feature_serializer.3 \ - Bio::DB::GFF::Adaptor::memory::iterator.3 \ - Bio::DB::GFF::Aggregator.3 \ - Bio::DB::GFF::Aggregator::alignment.3 \ - Bio::DB::GFF::Aggregator::clone.3 \ - Bio::DB::GFF::Aggregator::coding.3 \ - Bio::DB::GFF::Aggregator::match.3 \ - Bio::DB::GFF::Aggregator::none.3 \ - Bio::DB::GFF::Aggregator::processed_transcript.3 \ - Bio::DB::GFF::Aggregator::so_transcript.3 \ - Bio::DB::GFF::Aggregator::transcript.3 \ - Bio::DB::GFF::Aggregator::ucsc_acembly.3 \ - Bio::DB::GFF::Aggregator::ucsc_ensgene.3 \ - Bio::DB::GFF::Aggregator::ucsc_genscan.3 \ - Bio::DB::GFF::Aggregator::ucsc_refgene.3 \ - Bio::DB::GFF::Aggregator::ucsc_sanger22.3 \ - Bio::DB::GFF::Aggregator::ucsc_sanger22pseudo.3 \ - Bio::DB::GFF::Aggregator::ucsc_softberry.3 \ - Bio::DB::GFF::Aggregator::ucsc_twinscan.3 \ - Bio::DB::GFF::Aggregator::ucsc_unigene.3 \ - Bio::DB::GFF::Featname.3 \ - Bio::DB::GFF::Feature.3 \ - Bio::DB::GFF::Homol.3 \ - Bio::DB::GFF::RelSegment.3 \ - Bio::DB::GFF::Segment.3 \ - Bio::DB::GFF::Typename.3 \ - Bio::DB::GFF::Util::Binning.3 \ - Bio::DB::GFF::Util::Rearrange.3 \ - Bio::DB::GenBank.3 \ - Bio::DB::GenPept.3 \ - Bio::DB::InMemoryCache.3 \ - Bio::DB::LocationI.3 \ - Bio::DB::MeSH.3 \ - Bio::DB::NCBIHelper.3 \ - Bio::DB::Query::GenBank.3 \ - Bio::DB::Query::WebQuery.3 \ - Bio::DB::QueryI.3 \ - Bio::DB::RandomAccessI.3 \ - Bio::DB::ReferenceI.3 \ - Bio::DB::RefSeq.3 \ - Bio::DB::Registry.3 \ - Bio::DB::SeqFeature.3 \ - Bio::DB::SeqFeature::NormalizedFeature.3 \ - Bio::DB::SeqFeature::NormalizedFeatureI.3 \ - Bio::DB::SeqFeature::NormalizedTableFeatureI.3 \ - Bio::DB::SeqFeature::Segment.3 \ - Bio::DB::SeqFeature::Store.3 \ - Bio::DB::SeqFeature::Store::DBI::Iterator.3 \ - Bio::DB::SeqFeature::Store::DBI::mysql.3 \ - Bio::DB::SeqFeature::Store::GFF3Loader.3 \ - Bio::DB::SeqFeature::Store::bdb.3 \ - Bio::DB::SeqFeature::Store::berkeleydb.3 \ - Bio::DB::SeqFeature::Store::memory.3 \ - Bio::DB::SeqHound.3 \ - Bio::DB::SeqI.3 \ - Bio::DB::SeqVersion.3 \ - Bio::DB::SeqVersion::gi.3 \ - Bio::DB::SwissProt.3 \ - Bio::DB::Taxonomy.3 \ - Bio::DB::Taxonomy::entrez.3 \ - Bio::DB::Taxonomy::flatfile.3 \ - Bio::DB::Taxonomy::list.3 \ - Bio::DB::Universal.3 \ - Bio::DB::UpdateableSeqI.3 \ - Bio::DB::WebDBSeqI.3 \ - Bio::DB::XEMBL.3 \ - Bio::DB::XEMBLService.3 \ - Bio::DBLinkContainerI.3 \ - Bio::Das::FeatureTypeI.3 \ - Bio::Das::SegmentI.3 \ - Bio::DasI.3 \ - Bio::DescribableI.3 \ - Bio::Event::EventGeneratorI.3 \ - Bio::Event::EventHandlerI.3 \ - Bio::Expression::Contact.3 \ - Bio::Expression::DataSet.3 \ - Bio::Expression::FeatureGroup.3 \ - Bio::Expression::FeatureGroup::FeatureGroupMas50.3 \ - Bio::Expression::FeatureI.3 \ - Bio::Expression::FeatureSet::FeatureSetMas50.3 \ - Bio::Expression::Platform.3 \ - Bio::Expression::ProbeI.3 \ - Bio::Expression::Sample.3 \ - Bio::Factory::AnalysisI.3 \ - Bio::Factory::ApplicationFactoryI.3 \ - Bio::Factory::DriverFactory.3 \ - Bio::Factory::FTLocationFactory.3 \ - Bio::Factory::HitFactoryI.3 \ - Bio::Factory::LocationFactoryI.3 \ - Bio::Factory::MapFactoryI.3 \ - Bio::Factory::ObjectBuilderI.3 \ - Bio::Factory::ObjectFactory.3 \ - Bio::Factory::ObjectFactoryI.3 \ - Bio::Factory::ResultFactoryI.3 \ - Bio::Factory::SeqAnalysisParserFactory.3 \ - Bio::Factory::SeqAnalysisParserFactoryI.3 \ - Bio::Factory::SequenceFactoryI.3 \ - Bio::Factory::SequenceProcessorI.3 \ - Bio::Factory::SequenceStreamI.3 \ - Bio::Factory::TreeFactoryI.3 \ - Bio::FeatureHolderI.3 \ - Bio::FeatureIO.3 \ - Bio::FeatureIO::bed.3 \ - Bio::FeatureIO::gff.3 \ - Bio::FeatureIO::gtf.3 \ - Bio::FeatureIO::interpro.3 \ - Bio::FeatureIO::ptt.3 \ - Bio::Graph::Edge.3 \ - Bio::Graph::IO.3 \ - Bio::Graph::IO::dip.3 \ - Bio::Graph::IO::psi_xml.3 \ - Bio::Graph::ProteinGraph.3 \ - Bio::Graph::SimpleGraph.3 \ - Bio::Graph::SimpleGraph::Traversal.3 \ - Bio::Graphics.3 \ - Bio::Graphics::ConfiguratorI.3 \ - Bio::Graphics::Feature.3 \ - Bio::Graphics::FeatureBase.3 \ - Bio::Graphics::FeatureFile.3 \ - Bio::Graphics::FeatureFile::Iterator.3 \ - Bio::Graphics::Glyph.3 \ - Bio::Graphics::Glyph::Factory.3 \ - Bio::Graphics::Glyph::alignment.3 \ - Bio::Graphics::Glyph::anchored_arrow.3 \ - Bio::Graphics::Glyph::arrow.3 \ - Bio::Graphics::Glyph::box.3 \ - Bio::Graphics::Glyph::broken_line.3 \ - Bio::Graphics::Glyph::cds.3 \ - Bio::Graphics::Glyph::christmas_arrow.3 \ - Bio::Graphics::Glyph::crossbox.3 \ - Bio::Graphics::Glyph::dashed_line.3 \ - Bio::Graphics::Glyph::diamond.3 \ - Bio::Graphics::Glyph::dna.3 \ - Bio::Graphics::Glyph::dot.3 \ - Bio::Graphics::Glyph::dumbbell.3 \ - Bio::Graphics::Glyph::ellipse.3 \ - Bio::Graphics::Glyph::ex.3 \ - Bio::Graphics::Glyph::extending_arrow.3 \ - Bio::Graphics::Glyph::flag.3 \ - Bio::Graphics::Glyph::gene.3 \ - Bio::Graphics::Glyph::generic.3 \ - Bio::Graphics::Glyph::graded_segments.3 \ - Bio::Graphics::Glyph::group.3 \ - Bio::Graphics::Glyph::heterogeneous_segments.3 \ - Bio::Graphics::Glyph::image.3 \ - Bio::Graphics::Glyph::lightning.3 \ - Bio::Graphics::Glyph::line.3 \ - Bio::Graphics::Glyph::merge_parts.3 \ - Bio::Graphics::Glyph::merged_alignment.3 \ - Bio::Graphics::Glyph::minmax.3 \ - Bio::Graphics::Glyph::oval.3 \ - Bio::Graphics::Glyph::pentagram.3 \ - Bio::Graphics::Glyph::pinsertion.3 \ - Bio::Graphics::Glyph::primers.3 \ - Bio::Graphics::Glyph::processed_transcript.3 \ - Bio::Graphics::Glyph::protein.3 \ - Bio::Graphics::Glyph::ragged_ends.3 \ - Bio::Graphics::Glyph::redgreen_box.3 \ - Bio::Graphics::Glyph::redgreen_segment.3 \ - Bio::Graphics::Glyph::repeating_shape.3 \ - Bio::Graphics::Glyph::rndrect.3 \ - Bio::Graphics::Glyph::ruler_arrow.3 \ - Bio::Graphics::Glyph::saw_teeth.3 \ - Bio::Graphics::Glyph::segmented_keyglyph.3 \ - Bio::Graphics::Glyph::segments.3 \ - Bio::Graphics::Glyph::so_transcript.3 \ - Bio::Graphics::Glyph::span.3 \ - Bio::Graphics::Glyph::splice_site.3 \ - Bio::Graphics::Glyph::text_in_box.3 \ - Bio::Graphics::Glyph::three_letters.3 \ - Bio::Graphics::Glyph::tic_tac_toe.3 \ - Bio::Graphics::Glyph::toomany.3 \ - Bio::Graphics::Glyph::track.3 \ - Bio::Graphics::Glyph::transcript.3 \ - Bio::Graphics::Glyph::transcript2.3 \ - Bio::Graphics::Glyph::translation.3 \ - Bio::Graphics::Glyph::triangle.3 \ - Bio::Graphics::Glyph::two_bolts.3 \ - Bio::Graphics::Glyph::wave.3 \ - Bio::Graphics::Glyph::weighted_arrow.3 \ - Bio::Graphics::Glyph::whiskerplot.3 \ - Bio::Graphics::Glyph::xyplot.3 \ - Bio::Graphics::Panel.3 \ - Bio::Graphics::Pictogram.3 \ - Bio::Graphics::RendererI.3 \ - Bio::Graphics::Util.3 \ - Bio::IdCollectionI.3 \ - Bio::IdentifiableI.3 \ - Bio::Index::Abstract.3 \ - Bio::Index::AbstractSeq.3 \ - Bio::Index::Blast.3 \ - Bio::Index::EMBL.3 \ - Bio::Index::Fasta.3 \ - Bio::Index::Fastq.3 \ - Bio::Index::GenBank.3 \ - Bio::Index::Hmmer.3 \ - Bio::Index::Qual.3 \ - Bio::Index::SwissPfam.3 \ - Bio::Index::Swissprot.3 \ - Bio::LiveSeq::AARange.3 \ - Bio::LiveSeq::Chain.3 \ - Bio::LiveSeq::ChainI.3 \ - Bio::LiveSeq::DNA.3 \ - Bio::LiveSeq::Exon.3 \ - Bio::LiveSeq::Gene.3 \ - Bio::LiveSeq::IO::BioPerl.3 \ - Bio::LiveSeq::IO::Loader.3 \ - Bio::LiveSeq::Intron.3 \ - Bio::LiveSeq::Mutation.3 \ - Bio::LiveSeq::Mutator.3 \ - Bio::LiveSeq::Prim_Transcript.3 \ - Bio::LiveSeq::Range.3 \ - Bio::LiveSeq::Repeat_Region.3 \ - Bio::LiveSeq::Repeat_Unit.3 \ - Bio::LiveSeq::SeqI.3 \ - Bio::LiveSeq::Transcript.3 \ - Bio::LiveSeq::Translation.3 \ - Bio::LocatableSeq.3 \ - Bio::Location::Atomic.3 \ - Bio::Location::AvWithinCoordPolicy.3 \ - Bio::Location::CoordinatePolicyI.3 \ - Bio::Location::Fuzzy.3 \ - Bio::Location::FuzzyLocationI.3 \ - Bio::Location::NarrowestCoordPolicy.3 \ - Bio::Location::Simple.3 \ - Bio::Location::Split.3 \ - Bio::Location::SplitLocationI.3 \ - Bio::Location::WidestCoordPolicy.3 \ - Bio::LocationI.3 \ - Bio::Map::Clone.3 \ - Bio::Map::Contig.3 \ - Bio::Map::CytoMap.3 \ - Bio::Map::CytoMarker.3 \ - Bio::Map::CytoPosition.3 \ - Bio::Map::EntityI.3 \ - Bio::Map::FPCMarker.3 \ - Bio::Map::LinkageMap.3 \ - Bio::Map::LinkagePosition.3 \ - Bio::Map::MapI.3 \ - Bio::Map::Mappable.3 \ - Bio::Map::MappableI.3 \ - Bio::Map::Marker.3 \ - Bio::Map::MarkerI.3 \ - Bio::Map::Microsatellite.3 \ - Bio::Map::OrderedPosition.3 \ - Bio::Map::OrderedPositionWithDistance.3 \ - Bio::Map::PositionHandler.3 \ - Bio::Map::PositionHandlerI.3 \ - Bio::Map::Physical.3 \ - Bio::Map::Position.3 \ - Bio::Map::PositionI.3 \ - Bio::Map::Relative.3 \ - Bio::Map::RelativeI.3 \ - Bio::Map::SimpleMap.3 \ - Bio::MapIO.3 \ - Bio::MapIO::fpc.3 \ - Bio::MapIO::mapmaker.3 \ - Bio::Matrix::Generic.3 \ - Bio::Matrix::IO.3 \ - Bio::Matrix::IO::phylip.3 \ - Bio::Matrix::IO::scoring.3 \ - Bio::Matrix::MatrixI.3 \ - Bio::Matrix::PSM::IO.3 \ - Bio::Matrix::PSM::IO::mast.3 \ - Bio::Matrix::PSM::IO::masta.3 \ - Bio::Matrix::PSM::IO::meme.3 \ - Bio::Matrix::PSM::IO::psiblast.3 \ - Bio::Matrix::PSM::IO::transfac.3 \ - Bio::Matrix::PSM::InstanceSite.3 \ - Bio::Matrix::PSM::InstanceSiteI.3 \ - Bio::Matrix::PSM::ProtMatrix.3 \ - Bio::Matrix::PSM::ProtPsm.3 \ - Bio::Matrix::PSM::Psm.3 \ - Bio::Matrix::PSM::PsmHeader.3 \ - Bio::Matrix::PSM::PsmHeaderI.3 \ - Bio::Matrix::PSM::PsmI.3 \ - Bio::Matrix::PSM::SiteMatrix.3 \ - Bio::Matrix::PSM::SiteMatrixI.3 \ - Bio::Matrix::PhylipDist.3 \ - Bio::Matrix::Scoring.3 \ - Bio::Ontology::DocumentRegistry.3 \ - Bio::Ontology::GOterm.3 \ - Bio::Ontology::InterProTerm.3 \ - Bio::Ontology::OBOEngine.3 \ - Bio::Ontology::OBOterm.3 \ - Bio::Ontology::Ontology.3 \ - Bio::Ontology::OntologyEngineI.3 \ - Bio::Ontology::OntologyI.3 \ - Bio::OntologyIO::obo.3 \ - Bio::Ontology::OntologyStore.3 \ - Bio::Ontology::Path.3 \ - Bio::Ontology::PathI.3 \ - Bio::Ontology::Relationship.3 \ - Bio::Ontology::RelationshipFactory.3 \ - Bio::Ontology::RelationshipI.3 \ - Bio::Ontology::RelationshipType.3 \ - Bio::Ontology::SimpleGOEngine.3 \ - Bio::Ontology::SimpleGOEngine::GraphAdaptor.3 \ - Bio::Ontology::SimpleGOEngine::GraphAdaptor02.3 \ - Bio::Ontology::SimpleOntologyEngine.3 \ - Bio::Ontology::Term.3 \ - Bio::Ontology::TermFactory.3 \ - Bio::Ontology::TermI.3 \ - Bio::OntologyIO.3 \ - Bio::OntologyIO::Handlers::BaseSAXHandler.3 \ - Bio::OntologyIO::Handlers::InterProHandler.3 \ - Bio::OntologyIO::Handlers::InterPro_BioSQL_Handler.3 \ - Bio::OntologyIO::InterProParser.3 \ - Bio::OntologyIO::dagflat.3 \ - Bio::OntologyIO::goflat.3 \ - Bio::OntologyIO::simplehierarchy.3 \ - Bio::OntologyIO::soflat.