Version bump and cleanup

(Portage version: 2.2_rc30/cvs/Linux x86_64)

2 files changed, 92 insertions, 0 deletions

diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.8.3-disable-gd.patch b/sci-biology/vienna-rna/files/vienna-rna-1.8.3-disable-gd.patch
new file mode 100644
index 000000000000..2c5ac3041297
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-1.8.3-disable-gd.patch
@@ -0,0 +1,16 @@
+# unfortunately, vienna-rna's build system is a little broken and sometimes detects
+# gd in RNAforested but then realizes in g2 that it can't actually build it 
+# resulting in unresolved symbols.
+
+diff -durr ViennaRNA-1.8.3.orig/RNAforester/configure.in ViennaRNA-1.8.3/RNAforester/configure.in
+--- ViennaRNA-1.8.3.orig/RNAforester/configure.in	2009-09-10 13:05:40.507932827 +0000
++++ ViennaRNA-1.8.3/RNAforester/configure.in	2009-09-10 13:06:15.171952984 +0000
+@@ -47,7 +47,7 @@
+ save_CPPFLAGS=$CPPFLAGS	
+ CPPFLAGS=["-Ig2-0.70/src/ ${CPPFLAGS}"]
+ 
+-AC_CHECK_LIB(gd,main,,)
++dnl AC_CHECK_LIB(gd,main,,)
+ 		  
+ dnl Checks for header files.
+ AC_HEADER_STDC
diff --git a/sci-biology/vienna-rna/files/vienna-rna-1.8.3-gcc4.3.patch b/sci-biology/vienna-rna/files/vienna-rna-1.8.3-gcc4.3.patch
new file mode 100644
index 000000000000..025822f45c91
--- /dev/null
+++ b/sci-biology/vienna-rna/files/vienna-rna-1.8.3-gcc4.3.patch
@@ -0,0 +1,76 @@
+diff -durr ViennaRNA-1.8.3.orig/Cluster/AS_main.c ViennaRNA-1.8.3/Cluster/AS_main.c
+--- ViennaRNA-1.8.3.orig/Cluster/AS_main.c	2009-09-10 11:56:01.636674988 +0000
++++ ViennaRNA-1.8.3/Cluster/AS_main.c	2009-09-10 11:58:32.915952366 +0000
+@@ -1,5 +1,6 @@
+ #include <stdio.h>
+ #include <string.h>
++#include <stdlib.h>
+ #include "distance_matrix.h"
+ #include "statgeom.h"
+ #include "split.h"
+diff -durr ViennaRNA-1.8.3.orig/Cluster/statgeom.c ViennaRNA-1.8.3/Cluster/statgeom.c
+--- ViennaRNA-1.8.3.orig/Cluster/statgeom.c	2009-09-10 11:56:01.636674988 +0000
++++ ViennaRNA-1.8.3/Cluster/statgeom.c	2009-09-10 11:58:53.192452141 +0000
+@@ -7,6 +7,7 @@
+ #include <stdio.h>
+ #include <string.h>
+ #include <strings.h>
++#include <stdlib.h>
+ #include <ctype.h>
+ #include "utils.h"
+ #include "PS3D.h"
+diff -durr ViennaRNA-1.8.3.orig/Cluster/treeplot.c ViennaRNA-1.8.3/Cluster/treeplot.c
+--- ViennaRNA-1.8.3.orig/Cluster/treeplot.c	2009-09-10 11:56:01.636674988 +0000
++++ ViennaRNA-1.8.3/Cluster/treeplot.c	2009-09-10 11:59:22.457509165 +0000
+@@ -1,5 +1,6 @@
+ #include <stdio.h>
+ #include <string.h>
++#include <stdlib.h>
+ #include <math.h>
+ #include "distance_matrix.h"
+ #include "utils.h"
+diff -durr ViennaRNA-1.8.3.orig/RNAforester/src/main.cpp ViennaRNA-1.8.3/RNAforester/src/main.cpp
+--- ViennaRNA-1.8.3.orig/RNAforester/src/main.cpp	2009-09-10 11:56:01.624743558 +0000
++++ ViennaRNA-1.8.3/RNAforester/src/main.cpp	2009-09-10 12:00:37.693252890 +0000
+@@ -19,6 +19,8 @@
+ #include <list>
+ #include <sstream>
+ #include <string>
++#include <cstring>
++#include <climits>
+ #include <map>
+ 
+ //#include <sys/timeb.h>
+diff -durr ViennaRNA-1.8.3.orig/RNAforester/src/ppforestbase.h ViennaRNA-1.8.3/RNAforester/src/ppforestbase.h
+--- ViennaRNA-1.8.3.orig/RNAforester/src/ppforestbase.h	2009-09-10 11:56:01.624743558 +0000
++++ ViennaRNA-1.8.3/RNAforester/src/ppforestbase.h	2009-09-10 12:01:41.631932654 +0000
+@@ -16,6 +16,7 @@
+ 
+ #include <algorithm>
+ #include <cassert>
++#include <cstring>
+ 
+ #include "misc.h"
+ #include "types.h"
+diff -durr ViennaRNA-1.8.3.orig/RNAforester/src/rna_algebra.h ViennaRNA-1.8.3/RNAforester/src/rna_algebra.h
+--- ViennaRNA-1.8.3.orig/RNAforester/src/rna_algebra.h	2009-09-10 11:56:01.620703294 +0000
++++ ViennaRNA-1.8.3/RNAforester/src/rna_algebra.h	2009-09-10 12:02:29.687952726 +0000
+@@ -4,6 +4,7 @@
+ #include <assert.h>
+ #include <algorithm>
+ #include <climits>
++#include <cstring>
+ 
+ #include "algebra.h"
+ #include "debug.h"
+diff -durr ViennaRNA-1.8.3.orig/Readseq/ureadseq.c ViennaRNA-1.8.3/Readseq/ureadseq.c
+--- ViennaRNA-1.8.3.orig/Readseq/ureadseq.c	2009-09-10 11:56:01.632743452 +0000
++++ ViennaRNA-1.8.3/Readseq/ureadseq.c	2009-09-10 12:03:15.343952776 +0000
+@@ -20,6 +20,7 @@
+ #include <stdio.h>
+ #include <ctype.h>
+ #include <string.h>
++#include <stdlib.h>
+ 
+ #define UREADSEQ_G
+ #include "ureadseq.h"