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locks; strict; comment @# @; 1.5 date 2020.09.06.20.07.47; author wiz; state Exp; branches; next 1.4; commitid Hh2aMgDvnG5KF1nC; 1.4 date 2016.11.06.08.05.24; author wen; state Exp; branches; next 1.3; commitid 6tmsZiTCpIuMF2tz; 1.3 date 2014.02.20.14.44.16; author fhajny; state Exp; branches; next 1.2; commitid Ght08sVqZUkEGQpx; 1.2 date 2009.06.14.17.34.33; author joerg; state Exp; branches; next 1.1; 1.1 date 2001.10.31.21.27.53; author zuntum; state Exp; branches; next ; desc @@ 1.5 log @bioperl: update to 1.7.7. 1.7.7 2019-12-07 13:41:36-06:00 America/Chicago * The program bp_chaos_plot has been removed. * GD is now no longer a dependency, suggestion or requirement. * #321 - GenBank format fix for un-quoted features, text wrapping * Bio::DB::Query::WebQuery now includes methods for delay(), delay_policy(), and a 'private' _sleep() function that mirror those from Bio::DB::WebDBSeqI, primarily for compliance with potential website restrictions for the number and frequency of queries (e.g. NCBI eUtils). * Fix bug #329, related to Bio::Tree::Statistics::transfer_bootstrap_expectation in last release. 1.7.6 2019-08-28 12:37:01+01:00 Europe/London * The program bp_classify_hits_kingdom has been removed and is now part of the examples documentation instead. * GD is now listed as a suggestion instead of a requirement. The bp_chaos_plot program will now work with the GD module. * New method Bio::Tree::Statistics::transfer_bootstrap_expectation to compute Transfer Bootstrap Expectation (TBE) for internal nodes based on the methods outlined in Lemoine et al, Nature, 2018. * New method Bio::SeqIO::fasta::next_seq_fast to retrieve next sequence in the stream faster but not perfect. 1.7.5 2019-02-11 14:57:45+00:00 Europe/London * The following modules have been removed from the BioPerl distribution to be part of a separate distribution with independent development: Bio::Symbol::* * The Bio::Seq::SeqWithQuality module, which was deprecated since 2001, was finally removed. * The deprecated() method has been deprecated. It is recommended to use Carp::carp to warn. * The following methods have been deprecated for a long while and have now been removed: Bio::Align::AlignI->no_residues Bio::Align::AlignI->no_sequences Bio::LocatableSeq->no_gap Bio::LocatableSeq->no_sequences Bio::SeqFeature::Generic->slurp_gff_file Bio::SimpleAlign->no_residues Bio::SimpleAlign->no_sequences 1.7.4 2019-02-05 16:23:53+00:00 Europe/London * Fix Bio::Root::Test, and the testuite, to properly check for internet connection and the NO_NETWORK_TESTING environment variable. Previously, tests that required internet connection were not being skipped, causing tests to fail. 1.7.3 2019-01-30 13:30:34+00:00 Europe/London * The following modules have been removed from the BioPerl distribution to be part of a separate distribution. They have been integrated into other module distributions for independent development: Bio::Align::Graphics Bio::AlignIO::nexml Bio::AlignIO::stockholm Bio::Assembly::* Bio::Cluster::* Bio::ClusterI::* Bio::ClusterIO::* Bio::DB::Ace Bio::DB::BioFetch Bio::DB::CUTG Bio::DB::EMBL Bio::DB::EntrezGene Bio::DB::Expression::* Bio::DB::GFF Bio::DB::GFF::Adaptor::* Bio::DB::GFF::Aggregator::* Bio::DB::GFF::Featname Bio::DB::GFF::Feature Bio::DB::GFF::Homol Bio::DB::GFF::RelSegment Bio::DB::GFF::Segment Bio::DB::GFF::Typename Bio::DB::GenBank Bio::DB::GenPept Bio::DB::HIV::* Bio::DB::MeSH Bio::DB::NCBIHelper Bio::DB::Query::GenBank Bio::DB::Query::HIVQuery Bio::DB::RefSeq Bio::DB::SeqFeature::* Bio::DB::SeqVersion::* Bio::DB::SwissProt