gentoo resync : 31.12.2018

7 files changed, 152 insertions, 5 deletions

diff --git a/sci-libs/Manifest.gz b/sci-libs/Manifest.gz
index b1f7b53a0dc1..27a1a147000d 100644
--- a/sci-libs/Manifest.gz
+++ b/sci-libs/Manifest.gz
diff --git a/sci-libs/armadillo/Manifest b/sci-libs/armadillo/Manifest
index 969dbaa7c4be..b75b3480d5ad 100644
--- a/sci-libs/armadillo/Manifest
+++ b/sci-libs/armadillo/Manifest
@@ -1,5 +1,7 @@
 DIST armadillo-8.300.2.tar.xz 4593916 BLAKE2B 0cb9082d9452b43599dea810036a1cdcd8ef4ab6ce5b2bc7b9d9201f1f396666a2aecb81ffa62388e1ee3de9a8c7df083df594224af47e5df7ee4d3c2743d6cc SHA512 df069634db377e95e02dfca02312b082b34cab91bae0b1fd04a97339477074fc50c74f8adf92786ac6f0fc148044d527461617f382cc996523251b6d1287e41c
 DIST armadillo-9.200.5.tar.xz 4786264 BLAKE2B 3ac5e7e50c82927ba311860915d65426e5b71e6235a041b949166e02aa50dd50a6c32d34d44761052829471ce66df9a4a9a495e1da18deff2abfbd8d67b72d0f SHA512 31110ac0d9ef9e6cf6fcf97a846ad4bb7545aa2d16fc847d85d481d605942af62994562ba8b083d76b051002d6693c966ee4b4ad398711fe1d68d31bf12daea2
+DIST armadillo-9.200.6.tar.xz 4786904 BLAKE2B 4cd6245476b674ea325037fed4b9d613be399036328b72616631b26fec7b0d3d30a788689312d0c8f4bc8ce2041454ce5ff129523f1e3ef25de16c0668d7c958 SHA512 9375a5d8414ec6d34dfa07faa472ca8c56a0ed62761d6bdcb2c584f255fc212fadf00e5380e7b10e67836b93d17e609fe6714a7b233b6f0e5d9355ff504a15fd
 EBUILD armadillo-8.300.2.ebuild 3376 BLAKE2B 3919b3ff29586060911230a35fa61aa590cec61f982c9b817ad468eea146ea142cc6fe021a4240ffc7bc3562e1349e59f76a868a2632f03bc9a626da0811f08e SHA512 4983eb6be844203df5ebb1cc15d2005ec953c05af300ddcba5d656f4cbf03207998a0c198afee9e43d81d7788799b31d4e13a929f74399dc55120ede0538652b
 EBUILD armadillo-9.200.5.ebuild 3375 BLAKE2B bb7354dcba7e6eed511764a0234595a9909289b62912c0f8da36471e82dd785262f9f0aebedcf217e7cd2efb234b9cea7b1e9b71d24e0deb9e53f3d056c9d01f SHA512 645cb2e9f5b282e6fad87c793bbfca12ed3a289bb3ee50632b875dddb12e8c36e15fbac49e4c33b61e3fb32971c2a0f253bd46bdc7dd19cffc3518e88fe8cbfa
+EBUILD armadillo-9.200.6.ebuild 3276 BLAKE2B df197a91daa79362b04b5203ffd209ea40c199e0c0c7d8c515fbea7de8b26e7095b32fec028e6942864839aafc0cf11a139cce3843c590f29a7b48367867de3e SHA512 abcdee4251617e7c20de77660d6b61c84ea2f391db707476cda894de73e354c4d909a6a3e9b1452756c755edfb2e39acbcf0a424fb8eafa3cf67b087c9858ec9
 MISC metadata.xml 1537 BLAKE2B 5116cb259f8e27fb11430cc2b3ab3a351afcefa0734e7997c962596aab226cfdd052ba3186ea068d8d31d501520d063037185909bcf02de72f57b4c8dfd86e31 SHA512 206e3f8912bd753837b0e8301c1db0f94e3480d0f50ba83c1b9a4be44498507ccade8f0b317c3bf2baa8aa782a93c88806ddbe710eed9d8fecb135494c26bc71
