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 <[email protected]> +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() {
