File perl-BioPerl.changes of Package perl-BioPerl

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File perl-BioPerl.changes of Package perl-BioPerl (Revision 82ac477e5c2873730196234dfececcf2)

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Sun Dec  8 03:12:41 UTC 2019 -  <timueller+perl@suse.de>

- updated to 1.7.7
   see /usr/share/doc/packages/perl-BioPerl/Changes

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.

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Wed Sep 18 09:48:31 UTC 2019 -  <timueller+perl@suse.de>

- Add build dependency Gd
- Remove deps.patch (not used anymore)

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Wed Sep 18 09:35:33 UTC 2019 -  <timueller+perl@suse.de>

- updated to 1.7.6
   see /usr/share/doc/packages/perl-BioPerl/Changes

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.

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Wed Apr  3 06:45:03 UTC 2019 - Stephan Kulow <coolo@suse.com>

- updated to 1.7.5
   see /usr/share/doc/packages/perl-BioPerl/Changes

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Thu Sep 27 16:11:06 UTC 2018 - Christian Wittmer <chris@computersalat.de>

- fix for boo#1089992
  * nothing provides /usr/local/bin/perl
- fix license
- fix wrong end of line encoding (dos)

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Wed Feb  7 16:10:23 UTC 2018 - coolo@suse.com

- updated to 1.007002
   see /usr/share/doc/packages/perl-BioPerl/Changes

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Thu Jul 26 13:25:33 UTC 2012 - chris@computersalat.de

- update to 1.6.901
  - [Notes]
    * Use of AcePerl is deprecated; Ace.pm isn't actively maintained, and
      modules using Ace will also be deprecated [lds, cjfields]
    * Minor bug fix release
    * Bio::SeqIO::gbxml tests require XML::SAX [hartzell]
    * Address Build.PL issues when DBI is not present [hartzell]
    * Skip gbxml.t and Interpro tests when modules not installed [cjfields]
    * Remove deprecated code for perl 5.14.0 compat [cjfields]
    * Due to schema changes and lack of support for older versions, support
      for NeXML 0.9 is only (very) partially implemented.
      See: https://redmine.open-bio.org/issues/3207
  - [Bug fixes]
    * [3205] - small fix to Bio::Perl blast_sequence() to make compliant with
      docs [genehack, cjfields]
    * $VERSION for CPAN/cpanm-based installs was broken; force setting of
      module version from dist_version (probably not the best way to do this,
      but it seems to work) [rbuels, cjfields]
- update to 1.6.900 April 14, 2011
  - [Notes]
    * This will probably be the last release to add significant features to
      core modules; subsequent releases will be for bug fixes alone.
      We are planning on a restructuring of core for summer 2011, potentially
      as part of the Google Summer of Code.  This may become BioPerl 2.0.
    * Version bump represents 'just prior to v 1.7'.  We may have point
      releases to deal with bugs, with increments of 1.6.901, 1.6.902, etc.
      This code essentially is what is on the github master branch.
  - [New features]
    * Core code updated for perl 5.12.x [cjfields, Charle Tilford]
    * Bio::Tree refactor
        - major overhaul of Bio::Tree code by Greg Jordan, fixes several bugs
        - removal of Scalar::Util::weaken code, which was causing odd headaches
          with premature GC, memory leaks with perl 5.10.0, etc [cjfields]
    * Bio::DB::SeqFeature bug fixes for GBrowse2 compatibility [lds, scottcain,
          many others]
    * Bio::SeqIO::msout, Bio::SeqIO::mbsout - parsers for ms and mbs
          [Warren Kretzschmar]
    * Bio::SeqIO::gbxml
        - bug 2515 - new contribution [Ryan Golhar, jhannah]
    * Bio::Assembly::IO
        - support for reading Maq, Sam and Bowtie files [maj]
        - support for reading 454 GS Assembler (Newbler) ACE files [fangly]
        - bug 2483: support for writing ACE files [Joshua Udall, fangly]
        - bug 2599: support DBLINK annotation in GenBank files [cjfields]
        - bug 2726: reading/writing granularity: whole scaffold or one contig
          at a time [Joshua Udall, fangly]
    * Bio::OntologyIO
        - Added parsing of xrefs to OBO files, which are stored as secondary
            dbxrefs of the cvterm [Naama Menda]
        - General Interpro-related code refactors [dukeleto, rbuels, cjfields]
    * PAML code updated to work with PAML 4.4d [DaveMessina]
  - [Bug fixes]
    * [3198] - sort tabular BLAST hits by score [DaveMessina]
    * a lot of BUG fixes, please see Changes file for more info
- remove obsolete Build patch
- remove Authors from description
- add deps patch and send upstream

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Wed Dec  1 13:30:46 UTC 2010 - coolo@novell.com

- switch to perl_requires macro

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Mon Aug 16 15:02:25 UTC 2010 - chris@computersalat.de

- enabled some more optional tests
  o Algorithm::Munkres, Convert::Binary::C, GraphViz,
    PostScript::TextBlock, Spreadsheet::ParseExcel

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Wed Aug  4 16:11:26 UTC 2010 - chris@computersalat.de

- add Build patch
  o do not try to connect CPAN ;)
- added recommended pkgs
  o + BuildRequires (recommended) --with test

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Mon Aug  2 21:13:45 UTC 2010 - chris@computersalat.de

- initial package 1.6.1
  * created by cpanspec 1.78

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File perl-BioPerl.changes of Package perl-BioPerl (Revision 82ac477e5c2873730196234dfececcf2)

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