Merge pull request #49 from yixuan/Eigen3.3.4

Eigen 3.3.4

Author: eddelbuettel

ChangeLog

@@ -1,3 +1,17 @@
+2018-02-04  Yixuan Qiu  <yixuan.qiu@cos.name>
+
+	[ In RcppEigen 0.3.3.* branch ]
+
+	* inst/include/Eigen: Updated to the upstream 3.3 branch of Eigen
+	based on version 3.3.4
+	* inst/include/unsupported: Idem
+	* DESCRIPTION: Idem
+	* README.md: Idem
+
+	* inst/include/Eigen/src/Core/util/DisableStupidWarnings.h:
+	Patch from upstream Eigen that has not been ported to the 3.3 branch
+	(cf GitHub issue #48)
+
 2017-11-19  Dirk Eddelbuettel  <edd@debian.org>
 
 	* DESCRIPTION (Version, Date): Release 0.3.3.3.1

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: RcppEigen
 Type: Package
 Title: 'Rcpp' Integration for the 'Eigen' Templated Linear Algebra Library
-Version: 0.3.3.3.1
-Date: 2017-11-19
+Version: 0.3.3.4.0
+Date: 2018-02-04
 Author: Douglas Bates, Dirk Eddelbuettel, Romain Francois, and Yixuan Qiu;
  the authors of Eigen for the included version of Eigen
 Maintainer: Dirk Eddelbuettel <edd@debian.org>
@@ -14,7 +14,7 @@ Description: R and 'Eigen' integration using 'Rcpp'.
  such matrices, and solutions of linear systems. Its performance on many
  algorithms is comparable with some of the best implementations based on
  'Lapack' and level-3 'BLAS'. The 'RcppEigen' package includes the header
- files from the 'Eigen' C++ template library (currently version 3.3.3). Thus
+ files from the 'Eigen' C++ template library (currently version 3.3.4). Thus
  users do not need to install 'Eigen' itself in order to use 'RcppEigen'.
  Since version 3.1.1, 'Eigen' is licensed under the Mozilla Public License
  (version 2); earlier version were licensed under the GNU LGPL version 3 or

README.md

@@ -12,7 +12,7 @@ systems. Its performance on many algorithms is comparable with some of the
 best implementations based on `Lapack` and level-3 `BLAS`.
 
 The RcppEigen package includes the header files from the Eigen C++
-template library (currently version 3.3.3). Thus users do not need to
+template library (currently version 3.3.4). Thus users do not need to
 install Eigen itself in order to use RcppEigen.
 
 ### Status

inst/include/Eigen/Cholesky

@@ -9,6 +9,7 @@
 #define EIGEN_CHOLESKY_MODULE_H
 
 #include "Core"
+#include "Jacobi"
 
 #include "src/Core/util/DisableStupidWarnings.h"
 
@@ -31,7 +32,11 @@
 #include "src/Cholesky/LLT.h"
 #include "src/Cholesky/LDLT.h"
 #ifdef EIGEN_USE_LAPACKE
+#ifdef EIGEN_USE_MKL
+#include "mkl_lapacke.h"
+#else
 #include "src/misc/lapacke.h"
+#endif
 #include "src/Cholesky/LLT_LAPACKE.h"
 #endif
 

inst/include/Eigen/Core

@@ -14,6 +14,22 @@
 // first thing Eigen does: stop the compiler from committing suicide
 #include "src/Core/util/DisableStupidWarnings.h"
 
