reinit the tree, so we can have metadata

6 files changed, 208 insertions, 0 deletions

diff --git a/sci-libs/beagle/Manifest b/sci-libs/beagle/Manifest
new file mode 100644
index 000000000000..d86363a8b2f3
--- /dev/null
+++ b/sci-libs/beagle/Manifest
@@ -0,0 +1,8 @@
+AUX beagle-3.0.3-fix-c++14.patch 1087 SHA256 307180f16a137175b3700fbd309070222ba048a37c3b196b88bda177c7b3ba96 SHA512 fdbcd7bbde24943ad3327ee98078e25eea9c1a450c52594f50e59b3344a6c7a9a8d9be81665ccdef1dd95d2bc5945c8001309d4df013491238add0036835caca WHIRLPOOL 515adfa015fd7ce85ae21832c7ea00623ac7caa5f2211816f5adb15f678a100a635f041ee89092bf8efe2b0e30291764c81aaf06654a3ed76232d3df18df38b9
+AUX beagle-3.0.3-gcc43.patch 3096 SHA256 2c54696275ac9653fa30eddc1bc1640fffd5f68a7153fab896634b0b553f9487 SHA512 3611b41ea82030b192cf36cfa9636a72e874e69b60f69dcbe0745b21c98e8d89e09f52f902b6d4e174a5a64e05b14352227610b4780f917d29122ef03270e702 WHIRLPOOL c056115ca74ccb33297f55890c5ba1b19064b046a549eb570fc45d76ca3ca449f4c122541f09948df554b5c44aecb3a9589c6204f9451709624045ca35f3efab
+AUX beagle-3.0.3-gcc47.patch 447 SHA256 e881580d6689bb97619d1cb8c32e9b7f5e66c4e9eb029254d974a302b0927ae2 SHA512 693db5621625c8c3323a7f252041f5c2c2eb2609901f326891b782dbcc369f0bf531a2eda40ba08bddb824224e3863ee01917ad56cc99117b2a27aa63599b6d3 WHIRLPOOL d70df6d3108867d82f8506054ee2eec1ab1b68eab5fd9e43d3b28237f6024b04ed8fcba6c7ab5f6a03b7496a34f957ee7f50a9531fc7efe2f46c1da8047b2e5a
+DIST beagle-3.0.3.tar.gz 5002994 SHA256 2e481dc180bc1f665ade82f0568db4d67f4b8b3f32bc155f1358fd48630e2935 SHA512 2f8f027f3f24d0fd287e27a80fe5b24e18550144add06fb8157dd03f734f5ce212f62889720c81fd33246fa7086e9b913802ec0c5155df5bd801c36888b346cb WHIRLPOOL 7902d2bf149afb9c2dc1f89fbb6754250950d6df90e63b445939b9c7fdc21b59835ac840d3babb7b56056c24e1f159da9aef27105ff9e05e0298f283e6697bbb
+EBUILD beagle-3.0.3-r1.ebuild 1080 SHA256 133606ce52a609f807d09719db8b41b20257ff18c1dad9598226e9c48b521d19 SHA512 f95698da02a85c615c966a723dc464cf0b55ebeac3ba5e4ed41be6d9b7bb7db605f2e34dd949089ee6a5bd768eb7114c8d2600be97c61700c102f74f438a11b2 WHIRLPOOL efb6d1fefe16dd3f2b611fa81a39cc189f2a226943e00908578e01a5869232491d3f99369507eff6226c9c3279de718228e217831e1d7e8c7b96930daa90e8c3
+MISC ChangeLog 2928 SHA256 804c7b4f024aacff468d612689197c832364aa40a169aaf04ce97d7b52300117 SHA512 7097d251e33cd417598c858b21edf7064c7080df237ffa2caacf6a567bc15c440a8d8d908caf81a3925e2271359ffbb8b41cad9f1a1a2df7c1c825ebdda18c62 WHIRLPOOL 97a31956603023ef6b77fee60597cf3b719046aaffdd9efd436257475a46bf46200bb11cf768fdb0082648effdf3e9d7a21621d6e81e89e2d092866a6455f3df
+MISC ChangeLog-2015 2360 SHA256 b8a6c4098d8fe9c969c06b169ca9d06745dc53cec854433e2b447129ff5a2e72 SHA512 68d153c45046d06e165ad5e0f45d2b8f433137e959657ffe174fabf0ad849810f2549477fed1db8537a025a3f7c34c0e9f9feec3d2f18b304530374be4fb875a WHIRLPOOL 047af6a7b35f888784252e03ff297d95b22a639059e62c72ec2540cc08a2b2826c463dff2b14f7ddafb461fd966e1cf9e22a1d798ae5f570be57dfa04f8f54c0