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::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::withrefm.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::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::FastaHSP.3 \ - Bio::Search::HSP::GenericHSP.3 \ - Bio::Search::HSP::HMMERHSP.3 \ - Bio::Search::HSP::HmmpfamHSP.3 \ - Bio::Search::HSP::HSPFactory.3 \ - Bio::Search::HSP::HSPI.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::Fasta.3 \ - Bio::Search::Hit::GenericHit.3 \ - Bio::Search::Hit::HmmpfamHit.3 \ - Bio::Search::Hit::HMMERHit.3 \ - Bio::Search::Hit::HitFactory.3 \ - Bio::Search::Hit::HitI.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::BlastResult.3 \ - Bio::Search::Result::GenericResult.3 \ - Bio::Search::Result::HmmpfamResult.3 \ - Bio::Search::Result::HMMERResult.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::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::axt.3 \ - Bio::SearchIO::blast.3 \ - Bio::SearchIO::blasttable.3 \ - Bio::SearchIO::blastxml.3 \ - Bio::SearchIO::exonerate.3 \ - Bio::SearchIO::fasta.3 \ - Bio::SearchIO::hmmer.3 \ - Bio::SearchIO::hmmer_pull.3 \ - Bio::SearchIO::megablast.3 \ - Bio::SearchIO::psl.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::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::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::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::entrezgene.3 \ - Bio::SeqIO::excel.3 \ - Bio::SeqIO::exp.3 \ - Bio::SeqIO::fasta.3 \ - Bio::SeqIO::fastq.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::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::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::BPbl2seq.3 \ - Bio::Tools::BPlite.3 \ - Bio::Tools::BPlite::HSP.3 \ - Bio::Tools::BPlite::Iteration.3 \ - Bio::Tools::BPlite::Sbjct.3 \ - Bio::Tools::BPpsilite.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::ESTScan.3 \ - Bio::Tools::Eponine.3 \ - Bio::Tools::Est2Genome.3 \ - Bio::Tools::ERPIN.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::HMM.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::Lucy.3 \ - Bio::Tools::MZEF.3 \ - Bio::Tools::OddCodes.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::Pseudowise.3 \ - Bio::Tools::QRNA.3 \ - Bio::Tools::RandomDistFunctions.3 \ - Bio::Tools::RepeatMasker.3 \ - Bio::Tools::RestrictionEnzyme.3 \ - Bio::Tools::RNAMotif.3 \ - Bio::Tools::Run::GenericParameters.3 \ - Bio::Tools::Run::ParametersI.3 \ - Bio::Tools::Run::RemoteBlast.3 \ - Bio::Tools::Run::StandAloneBlast.3 \ - Bio::Tools::Run::WrapperBase.3 \ - Bio::Tools::Seg.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::Sim4::Exon.3 \ - Bio::Tools::Sim4::Results.3 \ - Bio::Tools::Spidey::Exon.3 \ - Bio::Tools::Spidey::Results.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::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::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 - -.include <bsd.port.pre.mk> - -.if ${PERL_LEVEL} < 500800 -BUILD_DEPENDS+= ${SITE_PERL}/File/Temp.pm:${PORTSDIR}/devel/p5-File-Temp -.if ${PERL_LEVEL} < 500600 -IGNORE= requires Perl 5.6 or better -.endif -.endif - -# now install all extra stuff (docs, examples, scripts, models) -post-install: - ${MKDIR} ${DATADIR} - ${CP} -R ${WRKSRC}/scripts ${WRKSRC}/models ${DATADIR} -.if !defined(NOPORTEXAMPLES) - ${MKDIR} ${EXAMPLESDIR} - ${CP} -R ${WRKSRC}/examples/* ${EXAMPLESDIR} -.endif -.if !defined(NOPORTDOCS) - ${MKDIR} ${DOCSDIR} -.for doc in AUTHORS BUGS Changes DEPENDENCIES DEPRECATED INSTALL LICENSE PLATFORMS README - ${INSTALL_MAN} ${WRKSRC}/${doc} ${DOCSDIR} -.endfor - ${CP} -R ${WRKSRC}/doc ${DOCSDIR} -.endif - -.include <bsd.port.post.mk> diff --git a/biology/p5-bioperl-devel/distinfo b/biology/p5-bioperl-devel/distinfo deleted file mode 100644 index 05e52069e19b..000000000000 --- a/biology/p5-bioperl-devel/distinfo +++ /dev/null @@ -1,3 +0,0 @@ -MD5 (bioperl-1.5.2_102.tar.gz) = 4890481c5beb33e129b65b922fb0c126 -SHA256 (bioperl-1.5.2_102.tar.gz) = 277c74c785afc05ad1d9dbe938677639c33130487d15bdc4a7a10e033137bada -SIZE (bioperl-1.5.2_102.tar.gz) = 5919092 diff --git a/biology/p5-bioperl-devel/files/patch-Build.PL b/biology/p5-bioperl-devel/files/patch-Build.PL deleted file mode 100644 index 58442ee46006..000000000000 --- a/biology/p5-bioperl-devel/files/patch-Build.PL +++ /dev/null @@ -1,19 +0,0 @@ ---- Build.PL.orig Wed Feb 14 05:37:47 2007 -+++ Build.PL Sun Jun 15 02:24:07 2008 -@@ -32,7 +32,6 @@ - 'Test::More' => 0, - 'Module::Build' => 0.2805, - 'Test::Harness' => 2.62, -- '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', -@@ -174,7 +173,7 @@ - } - - sub prompt_for_biodbgff { -- my $proceed = $build->y_n("Do you want to run the BioDBGFF live database tests? y/n", 'n'); -+ my $proceed = undef; # $build->y_n("Do you want to run the BioDBGFF live database tests? y/n", 'n'); - - if ($proceed) { - my @driver_choices; diff --git a/biology/p5-bioperl-devel/files/patch-ModuleBuildBioperl.pm b/biology/p5-bioperl-devel/files/patch-ModuleBuildBioperl.pm deleted file mode 100644 index 5f627035c3f3..000000000000 --- a/biology/p5-bioperl-devel/files/patch-ModuleBuildBioperl.pm +++ /dev/null @@ -1,20 +0,0 @@ ---- ModuleBuildBioperl.pm.orig 2007-02-14 05:37:47.000000000 -0600 -+++ ModuleBuildBioperl.pm 2008-10-17 23:16:52.000000000 -0500 -@@ -93,7 +93,7 @@ - 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 $prompt = $self->prompt($question, 'a'); -+ my $prompt = 'a'; # $self->prompt($question, 'a'); - - if ($prompt =~ /^[aA]/) { - $self->log_info(" - will install all scripts\n"); -@@ -328,7 +328,7 @@ - - $status->{message} .= "\n (wanted for $why, used by $by_what)"; - -- my $installed = $self->install_optional($modname, $preferred_version, $status->{message}); -+ my $installed = 'skip'; # $self->install_optional($modname, $preferred_version, $status->{message}); - next if $installed eq 'ok'; - $status->{message} = $installed unless $installed eq 'skip'; - } diff --git a/biology/p5-bioperl-devel/pkg-descr b/biology/p5-bioperl-devel/pkg-descr deleted file mode 100644 index 6ea2aedf8a8b..000000000000 --- a/biology/p5-bioperl-devel/pkg-descr +++ /dev/null @@ -1,11 +0,0 @@ -The Bioperl Project is an international association of developers of open -source Perl tools for bioinformatics, genomics and life science research. - -Bioperl is a collection of object-oriented Perl modules created by the -Bioperl Project. It forms the basis of a large number of bioinformatics and -genomics applications. - -(For an interesting aside on "How Perl saved the Human Genome Project", see -http://bioperl.org/GetStarted/tpj_ls_bio.html) - -WWW: http://bioperl.org/ diff --git a/biology/p5-bioperl-devel/pkg-plist b/biology/p5-bioperl-devel/pkg-plist deleted file mode 100644 index ef4214006d49..000000000000 --- a/biology/p5-bioperl-devel/pkg-plist +++ /dev/null @@ -1,1272 +0,0 @@ -bin/bp_sreformat.pl -bin/bp_contig_draw.pl -bin/bp_tree2pag.pl -bin/bp_meta_gff.pl -bin/bp_flanks.pl -bin/bp_heterogeneity_test.pl -bin/bp_feature_draw.pl -bin/bp_biogetseq.pl -bin/bp_genbank2gff.pl -bin/bp_seqfeature_load.pl -bin/bp_seq_length.pl -bin/bp_frend.pl -bin/bp_fastam9_to_table.pl -bin/bp_taxid4species.pl -bin/bp_glyphs1-demo.pl -bin/bp_blast2tree.pl -bin/bp_gccalc.pl -bin/bp_seqret.pl -bin/bp_query_entrez_taxa.pl -bin/bp_glyphs2-demo.pl -bin/bp_search2alnblocks.pl -bin/bp_taxonomy2tree.pl -bin/bp_mask_by_search.pl -bin/bp_aacomp.pl -bin/bp_composite_LD.pl -bin/bp_biblio.pl -bin/bp_process_wormbase.pl -bin/bp_embl2picture.pl -bin/bp_local_taxonomydb_query.pl -bin/bp_genbank2gff3.pl -bin/bp_search2BSML.pl -bin/bp_seqconvert.pl -bin/bp_parse_hmmsearch.pl -bin/bp_nexus2nh.pl -bin/bp_nrdb.pl -bin/bp_split_seq.pl -bin/bp_filter_search.pl -bin/bp_generate_histogram.pl -bin/bp_load_gff.pl -bin/bp_fetch.pl -bin/bp_mutate.pl -bin/bp_process_sgd.pl -bin/bp_index.pl -bin/bp_dbsplit.pl -bin/bp_oligo_count.pl -bin/bp_process_gadfly.pl -bin/bp_hmmer_to_table.pl -bin/bp_bulk_load_gff.pl -bin/bp_biofetch_genbank_proxy.pl -bin/bp_extract_feature_seq.pl -bin/bp_search2gff.pl -bin/bp_unflatten_seq.pl -bin/bp_make_mrna_protein.pl -bin/bp_mrtrans.pl -bin/bp_search2tribe.pl -bin/bp_bioflat_index.pl -bin/bp_pairwise_kaks.pl -bin/bp_fast_load_gff.pl -bin/bp_chaos_plot.pl -bin/bp_classify_hits_kingdom.pl -bin/bp_remote_blast.pl -bin/bp_search2table.pl -bin/bp_translate_seq.pl -bin/bp_search_overview.pl 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Bio::Tools::Run::PiseApplication::sampleseqs.3 \ - Bio::Tools::Run::PiseApplication::saps.3 \ - Bio::Tools::Run::PiseApplication::satellites.3 \ - Bio::Tools::Run::PiseApplication::scan_for_matches.3 \ - Bio::Tools::Run::PiseApplication::scope.3 \ - Bio::Tools::Run::PiseApplication::scopparse.3 \ - Bio::Tools::Run::PiseApplication::seqboot.3 \ - Bio::Tools::Run::PiseApplication::seqgen.3 \ - Bio::Tools::Run::PiseApplication::seqmatchall.3 \ - Bio::Tools::Run::PiseApplication::seqsblast.3 \ - Bio::Tools::Run::PiseApplication::seqstat.3 \ - Bio::Tools::Run::PiseApplication::showalign.3 \ - Bio::Tools::Run::PiseApplication::showfeat.3 \ - Bio::Tools::Run::PiseApplication::showorf.3 \ - Bio::Tools::Run::PiseApplication::showseq.3 \ - Bio::Tools::Run::PiseApplication::shuffleseq.3 \ - Bio::Tools::Run::PiseApplication::sigcleave.3 \ - Bio::Tools::Run::PiseApplication::siggen.3 \ - Bio::Tools::Run::PiseApplication::sigscan.3 \ - Bio::Tools::Run::PiseApplication::silent.3 \ - Bio::Tools::Run::PiseApplication::sirna.3 \ - Bio::Tools::Run::PiseApplication::splitter.3 \ - Bio::Tools::Run::PiseApplication::sreformat.3 \ - Bio::Tools::Run::PiseApplication::stretcher.3 \ - Bio::Tools::Run::PiseApplication::stride.3 \ - Bio::Tools::Run::PiseApplication::stssearch.3 \ - Bio::Tools::Run::PiseApplication::supermatcher.3 \ - Bio::Tools::Run::PiseApplication::syco.3 \ - Bio::Tools::Run::PiseApplication::tacg.3 \ - Bio::Tools::Run::PiseApplication::tfscan.3 \ - Bio::Tools::Run::PiseApplication::tipdate.3 \ - Bio::Tools::Run::PiseApplication::tmap.3 \ - Bio::Tools::Run::PiseApplication::toppred.3 \ - Bio::Tools::Run::PiseApplication::tranalign.3 \ - Bio::Tools::Run::PiseApplication::transeq.3 \ - Bio::Tools::Run::PiseApplication::treealign.3 \ - Bio::Tools::Run::PiseApplication::trimest.3 \ - Bio::Tools::Run::PiseApplication::trimseq.3 \ - Bio::Tools::Run::PiseApplication::trnascan.3 \ - Bio::Tools::Run::PiseApplication::twofeat.3 \ - Bio::Tools::Run::PiseApplication::unroot.3 \ - Bio::Tools::Run::PiseApplication::vectorstrip.3 \ - Bio::Tools::Run::PiseApplication::water.3 \ - Bio::Tools::Run::PiseApplication::weighbor.3 \ - Bio::Tools::Run::PiseApplication::whichdb.3 \ - Bio::Tools::Run::PiseApplication::wise2.3 \ - Bio::Tools::Run::PiseApplication::wobble.3 \ - Bio::Tools::Run::PiseApplication::wordcount.3 \ - Bio::Tools::Run::PiseApplication::wordmatch.3 \ - Bio::Tools::Run::PiseApplication::wublast2.3 \ - Bio::Tools::Run::PiseApplication::xblast.3 \ - Bio::Tools::Run::PiseApplication::xpound.3 \ - Bio::Tools::Run::PiseJob.3 \ - Bio::Tools::Run::PiseJobParser.3 \ - Bio::Tools::Run::PiseWorkflow.3 \ - Bio::Tools::Run::Primate.3 \ - Bio::Tools::Run::Primer3.3 \ - Bio::Tools::Run::Prints.3 \ - Bio::Tools::Run::Profile.3 \ - Bio::Tools::Run::Promoterwise.3 \ - Bio::Tools::Run::Pseudowise.3 \ - Bio::Tools::Run::RepeatMasker.3 \ - Bio::Tools::Run::Seg.3 \ - Bio::Tools::Run::Signalp.3 \ - Bio::Tools::Run::Tmhmm.3 \ - Bio::Tools::Run::TribeMCL.3 \ - Bio::Tools::Run::Vista.3 - -# now install all extra stuff (docs, examples, scripts) -post-install: - ${MKDIR} ${DATADIR} - @${CP} -Rv ${WRKSRC}/scripts ${DATADIR} - ${MKDIR} ${EXAMPLESDIR} - @${CP} -Rv ${WRKSRC}/examples/* ${EXAMPLESDIR} -.if !defined(NOPORTDOCS) - ${MKDIR} ${DOCSDIR} -.for doc in AUTHORS Changes INSTALL.PROGRAMS README - ${INSTALL_DATA} ${WRKSRC}/${doc} ${DOCSDIR} -.endfor -.endif - -.include <bsd.port.mk> diff --git a/biology/p5-bioperl-run-devel/distinfo b/biology/p5-bioperl-run-devel/distinfo deleted file mode 100644 index e20711cc19d2..000000000000 --- a/biology/p5-bioperl-run-devel/distinfo +++ /dev/null @@ -1,3 +0,0 @@ -MD5 (bioperl-run-1.5.1.tar.gz) = dbfce41fa5d86dab5fd1d6af4196c646 -SHA256 (bioperl-run-1.5.1.tar.gz) = d9e1f5bdff5541376cab1c8b7e8db9bedbbb7b6f76b965d55dc20122a98f93e8 -SIZE (bioperl-run-1.5.1.tar.gz) = 864369 diff --git a/biology/p5-bioperl-run-devel/pkg-descr b/biology/p5-bioperl-run-devel/pkg-descr deleted file mode 100644 index e6b90ec6ac9f..000000000000 --- a/biology/p5-bioperl-run-devel/pkg-descr +++ /dev/null @@ -1,5 +0,0 @@ -Bioperl-run contain modules that provides a PERL interface to various -bioinformatics applications. This allows various applications to be used -with common Bioperl objects. - -WWW: http://bioperl.org/ diff --git a/biology/p5-bioperl-run-devel/pkg-plist b/biology/p5-bioperl-run-devel/pkg-plist deleted file mode 100644 index f3d3e2196c37..000000000000 --- a/biology/p5-bioperl-run-devel/pkg-plist +++ /dev/null @@ -1,383 +0,0 @@ -%%SITE_PERL%%/Bio/Factory/EMBOSS.pm -%%SITE_PERL%%/Bio/Installer/Clustalw.pm -%%SITE_PERL%%/Bio/Installer/EMBOSS.pm -%%SITE_PERL%%/Bio/Installer/Generic.pm -%%SITE_PERL%%/Bio/Installer/PAML.pm -%%SITE_PERL%%/Bio/Installer/Probcons.pm -%%SITE_PERL%%/Bio/Installer/TCoffee.pm -%%SITE_PERL%%/Bio/Tools/Run/AbstractRunner.pm -%%SITE_PERL%%/Bio/Tools/Run/Alignment/Blat.pm -%%SITE_PERL%%/Bio/Tools/Run/Alignment/Clustalw.pm -%%SITE_PERL%%/Bio/Tools/Run/Alignment/DBA.pm -%%SITE_PERL%%/Bio/Tools/Run/Alignment/Exonerate.pm -%%SITE_PERL%%/Bio/Tools/Run/Alignment/Lagan.pm -%%SITE_PERL%%/Bio/Tools/Run/Alignment/MAFFT.pm -%%SITE_PERL%%/Bio/Tools/Run/Alignment/Muscle.pm 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-%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/sigcleave.pm -%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/siggen.pm -%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/sigscan.pm -%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/silent.pm -%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/sirna.pm -%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/splitter.pm -%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/sreformat.pm -%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/stretcher.pm -%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/stride.pm -%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/stssearch.pm -%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/supermatcher.pm -%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/syco.pm -%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/tacg.pm -%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/tfscan.pm -%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/tipdate.pm -%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/tmap.pm -%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/toppred.pm -%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/tranalign.pm -%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/transeq.pm -%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/treealign.pm -%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/trimest.pm -%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/trimseq.pm -%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/trnascan.pm -%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/twofeat.pm -%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/unroot.pm -%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/vectorstrip.pm -%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/water.pm -%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/weighbor.pm -%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/whichdb.pm -%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/wise2.pm -%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/wobble.pm -%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/wordcount.pm -%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/wordmatch.pm -%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/wublast2.pm -%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/xblast.pm -%%SITE_PERL%%/Bio/Tools/Run/PiseApplication/xpound.pm -%%SITE_PERL%%/Bio/Tools/Run/PiseJob.pm -%%SITE_PERL%%/Bio/Tools/Run/PiseJobParser.pm -%%SITE_PERL%%/Bio/Tools/Run/PiseWorkflow.pm -%%SITE_PERL%%/Bio/Tools/Run/Primate.pm -%%SITE_PERL%%/Bio/Tools/Run/Primer3.pm -%%SITE_PERL%%/Bio/Tools/Run/Prints.pm -%%SITE_PERL%%/Bio/Tools/Run/Profile.pm -%%SITE_PERL%%/Bio/Tools/Run/Promoterwise.pm -%%SITE_PERL%%/Bio/Tools/Run/Pseudowise.pm -%%SITE_PERL%%/Bio/Tools/Run/RepeatMasker.pm -%%SITE_PERL%%/Bio/Tools/Run/Seg.pm -%%SITE_PERL%%/Bio/Tools/Run/Signalp.pm -%%SITE_PERL%%/Bio/Tools/Run/Tmhmm.pm -%%SITE_PERL%%/Bio/Tools/Run/TribeMCL.pm -%%SITE_PERL%%/Bio/Tools/Run/Vista.pm -%%DATADIR%%/scripts/bioperl_application_installer.PLS -%%DATADIR%%/scripts/panalysis.PLS -%%DATADIR%%/scripts/papplmaker.PLS -%%DATADIR%%/scripts/run_neighbor.PLS -%%DATADIR%%/scripts/run_protdist.PLS -%%PORTDOCS%%%%DOCSDIR%%/AUTHORS -%%PORTDOCS%%%%DOCSDIR%%/Changes -%%PORTDOCS%%%%DOCSDIR%%/INSTALL.PROGRAMS -%%PORTDOCS%%%%DOCSDIR%%/README -%%EXAMPLESDIR%%/pise/blast-kun.pl -%%EXAMPLESDIR%%/pise/blast2.pl -%%EXAMPLESDIR%%/pise/clustalw.pl -%%EXAMPLESDIR%%/pise/dnadist.data -%%EXAMPLESDIR%%/pise/dnadist.pl -%%EXAMPLESDIR%%/pise/genscan.pl -%%EXAMPLESDIR%%/pise/needle.pl -%%EXAMPLESDIR%%/pise/phylo-kun.pl -%%EXAMPLESDIR%%/pise/toppred.pl -@dirrm %%EXAMPLESDIR%%/pise -@dirrm %%EXAMPLESDIR%% -%%PORTDOCS%%@dirrm %%DOCSDIR%% -@dirrm %%DATADIR%%/scripts -@dirrm %%DATADIR%% -@dirrmtry %%SITE_PERL%%/%%PERL_ARCH%%/auto/Bio -@dirrm %%SITE_PERL%%/Bio/Tools/Run/PiseApplication -@dirrm %%SITE_PERL%%/Bio/Tools/Run/Phylo/Phylip -@dirrm %%SITE_PERL%%/Bio/Tools/Run/Phylo/PAML -@dirrm %%SITE_PERL%%/Bio/Tools/Run/Phylo/Molphy -@dirrm %%SITE_PERL%%/Bio/Tools/Run/Phylo/Forester -@dirrm %%SITE_PERL%%/Bio/Tools/Run/Phylo -@dirrm %%SITE_PERL%%/Bio/Tools/Run/AnalysisFactory -@dirrm %%SITE_PERL%%/Bio/Tools/Run/Analysis -@dirrm %%SITE_PERL%%/Bio/Tools/Run/Alignment -@dirrmtry %%SITE_PERL%%/Bio/Tools/Run -@dirrmtry %%SITE_PERL%%/Bio/Tools -@dirrm %%SITE_PERL%%/Bio/Installer -@dirrmtry %%SITE_PERL%%/Bio/Factory -@dirrmtry %%SITE_PERL%%/Bio diff --git a/net-p2p/Makefile b/net-p2p/Makefile index daad08e010e4..c21fb96d2eee 100644 --- a/net-p2p/Makefile +++ b/net-p2p/Makefile @@ -22,7 +22,6 @@ SUBDIR += dctc-gui SUBDIR += dctc-gui-qt SUBDIR += deluge - SUBDIR += deluge05 SUBDIR += ed2k SUBDIR += edonkey-gui-gtk SUBDIR += edonkey-gui-gtk-urlslave diff --git a/net-p2p/deluge05/Makefile b/net-p2p/deluge05/Makefile deleted file mode 100644 index 10fbacd468f6..000000000000 --- a/net-p2p/deluge05/Makefile +++ /dev/null @@ -1,57 +0,0 @@ -# New ports collection makefile for: deluge -# Date created: 03 December 2006 -# Whom: Mezz <mezz@FreeBSD.org> -# -# $FreeBSD$ -# - -PORTNAME= deluge -PORTVERSION= 0.5.9.4 -CATEGORIES= net-p2p python -MASTER_SITES= http://ftp.osuosl.org/pub/deluge/source/${PORTVERSION}/ - -MAINTAINER= ports@FreeBSD.org -COMMENT= A Bittorrent client, using Python, GTK+2 and Rasterbar libtorrent - -LIB_DEPENDS= boost_thread.4:${PORTSDIR}/devel/boost -RUN_DEPENDS= xdg-open:${PORTSDIR}/devel/xdg-utils \ - ${PYTHON_SITELIBDIR}/xdg/__init__.py:${PORTSDIR}/devel/py-xdg \ - ${PYTHON_SITELIBDIR}/dbus/__init__.py:${PORTSDIR}/devel/py-dbus \ - ${PYTHON_SITELIBDIR}/gtk-2.0/pynotify/__init__.py:${PORTSDIR}/devel/py-notify \ - ${PYTHON_SITELIBDIR}/OpenSSL/__init__.py:${PORTSDIR}/security/py-openssl - -DEPRECIATED= use net-p2p/deluge instead -EXPIRATION_DATE= 2009-06-01 - -LATEST_LINK= ${PORTNAME}05 - -WRKSRC= ${WRKDIR}/${PORTNAME}-torrent-${PORTVERSION} -USE_GNOME= pygtk2 desktopfileutils librsvg2 -USE_GETTEXT= yes -USE_OPENSSL= yes -USE_PYTHON= yes -USE_PYDISTUTILS=yes -INSTALLS_ICONS= yes - -DOCS= LICENSE README - -.include <bsd.port.pre.mk> - -.if ${ARCH} == "sparc64" || ${ARCH} == "ia64" || ${ARCH} == "amd64" -CFLAGS+= -DAMD64 -.endif - -post-patch: - @${REINPLACE_CMD} -e 's|%%LOCALBASE%%|${LOCALBASE}|g ; \ - s|%%PTHREAD_LIBS%%|${PTHREAD_LIBS}|g' ${WRKSRC}/setup.py - -post-install: - @-update-desktop-database -.ifndef (NOPORTDOCS) - @${MKDIR} ${DOCSDIR} -.for i in ${DOCS} - @${INSTALL_DATA} ${WRKSRC}/${i} ${DOCSDIR} -.endfor -.endif - -.include <bsd.port.post.mk> diff --git a/net-p2p/deluge05/distinfo b/net-p2p/deluge05/distinfo deleted file mode 100644 index 391f9b33994d..000000000000 --- a/net-p2p/deluge05/distinfo +++ /dev/null @@ -1,3 +0,0 @@ -MD5 (deluge-0.5.9.4.tar.gz) = 8baee1df11074ca523d57ddc157a4ce4 -SHA256 (deluge-0.5.9.4.tar.gz) = 6454944e96b88819b92fd77aaa86f56d46fbbaaeb264424d7b3caf8cfec7442e -SIZE (deluge-0.5.9.4.tar.gz) = 2229519 diff --git a/net-p2p/deluge05/files/patch-disable_check_update b/net-p2p/deluge05/files/patch-disable_check_update deleted file mode 100644 index 90a7d315e5d1..000000000000 --- a/net-p2p/deluge05/files/patch-disable_check_update +++ /dev/null @@ -1,61 +0,0 @@ ---- glade/preferences_dialog.glade.orig 2008-01-30 13:03:26.000000000 -0600 -+++ glade/preferences_dialog.glade 2008-01-30 13:04:06.000000000 -0600 -@@ -2673,7 +2673,7 @@ - </child> - <child> - <widget class="GtkFrame" id="frame4"> -- <property name="visible">True</property> -+ <property name="visible">False</property> - <property name="events">GDK_POINTER_MOTION_MASK | GDK_POINTER_MOTION_HINT_MASK | GDK_BUTTON_PRESS_MASK | GDK_BUTTON_RELEASE_MASK</property> - <property name="label_xalign">0</property> - <property name="shadow_type">GTK_SHADOW_NONE</property> ---- src/interface.py.orig 2008-01-30 13:03:33.000000000 -0600 -+++ src/interface.py 2008-01-30 13:04:38.000000000 -0600 -@@ -1037,8 +1037,6 @@ - # Load plugins after we showed main window (if not started in tray) - self.load_plugins() - self.load_tabs_order() -- if self.config.get("new_releases"): -- self.new_release_check() - - try: - gobject.threads_init() -@@ -1048,38 +1046,6 @@ - except KeyboardInterrupt: - self.manager.quit() - -- def new_release_check(self): -- import socket -- import urllib -- timeout = 5 -- socket.setdefaulttimeout(timeout) -- try: -- gtk.gdk.threads_enter() -- except: -- pass -- try: -- new_release = urllib.urlopen("http://download.deluge-torrent.org/version").read().strip() -- except IOError: -- print "Network error while trying to check for a newer version of \ --Deluge" -- try: -- gtk.gdk.threads_leave() -- except: -- pass -- return -- -- if new_release > common.PROGRAM_VERSION: -- result = dialogs.show_popup_question(None, _("There is a newer version \ --of Deluge. Would you like to be taken to our download site?")) -- if result: -- common.open_url_in_browser('http://download.deluge-torrent.org/') -- else: -- pass -- try: -- gtk.gdk.threads_leave() -- except: -- pass -- - def load_plugins(self): - enable_plugins = self.config.get('enabled_plugins').split(':') - for plugin in enable_plugins: diff --git a/net-p2p/deluge05/files/patch-libtorrent-include-libtorrent-disk_io_thread.hpp b/net-p2p/deluge05/files/patch-libtorrent-include-libtorrent-disk_io_thread.hpp deleted file mode 100644 index b184e458762a..000000000000 --- a/net-p2p/deluge05/files/patch-libtorrent-include-libtorrent-disk_io_thread.hpp +++ /dev/null @@ -1,10 +0,0 @@ ---- libtorrent/include/libtorrent/disk_io_thread.hpp.orig 2008-07-23 00:04:51.000000000 +0400 -+++ libtorrent/include/libtorrent/disk_io_thread.hpp 2009-03-21 17:06:18.000000000 +0300 -@@ -41,6 +41,7 @@ - #include <boost/thread/thread.hpp> - #include <boost/function.hpp> - #include <boost/thread/mutex.hpp> -+#include <boost/thread/condition.hpp> - #include <boost/bind.hpp> - #include <boost/pool/pool.hpp> - #include <boost/noncopyable.hpp> diff --git a/net-p2p/deluge05/files/patch-setup.py b/net-p2p/deluge05/files/patch-setup.py deleted file mode 100644 index 2218f1fba390..000000000000 --- a/net-p2p/deluge05/files/patch-setup.py +++ /dev/null @@ -1,40 +0,0 @@ ---- setup.py.orig 2008-05-19 17:26:22.000000000 -0500 -+++ setup.py 2008-05-19 17:28:27.000000000 -0500 -@@ -103,13 +103,13 @@ - "-DHAVE_INCLUDE_LIBTORRENT_ASIO_SSL_STREAM_HPP=1", - "-DHAVE_INCLUDE_LIBTORRENT_ASIO_IP_TCP_HPP=1", - "-DHAVE_PTHREAD=1", "-DTORRENT_USE_OPENSSL=1", "-DHAVE_SSL=1", -- "-DNDEBUG=1", "-O2"] -- if ARCH == "x64": -- EXTRA_COMPILE_ARGS.append("-DAMD64") -+ "-DNDEBUG=1"] -+# if ARCH == "x64": -+# EXTRA_COMPILE_ARGS.append("-DAMD64") - - includedirs = ['./libtorrent', './libtorrent/include', - './libtorrent/include/libtorrent', -- '/usr/include/python' + python_version] -+ '%%LOCALBASE%%/include'] - - if OS == "linux": - if os.path.exists(os.path.join(sysconfig.get_config_vars()['LIBDIR'], \ -@@ -148,7 +148,7 @@ - boost_thread = "boost_thread-mt" - - librariestype = [boost_filesystem, boost_date_time, -- boost_thread, 'z', 'pthread', 'ssl', 'crypto'] -+ boost_thread, 'z', 'ssl', 'crypto'] - - if os == "linux": - librariestype += ['rt'] -@@ -205,8 +205,10 @@ - sources.remove('libtorrent/src/file_win.cpp') - deluge_core = Extension('deluge_core', - include_dirs = includedirs, -+ library_dirs = ['%%LOCALBASE%%/lib'], - libraries = librariestype, - extra_compile_args = EXTRA_COMPILE_ARGS, -+ extra_link_args = ['%%PTHREAD_LIBS%%'], - sources = sources) - else: - sources.remove('libtorrent\\src\\file.cpp') diff --git a/net-p2p/deluge05/pkg-descr b/net-p2p/deluge05/pkg-descr deleted file mode 100644 index fc985d391ad1..000000000000 --- a/net-p2p/deluge05/pkg-descr +++ /dev/null @@ -1,8 +0,0 @@ -Deluge is a Bittorrent client written in Python and GTK+. Deluge is intended -to bring a native, full-featured client to Linux, BSD, and other *NIX GTK -desktop environments such as Gnome and XFCE. - -Deluge uses Rasterbar's version of libtorrent as the main ingredient in its -bittorrent protocol backend. - -WWW: http://deluge-torrent.org/ diff --git a/net-p2p/deluge05/pkg-plist b/net-p2p/deluge05/pkg-plist deleted file mode 100644 index a7545ee8250d..000000000000 --- a/net-p2p/deluge05/pkg-plist +++ /dev/null @@ -1,844 +0,0 @@ -bin/deluge -%%PYTHON_SITELIBDIR%%/deluge/__init__.py -%%PYTHON_SITELIBDIR%%/deluge/__init__.pyc -%%PYTHON_SITELIBDIR%%/deluge/__init__.pyo -%%PYTHON_SITELIBDIR%%/deluge/_dbus.py -%%PYTHON_SITELIBDIR%%/deluge/_dbus.pyc -%%PYTHON_SITELIBDIR%%/deluge/_dbus.pyo -%%PYTHON_SITELIBDIR%%/deluge/common.py -%%PYTHON_SITELIBDIR%%/deluge/common.pyc -%%PYTHON_SITELIBDIR%%/deluge/common.pyo -%%PYTHON_SITELIBDIR%%/deluge/core.py -%%PYTHON_SITELIBDIR%%/deluge/core.pyc -%%PYTHON_SITELIBDIR%%/deluge/core.pyo 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%%DATADIR%%/plugins/WebUi -@dirrm %%DATADIR%%/plugins/WebSeed -@dirrm %%DATADIR%%/plugins/TorrentPeers -@dirrm %%DATADIR%%/plugins/TorrentNotification -@dirrm %%DATADIR%%/plugins/TorrentFiles -@dirrm %%DATADIR%%/plugins/TorrentCreator -@dirrm %%DATADIR%%/plugins/SpeedLimiter -@dirrm %%DATADIR%%/plugins/Search -@dirrm %%DATADIR%%/plugins/Scheduler -@dirrm %%DATADIR%%/plugins/NetworkHealth -@dirrm %%DATADIR%%/plugins/NetworkGraph -@dirrm %%DATADIR%%/plugins/MoveTorrent -@dirrm %%DATADIR%%/plugins/FlexRSS -@dirrm %%DATADIR%%/plugins/EventLogging -@dirrm %%DATADIR%%/plugins/DesiredRatio -@dirrm %%DATADIR%%/plugins/BlocklistImport -@dirrmtry %%DATADIR%%/plugins -@dirrm %%DATADIR%%/pixmaps/flags25x15 -@dirrm %%DATADIR%%/pixmaps/flags18x12 -@dirrm %%DATADIR%%/pixmaps -@dirrm %%DATADIR%%/icons/scalable/apps -@dirrm %%DATADIR%%/icons/scalable -@dirrm %%DATADIR%%/icons/hicolor -@dirrm %%DATADIR%%/icons -@dirrm %%DATADIR%%/glade -@dirrmtry %%DATADIR%% -@dirrmtry share/applications -@dirrm %%PYTHON_SITELIBDIR%%/deluge -@exec %%LOCALBASE%%/bin/update-desktop-database > /dev/null || /usr/bin/true -@unexec %%LOCALBASE%%/bin/update-desktop-database > /dev/null || /usr/bin/true diff --git a/textproc/Makefile b/textproc/Makefile index 947be7ed5476..96bfe23b1e51 100644 --- a/textproc/Makefile +++ b/textproc/Makefile @@ -186,7 +186,6 @@ SUBDIR += gladtex SUBDIR += glark SUBDIR += glimpse - SUBDIR += gmat SUBDIR += gmetadom SUBDIR += gnome-doc-utils SUBDIR += gnome-spell diff --git a/textproc/gmat/Makefile b/textproc/gmat/Makefile deleted file mode 100644 index a5c2b15840d1..000000000000 --- a/textproc/gmat/Makefile +++ /dev/null @@ -1,68 +0,0 @@ -# ports collection makefile for: gmat -# Date created: 31 December 2000 -# Whom: grog -# -# $FreeBSD$ -# - -PORTNAME= gmat -PORTVERSION= 0.2.4c -PORTREVISION= 2 -CATEGORIES= textproc -MASTER_SITES= ftp://ftp.ora.com/pub/gmat/ - -MAINTAINER= ports@FreeBSD.org -COMMENT= O'Reilly's SGML formatting package - -RUN_DEPENDS= nsgmls:${PORTSDIR}/textproc/jade \ - ${LOCALBASE}/bin/procmail:${PORTSDIR}/mail/procmail \ - docbook<2:${PORTSDIR}/textproc/docbook \ - ${LOCALBASE}/share/sgml/iso12083/book.dtd:${PORTSDIR}/textproc/iso12083 \ - gv:${PORTSDIR}/print/gv - -USE_PERL5_BUILD=yes -REINPLACE_ARGS= -i "" - -BROKEN= this port needs a larger cleanup -DEPRECATED= failed to build for a long time, no maintainer and apparently no users either -EXPIRATION_DATE=2009-06-03 - -WRKSRC= ${WRKDIR}/${PORTNAME}-0.2.4 -MAKE_ARGS= CC="${CC}" PRODROOT="${DATADIR}" SOELIMPATHNAME="/usr/bin/soelim" -SUB_FILES= pkg-message -PORTDOCS= README gmat.sgm - -DTDVER?