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

10 files changed, 433 insertions, 0 deletions

diff --git a/sci-libs/flann/Manifest b/sci-libs/flann/Manifest
new file mode 100644
index 000000000000..39203fd023cf
--- /dev/null
+++ b/sci-libs/flann/Manifest
@@ -0,0 +1,2 @@
+DIST flann-1.8.4-src.zip 561057 SHA256 dfbb9321b0d687626a644c70872a2c540b16200e7f4c7bd72f91ae032f445c08 SHA512 47ac6be66e3ec7303d28febc5a4cea2f8d1b3d81c3b7081f27cf17936074e06e91e30123569b41269a2b97c9960274dc485a575d77c1a386e8f539a76a8d3a0a WHIRLPOOL f7722d8c0a8482809920927353421ebb578464fe6746a4dba20a6c7b6f941715529d5be33aebd1726db36eae3b5d4080c6ae86b0f807e6e384af32b87735b83b
+DIST flann-1.8.4-testdata.tar.xz 26744244 SHA256 4eaecf3a221ea6611e841fa2f459a17b6a5fdd633338bb5bc46c434e37667141 SHA512 f2bee5e2dfe2fbb42953df563f178b67639b62e26fc31be14e07c196ba3e84db21804e594af44991f7cf45ca5e10ff753093cf160abf33e90d19735a9a0b51cb WHIRLPOOL e49e5a594464955241ebc9bdfa908bac8b93b2fb465fc08ab73ec4d57194a8b71361ecb67985cdc641013fb8c3fb51ea2033769f41e558ab86e8f71e477b97da
diff --git a/sci-libs/flann/files/flann-1.8.4-CUDA_NVCC_FLAGS.patch b/sci-libs/flann/files/flann-1.8.4-CUDA_NVCC_FLAGS.patch
new file mode 100644
index 000000000000..1a068af28351
--- /dev/null
+++ b/sci-libs/flann/files/flann-1.8.4-CUDA_NVCC_FLAGS.patch
@@ -0,0 +1,16 @@
+ src/cpp/CMakeLists.txt | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/src/cpp/CMakeLists.txt b/src/cpp/CMakeLists.txt
+index 8e72409..a4b35b1 100644
+--- a/src/cpp/CMakeLists.txt
++++ b/src/cpp/CMakeLists.txt
+@@ -15,7 +15,7 @@ endif()
+ set_property(TARGET flann_cpp_s PROPERTY COMPILE_DEFINITIONS FLANN_STATIC FLANN_USE_CUDA)
+ 
+ if (BUILD_CUDA_LIB)
+-    SET(CUDA_NVCC_FLAGS -DFLANN_USE_CUDA)
++    SET(CUDA_NVCC_FLAGS "${CUDA_NVCC_FLAGS};-DFLANN_USE_CUDA")
+     if(CMAKE_COMPILER_IS_GNUCC)
+ 		set(CUDA_NVCC_FLAGS "${CUDA_NVCC_FLAGS};-Xcompiler;-fPIC;-arch=sm_13" )
+         if (NVCC_COMPILER_BINDIR)
diff --git a/sci-libs/flann/files/flann-1.8.4-cuda5.5.patch b/sci-libs/flann/files/flann-1.8.4-cuda5.5.patch
new file mode 100644
index 000000000000..046b3252c36f
--- /dev/null
+++ b/sci-libs/flann/files/flann-1.8.4-cuda5.5.patch
@@ -0,0 +1,61 @@
+ src/cpp/flann/util/cuda/result_set.h | 12 ++++++------
+ 1 file changed, 6 insertions(+), 6 deletions(-)
+
+diff --git a/src/cpp/flann/util/cuda/result_set.h b/src/cpp/flann/util/cuda/result_set.h
+index 9ac8111..324ca1e 100644
+--- a/src/cpp/flann/util/cuda/result_set.h
++++ b/src/cpp/flann/util/cuda/result_set.h
+@@ -54,7 +54,7 @@ struct SingleResultSet
+     DistanceType bestDist;
+     const DistanceType epsError;
+ 
+-    __device__
++    __device__ __host__
+     SingleResultSet( DistanceType eps ) : bestIndex(-1),bestDist(INFINITY), epsError(eps){ }
+ 
+     __device__
+@@ -129,7 +129,7 @@ struct KnnResultSet
+     const DistanceType epsError;
+ 
+ 
+-    __device__
++    __device__ __host__
+     KnnResultSet(int knn, bool sortResults, DistanceType eps) : foundNeighbors(0),largestHeapDist(INFINITY),k(knn), sorted(sortResults), epsError(eps){ }
+ 
+     //          __host__ __device__
+@@ -229,7 +229,7 @@ struct CountingRadiusResultSet
+     DistanceType radius_sq_;
