Version bump from science overlay

Package-Manager: portage-2.2.14/cvs/Linux x86_64
Manifest-Sign-Key: 0x94BFDF4484AD142F

6 files changed, 159 insertions, 127 deletions

diff --git a/sci-libs/armadillo/ChangeLog b/sci-libs/armadillo/ChangeLog
index 46cdefb718eb..7ada27ed6d1b 100644
--- a/sci-libs/armadillo/ChangeLog
+++ b/sci-libs/armadillo/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-libs/armadillo
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/armadillo/ChangeLog,v 1.29 2015/01/05 16:30:03 aballier Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/armadillo/ChangeLog,v 1.30 2015/02/27 13:13:27 dilfridge Exp $
+
+*armadillo-4.600.4 (27 Feb 2015)
+
+  27 Feb 2015; Andreas K. Huettel <dilfridge@gentoo.org>
+  +armadillo-4.600.4.ebuild, -armadillo-3.6.0.ebuild, -armadillo-3.6.1.ebuild,
+  metadata.xml:
+  Version bump from science overlay
 
   05 Jan 2015; Alexis Ballier <aballier@gentoo.org> armadillo-3.6.2.ebuild:
   keyword ~arm
diff --git a/sci-libs/armadillo/Manifest b/sci-libs/armadillo/Manifest
index 3c5e6bd085c4..b9d853f7e2f0 100644
--- a/sci-libs/armadillo/Manifest
+++ b/sci-libs/armadillo/Manifest
@@ -2,19 +2,29 @@
 Hash: SHA256
 
 DIST armadillo-3.4.4.tar.gz 3006964 SHA256 ef94e12556421fa62ba7734f8b18bb12c188f43dd6192d3648a28e8d154e6ba7 SHA512 78fbb107b220d283a2404483ee38720fd8259bbf675d8753d706cc3c3ba9678d47412d156f24a4b3cc95e20ce3c935167e2f7657806b5b8e8b7c95938c4b3f3f WHIRLPOOL 2a1b6426b695569c10b13d3df1183c615fdb4261497eea405e61316a838a5744477db7bfd8344f25d741e69899f64a19c801bd068d366175a2c9898369090093
-DIST armadillo-3.6.0.tar.gz 3013210 SHA256 8eabbe5cc89d1541c27384175444caf99243402d0ae3ec5d52d53f55400e6927 SHA512 feeb11b49cbe88227c63aac1a28b50a88d1ee3df5fc8cc4d30ca893fbb12d17b9ba75d362403e0129106ea8309149205798d61db7bf7bec6a21284eca28a7545 WHIRLPOOL 67c4c2568476adbbcb85ee84b000b24f9f08d2f30dccded6099b7a2dae35b7d236102b3a1346cdcb18efd3187a88766b53e16383ec927ca63b722dd38b6de2e1
-DIST armadillo-3.6.1.tar.gz 3015353 SHA256 4ca5e0542754b70b1fb3008cc5f66c9152008f78ed89cee24a2b8e2c894f27a0 SHA512 e871808bd1f20bc2dbd6c8938715091d6f89ec7459a39a83462ebe6a0ee051c491454f729b2e9ed8e991fbaa1f3aa4c0dd4e13727bcc967013452bc8e6b3e62b WHIRLPOOL 643a61b497f7d6dbce17d9019bac65edb3d21e8594cbeb146ea28ff5b88ce66ad5c910a30482e2a5bc97941cb4f9edf1a25a5ba976eb396e6287ba8ec63d73f5
 DIST armadillo-3.6.2.tar.gz 3016818 SHA256 04f64c632e619989616c7f219310a06cb1618b16274bdac05b4798d49eb4f149 SHA512 0c769caad012f7893cc8ebb46969179f1175edac638f98fd2a0898aed062f7456536eecd12c9720f77caf4859cd0049e00dd71c9f096458b5fd5ce9cea517c66 WHIRLPOOL 898c29f7d0a7b02658f8d95a528be7d321a7d15f95ada6a4296d9822ee873556a49ccaafcaca16cb25e4a05321fa91b9711d7790b0910464b653398fb6ce4738