= 4.2 # docbook-xml version - -post-patch: - @${RM} ${WRKSRC}/src/crlf/crlf.o ${WRKSRC}/src/crlf/crlf ${WRKSRC}/bin/gmat.troff.orig - -pre-build: -# Change the pathnames in CATALOG & BOOKFILES -.for RP in /usr/local/prod %%PRODROOT%% - ${REINPLACE_CMD} -e "s|${RP}/sgml/ISO_12083-1993/dtds|${LOCALBASE}/share/sgml/iso12083|" \ - -e "s|${RP}/sgml/Davenport/dtds|${LOCALBASE}/share/sgml/docbook|" \ - -e "s|${RP}/sgml/DocBook-XML/iso|${LOCALBASE}/share/xml/docbook/${DTDVER}/ent/iso|" \ - -e "s|${RP}/sgml/DocBook-XML|${LOCALBASE}/share/xml/docbook/${DTDVER}|" \ - -e "s|${RP}/sgml/DocBook|${LOCALBASE}/share/sgml/docbook|" \ - ${WRKSRC}/test/CATALOG ${WRKSRC}/sgml/CATALOG -.endfor -.for FILE in BOOKFILES CATALOG - ${REINPLACE_CMD} -e "s|/usr/local/prod|${DATADIR}|" ${WRKSRC}/test/${FILE} -.endfor -.for FILE in checkaheads kern10sed kern10sed0 kern10sed1 - ${CHMOD} a+x ${WRKSRC}/bin/${FILE} -.endfor - ${REINPLACE_CMD} -e "s|/usr/local|${PREFIX}|" ${WRKSRC}/Makefile - -post-install: - @${STRIP_CMD} ${PREFIX}/bin/crlf - (cd ${WRKSRC}; tar cf - test) | (cd ${DATADIR}; tar xvf -) - ${CHOWN} -R ${SHAREOWN}:${SHAREGRP} ${DATADIR} -.if !defined(NOPORTDOCS) - ${MKDIR} ${DOCSDIR} - ${INSTALL_DATA} ${PORTDOCS:S|^|${WRKSRC}/|} ${DOCSDIR} -.endif - @${CAT} ${PKGMESSAGE} - -.include <bsd.port.mk> diff --git a/textproc/gmat/distinfo b/textproc/gmat/distinfo deleted file mode 100644 index 08aa26dec65f..000000000000 --- a/textproc/gmat/distinfo +++ /dev/null @@ -1,3 +0,0 @@ -MD5 (gmat-0.2.4c.tar.gz) = 184ba95d13d2a66c704ca7bb8586db7a -SHA256 (gmat-0.2.4c.tar.gz) = a421c2f2d50b7706a635f4a5dae4178db805c4707d323529dd82e8a696c8c2aa -SIZE (gmat-0.2.4c.tar.gz) = 332704 diff --git a/textproc/gmat/files/patch-ab b/textproc/gmat/files/patch-ab deleted file mode 100644 index ace0b2513727..000000000000 --- a/textproc/gmat/files/patch-ab +++ /dev/null @@ -1,28 +0,0 @@ ---- lib/oratoolsrc Thu Sep 7 00:48:19 2000 -+++ lib/oratoolsrc.new Thu Jan 11 12:05:38 2001 -@@ -58,9 +58,9 @@ - - action = view - --tbl = gtbl --pic = gpic --eqn = geqn -+tbl = tbl -+pic = pic -+eqn = eqn - - tbl_opts = - - pic_opts = - -@@ -94,9 +94,9 @@ - comment = This is really gmat.old - action = view - --tbl = gtbl --pic = gpic --eqn = geqn -+tbl = tbl -+pic = pic -+eqn = eqn - - tbl_opts = - - pic_opts = - diff --git a/textproc/gmat/files/patch-ac b/textproc/gmat/files/patch-ac deleted file mode 100644 index 8b154b5158f6..000000000000 --- a/textproc/gmat/files/patch-ac +++ /dev/null @@ -1,617 +0,0 @@ ---- gmat.sgm.orig Thu Jan 1 09:30:00 1970 -+++ gmat.sgm Sun Jan 7 12:44:25 2001 -@@ -0,0 +1,614 @@ -+<!-- $Id: gmat.sgm 1.2 1994/08/29 17:53:27 norm Exp $ --> -+ -+<chapter id=gmat><title>gmat</> -+ -+<sect1><title>Usage</> -+ -+<para> -+Usage: <command>gmat</> [switches] filename { [[switches] filename] } -+… -+</para> -+ -+</sect1> -+<sect1><title>Description</> -+ -+<para> -+<command>gmat</> handles the routine processing of text documents into -+printed or previewed output. Beginning with one or more input files (in -+a formatting language like troff or TeX; or in SGML), <command>gmat</> -+performs any necessary preprocessing (e.g. construction of an -+<acronym>SGML</acronym> driver file), executes the appropriate -+formatter, and previews or prints the resulting output file (generally -+PostScript). -+</para> -+ -+<para> -+Most aspects of <command>gmat</> are configurable through command line -+switches and/or configuration files. <command>gmat</> reads two -+configuration files: the <filename>oratoolsrc</> file and the -+<filename>bookfiles</> file. -+</para> -+ -+<para> -+The following command line switches are available: -+ -+<variablelist> -+ <varlistentry><term><option>–d</></term> -+ <listitem><para> -+ Enable debugging. If the <option>–d</option> switch is used, -+ temporary files -+ created by <command>gmat</> are not deleted when <command>gmat</> -+ ends. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term><option>–f</></term> -+ <listitem><para> -+ Keep the output file. If the <option>–f</option> switch is used, -+ the output file -+ is not deleted after previewing or printing. Ordinarily, -+ <command>gmat</> treats the output file as a temporary file. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term><option>–F</> <replaceable>file</></term> -+ <listitem><para> -+ Specify the name of the output file. The name of the output file -+ is controlled by the <filename>oratoolsrc</> variable -+ <literal>PS_BASE</> if the <option>–F</> option is not used. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term><option>–k</></term> -+ <listitem><para> -+ Keep the formatter input file. The <option>–k</> option is only meaningful -+ when <acronym>SGML</acronym> files are being processed by -+ <command>gmat</>. The <acronym>SGML</acronym> file is -+ automatically translated into a formatter input file; if the <option>–k</> -+ option isn't used, <command>gmat</> treats the output file as a -+ temporary file. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term><option>–K</> <replaceable>file</></term> -+ <listitem><para> -+ Specify the name of the formatter input file. The name of the -+ formatter input file is controlled by the <filename>oratoolsrc</> variables -+ <literal>EXT_BASE</> and <literal>EXT3L</> if the <option>–K</> option isn't used. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term><option>–o</> <replaceable>pages</></term> -+ <listitem><para> -+ Specify a list of pages. Only the pages specified will appear in -+ the output file. Pages are specified by page number. By default, -+ all of the pages in the formatter input file will appear in the -+ output file. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term><option>–p</></term> -+ <listitem><para> -+ Print the output file. Selection of the output action is -+ controlled by the <option>–p</> and <option>–v</> options and the <filename>oratoolsrc</> -+ variable <literal>ACTION</>. If the <option>–p</> option is used, the file will be -+ printed regardless of the action specified by the <filename>oratoolsrc</> -+ variable <literal>ACTION</>. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term><option>–P</> <replaceable>printer</></term> -+ <listitem><para> -+ Select printer. Output will be sent to the printer specified. If -+ the <option>–P</> option is not used, output will be sent to the printer -+ specified by the <filename>oratoolsrc</> variable <literal>PRINTER</>. This option has -+ no meaning if the output file is not printed (e.g. if the -+ previewer is used instead). Selection of the output action is -+ controlled by the <option>–p</> and <option>–v</> options and the <filename>oratoolsrc</> -+ variable <literal>ACTION</>. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term><option>–q</></term> -+ <listitem><para> -+ Suppress warning messages. The ``verbosity'' of messages is -+ controlled by the <filename>oratoolsrc</> variables <literal>QUIET</> and <literal>VERBOSE</> and -+ the <option>–q</> option. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term><option>–s</></term> -+ <listitem><para> -+ Save the <acronym>SGML</acronym> driver file. If the <option>–s</> option -+ is not used, <command>gmat</> treats the <acronym>SGML</acronym> -+ driver file (containing the <!DOCTYPE> declaration and the -+ locally defined entities) as a temporary file. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term><option>–S</></term> -+ <listitem><para> -+ Don't merge multiple <acronym>SGML</acronym> files together with -+ an <acronym>SGML</acronym> driver file. If the <option>–S</> option is -+ used, <command>gmat</> does not build a driver file. Each -+ <acronym>SGML</acronym> file must contain it's own <DOCTYPE> -+ specification. When multiple <acronym>SGML</acronym> files are -+ given on the command line, <command>gmat</> ordinarily merges them -+ together in the <acronym>SGML</acronym> driver. If the <option>–S</> -+ option is specified, each file is processed individually. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term><option>–T</> <replaceable>progname</></term> -+ <listitem><para> -+ Process the formatter input file with the specified program. This -+ option is not implemented yet. Ultimately, it will allow -+ <command>gmat</> to handle arbitrary document formatters instead -+ of just gtroff. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term><option>–v</></term> -+ <listitem><para> -+ Preview the output file. Selection of the output action is -+ controlled by the <option>–p</> and <option>–v</> options and the <filename>oratoolsrc</> -+ variable <literal>ACTION</>. If the <option>–v</> option is used, the file will be -+ previewed regardless of the action specified by the <filename>oratoolsrc</> -+ variable <literal>ACTION</>. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term><option>–W</></term> -+ <listitem><para> -+ Wait on error. If <command>gmat</> detects a user error (such as -+ an invalid option) it prints an error message and ends. If the -+ <option>–W</> option is specified, it also waits for the user to press -+ Enter. This option is useful if <command>gmat</> is executed by -+ shell script or batch file and subsequent processing might cause -+ the error message to scroll off of the screen before it could be -+ read or even noticed. