[med-svn] r9852 - in trunk/packages/bioperl/trunk/debian: . patches

[olivier sallou]

Author: osallou-guest
Date: 2012-03-02 10:43:54 +0000 (Fri, 02 Mar 2012)
New Revision: 9852

Added:
   trunk/packages/bioperl/trunk/debian/patches/
   trunk/packages/bioperl/trunk/debian/patches/fix_berkeleydb3_temp_file_creation
   trunk/packages/bioperl/trunk/debian/patches/series
Modified:
   trunk/packages/bioperl/trunk/debian/changelog
Log:
add patch fix_berkeleydb3_temp_file_creation to fix 661793

Modified: trunk/packages/bioperl/trunk/debian/changelog
===================================================================
--- trunk/packages/bioperl/trunk/debian/changelog	2012-03-02 05:25:32 UTC (rev 9851)
+++ trunk/packages/bioperl/trunk/debian/changelog	2012-03-02 10:43:54 UTC (rev 9852)
@@ -1,3 +1,12 @@
+bioperl (1.6.901-3) unstable; urgency=low
+
+  * Team upload.
+    [ Olivier Sallou ]
+    + add patch fix_berkeleydb3_temp_file_creation (Closes: #661793).
+      Fixed upstream for next release. 
+
+ -- Olivier Sallou <olivier.sallou at irisa.fr>  Fri, 02 Mar 2012 11:10:36 +0100
+
 bioperl (1.6.901-2) unstable; urgency=low
 
   [ Luca Capello ]

Added: trunk/packages/bioperl/trunk/debian/patches/fix_berkeleydb3_temp_file_creation
===================================================================
--- trunk/packages/bioperl/trunk/debian/patches/fix_berkeleydb3_temp_file_creation	                        (rev 0)
+++ trunk/packages/bioperl/trunk/debian/patches/fix_berkeleydb3_temp_file_creation	2012-03-02 10:43:54 UTC (rev 9852)
@@ -0,0 +1,17 @@
+Subject: wrong order in file creation
+Description: tie operation has flags and mode in the wrong order.
+ Fixed upstream with commit 2b0daf196e0f2acf373c2bc8f0bf2449c36edf40.
+ Patch should be removed with next upstream release.
+Author: Olivier Sallou <olivier.sallou at irisa.fr
+Last-Updated: 02/03/2012
+--- a/Bio/DB/SeqFeature/Store/berkeleydb3.pm
++++ b/Bio/DB/SeqFeature/Store/berkeleydb3.pm
+@@ -497,7 +497,7 @@
+     my $numeric_cmp         = DB_File::BTREEINFO->new;
+     $numeric_cmp->{compare} = sub { $_[0] <=> $_[1] };
+     $numeric_cmp->{flags}   = R_DUP;
+-    my $s = tie %sort,'DB_File',$name,0666,O_CREAT|O_RDWR,$numeric_cmp 
++    my $s = tie %sort,'DB_File',$name,O_CREAT|O_RDWR,0666,$numeric_cmp 
+ 	or $self->throw("Couldn't create temporary file for sorting: $!");
+ 
+     my $index    = $self->index_db('locations');

Added: trunk/packages/bioperl/trunk/debian/patches/series
===================================================================
--- trunk/packages/bioperl/trunk/debian/patches/series	                        (rev 0)
+++ trunk/packages/bioperl/trunk/debian/patches/series	2012-03-02 10:43:54 UTC (rev 9852)
@@ -0,0 +1 @@
+fix_berkeleydb3_temp_file_creation