Merged from HEAD to 1.5.1 branch, changes which remove old bug email …

…address and point to bugzilla.bioperl.org website for bug submission svn path=/bioperl-run/branches/bioperl-run-branch-1-5-1/; revision=13668
bioperl · Oct 9, 2005 · 3ee0b64 · 3ee0b64
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diff --git a/Bio/Factory/EMBOSS.pm b/Bio/Factory/EMBOSS.pm
@@ -70,11 +70,10 @@ Bioperl mailing lists  Your participation is much appreciated.
 
 =head2 Reporting Bugs
 
-report bugs to the Bioperl bug tracking system to help us keep track
- the bugs and their resolution.  Bug reports can be submitted via
- email or the web:
+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:
 
-  bioperl-bugs@bio.perl.org
   http://bugzilla.bioperl.org/
 
 =head1 AUTHOR - Heikki Lehvaslaiho

diff --git a/Bio/Tools/Run/Alignment/Blat.pm b/Bio/Tools/Run/Alignment/Blat.pm
@@ -19,26 +19,25 @@ Bio::Tools::Run::Alignment::Blat
 
 =head1 DESCRIPTION
 
- wrapper module for Blat  program
+wrapper module for Blat program
 
 =head1 FEEDBACK
 
 =head2 Mailing Lists
 
- User feedback is an integral part of the evolution of this and other
- Bioperl modules. Send your comments and suggestions preferably to one
- of the Bioperl mailing lists.  Your participation is much appreciated.
+User feedback is an integral part of the evolution of this and other
+Bioperl modules. Send your comments and suggestions preferably to one
+of the Bioperl mailing lists.  Your participation is much appreciated.
 
  bioperl-l@bioperl.org          - General discussion
  http://bio.perl.org/MailList.html             - About the mailing lists
 
 =head2 Reporting Bugs
 
- Report bugs to the Bioperl bug tracking system to help us keep track
- the bugs and their resolution.  Bug reports can be submitted via
- email or the web:
+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:
 
- bioperl-bugs@bioperl.org
  http://bugzilla.bioperl.org/
 
 =head1 AUTHOR - Bala
@@ -47,8 +46,8 @@ Bio::Tools::Run::Alignment::Blat
 
 =head1 APPENDIX
 
- The rest of the documentation details each of the object
- methods. Internal methods are usually preceded with a _
+The rest of the documentation details each of the object
+methods. Internal methods are usually preceded with a _
 
 =cut
 

diff --git a/Bio/Tools/Run/Alignment/Clustalw.pm b/Bio/Tools/Run/Alignment/Clustalw.pm
@@ -316,11 +316,10 @@ of the Bioperl mailing lists.  Your participation is much appreciated.
 =head2 Reporting Bugs
 
 Report bugs to the Bioperl bug tracking system to help us keep track
- the bugs and their resolution.  Bug reports can be submitted via
- email or the web:
+the bugs and their resolution.  Bug reports can be submitted via the
+web:
 
-  bioperl-bugs@bio.perl.org
-  http://bio.perl.org/bioperl-bugs/
+  http://bugzilla.bioperl.org/
 
 =head1 AUTHOR -  Peter Schattner
 

diff --git a/Bio/Tools/Run/Alignment/DBA.pm b/Bio/Tools/Run/Alignment/DBA.pm
@@ -56,11 +56,10 @@ of the Bioperl mailing lists.  Your participation is much appreciated.
 =head2 Reporting Bugs
 
 Report bugs to the Bioperl bug tracking system to help us keep track
- the bugs and their resolution.  Bug reports can be submitted via
- email or the web:
+the bugs and their resolution.  Bug reports can be submitted via the
+web:
 
-  bioperl-bugs@bio.perl.org
-  http://bio.perl.org/bioperl-bugs/
+  http://bugzilla.bioperl.org/
 
 =head1 AUTHOR - Shawn Hoon 
 

diff --git a/Bio/Tools/Run/Alignment/Lagan.pm b/Bio/Tools/Run/Alignment/Lagan.pm
@@ -94,10 +94,9 @@ the Bioperl mailing list.  Your participation is much appreciated.
 =head2 Reporting Bugs
 