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term><option>–x</></term> -+ <listitem><para> -+ Just check for errors. If the <option>–x</> option is specified, -+ <command>gmat</> does not preview or print the output file. -+ </para></listitem> -+ </varlistentry> -+</variablelist> -+</para> -+ -+<para> -+The <filename>oratoolsrc</> file provides another way to customize -+<command>gmat</>. <command>gmat</> loads each of the following -+<filename>oratoolsrc</> files if they exist: the system default file, the user -+default file, and the <filename>oratoolsrc</> file in the current directory. If a -+variable is set in more than one file, the value in the most recently -+loaded file is the value that <command>gmat</> uses. -+</para> -+ -+<para> -+The system default file is <filename>oratoolsrc</>. The location of the system -+default file is controlled by the environment variable <systemitem class=environvar>ORALIBDIR</>. If -+<systemitem class=environvar>ORALIBDIR</> is not set, the value <filename>/usr/local/prod/lib</> is used. The -+user default file is $HOME/.oratoolsrc. The <filename>oratoolsrc</> file in the -+current directory is <filename>.oratoolsrc</>. -+</para> -+ -+<para> -+The following variables are recognized by <command>gmat</> in the <literal>GMAT</> -+or global sections of the <filename>oratoolsrc</> configuration file. -+ -+<variablelist> -+ <varlistentry><term>action (view, print, check, file)</term> -+ <listitem><para> -+ Output file processing. Valid values are view (equivalent to the -+ <option>–v</> option), print (equivalent to the <option>–p</> option), check -+ (equivalent to the <option>–x</> option), and file (equivalent to the <option>–f</> -+ option). -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term>bindir dir</term> -+ <listitem><para> -+ Additional <systemitem class=environvar>PATH</> directory. <command>gmat</> adds the specified -+ directory to the <systemitem class=environvar>PATH</> environment variable before running -+ subprocesses. This variable allows the installer to place -+ <command>gmat</> in a standard place (e.g. <filename>/usr/local/bin</>) but -+ leave the rest of the executables somewhere else without requiring -+ that every user update their <systemitem class=environvar>PATH</>. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term>bookfiles filename</term> -+ <listitem><para> -+ Name of the <filename>bookfiles</> file. The <filename>bookfiles</> file is a -+ configuration file for a particular book. This variable should be -+ a simple filename (e.g. <filename>BOOKFILES</>) and not a path name. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term>debug boolean</term> -+ <listitem><para> -+ Enable debugging? Enabling this variable is equivalent to using -+ the <option>–d</> option. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term>debugdir dir</term> -+ <listitem><para> -+ Directory for temporary files. Temporary files are generally -+ placed in <filename>/tmp</>, but if this variable is set they are stored in -+ the directory specified. Temporary files are automatically -+ deleted when <command>gmat</> ends unless debugging is enabled. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term>entity_file filename { filename … }</term> -+ <listitem><para> -+ Local entities for the <DOCTYPE> declaration. This is used -+ only if <literal>entities</> is not set in the <filename>BOOKFILES</> -+ file. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term>eqn progname</term> -+ <listitem><para> -+ The <command>eqn</> preprocessor to use for gtroff files. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term>eqn_opts any</term> -+ <listitem><para> -+ Options for <command>eqn</> -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term>extension_3l ext</term> -+ <listitem><para> -+ The default extension for formatter input files. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term>ext_base rule</term> -+ <listitem><para> -+ The rule for constructing the base filename for the formatter -+ input file. See below. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term>gsoelim progname</term> -+ <listitem><para> -+ The <command>gsoelim</> preprocessor to use for gtroff files. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term>keep3l boolean</term> -+ <listitem><para> -+ Keep the formatter input file? -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term>macrodir dir</term> -+ <listitem><para> -+ Directory where local macro files are kept. This value should be a -+ path relative to the current directory, for example <filename>./macros</>. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term>pic progname</term> -+ <listitem><para> -+ The <command>pic</> preprocessor to use for gtroff files. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term>pic_opts any</term> -+ <listitem><para> -+ Options for <command>pic</> -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term>printer printer</term> -+ <listitem><para> -+ Name of the default printer. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term>ps_base rule</term> -+ <listitem><para> -+ The rule for constructing the base filename for the output file. -+ See below. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term>quiet</term> -+ <listitem><para> -+ Suppress warning messages? -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term>scriptdir dir</term> -+ <listitem><para> -+ Directory where local scripts are kept. This value should be a -+ path relative to the current directory, for example <filename>./scripts</>. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term>seddir dir</term> -+ <listitem><para> -+ Directory where <command>sed</> scripts are kept. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term>sgmlto3l progname</term> -+ <listitem><para> -+ Name of the program that converts an <acronym>SGML</acronym> -+ document instance into a formatter input file. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term>sgml_base rule</term> -+ <listitem><para> -+ The rule for constructing the base filename for the -+ <acronym>SGML</acronym> driver file. See below. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term>tbl progname</term> -+ <listitem><para> -+ The <command>tbl</> preprocessor to use for gtroff files. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term>tbl_opts any</term> -+ <listitem><para> -+ Options for <command>tbl</> -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term>temp_base rule</term> -+ <listitem><para> -+ The rule for constructing the base filename for temporary files. -+ See below. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term>verbose boolean</term> -+ <listitem><para> -+ Print additional informatory messages? -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term>wait_on_error boolean</term> -+ <listitem><para> -+ Wait on error? Enabling this variable is equivalent to using the -+ <option>–w</> switch. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term>workdir dir</term> -+ <listitem><para> -+ Additional <systemitem class=environvar>PATH</> directory. <command>gmat</> adds the specified -+ directory to the <systemitem class=environvar>PATH</> environment variable before running -+ subprocesses. Obsolete? -+ </para></listitem> -+ </varlistentry> -+</variablelist> -+</para> -+ -+<para> -+The following variables are recognized by -+<command>gmat</> in the <literal>GMAT</> or global sections of the <filename>bookfiles</> -+configuration file. -+ -+<variablelist> -+ <varlistentry><term>doctype</term> -+ <listitem><para> -+ The <DOCTYPE> definition for the <acronym>SGML</acronym> -+ driver file. For example, ``book system -+ “docbook.dtd”''. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term>sgmlto3l</term> -+ <listitem><para> -+ Name of the program that converts an <acronym>SGML</acronym> -+ document instance into a formatter input file. If this variable is -+ specfied in the <filename>bookfiles</> file, it takes precedence over the -+ value specified in the <filename>oratoolsrc</> file. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term>entities filename { filename … }</term> -+ <listitem><para> -+ Local entities for the <DOCTYPE> declaration. If this variable -+ is not set, the value of <literal>entity_file</> from the -+ <filename>oratoolsrc</> file is used. -+ </para></listitem> -+ </varlistentry> -+</variablelist> -+</para> -+ -+<para> -+<command>gmat</> uses the <filename>bookfiles</> configuration -+file to identify options for each file that it processes. Several of -+these options only apply to <acronym>SGML</acronym> files and a few only -+apply to files processed with the gtroff text formatter. -+</para> -+ -+<para> -+The following variables are recognized by <command>gmat</> in the -+section named by the file that is being processed (for example, the -+<filename>ch01.sgm</> section when the file <filename>ch01.sgm</> is being processed) or the -+global section of the <filename>bookfiles</> configuration file. Options that -+apply to the text formatter or text formatter input file (such as -+<literal>macros</> and <literal>scripts</>) should only be specified in the global section -+of a <filename>bookfiles</> configuration file for <acronym>SGML</acronym> files. -+Specifying options for each file does not make sense since they are all -+merged into a single driver file. -+</para> -+ -+<variablelist> -+ <varlistentry><term>appendix appletter</term> -+ <listitem><para> -+ Identifies the file as an appendix and specifies its appendix -+ letter (i.e. appendix number). -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term>chapter chapnum</term> -+ <listitem><para> -+ Specifies the chapter number of the file. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term>not_a_chapter</term> -+ <listitem><para> -+ Indicates that the file is not a chapter (or appendix). See -+ below. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term>page number</term> -+ <listitem><para> -+ Specifies the starting page number for the file. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term>part number</term> -+ <listitem><para> -+ Identifies the part of the book that contains the file. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term>part<emphasis>n</>_title</term> -+ <listitem><para> -+ Specifies the title of the <emphasis>n</>'th part of the book. This -+ information may be used in page headers or footers, for example. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term>pagecount number</term> -+ <listitem><para> -+ Identifies how many formatted pages occur in the file. This -+ information is used by <command>gmat</> to calculate starting page -+ numbers for files that do not have a <literal>page</> variable. It is -+ updated automatically each time <command>gmat</> processes the -+ file. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term>macros filenames</term> -+ <listitem><para> -+ Identifies the macro packages that should be used when the file is -+ processed. At present, this option only applies to files -+ processed with gtroff. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term>page number</term> -+ <listitem><para> -+ Identifies the starting page of the file. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term>scripts prognames</term> -+ <listitem><para> -+ A list of scripts that should be used to preprocess the text -+ formatter input file. Each script must be a filter (accepting -+ input on <filename>stdin</> and writing output to <filename>stdout</>. The first filter -+ will recieve the formatter input file as input and the output of -+ the last filter will become the new formatter input. -+ </para></listitem> -+ </varlistentry> -+ <varlistentry><term>wraptag</term> -+ <listitem><para> -+ When <command>gmat</> creates an <acronym>SGML</acronym> driver -+ file, it inserts the specified tag around the contents of the -+ files that are processed. -+ </para></listitem> -+ </varlistentry> -+</variablelist> -+ -+</sect1> -+<sect1><title>Rules</> -+ -+<para> -+The values of the <literal>ext_base</>, <literal>sgml_base</>, <literal>ps_base</>, and <literal>temp_base</> -+variables are interpreted as filenames with the following extensions. In -+order to make it possible for more than one person to work in the same -+directory at the same time (or for one person to run several concurrent -+<command>gmat</>s), it is neessary to specify that the temporary files -+have different names. <command>gmat</> accomplishes this by allowing -+you to use the special strings ``$WHOAMI'' and``$PID'' in the value for -+each of these variables. In addition, you can use the string -+``$BASEFILE'' to refer to the base name of the file that -+<command>gmat</> is processing. -+</para> -+ -+<para> -+For example, if ``norm'' processes ``<filename>myfile.tr</>'' with <literal>ps_base</> set -+to ``$BASEFILE-$WHOAMI.$PID.ps'' and <command>gmat</> happens to be -+process number 3142, the ouput file produced by <command>gmat</> would -+be ``<filename>myfile-norm.3142.ps</>''. -+</para> -+ -+</sect1> -+<sect1><title>Chapter and Appendix Numbering</> -+ -+<para> -+<command>gmat</> assumes that the sections in the <filename>bookfiles</> -+configuration file identify the chapters of a book. When files are -+listed on the command line, they are reordered into the order that they -+appear in the bookfiles file before processing. <command>gmat</> -+determines the chapter or appendix number of each chapter and the -+starting page number of each chapter by examining the <literal>chapter</>, -+<literal>appendix</>, <literal>page</>, and <literal>pagecount</> variables for each file. If a given -+file does not have a <literal>chapter</> variable, it is assumed to have a number -+one greater than the previous chapter. <command>gmat</> does not -+increment the chapter count when it processes a section that has the -+<literal>not_a_chapter</> variable set. After the first appendix has been -+encountered, <command>gmat</> begins enumerating chapters with letters -+rather than numbers. -+</para> -+ -+</sect1> -+<sect1><title>Handling <filename>BOOKFILES</></title> -+ -+<para> -+The <filename>bookfiles</> file is <emphasis>always</> read only. You must not -+edit the file by hand. Because <command>gmat</> updates the file each -+time it processes a document, any changes that you introduce while -+<command>gmat</> is running will potentially be lost. -+</para> -+ -+<para> -+Always use the <command>bookfiles</> program to update the <filename>bookfiles</> -+configuration file. -+</para> -+ -+</sect1> -+<sect1><title>Formating A Document</> -+ -+<para> -+When formatting a non-SGML document, <command>gmat</> reads the command -+line switches and filenames and verifies that they are correct. If all -+of the switches are valid, <command>gmat</> checks that each filename -+specified exists and that the most recent <acronym>RCS</acronym> -+version has been checked out (if applicable). -+</para> -+ -+<para> -+Each filename in turn is passed through the text formatter and the -+output file is processed as requested. -+</para> -+ -+<para> -+If switches are used before the first filename, the results of those -+switches become the default behavior for the rest of the files specified -+on the command line. -+</para> -+ -+</sect1> -+<sect1><title>Formating an SGML Document</> -+ -+<para> -+Formating and <acronym>SGML</acronym> document is slightly more -+complicated than formating a text document. If all of the filenames -+listed on the command line end in <filename>.sgm</> or <filename>.sgml</>, <command>gmat</> -+assumes that the files are SGML. Unless the <option>–S</> switch is used, -+<command>gmat</> will attempt to create a single driver file to process -+all of the specified files simultaneously. The general format of the -+driver file that <command>gmat</> produces is: -+</para> -+ -+<screen> -+<!DOCTYPE *doctype* [ -+<!ENTITY file1.sgm SYSTEM "file1.sgm"> -+<!ENTITY file2.sgm SYSTEM "file2.sgm"> -+<!ENTITY file3.sgm SYSTEM "file3.sgm"> -+*local entities* -+*wraptag* -+<?gmat-file "file1.3l"> -+<?gmat-part "part title"> -+<?gmat-chapter-number "1"> -+<?gmat-page-number "1"> -+&file1.sgm; -+<?gmat-file "file2.3l"> -+<?gmat-part "part title"> -+<?gmat-chapter-number "2"> -+<?gmat-page-number "17"> -+&file2.sgm; -+<?gmat-file "file3.3l"> -+<?gmat-part "part title"> -+<?gmat-chapter-number "3"> -+<?gmat-page-number "23"> -+&file3.sgm; -+*/wraptag* -+</screen> -+ -+<para> -+The files are arranged in the order that they appear in the <filename>bookfiles</> -+configuration file regardless of the order specified on the command -+line. -+</para> -+ -+</sect1> -+</chapter> -+<?troff .BLANK> -+ -+<!-- Keep this comment at the end of the file -+Local variables: -+mode: sgml -+sgml-default-dtd-file: "oraprod.ced" -+End: -+--> diff --git a/textproc/gmat/files/patch-ad b/textproc/gmat/files/patch-ad deleted file mode 100644 index ee262f18d278..000000000000 --- a/textproc/gmat/files/patch-ad +++ /dev/null @@ -1,11 +0,0 @@ ---- macros/tmac.G.orig Mon Mar 19 14:29:40 2001 -+++ macros/tmac.G Tue Dec 7 21:31:06 2004 -@@ -25,7 +25,7 @@ - .ds gmat_gmacroff %%BINDIR%%/gmacroff - .\" DEFINE THE FOLLOWING paths for your local environment! - .ds gmat_echo /bin/echo --.ds gmat_sed /bin/sed -+.ds gmat_sed /usr/bin/sed - .ds gmat_rm /bin/rm - .ds gmat_mv /bin/mv - .\" The following strings set variables to subdirectories of the book diff --git a/textproc/gmat/files/patch-ae b/textproc/gmat/files/patch-ae deleted file mode 100644 index e5c768fac553..000000000000 --- a/textproc/gmat/files/patch-ae +++ /dev/null @@ -1,24 +0,0 @@ ---- bin/gmat.troff.orig Tue Feb 1 21:49:18 2000 -+++ bin/gmat.troff Mon Dec 13 14:04:14 2004 -@@ -90,7 +90,7 @@ - - $PS_FONT_FILE = ($ENV{"PSFONTFILE"} - || &cfg($gmat, $PROGNAME, "ps-font-file") -- || "/usr/local/lib/groff/font/devps/download"); -+ || "/usr/share/groff_font/devps"); - - ############################################################################ - # Let's get to work, process each file with its options -@@ -519,10 +519,10 @@ - # HANDLE RETURN CODE! - } elsif ($preview) { - print STDERR "Previewing $file.\n" if $VERBOSE; -- print COMMANDS "ghostview $grops_temp\n"; -+ print COMMANDS "gv $grops_temp\n"; - close (COMMANDS); # so that you can see what's in there - # when the preview window is up... -- system "ghostview $grops_temp"; -+ system "gv $grops_temp"; - # HANDLE RETURN CODE! - } elsif ($checkonly) { - print STDERR "Checking completed.