New addition, written by me, #406401

Package-Manager: portage-2.2.0_alpha95/cvs/Linux x86_64

8 files changed, 295 insertions, 0 deletions

diff --git a/sci-chemistry/ball/ChangeLog b/sci-chemistry/ball/ChangeLog
new file mode 100644
index 000000000000..9acfc7b559f6
--- /dev/null
+++ b/sci-chemistry/ball/ChangeLog
@@ -0,0 +1,12 @@
+# ChangeLog for sci-chemistry/ball
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/ball/ChangeLog,v 1.1 2012/03/25 14:13:39 jlec Exp $
+
+*ball-1.4.1 (25 Mar 2012)
+
+  25 Mar 2012; Justin Lecher <jlec@gentoo.org> +ball-1.4.1.ebuild,
+  +files/ball-1.4.1-libsvm.patch, +files/ball-1.4.1-multilib.patch,
+  +files/ball-1.4.1-pthread.patch, +files/ball-1.4.1-python.patch,
+  +metadata.xml:
+  New addition, written by me, #406401
+
diff --git a/sci-chemistry/ball/Manifest b/sci-chemistry/ball/Manifest
new file mode 100644
index 000000000000..d0ee1ea77542
--- /dev/null
+++ b/sci-chemistry/ball/Manifest
@@ -0,0 +1,18 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA512
+
+AUX ball-1.4.1-libsvm.patch 814 RMD160 47017c89dc3217e28d8b08e37bc1d483b8463556 SHA1 e4e3e24b85bbf38e4fc0921517178635bc99312f SHA256 01d3e514d11260ca52a7d180219e62bd371ab48787d048321898d6ddf0eee219
+AUX ball-1.4.1-multilib.patch 1585 RMD160 6ef1f3dd73fd5ea964de8114873217da9f308081 SHA1 3a458df44a1e3dfd259f62cf84200f995b99f59a SHA256 ee246df89ca6f1559df359fb6af93462fda9c93fa8a81977f6a5b92190d6ceb5
+AUX ball-1.4.1-pthread.patch 418 RMD160 32393068ab23b6923d39a90c183d87a81862d4dd SHA1 7205c13f0b6414f1757f0df30f9bd2b0a14f4885 SHA256 be38df8bc184929b0db5c3716113a17ac0033ad53ee631a5881c56c664d23970
+AUX ball-1.4.1-python.patch 2780 RMD160 64a26b428557130b12997d2e4ecc77a22984a86c SHA1 868812268d8158d6c737891616bfeff612834447 SHA256 3abb2f70a4d8ea930da13cb68e8f57dd705fad42014bd2cc3912362cada48665
+DIST ball-1.4.1.tar.gz 23073541 RMD160 39425bf4f8c1f510ea877ce2de1330ac857d3904 SHA1 a01e93be9517212fd67af5b21664530f8724b7e9 SHA256 752b4487040d318bdcb1760c96c3293fed065fad7e0dd0efb5c927382e2aeb53
+EBUILD ball-1.4.1.ebuild 1599 RMD160 d9b342aa30c0f8f553534cdcc1d23477bfc5d338 SHA1 69ac277067efe28e80b5705fdf8ff29cfb0c0620 SHA256 484887558e1ef1d2490053499caf89b4f3a8e6c8f183018bacde574e59609fcd
+MISC ChangeLog 493 RMD160 3292b1387b26834488397aeceeb3fae3cd24ca31 SHA1 32bb8addc39c57252459d9ff1428017ceab0976f SHA256 a547eaced47a46ed712ea6676aed4ec1a35a6a02722b20721467d744f29efe7a
+MISC metadata.xml 1448 RMD160 dab47d2ed3c2e7884d728e782a23fd23565018df SHA1 5851bdc9106618e6206038fa4d349debf67b1340 SHA256 54512219e6ea9be9cd7a833def40b2d0102f4716b4507c4392673896d5150c5f
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.18 (GNU/Linux)
+
+iEYEAREKAAYFAk9vKBgACgkQgAnW8HDreRZ+AACgo/GXgwLBlo8zapjRnclTO9Nu
+qQ0AoM8HiJKtPM4IyWDN1+b63MtA/6gk
+=OjfE
+-----END PGP SIGNATURE-----
diff --git a/sci-chemistry/ball/ball-1.4.1.ebuild b/sci-chemistry/ball/ball-1.4.1.ebuild
new file mode 100644
index 000000000000..2101ecb92687
--- /dev/null
+++ b/sci-chemistry/ball/ball-1.4.1.ebuild
@@ -0,0 +1,69 @@
+# Copyright 1999-2012 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.ebuild,v 1.1 2012/03/25 14:13:39 jlec Exp $
+
+EAPI=4
+
+PYTHON_DEPEND="python? 2"
+
+inherit cmake-utils python
+
+DESCRIPTION="Biochemical Algorithms Library"
+HOMEPAGE="http://www.ball-project.org/"
+SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="LGPL-2 GPL-3"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="cuda mpi +python sql +threads +webkit"
+
+RDEPEND="
+	dev-cpp/eigen:3
+	dev-libs/boost
+	media-libs/glew
+	sci-libs/fftw:3.0[threads?]
