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

["Justin Lecher" <jlec@gentoo.org>]

commit:     e395a02c43d71ee8ea422d5092a4cc3ec3a1fe4c
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jan 15 19:34:44 2017 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jan 15 19:35:10 2017 +0000
URL:        https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=e395a02c

sci-libs/shogun: Backport fix for eigen-3.3

Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=604670

Package-Manager: Portage-2.3.3, Repoman-2.3.1
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 sci-libs/shogun/files/shogun-4.1.0-eigen-3.3.patch | 190 +++++++++++++++++++++
 sci-libs/shogun/shogun-4.1.0.ebuild                |   3 +-
 2 files changed, 192 insertions(+), 1 deletion(-)

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
new file mode 100644
index 00000000..ed57cec
--- /dev/null
+++ b/sci-libs/shogun/files/shogun-4.1.0-eigen-3.3.patch
@@ -0,0 +1,190 @@
+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/shogun-4.1.0.ebuild b/sci-libs/shogun/shogun-4.1.0.ebuild
index 3258b84..3f31f9d 100644
--- a/sci-libs/shogun/shogun-4.1.0.ebuild
+++ b/sci-libs/shogun/shogun-4.1.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
@@ -79,6 +79,7 @@ DEPEND="${RDEPEND}
 PATCHES=(
 	"${FILESDIR}"/${P}-fix-buildsystem.patch
 	"${FILESDIR}"/${P}-remove-C-linkage.patch
+	"${FILESDIR}"/${P}-eigen-3.3.patch
 )
 
 pkg_setup() {