Merge pull request #37 from yixuan/Eigen3.2.9

Update to Eigen 3.2.9

ChangeLog

@@ -1,10 +1,17 @@
+2016-08-19  Yixuan Qiu  <yixuan.qiu@cos.name>
+
+	* inst/include/Eigen: Updated to release 3.2.9 of Eigen
+    * DESCRIPTION: Idem
+
+	* README.md: Updated version number and fixed the NOTE from CRAN URL check
+
 2016-04-30  Dirk Eddelbuettel  <edd@debian.org>
 
 	* README.md: Expanded
 
 2016-04-28  James Joseph Balamuta <balamut2@illinois.edu>
 
-	* inst/include/RcppEigenWrap.h: Added an exporter class for Map::RowVectorX<t> per 
+	* inst/include/RcppEigenWrap.h: Added an exporter class for Map::RowVectorX<t> per
 	http://stackoverflow.com/questions/36920689/rowvectorxd-not-supported-in-rcppeigen
 	* inst/include/unitTests/runit.RcppEigen.R: Added row exporter unit test.
 

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: RcppEigen
 Type: Package
 Title: 'Rcpp' Integration for the 'Eigen' Templated Linear Algebra Library
-Version: 0.3.2.8.1
-Date: 2016-02-28
+Version: 0.3.2.9.0
+Date: 2016-08-19
 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>
@@ -16,7 +16,7 @@ Description: R and 'Eigen' integration using 'Rcpp'.
  implementations based on 'Lapack' and level-3 'BLAS'.
  .
  The 'RcppEigen' package includes the header files from the 'Eigen' C++
- template library (currently version 3.2.8). Thus users do not need to
+ template library (currently version 3.2.9). 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

README.md

@@ -1,6 +1,6 @@
 ## RcppEigen
 
-[![Build Status](https://travis-ci.org/RcppCore/RcppEigen.svg)](https://travis-ci.org/RcppCore/RcppEigen) [![License](http://img.shields.io/badge/license-GPL%20%28%3E=%202%29-brightgreen.svg?style=flat)](http://www.gnu.org/licenses/gpl-2.0.html) [![License](http://img.shields.io/badge/license-MPL2-brightgreen.svg?style=flat)](http://www.mozilla.org/MPL/2.0/) [![CRAN](http://www.r-pkg.org/badges/version/RcppEigen)](http://cran.rstudio.com/package=RcppEigen) [![Downloads](http://cranlogs.r-pkg.org/badges/RcppEigen?color=brightgreen)](http://www.r-pkg.org/pkg/RcppEigen)
+[![Build Status](https://travis-ci.org/RcppCore/RcppEigen.svg)](https://travis-ci.org/RcppCore/RcppEigen) [![License](http://img.shields.io/badge/license-GPL%20%28%3E=%202%29-brightgreen.svg?style=flat)](http://www.gnu.org/licenses/gpl-2.0.html) [![License](http://img.shields.io/badge/license-MPL2-brightgreen.svg?style=flat)](http://www.mozilla.org/MPL/2.0/) [![CRAN](http://www.r-pkg.org/badges/version/RcppEigen)](http://cran.r-project.org/package=RcppEigen) [![Downloads](http://cranlogs.r-pkg.org/badges/RcppEigen?color=brightgreen)](http://www.r-pkg.org/pkg/RcppEigen)
 
 ### Overview
 
@@ -12,18 +12,18 @@ 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 3.2.8). Thus users do not need to
+template library (currently version 3.2.9). Thus users do not need to
 install Eigen itself in order to use RcppEigen.
 
 ### Status
 
-The package is reasonably mature and under active development, following the 
+The package is reasonably mature and under active development, following the
 [Eigen](http://eigen.tuxfamily.org) release cycle.
 
 ### Documentation
 
 The package contains a pdf vignette which is a pre-print of the [paper by
-Bates and Eddelbuettel](https://www.jstatsoft.org/article/view/v052i05) 
+Bates and Eddelbuettel](https://www.jstatsoft.org/article/view/v052i05)
 in JSS (2013, v52i05).
 