+DIST armadillo-4.600.4.tar.gz 5347594 SHA256 308835440ce3b17d7652156bad6c9fbc6f6881859e07467623676d4a35229ca8 SHA512 a7378e2fe5a4485f5df755cd3af9e54034f1a701bd185161a9945422598dd7e20327cf945075bca71d31a18eaf9f932ff39f204e96a48855ef013a962dd07fd8 WHIRLPOOL 2c0544a243f5632445a740148dfd4266a20815c017aa0f52dd20ac5c6ab9531da7ad388605c136fdacf254b724648ab0f7a0354554b85af1ed82be21f5e0ea6b
 EBUILD armadillo-3.4.4.ebuild 1266 SHA256 2d771791965f7e24e57628042a03e1494ecc0d815071265fa067bbc7c5537e89 SHA512 7d6774f5555a024cf4e7a62114f2fcdef678eaa47adbd6eae01a59890e5ecf7fa36722be1072ad8220072f9a5e047e494fd85ed2f8ba794632f6ced22ddcddc5 WHIRLPOOL 6cb4003de7bbd8eb2b3b78beb1403e11ead745d3f991450be514ab8435465987908c5200a4981eab7283f6927714083c13369a2caff62c98b93b36d1d6119960
-EBUILD armadillo-3.6.0.ebuild 1273 SHA256 34e0c54531581dc0f07deb712146595c4fa9a5e16cf4903e219dc43a4512a04f SHA512 eb367d652ee372ac96c110ac52e782d4a0e5c9b77674b5f8e6466a0f5d4c4edb3bdaaacee46387a198bea5ae0ac6d7dd560234bf1af92b9808f16a4fe66dac56 WHIRLPOOL 47fcd294043a7b8ca9db5d4461585f218e3e33e1794e69de4dbb8462137b66e032751624ff137e1581798b28a5b5efd2733d2441b0c774a63626c2c63c85d10d
-EBUILD armadillo-3.6.1.ebuild 1273 SHA256 48f4856c793c007203182de1c706e4d2570145c73863f3054ec2f7c1e13d97cd SHA512 5b9d90a8ed8055281d517dc5708c06aa025c53d6621219041cbd2d4a3c47a3f284376300ecaaa5df793c86f30bfd657c34d67c6e3240ac287aec621a1f946c33 WHIRLPOOL bcb6d0e6aab01e90ffc518ea816fce00a1297ed9f618b205ad645361b2968121d3fe1a4578187da3f33dd7b3e2877c52b37bbabc2018baf6e6d8444b5b4bb483
 EBUILD armadillo-3.6.2.ebuild 1278 SHA256 6af0ef777d295f5825700fb3ae4d7fc0faa9e1ecf58438e65301584110cacbb3 SHA512 8b4e3abaaebe3d90aab80d1762f8ab1cb68035f11ffa974679289fa9776e744d705f83ba8740dd2cc970622f910a7d565e9f823ea96f6e05830f9c848c1cddde WHIRLPOOL 3834e7d60ba2b1cf16a0abe2deac6e481201fcd4f45ae6368d50e7d29c5db2b0a842c9948a0b78d4187d61c91e65e785d84ef812440452e8d69ed1932fb5962d
-MISC ChangeLog 4784 SHA256 e8327006f62210900658e19a576652f27a009b8d1f78bc6428b85b9c36e7119d SHA512 1520e1927d6969e0136a14ca3bf9c3061072bd553e9d87e95b39a25e61143efe37c3d9733db23932a633b71a24bd7ab703e030a5fac7049d01b93344a1fa6a1f WHIRLPOOL c654527e03be62a4c3b2b82d9deca0348ea0fcacb5a2a415a64222147d96bb15037a7fef4b54bf3daf6deadd670b74d155541bbbf8538046286c72393e7db24d
-MISC metadata.xml 808 SHA256 aa220a3aedeb9de18bd5ca69f9870579004258babf1e0509381a5c966476dd75 SHA512 1fe2e82eda7f1637cb13014f48e5688411ccf0fd8f517973a72ab7169a5be3f894dbd7aa21bcfd6c3aa16114cdacde4bf2b99a4cbe5103aaa5fa117e8b79aea1 WHIRLPOOL fb8e703eb875443fcc0fa294600f52595e5811bdd6af4ac8db4548c9300a489e84877102bb5a00974c3f335918916c4874182cbe2f9490fc77e2fce706007ec7
+EBUILD armadillo-4.600.4.ebuild 2989 SHA256 739788c20c6225ed46021990d3b88c9b73c79a5a49b6e778a7ec33c470190d5e SHA512 a4f6373e2122613590fe4b4cbd0c34b96068bafd09ced317ce1029e927f700a57e6719655e3e7338b19cb6a46eba1d9b54c30515c6575aa3860f1be26cc90e5c WHIRLPOOL fb22f5aac6947e3dd43a6017ec31a57f5ead566e5eca55c32172a3e5fcb30c34f7fda1fdbf05faf17894858db690828942a2b27fff2ee33d46ac2d8231c3e9a6
