sci-chemistry/ball: Version BUmp

Package-Manager: portage-2.2.10/cvs/Linux x86_64
Manifest-Sign-Key: 0xB9D4F231BD1558AB!

7 files changed, 232 insertions, 26 deletions

diff --git a/sci-chemistry/ball/ChangeLog b/sci-chemistry/ball/ChangeLog
index af2208ce4d81..86793ce83543 100644
--- a/sci-chemistry/ball/ChangeLog
+++ b/sci-chemistry/ball/ChangeLog
@@ -1,6 +1,15 @@
 # ChangeLog for sci-chemistry/ball
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ball/ChangeLog,v 1.12 2013/09/05 19:03:42 mgorny Exp $
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ball/ChangeLog,v 1.13 2014/03/26 11:20:39 jlec Exp $
+
+*ball-1.4.2 (26 Mar 2014)
+
+  26 Mar 2014; Justin Lecher <jlec@gentoo.org> ball-1.4.1-r1.ebuild,
+  +ball-1.4.2.ebuild,
+  +files/ball-1.4.2-Fix-compilation-of-sipModularWidget.patch,
+  +files/ball-1.4.2-PDBFile-Fix-compilation-with-gcc-4.8.patch,
+  +files/ball-1.4.2-QT4_EXTRACT_OPTIONS-CMake-macro-changed-in-CMake-2.8.patch:
+  Version BUmp
 
   05 Sep 2013; Michał Górny <mgorny@gentoo.org> ball-1.4.1-r1.ebuild:
   Clean up PYTHON_COMPAT from old implementations.
diff --git a/sci-chemistry/ball/Manifest b/sci-chemistry/ball/Manifest
index 33bc7c262955..ea5e484080aa 100644
--- a/sci-chemistry/ball/Manifest
+++ b/sci-chemistry/ball/Manifest
@@ -1,5 +1,5 @@
 -----BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA256
+Hash: SHA512
 
 AUX ball-1.4.1-Added-MAX_PENALTY-option-to-bond-order-assignment.patch 40315 SHA256 b3210eb9bc2356b7ae708d07b87c6132cda327311762475a8e9e476360decf43 SHA512 067b227d926d5ee1232f4c9cfe95aa915373f8a741094d2ce4a41527a1d67f03e82be0522b04471a1e6ac34231cdacc05ad164914eee41fe1b0811e594c61396 WHIRLPOOL 24b223a3ca34d343d180d6612e85ca213091f8ff02a636ae32631f84ecebf1785e3f3c419c029c6e22c5328de208a0d55fc0ae3ece0e9b7c465be613446228d8
 AUX ball-1.4.1-BondOrder.xml.patch 1675 SHA256 8aaecb9dc1bc729a0446c350b423b47779b8d82a3b00f570a55e4b4f0b7b02c3 SHA512 77e04209bebff5057ad549d1c1d7b638391fb063efb8635a72b46287a4c4975c2d0940267bce9002f3c9dc0f6fab7e21a3099506f57a44e0a325149ee134b2e0 WHIRLPOOL db3ecb2587e607f8257348d9e6dc558e2795807fd8c62e3fecf82bb426b54d18efba510c2b8990dd6fd74781b048be1e69373678977f723c11ed6624ad774d78
@@ -13,26 +13,31 @@ AUX ball-1.4.1-missing-signed.patch 985 SHA256 5bdeb4613e775e83bf219661f0e494f75
 AUX ball-1.4.1-multilib.patch 1585 SHA256 ee246df89ca6f1559df359fb6af93462fda9c93fa8a81977f6a5b92190d6ceb5 SHA512 5eebfdce5fba25967c252d0c83f6187079efc55c9481045d6c9e111930e1bb2bed31666b913eb12f46a723aa875559b54f658460efd7be10bbbe4c7cd2982341 WHIRLPOOL f4240a867e4ae503f49bffb986e8bd8a69e1914d6e770e7ae7cb7c03efd23eec3fa095c837e5874785ec4b6bf326c9fec15e16c746f48b89d9afe173f19eb0df
