[med-svn] r8174 - trunk/packages/gmod/gbrowse/trunk/debian/patches

[olivier sallou]

Author: osallou-guest
Date: 2011-10-18 17:00:41 +0000 (Tue, 18 Oct 2011)
New Revision: 8174

Modified:
   trunk/packages/gmod/gbrowse/trunk/debian/patches/manpages.patch
Log:
fix pod2man and what-is errors

Modified: trunk/packages/gmod/gbrowse/trunk/debian/patches/manpages.patch
===================================================================
--- trunk/packages/gmod/gbrowse/trunk/debian/patches/manpages.patch	2011-10-18 16:35:54 UTC (rev 8173)
+++ trunk/packages/gmod/gbrowse/trunk/debian/patches/manpages.patch	2011-10-18 17:00:41 UTC (rev 8174)
@@ -10,6 +10,15 @@
  
  =head1 VERSION
  
+@@ -1496,7 +1496,7 @@
+ =item C<< FATAL: Invalid value passed to strand: strand.  >>
+ 
+ This may indicate that your GTF file does not indicate the strand for
+-features that require it.  Consider using the DEFAULT_STRAND paramater
++features that require it.  Consider using the DEFAULT_STRAND parameter
+ in the config file.  It may also indicate a software bug.  Please
+ contact the author.
+ 
 --- a/bin/wiggle2gff3.pl
 +++ b/bin/wiggle2gff3.pl
 @@ -2,7 +2,7 @@
@@ -41,3 +50,104 @@
  
  =head1 SYNOPSIS
  
+--- a/lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm
++++ b/lib/Bio/Graphics/Browser2/AuthorizedFeatureFile.pm
+@@ -23,7 +23,6 @@
+ 
+ =head2 METHODS
+ 
+-=over 4
+ 
+ =cut
+ 
+--- a/lib/Bio/Graphics/Browser2/DataBase.pm
++++ b/lib/Bio/Graphics/Browser2/DataBase.pm
+@@ -63,12 +63,16 @@
+     $CACHE->delete($key);
+ }
+ 
++=over
++
+ =item Bio::Graphics::Browser2::DataBase->clone_databases()
+ 
+ Call this after a fork in the child process to make sure that all open
+ databases have had a chance to clone themselves if they need
+ to. Otherwise you will get random database failures.
+ 
++=back
++
+ =cut
+ 
+ sub clone_databases {
+--- a/lib/Bio/Graphics/Browser2/Plugin.pm
++++ b/lib/Bio/Graphics/Browser2/Plugin.pm
+@@ -238,7 +238,7 @@
+ 
+ The purpose of this methods is to suppress the 'Configure...'
+ or 'Find...' title that is printed at the top of the page when the 
+-plugin is loaded.  It will return false unless overriden by a plugin where
++plugin is loaded.  It will return false unless overridden by a plugin where
+ this behaviour is desired.
+ 
+ =item $type = $self->type()
+--- a/lib/Bio/Graphics/Browser2/Region.pm
++++ b/lib/Bio/Graphics/Browser2/Region.pm
+@@ -3,6 +3,12 @@
+ # provide method for fetching and manipulating the current
+ # region or regions.
+ 
++=head1 NAME
++
++Bio::Graphics::Browser2::Region -- Provide method for fetching and manipulating regions
++
++=cut
++
+ use strict;
+ use warnings;
+ use Bio::Graphics::Browser2::Shellwords;
+--- a/lib/Bio/Graphics/Browser2/Render.pm
++++ b/lib/Bio/Graphics/Browser2/Render.pm
+@@ -3,6 +3,12 @@
+ use strict;	
+ use warnings;
+ 
++=head1 NAME
++
++Bio::Graphics::Browser2::Render -- Provide methods to render regions
++
++=cut
++
+ use JSON;
+ use Digest::MD5 'md5_hex';
+ use CGI qw(:standard param request_method header url iframe img span div br center url_param);
+--- a/lib/Bio/Graphics/Browser2/RenderPanels.pm
++++ b/lib/Bio/Graphics/Browser2/RenderPanels.pm
+@@ -2,6 +2,13 @@
+ use strict;
+ use warnings;
+ 
++=head1 NAME
++
++Bio::Graphics::Browser2::RenderPanels-- Provide methods to render a panel
++
++=cut
++
++
+ use GD 'gdTransparent','gdStyled';
+ 
+ use Bio::Graphics;
+--- a/lib/Legacy/Graphics/Browser.pm
++++ b/lib/Legacy/Graphics/Browser.pm
+@@ -4,6 +4,12 @@
+ # This is an old version of Bio::Graphics::Browser retained for gbrowse_syn
+ # It is on the path to deprecation
+ 
++=head1 NAME
++
++Legacy::Graphics::Browser-- Old version, deprecated
++
++=cut
++
+ =head1 METHODS
+ 
+ The remainder of this document describes the methods available to the