+	sci-libs/gsl
+	sci-libs/libsvm
+	sci-mathematics/lpsolve
+	virtual/opengl
+	x11-libs/libX11
+	x11-libs/qt-core
+	x11-libs/qt-gui
+	x11-libs/qt-opengl
+	x11-libs/qt-test
+	x11-libs/qt-webkit
+	cuda? ( dev-util/nvidia-cuda-toolkit )
+	mpi? ( virtual/mpi )
+	sql? ( x11-libs/qt-sql )
+	webkit? ( x11-libs/qt-webkit )"
+DEPEND="${RDEPEND}
+	dev-python/sip
+	sys-devel/bison
+	virtual/yacc"
+
+S="${WORKDIR}"/BALL
+
+PATCHES=(
+	"${FILESDIR}"/${P}-multilib.patch
+	"${FILESDIR}"/${P}-libsvm.patch
+	"${FILESDIR}"/${P}-pthread.patch
+	"${FILESDIR}"/${P}-python.patch
+	)
+
+pkg_setup() {
+	use python \
+		&& python_set_active_version 2 \
+		&& python_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
+}
diff --git a/sci-chemistry/ball/files/ball-1.4.1-libsvm.patch b/sci-chemistry/ball/files/ball-1.4.1-libsvm.patch
new file mode 100644
index 000000000000..c85506d72733
--- /dev/null
+++ b/sci-chemistry/ball/files/ball-1.4.1-libsvm.patch
@@ -0,0 +1,24 @@
+From 60a5f677587046b3e2077872c21b005bad549b85 Mon Sep 17 00:00:00 2001
+Message-Id: <60a5f677587046b3e2077872c21b005bad549b85.1332678065.git.jlec@gentoo.org>
+From: Justin Lecher <jlec@gentoo.org>
+Date: Sun, 25 Mar 2012 14:15:16 +0200
+Subject: [PATCH 1/2] Correct deprecated usage of svm_destroy_model to
+ svm_free_and_destroy_model
+
+---
+ source/QSAR/libsvmModel.C |    2 +-
+ 1 files changed, 1 insertions(+), 1 deletions(-)
+
+diff --git a/source/QSAR/libsvmModel.C b/source/QSAR/libsvmModel.C
+index 58ce4dc..1f24e15 100644
+--- a/source/QSAR/libsvmModel.C
++++ b/source/QSAR/libsvmModel.C
+@@ -81,7 +81,7 @@ void LibsvmModel::train()
+ 		
+ 		//free(prob);
+ 		//free(prob->y); free(prob->x);
+-		svm_destroy_model((::svm_model*)svm_train_result_);
++		svm_free_and_destroy_model((::svm_model**)svm_train_result_);
+ 	}
+ }
+ 
diff --git a/sci-chemistry/ball/files/ball-1.4.1-multilib.patch b/sci-chemistry/ball/files/ball-1.4.1-multilib.patch
new file mode 100644
index 000000000000..317c4029c678
--- /dev/null
+++ b/sci-chemistry/ball/files/ball-1.4.1-multilib.patch
@@ -0,0 +1,39 @@
+From 5b8f4e58b4e54bcdfa6f287e01f91d9dfd4e5a14 Mon Sep 17 00:00:00 2001
+From: Justin Lecher <jlec@gentoo.org>
+Date: Sun, 25 Mar 2012 14:12:21 +0200
+Subject: [PATCH] Correct path for multilib installation.
+
+Libraries should go into lib64 not lib on native 64bit. Therefore we can use the LIBDIR detected by cmake.