 AUX ball-1.4.1-pthread.patch 418 SHA256 be38df8bc184929b0db5c3716113a17ac0033ad53ee631a5881c56c664d23970 SHA512 ce35b9f061534c250789f318a96196d3588d1cf875065a32007c6aeda0815809d42ebea0641c22d074f44125d5236450f887574af3624abc0f7eb6933e38343e WHIRLPOOL ee2152800b79e9f899ba5c194d2e9b7a7fd9503fc45e91d5a5ff75ba478c7694c7f14bca94fda675d04e9e45e7601bd87dfce53c127bf04dd480aa8a994bd0b3
 AUX ball-1.4.1-python.patch 2780 SHA256 3abb2f70a4d8ea930da13cb68e8f57dd705fad42014bd2cc3912362cada48665 SHA512 dd80af7e899bec2a2dff5b837f6b3eaca3f92d5b8b7c1e22cde5a8428b4e3036739212ef0fdea77955e4716d27638772b84d4516e5a15d5937f0d41692be1cdb WHIRLPOOL f82b11dcbc39ae4d434fe6425ff52253ba7c36e719cb103b30a8f01aee0f24699c4759e3c5e006ce168a586f1f012dee25a1b0f1ae23bd2454aac65983e71003
+AUX ball-1.4.2-Fix-compilation-of-sipModularWidget.patch 1565 SHA256 3644269518b8444d08de7348f799ba0dedaf644d84c89a55afefdfb64822dfff SHA512 15cc7b8583b5dfcefa152dac0fcf300ad2369f147dc4bb4061fd06586eea403a67442389b2eecca93144b02f73c0eb252794604b87348e63dddcaa03d2775882 WHIRLPOOL e184f70ec3d06e2ef1dc918f0b6e7390b01ce9695ec6bc6cb2ee8f9a637657d18fe74c34ef240d4f721e3d4d74953c9f6d080da7af3d41286d681ef83107e49d
+AUX ball-1.4.2-PDBFile-Fix-compilation-with-gcc-4.8.patch 1011 SHA256 7231441f971d95ec4845cd899d1d9c3c5c6adedc91156a312c1c76d6d8a096c0 SHA512 f99d0b42b6798b0f97aeb93f9aedf9dfd68c62f948dabab4cc1e7b6a4251b10ec8b4e109936f86456f77b1faecad5eff05bb40200d55490c7f82787b3f6951a1 WHIRLPOOL b54bfc73d6b4f674a7c3830ba142a9e55a13c5775d8174ea24c47759299f00b590df958e9213be892be103064e62f7e095ef543429c2a92884c1468f1660bd9c
+AUX ball-1.4.2-QT4_EXTRACT_OPTIONS-CMake-macro-changed-in-CMake-2.8.patch 1470 SHA256 be30e8dba38a385d53604c887436bae090aaae46bed97d87b02dd12083f8c19e SHA512 18cd445e4867878f73d74afef1ae74d02bb3a118fdeb379beb2463cef501a79eacfa9c5d487fa2656993f652cc0a7432c7d139a2df101416cc6d7139dc4af034 WHIRLPOOL 5a35d821789ddebe11d45f99866e052d345972d43193888346fbb5cf036288655a92d46c6b8d82291ba4ac6d3f8a57b350a5a71412ecd90b3ea1b4fcca00cbdb
+DIST BALL-1.4.2.tar.xz 16080664 SHA256 053931b2e050d7d5bceaa21ad3617a1ad0af00f94de56076ce02d544383cbf91 SHA512 c719af4ef2dc1076818d59b72350b704fbffea06bd44737519fb50d88da113ea509333d407f2330aa59bf1c4e6b81adfd3d28e05459f66d7c9707f8d85db7a87 WHIRLPOOL ba7ae340833ea5703d047a9dbc0ce50d9b9dc2b0047a0c6d9f9a17946956c684a09e0860f25c7214a2aa0adee9beb1d01eac38b0ab08259a2934f97cbef91379
