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authorJustin Lecher <jlec@gentoo.org>2012-06-14 14:11:08 +0200
committerJustin Lecher <jlec@gentoo.org>2012-06-14 14:11:08 +0200
commit3bdd9d0c7138075bded9befe7eb76591dfd9b8af (patch)
tree30e976543d00e30140b7db5d22f8c8ffd904d1da
parentMerge branch 'master' of git+ssh://git.overlays.gentoo.org/proj/sci (diff)
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sci-chemistry/coot: Fix for gcc-4.7
(Portage version: 2.2.0_alpha110/git/Linux x86_64, unsigned Manifest commit)
-rw-r--r--sci-chemistry/coot/ChangeLog4
-rw-r--r--sci-chemistry/coot/coot-9999.ebuild1
-rw-r--r--sci-chemistry/coot/files/coot-9999-gcc47.patch47
3 files changed, 52 insertions, 0 deletions
diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index 0b2d8a9f0..6facbcb7b 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 fc6ca945c..87215abba 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 000000000..465923a47
--- /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