sci-libs/shogun: Version bump to latest 4.1.0 release

Package-Manager: portage-2.2.28

3 files changed, 210 insertions, 0 deletions

diff --git a/sci-libs/shogun/Manifest b/sci-libs/shogun/Manifest
index 11c82bf05c0e..2cb0ed795c5a 100644
--- a/sci-libs/shogun/Manifest
+++ b/sci-libs/shogun/Manifest
@@ -1,6 +1,8 @@
 DIST shogun-1.1.0.tar.bz2 3485714 SHA256 9f69638f0bc18995358c38cd6eed6437e6b90c1fceab7c6e64c9739b7e6cc40b SHA512 853168e3d68ad02ef543391b78c51682d004af46acddfa09a76b41e373e27199fc9be0598892207e116a82f24437e3f1c0dc97c3e28ca32879594fbe112bd157 WHIRLPOOL dd044ff2cc9fd9376b80f1efd9bbcf901b11765a2f85eb2325ddd640ea547e513df8c9da548634e49758ef124147666f86b6b4082e118c6d35ef2d5010527cf9
 DIST shogun-2.0.0.tar.bz2 4106437 SHA256 b18e30515b9f4432d02602d0dd66dbc57c70a46f71636275071afaee94e245ee SHA512 e7c8d515afbcb3198aade32d2962e8d94b669b9c79ddbcd7425f04bbb0379803f7353c50ba8897356842cddb401d303fefaf8a7f9dd6a2e751e176deba1e46f1 WHIRLPOOL aa9ef89f28acc012ee2894c4ff6858f7bf01585d02160d5b2df33159c7c87593ea352833765a7a78cc0ed16fd10713d285eb711606f0e3771ec685778f703570
 DIST shogun-3.2.0.tar.bz2 4217245 SHA256 bc416b615ed90aef80c58a30546c5e2da779347bebb8742ecf11657073fc8f72 SHA512 7c420da7bf10c8971954964bce4dc13a8f64c6ff2a0976293f54947414ad2fe7171b1747cef3e2ceb969cf936d8fe862e940582f642cd2367897cda3191b186b WHIRLPOOL bce007c01ebee0e225d5cf858e042561a540416b349015ac566cce82b77096e8206b2f9e51572d9ee8149651a39aa30d6438b28d37ba43eb5aba593b10c5e497
+DIST shogun-4.1.0.tar.bz2 2908955 SHA256 0eb313a95606edee046768a4577d63f32f7ccce340bed7bf0ff0d69225567185 SHA512 01950d5186a94735df5331752e1b97a5464015973ddba38a70bc977f9872b3aad02b162ae87919631cce56d1f10b0bea1fa7b463bf959816e5a15a726214f52a WHIRLPOOL 300bd0d887fe8ee4a1ac2aca7f3fbaebd4344dcffe2b20f9b5bb05e83d6973e8a98e54a216d99329c03eea2c02666c557a3c50ff7e11556298d119b8c262f762
 DIST shogun-data-0.3.tar.bz2 126676026 SHA256 34272e3f5e6b6989a4941b925ab3a9cd1525d73180681884e948a673aff4ef89 SHA512 92c7e7dae1df5a7a79428a7f2116b1d9d825a37d4145edfdff1fb7b707853eab19ffe848c4ae2bc2338a93373e78c7cae4087df260411a9576b031e7a6f0de95 WHIRLPOOL 24987580c967b05e61ee5402fe30701cabe17d7ffb29b4966ff0abd0d03e197b928f018e617e254395c6939f93de3e397f5ce7df7c3d4ae7dfe4e782c345fe85