+---
+ CMakeLists.txt |    8 ++++----
+ 1 files changed, 4 insertions(+), 4 deletions(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 940ebf4..7eb3db4 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -426,8 +426,8 @@ SET(CMAKE_RUNTIME_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}/bin")
+ ## These variables are used in all install-targets
+ IF (NOT ${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
+ 	SET(BALL_RUNTIME_INSTALL_DIRECTORY "bin")
+-	SET(BALL_LIBRARY_INSTALL_DIRECTORY "lib")
+-	SET(BALL_ARCHIVE_INSTALL_DIRECTORY "lib")
++	SET(BALL_LIBRARY_INSTALL_DIRECTORY ${CMAKE_INSTALL_LIBDIR})
++	SET(BALL_ARCHIVE_INSTALL_DIRECTORY ${CMAKE_INSTALL_LIBDIR})
+ 	SET(BALL_HEADER_INSTALL_DIRECTORY   ".")
+ 	SET(BALL_DATA_INSTALL_DIRECTORY    "share/BALL")
+ 	SET(BALL_DOCUMENTATION_INSTALL_DIRECTORY    "share/BALL/doc")
+@@ -435,8 +435,8 @@ IF (NOT ${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
+ 		SET(BALL_PYTHON_INSTALL_DIRECTORY  "bin")
+ 		SET(BALL_PLUGIN_INSTALL_DIRECTORY  "bin")
+ 	ELSE()
+-		SET(BALL_PYTHON_INSTALL_DIRECTORY  "lib")
+-		SET(BALL_PLUGIN_INSTALL_DIRECTORY  "lib")
++		SET(BALL_PYTHON_INSTALL_DIRECTORY  ${CMAKE_INSTALL_LIBDIR})
++		SET(BALL_PLUGIN_INSTALL_DIRECTORY  ${CMAKE_INSTALL_LIBDIR})
+ 	ENDIF()
+ ELSE()
+ 	SET(BALL_BUNDLE_INSTALL_DIRECTORY  					"Applications")
+-- 
+1.7.8.5
+
diff --git a/sci-chemistry/ball/files/ball-1.4.1-pthread.patch b/sci-chemistry/ball/files/ball-1.4.1-pthread.patch
new file mode 100644
index 000000000000..5ca9699dc7bd
--- /dev/null
+++ b/sci-chemistry/ball/files/ball-1.4.1-pthread.patch
@@ -0,0 +1,19 @@
+ CMakeLists.txt |    5 +++++
+ 1 files changed, 5 insertions(+), 0 deletions(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index a68497f..264f321 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -426,6 +426,11 @@ LIST(APPEND BALL_DEP_LIBRARIES
+ 	${PYTHON_LIBRARIES}
+ )
+ 
++
++IF(UNIX)
++	LIST(APPEND BALL_DEP_LIBRARIES "pthread")
++ENDIF()
++
+ IF(TBB_FOUND)
+ 	LIST(APPEND BALL_DEP_LIBRARIES ${TBB_LIBRARIES})
+ ENDIF()
diff --git a/sci-chemistry/ball/files/ball-1.4.1-python.patch b/sci-chemistry/ball/files/ball-1.4.1-python.patch
new file mode 100644
index 000000000000..f7a235a3bd78
--- /dev/null
+++ b/sci-chemistry/ball/files/ball-1.4.1-python.patch
@@ -0,0 +1,82 @@
+ source/PYTHON/EXTENSIONS/BALL/file.sip             |    2 +-
+ source/PYTHON/EXTENSIONS/BALL/periodicBoundary.sip |    4 ++--
+ source/PYTHON/EXTENSIONS/VIEW/mainControl.sip      |    2 +-
+ source/PYTHON/pyInterpreter.C                      |    9 +++++----
+ 4 files changed, 9 insertions(+), 8 deletions(-)
+
+diff --git a/source/PYTHON/EXTENSIONS/BALL/file.sip b/source/PYTHON/EXTENSIONS/BALL/file.sip
+index e29170a..6ec6dc4 100644
+--- a/source/PYTHON/EXTENSIONS/BALL/file.sip
++++ b/source/PYTHON/EXTENSIONS/BALL/file.sip
+@@ -70,7 +70,7 @@ class File
+   // std::fstream& getFileStream();
+   bool copyTo(const String&);
+   bool moveTo(const String&);
+-  bool remove() const;
++  bool remove();
+   bool renameTo(const String&);
+   bool truncate(int) const;
+   bool operator == (const File& /file/) const;
+diff --git a/source/PYTHON/EXTENSIONS/BALL/periodicBoundary.sip b/source/PYTHON/EXTENSIONS/BALL/periodicBoundary.sip
+index 2b79778..46daade 100644
+--- a/source/PYTHON/EXTENSIONS/BALL/periodicBoundary.sip
++++ b/source/PYTHON/EXTENSIONS/BALL/periodicBoundary.sip