+     int max_neighbors_;
+ 
+-    __device__
++    __device__ __host__
+     CountingRadiusResultSet(DistanceType radius, int max_neighbors) : count_(0),radius_sq_(radius), max_neighbors_(max_neighbors){ }
+ 
+     __device__
+@@ -279,7 +279,7 @@ struct RadiusKnnResultSet
+     //          int count_;
+ 
+ 
+-    __device__
++    __device__ __host__
+     RadiusKnnResultSet(DistanceType radius, int knn, int* segment_starts, bool sortResults) : foundNeighbors(0),largestHeapDist(radius),k(knn), sorted(sortResults), radius_sq_(radius),segment_starts_(segment_starts) { }
+ 
+     //          __host__ __device__
+@@ -381,7 +381,7 @@ struct KnnRadiusResultSet
+     const DistanceType radius_sq;
+ 
+ 
+-    __device__
++    __device__ __host__
+     KnnRadiusResultSet(int knn, bool sortResults, DistanceType eps, DistanceType radius) : foundNeighbors(0),largestHeapDist(radius),k(knn), sorted(sortResults), epsError(eps),radius_sq(radius){ }
+ 
+     //          __host__ __device__
+@@ -484,7 +484,7 @@ struct RadiusResultSet
+     int count_;
+     bool sorted_;
+ 
+-    __device__
++    __device__ __host__
+     RadiusResultSet(DistanceType radius, int* segment_starts, bool sorted) : radius_sq_(radius), segment_starts_(segment_starts), count_(0), sorted_(sorted){ }
+ 
+     __device__
diff --git a/sci-libs/flann/files/flann-1.8.4-docdir.patch b/sci-libs/flann/files/flann-1.8.4-docdir.patch
new file mode 100644
index 000000000000..4b16684de14d
--- /dev/null
+++ b/sci-libs/flann/files/flann-1.8.4-docdir.patch
@@ -0,0 +1,24 @@
+ doc/CMakeLists.txt | 6 +++++-
+ 1 file changed, 5 insertions(+), 1 deletion(-)
+
+diff --git a/doc/CMakeLists.txt b/doc/CMakeLists.txt
+index 2d8eb24..aeac8ed 100644
+--- a/doc/CMakeLists.txt
++++ b/doc/CMakeLists.txt
+@@ -1,4 +1,8 @@
+ find_package(LATEX)
++
++if (NOT DOCDIR)
++  set(DOCDIR share/doc/flann)
++endif ()
+  
+ if (EXISTS ${PDFLATEX_COMPILER} AND EXISTS ${BIBTEX_COMPILER})
+     include(${PROJECT_SOURCE_DIR}/cmake/UseLATEX.cmake)
+@@ -14,6 +18,6 @@ endif()
+ 
+ install(
+     FILES manual.pdf
+-    DESTINATION share/doc/flann
++    DESTINATION ${DOCDIR}
+     OPTIONAL
+ )
diff --git a/sci-libs/flann/files/flann-1.8.4-examples.patch b/sci-libs/flann/files/flann-1.8.4-examples.patch
new file mode 100644
index 000000000000..b3346b35f73c
--- /dev/null
+++ b/sci-libs/flann/files/flann-1.8.4-examples.patch
@@ -0,0 +1,35 @@
+From 3922081fbd6710f4b72421069f6bf24dc37d35a8 Mon Sep 17 00:00:00 2001
+From: Casey Goodlett <casey.goodlett@kitware.com>
+Date: Thu, 8 Aug 2013 18:42:45 -0400
+Subject: [PATCH] Option to disable example building
+
+---
+ CMakeLists.txt | 5 ++++-
+ 1 file changed, 4 insertions(+), 1 deletion(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 5b19367..410a8f9 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -53,6 +53,7 @@ option(BUILD_C_BINDINGS "Build C bindings" ON)
+ option(BUILD_PYTHON_BINDINGS "Build Python bindings" ON)
+ option(BUILD_MATLAB_BINDINGS "Build Matlab bindings" ON)
+ option(BUILD_CUDA_LIB "Build CUDA library" OFF)
++option(BUILD_EXAMPLES "Build examples" ON)
+ option(USE_OPENMP "Use OpenMP multi-threading" ON)
+ option(USE_MPI "Use MPI" OFF)
+ 
+@@ -154,7 +155,9 @@ endif()
