| 1 |
weaver 09/09/10 18:43:01 |
| 2 |
|
| 3 |
Added: vienna-rna-1.8.3-gcc4.3.patch |
| 4 |
vienna-rna-1.8.3-disable-gd.patch |
| 5 |
Log: |
| 6 |
Version bump and cleanup |
| 7 |
(Portage version: 2.2_rc30/cvs/Linux x86_64) |
| 8 |
|
| 9 |
Revision Changes Path |
| 10 |
1.1 sci-biology/vienna-rna/files/vienna-rna-1.8.3-gcc4.3.patch |
| 11 |
|
| 12 |
file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/vienna-rna/files/vienna-rna-1.8.3-gcc4.3.patch?rev=1.1&view=markup |
| 13 |
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/vienna-rna/files/vienna-rna-1.8.3-gcc4.3.patch?rev=1.1&content-type=text/plain |
| 14 |
|
| 15 |
Index: vienna-rna-1.8.3-gcc4.3.patch |
| 16 |
=================================================================== |
| 17 |
diff -durr ViennaRNA-1.8.3.orig/Cluster/AS_main.c ViennaRNA-1.8.3/Cluster/AS_main.c |
| 18 |
--- ViennaRNA-1.8.3.orig/Cluster/AS_main.c 2009-09-10 11:56:01.636674988 +0000 |
| 19 |
+++ ViennaRNA-1.8.3/Cluster/AS_main.c 2009-09-10 11:58:32.915952366 +0000 |
| 20 |
@@ -1,5 +1,6 @@ |
| 21 |
#include <stdio.h> |
| 22 |
#include <string.h> |
| 23 |
+#include <stdlib.h> |
| 24 |
#include "distance_matrix.h" |
| 25 |
#include "statgeom.h" |
| 26 |
#include "split.h" |
| 27 |
diff -durr ViennaRNA-1.8.3.orig/Cluster/statgeom.c ViennaRNA-1.8.3/Cluster/statgeom.c |
| 28 |
--- ViennaRNA-1.8.3.orig/Cluster/statgeom.c 2009-09-10 11:56:01.636674988 +0000 |
| 29 |
+++ ViennaRNA-1.8.3/Cluster/statgeom.c 2009-09-10 11:58:53.192452141 +0000 |
| 30 |
@@ -7,6 +7,7 @@ |
| 31 |
#include <stdio.h> |
| 32 |
#include <string.h> |
| 33 |
#include <strings.h> |
| 34 |
+#include <stdlib.h> |
| 35 |
#include <ctype.h> |
| 36 |
#include "utils.h" |
| 37 |
#include "PS3D.h" |
| 38 |
diff -durr ViennaRNA-1.8.3.orig/Cluster/treeplot.c ViennaRNA-1.8.3/Cluster/treeplot.c |
| 39 |
--- ViennaRNA-1.8.3.orig/Cluster/treeplot.c 2009-09-10 11:56:01.636674988 +0000 |
| 40 |
+++ ViennaRNA-1.8.3/Cluster/treeplot.c 2009-09-10 11:59:22.457509165 +0000 |
| 41 |
@@ -1,5 +1,6 @@ |
| 42 |
#include <stdio.h> |
| 43 |
#include <string.h> |
| 44 |
+#include <stdlib.h> |
| 45 |
#include <math.h> |
| 46 |
#include "distance_matrix.h" |
| 47 |
#include "utils.h" |
| 48 |
diff -durr ViennaRNA-1.8.3.orig/RNAforester/src/main.cpp ViennaRNA-1.8.3/RNAforester/src/main.cpp |
| 49 |
--- ViennaRNA-1.8.3.orig/RNAforester/src/main.cpp 2009-09-10 11:56:01.624743558 +0000 |
| 50 |
+++ ViennaRNA-1.8.3/RNAforester/src/main.cpp 2009-09-10 12:00:37.693252890 +0000 |
| 51 |
@@ -19,6 +19,8 @@ |
| 52 |
#include <list> |
| 53 |
#include <sstream> |
| 54 |
#include <string> |
| 55 |
+#include <cstring> |
| 56 |
+#include <climits> |
| 57 |
#include <map> |
| 58 |
|
| 59 |
//#include <sys/timeb.h> |
| 60 |
diff -durr ViennaRNA-1.8.3.orig/RNAforester/src/ppforestbase.h ViennaRNA-1.8.3/RNAforester/src/ppforestbase.h |
