CVS commit: pkgsrc/biology/bioperl

To: pkgsrc-changes%NetBSD.org@localhost
Subject: CVS commit: pkgsrc/biology/bioperl
From: "Thomas Klausner" <wiz%netbsd.org@localhost>
Date: Sun, 6 Sep 2020 20:07:47 +0000

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.

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

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