 DIST ball-1.4.1.tar.gz 23073541 SHA256 752b4487040d318bdcb1760c96c3293fed065fad7e0dd0efb5c927382e2aeb53 SHA512 2ee1e3b4c9a7e84b581dd8566612f528b5337c2ab55ea57b44c06efa49bba9335604b64c3b618e8c5992d5854f3db77e247da31addf8dbcb6b02275ae4b328cf WHIRLPOOL 7a37b23825e6a7ef286995337ee4870192e89d0f42cc48d715f079431ab95db18aaa792c6cf6e0c3aca6c58e8f870058d87dd87b57931392fd27ecbf00b92c99
-EBUILD ball-1.4.1-r1.ebuild 2341 SHA256 505c1d5aa14a8f8e99f8621efff945fef779645cbebb2166c90ac79a24018e7a SHA512 b2662d5f7589fa2423ca2bfa3959be26226863938b60bffedb9468aeb5e84f757ebcbf7ff4a497c45447875ded1c3787d84f14c43e96b8021cc05aebcc55f9f1 WHIRLPOOL 3448fe32f2b9537f499e2bb94c6891c9af84840286288b791625a30042d619b6386f7987556921c5dd89c4b972894f3dc4bd176ca487f33c116c521326fb8281
-MISC ChangeLog 2448 SHA256 11b0965f1337718b4b3641e70a39c5f76e5fd831e231174ef1221bb5fc519f13 SHA512 ae3af08ba7eab7971a3bf30600894ce9e97bb0bf4dd1360411940af3925e8896de6c7a131a695395e9c4b27356b5c643a7ae71c0809a2b630f3479ae13c0d894 WHIRLPOOL d87576e47d7d51ea4cf5bbbaa95b864ea5819d77b973d372bf72399fcd40520c29771cedf8305097d6836694ead3698040227c4167a81cc56d91424f1afc3620
+EBUILD ball-1.4.1-r1.ebuild 2310 SHA256 1fce54353afe709dcca3146e314023e80cd9ac2c25feeedf087d99f40ef41112 SHA512 5ede5b995f9405a7254b48b6f52066d7ed70629c1978056cad4a2b3fe8686dc340b0f52a7b5c34460d0ddfc661a4ceb8e1480a267a759d08e7a511446024d0ab WHIRLPOOL 8a749cc5037af6da22c055983bee7ef88f40499399e5641d8a57af1154f6fdf03884c88ec1da84eab2f375b17781f045d126f89e21cb541f337a6639ed875902
+EBUILD ball-1.4.2.ebuild 2117 SHA256 a2cf62deb3c8b1cca28926b01f280f8c8a4becb2efe92345b6d2b4ab3654ee9f SHA512 d75aca9381af9b173ff6d3fff36e39681b812a3e1409b848b19b75dcd56a3b2e97889a2654d8303f4e875555aefccef02fc07f93a4e1966c138c5f283e0a8795 WHIRLPOOL e47b4b351a87e492076cf71d3ffc7a194272d064624193d0e1e26d30184a523df10d445e1613b485ebd549a32775a0111085d1a711b6a981c010a1d02de5d268
+MISC ChangeLog 2787 SHA256 caabcffb0eab64b14a680a17fb9e3fe5bdaaaf2daa3102dcb91f3658f2446ef7 SHA512 c61456ad6eb5fac236e750031ad850ea107b1a8226f25e1285643ceed3715d287bbb12a64f4a095702fee5342a4945f28ece292c3eccf3d85bab9d80d214a677 WHIRLPOOL ec6f9ae152b172b88781b0113346915619773076f69605cef0dcb6096eaa3b0e78773f45f692a2f60c71808076c50bc330d7eebe3a4a898b560b9e9665c489f9
 MISC metadata.xml 1469 SHA256 65ccda3e72400f4ddc1a1c502a10e0b0203fb918d56191f1bf704dc998ddf867 SHA512 2f1de58acc3f31aa91e3708beaac6bb8f68c247a7eed3033de35c5de037473abb8ad06a1e6273ee9879fe557ac1af6018eb17512850cee6ea5844c68b78bf82e WHIRLPOOL 5624b3f0767cd981ba58cafd731a173fb3faba519291c85b6387232a45d1654b055677e6f5a40c552fbb8e74a6621ec8816c189f52aa052bf37f934de3465c8e
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.21 (GNU/Linux)
+Version: GnuPG v2.0.22 (GNU/Linux)
 
-iQJ8BAEBCABmBQJSKNWwXxSAAAAAAC4AKGlzc3Vlci1mcHJAbm90YXRpb25zLm9w
