[gentoo-commits] repo/gentoo:master commit in: sci-libs/shogun/files/, sci-libs/shogun/

[David Seifert]

commit:     9d87880e06967309bde9877094080884b7d9c9ec
Author:     David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Feb  4 21:02:10 2017 +0000
Commit:     David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Feb  4 21:07:13 2017 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=9d87880e

sci-libs/shogun: Remove old

Package-Manager: Portage-2.3.3, Repoman-2.3.1
Closes: https://github.com/gentoo/gentoo/pull/3782

 sci-libs/shogun/Manifest                           |   1 -
 sci-libs/shogun/files/shogun-4.1.0-eigen-3.3.patch | 190 ---------------------
 .../files/shogun-4.1.0-fix-buildsystem.patch       |  81 ---------
 sci-libs/shogun/shogun-4.1.0.ebuild                | 129 --------------
 4 files changed, 401 deletions(-)

diff --git a/sci-libs/shogun/Manifest b/sci-libs/shogun/Manifest
index b92de5f..b827f90 100644
--- a/sci-libs/shogun/Manifest
+++ b/sci-libs/shogun/Manifest
@@ -1,3 +1,2 @@
-DIST shogun-4.1.0.tar.bz2 2908955 SHA256 0eb313a95606edee046768a4577d63f32f7ccce340bed7bf0ff0d69225567185 SHA512 01950d5186a94735df5331752e1b97a5464015973ddba38a70bc977f9872b3aad02b162ae87919631cce56d1f10b0bea1fa7b463bf959816e5a15a726214f52a WHIRLPOOL 300bd0d887fe8ee4a1ac2aca7f3fbaebd4344dcffe2b20f9b5bb05e83d6973e8a98e54a216d99329c03eea2c02666c557a3c50ff7e11556298d119b8c262f762
 DIST shogun-5.0.0.tar.bz2 2448509 SHA256 e82c6a58db9db6624192b018750b0e41f793481791fdc9a6d328bf278d0ae70d SHA512 fa8d9dee4596acce12022540a6927cbdb62e08f8468c8be3790de07ebf3a53055032bcc532b28334ca83284c38f2b0153602634f12bafe4019acb9121b9ff236 WHIRLPOOL 532058c44680909f3717785035c13fb3cf48efec22924101975d80990cb2a9e151814c673ad1a03fa33e363abbaf21fc9edc99d7d25686cc67e907547217bf69
 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-eigen-3.3.patch b/sci-libs/shogun/files/shogun-4.1.0-eigen-3.3.patch
deleted file mode 100644
index ed57cec..00000000
--- a/sci-libs/shogun/files/shogun-4.1.0-eigen-3.3.patch
+++ /dev/null
@@ -1,190 +0,0 @@
-From 57cd0958b153accf12f535ab9406dc8511bf22ec Mon Sep 17 00:00:00 2001
-From: Viktor Gal <viktor.gal@×××××.com>
-Date: Wed, 18 May 2016 06:35:28 +0200
-Subject: [PATCH] Fixing eigen 3.3 related errors
-
-porting fix for #3141 from lisitsyn/tapkee@7c74473d12809e4122527b6e003c74a942d8a25c
-fix #3140: provide a workaround for the eigen bug for calculating log of mapped matrices
----
- src/shogun/lib/tapkee/defines.hpp                  |  4 +--
- src/shogun/mathematics/eigen3.h                    |  7 +++++
- .../logdet/opfunc/DenseMatrixExactLog.cpp          |  5 ++++
- .../SerialComputationEngine_unittest.cc            |  5 ++++
- .../linalg/DenseExactLogJob_unittest.cc            |  5 ++++
- .../linalg/RationalApproximation_unittest.cc       | 10 ++++++++
- .../linalg/SparseMatrixOperator_unittest.cc        | 30 ++++++++++++----------
- 7 files changed, 51 insertions(+), 15 deletions(-)
-
-diff --git a/src/shogun/lib/tapkee/defines.hpp b/src/shogun/lib/tapkee/defines.hpp
-index fd02636..1be45fe 100644
---- a/src/shogun/lib/tapkee/defines.hpp
-+++ b/src/shogun/lib/tapkee/defines.hpp
-@@ -49,12 +49,12 @@ namespace tapkee
- 		TapkeeOutput(const tapkee::DenseMatrix& e, const tapkee::ProjectingFunction& p) :
- 			embedding(), projection(p)
- 		{
--			embedding.swap(e);
-+			embedding = e;
- 		}
- 		TapkeeOutput(const TapkeeOutput& that) :
- 			embedding(), projection(that.projection)
- 		{
--			this->embedding.swap(that.embedding);
-+			this->embedding = that.embedding;
- 		}
