gentoo resync : 07.07.2018

9 files changed, 181 insertions, 5 deletions

diff --git a/sci-libs/Manifest.gz b/sci-libs/Manifest.gz
index 294a12238757..59549242ae8a 100644
--- a/sci-libs/Manifest.gz
+++ b/sci-libs/Manifest.gz
diff --git a/sci-libs/Shapely/Manifest b/sci-libs/Shapely/Manifest
index dcfe5364f357..cba90c04cb00 100644
--- a/sci-libs/Shapely/Manifest
+++ b/sci-libs/Shapely/Manifest
@@ -4,7 +4,7 @@ DIST Shapely-1.3.2.tar.gz 120179 BLAKE2B bc10e017a546e715c05c4edb1aab4f86cb0fd6f
 DIST Shapely-1.5.17.tar.gz 180663 BLAKE2B 1a41de8c264989abeac27fe9b63abd81ad6f03f0eecd313131d04190b8bbebc6c6bd6b45b1782fbfd163025cda4977b7e93a24a711c76fddfaedb0fe880cea53 SHA512 eea241942ffbf377001445fab4017c9a2746d6bc0baa6c801a08ca95e608bbdaea7ad9568f00cbecdb559e634402bc6d213ebccb4074e59325e1cc4b3771626d
 EBUILD Shapely-1.3.0.ebuild 616 BLAKE2B 40b5772a42c752cd3a8b1af73c32522d13404d290e55679117f0b66ad8c1b73837ef547f2eccd1f80e92cd6b9340114a7852691641790102dd8fb219d9265bbd SHA512 572a36c51ded12facf3bf61da88b01e84838ed1ae76fd92f1afbbd0ca03d5feddfd9306a7b724e54be961abda8b1a242a5b26a02f018e7ecb4a81497f9faef4b
 EBUILD Shapely-1.3.2.ebuild 616 BLAKE2B 40b5772a42c752cd3a8b1af73c32522d13404d290e55679117f0b66ad8c1b73837ef547f2eccd1f80e92cd6b9340114a7852691641790102dd8fb219d9265bbd SHA512 572a36c51ded12facf3bf61da88b01e84838ed1ae76fd92f1afbbd0ca03d5feddfd9306a7b724e54be961abda8b1a242a5b26a02f018e7ecb4a81497f9faef4b
-EBUILD Shapely-1.5.17-r1.ebuild 1058 BLAKE2B 1767cd3f5e62169d5372c434a7756f113fb4905761a7fd539a3486d33c6f73cd4137821b6d06d20afc58d3bf030a202f3d23faa59143f158cad6c3e9c0bac228 SHA512 9b5550d65bb9c66c55e1a5284337f95e89cd506c61a7ac5aaacd1d26ad22ce217873030d6f281ab3713ca7fd48819b71b8c413b47ca7b2ce3d9208cc6b49611d
+EBUILD Shapely-1.5.17-r1.ebuild 1057 BLAKE2B 92b69b258b3febe176434d6128794ae7fc3a694c596e7961de3028af46b2b3d5039b79451088ff4728b4be10b05df7ceb9607876c6f151807e5741c34154fd57 SHA512 b56675fdec542e313beb09c4a5ef9433e489f7eeb83426616e8ada874169bf169c4dcc274efa073d0d756bbbc46ccc3fd797de538dc10a1e83b25fc24f7f8bf0
 EBUILD Shapely-1.5.17.ebuild 695 BLAKE2B f40613943d6bc8eed954e46d73a893a554b3ef4c2301e0318066c94972988ce8db5f552de0141387ddb3b01bffd66272bfb87dff55f6769cd1347d375976491a SHA512 cdf62837e50eee43531120a193ced8fa1a0df4da5577b01c153b90702caab4edcce35d6698c441e6dbb1e3a5946f57998c074b36375c516d58059c3658676368
 EBUILD Shapely-9999.ebuild 585 BLAKE2B cf9a5b6f9ed91b90573fab2c75ac0a1ba9f4d4521fb0861bb0433469185fb229e78b60a9a8084ffea9e84b069a8fc68bb389d59c4a762f32fa44de14e3ca8926 SHA512 c09c95c79b6e3d927fb0a3c91cdc2a6c2b8c2671c597196f62aa5aaaedfb4eb5820033664292fb10832718a2ca3481830557a05ab3ec0e1e91998067a96cdb43
 MISC metadata.xml 293 BLAKE2B 556bed997454d3e7c0a32291cae2326e9fcdd3cd91d5a3f43fd5934bb093daf397c3f3628b0f921460f7cb846b1c961a02de772437275193883d59c90f018e78 SHA512 850b4e0ef0b365030c29a55c20eba931ea283a3f1603d0c0f887e80fad352ffcee0c546cd68ada65d4ba9f33fc0bfb2a817b11e630e704a22928380c7180deb4