+ 
+ add_subdirectory( cmake )
+ add_subdirectory( src )
+-add_subdirectory( examples )
++if (BUILD_EXAMPLES)
++  add_subdirectory( examples )
++endif(BUILD_EXAMPLES)
+ add_subdirectory( test )
+ add_subdirectory( doc )
+ 
+-- 
+1.8.5.1
+
diff --git a/sci-libs/flann/files/flann-1.8.4-multilib.patch b/sci-libs/flann/files/flann-1.8.4-multilib.patch
new file mode 100644
index 000000000000..17a9d65dd778
--- /dev/null
+++ b/sci-libs/flann/files/flann-1.8.4-multilib.patch
@@ -0,0 +1,15 @@
+ cmake/flann_utils.cmake | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/cmake/flann_utils.cmake b/cmake/flann_utils.cmake
+index 1a10939..afe4742 100644
+--- a/cmake/flann_utils.cmake
++++ b/cmake/flann_utils.cmake
+@@ -1,6 +1,6 @@
+ macro(GET_OS_INFO)
+     string(REGEX MATCH "Linux" OS_IS_LINUX ${CMAKE_SYSTEM_NAME})
+-    set(FLANN_LIB_INSTALL_DIR "lib")
++    set(FLANN_LIB_INSTALL_DIR "lib${LIB_SUFFIX}")
+     set(FLANN_INCLUDE_INSTALL_DIR
+         "include/${PROJECT_NAME_LOWER}-${FLANN_MAJOR_VERSION}.${FLANN_MINOR_VERSION}")
+ endmacro(GET_OS_INFO)
diff --git a/sci-libs/flann/files/flann-1.8.4-options.patch b/sci-libs/flann/files/flann-1.8.4-options.patch
new file mode 100644
index 000000000000..dd212aca66a4
--- /dev/null
+++ b/sci-libs/flann/files/flann-1.8.4-options.patch
@@ -0,0 +1,41 @@
+ CMakeLists.txt | 13 +++++++++++--
+ 1 file changed, 11 insertions(+), 2 deletions(-)
+
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 410a8f9..b6244a4 100644
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -54,6 +54,8 @@ option(BUILD_PYTHON_BINDINGS "Build Python bindings" ON)
+ option(BUILD_MATLAB_BINDINGS "Build Matlab bindings" ON)
+ option(BUILD_CUDA_LIB "Build CUDA library" OFF)
+ option(BUILD_EXAMPLES "Build examples" ON)
++option(BUILD_TESTS "Build tests" ON)
++option(BUILD_DOC "Build documentation" ON)
+ option(USE_OPENMP "Use OpenMP multi-threading" ON)
+ option(USE_MPI "Use MPI" OFF)
+ 
+@@ -158,8 +160,12 @@ add_subdirectory( src )
+ if (BUILD_EXAMPLES)
+   add_subdirectory( examples )
+ endif(BUILD_EXAMPLES)
+-add_subdirectory( test )
+-add_subdirectory( doc )
++if (BUILD_TESTS)
++  add_subdirectory( test )
++endif (BUILD_TESTS)
++if (BUILD_DOC)
++  add_subdirectory( doc )
++endif (BUILD_DOC)
+ 
+ 
+ # CPACK options
+@@ -202,6 +208,9 @@ include(CPack)
+ message(STATUS "Install prefix: ${CMAKE_INSTALL_PREFIX}")
+ message(STATUS "Build type: ${CMAKE_BUILD_TYPE}")
+ message(STATUS "Building C bindings: ${BUILD_C_BINDINGS}")
++message(STATUS "Building examples: ${BUILD_EXAMPLES}")
++message(STATUS "Building tests: ${BUILD_TESTS}")
++message(STATUS "Building documentation: ${BUILD_DOC}")
+ message(STATUS "Building python bindings: ${BUILD_PYTHON_BINDINGS}")
+ message(STATUS "Building matlab bindings: ${BUILD_MATLAB_BINDINGS}")
+ message(STATUS "Building CUDA library: ${BUILD_CUDA_LIB}")
diff --git a/sci-libs/flann/flann-1.8.4-r1.ebuild b/sci-libs/flann/flann-1.8.4-r1.ebuild
new file mode 100644
index 000000000000..31ff4c5f1797
--- /dev/null
+++ b/sci-libs/flann/flann-1.8.4-r1.ebuild
@@ -0,0 +1,109 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit cmake-utils cuda eutils multilib toolchain-funcs
+