 DIST shogun-data-0.4.tar.bz2 127377123 SHA256 103ef944c7211f64957833cd6ace85e32629d73ef286273424e239fa454ecfcc SHA512 c178f6d5d8e4b6b6a94b74da5c133b01e83a1d4c7bf5d0fd66b4812b259934dbc998cfc1ef64f19b17b5099e8c389b8e359e69f1cc1bef6b82b940dc97cac46d WHIRLPOOL cef5d84f342523bad8b810fa3018669e9cd838c7c45bb37b8e7308dce448dc9b98f9aa6716aa724d64746539ef9c041a71cd2f3a1af71ed1077d276a192573d5
 DIST shogun-data-0.8.tar.bz2 261905079 SHA256 a2a0c8ccd754f0b893d97d77cfb60e25fcdb4e7033731434fb07e5483514a047 SHA512 9ea48706aae5ca116e8cf3507d1fcd06e24a8384abe6f2ebaf3c81735237d3beceee26ce5af97b85af24409eb47da684f7e7a56c0800a82c40ed214e6382978f WHIRLPOOL 3a3120a8e982c90c670ec0c206635abdcb152ae5f312172ec58ae21e1ee11f15c406b382bd3b8e8a63300302290590b83a977bd4d90375160ceb8ae516409c12
+DIST shogun-data-0.9.tar.bz2 287533841 SHA256 691dd37ccc9bdd4f56d6b7a8e061e80567c241219d70210f8148bc4b7b815559 SHA512 ab501640e2db650603899c857866b451fac5c7bbbc7b4ef98559581928869cea49aa326dfca1bb398eee7ebc8843dcc8ee3105c9f462718f1af672aac6b9340a WHIRLPOOL 19aa7a6d84be9ac7d8aaf7fb12747e17e0ba5a7ec8770b83cc1833b07cd1c6c397684a96eb8ebe709d544967ffaf23bcfbeea52dc8ddedf487fcf54a6d2b3ef7
diff --git a/sci-libs/shogun/files/shogun-4.1.0-fix-buildsystem.patch b/sci-libs/shogun/files/shogun-4.1.0-fix-buildsystem.patch
new file mode 100644
index 000000000000..e244c94e8e4c
--- /dev/null
+++ b/sci-libs/shogun/files/shogun-4.1.0-fix-buildsystem.patch
@@ -0,0 +1,81 @@
+Remove CFLAGS/CXXFLAGS setting which is not desired in Gentoo
+
+--- shogun-4.1.0/cmake/FindAtlas.cmake
++++ shogun-4.1.0/cmake/FindAtlas.cmake
+@@ -20,10 +20,10 @@
+   endif()
+   unset(CMAKE_REQUIRED_LIBRARIES CACHE)
+ else()
+-  find_file(ATLAS_LAPACK liblapack.so.3 PATHS /usr/lib/atlas /usr/lib64/atlas)
+-  find_library(ATLAS_LAPACK NAMES lapack)
+-  set(CMAKE_REQUIRED_LIBRARIES ${LAPACK_LIBRARIES} ${ATLAS_CBLAS})
+-  check_library_exists("${ATLAS_LAPACK}" clapack_dpotrf "" FOUND_CLAPACK)
++  # find_file(ATLAS_LAPACK liblapack.so.3 PATHS /usr/lib/atlas /usr/lib64/atlas)
++  # find_library(ATLAS_LAPACK NAMES lapack)
++  # set(CMAKE_REQUIRED_LIBRARIES ${LAPACK_LIBRARIES} ${ATLAS_CBLAS})
++  check_library_exists("${ATLAS_LIBRARIES}" clapack_dpotrf "" FOUND_CLAPACK)
+   if(NOT FOUND_CLAPACK)
+     unset(ATLAS_LAPACK CACHE)
+   endif()
+--- shogun-4.1.0/CMakeLists.txt
++++ shogun-4.1.0/CMakeLists.txt
+@@ -23,15 +23,6 @@
+ SET(EIGEN_VERSION_MINIMUM 3.1.2)
+ SET(VIENNACL_VERSION_MINIMUM 1.5.0)
+ 
+-# Store system's or distribution's C[XX]FLAGS.
