changes all issue tracking in preparation for switch to github issues

bioperl · Apr 21, 2014 · 7814d89 · 7814d89
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diff --git a/BUGS b/BUGS
@@ -3,15 +3,15 @@
 Known Bugs
 
 Bugs are tracked at this URL:
-https://redmine.open-bio.org/projects/bioperl/
+https://github.com/bioperl/bioperl-live/issues/
 
 Bioperl 1.6 series
 =============
 
 Though a stable release, some bugs and enhancements remain for this series
 that will be addressed in future point releases. For a full list please see:
 
-https://redmine.open-bio.org/projects/bioperl/
+https://github.com/bioperl/bioperl-live/issues/
 
 Bug     Summary (additional info)
 

diff --git a/Bio/Align/AlignI.pm b/Bio/Align/AlignI.pm
@@ -70,7 +70,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 of the bugs and their resolution. Bug reports can be submitted via the
 web:
 
-  https://redmine.open-bio.org/projects/bioperl/
+  https://github.com/bioperl/bioperl-live/issues
 
 =head1 AUTHOR - Jason Stajich
 

diff --git a/Bio/Align/DNAStatistics.pm b/Bio/Align/DNAStatistics.pm
@@ -313,7 +313,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 of the bugs and their resolution. Bug reports can be submitted via the
 web:
 
-  https://redmine.open-bio.org/projects/bioperl/
+  https://github.com/bioperl/bioperl-live/issues
 
 =head1 AUTHOR - Jason Stajich
 

diff --git a/Bio/Align/PairwiseStatistics.pm b/Bio/Align/PairwiseStatistics.pm
@@ -58,7 +58,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 of the bugs and their resolution. Bug reports can be submitted via the
 web:
 
-  https://redmine.open-bio.org/projects/bioperl/
+  https://github.com/bioperl/bioperl-live/issues
 
 =head1 AUTHOR - Jason Stajich
 

diff --git a/Bio/Align/ProteinStatistics.pm b/Bio/Align/ProteinStatistics.pm
@@ -68,7 +68,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 of the bugs and their resolution. Bug reports can be submitted via the
 web:
 
-  https://redmine.open-bio.org/projects/bioperl/
+  https://github.com/bioperl/bioperl-live/issues
 
 =head1 AUTHOR - Jason Stajich
 

diff --git a/Bio/Align/StatisticsI.pm b/Bio/Align/StatisticsI.pm
@@ -51,7 +51,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 of the bugs and their resolution. Bug reports can be submitted via the
 web:
 
-  https://redmine.open-bio.org/projects/bioperl/
+  https://github.com/bioperl/bioperl-live/issues
 
 =head1 AUTHOR - Jason Stajich
 

diff --git a/Bio/Align/Utilities.pm b/Bio/Align/Utilities.pm
@@ -91,7 +91,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 of the bugs and their resolution. Bug reports can be submitted via the
 web:
 
-  https://redmine.open-bio.org/projects/bioperl/
+  https://github.com/bioperl/bioperl-live/issues
 
 =head1 AUTHOR - Jason Stajich
 

diff --git a/Bio/AlignIO.pm b/Bio/AlignIO.pm
@@ -254,7 +254,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via the
 web:
 
-  https://redmine.open-bio.org/projects/bioperl/
+  https://github.com/bioperl/bioperl-live/issues
 
 =head1 AUTHOR - Peter Schattner
 

diff --git a/Bio/AlignIO/Handler/GenericAlignHandler.pm b/Bio/AlignIO/Handler/GenericAlignHandler.pm
@@ -562,7 +562,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via the
 web:
 
-  https://redmine.open-bio.org/projects/bioperl/
+  https://github.com/bioperl/bioperl-live/issues
 
 =head1 AUTHOR - Chris Fields
 

diff --git a/Bio/AlignIO/arp.pm b/Bio/AlignIO/arp.pm
@@ -77,7 +77,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via the
 web:
 