diff --git a/sci-libs/Shapely/Shapely-1.5.17-r1.ebuild b/sci-libs/Shapely/Shapely-1.5.17-r1.ebuild
index f89d281ffe3f..b7e7f9fc2839 100644
--- a/sci-libs/Shapely/Shapely-1.5.17-r1.ebuild
+++ b/sci-libs/Shapely/Shapely-1.5.17-r1.ebuild
@@ -16,7 +16,7 @@ if [[ ${PV} == "9999" ]] ; then
 	EGIT_REPO_URI="https://github.com/Toblerity/${PN}.git"
 else
 	SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-	KEYWORDS="amd64 ~x86"
+	KEYWORDS="amd64 x86"
 fi
 
 LICENSE="BSD"
diff --git a/sci-libs/cfitsio/Manifest b/sci-libs/cfitsio/Manifest
index c244e9feaa9f..8590adfe71d0 100644
--- a/sci-libs/cfitsio/Manifest
+++ b/sci-libs/cfitsio/Manifest
@@ -5,5 +5,5 @@ DIST cfitsio-3.410.tar.gz 4194529 BLAKE2B 31250b9add5b6a85c919c33251d127117ceab8
 EBUILD cfitsio-3.360.ebuild 1466 BLAKE2B 2fb223fb28e174080819389a09174685a77cb4ac1f96015e15932b16d81e059f908fa4052b7bee6fb1db20497eafa312e6fb92f2499b7cf01eb29af1ce052a02 SHA512 d0b05587db82dae7c49250b9e4a426b7d12c6a1c904210da1b08d0dbb0db44ae01cb53f0c28adba97f5487f74bcdc7c1c19b9c4286dcb3ea232a2e77c64b7068
 EBUILD cfitsio-3.38-r1.ebuild 1591 BLAKE2B 4a4360c3b04dee99f0b62d0a03b60c02798211fccc4d3f64af726ce0775337510125d35a1d51a38ddc78db46a2b9b6deff5ec4224d10e93b687a8ab8e1582c3d SHA512 ee50da814b874ab5f3d3835ab7658694d94940eba4e7d58f9dec53c4b8fe4c1a9c98b8f5b61e3d2a1b195d8839d72b046645f0eceb8354f703c350b0a5d92308
 EBUILD cfitsio-3.39.ebuild 1596 BLAKE2B 7a167a2855fdcb796610ac1b3a17701c003bae05d0b64d1e9272ba8541116e2a5df9ebf2ec1be457d840e753a07a39bcab8b5720667d81e8c8c4a1e445d2b290 SHA512 0e2d890700a61a280fd8330679babc890f046e4a7e3cc85c724e4b7a3bea6e5da7f17ecd88ac7f84286ef174aaedce2b483491a7b66b8c423775c51a68c8d395
-EBUILD cfitsio-3.410.ebuild 1594 BLAKE2B edac92f214f617c72a80ca8d7ac55840c7be32241c11f29967944c10b42bf3746cbcdb395381f6d63aeac811f323f64493edebc8431490678ed71b953c0da6e2 SHA512 6ade505cd5eceecfaca8d97080c2f6cfe64df58ea8aed5e748a6a780dc480077045456e49dfb4eec99194ac8eaacb42b1fb13b40641cdf2fcd8b47617474c42c
+EBUILD cfitsio-3.410.ebuild 1591 BLAKE2B b22a4cfbcd35f40b2ede042465cfbe9975380a5d81daf79ad02145efbdc79862e526949bf2e90687e34fb349cd8c62f38f63eb1f6cb1fe501836813e11008883 SHA512 59bdd0e3d7d931290df5004fa84b10efcf64e65f5213218616a4f6d8163450c62c7212093d8750a5fc3daea86df9a22a050884336dacca940c82bc23f34bf698
 MISC metadata.xml 840 BLAKE2B 6f024cc96a9da7bef155b5138d55b518a1ae917af045cd2970227ca1993461659eea8883dc3b6b9e4d3d2aaa5c49b4900e122dbb83a437aa3d94351c333934d7 SHA512 946044116d9a865e3b7e883b41f7d74a3f54c72cd857aed4dcb454cfe559385004b3e55562a306bfa3347cfc035a5af9a5aaa8a4d8dc7fe154b8d0dae7a7390b
diff --git a/sci-libs/cfitsio/cfitsio-3.410.ebuild b/sci-libs/cfitsio/cfitsio-3.410.ebuild
index b2f891ac2abd..e9cc7246e436 100644
--- a/sci-libs/cfitsio/cfitsio-3.410.ebuild
+++ b/sci-libs/cfitsio/cfitsio-3.410.ebuild
@@ -13,7 +13,7 @@ SRC_URI="https://dev.gentoo.org/~bicatali/distfiles/${P}.tar.gz"
 
 LICENSE="MIT"
 SLOT="0/5"
