[gentoo-commits] gentoo-x86 commit in sci-biology/vienna-rna/files: vienna-rna-1.7.2-gcc4.3.patch - gentoo-commits

From:	"Markus Dittrich (markusle)" <markusle@g.o>
To:	gentoo-commits@l.g.o
Subject:	[gentoo-commits] gentoo-x86 commit in sci-biology/vienna-rna/files: vienna-rna-1.7.2-gcc4.3.patch
Date:	Fri, 29 Aug 2008 01:21:42
Message-Id:	`E1KYsgF-0007nG-Tu@stork.gentoo.org`

1

markusle    08/08/29 01:21:39

2

3

  Added:                vienna-rna-1.7.2-gcc4.3.patch

4

  Log:

5

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

6

  (Portage version: 2.2_rc8/cvs/Linux 2.6.26-SENTINEL-2 i686)

7

8

Revision  Changes    Path

9

1.1                  sci-biology/vienna-rna/files/vienna-rna-1.7.2-gcc4.3.patch

10

11

file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/vienna-rna/files/vienna-rna-1.7.2-gcc4.3.patch?rev=1.1&view=markup

12

plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/vienna-rna/files/vienna-rna-1.7.2-gcc4.3.patch?rev=1.1&content-type=text/plain

13

14

Index: vienna-rna-1.7.2-gcc4.3.patch

15

===================================================================

16

diff -Naur ViennaRNA-1.7/Cluster/AS_main.c ViennaRNA-1.7.new/Cluster/AS_main.c

17

--- ViennaRNA-1.7/Cluster/AS_main.c	2001-04-05 04:36:41.000000000 -0400

18

+++ ViennaRNA-1.7.new/Cluster/AS_main.c	2008-08-28 10:53:11.000000000 -0400

19

@@ -1,5 +1,6 @@

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 #include <stdio.h>

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 #include <string.h>

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+#include <stdlib.h>

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 #include "distance_matrix.h"

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 #include "statgeom.h"

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 #include "split.h"

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diff -Naur ViennaRNA-1.7/Cluster/statgeom.c ViennaRNA-1.7.new/Cluster/statgeom.c

27

--- ViennaRNA-1.7/Cluster/statgeom.c	2001-04-05 04:36:41.000000000 -0400

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+++ ViennaRNA-1.7.new/Cluster/statgeom.c	2008-08-28 10:53:11.000000000 -0400

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@@ -7,6 +7,7 @@

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 #include <stdio.h>

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 #include <strings.h>

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 #include <ctype.h>

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+#include <stdlib.h>

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 #include "utils.h"

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 #include "PS3D.h"

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 #include "distance_matrix.h"

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diff -Naur ViennaRNA-1.7/Cluster/treeplot.c ViennaRNA-1.7.new/Cluster/treeplot.c

38

--- ViennaRNA-1.7/Cluster/treeplot.c	2001-04-05 04:36:41.000000000 -0400

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+++ ViennaRNA-1.7.new/Cluster/treeplot.c	2008-08-28 10:53:11.000000000 -0400

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@@ -1,6 +1,7 @@

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 #include <stdio.h>

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 #include <string.h>

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 #include <math.h>

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+#include <stdlib.h>

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 #include "distance_matrix.h"

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 #include "utils.h"

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diff -Naur ViennaRNA-1.7/RNAforester/src/main.cpp ViennaRNA-1.7.new/RNAforester/src/main.cpp

49

--- ViennaRNA-1.7/RNAforester/src/main.cpp	2005-08-05 10:14:10.000000000 -0400

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+++ ViennaRNA-1.7.new/RNAforester/src/main.cpp	2008-08-28 10:53:11.000000000 -0400

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@@ -19,6 +19,8 @@

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 #include <list>

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 #include <sstream>

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 #include <string>

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+#include <cstring>

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+#include <climits>

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 #include <map>

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 //#include <sys/timeb.h>

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diff -Naur ViennaRNA-1.7/RNAforester/src/ppforestbase.h ViennaRNA-1.7.new/RNAforester/src/ppforestbase.h

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--- ViennaRNA-1.7/RNAforester/src/ppforestbase.h	2006-05-08 07:49:33.000000000 -0400

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+++ ViennaRNA-1.7.new/RNAforester/src/ppforestbase.h	2008-08-28 10:53:11.000000000 -0400

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@@ -16,6 +16,7 @@

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 #include <algorithm>

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 #include <cassert>

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+#include <cstring>

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 #include "misc.h"

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 #include "types.h"

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diff -Naur ViennaRNA-1.7/RNAforester/src/rna_algebra.h ViennaRNA-1.7.new/RNAforester/src/rna_algebra.h

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--- ViennaRNA-1.7/RNAforester/src/rna_algebra.h	2004-09-01 17:55:22.000000000 -0400

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+++ ViennaRNA-1.7.new/RNAforester/src/rna_algebra.h	2008-08-28 10:53:11.000000000 -0400

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@@ -3,6 +3,8 @@

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 #include <assert.h>

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 #include <algorithm>

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+#include <cstring>

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+#include <climits>

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 #include "algebra.h"

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 #include "debug.h"

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diff -Naur ViennaRNA-1.7/Readseq/ureadseq.c ViennaRNA-1.7.new/Readseq/ureadseq.c

