gentoo resync : 20.03.2022

3 files changed, 177 insertions, 0 deletions

diff --git a/sci-libs/flann/Manifest b/sci-libs/flann/Manifest
index 8b2903604fb8..e015ffe243ed 100644
--- a/sci-libs/flann/Manifest
+++ b/sci-libs/flann/Manifest
@@ -1,3 +1,4 @@
+AUX flann-1.9.1-build-oct-rather-than-mex-files-for-octave.patch 3337 BLAKE2B c7d149672edd6a9870b614986ce33cf203f9954f9070c49d96d717467602cea0f07f0990b7961dda00612bc9e7f017ea5c4ce6f58d8fa7a11a37a04f509ff64a SHA512 34718d5bc357db532cdb41cbb0443ae90d53231a2b87adadbd66aafb9c456c2eb7765489f8af0362b04b2b0efadb8fb65da2c9581ee2133ad8eb7065bb47f587
 AUX flann-1.9.1-cmake-3.11-1.patch 663 BLAKE2B 7162cb27a4ba6e13ac6f65752224e53be4988b3bb2ab5b8a9afbbed69a262a36c394d445fbb006afe7edbc5c9e90c339a88040eb7bee4c5c6c3209e1ba21b4ef SHA512 6d5032c30c0509951aaa5afc3f24a423d275224f67e14e0c4defbbda92ec659cef86fcfa65d72265d000f8010f0117ca2b8905f2c6f496aeef74a98dee9ffa08
 AUX flann-1.9.1-cmake-3.11.patch 2998 BLAKE2B 85c6b6feb800ab1a21af86a4001b0056fda416a6b61147f614670968cca13fa2b63d06673a11a2ef72b6f0d0876539ccb68134f4817975d4b796b66a716e606d SHA512 5cdffa2da3538965c0d20fb091a13124cdc301669b622ca35a131680db8abb58cf8e02f1366604a19a5cd10dd67f14861caa1c12da3154d82d576cb8052a4b87
 AUX flann-1.9.1-cuda-9.patch 850 BLAKE2B f193a6fd25a1d2cd45201d547fb444393cb82f344da6f5d1e2a012599170a412b261f6cf35d8943da7e96fd9f204991580d5ea045b43e2aa33ea5ad9fa9307d4 SHA512 0b5cad7b928319b922bdaa27d07fd38f1c359799ef9c217b6c1979f8ac9a86706e7ad1547f484aeb1db449a37693d18b2710b877483266915a869372c29ee1e4
@@ -5,4 +6,5 @@ AUX flann-1.9.1-system-lz4-pkgconfig.patch 1168 BLAKE2B 9fadff93a2d603aee3eadd72
 AUX flann-1.9.1-system-lz4.patch 4934 BLAKE2B eea32abae8b13d5d0e5149c58b2639c1b6f3bbbedfa8aa91f5fb83afca4726571eb4e01eb440eb913b54f8a03124bc0266c8b039b6448bcdc0bc5e87a9512c6f SHA512 acb67eb59b400b82722f064e529fc86f43c4e16ba097a3742b5717b33fcd35a619c73ec6ea6391b23f906d4bc40a5167b56cffd0267bc2c8259b7298ad414e65
 DIST flann-1.9.1.tar.gz 485391 BLAKE2B bf1e1e7feb33e939e1d0586db593bea3fdf66726fbadec63df9ed9c7bdb678babb11001769f0d041a7a569186b3d700db8b96af5eb9740615f6dfd880460f68b SHA512 0da78bb14111013318160dd3dee1f93eb6ed077b18439fd6496017b62a8a6070cc859cfb3e08dad4c614e48d9dc1da5f7c4a21726ee45896d360506da074a6f7
 EBUILD flann-1.9.1-r4.ebuild 2380 BLAKE2B ee30376d1c3a968a0a92ea5bfa9062db6773b087b5ee60517d1d9dde512d48b931a91fa83c9fef49a6eb4cf8e5117cc1f77085df1913fed3875d97a9edd02786 SHA512 8d18d6a7d8e6f3f5e0cce5b0d40b258768a59254f6d20e40256ec3d46cd5c304919623cd0ed109fd053f9a55552149d6a04e7f7b6184e31fa11473fb783af39b
+EBUILD flann-1.9.1-r5.ebuild 2281 BLAKE2B 1a33a7fab92e4542139cddda111c20fec37b6494f366921b9cf4110727e88cccfdeebfc7eb0b6c9138a85028776a6dd2b3efe6048a80c100f3a88702d3c4bbe8 SHA512 66eea1bb95529e2f72442657e09c391681f23a567bbd959a1f9e51fa861aec932f6b99da1f5c7d8a3e8089a2a409764aac23ebaf657a55edf45c65ea8688b45e
 MISC metadata.xml 972 BLAKE2B b192aee4ab043f8c3f69526727aad60e2613a6b94c5b686404593ab40213afeacde74009d305fee83c6d670d50af59207ad95189a03c53fb8193abcfdfd69c97 SHA512 77b1bf0f269cd7bd63c06442cf2cd9d1405f2a40925da469a23827a1e2461e89b8ab1b80d202ead404e7fe25f9d24a91cc4b36d775349ddd9dd50168097d3db4
