Changelog for perl-BioPerl-1.6.901-1.1.noarch.rpm :
Thu Jul 26 14:00:00 2012 chrisAATTcomputersalat.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

Wed Dec 1 13:00:00 2010 cooloAATTnovell.com
- switch to perl_requires macro

Mon Aug 16 14:00:00 2010 chrisAATTcomputersalat.de
- enabled some more optional tests
o Algorithm::Munkres, Convert::Binary::C, GraphViz,
PostScript::TextBlock, Spreadsheet::ParseExcel

Wed Aug 4 14:00:00 2010 chrisAATTcomputersalat.de
- add Build patch
o do not try to connect CPAN ;)
- added recommended pkgs
o + BuildRequires (recommended) --with test

Mon Aug 2 14:00:00 2010 chrisAATTcomputersalat.de
- initial package 1.6.1

* created by cpanspec 1.78