Bio::DB::TFBS::* Bio::DB::Taxonomy::entrez Bio::DB::Taxonomy::sqlite Bio::DB::Universal Bio::Draw::Pictogram Bio::Factory::MapFactoryI Bio::Index::Hmmer Bio::Index::Stockholm Bio::LiveSeq::* Bio::Map::* Bio::MapIO::* Bio::MolEvol::CodonModel Bio::Nexml::Factory Bio::NexmlIO Bio::Perl Bio::Phenotype::* Bio::PhyloNetwork::* Bio::PopGen::* Bio::Restriction::* Bio::Root::Build Bio::Search::HSP::HMMERHSP Bio::Search::HSP::HmmpfamHSP Bio::Search::Hit::HMMERHit Bio::Search::Hit::HmmpfamHit Bio::Search::Hit::hmmer3Hit Bio::Search::Result::HMMERResult Bio::Search::Result::HmmpfamResult Bio::Search::Result::hmmer3Result Bio::SearchDist Bio::SearchIO::hmmer Bio::SearchIO::hmmer2 Bio::SearchIO::hmmer3 Bio::SearchIO::hmmer_pull Bio::SeqEvolution::* Bio::SeqFeature::SiRNA::* Bio::SeqIO::abi Bio::SeqIO::agave Bio::SeqIO::alf Bio::SeqIO::chadoxml Bio::SeqIO::chaos Bio::SeqIO::chaosxml Bio::SeqIO::ctf Bio::SeqIO::entrezgene Bio::SeqIO::excel Bio::SeqIO::exp Bio::SeqIO::flybase_chadoxml Bio::SeqIO::lasergene Bio::SeqIO::nexml Bio::SeqIO::pln Bio::SeqIO::strider Bio::SeqIO::ztr Bio::Structure::* Bio::Taxonomy::* Bio::Tools::AlignFactory Bio::Tools::Analysis::* (except SimpleAnalysisBase) Bio::Tools::Gel Bio::Tools::HMMER::* Bio::Tools::Hmmpfam Bio::Tools::Phylo::Gumby Bio::Tools::Protparam Bio::Tools::Run::RemoteBlast Bio::Tools::SiRNA::* Bio::Tools::dpAlign Bio::Tools::pSW Bio::Tree::AlleleNode Bio::Tree::Draw::Cladogram Bio::TreeIO::nexml Bio::TreeIO::svggraph Bio::Variation::* * The following modules are new in the BioPerl distribution. They have been previously released in the BioPerl-Run distribution. This will enable smaller distributions that provide a Bio::Tool::Run interface, to be only dependent on the BioPerl distribution instead of the whole (very large) BioPerl-Run: Bio::Tools::Run::Analysis Bio::Tools::Run::AnalysisFactory Bio::Tools::Run::Phylo::PhyloBase Bio::Tools::Run::WrapperBase Bio::Tools::Run::WrapperBase::CommandExts * The following programs have been removed: bp_biofetch_genbank_proxy bp_blast2tree bp_bulk_load_gff bp_composite_LD bp_das_server bp_download_query_genbank bp_fast_load_gff bp_flanks bp_genbank2gff bp_generate_histogram bp_heterogeneity_test bp_hivq bp_hmmer_to_table bp_load_gff bp_meta_gff bp_netinstall bp_parse_hmmsearch bp_process_wormbase bp_query_entrez_taxa bp_remote_blast bp_seqfeature_delete bp_seqfeature_gff3 bp_seqfeature_load * Because of the move of so many modules and programs into separate distributions, the following modules are no longer prerequisites: Ace Ace::Sequence::Homol Algorithm::Munkres Apache::DBI Archive::Tar Array::Compare Bio::ASN1::EntrezGene Bio::Expression::Contact Bio::Expression::DataSet Bio::Expression::Platform Bio::Expression::Sample Bio::Ext::Align Bio::GMOD::CMap::Utils Bio::Phylo::Factory Bio::Phylo::Forest::Tree Bio::Phylo::IO Bio::Phylo::Matrices Bio::Phylo::Matrices::Datum Bio::Phylo::Matrices::Matrix Bio::SeqFeature::Annotated Bio::SeqIO::staden::read Bio::Tools::Run::Alignment::Clustalw Bio::Tools::Run::Ensembl Bio::Tools::Run::Phylo::Molphy::ProtML Bio::Tools::Run::Phylo::Phylip::Neighbor Bio::Tools::Run::Phylo::Phylip::ProtDist Bio::Tools::Run::Phylo::Phylip::ProtPars Bio::Tools::Run::Samtools CGI CPAN Cache::FileCache Config Convert::Binary::C DBD::Pg DBD::SQLite Data::Stag::XMLWriter Encode English ExtUtils::Install ExtUtils::Manifest File::Glob GD::Simple Getopt::Std Graph::Undirected GraphViz HTML::HeadParser HTML::TableExtract LWP LWP::Simple MIME::Base64 Memoize PostScript::TextBlock SVG SVG::Graph SVG::Graph::Data SVG::Graph::Data::Node SVG::Graph::Data::Tree Sort::Naturally