 ### Authors
@@ -33,4 +33,3 @@ Douglas Bates, Dirk Eddelbuettel, Romain Francois, and Yixuan Qiu
 ### License
 
 GPL (>= 2)
-

inst/NEWS.Rd

@@ -3,10 +3,11 @@
 \newcommand{\ghpr}{\href{https://github.com/RcppCore/RcppEigen/pull/#1}{##1}}
 \newcommand{\ghit}{\href{https://github.com/RcppCore/RcppEigen/issues/#1}{##1}}
 
-\section{Changes in RcppEigen version 0.3.X.Y.Z (2016-XX-YY)}{
+\section{Changes in RcppEigen version 0.3.2.9.0 (2016-08-19)}{
   \itemize{
     \item An exporter for RowVectorX was added (thanks to PR \ghpr{32}
-    by James Balamuta) 
+    by James Balamuta)
+    \item Updated to version 3.2.9 of Eigen
   }
 }
 
@@ -54,7 +55,7 @@
     \CRANpkg{pkgKitten} if available
   }
 }
-    
+
 \section{Changes in RcppEigen version 0.3.2.3.0 (2014-12-22)}{
   \itemize{
     \item Updated to version 3.2.3 of Eigen
@@ -85,7 +86,7 @@
     the cpu id comparison, with thanks to Gael Guennebaud for the patch
   }
 }
-    
+
 \section{Changes in RcppEigen version 0.3.2.1.1 (2014-03-06)}{
   \itemize{
     \item Better \code{ifdef} on one directory entry feature, with
@@ -103,7 +104,7 @@
   \itemize{
     \item Updated and extended \code{RcppEigen.package.skeleton()} to
     use several examples via \CRANpkg{Rcpp} Attributes; also removed the
-    deprecated \code{namespace} argument 
+    deprecated \code{namespace} argument
     \item Updated skeleton package example for \CRANpkg{Rcpp} 0.11.0 or
     later by removing needed for linking with user library
     \item Updated files \code{DESCRIPTION}, \code{NAMESPACE},
@@ -128,7 +129,7 @@
     \item Applied two small patches to deal with non-g++ compilrs
     \item Clarifications concerning license and authorship of
     Eigen (as opposed to RcppEigen) code added to \code{DESCRIPTION} at
-    the request of CRAN 
+    the request of CRAN
   }
 }
 
@@ -157,7 +158,7 @@
     which cannot be changed to a ColMajor form.
     \item Because of changes in R, -DNDEBUG is automatic. One must
     override it with -UNDEBUG in the local ~/.R/Makevars to activate the
-    debugging code. 
+    debugging code.
     \item New (unexported) functions CxxFlags() and RcppEigenCxxFlags()
     for use in Makefiles
     \item Fixes related to Rcpp 0.10.*
@@ -210,5 +211,3 @@
     some difficulty with combining testthat, inline and R CMD check.
   }
 }
-
-

inst/include/Eigen/src/Core/CommaInitializer.h

@@ -76,8 +76,11 @@ struct CommaInitializer
   template<typename OtherDerived>
   CommaInitializer& operator,(const DenseBase<OtherDerived>& other)
   {
-    if(other.cols()==0 || other.rows()==0)
+    if(other.rows()==0)
+    {
+      m_col += other.cols();
       return *this;
+    }
     if (m_col==m_xpr.cols())
     {
       m_row+=m_currentBlockRows;
@@ -86,7 +89,7 @@ struct CommaInitializer
       eigen_assert(m_row+m_currentBlockRows<=m_xpr.rows()
         && "Too many rows passed to comma initializer (operator<<)");
     }
-    eigen_assert(m_col<m_xpr.cols()
+    eigen_assert((m_col<m_xpr.cols() || (m_xpr.cols()==0 && m_col==0))
       && "Too many coefficients passed to comma initializer (operator<<)");
     eigen_assert(m_currentBlockRows==other.rows());
     if (OtherDerived::SizeAtCompileTime != Dynamic)

inst/include/Eigen/src/Core/DiagonalMatrix.h

@@ -44,10 +44,10 @@ class DiagonalBase : public EigenBase<Derived>
     template<typename DenseDerived>
     void evalTo(MatrixBase<DenseDerived> &other) const;
     template<typename DenseDerived>
-    void addTo(MatrixBase<DenseDerived> &other) const
+    inline void addTo(MatrixBase<DenseDerived> &other) const
     { other.diagonal() += diagonal(); }
     template<typename DenseDerived>
-    void subTo(MatrixBase<DenseDerived> &other) const
+    inline void subTo(MatrixBase<DenseDerived> &other) const
     { other.diagonal() -= diagonal(); }
 
     inline const DiagonalVectorType& diagonal() const { return derived().diagonal(); }
@@ -98,7 +98,7 @@ class DiagonalBase : public EigenBase<Derived>
 
 template<typename Derived>
 template<typename DenseDerived>
-void DiagonalBase<Derived>::evalTo(MatrixBase<DenseDerived> &other) const
+inline void DiagonalBase<Derived>::evalTo(MatrixBase<DenseDerived> &other) const
 {
   other.setZero();
   other.diagonal() = diagonal();

