Received: by mail.netbsd.org (Postfix, from userid 605) id 5E24A84D3A; Sun, 6 Sep 2020 20:07:49 +0000 (UTC) Received: from localhost (localhost [127.0.0.1]) by mail.netbsd.org (Postfix) with ESMTP id D7AF284D37 for ; Sun, 6 Sep 2020 20:07:48 +0000 (UTC) X-Virus-Scanned: amavisd-new at netbsd.org Received: from mail.netbsd.org ([127.0.0.1]) by localhost (mail.netbsd.org [127.0.0.1]) (amavisd-new, port 10025) with ESMTP id zDiAQkj754zY for ; Sun, 6 Sep 2020 20:07:47 +0000 (UTC) Received: from cvs.NetBSD.org (ivanova.NetBSD.org [IPv6:2001:470:a085:999:28c:faff:fe03:5984]) by mail.netbsd.org (Postfix) with ESMTP id BC61E84D2E for ; Sun, 6 Sep 2020 20:07:47 +0000 (UTC) Received: by cvs.NetBSD.org (Postfix, from userid 500) id B48D5FB28; Sun, 6 Sep 2020 20:07:47 +0000 (UTC) Content-Transfer-Encoding: 7bit Content-Type: multipart/mixed; boundary="_----------=_1599422867155680" MIME-Version: 1.0 Date: Sun, 6 Sep 2020 20:07:47 +0000 From: "Thomas Klausner" Subject: CVS commit: pkgsrc/biology/bioperl To: pkgsrc-changes@NetBSD.org Reply-To: wiz@netbsd.org X-Mailer: log_accum Message-Id: <20200906200747.B48D5FB28@cvs.NetBSD.org> Sender: pkgsrc-changes-owner@NetBSD.org List-Id: pkgsrc-changes.NetBSD.org Precedence: bulk List-Unsubscribe: This is a multi-part message in MIME format. --_----------=_1599422867155680 Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="US-ASCII" Module Name: pkgsrc Committed By: wiz Date: Sun Sep 6 20:07:47 UTC 2020 Modified Files: pkgsrc/biology/bioperl: Makefile PLIST distinfo Log Message: 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 To generate a diff of this commit: cvs rdiff -u -r1.39 -r1.40 pkgsrc/biology/bioperl/Makefile cvs rdiff -u -r1.4 -r1.5 pkgsrc/biology/bioperl/PLIST cvs rdiff -u -r1.9 -r1.10 pkgsrc/biology/bioperl/distinfo Please note that diffs are not public domain; they are subject to the copyright notices on the relevant files. --_----------=_1599422867155680 Content-Disposition: inline Content-Length: 4772 Content-Transfer-Encoding: binary Content-Type: text/x-diff; charset=us-ascii Modified files: Index: pkgsrc/biology/bioperl/Makefile diff -u pkgsrc/biology/bioperl/Makefile:1.39 pkgsrc/biology/bioperl/Makefile:1.40 --- pkgsrc/biology/bioperl/Makefile:1.39 Mon Aug 31 18:06:38 2020 +++ pkgsrc/biology/bioperl/Makefile Sun Sep 6 20:07:47 2020 @@ -1,8 +1,7 @@ -# $NetBSD: Makefile,v 1.39 2020/08/31 18:06:38 wiz Exp $ +# $NetBSD: Makefile,v 1.40 2020/09/06 20:07:47 wiz Exp $ -DISTNAME= BioPerl-1.007002 +DISTNAME= BioPerl-1.7.7 PKGNAME= ${DISTNAME:tl} -PKGREVISION= 3 CATEGORIES= biology perl5 MASTER_SITES= ${MASTER_SITE_PERL_CPAN:=Bio/} @@ -11,7 +10,6 @@ HOMEPAGE= http://www.bioperl.org/ COMMENT= Perl tools for computational molecular biology LICENSE= ${PERL5_LICENSE} -#BUILD_DEPENDS+= {perl>=5.19.6,p5-Module-Build>0.42}:../../devel/p5-Module-Build BUILD_DEPENDS+= p5-Test-Most-[0-9]*:../../devel/p5-Test-Most DEPENDS+= p5-Algorithm-Munkres-[0-9]*:../../math/p5-Algorithm-Munkres @@ -55,10 +53,11 @@ BUILD_DEPENDS+= p5-Text-Diff-[0-9]*:../. USE_TOOLS+= pax -REPLACE_PERL+= scripts/*/*.pl Bio/LiveSeq/Chain.pm +REPLACE_PERL+= examples/*.pl +REPLACE_PERL+= examples/*/*.pl -PERL5_MODULE_TYPE= Module::Build -PERL5_PACKLIST= auto/Bio/.packlist +PERL5_MODULE_TYPE= Module::Install +PERL5_PACKLIST= auto/BioPerl/.packlist INSTALLATION_DIRS= share/examples/bioperl Index: pkgsrc/biology/bioperl/PLIST diff -u pkgsrc/biology/bioperl/PLIST:1.4 pkgsrc/biology/bioperl/PLIST:1.5 --- pkgsrc/biology/bioperl/PLIST:1.4 Sun Nov 6 08:05:24 2016 +++ pkgsrc/biology/bioperl/PLIST Sun Sep 6 20:07:47 2020 @@ -1,27 +1,20 @@ -@comment $NetBSD: PLIST,v 1.4 2016/11/06 08:05:24 wen Exp $ +@comment $NetBSD: PLIST,v 1.5 2020/09/06 20:07:47 wiz Exp $ 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/clustalw.pl share/examples/bioperl/align/simplealign.pl -share/examples/bioperl/bioperl.pl -share/examples/bioperl/cluster/dbsnp.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/dbfetch share/examples/bioperl/db/est_tissue_query.pl -share/examples/bioperl/db/gb2features.pl -share/examples/bioperl/db/getGenBank.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/liveseq/change_gene.pl share/examples/bioperl/longorf.pl share/examples/bioperl/make_primers.pl -share/examples/bioperl/popgen/parse_calc_stats.pl share/examples/bioperl/quality/svgtrace.pl share/examples/bioperl/rev_and_trans.pl share/examples/bioperl/revcom_dir.pl @@ -41,17 +34,12 @@ share/examples/bioperl/searchio/rawwrite share/examples/bioperl/searchio/resultwriter.pl share/examples/bioperl/searchio/waba2gff.pl share/examples/bioperl/searchio/waba2gff3.pl -share/examples/bioperl/sirna/TAG -share/examples/bioperl/sirna/rnai_finder.cgi -share/examples/bioperl/structure/structure-io.pl -share/examples/bioperl/subsequence.cgi 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/psw.pl share/examples/bioperl/tools/reverse-translate.pl share/examples/bioperl/tools/run_genscan.pl share/examples/bioperl/tools/run_primer3.pl Index: pkgsrc/biology/bioperl/distinfo diff -u pkgsrc/biology/bioperl/distinfo:1.9 pkgsrc/biology/bioperl/distinfo:1.10 --- pkgsrc/biology/bioperl/distinfo:1.9 Sun Sep 17 07:48:11 2017 +++ pkgsrc/biology/bioperl/distinfo Sun Sep 6 20:07:47 2020 @@ -1,6 +1,6 @@ -$NetBSD: distinfo,v 1.9 2017/09/17 07:48:11 wiz Exp $ +$NetBSD: distinfo,v 1.10 2020/09/06 20:07:47 wiz Exp $ -SHA1 (BioPerl-1.007002.tar.gz) = 21ab4653fde8cd8520bd7f59f790535f99358eaa -RMD160 (BioPerl-1.007002.tar.gz) = 6c38bb83464a36546e22629675f881d42dbda4bd -SHA512 (BioPerl-1.007002.tar.gz) = d89502dd0561a9a969d816e6d66df7f11e57709934095a87027d2637d16a463f0669f7d7392d95a1c8a9db94bfa8d6ec714668a4b9f81fa8b9b512796138d287 -Size (BioPerl-1.007002.tar.gz) = 12362741 bytes +SHA1 (BioPerl-1.7.7.tar.gz) = 06a6d7a9faebe6e63c02ba5b31d1f7618289f534 +RMD160 (BioPerl-1.7.7.tar.gz) = 7aa9377f07e6b8fa0095f06898655acc11cfc27e +SHA512 (BioPerl-1.7.7.tar.gz) = adcb04b5aa8af2c15edd85b057842ba5f2f8c269a2c9d1b65b96c265539e49b0bb27901d687ec7382cf96c07c576e95c50a32caddf9286eb19c9591a56a12c82 +Size (BioPerl-1.7.7.tar.gz) = 7532782 bytes --_----------=_1599422867155680--