Version bump and removed old ebuilds (fixes bug #235943).

Package-Manager: portage-2.2_rc8/cvs/Linux 2.6.26-SENTINEL-2 i686

1 files changed, 79 insertions, 0 deletions

diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.7.2-gcc4.3.patch b/sci-biology/vienna-rna/files/vienna-rna-1.7.2-gcc4.3.patch
new file mode 100644
index 000000000000..4f5bd37f3a77
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-1.7.2-gcc4.3.patch
@@ -0,0 +1,79 @@
+diff -Naur ViennaRNA-1.7/Cluster/AS_main.c ViennaRNA-1.7.new/Cluster/AS_main.c
+--- ViennaRNA-1.7/Cluster/AS_main.c	2001-04-05 04:36:41.000000000 -0400
++++ ViennaRNA-1.7.new/Cluster/AS_main.c	2008-08-28 10:53:11.000000000 -0400
+@@ -1,5 +1,6 @@
+ #include <stdio.h>
+ #include <string.h>
++#include <stdlib.h>
+ #include "distance_matrix.h"
+ #include "statgeom.h"
+ #include "split.h"
+diff -Naur ViennaRNA-1.7/Cluster/statgeom.c ViennaRNA-1.7.new/Cluster/statgeom.c
+--- ViennaRNA-1.7/Cluster/statgeom.c	2001-04-05 04:36:41.000000000 -0400
++++ ViennaRNA-1.7.new/Cluster/statgeom.c	2008-08-28 10:53:11.000000000 -0400
+@@ -7,6 +7,7 @@
+ #include <stdio.h>
+ #include <strings.h>
+ #include <ctype.h>
++#include <stdlib.h>
+ #include "utils.h"
+ #include "PS3D.h"
+ #include "distance_matrix.h"
+diff -Naur ViennaRNA-1.7/Cluster/treeplot.c ViennaRNA-1.7.new/Cluster/treeplot.c
+--- ViennaRNA-1.7/Cluster/treeplot.c	2001-04-05 04:36:41.000000000 -0400
++++ ViennaRNA-1.7.new/Cluster/treeplot.c	2008-08-28 10:53:11.000000000 -0400
+@@ -1,6 +1,7 @@
+ #include <stdio.h>
+ #include <string.h>
+ #include <math.h>
++#include <stdlib.h>
+ #include "distance_matrix.h"
+ #include "utils.h"
+ 
+diff -Naur ViennaRNA-1.7/RNAforester/src/main.cpp ViennaRNA-1.7.new/RNAforester/src/main.cpp
+--- ViennaRNA-1.7/RNAforester/src/main.cpp	2005-08-05 10:14:10.000000000 -0400
++++ ViennaRNA-1.7.new/RNAforester/src/main.cpp	2008-08-28 10:53:11.000000000 -0400
+@@ -19,6 +19,8 @@
+ #include <list>
+ #include <sstream>
+ #include <string>
++#include <cstring>
++#include <climits>
+ #include <map>
+ 
+ //#include <sys/timeb.h>

+diff -Naur ViennaRNA-1.7/RNAforester/src/ppforestbase.h ViennaRNA-1.7.new/RNAforester/src/ppforestbase.h
+--- ViennaRNA-1.7/RNAforester/src/ppforestbase.h	2006-05-08 07:49:33.000000000 -0400
++++ ViennaRNA-1.7.new/RNAforester/src/ppforestbase.h	2008-08-28 10:53:11.000000000 -0400
+@@ -16,6 +16,7 @@
+ 
+ #include <algorithm>
+ #include <cassert>
++#include <cstring>
+ 
+ #include "misc.h"
+ #include "types.h"
+diff -Naur ViennaRNA-1.7/RNAforester/src/rna_algebra.h ViennaRNA-1.7.new/RNAforester/src/rna_algebra.h
+--- ViennaRNA-1.7/RNAforester/src/rna_algebra.h	2004-09-01 17:55:22.000000000 -0400
++++ ViennaRNA-1.7.new/RNAforester/src/rna_algebra.h	2008-08-28 10:53:11.000000000 -0400
+@@ -3,6 +3,8 @@
+ 

+ #include <assert.h>
+ #include <algorithm>
++#include <cstring>
++#include <climits>
+ 
+ #include "algebra.h"
+ #include "debug.h"
+diff -Naur ViennaRNA-1.7/Readseq/ureadseq.c ViennaRNA-1.7.new/Readseq/ureadseq.c
+--- ViennaRNA-1.7/Readseq/ureadseq.c	2002-11-27 06:23:56.000000000 -0500
++++ ViennaRNA-1.7.new/Readseq/ureadseq.c	2008-08-28 10:53:11.000000000 -0400
+@@ -16,7 +16,7 @@
+  *
+  */
+ 
+-
++#include <stdlib.h>
+ #include <stdio.h>
+ #include <ctype.h>
+ #include <string.h>