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 <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> +## +## All lines beginning with `## DP:' are a description of the patch. +## DP: exit not found + [EMAIL PROTECTED]@ + +--- 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" _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