 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
-email or the web:
+of the bugs and their resolution. Bug reports can be submitted via the
+web:
 
-  bioperl-bugs@bioperl.org
   http://bugzilla.bioperl.org/
 
 =head1 AUTHOR - Stephen Montgomery

diff --git a/Bio/Tools/Run/Alignment/Sim4.pm b/Bio/Tools/Run/Alignment/Sim4.pm
@@ -64,11 +64,10 @@ of the Bioperl mailing lists.  Your participation is much appreciated.
 =head2 Reporting Bugs
 
 Report bugs to the Bioperl bug tracking system to help us keep track
- the bugs and their resolution.  Bug reports can be submitted via
- email or the web:
+the bugs and their resolution.  Bug reports can be submitted via the
+web:
 
-  bioperl-bugs@bio.perl.org
-  http://bio.perl.org/bioperl-bugs/
+  http://bugzilla.bioperl.org/
 
 =head1 AUTHOR - Shawn Hoon 
 

diff --git a/Bio/Tools/Run/Alignment/StandAloneFasta.pm b/Bio/Tools/Run/Alignment/StandAloneFasta.pm
@@ -87,9 +87,10 @@ of the Bioperl mailing lists.  Your participation is much appreciated.
 =head2 Reporting Bugs
 
 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:
+the bugs and their resolution.  Bug reports can be submitted via the
+web:
 
-  http://bio.perl.org/bioperl-bugs/
+                                                                http://bugzilla.bioperl.org/
 
 =head1 AUTHOR -  Tiequan Zhang
 

diff --git a/Bio/Tools/Run/Analysis.pm b/Bio/Tools/Run/Analysis.pm
@@ -158,7 +158,7 @@ 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:
 
-  http://bioperl.org/bioperl-bugs/
+  http://bugzilla.bioperl.org/
 
 =head1 AUTHOR
 

diff --git a/Bio/Tools/Run/Analysis/soap.pm b/Bio/Tools/Run/Analysis/soap.pm
@@ -46,7 +46,7 @@ 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:
 
-  http://bioperl.org/bioperl-bugs/
+  http://bugzilla.bioperl.org/
 
 =head1 AUTHOR
 

diff --git a/Bio/Tools/Run/AnalysisFactory.pm b/Bio/Tools/Run/AnalysisFactory.pm
@@ -91,11 +91,10 @@ the Bioperl mailing list.  Your participation is much appreciated.
 =head2 Reporting Bugs
 
 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
-email or the web:
+of the bugs and their resolution. Bug reports can be submitted via the
+web:
 
-  bioperl-bugs@bioperl.org
-  http://bioperl.org/bioperl-bugs/
+  http://bugzilla.bioperl.org/
 
 =head1 AUTHOR
 

diff --git a/Bio/Tools/Run/AnalysisFactory/Pise.pm b/Bio/Tools/Run/AnalysisFactory/Pise.pm
@@ -109,11 +109,10 @@ the Bioperl mailing list.  Your participation is much appreciated.
 =head2 Reporting Bugs
 
 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
-email or the web:
+of the bugs and their resolution. Bug reports can be submitted via the
+web:
 
-  bioperl-bugs@bioperl.org
-  http://bioperl.org/bioperl-bugs/
+  http://bugzilla.bioperl.org/
 
 =head1 AUTHOR
 

diff --git a/Bio/Tools/Run/AnalysisFactory/soap.pm b/Bio/Tools/Run/AnalysisFactory/soap.pm
@@ -43,7 +43,7 @@ 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:
 
-  http://bioperl.org/bioperl-bugs/
+  http://bugzilla.bioperl.org/
 
 =head1 AUTHOR
 

diff --git a/Bio/Tools/Run/Coil.pm b/Bio/Tools/Run/Coil.pm
@@ -25,26 +25,25 @@ Bio::Tools::Run::Coil
 
 =head1 DESCRIPTION
 
- Wrapper module for Coil
+Wrapper module for Coil
 
 =head1 FEEDBACK
 
 =head2 Mailing Lists
 
- User feedback is an integral part of the evolution of this and other
- Bioperl modules. Send your comments and suggestions preferably to one
- of the Bioperl mailing lists.  Your participation is much appreciated.
+User feedback is an integral part of the evolution of this and other
+Bioperl modules. Send your comments and suggestions preferably to one
+of the Bioperl mailing lists.  Your participation is much appreciated.
 