+MISC ChangeLog 5008 SHA256 06255a2082f17526bba50f0e00d0d908c749c0f6e9b260cd85b718c02ae8efeb SHA512 996d073667fcad39cd51e920a10ec076974f20c87e9b69845c01d32b07ca3bffbd4ad63d9b8e88d1fe3487032e4888c3f4c69f1d0a6dc0fda0e937dd2f781e50 WHIRLPOOL 06a8ab719efaac7faefd6e44f034e04534ee4c3a124234bcd06dfa3351df0cae818fb6747969a89374f571c8435080642ce162575f5e18c01f269ad25d398457
+MISC metadata.xml 1311 SHA256 4672019057812589e86d4cd9d59ccecb3f3aa0ad2b7ccb35cc33c53b8f7729a2 SHA512 08a2b35bb2adb32526404ab186130e52e8ec75e72027dc46406b9ac61839cb2ca59fbd4d6160baf04d9b0a8294c28304465ba6fd246b25664861339ab9eda8e2 WHIRLPOOL 725444c27e30f41f5dec79e8b94dfbffb121628289a1f885f166362a0d9f9adb0eaa40a00e0e5711f6d23e5a0993a2107ab7b1374feedd0e4f6dd05cfa9450c8
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2
+Version: GnuPG v2.0
 
-iEYEAREIAAYFAlSqvAwACgkQvFcC4BYPU0pSPgCfUSgx9x6vsX7a8qzwwnive7+6
-5ZIAoLiZKDkd5s+lpdGoivLsmFsNEoeA
-=86Ld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+=g8V3
 -----END PGP SIGNATURE-----
diff --git a/sci-libs/armadillo/armadillo-3.6.0.ebuild b/sci-libs/armadillo/armadillo-3.6.0.ebuild
deleted file mode 100644
index c927983935e8..000000000000
--- a/sci-libs/armadillo/armadillo-3.6.0.ebuild
+++ /dev/null
@@ -1,57 +0,0 @@
-# Copyright 1999-2012 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/armadillo/armadillo-3.6.0.ebuild,v 1.1 2012/12/12 18:23:10 bicatali Exp $
-
-EAPI=4
-
-CMAKE_IN_SOURCE_BUILD=1
-
-inherit cmake-utils toolchain-funcs
-
-DESCRIPTION="Streamlined C++ linear algebra library"
-HOMEPAGE="http://arma.sourceforge.net/"
-SRC_URI="mirror://sourceforge/arma/${P}.tar.gz"
-
-LICENSE="LGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="blas doc examples lapack"
-
-RDEPEND="
-	dev-libs/boost
-	blas? ( virtual/blas )
-	lapack? ( virtual/lapack )"
-DEPEND="${DEPEND}
-	virtual/pkgconfig"
-
-src_prepare() {
-	# avoid the automagic cmake macros
-	sed -i -e '/ARMA_Find/d' CMakeLists.txt || die
-}
-
-src_configure() {
-	local mycmakeargs=()
-	if use blas; then
-		mycmakeargs+=(
-			-DBLAS_FOUND=ON
-			-DBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs blas)"
-		)
-	fi
-	if use lapack; then
-		mycmakeargs+=(
-			-DLAPACK_FOUND=ON
-			-DLAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs lapack)"
-		)
-	fi
-	cmake-utils_src_configure
-}
-
-src_install() {
-	cmake-utils_src_install
-	dodoc README.txt
-	use doc && dodoc *pdf && dohtml *html
-	if use examples; then
-		insinto /usr/share/doc/${PF}
-		doins -r examples
-	fi
-}
diff --git a/sci-libs/armadillo/armadillo-3.6.1.ebuild b/sci-libs/armadillo/armadillo-3.6.1.ebuild
deleted file mode 100644
index abbd726b9084..000000000000
--- a/sci-libs/armadillo/armadillo-3.6.1.ebuild
+++ /dev/null
@@ -1,57 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-libs/armadillo/armadillo-3.6.1.ebuild,v 1.1 2013/01/21 19:38:49 bicatali Exp $