diff --git a/sci-libs/armadillo/armadillo-9.200.6.ebuild b/sci-libs/armadillo/armadillo-9.200.6.ebuild
new file mode 100644
index 000000000000..c0be49813cfa
--- /dev/null
+++ b/sci-libs/armadillo/armadillo-9.200.6.ebuild
@@ -0,0 +1,145 @@
+# Copyright 1999-2018 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+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/${P}.tar.xz"
+
+LICENSE="Apache-2.0"
+SLOT="0/9"
+KEYWORDS="~amd64 ~arm ~ppc64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="arpack blas doc examples hdf5 lapack mkl superlu test"
+REQUIRED_USE="test? ( lapack )"
+
+#	atlas? ( sci-libs/atlas[lapack] )
+
+RDEPEND="
+	dev-libs/boost
+	arpack? ( sci-libs/arpack )
+	blas? ( virtual/blas )
+	lapack? ( virtual/lapack )
+	superlu? ( >=sci-libs/superlu-5.2 )
+"
+
+DEPEND="${RDEPEND}
+	arpack? ( virtual/pkgconfig )
+	blas? ( virtual/pkgconfig )
+	hdf5? ( sci-libs/hdf5 )
+	lapack? ( virtual/pkgconfig )
+	mkl? ( sci-libs/mkl )
+"
+PDEPEND="${RDEPEND}
+	hdf5? ( sci-libs/hdf5 )
+	mkl? ( sci-libs/mkl )
+"
+
+src_prepare() {
+	# avoid the automagic cmake macros
+	sed -i -e '/ARMA_Find/d' CMakeLists.txt || die
+	cmake-utils_src_prepare
+}
+
+src_configure() {
+	local mycmakeargs=(
+		-DINSTALL_LIB_DIR="${EPREFIX}/usr/$(get_libdir)"
+	)
+	if ! use mkl; then
+		mycmakeargs+=(
+			-DMKL_FOUND=OFF
+		)
+	fi
+	if use arpack; then
+		mycmakeargs+=(
+			-DARPACK_FOUND=ON
+			-DARPACK_LIBRARY="$($(tc-getPKG_CONFIG) --libs arpack)"
+		)
+	else
+		mycmakeargs+=(
+			-DARPACK_FOUND=OFF
+		)
+	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 ${l})"
+#		)
+#	fi
+	if use blas; then
+		mycmakeargs+=(
+			-DBLAS_FOUND=ON
+			-DBLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs blas)"
+		)
+	else
+		mycmakeargs+=(
+			-DBLAS_FOUND=OFF
+		)
+	fi
+	if use hdf5; then
+		mycmakeargs+=(
+			-DHDF5_FOUND=ON
+			-DHDF5_LIBRARIES="-lhdf5"
+		)
+	else
+		mycmakeargs+=(
+			-DHDF5_FOUND=OFF
+		)
+	fi
+	if use lapack; then
+		mycmakeargs+=(
+			-DLAPACK_FOUND=ON
+			-DLAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs lapack)"
+		)
+	else
+		mycmakeargs+=(
+			-DLAPACK_FOUND=OFF
+		)
+	fi
+	if use superlu; then
+		mycmakeargs+=(
+			-DSuperLU_FOUND=ON
+			-DSuperLU_LIBRARY="$($(tc-getPKG_CONFIG) --libs superlu)"
+			-DSuperLU_INCLUDE_DIR="$($(tc-getPKG_CONFIG) --cflags-only-I superlu | awk '{print $1}' | sed 's/-I//')"
+		)
+	else
+		mycmakeargs+=(
+			-DSuperLU_FOUND=OFF
+		)
+	fi
+
+	cmake-utils_src_configure