  bioperl-l@bioperl.org          - General discussion
  http://bio.perl.org/MailList.html             - About the mailing lists
 
 =head2 Reporting Bugs
 
- Report bugs to the Bioperl bug tracking system to help us keep track
- the bugs and their resolution.  Bug reports can be submitted via
- email or the web:
+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:
 
- bioperl-bugs@bioperl.org
  http://bugzilla.bioperl.org/
 
 =head1 AUTHOR
@@ -56,8 +55,8 @@ Bio::Tools::Run::Coil
 
 =head1 APPENDIX
 
- The rest of the documentation details each of the object
- methods. Internal methods are usually preceded with a _
+The rest of the documentation details each of the object
+methods. Internal methods are usually preceded with a _
 
 =cut
 

diff --git a/Bio/Tools/Run/EMBOSSApplication.pm b/Bio/Tools/Run/EMBOSSApplication.pm
@@ -74,11 +74,10 @@ Bioperl mailing lists  Your participation is much appreciated.
 =head2 Reporting Bugs
 
 report bugs to the Bioperl bug tracking system to help us keep track
- the bugs and their resolution.  Bug reports can be submitted via
- email or the web:
+the bugs and their resolution.  Bug reports can be submitted via the
+web:
 
-  bioperl-bugs@bio.perl.org
-  http://bio.perl.org/bioperl-bugs/
+   http://bugzilla.bioperl.org/
 
 =head1 AUTHOR - Heikki Lehvaslaiho
 

diff --git a/Bio/Tools/Run/EMBOSSacd.pm b/Bio/Tools/Run/EMBOSSacd.pm
@@ -80,11 +80,10 @@ Bioperl mailing lists  Your participation is much appreciated.
 =head2 Reporting Bugs
 
 report bugs to the Bioperl bug tracking system to help us keep track
- the bugs and their resolution.  Bug reports can be submitted via
- email or the web:
+the bugs and their resolution.  Bug reports can be submitted via the
+web:
 
-  bioperl-bugs@bio.perl.org
-  http://bio.perl.org/bioperl-bugs/
+  http://bugzilla.bioperl.org/
 
 =head1 AUTHOR - Heikki Lehvaslaiho
 

diff --git a/Bio/Tools/Run/Eponine.pm b/Bio/Tools/Run/Eponine.pm
@@ -61,11 +61,10 @@ of the Bioperl mailing lists.  Your participation is much appreciated.
 =head2 Reporting Bugs
 
 Report bugs to the Bioperl bug tracking system to help us keep track
-the bugs and their resolution.  Bug reports can be submitted via email
-or the web:
+the bugs and their resolution.  Bug reports can be submitted via the
+web:
 
-  bioperl-bugs@bio.perl.org
-  http://bio.perl.org/bioperl-bugs/
+  http://bugzilla.bioperl.org/
 
 =head1 AUTHOR
 

diff --git a/Bio/Tools/Run/FootPrinter.pm b/Bio/Tools/Run/FootPrinter.pm
@@ -134,11 +134,10 @@ of the Bioperl mailing lists. Your participation is much appreciated.
 =head2 Reporting Bugs
 
 Report bugs to the Bioperl bug tracking system to help us keep track
-the bugs and their resolution.  Bug reports can be submitted via email
-or the web:
+the bugs and their resolution.  Bug reports can be submitted via the
+web:
 
-  bioperl-bugs@bioperl.org
-  http://bio.perl.org/bioperl-bugs/
+  http://bugzilla.bioperl.org/
 
 =head1 AUTHOR - Shawn Hoon
 

diff --git a/Bio/Tools/Run/Genscan.pm b/Bio/Tools/Run/Genscan.pm
@@ -24,7 +24,7 @@ given sequence given a matrix(for appropriate organisms).
 
