Accepting request 129021 from home:computersalat:devel:perl

update to 1.6.901 OBS-URL: https://build.opensuse.org/request/show/129021 OBS-URL: https://build.opensuse.org/package/show/devel:languages:perl/perl-BioPerl?expand=0&rev=4
2012-07-26 14:27:51 +00:00
parent a69a704fdf
commit 5f59bd50c1
6 changed files with 117 additions and 41 deletions
--- a/perl-BioPerl.changes
+++ b/perl-BioPerl.changes
@@ -1,3 +1,64 @@
+-------------------------------------------------------------------
+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