+}
+
+src_test() {
+	pushd examples > /dev/null
+	emake \
+		CXX="$(tc-getCXX)" \
+		CXXFLAGS="-I../include ${CXXFLAGS} -DARMA_USE_BLAS -DARMA_USE_LAPACK" \
+		LIB_FLAGS="-L.. -larmadillo $($(tc-getPKG_CONFIG) --libs blas lapack)"
+	LD_LIBRARY_PATH="..:${LD_LIBRARY_PATH}" ./example1 || die
+	emake clean
+	popd > /dev/null
+}
+
+src_install() {
+	cmake-utils_src_install
+	dodoc README.md
+	use doc && dodoc *pdf *html
+	if use examples; then
+		insinto /usr/share/doc/${PF}/examples
+		doins -r examples/*
+		docompress -x /usr/share/doc/${PF}/examples
+	fi
+}
diff --git a/sci-libs/cholmod/Manifest b/sci-libs/cholmod/Manifest
index c77e71f597b5..9abab49a38c7 100644
--- a/sci-libs/cholmod/Manifest
+++ b/sci-libs/cholmod/Manifest
@@ -1,4 +1,4 @@
 AUX cholmod-1.7.4-parmetis32.patch 702 BLAKE2B 241d68fa25ac2ab3f9a425702559736fb15657eda82c5ba0a413174c146c09e0be167746f866a64189d027892d180445adcf92f55fc913c9bff0085f87051c94 SHA512 a1694a7f42f10c7619e23817e93f76df35bc208200918b74a6dd68bb4662d57ce2f3665be424ad4b5c8a4ea9c3957676c48716aa0e47d9fb19337dc43e759ecc
 DIST cholmod-2.1.2.tar.bz2 656458 BLAKE2B 83a574ad7d3755428d8d732f3f60b07908b8315d73d5a3d3aaf9aac50b54590c532389dd90efc569e67639993095706eb546e72313b735e35af34a1fea398be2 SHA512 7aca97de4c60ff2d7a76a776be4c2d61243a159a51b9e147fa2480f2aaf61a5d966eb0f1cb57c0145510437f6c478fa30384b741709d0a02432b74ada3e78089
-EBUILD cholmod-2.1.2.ebuild 1776 BLAKE2B 5feefb87959a48831d2be1f9ff811230ea2941e1c8a2a19a904ed6846eb24f6d7ce92932d5df9555f024716af2cee46af69c4f66628363113d086eda71b840e4 SHA512 f83dc657b727a3b160fa8491d013e3c78a401ab9e1e79d620c2db23e003c84ac5375d6651ccacf8bafc0bd00e983effa382710fb092e1e99ff48cf8992c7200d
+EBUILD cholmod-2.1.2.ebuild 1775 BLAKE2B 6540adeeb55b8f0503041f5f21c93c7e0fc0b33dc36984112c44cba4308f4181f5429ae62e1c275da39272f90024f640939976e7e37010350f1e051bdbfe3914 SHA512 1f088d390bb3fa40f99308b0fa3a24d10b2de86abc0dc00ae77ca5807e9e2c7b793ecc6c2e526f5b99d0b508fea845fd63cb07a62d3eaa46d0ebbc7e07b6dc1b
 MISC metadata.xml 603 BLAKE2B ce6355915a22fd4bb81f619a1b946f83b971b43caf86929441452938c1bee5971c5f95d0349d13d740efcf51883015334db167d2fab49c8954ac6af1d5ca3348 SHA512 da9db58edeab0b40813e47567cbaa4e54ae8aa9f4cdc89cd87f1e35bb65991c305bc955e6aba744d322c6375de0e8ba1253415814175cf1f4bc2a01de2e11d22
diff --git a/sci-libs/cholmod/cholmod-2.1.2.ebuild b/sci-libs/cholmod/cholmod-2.1.2.ebuild
index 32bd49515a4b..a0460f5c4b64 100644
--- a/sci-libs/cholmod/cholmod-2.1.2.ebuild
+++ b/sci-libs/cholmod/cholmod-2.1.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5
