[pkgsrc/trunk]: pkgsrc/biology/bioperl Update to 1.007001

[wen <wen%pkgsrc.org@localhost>]

details:   https://anonhg.NetBSD.org/pkgsrc/rev/730a7182c04e
branches:  trunk
changeset: 354655:730a7182c04e
user:      wen <wen%pkgsrc.org@localhost>
date:      Sun Nov 06 08:05:24 2016 +0000

description:
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!

diffstat:

 biology/bioperl/Makefile |   5 ++---
 biology/bioperl/PLIST    |   4 +---
 biology/bioperl/distinfo |  10 +++++-----
 3 files changed, 8 insertions(+), 11 deletions(-)

diffs (47 lines):

diff -r 9529170ec513 -r 730a7182c04e biology/bioperl/Makefile
--- a/biology/bioperl/Makefile  Sun Nov 06 06:33:58 2016 +0000
+++ b/biology/bioperl/Makefile  Sun Nov 06 08:05:24 2016 +0000
@@ -1,8 +1,7 @@
-# $NetBSD: Makefile,v 1.32 2016/07/09 06:37:50 wiz Exp $
+# $NetBSD: Makefile,v 1.33 2016/11/06 08:05:24 wen Exp $
 
-DISTNAME=      BioPerl-1.6.924
+DISTNAME=      BioPerl-1.007001
 PKGNAME=       ${DISTNAME:tl}
-PKGREVISION=   2
 CATEGORIES=    biology perl5
 MASTER_SITES=  ${MASTER_SITE_PERL_CPAN:=Bio/}
 
diff -r 9529170ec513 -r 730a7182c04e biology/bioperl/PLIST
--- a/biology/bioperl/PLIST     Sun Nov 06 06:33:58 2016 +0000
+++ b/biology/bioperl/PLIST     Sun Nov 06 08:05:24 2016 +0000
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.3 2014/02/20 14:44:16 fhajny Exp $
+@comment $NetBSD: PLIST,v 1.4 2016/11/06 08:05:24 wen Exp $
 share/examples/bioperl/Bio-DB-GFF/load_ucsc.pl
 share/examples/bioperl/align/FastAlign.pl
 share/examples/bioperl/align/align_on_codons.pl
@@ -30,8 +30,6 @@
 share/examples/bioperl/root/exceptions2.pl
 share/examples/bioperl/root/exceptions3.pl
 share/examples/bioperl/root/exceptions4.pl
-share/examples/bioperl/root/lib/TestInterface.pm
-share/examples/bioperl/root/lib/TestObject.pm
 share/examples/bioperl/searchio/blast_example.pl
 share/examples/bioperl/searchio/custom_writer.pl
 share/examples/bioperl/searchio/hitwriter.pl
diff -r 9529170ec513 -r 730a7182c04e biology/bioperl/distinfo
--- a/biology/bioperl/distinfo  Sun Nov 06 06:33:58 2016 +0000
+++ b/biology/bioperl/distinfo  Sun Nov 06 08:05:24 2016 +0000
@@ -1,6 +1,6 @@
-$NetBSD: distinfo,v 1.7 2015/11/02 18:42:20 agc Exp $
+$NetBSD: distinfo,v 1.8 2016/11/06 08:05:24 wen Exp $
 
-SHA1 (BioPerl-1.6.924.tar.gz) = 74986dad54192a1e53b1da6b632877a782763140
-RMD160 (BioPerl-1.6.924.tar.gz) = 0723177a285607b95bf32114f6723f74873fe553
-SHA512 (BioPerl-1.6.924.tar.gz) = 49f732ece2c1d9ed39f951e51dd1c201f1ed528d3e5b765cd770b8992ecf5c4ef6bce2d38a261581c25d8d49dbbb17f1e15c897be1beed800ff5b8079b68503a
-Size (BioPerl-1.6.924.tar.gz) = 12623118 bytes
+SHA1 (BioPerl-1.007001.tar.gz) = 13a3e7a30d68ee32d735921668839eda668771f4
+RMD160 (BioPerl-1.007001.tar.gz) = c433044f47f5827f480836329487bf5780c9f480
+SHA512 (BioPerl-1.007001.tar.gz) = 6ab6af9d8fa74a299870273f2843872af099764997aa1b03f88248502f9ed1b74f4f577b67befa1ae8c18ee2640c029a08a403e2dec5b1cdea41f2b86c82c11b
+Size (BioPerl-1.007001.tar.gz) = 12486953 bytes