-KEYWORDS="alpha ~amd64 ~hppa ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos ~sparc-solaris ~sparc64-solaris"
+KEYWORDS="alpha amd64 hppa ppc ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~x86-macos ~sparc-solaris ~sparc64-solaris"
 IUSE="bzip2 doc examples fortran static-libs +tools threads"
 
 RDEPEND="
diff --git a/sci-libs/flann/Manifest b/sci-libs/flann/Manifest
index dda7e23477f2..4c58fa58fcbf 100644
--- a/sci-libs/flann/Manifest
+++ b/sci-libs/flann/Manifest
@@ -1,4 +1,6 @@
+AUX flann-1.9.1-cmake-3.11.patch 2998 BLAKE2B 85c6b6feb800ab1a21af86a4001b0056fda416a6b61147f614670968cca13fa2b63d06673a11a2ef72b6f0d0876539ccb68134f4817975d4b796b66a716e606d SHA512 5cdffa2da3538965c0d20fb091a13124cdc301669b622ca35a131680db8abb58cf8e02f1366604a19a5cd10dd67f14861caa1c12da3154d82d576cb8052a4b87
 DIST flann-1.9.1.tar.gz 485391 BLAKE2B bf1e1e7feb33e939e1d0586db593bea3fdf66726fbadec63df9ed9c7bdb678babb11001769f0d041a7a569186b3d700db8b96af5eb9740615f6dfd880460f68b SHA512 0da78bb14111013318160dd3dee1f93eb6ed077b18439fd6496017b62a8a6070cc859cfb3e08dad4c614e48d9dc1da5f7c4a21726ee45896d360506da074a6f7
+EBUILD flann-1.9.1-r1.ebuild 2242 BLAKE2B c36832b645ca46e3aa622882cca34b644d8b667def8b900f1e5eea83fa0d55677f65c14c4a17134f080b4b7fe863023a71a7aeac72385bc25a9c2a4048fb33bb SHA512 08de8ba5d423999f8403104be8efbd678e6c4981790a314e717944d6f5ca714cf97219efa445894145acc47d896ce11a49867e19c654b6c403db3b55700b5ab0
 EBUILD flann-1.9.1.ebuild 2184 BLAKE2B b30802c31a247f9665be199ed77ffe5dbaf9d5f5d7650b2a8c8cf472af63cebdd1bc7b7a258136d23b43f96c015069c8905fe9300a34a51e4b8dcbba8a331a2b SHA512 eba3ebb2798f06e6785c008077a664136ab4e58fda5d647e411e03778036895d43884838176f0a761b2dd392f09abdb4e5dd91f4ff5ea3b27eb1048d620bf930
-EBUILD flann-9999.ebuild 2121 BLAKE2B 336e31bc0e5ece6c63ca3c82e3b61605fbfa46e76ab111574b3d05303add959c31b2339c60768d7ab32f56e534b7cb08f08c1a29fb15279bf2d048a02d00df06 SHA512 6e3978c5c92f2723eed4615cc292aedd3be146a9afe0fc47cd1922a12fb9fb58d81d2f284f2946d96c5f4c2d235f06c0dc5929b37258ea83bf412d36a0ac1e2e
+EBUILD flann-9999.ebuild 2178 BLAKE2B de6de98ab61428b3f19b8b229b5ad947a3e73478f21c45900b0752bcf6e382317d59020618d876e8a3908f2ae9ae770ef204959fff5f3f8bdd0d67825fb62256 SHA512 0ff48c8f14166bf2a4a77ec562618156b7ec7a40282ea0f61d233ff79a9fb3bb84195ac0465dd7b9dde7fc25889dae11a3f0088a0db3a51de00cb9627343d6bd
 MISC metadata.xml 971 BLAKE2B 5cffd393d18c3719d8b61069dbc84f4ce4e16e6746637b1203dcba3719fb672d8db082afa93add6be9ebc4203df85391d20eb824a7a9ea3550b37295186538ff SHA512 b8416b149e26ede6d3f207d7e48316a8b880436c40c4ed5610953ceda0fee4e5b97f1b99f778678514dd115c257fb419b365ed46fdd90a19d444bca8e3e0fe03
diff --git a/sci-libs/flann/files/flann-1.9.1-cmake-3.11.patch b/sci-libs/flann/files/flann-1.9.1-cmake-3.11.patch
new file mode 100644
index 000000000000..b37bedcf6d50
--- /dev/null
+++ b/sci-libs/flann/files/flann-1.9.1-cmake-3.11.patch
@@ -0,0 +1,80 @@
+From fa5ec96a94646492a3f908e12905b3e48a8e800b Mon Sep 17 00:00:00 2001
