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

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

commit:     cfad9afcc75652e395adf780dfb3a2d4df72a032
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Jun 11 12:12:17 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Jun 11 14:22:52 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=cfad9afc

update to new lange patches
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

---
 .../rosetta/files/rosetta-3.4-gcc4.78.patch        | 32 ++++++++++++++++++++++
 .../rosetta/files/rosetta-3.4-lange-fix.patch      | 22 +++++++++++++++
 sci-chemistry/rosetta/rosetta-3.4.ebuild           | 12 ++++++--
 3 files changed, 63 insertions(+), 3 deletions(-)

diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.78.patch b/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.78.patch
new file mode 100644
index 0000000..882534b
--- /dev/null
+++ b/sci-chemistry/rosetta/files/rosetta-3.4-gcc4.78.patch
@@ -0,0 +1,32 @@
+ tools/build/options.settings | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/tools/build/options.settings b/tools/build/options.settings
+index 30fb65e..f79ef5b 100644
+--- a/tools/build/options.settings
++++ b/tools/build/options.settings
+@@ -9,7 +9,7 @@
+ options = {
+ 
+     "cxx" : {
+-        "gcc"     : [ "3.3", "3.4", "4.0", "4.1", "4.2", "4.3","4.4","4.5", "4.6", "*" ],
++        "gcc"     : [ "3.3", "3.4", "4.0", "4.1", "4.2", "4.3","4.4","4.5", "4.6", "4.7", "4.8", "*" ],
+         "icc"     : [ "8.0", "8.1", "9.0", "9.1", "10.0", "10.1", "11.1", "*" ], #PBHACK
+         "msvc"    : [ "7.0", "7.1", "8.0", "8.1", "*" ],
+         "xlc"     : [ "7.0", "8.0", "9.0", "XL", "*" ],
+ src/protocols/jd2/SingleFileBuffer.cc | 2 ++
+ 1 file changed, 2 insertions(+)
+
+diff --git a/src/protocols/jd2/SingleFileBuffer.cc b/src/protocols/jd2/SingleFileBuffer.cc
+index aa78d91..61ca823 100644
+--- a/src/protocols/jd2/SingleFileBuffer.cc
++++ b/src/protocols/jd2/SingleFileBuffer.cc
+@@ -28,6 +28,8 @@
+ #include <ctime>      // for clock()
+ #endif
+ 
++#include <unistd.h>
++
+ namespace protocols {
+ namespace jd2 {
+ using namespace core;

diff --git a/sci-chemistry/rosetta/files/rosetta-3.4-lange-fix.patch b/sci-chemistry/rosetta/files/rosetta-3.4-lange-fix.patch
new file mode 100644
index 0000000..17e85f8
--- /dev/null
+++ b/sci-chemistry/rosetta/files/rosetta-3.4-lange-fix.patch
@@ -0,0 +1,22 @@
+ tools/build/setup.py | 8 +++++++-
+ 1 file changed, 7 insertions(+), 1 deletion(-)
+
+diff --git a/tools/build/setup.py b/tools/build/setup.py
+index 4e57ff6..d8a2a08 100644
+--- a/tools/build/setup.py
++++ b/tools/build/setup.py
+@@ -354,7 +354,13 @@ what SCons will use to build the system.
+             symbols = setting.appends.symbols()
+             if symbols.has_key("ENV"):
+                 for key, value in symbols["ENV"].items():
+-                    env["ENV"][key] += value
++                    if key == "PATH":
++                        env["ENV"][key] = value
++                    else:
++                        try:
++                            env["ENV"][key] += value
++                        except:
++                            print key, value
+                 del symbols["ENV"]
+             env.Append(**symbols)
+         if setting.prepends:

diff --git a/sci-chemistry/rosetta/rosetta-3.4.ebuild b/sci-chemistry/rosetta/rosetta-3.4.ebuild
index 6ffe8df..518e746 100644
--- a/sci-chemistry/rosetta/rosetta-3.4.ebuild
+++ b/sci-chemistry/rosetta/rosetta-3.4.ebuild
@@ -13,12 +13,12 @@ MY_P="${PN}${PV}_source"
 
 DESCRIPTION="Prediction and design of protein structures, folding mechanisms, and protein-protein interactions"
 HOMEPAGE="http://www.rosettacommons.org/"
-SRC_URI="${MY_P}.tgz"
+SRC_URI="${MY_P}.tgz patch_rosetta3.4_to_CSROSETTA3_ver1.3.txt"
 
 LICENSE="|| ( rosetta-academic rosetta-commercial )"
 SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="boinc +boost custom-cflags debug doc float mpi +openmp X"
+IUSE="boinc +boost custom-cflags debug doc float +lange mpi +openmp X"
 
 REQUIRED_USE="?? ( mpi boinc )"
 
@@ -51,13 +51,19 @@ src_prepare() {
 	use custom-cflags || \
 		export CXXFLAGS="-O3 -ffast-math -funroll-loops -finline-functions -finline-limit=20000 -pipe"
 
+	export LD_LIBRARY_PATH=""
+	use lange && \
+		epatch \
+			"${DISTDIR}"/patch_${PN}${PV}_to_CSROSETTA3_ver1.3.txt \
+			"${FILESDIR}"/${P}-lange-fix.patch
+
 	epatch \
 		"${FILESDIR}"/${P}-platform.patch \
 		"${FILESDIR}"/${P}-user-settings.patch \
 		"${FILESDIR}"/${P}-fix-valgrind.patch \
 		"${FILESDIR}"/${P}-boinc.patch \
 		"${FILESDIR}"/${P}-boost.patch \
-		"${FILESDIR}"/${P}-gcc4.7.patch
+		"${FILESDIR}"/${P}-gcc4.78.patch
 
 	eprefixify tools/build/*