Spreadsheet::ParseExcel Term::ReadLine Text::NSP::Measures::2D::Fisher2::twotailed Text::ParseWords Time::Local Tree::DAG_Node URI::Escape WWW::Mechanize XML::Simple * The following is a new prerequisite: Test::RequiresInternet * The deobfuscator has been removed. * The emacs bioperl minor mode is no longer distributed as part of the perl module distributions. See https://github.com/bioperl/emacs-bioperl-mode @ text @@@comment $NetBSD$ share/examples/bioperl/Bio-DB-GFF/load_ucsc.pl share/examples/bioperl/align/FastAlign.pl share/examples/bioperl/align/align_on_codons.pl share/examples/bioperl/align/aligntutorial.pl share/examples/bioperl/align/simplealign.pl share/examples/bioperl/classify_hits_kingdom share/examples/bioperl/contributed/nmrpdb_parse.pl share/examples/bioperl/contributed/prosite2perl.pl share/examples/bioperl/contributed/rebase2list.pl share/examples/bioperl/db/est_tissue_query.pl share/examples/bioperl/db/get_seqs.pl share/examples/bioperl/db/rfetch.pl share/examples/bioperl/db/use_registry.pl share/examples/bioperl/generate_random_seq.pl share/examples/bioperl/longorf.pl share/examples/bioperl/make_primers.pl share/examples/bioperl/quality/svgtrace.pl share/examples/bioperl/rev_and_trans.pl share/examples/bioperl/revcom_dir.pl share/examples/bioperl/root/README share/examples/bioperl/root/exceptions1.pl share/examples/bioperl/root/exceptions2.pl share/examples/bioperl/root/exceptions3.pl share/examples/bioperl/root/exceptions4.pl share/examples/bioperl/searchio/blast_example.pl share/examples/bioperl/searchio/custom_writer.pl share/examples/bioperl/searchio/hitwriter.pl share/examples/bioperl/searchio/hspwriter.pl share/examples/bioperl/searchio/htmlwriter.pl share/examples/bioperl/searchio/psiblast_features.pl share/examples/bioperl/searchio/psiblast_iterations.pl share/examples/bioperl/searchio/rawwriter.pl share/examples/bioperl/searchio/resultwriter.pl share/examples/bioperl/searchio/waba2gff.pl share/examples/bioperl/searchio/waba2gff3.pl share/examples/bioperl/tk/gsequence.pl share/examples/bioperl/tk/hitdisplay.pl share/examples/bioperl/tools/extract_genes.pl share/examples/bioperl/tools/gb_to_gff.pl share/examples/bioperl/tools/gff2ps.pl share/examples/bioperl/tools/parse_codeml.pl share/examples/bioperl/tools/reverse-translate.pl share/examples/bioperl/tools/run_genscan.pl share/examples/bioperl/tools/run_primer3.pl share/examples/bioperl/tools/seq_pattern.pl share/examples/bioperl/tools/standaloneblast.pl share/examples/bioperl/tree/paup2phylip.pl @ 1.4 log @Update to 1.007001 Upstream changes: 1.7.1 - "Election" [Bugs] * Minor release to incorporate fix for CPAN indexing, which prevented proper updates [cjfields] * Fix problem in managing Target attribute for gff3 [Jukes34] * Minor bug fixes related to NCBI HTTPS support [cjfields] 1.7.0 - "Disney" [New site] * We have migrated to Github Pages. This was actually planned, but the recent OBF server compromise forced our hand. Brian Osborne [bosborne] took this under his wing to move docs and has done a tremendous amount of work formatting the site and working out some of the idiosyncracies with the new Jekyll-based design. Mark Jensen, Paul Cantalupo and Franscison Ossandon also helped. Kudos!! * Similarly, the official issue tracker is now Github Issues. This has been updated in the relevant documentation bits (we hope!) [Code changes] * Previously deprecated modules removed * Bio::Tools::Infernal, Bio::Tools::ERPIN, Bio::Tools::RNAMotif * Bio::DB::SeqHound has been removed due to the service no longer being available * Bio::Tools::Analysis::Protein::Mitoprot has been removed for security