@@ -6,7 +6,7 @@ EAPI=5
 inherit autotools-utils multilib toolchain-funcs
 
 DESCRIPTION="Sparse Cholesky factorization and update/downdate library"
-HOMEPAGE="http://www.cise.ufl.edu/research/sparse/cholmod/"
+HOMEPAGE="http://faculty.cse.tamu.edu/davis/suitesparse.html"
 SRC_URI="https://dev.gentoo.org/~bicatali/distfiles/${P}.tar.bz2"
 
 LICENSE="minimal? ( LGPL-2.1 ) !minimal? ( GPL-2 )"
diff --git a/sci-libs/dmlc-core/Manifest b/sci-libs/dmlc-core/Manifest
index 05cb4dad400e..4fb999204d08 100644
--- a/sci-libs/dmlc-core/Manifest
+++ b/sci-libs/dmlc-core/Manifest
@@ -1,4 +1,4 @@
 AUX dmlc-core-install-dirs.patch 1206 BLAKE2B df1f1520f3e6b21ef7dc30d6f2d73f888c639bdbbfe824ed89a5a7a9fa7b9dabb94704d6ba1ee9a95274b66b5160c560538cdb252804cfdeb304f7b8727cddb5 SHA512 ceee3e6f6f02e4a96167f12ffb50cbbc3bfbf07d025acb002139072ac73cf02adcd9c8f7a7b371055a68a61a104bf16ad95d7a3769edc3ad2dc63be36ff45ff5
 DIST dmlc-core-0_p20170719.tar.gz 160242 BLAKE2B 2752968c831b5468cb926fbd2783098d1d66f5dd7f06b1abf138e165c637a3c16d477b04b709a05826528ee8e35ed61b563bdaae958fb91c78591dd57761a5f4 SHA512 2e2d79800839652772f07deb5ea3aa470cc5a18d2d0e480b8f4a1598aca72443546a438f3309708268cc49cf2d65684c3366cfc6c33c085baf1b804b4c04f02e
 EBUILD dmlc-core-0_p20170719.ebuild 2250 BLAKE2B 01afde6458c15d1f70e0954b34df30e6062994ab5ca8a55cef2a56ce3f15fe129b892cb93b0ceae74a4f83c697d277ad166b2217964d5ce79f9e34a194ed3bf1 SHA512 2e2e067d276fe36d505f89d131ea8b0d935bbb6290c3bb9c93d43d755e985dcc28e8d15a7da6f4e18b8371def749b80d4e06d65a3c1420999d7f7b91e13e79a7
-MISC metadata.xml 704 BLAKE2B f301b3c1695a218b9b6799dae9314836400a29134ba85ea0bf4cc8d44c3bade740b25b9fa00d91d9e7ac734e22c8da98567e88deb74ec2227b08f8da3fb2c22f SHA512 daa2fd03eb40932f9b28fe3e624a44dd16862952d473c6beba4a60dc7ddae17935858191909dddb471830bfb23de1a98887fd2fd401f353e77d3cd8acd690896
+MISC metadata.xml 702 BLAKE2B 085ca9f33a3772884d2b401b8339c2f0862a834ccfbe28ecd141c97b26b50f00f499ff7ea917db0eb0fd0b5c3618efadc82300f3bb6c4475c7cf10dc58657bf8 SHA512 ab1359ef913665692ab9fd32c0a18ad6ac9315cb3dbb6299cc4ea642ec7d649f31a79814017e8ad29062fc0c10c8ca27201dbad157a662432bc2b04f4105fe83
diff --git a/sci-libs/dmlc-core/metadata.xml b/sci-libs/dmlc-core/metadata.xml
index 7fb45e55273f..a9cd5175551b 100644
--- a/sci-libs/dmlc-core/metadata.xml
+++ b/sci-libs/dmlc-core/metadata.xml
@@ -15,5 +15,5 @@
   </upstream>
   <use>
     <flag name="s3">Support for the Amazon Simple Storage Service</flag>
-  </use>		
+  </use>
 </pkgmetadata>