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--- ViennaRNA-1.7/Readseq/ureadseq.c	2002-11-27 06:23:56.000000000 -0500

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+++ ViennaRNA-1.7.new/Readseq/ureadseq.c	2008-08-28 10:53:11.000000000 -0400

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@@ -16,7 +16,7 @@

87

*

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*/

89

90

-

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+#include <stdlib.h>

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 #include <stdio.h>

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 #include <ctype.h>

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 #include <string.h>

1	markusle 08/08/29 01:21:39
2
3	Added: vienna-rna-1.7.2-gcc4.3.patch
4	Log:
5	Version bump and removed old ebuilds (fixes bug #235943).
6	(Portage version: 2.2_rc8/cvs/Linux 2.6.26-SENTINEL-2 i686)
7
8	Revision Changes Path
9	1.1 sci-biology/vienna-rna/files/vienna-rna-1.7.2-gcc4.3.patch
10
11	file : http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/vienna-rna/files/vienna-rna-1.7.2-gcc4.3.patch?rev=1.1&view=markup
12	plain: http://sources.gentoo.org/viewcvs.py/gentoo-x86/sci-biology/vienna-rna/files/vienna-rna-1.7.2-gcc4.3.patch?rev=1.1&content-type=text/plain
13
14	Index: vienna-rna-1.7.2-gcc4.3.patch
15	===================================================================
16	diff -Naur ViennaRNA-1.7/Cluster/AS_main.c ViennaRNA-1.7.new/Cluster/AS_main.c
17	--- ViennaRNA-1.7/Cluster/AS_main.c 2001-04-05 04:36:41.000000000 -0400
18	+++ ViennaRNA-1.7.new/Cluster/AS_main.c 2008-08-28 10:53:11.000000000 -0400
19	@@ -1,5 +1,6 @@
20	#include <stdio.h>
21	#include <string.h>
22	+#include <stdlib.h>
23	#include "distance_matrix.h"
24	#include "statgeom.h"
25	#include "split.h"
26	diff -Naur ViennaRNA-1.7/Cluster/statgeom.c ViennaRNA-1.7.new/Cluster/statgeom.c
27	--- ViennaRNA-1.7/Cluster/statgeom.c 2001-04-05 04:36:41.000000000 -0400
28	+++ ViennaRNA-1.7.new/Cluster/statgeom.c 2008-08-28 10:53:11.000000000 -0400
29	@@ -7,6 +7,7 @@
30	#include <stdio.h>
31	#include <strings.h>
32	#include <ctype.h>
33	+#include <stdlib.h>
34	#include "utils.h"
35	#include "PS3D.h"
36	#include "distance_matrix.h"
37	diff -Naur ViennaRNA-1.7/Cluster/treeplot.c ViennaRNA-1.7.new/Cluster/treeplot.c
38	--- ViennaRNA-1.7/Cluster/treeplot.c 2001-04-05 04:36:41.000000000 -0400
39	+++ ViennaRNA-1.7.new/Cluster/treeplot.c 2008-08-28 10:53:11.000000000 -0400
40	@@ -1,6 +1,7 @@
41	#include <stdio.h>
42	#include <string.h>
43	#include <math.h>
44	+#include <stdlib.h>
45	#include "distance_matrix.h"
46	#include "utils.h"
47
48	diff -Naur ViennaRNA-1.7/RNAforester/src/main.cpp ViennaRNA-1.7.new/RNAforester/src/main.cpp
49	--- ViennaRNA-1.7/RNAforester/src/main.cpp 2005-08-05 10:14:10.000000000 -0400
50	+++ ViennaRNA-1.7.new/RNAforester/src/main.cpp 2008-08-28 10:53:11.000000000 -0400
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 -Naur ViennaRNA-1.7/RNAforester/src/ppforestbase.h ViennaRNA-1.7.new/RNAforester/src/ppforestbase.h
61	--- ViennaRNA-1.7/RNAforester/src/ppforestbase.h 2006-05-08 07:49:33.000000000 -0400
62	+++ ViennaRNA-1.7.new/RNAforester/src/ppforestbase.h 2008-08-28 10:53:11.000000000 -0400
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 -Naur ViennaRNA-1.7/RNAforester/src/rna_algebra.h ViennaRNA-1.7.new/RNAforester/src/rna_algebra.h
72	--- ViennaRNA-1.7/RNAforester/src/rna_algebra.h 2004-09-01 17:55:22.000000000 -0400
73	+++ ViennaRNA-1.7.new/RNAforester/src/rna_algebra.h 2008-08-28 10:53:11.000000000 -0400
74	@@ -3,6 +3,8 @@
75
76	#include <assert.h>
77	#include <algorithm>
78	+#include <cstring>
79	+#include <climits>
80
81	#include "algebra.h"
82	#include "debug.h"
83	diff -Naur ViennaRNA-1.7/Readseq/ureadseq.c ViennaRNA-1.7.new/Readseq/ureadseq.c
84	--- ViennaRNA-1.7/Readseq/ureadseq.c 2002-11-27 06:23:56.000000000 -0500
85	+++ ViennaRNA-1.7.new/Readseq/ureadseq.c 2008-08-28 10:53:11.000000000 -0400
86	@@ -16,7 +16,7 @@
87	*
88	*/
89
90	-
91	+#include <stdlib.h>
92	#include <stdio.h>
93	#include <ctype.h>
94	#include <string.h>

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