reasons due to the server no longer having a valid cert * Bio::EUtilities, Bio::Biblio are now separate releases on CPAN * Bio::Coordinate, Bio::SearchIO::blastxml, Bio::SearchIO::Writer::BSMLResultWriter are now separate releases to be added on CPAN [New features] * Docker instances of tagged releases are available! [hlapp] * NCBI HTTPS support [mjohnson and others] * Bio::SearchIO::infernal - Issue #131: added CMSEARCH parsing support for Infernal 1.1 [pcantalupo] * Bio::Search::HSP::ModelHSP - Added a 'noncanonical_string' method to retrieve the NC line from CMSEARCH reports [pcantalupo] * Bio::Search::Result::INFERNALResult - Added new module to represent features of Infernal reports [pcantalupo] * Bio::DB::Taxonomy SQLite option [cjfields] * WrapperBase quoted option values [majensen] * Various documentation fixes and updates [bosborne] [Bug Fixes] * Fixes in Bio::Root::Build to deal with META.json/yml for CPAN indexing [cjfields] * Bio::SeqFeature::Generic spliced_seq() bug fix [Eric Snyder, via bosborne] * NeXML parser fixes [fjossandon] * Bug fix for Bio::DB::SeqFeature memory adapter [lstein] * RT 103272 : SeqFeature database deletion skipped features with a decimal - Joshua Fortriede (Xenbase) * RT 98374: AlignIO issues with sequence names not correctly parsing - Xiaoyu Zhuo * Issue #70: CONTIG parsing in GenBank output fixed [fjossandon] * Issue #76: Circular genome fixes with Bio::Location::Split [fjossandon] * Issue #80: Fix lack of caching issue with Bio::DB::Taxonomy [fjossandon] * Issue #81: Small updates to make sure possible memory leaks are detected [cjfields] * Issue #84: EMBL format wrapping problem [nyamned] * Issue #90: Missing entries for translation tables 24 and 25 [fjossandon] * Issue #95: Speed up of Bio::DB::Fasta::subseq by using a compiled regex or compiled C code (when Inline::C is installed) [rocky] * Fix various Bio::Tools::Analysis remote server config problems [cjfields] * Added several missing 'Data::Stag' and 'LWP::UserAgent' requirements [fjossandon] * Added a workaround in Bio::DB::Registry to get Username in Windows [fjossandon] * For HMMer report parsing, changed "$hsp->bits" to return 0 instead of undef to be consistent with "$hit->bits" behaviour [fjossandon] * Fixed a bug in HMMer3 parsing, where an homology line ending in CS or RF aminoacids made "next_seq" confused and broke the parser [fjossandon] * Adjusted FTLocationFactory.pm to comply with current GenBank Feature Table Definition, so now "join(complement(C..D),complement(A..B))" is equivalent to "complement(join(A..B,C..D))" [fjossandon] * For the many many many fixes that weren't mentioned - blame the release guy! @ text @a5 1 share/examples/bioperl/align/clustalw.pl d7 1 a7 2 share/examples/bioperl/bioperl.pl share/examples/bioperl/cluster/dbsnp.pl a10 1 share/examples/bioperl/db/dbfetch a11 2 share/examples/bioperl/db/gb2features.pl share/examples/bioperl/db/getGenBank.pl a15 1 share/examples/bioperl/liveseq/change_gene.pl a17 1 share/examples/bioperl/popgen/parse_calc_stats.pl a36 4 share/examples/bioperl/sirna/TAG share/examples/bioperl/sirna/rnai_finder.cgi share/examples/bioperl/structure/structure-io.pl share/examples/bioperl/subsequence.cgi a42 1 share/examples/bioperl/tools/psw.pl @ 1.3 log @Update biology/bioperl to 1.6.923. Way too many changes (0.7.0 was released in 2001!). See changelog at: https://github.com/bioperl/bioperl-live/blob/master/Changes @ text @a32 2 share/examples/bioperl/root/lib/TestInterface.pm share/examples/bioperl/root/lib/TestObject.pm @ 1.2 log @Remove @@dirrm entries from PLISTs @ text @d1 25 a25 42 @@comment $NetBSD: PLIST,v 