inst/include/Eigen/src/Core/Dot.h

@@ -59,7 +59,7 @@ struct dot_nocheck<T, U, true>
   */
 template<typename Derived>
 template<typename OtherDerived>
-typename internal::scalar_product_traits<typename internal::traits<Derived>::Scalar,typename internal::traits<OtherDerived>::Scalar>::ReturnType
+inline typename internal::scalar_product_traits<typename internal::traits<Derived>::Scalar,typename internal::traits<OtherDerived>::Scalar>::ReturnType
 MatrixBase<Derived>::dot(const MatrixBase<OtherDerived>& other) const
 {
   EIGEN_STATIC_ASSERT_VECTOR_ONLY(Derived)

inst/include/Eigen/src/Core/GeneralProduct.h

@@ -205,9 +205,6 @@ class GeneralProduct<Lhs, Rhs, InnerProduct>
   public:
     GeneralProduct(const Lhs& lhs, const Rhs& rhs)
     {
-      EIGEN_STATIC_ASSERT((internal::is_same<typename Lhs::RealScalar, typename Rhs::RealScalar>::value),
-        YOU_MIXED_DIFFERENT_NUMERIC_TYPES__YOU_NEED_TO_USE_THE_CAST_METHOD_OF_MATRIXBASE_TO_CAST_NUMERIC_TYPES_EXPLICITLY)
-
       Base::coeffRef(0,0) = (lhs.transpose().cwiseProduct(rhs)).sum();
     }
 
@@ -264,8 +261,6 @@ class GeneralProduct<Lhs, Rhs, OuterProduct>
 
     GeneralProduct(const Lhs& lhs, const Rhs& rhs) : Base(lhs,rhs)
     {
-      EIGEN_STATIC_ASSERT((internal::is_same<typename Lhs::RealScalar, typename Rhs::RealScalar>::value),
-        YOU_MIXED_DIFFERENT_NUMERIC_TYPES__YOU_NEED_TO_USE_THE_CAST_METHOD_OF_MATRIXBASE_TO_CAST_NUMERIC_TYPES_EXPLICITLY)
     }
 
     struct set  { template<typename Dst, typename Src> void operator()(const Dst& dst, const Src& src) const { dst.const_cast_derived()  = src; } };

inst/include/Eigen/src/Core/MathFunctions.h

@@ -218,8 +218,8 @@ struct conj_retval
 * Implementation of abs2                                                 *
 ****************************************************************************/
 
-template<typename Scalar>
-struct abs2_impl
+template<typename Scalar,bool IsComplex>
+struct abs2_impl_default
 {
   typedef typename NumTraits<Scalar>::Real RealScalar;
   static inline RealScalar run(const Scalar& x)
@@ -228,15 +228,26 @@ struct abs2_impl
   }
 };
 
-template<typename RealScalar>
-struct abs2_impl<std::complex<RealScalar> >
+template<typename Scalar>
+struct abs2_impl_default<Scalar, true> // IsComplex
 {
-  static inline RealScalar run(const std::complex<RealScalar>& x)
+  typedef typename NumTraits<Scalar>::Real RealScalar;
+  static inline RealScalar run(const Scalar& x)
   {
     return real(x)*real(x) + imag(x)*imag(x);
   }
 };
 
+template<typename Scalar>
+struct abs2_impl
+{
+  typedef typename NumTraits<Scalar>::Real RealScalar;
+  static inline RealScalar run(const Scalar& x)
+  {
+    return abs2_impl_default<Scalar,NumTraits<Scalar>::IsComplex>::run(x);
+  }
+};
+
 template<typename Scalar>
 struct abs2_retval
 {

inst/include/Eigen/src/Core/PermutationMatrix.h

@@ -584,10 +584,11 @@ struct permut_matrix_product_retval
       const Index n = Side==OnTheLeft ? rows() : cols();
       // FIXME we need an is_same for expression that is not sensitive to constness. For instance
       // is_same_xpr<Block<const Matrix>, Block<Matrix> >::value should be true.
+      const typename Dest::Scalar *dst_data = internal::extract_data(dst);
       if(    is_same<MatrixTypeNestedCleaned,Dest>::value
           && blas_traits<MatrixTypeNestedCleaned>::HasUsableDirectAccess
           && blas_traits<Dest>::HasUsableDirectAccess
-          && extract_data(dst) == extract_data(m_matrix))
+          && dst_data!=0 && dst_data == extract_data(m_matrix))
       {
         // apply the permutation inplace
         Matrix<bool,PermutationType::RowsAtCompileTime,1,0,PermutationType::MaxRowsAtCompileTime> mask(m_permutation.size());

