proj/gentoo: Initial commit

This commit represents a new era for Gentoo:
Storing the gentoo-x86 tree in Git, as converted from CVS.

This commit is the start of the NEW history.
Any historical data is intended to be grafted onto this point.

Creation process:
1. Take final CVS checkout snapshot
2. Remove ALL ChangeLog* files
3. Transform all Manifests to thin
4. Remove empty Manifests
5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$
5.1. Do not touch files with -kb/-ko keyword flags.

Signed-off-by: Robin H. Johnson <robbat2@gentoo.org>
X-Thanks: Alec Warner <antarus@gentoo.org> - did the GSoC 2006 migration tests
X-Thanks: Robin H. Johnson <robbat2@gentoo.org> - infra guy, herding this project
X-Thanks: Nguyen Thai Ngoc Duy <pclouds@gentoo.org> - Former Gentoo developer, wrote Git features for the migration
X-Thanks: Brian Harring <ferringb@gentoo.org> - wrote much python to improve cvs2svn
X-Thanks: Rich Freeman <rich0@gentoo.org> - validation scripts
X-Thanks: Patrick Lauer <patrick@gentoo.org> - Gentoo dev, running new 2014 work in migration
X-Thanks: Michał Górny <mgorny@gentoo.org> - scripts, QA, nagging
X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed

5 files changed, 166 insertions, 0 deletions

diff --git a/sci-libs/beagle/Manifest b/sci-libs/beagle/Manifest
new file mode 100644
index 000000000000..6e60f608bfcf
--- /dev/null
+++ b/sci-libs/beagle/Manifest
@@ -0,0 +1 @@
+DIST beagle-3.0.3.tar.gz 5002994 SHA256 2e481dc180bc1f665ade82f0568db4d67f4b8b3f32bc155f1358fd48630e2935 SHA512 2f8f027f3f24d0fd287e27a80fe5b24e18550144add06fb8157dd03f734f5ce212f62889720c81fd33246fa7086e9b913802ec0c5155df5bd801c36888b346cb WHIRLPOOL 7902d2bf149afb9c2dc1f89fbb6754250950d6df90e63b445939b9c7fdc21b59835ac840d3babb7b56056c24e1f159da9aef27105ff9e05e0298f283e6697bbb
diff --git a/sci-libs/beagle/beagle-3.0.3.ebuild b/sci-libs/beagle/beagle-3.0.3.ebuild
new file mode 100644
index 000000000000..52ba7e8f86b2
--- /dev/null
+++ b/sci-libs/beagle/beagle-3.0.3.ebuild
@@ -0,0 +1,55 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit autotools-utils
+
+DESCRIPTION="Open BEAGLE, a versatile EC/GA/GP framework"
+SRC_URI="mirror://sourceforge/beagle/${P}.tar.gz"
+HOMEPAGE="http://beagle.gel.ulaval.ca/"
+
+SLOT="0"
+LICENSE="LGPL-2.1"
+KEYWORDS="~amd64 x86"
+IUSE="doc static-libs"
+
+RDEPEND="
+	sys-libs/zlib
+	!app-misc/beagle
+	!dev-libs/libbeagle"
+DEPEND="${DEPEND}
+	doc? ( app-doc/doxygen )"
+
+PATCHES=( "${FILESDIR}"/${PN}-3.0.3-gcc43.patch "${FILESDIR}"/${PN}-3.0.3-gcc47.patch )
+
+AUTOTOOLS_IN_SOURCE_BUILD=1
+
+src_prepare() {
+	autotools-utils_src_prepare
+	sed -e "s:@LIBS@:@LIBS@ -lpthread:" \
+		-i PACC/Threading/Makefile.in || \
+		die "Failed to fix threading libs makefile."
+}
+
+src_configure() {
+	local myeconfargs=( --enable-optimization )
+	autotools-utils_src_configure
+}
+
+src_compile() {
+	autotools-utils_src_compile
+
+	use doc && autotools-utils_src_compile doc
+}
+
+src_install () {
+	autotools-utils_src_install
+
+	if use doc; then
+		cp -pPR examples "${D}"/usr/share/doc/${PF} || \
+			die "Failed to install examples."
+		dohtml -r refman/*
+	fi
+}
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..cb3546c68a5c
--- /dev/null
+++ b/sci-libs/beagle/files/beagle-3.0.3-gcc47.patch
@@ -0,0 +1,10 @@
+--- beagle/include/beagle/RouletteT.hpp
++++ 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..4b2a7479afe8
--- /dev/null
+++ b/sci-libs/beagle/metadata.xml
@@ -0,0 +1,11 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<herd>sci</herd>
+	<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>