+MISC metadata.xml 624 SHA256 0c4f86d0ec1ba89151fcab323af5231d472b367513e98e5a673bbed2011a1e9a SHA512 2f9f6ce205603a1a13125daaa1470499b699a836279633afe00156e07b31515037a1f8f0c236a553a8afde718202afb16fa68760de37c5549ace17227de64b71 WHIRLPOOL f37444cf98903fe49d2af9de2b8fbbb841a3f47395e80ecd7e6abd8c855a748f8d261e9b8522ec1a64dcf878a3797316df7c116a70e0159db04a1d6592662d02
diff --git a/sci-libs/beagle/beagle-3.0.3-r1.ebuild b/sci-libs/beagle/beagle-3.0.3-r1.ebuild
new file mode 100644
index 000000000000..65436b9733a4
--- /dev/null
+++ b/sci-libs/beagle/beagle-3.0.3-r1.ebuild
@@ -0,0 +1,57 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+DESCRIPTION="Open BEAGLE, a versatile EC/GA/GP framework"
+SRC_URI="mirror://sourceforge/beagle/${P}.tar.gz"
+HOMEPAGE="http://beagle.gel.ulaval.ca/"
+
+SLOT="0"
+LICENSE="LGPL-2.1"
+KEYWORDS="~amd64 ~x86"
+IUSE="doc examples static-libs"
+
+RDEPEND="
+	sys-libs/zlib
+	!app-misc/beagle
+	!dev-libs/libbeagle"
+DEPEND="${RDEPEND}
+	doc? ( app-doc/doxygen )"
+
+PATCHES=(
+	"${FILESDIR}/${PN}-3.0.3-gcc43.patch"
+	"${FILESDIR}/${PN}-3.0.3-gcc47.patch"
+	"${FILESDIR}/${PN}-3.0.3-fix-c++14.patch"
+)
+
+src_prepare() {
+	default
+	sed -e "s:@LIBS@:@LIBS@ -lpthread:" \
+		-i PACC/Threading/Makefile.in || die
+}
+
+src_configure() {
+	econf \
+		--enable-optimization \
+		$(use_enable static-libs static)
+}
+
+src_compile() {
+	default
+	use doc && emake doc
+}
+
+src_install () {
+	use doc && local HTML_DOCS=( refman/. )
+	if use examples; then
+		dodoc -r examples
+		docompress -x /usr/share/doc/${PF}/examples
+	fi
+
+	default
+
+	if ! use static-libs; then
+		find "${D}" -name '*.la' -delete || die
+	fi
+}
diff --git a/sci-libs/beagle/files/beagle-3.0.3-fix-c++14.patch b/sci-libs/beagle/files/beagle-3.0.3-fix-c++14.patch
new file mode 100644
index 000000000000..896b58225890
--- /dev/null
+++ b/sci-libs/beagle/files/beagle-3.0.3-fix-c++14.patch
@@ -0,0 +1,30 @@
+Fix building with C++14, where destructors are noexcept(true) by default.
+See also: https://bugs.gentoo.org/show_bug.cgi?id=597342
+
+--- a/PACC/Threading/Thread.cpp
++++ b/PACC/Threading/Thread.cpp
+@@ -79,6 +79,9 @@
+ \attention If the destructor in the derived thread class (e.g. MyThread above) does not wait for thread termination, the potential hazardous situation is that the runtime system will have deleted all of its members before calling this destructor (in C++, class destructors are called in reversed sequence). Thus, the still running thread could access deleted data members with unpredictable and unexpected results. So beware!