- 		tapkee::DenseMatrix embedding;
- 		tapkee::ProjectingFunction projection;
-diff --git a/src/shogun/mathematics/eigen3.h b/src/shogun/mathematics/eigen3.h
-index 0fb8522..734be6c 100644
---- a/src/shogun/mathematics/eigen3.h
-+++ b/src/shogun/mathematics/eigen3.h
-@@ -61,6 +61,13 @@
- 
- 	#endif	//EIGEN_VERSION_AT_LEAST(3,0,93)
- 
-+#if ((EIGEN_WORLD_VERSION == 3) && (EIGEN_MAJOR_VERSION == 2) && \
-+	((EIGEN_MINOR_VERSION == 91) || (EIGEN_MINOR_VERSION == 92)))
-+	// Regression has been introduced to eigen develop (3.3alpha1+):
-+	// http://eigen.tuxfamily.org/bz/show_bug.cgi?id=1229
-+	// until this is not fixed we need to copy the matrix and calculate the log
-+	#define EIGEN_WITH_LOG_BUG_1229 1
-+#endif
- namespace shogun
- {
- template<class T> class SGSparseMatrix;
-diff --git a/src/shogun/mathematics/linalg/ratapprox/logdet/opfunc/DenseMatrixExactLog.cpp b/src/shogun/mathematics/linalg/ratapprox/logdet/opfunc/DenseMatrixExactLog.cpp
-index a7918e6..1002a6c 100644
---- a/src/shogun/mathematics/linalg/ratapprox/logdet/opfunc/DenseMatrixExactLog.cpp
-+++ b/src/shogun/mathematics/linalg/ratapprox/logdet/opfunc/DenseMatrixExactLog.cpp
-@@ -62,7 +62,12 @@ void CDenseMatrixExactLog::precompute()
- 	Map<MatrixXd> mat(m.matrix, m.num_rows, m.num_cols);
- 	SGMatrix<float64_t> log_m(m.num_rows, m.num_cols);
- 	Map<MatrixXd> log_mat(log_m.matrix, log_m.num_rows, log_m.num_cols);
-+#if EIGEN_WITH_LOG_BUG_1229
-+	MatrixXd tmp = mat;
-+	log_mat=tmp.log();
-+#else
- 	log_mat=mat.log();
-+#endif
- 
- 	// the log(C) is also a linear operator here
- 	// reset the operator of this function with log(C)
-diff --git a/tests/unit/lib/computation/SerialComputationEngine_unittest.cc b/tests/unit/lib/computation/SerialComputationEngine_unittest.cc
-index c41a69a..7f96df1 100644
---- a/tests/unit/lib/computation/SerialComputationEngine_unittest.cc
-+++ b/tests/unit/lib/computation/SerialComputationEngine_unittest.cc
-@@ -40,7 +40,12 @@ TEST(SerialComputationEngine, dense_log_det)
- 	mat(1,1)=3.0;
- 	Map<MatrixXd> m(mat.matrix, mat.num_rows, mat.num_cols);
- 	Map<MatrixXd> log_m(log_mat.matrix, log_mat.num_rows, log_mat.num_cols);
-+#if EIGEN_WITH_LOG_BUG_1229
-+	MatrixXd tmp = m;
-+	log_m=tmp.log();
-+#else
- 	log_m=m.log();
-+#endif
- 
- 	// create linear operator and aggregator
- 	CDenseMatrixOperator<float64_t>* log_op=new CDenseMatrixOperator<float64_t>(log_mat);
-diff --git a/tests/unit/mathematics/linalg/DenseExactLogJob_unittest.cc b/tests/unit/mathematics/linalg/DenseExactLogJob_unittest.cc
-index a5a12cf..60daf40 100644
---- a/tests/unit/mathematics/linalg/DenseExactLogJob_unittest.cc
-+++ b/tests/unit/mathematics/linalg/DenseExactLogJob_unittest.cc
-@@ -38,7 +38,12 @@ TEST(DenseExactLogJob, log_det)
- 	mat(1,1)=3.0;
- 	Map<MatrixXd> m(mat.matrix, mat.num_rows, mat.num_cols);
- 	Map<MatrixXd> log_m(log_mat.matrix, log_mat.num_rows, log_mat.num_cols);
-+#if EIGEN_WITH_LOG_BUG_1229
-+	MatrixXd tmp = m;
-+	log_m=tmp.log();
-+#else
- 	log_m=m.log();
-+#endif
- 
- 	// create linear operator and aggregator
- 	CDenseMatrixOperator<float64_t>* log_op=new CDenseMatrixOperator<float64_t>(log_mat);
-diff --git a/tests/unit/mathematics/linalg/RationalApproximation_unittest.cc b/tests/unit/mathematics/linalg/RationalApproximation_unittest.cc
-index f401d06..682ed66 100644
---- a/tests/unit/mathematics/linalg/RationalApproximation_unittest.cc
-+++ b/tests/unit/mathematics/linalg/RationalApproximation_unittest.cc
-@@ -182,7 +182,12 @@ TEST(RationalApproximation, trace_accuracy)
- #if EIGEN_VERSION_AT_LEAST(3,1,0)