1.1 2001/10/31 21:27:53 zuntum Exp $ share/examples/bioperl/blast/out/blastn.2.gz share/examples/bioperl/blast/out/blastn.2.wu.gz share/examples/bioperl/blast/out/blastp.1.gcg.gz share/examples/bioperl/blast/out/blastp.1.gz share/examples/bioperl/blast/out/blastp.2.gz share/examples/bioperl/blast/out/blastp.2.nogap.gz share/examples/bioperl/blast/out/blastp.2.wu share/examples/bioperl/blast/out/blastp.205.gz share/examples/bioperl/blast/out/blastp.2a.gz share/examples/bioperl/blast/out/blastp.2b.gz share/examples/bioperl/blast/out/blastp.email.html.gz share/examples/bioperl/blast/out/blastx.2 share/examples/bioperl/blast/out/blastx.2.email.gz share/examples/bioperl/blast/out/blastx.208.gz share/examples/bioperl/blast/out/tblastn.206.out.gz share/examples/bioperl/blast/seq/acc1.dna.fasta share/examples/bioperl/blast/seq/seqs.fasta share/examples/bioperl/blast/seq/yal011w.dna.fasta share/examples/bioperl/blast/seq/yel009c.fasta share/examples/bioperl/blast/seq/ymr284w.fasta share/examples/bioperl/blast/blast_config.pl share/examples/bioperl/blast/blast_seq.pl share/examples/bioperl/blast/example.table1 share/examples/bioperl/blast/example.table2 share/examples/bioperl/blast/html.pl share/examples/bioperl/blast/parse_blast.pl share/examples/bioperl/blast/parse_blast2.pl share/examples/bioperl/blast/parse_multi.pl share/examples/bioperl/blast/parse_positions.pl share/examples/bioperl/blast/print_blasts.pl share/examples/bioperl/blast/retrieve_blast.pl share/examples/bioperl/blast/run_blast_remote.pl share/examples/bioperl/blosum62.bla share/examples/bioperl/change_gene.pl share/examples/bioperl/clustalw.pl share/examples/bioperl/getGenBank.pl share/examples/bioperl/gon250.bla share/examples/bioperl/gsequence share/examples/bioperl/hitdisplay.pl share/examples/bioperl/psw.pl share/examples/bioperl/restriction.pl d27 36 a62 31 share/examples/bioperl/seq_pattern.pl share/examples/bioperl/simplealign.pl share/examples/bioperl/standaloneblast.pl share/examples/bioperl/test-genscan.pl share/examples/bioperl/root_object/Outer.pm share/examples/bioperl/root_object/Bar.pm share/examples/bioperl/root_object/Foo.pm share/examples/bioperl/root_object/vector/Person.pm share/examples/bioperl/root_object/vector/PersonManager.pm share/examples/bioperl/root_object/vector/vector.out share/examples/bioperl/root_object/vector/vector.pl share/examples/bioperl/root_object/destroy.pl share/examples/bioperl/root_object/error.out share/examples/bioperl/root_object/error.pl share/examples/bioperl/root_object/filehandle.out share/examples/bioperl/root_object/filehandle.pl share/examples/bioperl/root_object/io.out share/examples/bioperl/root_object/io.pl share/examples/bioperl/root_object/read.pl share/examples/bioperl/root_object/read.test share/examples/bioperl/root_object/read.test2 share/examples/bioperl/root_object/read.test3 share/examples/bioperl/root_object/utilities.pl share/examples/bioperl/seq/seq.fasta.gz share/examples/bioperl/seq/id.list share/examples/bioperl/seq/seq1.fasta share/examples/bioperl/seq/seq2.fasta share/examples/bioperl/seq/seqs1.pl share/examples/bioperl/seq/seqs2.pl share/examples/bioperl/seq/seqs3.pl share/examples/bioperl/seq/seqtools.pl @ 1.1 log @Move pkg/ files into package's toplevel directory @ text @d1 1 a1 1 @@comment $NetBSD: PLIST,v 1.3 2001/04/05 21:48:41 jtb Exp $ a74 7 @@dirrm share/examples/bioperl/seq @@dirrm share/examples/bioperl/root_object/vector @@dirrm share/examples/bioperl/root_object @@dirrm share/examples/bioperl/blast/seq @@dirrm share/examples/bioperl/blast/out @@dirrm share/examples/bioperl/blast @@dirrm share/examples/bioperl @