-
-EAPI=4
-
-CMAKE_IN_SOURCE_BUILD=1
-
-inherit cmake-utils toolchain-funcs
-
-DESCRIPTION="Streamlined C++ linear algebra library"
-HOMEPAGE="http://arma.sourceforge.net/"
-SRC_URI="mirror://sourceforge/arma/${P}.tar.gz"
-
-LICENSE="LGPL-3"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~ppc64 ~x86 ~amd64-linux ~x86-linux"
-IUSE="blas doc examples lapack"
-
-RDEPEND="
-	dev-libs/boost
-	blas? ( virtual/blas )
-	lapack? ( virtual/lapack )"
-DEPEND="${DEPEND}
-	virtual/pkgconfig"
-
-src_prepare() {
-	# avoid the automagic cmake macros
-	sed -i -e '/ARMA_Find/d' CMakeLists.txt || die
-}
-
-src_configure() {
-	local mycmakeargs=()
-	if use blas; then
-		mycmakeargs+=(
-			-DBLAS_FOUND=ON
-			-DBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs blas)"
-		)
-	fi
-	if use lapack; then
-		mycmakeargs+=(
-			-DLAPACK_FOUND=ON
-			-DLAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs lapack)"
-		)
-	fi
-	cmake-utils_src_configure
-}
-
-src_install() {
-	cmake-utils_src_install
-	dodoc README.txt
-	use doc && dodoc *pdf && dohtml *html
-	if use examples; then
-		insinto /usr/share/doc/${PF}
-		doins -r examples
-	fi
-}
diff --git a/sci-libs/armadillo/armadillo-4.600.4.ebuild b/sci-libs/armadillo/armadillo-4.600.4.ebuild
new file mode 100644
index 000000000000..9e3bc6e93ee0
--- /dev/null
+++ b/sci-libs/armadillo/armadillo-4.600.4.ebuild
@@ -0,0 +1,112 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-libs/armadillo/armadillo-4.600.4.ebuild,v 1.1 2015/02/27 13:13:27 dilfridge Exp $
+
+EAPI=5
+
+CMAKE_IN_SOURCE_BUILD=1
+
+inherit cmake-utils toolchain-funcs multilib eutils
+
+DESCRIPTION="Streamlined C++ linear algebra library"
+HOMEPAGE="http://arma.sourceforge.net/"
+SRC_URI="mirror://sourceforge/arma/${P}.tar.gz"
+
+LICENSE="MPL-2.0"
+SLOT="0/4"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="arpack atlas blas debug doc examples hdf5 lapack mkl tbb test"
+REQUIRED_USE="test? ( lapack )"
+
+RDEPEND="
+	dev-libs/boost
+	arpack? ( sci-libs/arpack )
+	atlas? ( sci-libs/atlas[lapack] )
+	blas? ( virtual/blas )
+	lapack? ( virtual/lapack )"
+DEPEND="${RDEPEND}
+	arpack? ( virtual/pkgconfig )
+	atlas? ( virtual/pkgconfig )
+	blas? ( virtual/pkgconfig )
+	hdf5? ( sci-libs/hdf5 )
+	lapack? ( virtual/pkgconfig )
+	mkl? ( sci-libs/mkl )
+	tbb? ( dev-cpp/tbb )"
+PDEPEND="${RDEPEND}
+	hdf5? ( sci-libs/hdf5 )
+	mkl? ( sci-libs/mkl )
+	tbb? ( dev-cpp/tbb )"
+
+src_prepare() {
+	# avoid the automagic cmake macros
+	sed -i -e '/ARMA_Find/d' CMakeLists.txt || die
+	cmake-utils_src_prepare
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DINSTALL_LIB_DIR="${EPREFIX}/usr/$(get_libdir)"
+		$(cmake-utils_use debug ARMA_EXTRA_DEBUG)
+		$(cmake-utils_use mkl ARMA_USE_MKL_ALLOC)
+		$(cmake-utils_use tbb ARMA_USE_TBB_ALLOC)
+	)
+	if use arpack; then
+		mycmakeargs+=(
