[med-svn] r10157 - trunk/packages/proda/trunk/debian/patches

[Andreas Tille]

Author: tille
Date: 2012-03-29 13:43:37 +0000 (Thu, 29 Mar 2012)
New Revision: 10157

Modified:
   trunk/packages/proda/trunk/debian/patches/01-fix_gcc4.3_warnings.patch
   trunk/packages/proda/trunk/debian/patches/03-fix_FTBFS_gcc4.3_missing_includes.patch
Log:
Refreshed patches


Modified: trunk/packages/proda/trunk/debian/patches/01-fix_gcc4.3_warnings.patch
===================================================================
--- trunk/packages/proda/trunk/debian/patches/01-fix_gcc4.3_warnings.patch	2012-03-29 13:38:08 UTC (rev 10156)
+++ trunk/packages/proda/trunk/debian/patches/01-fix_gcc4.3_warnings.patch	2012-03-29 13:43:37 UTC (rev 10157)
@@ -3,10 +3,8 @@
 Description: Corrects deprecated conversion from string constant to ‘char*’.
 License: Use, modify, redistribute under the same terms as Proda iteslf.
 
-Index: proda-1.0/Assert.cc
-===================================================================
---- proda-1.0.orig/Assert.cc	2007-12-16 01:36:01.000000000 +0100
-+++ proda-1.0/Assert.cc	2007-12-16 01:36:25.000000000 +0100
+--- proda.orig/Assert.cc
++++ proda/Assert.cc
 @@ -10,7 +10,7 @@
  // Write out assertion error message
  //////////////////////////////////////////////////////////////////////
@@ -16,10 +14,8 @@
    fprintf (stderr, "Assertion failed in file \"%s\", line %d: %s\n",
  	   filename, line_number, error_msg);
    abort();
-Index: proda-1.0/Assert.h
-===================================================================
---- proda-1.0.orig/Assert.h	2007-12-16 01:36:44.000000000 +0100
-+++ proda-1.0/Assert.h	2007-12-16 01:36:54.000000000 +0100
+--- proda.orig/Assert.h
++++ proda/Assert.h
 @@ -7,7 +7,7 @@
  #ifndef ASSERT_H
  #define ASSERT_H
@@ -29,10 +25,8 @@
  
  #ifdef NDEBUG
  #define ASSERT(test,error_msg)
-Index: proda-1.0/MultiSequence.cc
-===================================================================
---- proda-1.0.orig/MultiSequence.cc	2007-12-16 01:36:44.000000000 +0100
-+++ proda-1.0/MultiSequence.cc	2007-12-16 01:37:20.000000000 +0100
+--- proda.orig/MultiSequence.cc
++++ proda/MultiSequence.cc
 @@ -386,7 +386,7 @@
  //////////////////////////////////////////////////////////////////////
  
@@ -42,10 +36,8 @@
      
      // Identities
      "A", "B", "C", "D", "E", "F", "G", "H", "I", "J", "K", "L", "M", 
-Index: proda-1.0/ProbModel.cc
-===================================================================
---- proda-1.0.orig/ProbModel.cc	2007-12-16 01:36:44.000000000 +0100
-+++ proda-1.0/ProbModel.cc	2007-12-16 01:37:26.000000000 +0100
+--- proda.orig/ProbModel.cc
++++ proda/ProbModel.cc
 @@ -30,7 +30,7 @@
    { 0, 0, 0, 0, 0, 0, 1 }
  };

Modified: trunk/packages/proda/trunk/debian/patches/03-fix_FTBFS_gcc4.3_missing_includes.patch
===================================================================
--- trunk/packages/proda/trunk/debian/patches/03-fix_FTBFS_gcc4.3_missing_includes.patch	2012-03-29 13:38:08 UTC (rev 10156)
+++ trunk/packages/proda/trunk/debian/patches/03-fix_FTBFS_gcc4.3_missing_includes.patch	2012-03-29 13:43:37 UTC (rev 10157)
@@ -4,10 +4,8 @@
  GCC 4.3 has a stricter requirements for the declaration of includes. Without
  this patch, ProDA would not build with g++4.3.
 License: Use, modify, redistribute under the same terms as Proda iteslf.
-Index: proda-1.0/AlignedFragment.cc
-===================================================================
---- proda-1.0.orig/AlignedFragment.cc	2007-12-16 01:39:42.000000000 +0100
-+++ proda-1.0/AlignedFragment.cc	2007-12-16 01:39:50.000000000 +0100
+--- proda.orig/AlignedFragment.cc
++++ proda/AlignedFragment.cc
 @@ -2,6 +2,7 @@
  //
  //////////////////////////////////////////////////////////////////////
@@ -16,24 +14,20 @@
  #include "AlignedFragment.h"
  #include "Assert.h"
  #include "Utilities.h"
-Index: proda-1.0/AlignedFragment.h
-===================================================================
 --- proda.orig/AlignedFragment.h
 +++ proda/AlignedFragment.h
 @@ -7,7 +7,9 @@
  #ifndef ALIGNFRAGMENT_H
  #define ALIGNFRAGMENT_H
-
+ 
 +#include <cstdio>
  #include <vector>
 +#include <fstream>
-
+ 
  class Fragment;
  class AlignedFragment;
-Index: proda-1.0/Block.cc
-===================================================================
---- proda-1.0.orig/Block.cc	2007-12-16 01:39:42.000000000 +0100
-+++ proda-1.0/Block.cc	2007-12-16 01:40:04.000000000 +0100
+--- proda.orig/Block.cc
++++ proda/Block.cc
 @@ -2,6 +2,7 @@
  //
  //////////////////////////////////////////////////////////////////////
@@ -42,10 +36,8 @@
  #include "Block.h"
  #include "AlignedFragment.h"
  #include "Sequence.h"
-Index: proda-1.0/Main.cc
-===================================================================
---- proda-1.0.orig/Main.cc	2007-12-16 01:39:42.000000000 +0100
-+++ proda-1.0/Main.cc	2007-12-16 01:40:10.000000000 +0100
+--- proda.orig/Main.cc
++++ proda/Main.cc
 @@ -6,6 +6,7 @@
  #include <stdlib.h>
  #include <string.h>
@@ -54,10 +46,8 @@
  #include "Assert.h"
  #include "MultiSequence.h"
  #include "ProbModel.h"
-Index: proda-1.0/PairAligner.cc
-===================================================================
---- proda-1.0.orig/PairAligner.cc	2007-12-16 01:39:42.000000000 +0100
-+++ proda-1.0/PairAligner.cc	2007-12-16 01:40:25.000000000 +0100
+--- proda.orig/PairAligner.cc
++++ proda/PairAligner.cc
 @@ -4,6 +4,8 @@
  // Implementation of PairAligner class
  ////////////////////////////////////////////////////////////////////
@@ -67,10 +57,8 @@
  #include "PairAligner.h"
  #include "Utilities.h"
  #include "LocalAlign.h"
-Index: proda-1.0/ProbModel.cc
-===================================================================
---- proda-1.0.orig/ProbModel.cc	2007-12-16 01:39:42.000000000 +0100
-+++ proda-1.0/ProbModel.cc	2007-12-16 01:40:33.000000000 +0100
+--- proda.orig/ProbModel.cc
++++ proda/ProbModel.cc
 @@ -4,6 +4,7 @@
  
  #include <stdio.h>