./biology/bioperl, Perl tools for computational molecular biology

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Branch: CURRENT, Version: 1.007002nb1, Package name: bioperl-1.007002nb1, Maintainer: pkgsrc-users

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.


Required to run:
[textproc/p5-XML-Simple] [textproc/p5-libxml] [textproc/p5-YAML] [textproc/p5-XML-DOM] [textproc/p5-XML-Parser] [textproc/p5-XML-SAX] [textproc/p5-XML-SAX-Writer] [textproc/p5-XML-Twig] [textproc/p5-XML-Writer] [www/p5-HTML-TableExtract] [www/p5-libwww] [www/p5-HTML-Parser] [graphics/p5-GraphViz] [graphics/p5-GD] [lang/perl5] [net/p5-SOAP-Lite] [math/p5-Spreadsheet-ParseExcel] [devel/p5-Error] [devel/p5-Array-Compare] [devel/p5-List-MoreUtils] [devel/p5-Set-Scalar] [devel/p5-Graph] [devel/p5-IO-String] [devel/p5-Clone] [graphics/p5-SVG] [devel/p5-Sort-Naturally] [biology/p5-Bio-ASN1-EntrezGene] [graphics/p5-SVG-Graph] [print/p5-PostScript] [math/p5-Algorithm-Munkres] [devel/p5-Convert-Binary-C] [devel/p5-Data-Stag]

Required to build:
[textproc/p5-Text-Diff] [devel/p5-Module-Build] [devel/p5-Test-Most] [pkgtools/cwrappers]

Master sites: (Expand)

SHA1: 21ab4653fde8cd8520bd7f59f790535f99358eaa
RMD160: 6c38bb83464a36546e22629675f881d42dbda4bd
Filesize: 12072.989 KB

Version history: (Expand)


CVS history: (Expand)


   2018-08-22 11:48:07 by Thomas Klausner | Files touched by this commit (3558)
Log message:
Recursive bump for perl5-5.28.0
   2017-09-17 09:48:11 by Thomas Klausner | Files touched by this commit (2) | Package updated
Log message:
bioperl: update to 1.007002.

Add p5-Text-Diff as test dependency.

1.7.2 - "Entebbe"

    [Bugs]

    * #247 - Omit unnecessary parent_id attribute added by GFF3Loader [nathanweeks]
    * #245 - Code coverage fixes [zmughal,cjfields]
    * #237 - Fix warning in Bio::DB::IndexedBase [willmclaren,bosborne]
    * #238 - Use a Travis cron job for network tests [zmughal,cjfields]
    * #218 - Bio::DB::Flat::BinarySearch should use _fh() instead of fh() as \ 
fh() does not take arguments in [thibauthourlier,bosborne]
    * #227 - Bio::SeqIO Ignores first line of sequence [VAR121,bosborne]
    * #223 - Use Travis Perl helper script and enable coverage [zmughal,cjfields]
    * #222 - Fix test RemoteDB/Taxonomy.t: requires networking [zmughal,cjfields]
    * #216 - Apply carsonhh's patch (Inline::C fixes) [carsonh,bosborne]
    * #213 - Support FTS5 in Bio::DB::SeqFeature::Store::DBI::SQLite \ 
[nathanweeks,bosborne]
    * #210 - Sorting qualifiers while write embl files [hdevillers,cjfields]
    * #209 - Fixed bug in _toDsspKey() [jvolkening,hlapp]

    [Code changes]

    * PAML-related code from bioperl and bioperl-run are now in a separate \ 
distribution on CPAN [carandraug]
   2016-11-10 15:00:17 by Filip Hajny | Files touched by this commit (1)
Log message:
Give up maintainership.
   2016-11-06 09:05:24 by Wen Heping | Files touched by this commit (3) | Package updated
Log message:
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!
   2016-07-09 08:39:18 by Thomas Klausner | Files touched by this commit (1068) | Package updated
Log message:
Bump PKGREVISION for perl-5.24.0 for everything mentioning perl.
   2015-11-02 19:42:23 by Alistair G. Crooks | Files touched by this commit (38)
Log message:
Add SHA512 digests for distfiles for biology category.

Existing SHA1 digests verified, all found to be the same on the
machine holding the existing distfiles (morden).  Existing SHA1
digests retained for now as an audit trail.
   2015-07-12 20:56:37 by Thomas Klausner | Files touched by this commit (405)
Log message:
Comment out dependencies of the style
{perl>=5.16.6,p5-ExtUtils-ParseXS>=3.15}:../../devel/p5-ExtUtils-ParseXS
since pkgsrc enforces the newest perl version anyway, so they
should always pick perl, but sometimes (pkg_add) don't due to the
design of the {,} syntax.

No effective change for the above reason.

Ok joerg
   2015-06-12 12:52:19 by Thomas Klausner | Files touched by this commit (3152)
Log message:
Recursive PKGREVISION bump for all packages mentioning 'perl',
having a PKGNAME of p5-*, or depending such a package,
for perl-5.22.0.