-ZW5wZ3AuZmlmdGhob3JzZW1hbi5uZXQ2REJCMDdDQzRGMERBRDA2RUEwQUZFNDFC
-MDdBMUFFQUVGQjQ0NjRFAAoJELB6GurvtEZOD98QAIx5Zos85DIHkZ8+5x58+L60
-l5wzXmVhr/O+muWTNM4YfuJYpTXbt+ILgewiftXAP5S4wWiOZXC6SriuPLOVvlK4
-5bdtcqju5+KTeyVR7KQ/IEdSzL8yyu7OingWJxXbdpuLDXATpqYTUH+P3eZtzBkW
-6gz2n4583DLYHU+XbPOags9U32yXGpURlU2nUU1azOVMv2b55KC6Au3E0FtNuAfN
-8w/FF19Ru2Qji+5HsC6iLjh7V1g3O6BzgGgf382r4/9OU106MIGOctz+UEWkUOtm
-7zXwn2KDzVGZ+ivQpJTX3Wr1gNp1cs/EBthKi+rjAa135+UDM/neWzL9QF6NmMgX
-YcGoDKdjmuIFnvXeCqKxq7RN1Gf5XCBLv6wCN2mk0r0lJKcvJAFhEn/DKT8T1ABu
-5fb74Mt/d85rCLZhKF0/vo7fxO5Q8aRvcHYspQSPTOGC5XxU9EUIRE98r0aO/cBX
-xHuhAyeKPNuScG5r7yYb3YI4+YdXmLwLSKJe95W3vtgXj2VC2T0X0/vcB3axSDQg
-KOILHEtvLAsRLH6GbV2cPSN8ZXP9f3vi0759v6tSRghnRr2LmFlD5dHZnqeOCF47
-MiXJIe+NDGGM+0H4x9US8pqDcoyuwHC7r5H3vASZ52UMx59dY1iU9u9K27aD/QLe
-ZW/V405CgprSUn17IhS0
-=yQmv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+=Z7us
 -----END PGP SIGNATURE-----
diff --git a/sci-chemistry/ball/ball-1.4.1-r1.ebuild b/sci-chemistry/ball/ball-1.4.1-r1.ebuild
index c6eaa4f0bb2f..ba23080fc497 100644
--- a/sci-chemistry/ball/ball-1.4.1-r1.ebuild
+++ b/sci-chemistry/ball/ball-1.4.1-r1.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2013 Gentoo Foundation
+# Copyright 1999-2014 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ball/ball-1.4.1-r1.ebuild,v 1.6 2013/09/05 19:03:42 mgorny Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ball/ball-1.4.1-r1.ebuild,v 1.7 2014/03/26 11:20:39 jlec Exp $
 
 EAPI=5
 
@@ -61,9 +61,7 @@ PATCHES=(
 	)
 
 pkg_setup() {
-	use python \
-		&& python_set_active_version 2 \
-		&& python_pkg_setup
+	use python && python-single-r1_pkg_setup
 }
 
 src_configure() {
diff --git a/sci-chemistry/ball/ball-1.4.2.ebuild b/sci-chemistry/ball/ball-1.4.2.ebuild
new file mode 100644
index 000000000000..3c8129aa4d6b
--- /dev/null
+++ b/sci-chemistry/ball/ball-1.4.2.ebuild
@@ -0,0 +1,82 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ball/ball-1.4.2.ebuild,v 1.1 2014/03/26 11:20:39 jlec Exp $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit cmake-utils python-single-r1
+
+DESCRIPTION="Biochemical Algorithms Library"
+HOMEPAGE="http://www.ball-project.org/"
+SRC_URI="http://www.ball-project.org/Downloads/v${PV}/BALL-${PV}.tar.xz"
+
+SLOT="0"
+LICENSE="LGPL-2 GPL-3"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="cuda mpi +python sql test +threads +webkit"
+
+REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
+
+RDEPEND="
+	dev-cpp/eigen:3
+	dev-libs/boost
+	dev-qt/qtcore:4
+	dev-qt/qtgui:4
+	dev-qt/qtopengl:4
+	dev-qt/qttest:4
+	dev-qt/qtwebkit:4
+	media-libs/glew
+	sci-libs/fftw:3.0[threads?]
