[med-svn] r4155 - in trunk/packages/mustang/trunk/debian: . patches

[Morten Kjeldgaard]

Author: mok0-guest
Date: 2009-10-05 13:16:55 +0000 (Mon, 05 Oct 2009)
New Revision: 4155

Removed:
   trunk/packages/mustang/trunk/debian/patches/02-main.cpp.patch
   trunk/packages/mustang/trunk/debian/patches/04-gcc-4.3-exit.patch
Modified:
   trunk/packages/mustang/trunk/debian/runtest
   trunk/packages/mustang/trunk/debian/test_zf-CCHH-small
Log:
fix runtest script

Deleted: trunk/packages/mustang/trunk/debian/patches/02-main.cpp.patch
===================================================================
--- trunk/packages/mustang/trunk/debian/patches/02-main.cpp.patch	2009-10-05 12:46:54 UTC (rev 4154)
+++ trunk/packages/mustang/trunk/debian/patches/02-main.cpp.patch	2009-10-05 13:16:55 UTC (rev 4155)
@@ -1,27 +0,0 @@
-
---- trunk.orig/src/main.cpp
-+++ trunk/src/main.cpp
-@@ -64,17 +64,17 @@
- 	if(!meditate)
- 	{
- 		cout << "\n" ;
--		cout << "\t\t\t\t\033[0;37;1;41m";
--		cout << "       MUSTANG (v.3): A MUltiple STuructural AligNment alGorithm.       \033[0;0m\n" ;
-+		cout << "\033[0;37;1;41m";
-+		cout << "       MUSTANG (v.3): A MUltiple STructural AligNment alGorithm.        \033[0;0m\n" ;
- 		//cout << "\033[0;49m" ;
--		cout << "\t\t\t\t\033[1;33;4;1;46m";
-+		cout << "\033[1;33;4;1;46m";
- 		cout << "Authors:     " ; 
- 		cout << "\033[0;1;37;4;1;46m" ;
--		cout << "    A S Konagurthu,  J Whisstock, and P J Stuckey, A M Lesk.\033[0m\n";
-+		cout << "  A S Konagurthu,  J Whisstock, and P J Stuckey, A M Lesk.  \033[0m\n";
- 		//cout << "\033[0m" ;
--		cout << "\t\t\t\t\033[0;33;4;1;46m";
-+		cout << "\033[0;33;4;1;46m";
- 		cout << "(Mis)Coding: " ; cout << "\033[0;37;4;1;46m" ;
--		cout << "    A S Konagurthu.                                         \033[0m\n";
-+		cout << "  A S Konagurthu.                                           \033[0m\n";
- 		cout << "\033[0m" ;
- 		cout << "\n\n" ;
- 	}

Deleted: trunk/packages/mustang/trunk/debian/patches/04-gcc-4.3-exit.patch
===================================================================
--- trunk/packages/mustang/trunk/debian/patches/04-gcc-4.3-exit.patch	2009-10-05 12:46:54 UTC (rev 4154)
+++ trunk/packages/mustang/trunk/debian/patches/04-gcc-4.3-exit.patch	2009-10-05 13:16:55 UTC (rev 4155)
@@ -1,60 +0,0 @@
-
---- trunk.orig/src/ew_2.cpp
-+++ trunk/src/ew_2.cpp
-@@ -35,6 +35,8 @@
- #include <fstream>
- using std::ifstream;
- 
-+#include <stdlib.h>
-+
- #include<math.h>
- #include "macros.h"
- #include "globals.h"
---- trunk.orig/src/multiple_superposition.cpp
-+++ trunk/src/multiple_superposition.cpp
-@@ -43,10 +43,11 @@
- using std::flush; 	using std::endl; 	using std::ios;
- using std::fixed;
- 
--
- #include<iomanip>
- using std::setprecision ; using std::setw ; 
- 
-+#include<stdlib.h>
-+
- #include "jacobi.h"
- #include "alloc_routines.h"
- #include "de_alloc_routines.h"
---- trunk.orig/src/pdb_ripper_2.cpp
-+++ trunk/src/pdb_ripper_2.cpp
-@@ -35,6 +35,8 @@
- #include <cstring>
- using std::ifstream ;
- 
-+#include <stdlib.h>
-+
- #include "macros.h"
- #include "globals.h"
- #include "pdb_ripper.h"
---- trunk.orig/src/progress_align_3.cpp
-+++ trunk/src/progress_align_3.cpp
-@@ -34,6 +34,8 @@
- #include<cmath>
- #include<cstring>
- 
-+#include<stdlib.h>
-+
- 
- #include "macros.h"
- #include "globals.h"
---- trunk.orig/src/read_structures.cpp
-+++ trunk/src/read_structures.cpp
-@@ -35,6 +35,8 @@
- using std::ifstream ;
- using std::ofstream ;
- 
-+#include <stdlib.h>
-+
- #include "macros.h"
- #include "globals.h"
- #include "read_structures.h"

Modified: trunk/packages/mustang/trunk/debian/runtest
===================================================================
--- trunk/packages/mustang/trunk/debian/runtest	2009-10-05 12:46:54 UTC (rev 4154)
+++ trunk/packages/mustang/trunk/debian/runtest	2009-10-05 13:16:55 UTC (rev 4155)
@@ -17,7 +17,8 @@
 tmpdir=/tmp/mustang
 
 savedir=$PWD
-mkdir $tmpdir
+rm -rf $tmpdir
+mkdir -p $tmpdir
 cd $tmpdir
 pdb_fetch $entries
 for f in $entries; do gzip -dc $f.pdb.gz > $f.pdb ; done

Modified: trunk/packages/mustang/trunk/debian/test_zf-CCHH-small
===================================================================
--- trunk/packages/mustang/trunk/debian/test_zf-CCHH-small	2009-10-05 12:46:54 UTC (rev 4154)
+++ trunk/packages/mustang/trunk/debian/test_zf-CCHH-small	2009-10-05 13:16:55 UTC (rev 4155)
@@ -16,7 +16,7 @@
 ## symbols to show that the whitespaces are ignored                                          ##
 ###############################################################################################
 
- >  /tmp
+ >  /tmp/mustang
 
 +1sp1.pdb
 +1sp2.pdb