\n" if $VERBOSE; diff --git a/textproc/gmat/files/pkg-message.in b/textproc/gmat/files/pkg-message.in deleted file mode 100644 index a93a80846d24..000000000000 --- a/textproc/gmat/files/pkg-message.in +++ /dev/null @@ -1,8 +0,0 @@ -=============================================================================== -To use the programs in this package, add the path -%%DATADIR%%/bin to your PATH environment variable. - -Then, type -gmat --job %%DATADIR%%/test/BOOKFILES %%DOCSDIR%%/gmat.sgm -to format the documentation. -=============================================================================== diff --git a/textproc/gmat/pkg-descr b/textproc/gmat/pkg-descr deleted file mode 100644 index 47aeb09c207d..000000000000 --- a/textproc/gmat/pkg-descr +++ /dev/null @@ -1,21 +0,0 @@ -O'Reilly's SGML formatting package. - -This package processes the complete sources for a book in DocBook -format and formats it with groff. - -This port is the first port of what was previously an internal -O'Reilly product. Consider it beta quality. The copyright -information in the README file states: - - # This is ALPHA software. Permission to redistribute this alpha - # version is expressly denied. - -According to Lenny Muellner <len@oreilly.com>, this is out of date, -but the archive has not yet been updated. - -The only documentation is gmat.sgm. To format, - - # gmat gmat.sgm - -The results of the formatting are not exactly production quality. -There is still a lot of work to be done. diff --git a/textproc/gmat/pkg-plist b/textproc/gmat/pkg-plist deleted file mode 100644 index d060b48439a9..000000000000 --- a/textproc/gmat/pkg-plist +++ /dev/null @@ -1,251 +0,0 @@ -bin/crlf -%%DATADIR%%/bin/bookfiles -%%DATADIR%%/bin/bookpage -%%DATADIR%%/bin/checkaheads -%%DATADIR%%/bin/dbtohtml -%%DATADIR%%/bin/dbtohtml.cls -%%DATADIR%%/bin/dbtohtml.sup -%%DATADIR%%/bin/dbtoltx -%%DATADIR%%/bin/dbtoltx.cls -%%DATADIR%%/bin/dbtoltx.sup -%%DATADIR%%/bin/dbtotexi -%%DATADIR%%/bin/dbtotexi.cls -%%DATADIR%%/bin/dbtotexi.sup -%%DATADIR%%/bin/epsbbox -%%DATADIR%%/bin/fontstack -%%DATADIR%%/bin/gmacroff -%%DATADIR%%/bin/gmat -%%DATADIR%%/bin/gmat.cat -%%DATADIR%%/bin/gmat.driver -%%DATADIR%%/bin/gmat.latex -%%DATADIR%%/bin/gmat.nop -%%DATADIR%%/bin/gmat.sgmls -%%DATADIR%%/bin/gmat.troff -%%DATADIR%%/bin/gnct -%%DATADIR%%/bin/inx -%%DATADIR%%/bin/kern10sed -%%DATADIR%%/bin/kern10sed0 -%%DATADIR%%/bin/kern10sed1 -%%DATADIR%%/bin/lowres -%%DATADIR%%/bin/memototxt -%%DATADIR%%/bin/memototxt.cls -%%DATADIR%%/bin/memototxt.sup -%%DATADIR%%/bin/rcs-lock-list -%%DATADIR%%/bin/rcsvdate -%%DATADIR%%/bin/sgml-checkindex -%%DATADIR%%/bin/sgml-fixindex -%%DATADIR%%/bin/sgmlfiglist -%%DATADIR%%/bin/tbltodb -%%DATADIR%%/bin/wraplines -%%DATADIR%%/bin/xdbto3l -%%DATADIR%%/bin/xdbto3l.cls -%%DATADIR%%/bin/xdbto3l.sup -%%DATADIR%%/bin/yadc-strings -%%DATADIR%%/lib/commonlock5.pl -%%DATADIR%%/lib/dbtohtml.ent -%%DATADIR%%/lib/dbtohtml.tag -%%DATADIR%%/lib/dbtoltx.tag -%%DATADIR%%/lib/dbtortf.tag -%%DATADIR%%/lib/dbtotexi.ent -%%DATADIR%%/lib/dbtotexi.tag -%%DATADIR%%/lib/gmat.pl -%%DATADIR%%/lib/html.mkp -%%DATADIR%%/lib/inx.preamble -%%DATADIR%%/lib/longopts5.pl -%%DATADIR%%/lib/memototxt.tag -%%DATADIR%%/lib/oragetopts.pl -%%DATADIR%%/lib/oratoolsrc -%%DATADIR%%/lib/oratoolsrc.orig -%%DATADIR%%/lib/parsecfg5.pl -%%DATADIR%%/lib/psgmls.pl -%%DATADIR%%/lib/sgmlesis.pl -%%DATADIR%%/lib/sgmlpars.pl -%%DATADIR%%/lib/sgmls3l.pl -%%DATADIR%%/lib/sparser.pl -%%DATADIR%%/lib/xdbto3l.ent -%%DATADIR%%/lib/xdbto3l.tag -%%DATADIR%%/macros/sgmlmacs -%%DATADIR%%/macros/tmac.G -%%DATADIR%%/macros/tmac.G.orig -%%DATADIR%%/macros/tmac.Gdraft -%%DATADIR%%/macros/tmac.Ginanut -%%DATADIR%%/macros/tmac.Ginit -%%DATADIR%%/macros/tmac.gs -%%DATADIR%%/macros/tmac.paras -%%DATADIR%%/macros/tmac.sgmlmacs -%%DATADIR%%/sed/gcleanup-d.sed -%%DATADIR%%/sed/gcleanup.sed -%%DATADIR%%/sed/gcleanup.sed.gr -%%DATADIR%%/sgml/CATALOG -%%DATADIR%%/sgml/ECAT -%%DATADIR%%/sgml/ISO_8879-1986/entities/Added_Latin_1 -%%DATADIR%%/sgml/ISO_8879-1986/entities/Added_Latin_2 -%%DATADIR%%/sgml/ISO_8879-1986/entities/Added_Math_Symbols_Arrow_Relations -%%DATADIR%%/sgml/ISO_8879-1986/entities/Added_Math_Symbols_Binary_Operators -%%DATADIR%%/sgml/ISO_8879-1986/entities/Added_Math_Symbols_Delimiters -%%DATADIR%%/sgml/ISO_8879-1986/entities/Added_Math_Symbols_Negated_Relations -%%DATADIR%%/sgml/ISO_8879-1986/entities/Added_Math_Symbols_Ordinary -%%DATADIR%%/sgml/ISO_8879-1986/entities/Added_Math_Symbols_Relations -%%DATADIR%%/sgml/ISO_8879-1986/entities/Alternative_Greek_Symbols -%%DATADIR%%/sgml/ISO_8879-1986/entities/Box_and_Line_Drawing -%%DATADIR%%/sgml/ISO_8879-1986/entities/Diacritical_Marks -%%DATADIR%%/sgml/ISO_8879-1986/entities/General_Technical -%%DATADIR%%/sgml/ISO_8879-1986/entities/Greek_Letters -%%DATADIR%%/sgml/ISO_8879-1986/entities/Greek_Symbols -%%DATADIR%%/sgml/ISO_8879-1986/entities/Monotoniko_Greek -%%DATADIR%%/sgml/ISO_8879-1986/entities/Non-Russian_Cyrillic -%%DATADIR%%/sgml/ISO_8879-1986/entities/Numeric_and_Special_Graphic -%%DATADIR%%/sgml/ISO_8879-1986/entities/Publishing -%%DATADIR%%/sgml/ISO_8879-1986/entities/Russian_Cyrillic -%%DATADIR%%/sgml/ISO_8879-1986/entities/iso-amsa.gml -%%DATADIR%%/sgml/ISO_8879-1986/entities/iso-amsb.gml -%%DATADIR%%/sgml/ISO_8879-1986/entities/iso-amsc.gml -%%DATADIR%%/sgml/ISO_8879-1986/entities/iso-amsn.gml -%%DATADIR%%/sgml/ISO_8879-1986/entities/iso-amso.gml -%%DATADIR%%/sgml/ISO_8879-1986/entities/iso-amsr.gml -%%DATADIR%%/sgml/ISO_8879-1986/entities/iso-box.gml -%%DATADIR%%/sgml/ISO_8879-1986/entities/iso-cyr1.gml -%%DATADIR%%/sgml/ISO_8879-1986/entities/iso-cyr2.gml -%%DATADIR%%/sgml/ISO_8879-1986/entities/iso-dia.gml -%%DATADIR%%/sgml/ISO_8879-1986/entities/iso-grk1.gml -%%DATADIR%%/sgml/ISO_8879-1986/entities/iso-grk2.gml -%%DATADIR%%/sgml/ISO_8879-1986/entities/iso-grk3.gml -%%DATADIR%%/sgml/ISO_8879-1986/entities/iso-grk4.gml -%%DATADIR%%/sgml/ISO_8879-1986/entities/iso-lat1.gml -%%DATADIR%%/sgml/ISO_8879-1986/entities/iso-lat2.gml -%%DATADIR%%/sgml/ISO_8879-1986/entities/iso-num.gml -%%DATADIR%%/sgml/ISO_8879-1986/entities/iso-pub.gml -%%DATADIR%%/sgml/ISO_8879-1986/entities/iso-tech.gml -%%DATADIR%%/sgml/ISO_9573-13-1991/entities/Math_Alphabets_Fraktur -%%DATADIR%%/sgml/ISO_9573-13-1991/entities/Math_Alphabets_Open_Face -%%DATADIR%%/sgml/ISO_9573-13-1991/entities/Math_Alphabets_Script -%%DATADIR%%/sgml/ORA/dtds/memo.dtd -%%DATADIR%%/sgml/ORA/dtds/nutshell.1.1.dtd -%%DATADIR%%/sgml/ORA/dtds/nutshell.dtd -%%DATADIR%%/sgml/ORA/dtds/orahtml.dtd -%%DATADIR%%/sgml/ORA/dtds/oraprod.2.2.1.dtd -%%DATADIR%%/sgml/ORA/dtds/oraprod.2.4.dtd -%%DATADIR%%/sgml/ORA/dtds/oraprod.3.0.dtd -%%DATADIR%%/sgml/ORA/dtds/oraprod.3.1.dtd -%%DATADIR%%/sgml/ORA/entities/Common_Entities -%%DATADIR%%/sgml/ORA/entities/DNS_and_Bind -%%DATADIR%%/sgml/ORA/entities/Essential_System_Administration -%%DATADIR%%/sgml/ORA/entities/MIF_Entities -%%DATADIR%%/sgml/ORA/entities/Managing_NFS_and_NIS -%%DATADIR%%/sgml/ORA/entities/Nutshell_Legal_Notice -%%DATADIR%%/sgml/ORA/entities/ORA_Entities -%%DATADIR%%/sgml/ORA/entities/ORA_X_Books -%%DATADIR%%/sgml/ORA/entities/System_Entities -%%DATADIR%%/sgml/ORA/entities/X_Legal_Notice_1 -%%DATADIR%%/sgml/ORA/entities/X_Legal_Notice_2 -%%DATADIR%%/sgml/ORA/entities/bulksales -%%DATADIR%%/sgml/ORA/entities/iso-lat1.gml -%%DATADIR%%/sgml/ORA/entities/iso-lat2 -%%DATADIR%%/sgml/ORA/entities/orachars -%%DATADIR%%/sgml/ORA/entities/oraxbooks -%%DATADIR%%/sgml/ORA/entities/oraxrelated -%%DATADIR%%/sgml/ORA/entities/xreqforcomments -%%DATADIR%%/sgml/cdtds/html -%%DATADIR%%/sgml/cdtds/memo -%%DATADIR%%/sgml/cdtds/orahtml -%%DATADIR%%/sgml/cdtds/oraprod.2.2.1 -%%DATADIR%%/sgml/doctype.close -%%DATADIR%%/sgml/doctype.open -%%DATADIR%%/sgml/foo.len -%%DATADIR%%/sgml/html.sdecl -%%DATADIR%%/sgml/sdecl -%%DATADIR%%/test/BOOKFILES -%%DATADIR%%/test/BOOKFILES~ -%%DATADIR%%/test/BOOKIDS -%%DATADIR%%/test/CATALOG -%%DATADIR%%/test/ch00.sgm -%%DATADIR%%/test/ch01.sgm -%%DATADIR%%/test/ch02.sgm -%%DATADIR%%/test/fmt/exlist/ch00.3l -%%DATADIR%%/test/fmt/exlist/ch01-new.3l -%%DATADIR%%/test/fmt/exlist/ch01.3l -%%DATADIR%%/test/fmt/exlist/ch02.3l -%%DATADIR%%/test/fmt/exlist/ch03.3l -%%DATADIR%%/test/fmt/exlist/ch05.3l -%%DATADIR%%/test/fmt/exlist/ch06.3l -%%DATADIR%%/test/fmt/exlist/ch07.3l -%%DATADIR%%/test/fmt/exlist/fptest -%%DATADIR%%/test/fmt/exlist/toc -%%DATADIR%%/test/fmt/figlist/ch00.3l -%%DATADIR%%/test/fmt/figlist/ch01-new.3l -%%DATADIR%%/test/fmt/figlist/ch01.3l -%%DATADIR%%/test/fmt/figlist/ch02.3l -%%DATADIR%%/test/fmt/figlist/ch03.3l -%%DATADIR%%/test/fmt/figlist/ch05.3l -%%DATADIR%%/test/fmt/figlist/ch06.3l -%%DATADIR%%/test/fmt/figlist/ch07.3l -%%DATADIR%%/test/fmt/figlist/fptest -%%DATADIR%%/test/fmt/figlist/toc -%%DATADIR%%/test/fmt/index/ch00.3l -%%DATADIR%%/test/fmt/index/ch01-new.3l -%%DATADIR%%/test/fmt/index/ch01.3l -%%DATADIR%%/test/fmt/index/ch02.3l -%%DATADIR%%/test/fmt/index/ch03.3l -%%DATADIR%%/test/fmt/index/ch05.3l -%%DATADIR%%/test/fmt/index/ch06.3l -%%DATADIR%%/test/fmt/index/ch07.3l -%%DATADIR%%/test/fmt/index/fptest -%%DATADIR%%/test/fmt/index/toc -%%DATADIR%%/test/fmt/tablist/ch00.3l -%%DATADIR%%/test/fmt/tablist/ch01-new.3l -%%DATADIR%%/test/fmt/tablist/ch01.3l -%%DATADIR%%/test/fmt/tablist/ch02.3l -%%DATADIR%%/test/fmt/tablist/ch03.3l -%%DATADIR%%/test/fmt/tablist/ch05.3l -%%DATADIR%%/test/fmt/tablist/ch06.3l -%%DATADIR%%/test/fmt/tablist/ch07.3l -%%DATADIR%%/test/fmt/tablist/fptest -%%DATADIR%%/test/fmt/tablist/toc -%%DATADIR%%/test/fmt/toc/Se.ch00.3l -%%DATADIR%%/test/fmt/toc/Se.ch00.3l.flag -%%DATADIR%%/test/fmt/toc/Se.ch01-new.3l -%%DATADIR%%/test/fmt/toc/Se.ch01-new.3l.flag -%%DATADIR%%/test/fmt/toc/Se.ch01.3l -%%DATADIR%%/test/fmt/toc/Se.ch01.3l.flag -%%DATADIR%%/test/fmt/toc/Se.ch02.3l -%%DATADIR%%/test/fmt/toc/Se.ch02.3l.flag -%%DATADIR%%/test/fmt/toc/Se.ch03.3l -%%DATADIR%%/test/fmt/toc/Se.ch03.3l.flag -%%DATADIR%%/test/fmt/toc/Se.ch05.3l.flag -%%DATADIR%%/test/fmt/toc/Se.ch06.3l -%%DATADIR%%/test/fmt/toc/Se.ch06.3l.flag -%%DATADIR%%/test/fmt/toc/Se.ch07.3l -%%DATADIR%%/test/fmt/toc/Se.ch07.3l.flag -%%DATADIR%%/test/fmt/toc/ch00.3l -%%DATADIR%%/test/fmt/toc/ch01-new.3l -%%DATADIR%%/test/fmt/toc/ch01.3l -%%DATADIR%%/test/fmt/toc/ch02.3l -%%DATADIR%%/test/fmt/toc/ch03.3l -%%DATADIR%%/test/fmt/toc/ch05.3l -%%DATADIR%%/test/fmt/toc/ch06.3l -%%DATADIR%%/test/fmt/toc/ch07.3l -%%DATADIR%%/test/fmt/toc/fptest -%%DATADIR%%/test/fmt/toc/toc -%%DATADIR%%/test/nsgmls.err -@dirrm %%DATADIR%%/bin -@dirrm %%DATADIR%%/lib -@dirrm %%DATADIR%%/macros -@dirrm %%DATADIR%%/sed -@dirrm %%DATADIR%%/sgml/ISO_8879-1986/entities -@dirrm %%DATADIR%%/sgml/ISO_8879-1986 -@dirrm %%DATADIR%%/sgml/ISO_9573-13-1991/entities -@dirrm %%DATADIR%%/sgml/ISO_9573-13-1991 -@dirrm %%DATADIR%%/sgml/ORA/dtds -@dirrm %%DATADIR%%/sgml/ORA/entities -@dirrm %%DATADIR%%/sgml/ORA -@dirrm %%DATADIR%%/sgml/cdtds -@dirrm %%DATADIR%%/sgml -@dirrm %%DATADIR%%/test/fmt/toc -@dirrm %%DATADIR%%/test/fmt/index -@dirrm %%DATADIR%%/test/fmt/exlist -@dirrm %%DATADIR%%/test/fmt/figlist -@dirrm %%DATADIR%%/test/fmt/tablist -@dirrm %%DATADIR%%/test/fmt -@dirrm %%DATADIR%%/test/tools-debug -@dirrm %%DATADIR%%/test -@dirrm %%DATADIR%% |