+ */
+ Threading::Thread::~Thread(void)
++#if __cplusplus >= 201103L
++	noexcept(false)
++#endif
+ {
+ 	lock();
+ 	if(mThread) {
+--- a/PACC/Threading/Thread.hpp
++++ b/PACC/Threading/Thread.hpp
+@@ -53,7 +53,11 @@
+ 		class Thread : public Condition {
+ 		 public:
+ 			Thread(void);
+-			virtual ~Thread(void);
++			virtual ~Thread(void)
++#if __cplusplus >= 201103L
++			noexcept(false)
++#endif
++			;
+ 			
+ 			void cancel(void);
+ 			bool isRunning(void) const;
diff --git a/sci-libs/beagle/files/beagle-3.0.3-gcc43.patch b/sci-libs/beagle/files/beagle-3.0.3-gcc43.patch
new file mode 100644
index 000000000000..608ce388e793
--- /dev/null
+++ b/sci-libs/beagle/files/beagle-3.0.3-gcc43.patch
@@ -0,0 +1,89 @@
+diff -rupN beagle-3.0.3b/PACC/Math/Matrix.cpp beagle-3.0.3/PACC/Math/Matrix.cpp
+--- beagle-3.0.3b/PACC/Math/Matrix.cpp	2009-01-20 23:38:39.000000000 -0400
++++ beagle-3.0.3/PACC/Math/Matrix.cpp	2009-01-21 00:26:46.000000000 -0400
+@@ -40,6 +40,7 @@
+ #include <stdexcept>
+ #include <iomanip>
+ #include <cmath>
++#include <climits>
+ 
+ using namespace std;
+ using namespace PACC;
+diff -rupN beagle-3.0.3b/PACC/Math/Vector.hpp beagle-3.0.3/PACC/Math/Vector.hpp
+--- beagle-3.0.3b/PACC/Math/Vector.hpp	2009-01-20 23:38:39.000000000 -0400
++++ beagle-3.0.3/PACC/Math/Vector.hpp	2009-01-21 00:26:29.000000000 -0400
+@@ -42,6 +42,7 @@
+ #include "XML/Document.hpp"
+ #include "XML/Streamer.hpp"
+ #include <cmath>
++#include <algorithm>
+ 
+ namespace PACC {
+ 	
+diff -rupN beagle-3.0.3b/PACC/Socket/Cafe.cpp beagle-3.0.3/PACC/Socket/Cafe.cpp
+--- beagle-3.0.3b/PACC/Socket/Cafe.cpp	2009-01-20 23:38:39.000000000 -0400
++++ beagle-3.0.3/PACC/Socket/Cafe.cpp	2009-01-21 00:31:09.000000000 -0400
+@@ -35,6 +35,7 @@
+ 
+ #include "Socket/Cafe.hpp"
+ #include <iostream>
++#include <cstring>
+ 
+ #ifdef WIN32
+ ///////////// specifics for windows /////////////
+diff -rupN beagle-3.0.3b/PACC/Socket/Port.cpp beagle-3.0.3/PACC/Socket/Port.cpp
+--- beagle-3.0.3b/PACC/Socket/Port.cpp	2009-01-20 23:38:39.000000000 -0400
++++ beagle-3.0.3/PACC/Socket/Port.cpp	2009-01-21 00:30:54.000000000 -0400
+@@ -34,6 +34,7 @@
+  */
+ 
+ #include "Socket/Port.hpp"
++#include <cstring>
+ 
+ #ifdef WIN32
+ ///////////// specifics for windows /////////////
+diff -rupN beagle-3.0.3b/PACC/Threading/Thread.cpp beagle-3.0.3/PACC/Threading/Thread.cpp
+--- beagle-3.0.3b/PACC/Threading/Thread.cpp	2009-01-20 23:38:39.000000000 -0400
++++ beagle-3.0.3/PACC/Threading/Thread.cpp	2009-01-21 00:28:02.000000000 -0400
+@@ -35,6 +35,7 @@
+ 
+ #include "Threading/Thread.hpp"
+ #include "Util/Assert.hpp"
++#include <cstdlib>
+ 
+ #ifdef WIN32