+DESCRIPTION="Library for performing fast approximate nearest neighbor searches in high dimensional spaces"
+HOMEPAGE="http://www.cs.ubc.ca/research/flann/"
+SRC_URI="
+	http://people.cs.ubc.ca/~mariusm/uploads/FLANN/${P}-src.zip
+	test? ( http://dev.gentoo.org/~bicatali/distfiles/${P}-testdata.tar.xz )"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="amd64 ~arm ~ppc x86 ~amd64-linux ~x86-linux"
+IUSE="cuda doc examples mpi openmp octave static-libs test"
+
+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="${RDEPEND}
+	app-arch/unzip
+	doc? ( dev-tex/latex2html )
+	test? (
+		dev-cpp/gtest
+		cuda? ( sci-libs/hdf5 )
+	)
+"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-examples.patch
+	"${FILESDIR}"/${P}-options.patch
+	"${FILESDIR}"/${P}-CUDA_NVCC_FLAGS.patch
+	"${FILESDIR}"/${P}-cuda5.5.patch
+	"${FILESDIR}"/${P}-multilib.patch
+	"${FILESDIR}"/${P}-docdir.patch
+)
+
+S="${WORKDIR}"/${P}-src
+
+pkg_setup() {
+	if use openmp; then
+		if [[ $(tc-getCC) == *gcc ]] && ! tc-has-openmp ; then
+			ewarn "OpenMP is not available in your current selected gcc"
+			die "need openmp capable gcc"
+		fi
+	fi
+}
+
+src_prepare() {
+	# bug #302621
+	use mpi && export CXX=mpicxx
+	# produce pure octave files
+	# octave gentoo installation for .m files respected
+	sed -i \
+		-e 's/--mex//' \
+		-e 's/\.mex/\.oct/' \
+		-e '/FILES/s/${MEX_FILE}//' \
+		-e 's:share/flann/octave:share/octave/site/m:' \
+		-e "/CUSTOM_TARGET/a\INSTALL(FILES \${MEX_FILE} DESTINATION libexec/octave/site/oct/${CHOST})" \
+		src/matlab/CMakeLists.txt || die
+	use cuda && cuda_src_prepare
+
+	cmake-utils_src_prepare
+}
+
+src_configure() {
+	# python bindings are split
+	local mycmakeargs=(
+		-DBUILD_C_BINDINGS=ON
+		-DBUILD_PYTHON_BINDINGS=OFF
+		-DPYTHON_EXECUTABLE=
+		-DDOCDIR=share/doc/${PF}
+		$(cmake-utils_use_build cuda CUDA_LIB)
+		$(cmake-utils_use_build examples)
+		$(cmake-utils_use_build doc)
+		$(cmake-utils_use_build test TESTS)
+		$(cmake-utils_use_build octave MATLAB_BINDINGS)
+		$(cmake-utils_use_use mpi)
+		$(cmake-utils_use_use openmp)
+	)
+	use cuda && \
+		mycmakeargs+=(
+		-DCUDA_NVCC_FLAGS="${NVCCFLAGS},-arsch"
+		)
+	cmake-utils_src_configure
+}
+
+src_test() {
+	ln -s "${WORKDIR}"/testdata/* test/ || die
+	# -j1 to avoid obversubscribing jobs
+	LD_LIBRARY_PATH="${BUILD_DIR}/lib" \
+		cmake-utils_src_compile -j1 test
+}
+
+src_install() {
+	cmake-utils_src_install
+	dodoc README.md
+	if ! use static-libs; then
+		find "${ED}" -name 'lib*.a' -exec rm -rf '{}' '+' || die
+	fi
+}
diff --git a/sci-libs/flann/flann-9999.ebuild b/sci-libs/flann/flann-9999.ebuild
new file mode 100644
index 000000000000..ebc34bb597bd
--- /dev/null
+++ b/sci-libs/flann/flann-9999.ebuild
@@ -0,0 +1,111 @@
+# Copyright 1999-2013 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+inherit cmake-utils cuda eutils git-r3 multilib toolchain-funcs
+
+DESCRIPTION="Library for performing fast approximate nearest neighbor searches in high dimensional spaces"
+HOMEPAGE="http://www.cs.ubc.ca/research/flann/"
+SRC_URI="test? ( http://dev.gentoo.org/~bicatali/distfiles/${PN}-1.8.4-testdata.tar.xz )"
+EGIT_REPO_URI="https://github.com/mariusmuja/flann.git"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS=""
