[med-svn] r5610 - in trunk/packages/probcons/trunk/debian: . patches

[Charles Plessy]

Author: plessy
Date: 2010-12-21 17:59:20 +0000 (Tue, 21 Dec 2010)
New Revision: 5610

Added:
   trunk/packages/probcons/trunk/debian/patches/gcc-4.5.diff
Removed:
   trunk/packages/probcons/trunk/debian/patches/fix-gcc-4.3-headers
Modified:
   trunk/packages/probcons/trunk/debian/changelog
   trunk/packages/probcons/trunk/debian/patches/series
Log:
To build with GCC 4.5.


Modified: trunk/packages/probcons/trunk/debian/changelog
===================================================================
--- trunk/packages/probcons/trunk/debian/changelog	2010-12-21 07:18:46 UTC (rev 5609)
+++ trunk/packages/probcons/trunk/debian/changelog	2010-12-21 17:59:20 UTC (rev 5610)
@@ -1,3 +1,11 @@
+probcons (1.12-6) UNRELEASED; urgency=low
+
+  * Renamed and updated the patch to build with GCC (debian/patches/series,
+    debian/patches/fix-gcc-4.3-headers, debian/patches/gcc-4.5.diff)
+    Closes: #607728
+
+ -- Charles Plessy <plessy at debian.org>  Wed, 22 Dec 2010 02:05:41 +0900
+
 probcons (1.12-5) unstable; urgency=low
 
   [ Charles Plessy ]

Deleted: trunk/packages/probcons/trunk/debian/patches/fix-gcc-4.3-headers
===================================================================
--- trunk/packages/probcons/trunk/debian/patches/fix-gcc-4.3-headers	2010-12-21 07:18:46 UTC (rev 5609)
+++ trunk/packages/probcons/trunk/debian/patches/fix-gcc-4.3-headers	2010-12-21 17:59:20 UTC (rev 5610)
@@ -1,33 +0,0 @@
---- a/CompareToRef.cc
-+++ b/CompareToRef.cc
-@@ -7,7 +7,7 @@
- 
- #include "SafeVector.h"
- #include "MultiSequence.h"
--#include <string>
-+#include <string.h>
- #include <sstream>
- #include <iomanip>
- #include <iostream>
---- a/Main.cc
-+++ b/Main.cc
-@@ -11,7 +11,7 @@
- #include "ProbabilisticModel.h"
- #include "EvolutionaryTree.h"
- #include "SparseMatrix.h"
--#include <string>
-+#include <string.h>
- #include <sstream>
- #include <iomanip>
- #include <iostream>
---- a/ProjectPairwise.cc
-+++ b/ProjectPairwise.cc
-@@ -7,7 +7,7 @@
- 
- #include "SafeVector.h"
- #include "MultiSequence.h"
--#include <string>
-+#include <string.h>
- #include <sstream>
- #include <iomanip>
- #include <iostream>

Added: trunk/packages/probcons/trunk/debian/patches/gcc-4.5.diff
===================================================================
--- trunk/packages/probcons/trunk/debian/patches/gcc-4.5.diff	                        (rev 0)
+++ trunk/packages/probcons/trunk/debian/patches/gcc-4.5.diff	2010-12-21 17:59:20 UTC (rev 5610)
@@ -0,0 +1,64 @@
+Description: To build ProbCons with gcc-4.5 by including additional headers.
+Origin: http://bugs.debian.org/607728
+Forwarded: yes
+
+Index: probcons-1.12/ProbabilisticModel.h
+===================================================================
+--- probcons-1.12.orig/ProbabilisticModel.h	2010-12-21 13:01:04.548229000 +0000
++++ probcons-1.12/ProbabilisticModel.h	2010-12-21 13:01:04.868229000 +0000
+@@ -12,6 +12,7 @@
+ #include <list>
+ #include <cmath>
+ #include <cstdio>
++#include <cstring>
+ #include "SafeVector.h"
+ #include "ScoreType.h"
+ #include "SparseMatrix.h"
+Index: probcons-1.12/ProjectPairwise.cc
+===================================================================
+--- probcons-1.12.orig/ProjectPairwise.cc	2010-12-21 13:01:04.858229000 +0000
++++ probcons-1.12/ProjectPairwise.cc	2010-12-21 13:01:04.868229000 +0000
+@@ -16,6 +16,7 @@
+ #include <limits>
+ #include <cstdio>
+ #include <cstdlib>
++#include <cstring>
+ #include <cerrno>
+ #include <iomanip>
+ 
+Index: probcons-1.12/CompareToRef.cc
+===================================================================
+--- probcons-1.12.orig/CompareToRef.cc	2010-12-21 13:04:39.418227395 +0000
++++ probcons-1.12/CompareToRef.cc	2010-12-21 13:05:16.438228987 +0000
+@@ -16,6 +16,7 @@
+ #include <limits>
+ #include <cstdio>
+ #include <cstdlib>
++#include <cstring>
+ #include <cerrno>
+ #include <iomanip>
+ 
+Index: probcons-1.12/FixRef.cc
+===================================================================
+--- probcons-1.12.orig/FixRef.cc	2010-12-21 13:04:39.398225710 +0000
++++ probcons-1.12/FixRef.cc	2010-12-21 13:05:11.058229036 +0000
+@@ -17,6 +17,7 @@
+ #include <algorithm>
+ #include <cstdio>
+ #include <cstdlib>
++#include <cstring>
+ #include <cerrno>
+ #include <iomanip>
+ 
+Index: probcons-1.12/Main.cc
+===================================================================
+--- probcons-1.12.orig/Main.cc	2010-12-21 13:04:39.438228258 +0000
++++ probcons-1.12/Main.cc	2010-12-21 13:05:32.688228993 +0000
+@@ -21,6 +21,7 @@
+ #include <climits>
+ #include <cstdio>
+ #include <cstdlib>
++#include <cstring>
+ #include <cerrno>
+ #include <iomanip>
+ 

Modified: trunk/packages/probcons/trunk/debian/patches/series
===================================================================
--- trunk/packages/probcons/trunk/debian/patches/series	2010-12-21 07:18:46 UTC (rev 5609)
+++ trunk/packages/probcons/trunk/debian/patches/series	2010-12-21 17:59:20 UTC (rev 5610)
@@ -1,3 +1,3 @@
 10_add-RNA-in-Makefile.diff
 11-Rename-programs-in-Makefile.diff
-fix-gcc-4.3-headers
+gcc-4.5.diff