+From: Romain Naour <romain.naour@gmail.com>
+Date: Wed, 18 Apr 2018 20:24:13 +0200
+Subject: [PATCH] src/cpp: fix cmake >= 3.11 build
+
+CMake < 3.11 doesn't support add_library() without any source file
+(i.e add_library(foo SHARED)). But flann CMake use a trick that use
+an empty string "" as source list (i.e add_library(foo SHARED "")).
+This look like a bug in CMake < 3.11.
+
+With CMake >= 3.11, the new behaviour of add_library() break the
+existing flann CMake code.
+
+From CMake Changelog [1]:
+"add_library() and add_executable() commands can now be called without
+ any sources and will not complain as long as sources are added later
+ via the target_sources() command."
+
+Note: flann CMake code doesn't use target_sources() since no source file
+are provided intentionally since the flann shared library is created by
+linking with the flann_cpp_s static library with this line:
+
+target_link_libraries(flann_cpp -Wl,-whole-archive flann_cpp_s -Wl,-no-whole-archive)
+
+If you try to use "add_library(flann_cpp SHARED ${CPP_SOURCES})" (as it should
+be normally done), the link fail due to already defined symbol.
+
+They are building the shared version using the static library "to speedup the
+build time" [3]
+
+This issue is already reported upstream [2] with a proposed solution.
+
+Upstream status: Pending
+
+Fixes:
+http://autobuild.buildroot.net/results/b2f/b2febfaf8c44ce477b3e4a5b9b976fd25e8d7454
+
+[1] https://cmake.org/cmake/help/v3.11/release/3.11.html
+[2] https://github.com/mariusmuja/flann/issues/369
+[3] https://github.com/mariusmuja/flann/commit/0fd62b43be2fbb0b8d791ee36290791224dc030c
+
+Signed-off-by: Romain Naour <romain.naour@gmail.com>
+---
+ src/cpp/CMakeLists.txt | 4 ++--
+ src/cpp/empty.cpp      | 1 +
+ 2 files changed, 3 insertions(+), 2 deletions(-)
+ create mode 100644 src/cpp/empty.cpp
+
+diff --git a/src/cpp/CMakeLists.txt b/src/cpp/CMakeLists.txt
+index b44a735..a816863 100644
+--- a/src/cpp/CMakeLists.txt
++++ b/src/cpp/CMakeLists.txt
+@@ -29,7 +29,7 @@ if (BUILD_CUDA_LIB)
+ endif()
+ 
+ if(CMAKE_SYSTEM_NAME STREQUAL "Linux" AND CMAKE_COMPILER_IS_GNUCC)
+-    add_library(flann_cpp SHARED "")
++    add_library(flann_cpp SHARED "empty.cpp")
+     set_target_properties(flann_cpp PROPERTIES LINKER_LANGUAGE CXX)
+     target_link_libraries(flann_cpp -Wl,-whole-archive flann_cpp_s -Wl,-no-whole-archive)
+ 
+@@ -85,7 +85,7 @@ if (BUILD_C_BINDINGS)
+     set_property(TARGET flann_s PROPERTY COMPILE_DEFINITIONS FLANN_STATIC)
+ 
+     if(CMAKE_SYSTEM_NAME STREQUAL "Linux" AND CMAKE_COMPILER_IS_GNUCC)
+-        add_library(flann SHARED "")
++        add_library(flann SHARED "empty.cpp")
+         set_target_properties(flann PROPERTIES LINKER_LANGUAGE CXX)
+         target_link_libraries(flann -Wl,-whole-archive flann_s -Wl,-no-whole-archive)
+     else()
+diff --git a/src/cpp/empty.cpp b/src/cpp/empty.cpp
+new file mode 100644
+index 0000000..40a8c17
+--- /dev/null