+IUSE="cuda doc examples mpi openmp octave static-libs test"
+
+RDEPEND="
+	cuda? ( >=dev-util/nvidia-cuda-toolkit-5.5 )
+	mpi? (
+		sci-libs/hdf5[mpi]
+		dev-libs/boost[mpi]
+	)
+	!mpi? ( !sci-libs/hdf5[mpi] )
+	octave? ( >=sci-mathematics/octave-3.6.4-r1 )"
+DEPEND="${RDEPEND}
+	app-arch/unzip
+	doc? ( dev-tex/latex2html )
+	test? (
+		dev-cpp/gtest
+		cuda? ( sci-libs/hdf5 )
+	)
+"
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-1.8.4-options.patch
+	"${FILESDIR}"/${PN}-1.8.4-CUDA_NVCC_FLAGS.patch
+	"${FILESDIR}"/${PN}-1.8.4-cuda5.5.patch
+	"${FILESDIR}"/${PN}-1.8.4-multilib.patch
+	"${FILESDIR}"/${PN}-1.8.4-docdir.patch
+)
+
+pkg_setup() {
+	if use openmp; then
+		if [[ $(tc-getCC) == *gcc ]] && ! tc-has-openmp ; then
+			ewarn "OpenMP is not available in your current selected gcc"
+			die "need openmp capable gcc"
+		fi
+	fi
+}
+
+src_unpack() {
+	default
+	git-r3_src_unpack
+}
+
+src_prepare() {
+	# bug #302621
+	use mpi && export CXX=mpicxx
+
+	# produce pure octave files
+	# octave gentoo installation for .m files respected
+	sed -i \
+		-e 's/--mex//' \
+		-e 's/\.mex/\.oct/' \
+		-e '/FILES/s/${MEX_FILE}//' \
+		-e 's:share/flann/octave:share/octave/site/m:' \
+		-e "/CUSTOM_TARGET/a\INSTALL(FILES \${MEX_FILE} DESTINATION libexec/octave/site/oct/${CHOST})" \
+		src/matlab/CMakeLists.txt || die
+	use cuda && cuda_src_prepare
+
+	cmake-utils_src_prepare
+}
+
+src_configure() {
+	# python bindings are split
+	local mycmakeargs=(
+		-DBUILD_C_BINDINGS=ON
+		-DBUILD_PYTHON_BINDINGS=OFF
+		-DPYTHON_EXECUTABLE=
+		-DDOCDIR=share/doc/${PF}
+		$(cmake-utils_use_build cuda CUDA_LIB)
+		$(cmake-utils_use_build examples)
+		$(cmake-utils_use_build doc)
+		$(cmake-utils_use_build test TESTS)
+		$(cmake-utils_use_build octave MATLAB_BINDINGS)
+		$(cmake-utils_use_use mpi)
+		$(cmake-utils_use_use openmp)
+	)
+	use cuda && \
+		mycmakeargs+=(
+		-DCUDA_NVCC_FLAGS="${NVCCFLAGS},-arsch"
+		)
+	cmake-utils_src_configure
+}
+
+src_test() {
+	ln -s "${WORKDIR}"/testdata/* test/ || die
+	# -j1 to avoid obversubscribing jobs
+	LD_LIBRARY_PATH="${BUILD_DIR}/lib" \
+		cmake-utils_src_compile -j1 test
+}
+
+src_install() {
+	cmake-utils_src_install
+	dodoc README.md
+	if ! use static-libs; then
+		find "${ED}" -name 'lib*.a' -exec rm -rf '{}' '+' || die
+	fi
+}
diff --git a/sci-libs/flann/metadata.xml b/sci-libs/flann/metadata.xml
new file mode 100644
index 000000000000..3b08417e4cab
--- /dev/null
+++ b/sci-libs/flann/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci</herd>
+  <longdescription lang="en">
+  FLANN is a library for performing fast approximate nearest neighbor
+  searches in high dimensional spaces. It contains a collection of
+  algorithms we found to work best for nearest neighbor search and a
+  system for automatically choosing the best algorithm and optimum
+  parameters depending on the dataset.
+  FLANN is written in C++ and contains bindings for the following
+  languages: C, MATLAB and Python.
+</longdescription>
+  <use>
+    <flag name="octave">Add bindings for
+  <pkg>sci-mathematics/octave</pkg></flag>
+    <flag name="cuda">Enable support for nVidia CUDA</flag>
+  </use>
+</pkgmetadata>