inst/include/Eigen/src/Core/PlainObjectBase.h

@@ -315,8 +315,8 @@ class PlainObjectBase : public internal::dense_xpr_base<Derived>::type
     EIGEN_STRONG_INLINE void resizeLike(const EigenBase<OtherDerived>& _other)
     {
       const OtherDerived& other = _other.derived();
-      internal::check_rows_cols_for_overflow<MaxSizeAtCompileTime>::run(other.rows(), other.cols());
-      const Index othersize = other.rows()*other.cols();
+      internal::check_rows_cols_for_overflow<MaxSizeAtCompileTime>::run(Index(other.rows()), Index(other.cols()));
+      const Index othersize = Index(other.rows())*Index(other.cols());
       if(RowsAtCompileTime == 1)
       {
         eigen_assert(other.rows() == 1 || other.cols() == 1);
@@ -487,7 +487,7 @@ class PlainObjectBase : public internal::dense_xpr_base<Derived>::type
     /** \sa MatrixBase::operator=(const EigenBase<OtherDerived>&) */
     template<typename OtherDerived>
     EIGEN_STRONG_INLINE PlainObjectBase(const EigenBase<OtherDerived> &other)
-      : m_storage(other.derived().rows() * other.derived().cols(), other.derived().rows(), other.derived().cols())
+      : m_storage(Index(other.derived().rows()) * Index(other.derived().cols()), other.derived().rows(), other.derived().cols())
     {
       _check_template_params();
       internal::check_rows_cols_for_overflow<MaxSizeAtCompileTime>::run(other.derived().rows(), other.derived().cols());

inst/include/Eigen/src/Core/SolveTriangular.h

@@ -243,7 +243,8 @@ template<int Side, typename TriangularType, typename Rhs> struct triangular_solv
 
   template<typename Dest> inline void evalTo(Dest& dst) const
   {
-    if(!(is_same<RhsNestedCleaned,Dest>::value && extract_data(dst) == extract_data(m_rhs)))
+    const typename Dest::Scalar *dst_data = internal::extract_data(dst);
+    if(!(is_same<RhsNestedCleaned,Dest>::value && dst_data!=0 && extract_data(dst) == extract_data(m_rhs)))
       dst = m_rhs;
     m_triangularMatrix.template solveInPlace<Side>(dst);
   }

inst/include/Eigen/src/Core/Transpose.h

@@ -331,11 +331,11 @@ inline void MatrixBase<Derived>::adjointInPlace()
 
 namespace internal {
 
-template<typename BinOp,typename NestedXpr,typename Rhs>
-struct blas_traits<SelfCwiseBinaryOp<BinOp,NestedXpr,Rhs> >
- : blas_traits<NestedXpr>
+template<typename BinOp,typename Xpr,typename Rhs>
+struct blas_traits<SelfCwiseBinaryOp<BinOp,Xpr,Rhs> >
+ : blas_traits<typename internal::remove_all<typename Xpr::Nested>::type>
 {
-  typedef SelfCwiseBinaryOp<BinOp,NestedXpr,Rhs> XprType;
+  typedef SelfCwiseBinaryOp<BinOp,Xpr,Rhs> XprType;
   static inline const XprType extract(const XprType& x) { return x; }
 };
 
@@ -392,7 +392,6 @@ struct checkTransposeAliasing_impl
                       ::run(extract_data(dst), other))
           && "aliasing detected during transposition, use transposeInPlace() "
              "or evaluate the rhs into a temporary using .eval()");
-
     }
 };
 

inst/include/Eigen/src/Core/Transpositions.h

@@ -376,7 +376,8 @@ struct transposition_matrix_product_retval
       const int size = m_transpositions.size();
       Index j = 0;
 
-      if(!(is_same<MatrixTypeNestedCleaned,Dest>::value && extract_data(dst) == extract_data(m_matrix)))
+      const typename Dest::Scalar *dst_data = internal::extract_data(dst);
+      if(!(is_same<MatrixTypeNestedCleaned,Dest>::value && dst_data!=0 && dst_data == extract_data(m_matrix)))
         dst = m_matrix;
 
       for(int k=(Transposed?size-1:0) ; Transposed?k>=0:k<size ; Transposed?--k:++k)

inst/include/Eigen/src/Core/products/TriangularSolverMatrix.h

@@ -81,7 +81,7 @@ EIGEN_DONT_INLINE void triangular_solve_matrix<Scalar,Index,OnTheLeft,Mode,Conju
     // coherence when accessing the rhs elements
     std::ptrdiff_t l1, l2;
     manage_caching_sizes(GetAction, &l1, &l2);
-    Index subcols = cols>0 ? l2/(4 * sizeof(Scalar) * otherStride) : 0;
+    Index subcols = cols>0 ? l2/(4 * sizeof(Scalar) *  std::max<Index>(otherStride,size)) : 0;
     subcols = std::max<Index>((subcols/Traits::nr)*Traits::nr, Traits::nr);
 
     for(Index k2=IsLower ? 0 : size;