+-SET(SYSTEM_C_FLAGS "${CMAKE_C_FLAGS}")
+-SET(SYSTEM_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
+-STRING(TOUPPER "${CMAKE_BUILD_TYPE}" BUILD_TYPE_UC)
+-IF(NOT ("${BUILD_TYPE_UC}" STREQUAL "DISTRIBUTION"))
+-	SET(CMAKE_C_FLAGS "")
+-	SET(CMAKE_CXX_FLAGS "")
+-ENDIF(NOT ("${BUILD_TYPE_UC}" STREQUAL "DISTRIBUTION"))
+-
+ # CCACHE
+ OPTION(ENABLE_CCACHE "Enable ccache for compilation" ON)
+ FIND_PACKAGE(CCache)
+@@ -145,20 +136,8 @@
+ 	SET(COMPILER_WARNINGS "-Wall -Wno-unused-parameter -Wformat -Wformat-security -Wparentheses -Wshadow -Wno-unknown-pragmas -Wno-deprecated")
+ ENDIF()
+ 
+-IF(CMAKE_COMPILER_IS_GNUCXX)
+-	SET(RELEASE_COMPILER_FLAGS "-fexpensive-optimizations -frerun-cse-after-loop -fcse-follow-jumps -finline-functions -fschedule-insns2 -fthread-jumps -fforce-addr -fstrength-reduce -funroll-loops -mfpmath=sse")
+-ELSEIF("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
+-	SET(RELEASE_COMPILER_FLAGS "-funroll-loops")
+-ENDIF()
+-SET(SWIG_CXX_COMPILER_FLAGS "-O0 -g")
+ SET(CMAKE_C_FLAGS "${COMPILER_WARNINGS} ${CMAKE_C_FLAGS}")
+ SET(CMAKE_CXX_FLAGS "${COMPILER_WARNINGS} ${CMAKE_CXX_FLAGS}")
+-SET(CMAKE_C_FLAGS_RELEASE "-O3 ${RELEASE_COMPILER_FLAGS}")
+-SET(CMAKE_CXX_FLAGS_RELEASE "-O3 ${RELEASE_COMPILER_FLAGS}")
+-SET(CMAKE_C_FLAGS_DISTRIBUTION "-O2")
+-SET(CMAKE_CXX_FLAGS_DISTRIBUTION "-O2")
+-SET(CMAKE_C_FLAGS_DEBUG "-g")
+-SET(CMAKE_CXX_FLAGS_DEBUG "-g")
+ 
+ OPTION(ENABLE_COVERAGE "Enable code coverage" OFF)
+ IF(ENABLE_COVERAGE)
+@@ -881,21 +860,7 @@
+ OPTION(USE_SWIG_DIRECTORS "Enable SWIG director classes" OFF)
+ 
+ # Respect system's or distribution's C[XX]FLAGS.
+-OPTION(SWIG_WITH_SYSTEM_CFLAGS "Enable system's C[XX]FLAGS for compilation of swig-binaries" ON)
+-
+-IF(NOT ("${BUILD_TYPE_UC}" STREQUAL "DISTRIBUTION"))
+-	SET(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${SYSTEM_C_FLAGS}")
+-	SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${SYSTEM_CXX_FLAGS}")
+-ENDIF(NOT ("${BUILD_TYPE_UC}" STREQUAL "DISTRIBUTION"))
+-
+-IF(SWIG_WITH_SYSTEM_CFLAGS)
+-	SET(SWIG_CXX_COMPILER_FLAGS "${SWIG_CXX_COMPILER_FLAGS} ${SYSTEM_CXX_FLAGS}")
+-ENDIF(SWIG_WITH_SYSTEM_CFLAGS)
+-
+-OPTION(REDUCE_SWIG_DEBUG "Reduce debuginfo when compiling interfaces" OFF)
+-IF(REDUCE_SWIG_DEBUG)
+-	SET(SWIG_CXX_COMPILER_FLAGS "${SWIG_CXX_COMPILER_FLAGS} -g1")
+-ENDIF(REDUCE_SWIG_DEBUG)
++SET(SWIG_CXX_COMPILER_FLAGS "${CMAKE_CXX_FLAGS}")
+ 
+ # python modular
+ IF (PythonModular OR PythonStatic)
diff --git a/sci-libs/shogun/shogun-4.1.0.ebuild b/sci-libs/shogun/shogun-4.1.0.ebuild
new file mode 100644
index 000000000000..651f7bbc8652
--- /dev/null
+++ b/sci-libs/shogun/shogun-4.1.0.ebuild
@@ -0,0 +1,127 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 python3_{4,5} )
+
+inherit cmake-utils flag-o-matic python-single-r1 toolchain-funcs versionator
+
+MYPV=$(get_version_component_range 1-2)
+MYPD=${PN}-data-0.9
+
+DESCRIPTION="Large Scale Machine Learning Toolbox"
+HOMEPAGE="http://shogun-toolbox.org/"
+SRC_URI="
