[med-svn] r2380 - in trunk/packages/mustang/trunk/debian: . patches

[smoe-guest at alioth.debian.org]

Author: smoe-guest
Date: 2008-08-03 23:54:44 +0000 (Sun, 03 Aug 2008)
New Revision: 2380

Added:
   trunk/packages/mustang/trunk/debian/patches/04-gcc-4.3-exit
Modified:
   trunk/packages/mustang/trunk/debian/changelog
   trunk/packages/mustang/trunk/debian/control
   trunk/packages/mustang/trunk/debian/patches/00list
Log:
Why was this not uploaded? It seems nice!

  * Policy 3.8.0
  * Patch for gcc-4.3
  * debian/control has less redundany and easier working, added ref to paper.



Modified: trunk/packages/mustang/trunk/debian/changelog
===================================================================
--- trunk/packages/mustang/trunk/debian/changelog	2008-08-03 15:26:17 UTC (rev 2379)
+++ trunk/packages/mustang/trunk/debian/changelog	2008-08-03 23:54:44 UTC (rev 2380)
@@ -23,6 +23,11 @@
   * XS-DM-Upload-Allowed: Yes
   * Vcs-Browser, Vcs-Svn
 
+  [ Steffen Moeller ]
+  * Policy 3.8.0
+  * Patch for gcc-4.3
+  * debian/control has less redundany and easier working, added ref to paper.
+
  -- Morten Kjeldgaard <mok at bioxray.dk>  Thu, 10 Jan 2008 16:53:32 +0100
 
 mustang (3.0-0ubuntu1) gutsy; urgency=low

Modified: trunk/packages/mustang/trunk/debian/control
===================================================================
--- trunk/packages/mustang/trunk/debian/control	2008-08-03 15:26:17 UTC (rev 2379)
+++ trunk/packages/mustang/trunk/debian/control	2008-08-03 23:54:44 UTC (rev 2380)
@@ -6,7 +6,7 @@
 DM-Upload-Allowed: yes
 Homepage: http://www.cs.mu.oz.au/~arun/mustang/
 Build-Depends: debhelper (>= 5), dpatch
-Standards-Version: 3.7.3
+Standards-Version: 3.8.0
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mustang/trunk/?rev=0&sc=0
 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/mustang/trunk/
 
@@ -15,23 +15,20 @@
 Depends: ${shlibs:Depends}, ${misc:Depends}
 Suggests: mustang-testdata
 Description: multiple structural alignment of proteins
- Mustang is an algorithm for structural alignment of multiple
- protein structures. Given a set of PDB files, the program uses the spatial
+ Mustang is an algorithm to align multiple protein structures.
+ Given a set of PDB files, the program uses the spatial
  information in the Calpha atoms of the set to produce a sequence alignment.
  Based on a progressive pairwise heuristic the algorithm then proceeds
  through a number of refinement passes. Mustang reports the multiple
  sequence alignment and the corresponding superposition of structures.
+ .
+ When using this program please cite A.S. Konagurthu, J.C. Whisstock,
+ P.J. Stuckey, A.M. Lesk, "MUSTANG: A multiple structural alignment
+ algorithm." Proteins: Structure, Function, and Bioinformatics. 64(3):559-574.
 
 Package: mustang-testdata
 Architecture: all
 Enhances: mustang
 Description: multiple structural alignment of proteins, test data
- Mustang is an algorithm for structural alignment of multiple
- protein structures. Given a set of PDB files, the program uses the spatial
- information in the Calpha atoms of the set to produce a sequence alignment.
- Based on a progressive pairwise heuristic the algorithm then proceeds
- through a number of refinement passes. Mustang reports the multiple
- sequence alignment and the corresponding superposition of structures.
- .
  This package contains a larger set of test data than what
  comes with the binary package.

Modified: trunk/packages/mustang/trunk/debian/patches/00list
===================================================================
--- trunk/packages/mustang/trunk/debian/patches/00list	2008-08-03 15:26:17 UTC (rev 2379)
+++ trunk/packages/mustang/trunk/debian/patches/00list	2008-08-03 23:54:44 UTC (rev 2380)
@@ -1,3 +1,4 @@
 01-upstream.dpatch
 02-main.cpp.dpatch
 03-test_zf-cchh.dpatch
+04-gcc-4.3-exit

Added: trunk/packages/mustang/trunk/debian/patches/04-gcc-4.3-exit
===================================================================
--- trunk/packages/mustang/trunk/debian/patches/04-gcc-4.3-exit	                        (rev 0)
+++ trunk/packages/mustang/trunk/debian/patches/04-gcc-4.3-exit	2008-08-03 23:54:44 UTC (rev 2380)
@@ -0,0 +1,67 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 04-gcc-4.3-exit.dpatch by  <steffen_moeller at gmx.de>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: exit not found
+
+ at DPATCH@
+
+--- mustang.old/src/ew_2.cpp.orig	2008-08-04 01:01:45.509512156 +0200
++++ mustang/src/ew_2.cpp	2008-08-04 01:02:08.001463089 +0200
+@@ -35,6 +35,8 @@
+ #include <fstream>
+ using std::ifstream;
+ 
++#include <stdlib.h>
++
+ #include<math.h>
+ #include "macros.h"
+ #include "globals.h"
+--- mustang.old/src/multiple_superposition.cpp.orig	2008-08-04 01:03:34.018459733 +0200
++++ mustang/src/multiple_superposition.cpp	2008-08-04 01:03:59.790460503 +0200
+@@ -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"
+--- mustang.old/src/pdb_ripper_2.cpp.orig	2008-08-04 01:01:06.014501128 +0200
++++ mustang/src/pdb_ripper_2.cpp	2008-08-04 01:01:25.510476525 +0200
+@@ -35,6 +35,8 @@
+ #include <cstring>
+ using std::ifstream ;
+ 
++#include <stdlib.h>
++
+ #include "macros.h"
+ #include "globals.h"
+ #include "pdb_ripper.h"
+--- mustang.old/src/progress_align_3.cpp.orig	2008-08-04 01:02:32.922510805 +0200
++++ mustang/src/progress_align_3.cpp	2008-08-04 01:02:48.657512880 +0200
+@@ -34,6 +34,8 @@
+ #include<cmath>
+ #include<cstring>
+ 
++#include<stdlib.h>
++
+ 
+ #include "macros.h"
+ #include "globals.h"
+--- mustang.old/src/read_structures.cpp.orig	2008-08-04 00:57:19.561501585 +0200
++++ mustang/src/read_structures.cpp	2008-08-04 01:00:10.961466245 +0200
+@@ -35,6 +35,8 @@
+ using std::ifstream ;
+ using std::ofstream ;
+ 
++#include <stdlib.h>
++
+ #include "macros.h"
+ #include "globals.h"
+ #include "read_structures.h"