diff --git a/sci-libs/flann/files/flann-1.9.1-build-oct-rather-than-mex-files-for-octave.patch b/sci-libs/flann/files/flann-1.9.1-build-oct-rather-than-mex-files-for-octave.patch
new file mode 100644
index 000000000000..f29aef41977c
--- /dev/null
+++ b/sci-libs/flann/files/flann-1.9.1-build-oct-rather-than-mex-files-for-octave.patch
@@ -0,0 +1,81 @@
+From 85d2acc120b0640d02d189089bf113d351c14bba Mon Sep 17 00:00:00 2001
+From: Alexander Golubev <fatzer2@gmail.com>
+Date: Wed, 16 Feb 2022 21:37:55 +0300
+Subject: [PATCH] build *.oct rather than *.mex files for octave
+
+ * build .oct filse rather than *.mex
+ * install the file to a sane location obtained from octave-config
+ * fix a build issue with a recent cmake doesn't like querying target
+   LOCATION
+
+Signed-off-by: Alexander Golubev <fatzer2@gmail.com>
+---
+ src/matlab/CMakeLists.txt | 28 ++++++++++++++++++----------
+ 1 file changed, 18 insertions(+), 10 deletions(-)
+
+diff --git a/src/matlab/CMakeLists.txt b/src/matlab/CMakeLists.txt
+index a89b6b8..ebacaea 100755
+--- a/src/matlab/CMakeLists.txt
++++ b/src/matlab/CMakeLists.txt
+@@ -16,9 +16,6 @@ endif()
+ 
+ find_program(OCT_CMD mkoctfile)
+ 
+-get_property(FLANN_LIB_LOCATION TARGET flann_s PROPERTY LOCATION)
+-get_filename_component(FLANN_LIB_PATH ${FLANN_LIB_LOCATION} PATH)
+-
+ if(MEX_CMD AND MEXEXT_CMD)
+ 
+     get_filename_component(MEX_REAL_CMD ${MEX_CMD} ABSOLUTE)
+@@ -48,7 +45,7 @@ if(MEX_CMD AND MEXEXT_CMD)
+         ADD_CUSTOM_COMMAND(
+             OUTPUT ${MEX_FILE}
+             COMMAND ${MEX_REAL_CMD}
+-            ARGS ${CMAKE_CURRENT_SOURCE_DIR}/${MEX_NAME}.cpp -I${PROJECT_SOURCE_DIR}/src/cpp -L${FLANN_LIB_PATH} -lflann_s ${MEX_BUILD_FLAGS}
++            ARGS ${CMAKE_CURRENT_SOURCE_DIR}/${MEX_NAME}.cpp -I${PROJECT_SOURCE_DIR}/src/cpp -L${PROJECT_BINARY_DIR}/lib -lflann_s ${MEX_BUILD_FLAGS}
+             DEPENDS flann_s ${CMAKE_CURRENT_SOURCE_DIR}/${MEX_NAME}.cpp
+             COMMENT "Building MEX extension ${MEX_FILE}"
+         )
+@@ -66,11 +63,11 @@ if(MEX_CMD AND MEXEXT_CMD)
+         set(BUILD_MATLAB_BINDINGS OFF) 
+     endif()
+ elseif(OCT_CMD)
+-  SET(MEX_FILE ${CMAKE_CURRENT_BINARY_DIR}/${MEX_NAME}.mex)
++  SET(MEX_FILE ${CMAKE_CURRENT_BINARY_DIR}/${MEX_NAME}.oct)
+   ADD_CUSTOM_COMMAND(
+     OUTPUT ${MEX_FILE}
+     COMMAND ${OCT_CMD}
+-    ARGS ${CMAKE_CURRENT_SOURCE_DIR}/${MEX_NAME}.cpp -I${PROJECT_SOURCE_DIR}/src/cpp -L${FLANN_LIB_PATH} -DFLANN_STATIC -lflann_s -lgomp --mex
++    ARGS ${CMAKE_CURRENT_SOURCE_DIR}/${MEX_NAME}.cpp -I${PROJECT_SOURCE_DIR}/src/cpp -L${PROJECT_BINARY_DIR}/lib -DFLANN_STATIC -lflann_s -lgomp
+     DEPENDS flann_s ${CMAKE_CURRENT_SOURCE_DIR}/${MEX_NAME}.cpp
+     COMMENT "Building MEX extension ${MEX_FILE}"
+     )
+@@ -79,10 +76,21 @@ elseif(OCT_CMD)
+ 
+   FILE(GLOB MATLAB_SOURCES *.m)
+ 
+-  INSTALL (
+-    FILES ${MEX_FILE} ${MATLAB_SOURCES}
+-    DESTINATION share/flann/octave
+-    )
++  find_program(OCTAVE_CONFIG_EXECUTABLE NAMES octave-config)