-  https://redmine.open-bio.org/projects/bioperl/
+  https://github.com/bioperl/bioperl-live/issues
 
 =head1 AUTHORS
 

diff --git a/Bio/AlignIO/bl2seq.pm b/Bio/AlignIO/bl2seq.pm
@@ -87,7 +87,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via the
 web:
 
-  https://redmine.open-bio.org/projects/bioperl/
+  https://github.com/bioperl/bioperl-live/issues
 
 =head1 AUTHOR - Peter Schattner
 

diff --git a/Bio/AlignIO/clustalw.pm b/Bio/AlignIO/clustalw.pm
@@ -54,7 +54,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via the
 web:
 
-  https://redmine.open-bio.org/projects/bioperl/
+  https://github.com/bioperl/bioperl-live/issues
 
 =head1 AUTHORS - Peter Schattner
 

diff --git a/Bio/AlignIO/emboss.pm b/Bio/AlignIO/emboss.pm
@@ -59,7 +59,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 of the bugs and their resolution. Bug reports can be submitted via the
 web:
 
-  https://redmine.open-bio.org/projects/bioperl/
+  https://github.com/bioperl/bioperl-live/issues
 
 =head1 AUTHOR - Jason Stajich
 

diff --git a/Bio/AlignIO/fasta.pm b/Bio/AlignIO/fasta.pm
@@ -41,7 +41,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via the
 web:
 
-  https://redmine.open-bio.org/projects/bioperl/
+  https://github.com/bioperl/bioperl-live/issues
 
 =head1 AUTHORS
 

diff --git a/Bio/AlignIO/largemultifasta.pm b/Bio/AlignIO/largemultifasta.pm
@@ -53,7 +53,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via the
 web:
 
-  https://redmine.open-bio.org/projects/bioperl/
+  https://github.com/bioperl/bioperl-live/issues
 
 =head1 AUTHORS - Albert Vilella, Heikki Lehvaslaiho
 

diff --git a/Bio/AlignIO/maf.pm b/Bio/AlignIO/maf.pm
@@ -64,7 +64,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via the
 web:
 
-  https://redmine.open-bio.org/projects/bioperl/
+  https://github.com/bioperl/bioperl-live/issues
 
 =head1 AUTHORS - Allen Day
 

diff --git a/Bio/AlignIO/mase.pm b/Bio/AlignIO/mase.pm
@@ -46,7 +46,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via the
 web:
 
-  https://redmine.open-bio.org/projects/bioperl/
+  https://github.com/bioperl/bioperl-live/issues
 
 =head1 AUTHORS - Peter Schattner
 

diff --git a/Bio/AlignIO/mega.pm b/Bio/AlignIO/mega.pm
@@ -59,7 +59,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 of the bugs and their resolution. Bug reports can be submitted the
 web:
 
-  https://redmine.open-bio.org/projects/bioperl/
+  https://github.com/bioperl/bioperl-live/issues
 
 =head1 AUTHOR - Jason Stajich
 

diff --git a/Bio/AlignIO/meme.pm b/Bio/AlignIO/meme.pm
@@ -59,7 +59,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via the
 web:
 
-  https://redmine.open-bio.org/projects/bioperl/
+  https://github.com/bioperl/bioperl-live/issues
 
 =head1 AUTHORS - Benjamin Berman
 

diff --git a/Bio/AlignIO/metafasta.pm b/Bio/AlignIO/metafasta.pm
@@ -58,7 +58,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via the
 web:
 
-  https://redmine.open-bio.org/projects/bioperl/
+  https://github.com/bioperl/bioperl-live/issues
 
 =head1 AUTHOR - Heikki Lehvaslaiho
 

diff --git a/Bio/AlignIO/msf.pm b/Bio/AlignIO/msf.pm
@@ -45,7 +45,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via the
 web:
 
-  https://redmine.open-bio.org/projects/bioperl/
+  https://github.com/bioperl/bioperl-live/issues
 