+ #include <windows.h>
+diff -rupN beagle-3.0.3b/PACC/Util/SignalHandler.cpp beagle-3.0.3/PACC/Util/SignalHandler.cpp
+--- beagle-3.0.3b/PACC/Util/SignalHandler.cpp	2009-01-20 23:38:39.000000000 -0400
++++ beagle-3.0.3/PACC/Util/SignalHandler.cpp	2009-01-20 23:44:20.000000000 -0400
+@@ -37,6 +37,7 @@
+ #include "Util/Assert.hpp"
+ #include <signal.h>
+ #include <stdexcept>
++#include <cstdlib>
+ 
+ using namespace std;
+ using namespace PACC;
+diff -rupN beagle-3.0.3b/PACC/Util/Tokenizer.cpp beagle-3.0.3/PACC/Util/Tokenizer.cpp
+--- beagle-3.0.3b/PACC/Util/Tokenizer.cpp	2009-01-20 23:38:39.000000000 -0400
++++ beagle-3.0.3/PACC/Util/Tokenizer.cpp	2009-01-20 23:44:10.000000000 -0400
+@@ -36,6 +36,8 @@
+ #include "Util/Tokenizer.hpp"
+ #include "Util/Assert.hpp"
+ #include <stdexcept>
++#include <cstring>
++#include <cstdlib>
+ 
+ using namespace std;
+ using namespace PACC;
+diff -rupN beagle-3.0.3b/PACC/XML/Node.cpp beagle-3.0.3/PACC/XML/Node.cpp
+--- beagle-3.0.3b/PACC/XML/Node.cpp	2009-01-20 23:38:39.000000000 -0400
++++ beagle-3.0.3/PACC/XML/Node.cpp	2009-01-20 23:45:09.000000000 -0400
+@@ -39,6 +39,7 @@
+ #include "Util/Assert.hpp"
+ #include <sstream>
+ #include <stdexcept>
++#include <cstring>
+ 
+ using namespace std;
+ using namespace PACC;
diff --git a/sci-libs/beagle/files/beagle-3.0.3-gcc47.patch b/sci-libs/beagle/files/beagle-3.0.3-gcc47.patch
new file mode 100644
index 000000000000..b74fb32b9989
--- /dev/null
+++ b/sci-libs/beagle/files/beagle-3.0.3-gcc47.patch
@@ -0,0 +1,10 @@
+--- a/beagle/include/beagle/RouletteT.hpp
++++ b/beagle/include/beagle/RouletteT.hpp
+@@ -87,7 +87,7 @@
+     Beagle_StackTraceBeginM();
+     Beagle_AssertM(inWeight>=0.0);
+     if(VectorType::empty()==false) inWeight += VectorType::back().first;
+-    push_back(std::make_pair(inWeight,inValue));
++    this->push_back(std::make_pair(inWeight,inValue));
+     Beagle_StackTraceEndM("void RouletteT<T>::insert(const T& inValue, double inWeight)");
+   }
diff --git a/sci-libs/beagle/metadata.xml b/sci-libs/beagle/metadata.xml
new file mode 100644
index 000000000000..c7ddf2e763fe
--- /dev/null
+++ b/sci-libs/beagle/metadata.xml
@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science Project</name>
+	</maintainer>
+	<longdescription>
+    Open BEAGLE is a C++ Evolutionary Computation (EC) framework. It provides an high-level software environment to do any kind of EC, with support for tree-based genetic programming, bit string and real-valued genetic algorithms, and evolution strategy.
+  </longdescription>
+	<upstream>
+		<remote-id type="sourceforge">beagle</remote-id>
+	</upstream>
+</pkgmetadata>