rpms/lagan/devel lagan.spec,1.5,1.6 lagan20-chris.patch,1.1,1.2

[Christian Iseli (c4chris)]

Author: c4chris

Update of /cvs/extras/rpms/lagan/devel
In directory cvs-int.fedora.redhat.com:/tmp/cvs-serv29581

Modified Files:
	lagan.spec lagan20-chris.patch 
Log Message:
Update patch to fix gcc-4.3 compilation issues.


Index: lagan.spec
===================================================================
RCS file: /cvs/extras/rpms/lagan/devel/lagan.spec,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- lagan.spec	18 Sep 2007 15:52:55 -0000	1.5
+++ lagan.spec	26 Jan 2008 23:47:49 -0000	1.6
@@ -1,6 +1,6 @@
 Name:           lagan
 Version:        2.0
-Release:        1%{?dist}
+Release:        2%{?dist}
 Summary:        Local, global, and multiple alignment of DNA sequences
 
 Group:          Applications/Engineering
@@ -80,6 +80,9 @@
 
 
 %changelog
+* Sun Jan 27 2008 Christian Iseli <Christian.Iseli at licr.org> 2.0-2
+ - Update patch to fix gcc-4.3 compilation issues.
+
 * Tue Sep 18 2007 Christian Iseli <Christian.Iseli at licr.org> 2.0-1
  - New upstream release.
 

lagan20-chris.patch:

Index: lagan20-chris.patch
===================================================================
RCS file: /cvs/extras/rpms/lagan/devel/lagan20-chris.patch,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- lagan20-chris.patch	18 Sep 2007 15:52:55 -0000	1.1
+++ lagan20-chris.patch	26 Jan 2008 23:47:49 -0000	1.2
@@ -77,8 +77,16 @@
    fprintf (stderr, "%s\n", line);
 diff -up lagan20/src/utils/Glue.cpp.chris lagan20/src/utils/Glue.cpp
 --- lagan20/src/utils/Glue.cpp.chris	2006-09-14 22:40:18.000000000 +0200
-+++ lagan20/src/utils/Glue.cpp	2007-09-18 17:27:46.000000000 +0200
-@@ -30,10 +30,6 @@ void readScoreMatrix (char *filename){
++++ lagan20/src/utils/Glue.cpp	2008-01-27 00:10:28.000000000 +0100
+@@ -6,6 +6,7 @@
+ #include <fstream>
+ #include <iostream>
+ #include <algorithm>
++#include <cstring>
+ 
+ #define NUCLEOTIDE_MATRIX_FILE "nucmatrix.txt"
+ #define MAX_LINE_LENGTH 1024
+@@ -30,10 +31,6 @@ void readScoreMatrix (char *filename){
    char *lagan_dir;
  
    lagan_dir = getenv ("LAGAN_DIR");
@@ -606,3 +614,15 @@
  
  open(IN, "< glue.out");
  my @glue_out = <IN>;
+diff -up lagan20/src/glocal/score.cpp.chris lagan20/src/glocal/score.cpp
+--- lagan20/src/glocal/score.cpp.chris	2008-01-27 00:10:50.000000000 +0100
++++ lagan20/src/glocal/score.cpp	2008-01-27 00:11:01.000000000 +0100
+@@ -2,7 +2,7 @@
+ #include<score.h>
+ #include<leftinfluence.h>
+ #include<rightinfluence.h>
+-#include<fstream.h>
++#include<fstream>
+ 
+ extern vector<class Score*> scoreFunctions[1<<(UPSTRANDBITS+DOWNSTRANDBITS+RELPOSBITS)];
+