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authorJustin Lecher <jlec@gentoo.org>2017-01-15 19:34:44 +0000
committerJustin Lecher <jlec@gentoo.org>2017-01-15 19:35:10 +0000
commite395a02c43d71ee8ea422d5092a4cc3ec3a1fe4c (patch)
treee5e81141bfb19f91af8d77efa6e8f2a5729b76e9 /sci-libs/shogun
parentdev-perl/Mozilla-CA: Remove old (diff)
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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@gentoo.org>
Diffstat (limited to 'sci-libs/shogun')
-rw-r--r--sci-libs/shogun/files/shogun-4.1.0-eigen-3.3.patch190
-rw-r--r--sci-libs/shogun/shogun-4.1.0.ebuild3
2 files changed, 192 insertions, 1 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
new file mode 100644
index 00000000000..ed57ceca9b9
--- /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 3258b84c830..3f31f9d833c 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() {