sci-libs/shogun: Remove old

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

2 files changed, 0 insertions, 271 deletions

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 ed57ceca9b9d..000000000000
--- 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@maeth.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 e244c94e8e4c..000000000000
--- 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)