+@@ -22,8 +22,8 @@ using namespace BALL;
+   void disable();
+   SimpleBox3 getBox() const;
+   void setBox(const SimpleBox3&);
+-  int addSolvent(const String&) const;
+-  int removeSolvent() const;
++  int addSolvent(const String& /In/);
++  int removeSolvent();
+   bool isEnabled() const;
+   void updateMolecules();
+   Options* options;
+diff --git a/source/PYTHON/EXTENSIONS/VIEW/mainControl.sip b/source/PYTHON/EXTENSIONS/VIEW/mainControl.sip
+index 0a6c319..61d4596 100644
+--- a/source/PYTHON/EXTENSIONS/VIEW/mainControl.sip
++++ b/source/PYTHON/EXTENSIONS/VIEW/mainControl.sip
+@@ -139,7 +139,7 @@ class MainControl
+ 	virtual void openFile(const String&) throw();
+ 	void saveBALLViewProjectFile(const String&);
+ 	void loadBALLViewProjectFile(const String&) throw();
+-	void quickSave() const;
++	void quickSave();
+ 	void quickLoad();
+ 	void processEvents(Size);
+ };
+diff --git a/source/PYTHON/pyInterpreter.C b/source/PYTHON/pyInterpreter.C
+index 155a09f..7a12c33 100644
+--- a/source/PYTHON/pyInterpreter.C
++++ b/source/PYTHON/pyInterpreter.C
+@@ -4,9 +4,9 @@
+ // $Id: ball-1.4.1-python.patch,v 1.1 2012/03/25 14:13:39 jlec Exp $
+ //
+ 
+-#include <Python.h>
+-
+ #include <BALL/PYTHON/pyInterpreter.h>
++#include <Python.h>
++
+ #include <BALL/PYTHON/BALLPythonConfig.h>
+ 
+ #include <BALL/FORMAT/lineBasedFile.h>
+@@ -34,7 +34,6 @@ namespace BALL
+ 		PyObject* result = PyRun_String(const_cast<char*>(str.c_str()), mode, context_, context_);
+ 		if (PyErr_Occurred())
+ 		{
+-			PyErr_Print();
+ 			PyObject* type;
+ 			PyObject* value;
+ 			PyObject* range;
+@@ -50,7 +49,9 @@ namespace BALL
+ 			{	
+ 				error_message_ += " (error message could not be parsed)";
+ 			}
+-			
++
++			PyErr_Print();
++
+ 			error_message_ += "\n";
+ 
+ 			return 0;
diff --git a/sci-chemistry/ball/metadata.xml b/sci-chemistry/ball/metadata.xml
new file mode 100644
index 000000000000..8c954a23afc5
--- /dev/null
+++ b/sci-chemistry/ball/metadata.xml
@@ -0,0 +1,32 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<herd>sci</herd>
+	<maintainer>
+		<email>jlec@gentoo.org</email>
+	</maintainer>
+	<longdescription>
+Rapid Software Prototyping can significantly reduce development times in the 
+field of Computational Molecular Biology and Molecular Modeling. 
+BALL (Biochemical Algorithms Library) is an application framework in C++ that 
+has been specifically designed for this purpose. It provides an extensive set 
+of data structures as well as classes for Molecular Mechanics, advanced 
+solvation methods, comparison and analysis of protein structures, file 
+import/export, and visualization .
+
+BALL has been carefully designed to be robust, easy to use, and open to 
+extensions. Especially its extensibility which results from an object-oriented 
+and generic programming approach distinguishes it from other software packages.
+BALL is well suited to serve as a public repository for reliable data 
+structures and algorithms.
+
+Based on BALL we have developed a stand-alone tool for molecular visualization,
+BALLView . BALLView makes the broad functionality available through an 
+integrated user-friendly GUI.
+</longdescription>
+	<use>
+		<flag name="sql">Include SQL database support</flag>
+		<flag name="cuda">Include cuda support</flag>
+		<flag name="webkit">Uses <pkg>x11-libs/qt-webkit</pkg> for drawing</flag>
+	</use>
+</pkgmetadata>