+#if defined(__CUDACC__) && !defined(EIGEN_NO_CUDA)
+  #define EIGEN_CUDACC __CUDACC__
+#endif
+
+#if defined(__CUDA_ARCH__) && !defined(EIGEN_NO_CUDA)
+  #define EIGEN_CUDA_ARCH __CUDA_ARCH__
+#endif
+
+#if defined(__CUDACC_VER_MAJOR__) && (__CUDACC_VER_MAJOR__ >= 9)
+#define EIGEN_CUDACC_VER  ((__CUDACC_VER_MAJOR__ * 10000) + (__CUDACC_VER_MINOR__ * 100))
+#elif defined(__CUDACC_VER__)
+#define EIGEN_CUDACC_VER __CUDACC_VER__
+#else
+#define EIGEN_CUDACC_VER 0
+#endif
+
 // Handle NVCC/CUDA/SYCL
 #if defined(__CUDACC__) || defined(__SYCL_DEVICE_ONLY__)
   // Do not try asserts on CUDA and SYCL!
@@ -229,7 +245,7 @@
 #if defined __CUDACC__
   #define EIGEN_VECTORIZE_CUDA
   #include <vector_types.h>
-  #if defined __CUDACC_VER__ && __CUDACC_VER__ >= 70500
+  #if EIGEN_CUDACC_VER >= 70500
     #define EIGEN_HAS_CUDA_FP16
   #endif
 #endif
@@ -352,6 +368,7 @@ using std::ptrdiff_t;
 #include "src/Core/MathFunctions.h"
 #include "src/Core/GenericPacketMath.h"
 #include "src/Core/MathFunctionsImpl.h"
+#include "src/Core/arch/Default/ConjHelper.h"
 
 #if defined EIGEN_VECTORIZE_AVX512
   #include "src/Core/arch/SSE/PacketMath.h"

inst/include/Eigen/Eigenvalues

@@ -45,7 +45,11 @@
 #include "src/Eigenvalues/GeneralizedEigenSolver.h"
 #include "src/Eigenvalues/MatrixBaseEigenvalues.h"
 #ifdef EIGEN_USE_LAPACKE
+#ifdef EIGEN_USE_MKL
+#include "mkl_lapacke.h"
+#else
 #include "src/misc/lapacke.h"
+#endif
 #include "src/Eigenvalues/RealSchur_LAPACKE.h"
 #include "src/Eigenvalues/ComplexSchur_LAPACKE.h"
 #include "src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h"

inst/include/Eigen/LU

@@ -28,7 +28,11 @@
 #include "src/LU/FullPivLU.h"
 #include "src/LU/PartialPivLU.h"
 #ifdef EIGEN_USE_LAPACKE
+#ifdef EIGEN_USE_MKL
+#include "mkl_lapacke.h"
+#else
 #include "src/misc/lapacke.h"
+#endif
 #include "src/LU/PartialPivLU_LAPACKE.h"
 #endif
 #include "src/LU/Determinant.h"

inst/include/Eigen/QR

@@ -36,7 +36,11 @@
 #include "src/QR/ColPivHouseholderQR.h"
 #include "src/QR/CompleteOrthogonalDecomposition.h"
 #ifdef EIGEN_USE_LAPACKE
+#ifdef EIGEN_USE_MKL
+#include "mkl_lapacke.h"
+#else
 #include "src/misc/lapacke.h"
+#endif
 #include "src/QR/HouseholderQR_LAPACKE.h"
 #include "src/QR/ColPivHouseholderQR_LAPACKE.h"
 #endif

inst/include/Eigen/QtAlignedMalloc

@@ -27,7 +27,7 @@ void qFree(void *ptr)
 void *qRealloc(void *ptr, std::size_t size)
 {
   void* newPtr = Eigen::internal::aligned_malloc(size);
-  memcpy(newPtr, ptr, size);
+  std::memcpy(newPtr, ptr, size);
   Eigen::internal::aligned_free(ptr);
   return newPtr;
 }

inst/include/Eigen/SVD

@@ -37,7 +37,11 @@
 #include "src/SVD/JacobiSVD.h"
 #include "src/SVD/BDCSVD.h"
 #if defined(EIGEN_USE_LAPACKE) && !defined(EIGEN_USE_LAPACKE_STRICT)
+#ifdef EIGEN_USE_MKL
+#include "mkl_lapacke.h"
+#else
 #include "src/misc/lapacke.h"
+#endif
 #include "src/SVD/JacobiSVD_LAPACKE.h"
 #endif