- 	// compute the trace of log(m) using Eigen3 that uses Schur-Parlett algorithm
- 	Map<MatrixXd> eig_m(m.matrix, m.num_rows, m.num_cols);
-+#if EIGEN_WITH_LOG_BUG_1229
-+	MatrixXd tmp = eig_m;
-+	float64_t trace_log_m=tmp.log().diagonal().sum();
-+#else
- 	float64_t trace_log_m=eig_m.log().diagonal().sum();
-+#endif
- #else
- 	float64_t trace_log_m=-11.51292546497021618279;
- #endif // EIGEN_VERSION_AT_LEAST(3,1,0)
-@@ -364,7 +369,12 @@ TEST(RationalApproximation, trace_accuracy_cg_m)
- #if EIGEN_VERSION_AT_LEAST(3,1,0)
- 	// compute the trace of log(m) using Eigen3 that uses Schur-Parlett algorithm
- 	Map<MatrixXd> eig_m(m.matrix, m.num_rows, m.num_cols);
-+#if EIGEN_WITH_LOG_BUG_1229
-+	MatrixXd tmp = eig_m;
-+	float64_t trace_log_m=tmp.log().diagonal().sum();
-+#else
- 	float64_t trace_log_m=eig_m.log().diagonal().sum();
-+#endif
- #else
- 	float64_t trace_log_m=-11.51292546497021618279;
- #endif // EIGEN_VERSION_AT_LEAST(3,1,0)
-diff --git a/tests/unit/mathematics/linalg/SparseMatrixOperator_unittest.cc b/tests/unit/mathematics/linalg/SparseMatrixOperator_unittest.cc
-index 4d30724..9d171cc 100644
---- a/tests/unit/mathematics/linalg/SparseMatrixOperator_unittest.cc
-+++ b/tests/unit/mathematics/linalg/SparseMatrixOperator_unittest.cc
-@@ -219,33 +219,37 @@ TEST(SparseMatrixOperator, get_set_diagonal_realloc_complex128)
- 
- TEST(SparseMatrixOperator, get_sparsity_structure)
- {
--	const int size=9;
--	const int max_pow=10;
-+	const int32_t size=9;
-+	const int32_t max_pow=10;
- 
--	SGMatrix<double> m(size, size);
-+	SGMatrix<float64_t> m(size, size);
- 
- 	m.set_const(0.0);
--	for (int i=0; i<size; ++i)
-+	for (int32_t i=0; i<size; ++i)
- 		m(i,i)=2.0;
--	for (int i=0; i<size; i+=4)
-+	for (int32_t i=0; i<size; i+=4)
- 		m(i,size-1)=2.0;
--	for (int i=0; i<size; i+=4)
-+	for (int32_t i=0; i<size; i+=4)
- 		m(size-1,i)=2.0;
- 
--	CSparseFeatures<double> feat(m);
--	SGSparseMatrix<double> sm=feat.get_sparse_feature_matrix();
--	CSparseMatrixOperator<double> op(sm);
-+	CSparseFeatures<float64_t> feat(m);
-+	SGSparseMatrix<float64_t> sm=feat.get_sparse_feature_matrix();
-+	CSparseMatrixOperator<float64_t> op(sm);
- 	CSparseMatrixOperator<bool>* b_op
- 		=static_cast<CSparseMatrixOperator<bool>*>(op);
- 
--	SparseMatrix<bool, RowMajor, int> sp
-+	SparseMatrix<bool, RowMajor, int32_t> sp
- 		=EigenSparseUtil<bool>::toEigenSparse(b_op->get_matrix_operator());
--	SparseMatrix<double, RowMajor, int> sm2
--		=EigenSparseUtil<double>::toEigenSparse(sm);
-+	SparseMatrix<float64_t, RowMajor, int32_t> sm2
-+		=EigenSparseUtil<float64_t>::toEigenSparse(sm);
- 
- 	// compute direct matrix power and then the sparsity structure
--	for (int i=2; i<=max_pow; ++i)
-+	for (int32_t i=2; i<=max_pow; ++i)
-+#if EIGEN_VERSION_AT_LEAST(3,2,91)
-+		sp=(sp.cast<float64_t>()*sm2).cast<bool>();
-+#else
- 		sp=sp*sm2;
-+#endif
- 
- 	int32_t* outerIndexPtr=const_cast<int32_t*>(sp.outerIndexPtr());
- 	int32_t* innerIndexPtr=const_cast<int32_t*>(sp.innerIndexPtr());

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
deleted file mode 100644
index e244c94..00000000
--- a/sci-libs/shogun/files/shogun-4.1.0-fix-buildsystem.patch
+++ /dev/null
@@ -1,81 +0,0 @@
-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
deleted file mode 100644
index 3f31f9d..00000000
--- a/sci-libs/shogun/shogun-4.1.0.ebuild
+++ /dev/null
@@ -1,129 +0,0 @@
-# Copyright 1999-2017 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
-	"${FILESDIR}"/${P}-remove-C-linkage.patch
-	"${FILESDIR}"/${P}-eigen-3.3.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 "${BUILD_DIR}"/doc
-}