 =head1 AUTHORS - Peter Schattner
 

diff --git a/Bio/AlignIO/nexml.pm b/Bio/AlignIO/nexml.pm
@@ -38,7 +38,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via the
 web:
 
-  https://redmine.open-bio.org/projects/bioperl/
+  https://github.com/bioperl/bioperl-live/issues
 
 =head1 AUTHORS
 

diff --git a/Bio/AlignIO/nexus.pm b/Bio/AlignIO/nexus.pm
@@ -49,7 +49,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via the
 web:
 
-  https://redmine.open-bio.org/projects/bioperl/
+  https://github.com/bioperl/bioperl-live/issues
 
 =head1 AUTHORS - Heikki Lehvaslaiho
 

diff --git a/Bio/AlignIO/pfam.pm b/Bio/AlignIO/pfam.pm
@@ -46,7 +46,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via the
 web:
 
-  https://redmine.open-bio.org/projects/bioperl/
+  https://github.com/bioperl/bioperl-live/issues
 
 =head1 AUTHORS - Peter Schattner
 

diff --git a/Bio/AlignIO/phylip.pm b/Bio/AlignIO/phylip.pm
@@ -71,7 +71,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution. Bug reports can be submitted via the
 web:
 
-  https://redmine.open-bio.org/projects/bioperl/
+  https://github.com/bioperl/bioperl-live/issues
 
 =head1 AUTHORS - Heikki Lehvaslaiho and Jason Stajich
 

diff --git a/Bio/AlignIO/po.pm b/Bio/AlignIO/po.pm
@@ -46,7 +46,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via the
 web:
 
-  https://redmine.open-bio.org/projects/bioperl/
+  https://github.com/bioperl/bioperl-live/issues
 
 =head1 AUTHORS - Matthew Betts
 

diff --git a/Bio/AlignIO/proda.pm b/Bio/AlignIO/proda.pm
@@ -56,7 +56,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via the
 web:
 
-  https://redmine.open-bio.org/projects/bioperl/
+  https://github.com/bioperl/bioperl-live/issues
 
 =head1 AUTHORS - Albert Vilella
 

diff --git a/Bio/AlignIO/prodom.pm b/Bio/AlignIO/prodom.pm
@@ -46,7 +46,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via the
 web:
 
-  https://redmine.open-bio.org/projects/bioperl/
+  https://github.com/bioperl/bioperl-live/issues
 
 =head1 AUTHORS - Peter Schattner
 

diff --git a/Bio/AlignIO/psi.pm b/Bio/AlignIO/psi.pm
@@ -51,7 +51,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 of the bugs and their resolution. Bug reports can be submitted via
 the web:
 
-  https://redmine.open-bio.org/projects/bioperl/
+  https://github.com/bioperl/bioperl-live/issues
 
 =head1 AUTHOR - Jason Stajich
 

diff --git a/Bio/AlignIO/selex.pm b/Bio/AlignIO/selex.pm
@@ -55,7 +55,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution. Bug reports can be submitted via the
 web:
 
-  https://redmine.open-bio.org/projects/bioperl/
+  https://github.com/bioperl/bioperl-live/issues
 
 =head1 AUTHORS - Peter Schattner
 

diff --git a/Bio/AlignIO/stockholm.pm b/Bio/AlignIO/stockholm.pm
@@ -198,7 +198,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via the
 web:
 
-  https://redmine.open-bio.org/projects/bioperl/
+  https://github.com/bioperl/bioperl-live/issues
 
 =head1 AUTHORS - Chris Fields, Peter Schattner
 

diff --git a/Bio/AlignIO/xmfa.pm b/Bio/AlignIO/xmfa.pm
@@ -49,7 +49,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via the
 web:
 
-  https://redmine.open-bio.org/projects/bioperl/
+  https://github.com/bioperl/bioperl-live/issues
 
 =head1 AUTHORS
 

diff --git a/Bio/AnalysisI.pm b/Bio/AnalysisI.pm
@@ -55,7 +55,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 of the bugs and their resolution. Bug reports can be submitted via the
 web:
 