 =head1 DESCRIPTION
 
- Genscan is a gene identifying program developed by Christopher Burge
+Genscan is a gene identifying program developed by Christopher Burge
 http://genes.mit.edu/burgelab/
 
 =head1 FEEDBACK
@@ -41,11 +41,10 @@ of the Bioperl mailing lists.  Your participation is much appreciated.
 =head2 Reporting Bugs
 
 Report bugs to the Bioperl bug tracking system to help us keep track
- the bugs and their resolution.  Bug reports can be submitted via
- email or the web:
+the bugs and their resolution.  Bug reports can be submitted via the
+web:
 
-  bioperl-bugs@bio.perl.org
-  http://bio.perl.org/bioperl-bugs/
+  http://bugzilla.bioperl.org/
 
 =head1 AUTHOR - Bala
 

diff --git a/Bio/Tools/Run/Phrap.pm b/Bio/Tools/Run/Phrap.pm
@@ -42,9 +42,9 @@ Bio::Tools::Run::Phrap - a wrapper for running Phrap
 
 =head2 Mailing Lists
 
- User feedback is an integral part of the evolution of this and other
- Bioperl modules. Send your comments and suggestions preferably to one
- of the Bioperl mailing lists.  Your participation is much appreciated.
+User feedback is an integral part of the evolution of this and other
+Bioperl modules. Send your comments and suggestions preferably to one
+of the Bioperl mailing lists.  Your participation is much appreciated.
 
  bioperl-l@bioperl.org               - General discussion
  http://bio.perl.org/MailList.html   - About the mailing lists

diff --git a/Bio/Tools/Run/Phylo/LVB.pm b/Bio/Tools/Run/Phylo/LVB.pm
@@ -58,11 +58,10 @@ of the Bioperl mailing lists.  Your participation is much appreciated.
 =head2 Reporting Bugs
 
 Report bugs to the Bioperl bug tracking system to help us keep track
-the bugs and their resolution.  Bug reports can be submitted via email
-or the web:
+the bugs and their resolution.  Bug reports can be submitted via the
+web:
 
-  bioperl-bugs@bio.perl.org
-  http://bio.perl.org/bioperl-bugs/
+  http://bugzilla.bioperl.org/
 
 =head1 PARAMETERS FOR LVB COMPUTATION
 

diff --git a/Bio/Tools/Run/Phylo/Molphy/ProtML.pm b/Bio/Tools/Run/Phylo/Molphy/ProtML.pm
@@ -136,11 +136,10 @@ the Bioperl mailing list.  Your participation is much appreciated.
 =head2 Reporting Bugs
 
 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
-email or the web:
+of the bugs and their resolution. Bug reports can be submitted via the
+web:
 
-  bioperl-bugs@bioperl.org
-  http://bioperl.org/bioperl-bugs/
+  http://bugzilla.bioperl.org/
 
 =head1 AUTHOR - Jason Stajich
 

diff --git a/Bio/Tools/Run/Phylo/PAML/Baseml.pm b/Bio/Tools/Run/Phylo/PAML/Baseml.pm
@@ -132,10 +132,10 @@ the Bioperl mailing list.  Your participation is much appreciated.
 =head2 Reporting Bugs
 
 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
-email or the web:
+of the bugs and their resolution. Bug reports can be submitted via the
+web:
 
-  http://bioperl.org/bioperl-bugs/
+ http://bugzilla.bioperl.org/
 
 =head1 AUTHOR - Jason Stajich
 

diff --git a/Bio/Tools/Run/Phylo/PAML/Codeml.pm b/Bio/Tools/Run/Phylo/PAML/Codeml.pm
@@ -57,10 +57,9 @@ the Bioperl mailing list.  Your participation is much appreciated.
 =head2 Reporting Bugs
 
 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:
+of the bugs and their resolution. Bug reports can be submitted via:
 
-  http://bioperl.org/bioperl-bugs/
+  http://bugzilla.bioperl.org/
 
 =head1 AUTHOR - Jason Stajich
 

diff --git a/Bio/Tools/Run/Phylo/PAML/Yn00.pm b/Bio/Tools/Run/Phylo/PAML/Yn00.pm
@@ -60,10 +60,9 @@ the Bioperl mailing list.  Your participation is much appreciated.
 =head2 Reporting Bugs
 
 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
-email or the web:
+of the bugs and their resolution. Bug reports can be submitted via the
+web:
 
-  http://bioperl.org/bioperl-bugs/
 
 =head1 AUTHOR - Jason Stajich