sci-chemistry/mustang: Fix for gcc-4.7, #413945

(Portage version: 2.2.0_alpha101/cvs/Linux x86_64)

3 files changed, 28 insertions, 4 deletions

diff --git a/sci-chemistry/mustang/ChangeLog b/sci-chemistry/mustang/ChangeLog
index 8f89c9dbf9c8..9de17907e869 100644
--- a/sci-chemistry/mustang/ChangeLog
+++ b/sci-chemistry/mustang/ChangeLog
@@ -1,6 +1,10 @@
 # ChangeLog for sci-chemistry/mustang
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/mustang/ChangeLog,v 1.12 2012/01/21 16:20:22 phajdan.jr Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/mustang/ChangeLog,v 1.13 2012/04/29 10:36:13 jlec Exp $
+
+  29 Apr 2012; Justin Lecher <jlec@gentoo.org> mustang-3.2.1.ebuild,
+  +files/mustang-3.2.1-gcc-4.7.patch:
+  Fix for gcc-4.7, #413945
 
   21 Jan 2012; Pawel Hajdan jr <phajdan.jr@gentoo.org> mustang-3.2.1.ebuild:
   x86 stable wrt bug #398541
diff --git a/sci-chemistry/mustang/files/mustang-3.2.1-gcc-4.7.patch b/sci-chemistry/mustang/files/mustang-3.2.1-gcc-4.7.patch
new file mode 100644
index 000000000000..9e5dea85afeb
--- /dev/null
+++ b/sci-chemistry/mustang/files/mustang-3.2.1-gcc-4.7.patch
@@ -0,0 +1,16 @@
+ src/superpose_on_core_2.cpp |    2 ++
+ 1 files changed, 2 insertions(+), 0 deletions(-)
+
+diff --git a/src/superpose_on_core_2.cpp b/src/superpose_on_core_2.cpp
+index ae137de..059dfe3 100644
+--- a/src/superpose_on_core_2.cpp
++++ b/src/superpose_on_core_2.cpp
+@@ -55,6 +55,8 @@ using std::ofstream ;
+ #include "multiple_superposition.h"
+ #include "3D_manip_functions.h"
+ 
++#include <unistd.h>
++
+ int **core_columns ;
+ int *core_columns_2 , NCORE = 0 ;
+ int **algn_to_seq_hash ;
diff --git a/sci-chemistry/mustang/mustang-3.2.1.ebuild b/sci-chemistry/mustang/mustang-3.2.1.ebuild
index dc80d0851972..1a6b04bb48ad 100644
--- a/sci-chemistry/mustang/mustang-3.2.1.ebuild
+++ b/sci-chemistry/mustang/mustang-3.2.1.ebuild
@@ -1,16 +1,16 @@
 # Copyright 1999-2012 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/mustang/mustang-3.2.1.ebuild,v 1.8 2012/01/21 16:20:22 phajdan.jr Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/mustang/mustang-3.2.1.ebuild,v 1.9 2012/04/29 10:36:13 jlec Exp $
 
 EAPI=4
 
-inherit base toolchain-funcs
+inherit eutils toolchain-funcs
 
 MY_PN="MUSTANG"
 SRC_P="${PN}_v${PV}"
 MY_P="${MY_PN}_v${PV}"
 
-DESCRIPTION="MUltiple STructural AligNment AlGorithm."
+DESCRIPTION="MUltiple STructural AligNment AlGorithm"
 HOMEPAGE="http://www.csse.monash.edu.au/~karun/Site/mustang.html"
 SRC_URI="http://www.csse.unimelb.edu.au/~arun/${PN}/${SRC_P}.tgz"
 
@@ -21,6 +21,10 @@ IUSE=""
 
 S="${WORKDIR}/${MY_P}"
 
+src_prepare() {
+	epatch "${FILESDIR}"/${P}-gcc-4.7.patch
+}
+
 src_compile() {
 	emake \
 		CPP=$(tc-getCXX) \