-  https://redmine.open-bio.org/projects/bioperl/
+  https://github.com/bioperl/bioperl-live/issues
 
 =head1 AUTHOR
 

diff --git a/Bio/AnalysisParserI.pm b/Bio/AnalysisParserI.pm
@@ -108,7 +108,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via the
 web:
 
-  https://redmine.open-bio.org/projects/bioperl/
+  https://github.com/bioperl/bioperl-live/issues
 
 =head1 AUTHOR - Steve Chervitz, Jason Stajich, Hilmar Lapp
 

diff --git a/Bio/AnalysisResultI.pm b/Bio/AnalysisResultI.pm
@@ -68,7 +68,7 @@ with code and data examples if at all possible.
 Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via the web:
 
-  https://redmine.open-bio.org/projects/bioperl/
+  https://github.com/bioperl/bioperl-live/issues
 
 =head1 AUTHOR - Steve Chervitz, Hilmar Lapp
 

diff --git a/Bio/AnnotatableI.pm b/Bio/AnnotatableI.pm
@@ -62,7 +62,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 of the bugs and their resolution. Bug reports can be submitted via the
 web:
 
-  https://redmine.open-bio.org/projects/bioperl/
+  https://github.com/bioperl/bioperl-live/issues
 
 =head1 AUTHOR
 

diff --git a/Bio/Annotation/AnnotationFactory.pm b/Bio/Annotation/AnnotationFactory.pm
@@ -72,7 +72,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 of the bugs and their resolution. Bug reports can be submitted via
 the web:
 
-  https://redmine.open-bio.org/projects/bioperl/
+  https://github.com/bioperl/bioperl-live/issues
 
 =head1 AUTHOR - Hilmar Lapp
 

diff --git a/Bio/Annotation/Collection.pm b/Bio/Annotation/Collection.pm
@@ -66,7 +66,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via
 the web:
 
-  https://redmine.open-bio.org/projects/bioperl/
+  https://github.com/bioperl/bioperl-live/issues
 
 =head1 AUTHOR - Ewan Birney
 

diff --git a/Bio/Annotation/OntologyTerm.pm b/Bio/Annotation/OntologyTerm.pm
@@ -85,7 +85,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via
 the web:
 
-  https://redmine.open-bio.org/projects/bioperl/
+  https://github.com/bioperl/bioperl-live/issues
 
 =head1 AUTHOR - Hilmar Lapp
 

diff --git a/Bio/Annotation/Relation.pm b/Bio/Annotation/Relation.pm
@@ -57,7 +57,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via
 the web:
 
-  https://redmine.open-bio.org/projects/bioperl/
+  https://github.com/bioperl/bioperl-live/issues
 
 =head1 AUTHOR  - Mira Han
 

diff --git a/Bio/Annotation/SimpleValue.pm b/Bio/Annotation/SimpleValue.pm
@@ -56,7 +56,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via
 the web:
 
-  https://redmine.open-bio.org/projects/bioperl/
+  https://github.com/bioperl/bioperl-live/issues
 
 =head1 AUTHOR  - Ewan Birney 
 

diff --git a/Bio/Annotation/StructuredValue.pm b/Bio/Annotation/StructuredValue.pm
@@ -65,7 +65,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via
 or the web:
 
-  https://redmine.open-bio.org/projects/bioperl/
+  https://github.com/bioperl/bioperl-live/issues
 
 =head1 AUTHOR - Hilmar Lapp
 

diff --git a/Bio/Annotation/TagTree.pm b/Bio/Annotation/TagTree.pm
@@ -99,7 +99,7 @@ Report bugs to the Bioperl bug tracking system to help us keep track
 the bugs and their resolution.  Bug reports can be submitted via
 or the web:
 
-  https://redmine.open-bio.org/projects/bioperl/
+  https://github.com/bioperl/bioperl-live/issues
 
 =head1 AUTHOR