| 61 |
--- ViennaRNA-1.8.3.orig/RNAforester/src/ppforestbase.h 2009-09-10 11:56:01.624743558 +0000 |
| 62 |
+++ ViennaRNA-1.8.3/RNAforester/src/ppforestbase.h 2009-09-10 12:01:41.631932654 +0000 |
| 63 |
@@ -16,6 +16,7 @@ |
| 64 |
|
| 65 |
#include <algorithm> |
| 66 |
#include <cassert> |
| 67 |
+#include <cstring> |
| 68 |
|
| 69 |
#include "misc.h" |
| 70 |
#include "types.h" |
| 71 |
diff -durr ViennaRNA-1.8.3.orig/RNAforester/src/rna_algebra.h ViennaRNA-1.8.3/RNAforester/src/rna_algebra.h |
| 72 |
--- ViennaRNA-1.8.3.orig/RNAforester/src/rna_algebra.h 2009-09-10 11:56:01.620703294 +0000 |
| 73 |
+++ ViennaRNA-1.8.3/RNAforester/src/rna_algebra.h 2009-09-10 12:02:29.687952726 +0000 |
| 74 |
@@ -4,6 +4,7 @@ |
| 75 |
#include <assert.h> |
| 76 |
#include <algorithm> |
| 77 |
#include <climits> |
| 78 |
+#include <cstring> |
| 79 |
|
| 80 |
#include "algebra.h" |
| 81 |
#include "debug.h" |
| 82 |
diff -durr ViennaRNA-1.8.3.orig/Readseq/ureadseq.c ViennaRNA-1.8.3/Readseq/ureadseq.c |
| 83 |
--- ViennaRNA-1.8.3.orig/Readseq/ureadseq.c 2009-09-10 11:56:01.632743452 +0000 |
| 84 |
+++ ViennaRNA-1.8.3/Readseq/ureadseq.c 2009-09-10 12:03:15.343952776 +0000 |
| 85 |
@@ -20,6 +20,7 @@ |
| 86 |
#include <stdio.h> |
| 87 |
#include <ctype.h> |
| 88 |
#include <string.h> |
| 89 |
+#include <stdlib.h> |
| 90 |
|
| 91 |
#define UREADSEQ_G |
| 92 |
#include "ureadseq.h" |
| 93 |
|
| 94 |
|
| 95 |
|
| 96 |
1.1 sci-biology/vienna-rna/files/vienna-rna-1.8.3-disable-gd.patch |
| 97 |
|
| 98 |
file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/vienna-rna/files/vienna-rna-1.8.3-disable-gd.patch?rev=1.1&view=markup |
| 99 |
plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/vienna-rna/files/vienna-rna-1.8.3-disable-gd.patch?rev=1.1&content-type=text/plain |
| 100 |
|
| 101 |
Index: vienna-rna-1.8.3-disable-gd.patch |
| 102 |
=================================================================== |
| 103 |
# unfortunately, vienna-rna's build system is a little broken and sometimes detects |
| 104 |
# gd in RNAforested but then realizes in g2 that it can't actually build it |
| 105 |
# resulting in unresolved symbols. |
| 106 |
|
| 107 |
diff -durr ViennaRNA-1.8.3.orig/RNAforester/configure.in ViennaRNA-1.8.3/RNAforester/configure.in |
| 108 |
--- ViennaRNA-1.8.3.orig/RNAforester/configure.in 2009-09-10 13:05:40.507932827 +0000 |
| 109 |
+++ ViennaRNA-1.8.3/RNAforester/configure.in 2009-09-10 13:06:15.171952984 +0000 |
| 110 |
@@ -47,7 +47,7 @@ |
| 111 |
save_CPPFLAGS=$CPPFLAGS |
| 112 |
CPPFLAGS=["-Ig2-0.70/src/ ${CPPFLAGS}"] |
| 113 |
|
| 114 |
-AC_CHECK_LIB(gd,main,,) |
| 115 |
+dnl AC_CHECK_LIB(gd,main,,) |
| 116 |
|
| 117 |
dnl Checks for header files. |
| 118 |
AC_HEADER_STDC |
Archives