+	sci-libs/gsl
+	sci-libs/libsvm
+	sci-mathematics/lpsolve
+	virtual/opengl
+	x11-libs/libX11
+	cuda? ( dev-util/nvidia-cuda-toolkit )
+	mpi? ( virtual/mpi )
+	python? ( ${PYTHON_DEPS} )
+	sql? ( dev-qt/qtsql:4 )
+	webkit? ( dev-qt/qtwebkit:4 )"
+DEPEND="${RDEPEND}
+	dev-python/sip
+	sys-devel/bison
+	virtual/yacc"
+
+S="${WORKDIR}"/BALL-${PV}
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-1.4.1-multilib.patch
+	"${FILESDIR}"/${PN}-1.4.1-missing-signed.patch
+	"${FILESDIR}"/${P}-PDBFile-Fix-compilation-with-gcc-4.8.patch
+	"${FILESDIR}"/${P}-QT4_EXTRACT_OPTIONS-CMake-macro-changed-in-CMake-2.8.patch
+	"${FILESDIR}"/${PN}-1.4.1-BondOrder.xml.patch
+	"${FILESDIR}"/${P}-Fix-compilation-of-sipModularWidget.patch
+	)
+
+pkg_setup() {
+	use python && python-single-r1_pkg_setup
+}
+
+src_configure() {
+	local mycmakeargs=(
+		$(cmake-utils_use_use threads FFTW_THREADS)
+		$(cmake-utils_use cuda MT_ENABLE_CUDA)
+		$(cmake-utils_use mpi MT_ENABLE_MPI)
+		$(cmake-utils_use sql BALL_HAS_QTSQL)
+		$(cmake-utils_use_use webkit USE_QTWEBKIT)
+		$(cmake-utils_use python BALL_PYTHON_SUPPORT)
+	)
+	cmake-utils_src_configure
+	local i
+	for i in "${S}"/data/*; do
+		ln -sf "${i}" "${BUILD_DIR}"/source/TEST/ || die
+		ln -sf "${i}" "${S}"/source/TEST/ || die
+	done
+}
+
+src_compile() {
+	cmake-utils_src_compile
+	use test && cmake-utils_src_make build_tests
+}
diff --git a/sci-chemistry/ball/files/ball-1.4.2-Fix-compilation-of-sipModularWidget.patch b/sci-chemistry/ball/files/ball-1.4.2-Fix-compilation-of-sipModularWidget.patch
new file mode 100644
index 000000000000..3ec2f6e983a8
--- /dev/null
+++ b/sci-chemistry/ball/files/ball-1.4.2-Fix-compilation-of-sipModularWidget.patch
@@ -0,0 +1,40 @@
+From da49802f8620562f91ac2c947520dccd223ee26b Mon Sep 17 00:00:00 2001
+From: Andreas Hildebrandt <andreas.hildebrandt@uni-mainz.de>
+Date: Wed, 15 Jan 2014 17:42:01 +0100
+Subject: [PATCH] Fix compilation of sipModularWidget
+
+---
+ source/PYTHON/EXTENSIONS/VIEW/modularWidget.sip | 10 +++++-----
+ 1 file changed, 5 insertions(+), 5 deletions(-)
+
+diff --git a/source/PYTHON/EXTENSIONS/VIEW/modularWidget.sip b/source/PYTHON/EXTENSIONS/VIEW/modularWidget.sip
+index 522b0ed..7b8ba3e 100644
+--- a/source/PYTHON/EXTENSIONS/VIEW/modularWidget.sip
++++ b/source/PYTHON/EXTENSIONS/VIEW/modularWidget.sip
+@@ -22,18 +22,18 @@ class ModularWidget
+ 	static Size countInstances();
+ 	static ModularWidget* getInstance(Position);
+ 
+-  ModularWidget(const char* = "<ModularWidget>")	throw();
+-	ModularWidget(const ModularWidget&) throw();
++  ModularWidget(const char* = "<ModularWidget>");
++	ModularWidget(const ModularWidget&);
+  	~ModularWidget() throw();
+ 				
+-	virtual void destroy() throw();
+-	virtual void clear() throw();
++//	virtual void destroy();
++	virtual void clear();
+ 
+ 	static void registerWidget(ModularWidget*) throw(NullPointer);
+ //	virtual void initializeWidget(MainControl&);
+ // 	virtual void finalizeWidget(MainControl&);
+ 	virtual void checkMenu(MainControl&) throw();
+-//	virtual void initializePreferencesTab(Preferences&)	throw();
++//	virtual void initializePreferencesTab(Preferences&);
+ //	virtual void finalizePreferencesTab(Preferences&)	throw();
+ 	virtual void applyPreferences() throw();
+   virtual void fetchPreferences(INIFile&) throw();
+-- 
+1.9.1
+
diff --git a/sci-chemistry/ball/files/ball-1.4.2-PDBFile-Fix-compilation-with-gcc-4.8.patch b/sci-chemistry/ball/files/ball-1.4.2-PDBFile-Fix-compilation-with-gcc-4.8.patch
new file mode 100644
index 000000000000..f6b8ff45fa7f
--- /dev/null
+++ b/sci-chemistry/ball/files/ball-1.4.2-PDBFile-Fix-compilation-with-gcc-4.8.patch
@@ -0,0 +1,28 @@
+From e7cc50705bed20e160bd4b637b23f57270f580a8 Mon Sep 17 00:00:00 2001
+From: Daniel Stoeckel <dstoeckel@bioinf.uni-sb.de>
+Date: Sat, 6 Apr 2013 01:06:55 +0200
+Subject: [PATCH] PDBFile:Fix compilation with gcc 4.8
+
+Apparently the automatic conversion from boost::shared_ptr<CrystalInfo>
+to boost::shared_ptr<PersistentObject> is no longer supported.