++
++  if (OCTAVE_CONFIG_EXECUTABLE)
++    execute_process (COMMAND ${OCTAVE_CONFIG_EXECUTABLE} --m-site-dir
++                     OUTPUT_VARIABLE OCTAVE_M_SITE_DIR
++                     OUTPUT_STRIP_TRAILING_WHITESPACE)
++
++    execute_process (COMMAND ${OCTAVE_CONFIG_EXECUTABLE} --oct-site-dir
++                      OUTPUT_VARIABLE OCTAVE_OCT_SITE_DIR
++                      OUTPUT_STRIP_TRAILING_WHITESPACE)
++
++  endif()
++
++  INSTALL (FILES ${MEX_FILE} DESTINATION ${OCTAVE_OCT_SITE_DIR})
++  INSTALL (FILES ${MATLAB_SOURCES} DESTINATION ${OCTAVE_M_SITE_DIR})
+ else()
+     message(WARNING "Cannot find MATLAB or Octave instalation. Make sure that the 'bin' directory from the MATLAB instalation or that mkoctfile is in PATH")
+     set(BUILD_MATLAB_BINDINGS OFF) 
+-- 
+2.34.1
+
diff --git a/sci-libs/flann/flann-1.9.1-r5.ebuild b/sci-libs/flann/flann-1.9.1-r5.ebuild
new file mode 100644
index 000000000000..788c2733be10
--- /dev/null
+++ b/sci-libs/flann/flann-1.9.1-r5.ebuild
@@ -0,0 +1,94 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit cmake cuda flag-o-matic toolchain-funcs
+
+DESCRIPTION="Fast approximate nearest neighbor searches in high dimensional spaces"
+HOMEPAGE="https://github.com/mariusmuja/flann"
+SRC_URI="https://github.com/mariusmuja/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~arm ~arm64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE="cuda doc examples mpi octave openmp"
+
+BDEPEND="
+	app-arch/unzip
+	doc? ( dev-tex/latex2html )
+	mpi? ( app-admin/chrpath )
+"
+DEPEND="
+	app-arch/lz4:=
+	cuda? ( >=dev-util/nvidia-cuda-toolkit-5.5 )
+	mpi? (
+		dev-libs/boost:=[mpi]
+		sci-libs/hdf5[mpi]
+	)
+	!mpi? ( !sci-libs/hdf5[mpi] )
+	octave? ( >=sci-mathematics/octave-3.6.4-r1:= )
+"
+RDEPEND="${DEPEND}"
+# TODO:
+# readd dependencies for test suite,
+# requires multiple ruby dependencies
+
+PATCHES=(
+	"${FILESDIR}"/${P}-cmake-3.11{,-1}.patch # bug 678030
+	"${FILESDIR}"/${P}-cuda-9.patch
+	"${FILESDIR}"/${P}-system-lz4.patch # bug 681898
+	"${FILESDIR}"/${P}-system-lz4-pkgconfig.patch # bug 827263
+	"${FILESDIR}"/${P}-build-oct-rather-than-mex-files-for-octave.patch # bug 830424
+)
+
+pkg_pretend() {
+	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+}
+
+pkg_setup() {
+	[[ ${MERGE_TYPE} != binary ]] && use openmp && tc-check-openmp
+}
+
+src_prepare() {
+	# bug #302621
+	use mpi && export CXX=mpicxx
+
+	use cuda && cuda_src_prepare
+
+	cmake_src_prepare
+}
+
+src_configure() {
+	append-cxxflags -std=c++11
+
+	# python bindings are split off into dev-python/pyflann
+	local mycmakeargs=(
+		-DBUILD_C_BINDINGS=ON
+		-DBUILD_PYTHON_BINDINGS=OFF
+		-DPYTHON_EXECUTABLE=
+		-DBUILD_CUDA_LIB=$(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\""
+	)
+	use doc && mycmakeargs+=( -DDOCDIR=share/doc/${PF} )
+
+	cmake_src_configure
+}
+
+src_install() {
+	cmake_src_install
+	find "${D}" -name 'lib*.a' -delete || die
+
+	# bug 795828; mpicc volunterely adds some runpaths
+	if use mpi; then
+		chrpath -d "${ED}"/usr/bin/flann_mpi_{client,server} || die
+	fi
+}