+			-DARPACK_FOUND=ON
+			-DARPACK_LIBRARY="$($(tc-getPKG_CONFIG) --libs arpack)"
+		)
+	fi
+	if use atlas; then
+		local c=atlas-cblas l=atlas-clapack
+		$(tc-getPKG_CONFIG) --exists ${c}-threads && c+=-threads
+		$(tc-getPKG_CONFIG) --exists ${l}-threads && l+=-threads
+		mycmakeargs+=(
+			-DCBLAS_FOUND=ON
+			-DCBLAS_INCLUDE_DIR="$($(tc-getPKG_CONFIG) --cflags-only-I ${c} | sed 's/-I//')"
+			-DCBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs ${c})"
+			-DCLAPACK_FOUND=ON
+			-DCLAPACK_INCLUDE_DIR="$($(tc-getPKG_CONFIG) --cflags-only-I ${l} | sed 's/-I//')"
+			-DCLAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs ${l})"
+		)
+	fi
+	if use blas; then
+		mycmakeargs+=(
+			-DBLAS_FOUND=ON
+			-DBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs blas)"
+		)
+	fi
+	if use hdf5; then
+		mycmakeargs+=(
+			-DHDF5_FOUND=ON
+			-DHDF5_LIBRARIES="-lhdf5"
+		)
+	fi
+	if use lapack; then
+		mycmakeargs+=(
+			-DLAPACK_FOUND=ON
+			-DLAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs lapack)"
+		)
+	fi
+	cmake-utils_src_configure
+}
+
+src_test() {
+	pushd examples > /dev/null
+	emake \
+		CXXFLAGS="-I../include ${CXXFLAGS} -DARMA_USE_BLAS -DARMA_USE_LAPACK" \
+		EXTRA_LIB_FLAGS="-L.. $($(tc-getPKG_CONFIG) --libs blas lapack)"
+	LD_LIBRARY_PATH="..:${LD_LIBRARY_PATH}" ./example1 || die
+	LD_LIBRARY_PATH="..:${LD_LIBRARY_PATH}" ./example2 || die
+	emake clean
+	popd > /dev/null
+}
+
+src_install() {
+	cmake-utils_src_install
+	dodoc README.txt
+	use doc && dodoc *pdf && dohtml *html
+	if use examples; then
+		insinto /usr/share/examples/${PF}
+		doins -r examples/*
+	fi
+}
diff --git a/sci-libs/armadillo/metadata.xml b/sci-libs/armadillo/metadata.xml
index 13f3be1f60ae..95877e7a0397 100644
--- a/sci-libs/armadillo/metadata.xml
+++ b/sci-libs/armadillo/metadata.xml
@@ -1,8 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-  <herd>sci</herd>
-  <longdescription lang="en">
+<herd>sci</herd>
+<maintainer><email>dilfridge@gentoo.org</email></maintainer>
+<longdescription lang="en">
   Armadillo is a C++ linear algebra library (matrix maths) aiming
   towards a good balance between speed and ease of use. Integer,
   floating point and complex numbers are supported, as well as a
@@ -14,4 +15,20 @@
   need for temporaries. This is accomplished through recursive
   templates and template meta-programming.
 </longdescription>
+<use>
+  <flag name="atlas">
+    Link with <pkg>sci-libs/atlas</pkg> libraries for cblas and
+    clapack
+  </flag>
+  <flag name="arpack">
+    Link with <pkg>sci-libs/arpack</pkg> libraries for eigen decomposition
+  </flag>
+  <flag name='mkl'>
+    Use matrix allocation from the Intel MKL <pkg>sci-libs/mkl</pkg>
+  </flag> 
+  <flag name='tbb'>
+    Use matrix allocation from the Threads Building Blocks
+    <pkg>dev-cpp/tbb</pkg>
+  </flag> 
+</use>
 </pkgmetadata>