+Just change the type of the pointer and work around this issue.
+---
+ source/FORMAT/PDBFileDetails.C | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/source/FORMAT/PDBFileDetails.C b/source/FORMAT/PDBFileDetails.C
+index 97c2572..aedc5db 100644
+--- a/source/FORMAT/PDBFileDetails.C
++++ b/source/FORMAT/PDBFileDetails.C
+@@ -901,7 +901,7 @@ namespace BALL
+ 	{
+ 		if (!(current_protein_->hasProperty("CRYSTALINFO")))
+ 		{
+-			boost::shared_ptr<CrystalInfo> temp_ptr(new CrystalInfo());
++			boost::shared_ptr<PersistentObject> temp_ptr(new CrystalInfo());
+ 			current_protein_->setProperty(NamedProperty("CRYSTALINFO", temp_ptr));
+ 		}
+ 
+-- 
+1.9.1
+
diff --git a/sci-chemistry/ball/files/ball-1.4.2-QT4_EXTRACT_OPTIONS-CMake-macro-changed-in-CMake-2.8.patch b/sci-chemistry/ball/files/ball-1.4.2-QT4_EXTRACT_OPTIONS-CMake-macro-changed-in-CMake-2.8.patch
new file mode 100644
index 000000000000..615a92290805
--- /dev/null
+++ b/sci-chemistry/ball/files/ball-1.4.2-QT4_EXTRACT_OPTIONS-CMake-macro-changed-in-CMake-2.8.patch
@@ -0,0 +1,44 @@
+From 1e76c9cb1920e9176b725269985c7eb43126d188 Mon Sep 17 00:00:00 2001
+From: Luis de la Garza <delagarza@informatik.uni-tuebingen.de>
+Date: Fri, 22 Nov 2013 15:18:55 +0100
+Subject: [PATCH] QT4_EXTRACT_OPTIONS CMake macro changed in CMake 2.8.12;
+ fixed BALLMacros.cmake
+
+---
+ cmake/BALLMacros.cmake | 14 ++++++++++----
+ 1 file changed, 10 insertions(+), 4 deletions(-)
+
+diff --git a/cmake/BALLMacros.cmake b/cmake/BALLMacros.cmake
+index f81ab89..0ac1b87 100644
+--- a/cmake/BALLMacros.cmake
++++ b/cmake/BALLMacros.cmake
+@@ -6,16 +6,22 @@
+ ### minor modifications (marked with ## BALL ###)
+ ###
+ MACRO(QT4_WRAP_UI_BALL outfiles )
+-  QT4_EXTRACT_OPTIONS(ui_files ui_options ${ARGN})
+-
+-	### BALL ###
++  # since 2.8.12 qt4_extract_options has an additional argument
++  # copied fix from OpenMS
++  IF(${CMAKE_VERSION} VERSION_LESS "2.8.12")
++      QT4_EXTRACT_OPTIONS(ui_files ui_options ${ARGN})
++  ELSE()
++      QT4_EXTRACT_OPTIONS(ui_files ui_options ui_target ${ARGN})
++  ENDIF()
++
++  ### BALL ###
+   # create output directory (will not exist for out-of-source builds)
+   FILE(MAKE_DIRECTORY ${PROJECT_BINARY_DIR}/include/BALL/VIEW/UIC/)
+ 
+   FOREACH (it ${ui_files})
+     GET_FILENAME_COMPONENT(outfile ${it} NAME_WE)
+     GET_FILENAME_COMPONENT(infile ${it} ABSOLUTE)
+-		### BALL ###
++    ### BALL ###
+     SET(outfile ${PROJECT_BINARY_DIR}/include/BALL/VIEW/UIC/ui_${outfile}.h)
+     ADD_CUSTOM_COMMAND(OUTPUT ${outfile}
+       COMMAND ${QT_UIC_EXECUTABLE}
+-- 
+1.9.1
+