+	ftp://shogun-toolbox.org/shogun/releases/${MYPV}/sources/${P}.tar.bz2
+	test? ( ftp://shogun-toolbox.org/shogun/data/${MYPD}.tar.bz2 )
+	examples? ( ftp://shogun-toolbox.org/shogun/data/${MYPD}.tar.bz2 )"
+
+LICENSE="GPL-3 free-noncomm"
+SLOT="0/16"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE="doc examples lua mono octave python R ruby static-libs test"
+
+REQUIRED_USE="
+	python? ( ${PYTHON_REQUIRED_USE} )
+	test? ( python )"
+
+RDEPEND="
+	app-arch/bzip2:=
+	app-arch/gzip:=
+	app-arch/lzma:=
+	app-arch/snappy:=
+	dev-libs/lzo:=
+	>=dev-cpp/eigen-3.1
+	dev-libs/json-c:=
+	dev-libs/libxml2:=
+	dev-libs/protobuf:=
+	net-misc/curl:=
+	sci-libs/arpack:=
+	sci-libs/arprec:=
+	sci-libs/colpack:=
+	sci-libs/hdf5:=
+	sci-libs/nlopt:=
+	sci-mathematics/glpk:=
+	sci-mathematics/lpsolve:=
+	sys-libs/readline:0
+	sys-libs/zlib:=
+	virtual/blas
+	virtual/cblas
+	virtual/lapack
+	lua? ( dev-lang/lua:0 )
+	mono? ( dev-lang/mono )
+	octave? ( <sci-mathematics/octave-3.8.0[hdf5] )
+	python? ( dev-python/numpy[${PYTHON_USEDEP}] )
+	R? ( dev-lang/R )
+	ruby? ( dev-ruby/narray )"
+
+DEPEND="${RDEPEND}
+	virtual/pkgconfig
+	doc? ( app-doc/doxygen[dot] )
+	lua? ( >=dev-lang/swig-2.0.4 )
+	mono? ( >=dev-lang/swig-2.0.4 )
+	octave? ( >=dev-lang/swig-2.0.4 )
+	python? ( >=dev-lang/swig-2.0.4 test? ( sci-libs/scipy ) )
+	R? ( >=dev-lang/swig-2.0.4 )
+	ruby? ( >=dev-lang/swig-2.0.4 )
+	test? (
+		dev-python/jinja[${PYTHON_USEDEP}]
+		dev-cpp/gmock
+		)"
+
+# javamodular needs jblas (painful to package properly)
+# permodular work in progress (as 3.2.0)
+# could actually support multiple pythons, multiple rubys
+# feel free to do work for it
+
+PATCHES=(
+	"${FILESDIR}"/${P}-fix-buildsystem.patch
+)
+
+pkg_setup() {
+	use python && python-single-r1_pkg_setup
+}
+
+src_configure() {
+	export ATLAS_LIBRARY="$($(tc-getPKG_CONFIG) --libs cblas lapack)"
+	export CBLAS_LIBRARY="$($(tc-getPKG_CONFIG) --libs cblas)"
+	export ATLAS_LIBRARIES="$($(tc-getPKG_CONFIG) --libs blas cblas lapack)"
+	export LAPACK_LIBRARIES="$($(tc-getPKG_CONFIG) --libs lapack)"
+
+	append-cppflags "$($(tc-getPKG_CONFIG) --cflags cblas)"
+
+	local mycmakeargs=(
+		-DCMAKE_SKIP_INSTALL_RPATH=ON
+		-DCMAKE_SKIP_RPATH=ON
+		-DBUNDLE_ARPREC=OFF
+		-DBUNDLE_COLPACK=OFF
+		-DBUNDLE_EIGEN=OFF
+		-DBUNDLE_JSON=OFF
+		-DBUNDLE_NLOPT=OFF
+		-DENABLE_COVERAGE=OFF
+		-DJavaModular=OFF
+		-DPerlModular=OFF
+		-DLIB_INSTALL_DIR=$(get_libdir)
+		-DLuaModular="$(usex lua)"
+		-DCSharpModular="$(usex mono)"
+		-DOctaveModular="$(usex octave)"
+		-DOctaveStatic="$(usex octave)"
+		-DPythonModular="$(usex python)"
+		-DPythonStatic="$(usex python)"
+		-DRModular="$(usex R)"
+		-DRStatic="$(usex R)"
+		-DRubyModular="$(usex ruby)"
+		-DENABLE_TESTING="$(usex test)"
+		-DBUILD_EXAMPLES="$(usex examples)"
+	)
+	cmake-utils_src_configure
+	# gentoo bug #302621
+	has_version sci-libs/hdf5[mpi] && export CXX=mpicxx CC=mpicc
+}
+
+src_compile() {
+	cmake-utils_src_compile
+	use doc && emake -C doc
+}