++++ b/src/cpp/empty.cpp
+@@ -0,0 +1 @@
++/* empty */
+-- 
+2.14.3
+
diff --git a/sci-libs/flann/flann-1.9.1-r1.ebuild b/sci-libs/flann/flann-1.9.1-r1.ebuild
new file mode 100644
index 000000000000..fcb4ef999dff
--- /dev/null
+++ b/sci-libs/flann/flann-1.9.1-r1.ebuild
@@ -0,0 +1,90 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit cmake-utils cuda flag-o-matic toolchain-funcs
+
+DESCRIPTION="Fast approximate nearest neighbor searches in high dimensional spaces"
+HOMEPAGE="http://www.cs.ubc.ca/research/flann/"
+SRC_URI="https://github.com/mariusmuja/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~arm ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE="cuda doc examples mpi openmp octave static-libs"
+
+RDEPEND="
+	cuda? ( >=dev-util/nvidia-cuda-toolkit-5.5 )
+	mpi? (
+		sci-libs/hdf5[mpi]
+		dev-libs/boost:=[mpi]
+	)
+	!mpi? ( !sci-libs/hdf5[mpi] )
+	octave? ( >=sci-mathematics/octave-3.6.4-r1 )"
+DEPEND="${RDEPEND}
+	app-arch/unzip
+	doc? ( dev-tex/latex2html )"
+# TODO:
+# readd dependencies for test suite,
+# requires multiple ruby dependencies
+
+PATCHES=(
+	"${FILESDIR}"/flann-1.9.1-cmake-3.11.patch
+)
+
+pkg_pretend() {
+	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+}
+
+pkg_setup() {
+	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+}
+
+src_prepare() {
+	# bug #302621
+	use mpi && export CXX=mpicxx
+	# produce pure octave files
+	# octave gentoo installation for .m files respected
+	sed -i \
+		-e 's/--mex//' \
+		-e 's/\.mex/\.oct/' \
+		-e '/FILES/s/${MEX_FILE}//' \
+		-e 's:share/flann/octave:share/octave/site/m:' \
+		-e "/CUSTOM_TARGET/a\INSTALL(FILES \${MEX_FILE} DESTINATION libexec/octave/site/oct/${CHOST})" \
+		src/matlab/CMakeLists.txt || die
+	use cuda && cuda_src_prepare
+
+	cmake-utils_src_prepare
+}
+
+src_configure() {
+	append-cxxflags -std=c++11
+
+	# python bindings are split
+	# off into dev-python/pyflann
+	local mycmakeargs=(
+		-DBUILD_C_BINDINGS=ON
+		-DBUILD_PYTHON_BINDINGS=OFF
+		-DPYTHON_EXECUTABLE=
+		-DDOCDIR=share/doc/${PF}
+		-DBUILD_CUDA_LIB=$(usex cuda)
+		-DBUILD_EXAMPLES=$(usex examples)
+		-DBUILD_DOC=$(usex doc)
+		-DBUILD_TESTS=OFF
+		-DBUILD_MATLAB_BINDINGS=$(usex octave)
+		-DUSE_MPI=$(usex mpi)
+		-DUSE_OPENMP=$(usex openmp)
+	)
+	use cuda && mycmakeargs+=(
+		-DCUDA_NVCC_FLAGS="${NVCCFLAGS} --linker-options \"-arsch\""
+	)
+	cmake-utils_src_configure
+}
+
+src_install() {
+	cmake-utils_src_install
+	if ! use static-libs; then
+		find "${D}" -name 'lib*.a' -delete || die
+	fi
+}
diff --git a/sci-libs/flann/flann-9999.ebuild b/sci-libs/flann/flann-9999.ebuild
index 06d78eb963d7..e8b80e9f855f 100644
--- a/sci-libs/flann/flann-9999.ebuild
+++ b/sci-libs/flann/flann-9999.ebuild
@@ -29,6 +29,10 @@ DEPEND="${RDEPEND}
 # readd dependencies for test suite,
 # requires multiple ruby dependencies
 
+PATCHES=(
+	"${FILESDIR}"/flann-1.9.1-cmake-3.11.patch
+)
+
 pkg_pretend() {
 	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
 }