[gentoo-commits] proj/sci:master commit in: sci-chemistry/coot/files/, sci-chemistry/coot/

["Justin Lecher" <jlec@gentoo.org>]

commit:     3bdd9d0c7138075bded9befe7eb76591dfd9b8af
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Jun 14 12:11:08 2012 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Jun 14 12:11:08 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=3bdd9d0c

sci-chemistry/coot: Fix for gcc-4.7

(Portage version: 2.2.0_alpha110/git/Linux x86_64, unsigned Manifest commit)

---
 sci-chemistry/coot/ChangeLog                   |    4 ++
 sci-chemistry/coot/coot-9999.ebuild            |    1 +
 sci-chemistry/coot/files/coot-9999-gcc47.patch |   47 ++++++++++++++++++++++++
 3 files changed, 52 insertions(+), 0 deletions(-)

diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index 0b2d8a9..6facbcb 100644
--- a/sci-chemistry/coot/ChangeLog
+++ b/sci-chemistry/coot/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  14 Jun 2012; Justin Lecher <jlec@gentoo.org> coot-9999.ebuild,
+  +files/coot-9999-gcc47.patch:
+  Fix for gcc-4.7
+
   25 Apr 2012; Justin Lecher <jlec@gentoo.org> -files/9999-libpng-1.5.patch,
   coot-9999.ebuild:
   Drop libpng-1.5 patch, included upstream

diff --git a/sci-chemistry/coot/coot-9999.ebuild b/sci-chemistry/coot/coot-9999.ebuild
index fc6ca94..87215ab 100644
--- a/sci-chemistry/coot/coot-9999.ebuild
+++ b/sci-chemistry/coot/coot-9999.ebuild
@@ -85,6 +85,7 @@ PATCHES=(
 	"${FILESDIR}"/${PV}-goocanvas.patch
 	"${FILESDIR}"/${PV}-mmdb-config.patch
 	"${FILESDIR}"/${PV}-ssm.patch
+	"${FILESDIR}"/${P}-gcc47.patch
 	)
 
 src_unpack() {

diff --git a/sci-chemistry/coot/files/coot-9999-gcc47.patch b/sci-chemistry/coot/files/coot-9999-gcc47.patch
new file mode 100644
index 0000000..465923a
--- /dev/null
+++ b/sci-chemistry/coot/files/coot-9999-gcc47.patch
@@ -0,0 +1,47 @@
+Index: utils/coot-utils.cc
+===================================================================
+--- utils/coot-utils.cc	(revision 4235)
++++ utils/coot-utils.cc	(working copy)
+@@ -28,6 +28,7 @@
+ #include <stdexcept> // for string_to_int.
+ #include <sstream>   // ditto.
+ #include <cstdio>    // 20090806 Justin Lecher says we need this on Gentoo 
++#include <unistd.h>
+ 
+ #include "coot-sysdep.h"
+ #if defined _MSC_VER
+Index: coot-utils/coot-coord-utils.cc
+===================================================================
+--- coot-utils/coot-coord-utils.cc	(revision 4235)
++++ coot-utils/coot-coord-utils.cc	(working copy)
+@@ -196,7 +196,7 @@
+       clipper::Coord_frac cf = coot::util::shift_to_origin(mol);
+       clipper::Coord_orth co = cf.coord_orth(csp.first);
+       for(int imod = 1; imod<=mol->GetNumberOfModels(); imod++) {
+-	 int imod = 1;
++//	 int imod = 1;
+ 	 CModel *model_p = mol->GetModel(imod);
+ 	 CChain *chain_p;
+ 	 int nchains = model_p->GetNumberOfChains();
+@@ -2779,7 +2779,7 @@
+    short int whole_res_flag = 1;
+ 
+    for(int imod = 1; imod<=mol_in->GetNumberOfModels(); imod++) {
+-     int imod = 1;
++//     int imod = 1;
+      CModel *model_p = mol_in->GetModel(imod);
+      CModel *new_model_p = new CModel;
+      int nchains = model_p->GetNumberOfChains();
+Index: src/molecule-class-info-residues.cc
+===================================================================
+--- src/molecule-class-info-residues.cc	(revision 4235)
++++ src/molecule-class-info-residues.cc	(working copy)
+@@ -145,7 +145,7 @@
+ 
+    int r = 0;
+    for(int imod = 1; imod<=atom_sel.mol->GetNumberOfModels(); imod++) {
+-      int imod = 1;
++//      int imod = 1;
+       CModel *model_p = atom_sel.mol->GetModel(imod);
+       CChain *chain_p;
+       // run over chains of the existing mol