Sun Jun 12 02:22:34 CEST 2011

Author: dmbates
Date: 2011-06-12 02:22:33 +0200 (Sun, 12 Jun 2011)
New Revision: 3053

Added:
   pkg/RcppEigen/
   pkg/RcppEigen/DESCRIPTION
   pkg/RcppEigen/NAMESPACE
   pkg/RcppEigen/R/
   pkg/RcppEigen/R/fastLm.R
   pkg/RcppEigen/R/zzz.R
   pkg/RcppEigen/inst/
   pkg/RcppEigen/inst/include/
   pkg/RcppEigen/inst/include/Eigen/
   pkg/RcppEigen/inst/include/Eigen/Array
   pkg/RcppEigen/inst/include/Eigen/CMakeLists.txt
   pkg/RcppEigen/inst/include/Eigen/Cholesky
   pkg/RcppEigen/inst/include/Eigen/Core
   pkg/RcppEigen/inst/include/Eigen/Dense
   pkg/RcppEigen/inst/include/Eigen/Eigen
   pkg/RcppEigen/inst/include/Eigen/Eigen2Support
   pkg/RcppEigen/inst/include/Eigen/Eigenvalues
   pkg/RcppEigen/inst/include/Eigen/Geometry
   pkg/RcppEigen/inst/include/Eigen/Householder
   pkg/RcppEigen/inst/include/Eigen/Jacobi
   pkg/RcppEigen/inst/include/Eigen/LU
   pkg/RcppEigen/inst/include/Eigen/LeastSquares
   pkg/RcppEigen/inst/include/Eigen/QR
   pkg/RcppEigen/inst/include/Eigen/QtAlignedMalloc
   pkg/RcppEigen/inst/include/Eigen/SVD
   pkg/RcppEigen/inst/include/Eigen/Sparse
   pkg/RcppEigen/inst/include/Eigen/StdDeque
   pkg/RcppEigen/inst/include/Eigen/StdList
   pkg/RcppEigen/inst/include/Eigen/StdVector
   pkg/RcppEigen/inst/include/Eigen/src/
   pkg/RcppEigen/inst/include/Eigen/src/CMakeLists.txt
   pkg/RcppEigen/inst/include/Eigen/src/Cholesky/
   pkg/RcppEigen/inst/include/Eigen/src/Cholesky/CMakeLists.txt
   pkg/RcppEigen/inst/include/Eigen/src/Cholesky/LDLT.h
   pkg/RcppEigen/inst/include/Eigen/src/Cholesky/LLT.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/
   pkg/RcppEigen/inst/include/Eigen/src/Core/Array.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/ArrayBase.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/ArrayWrapper.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/Assign.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/BandMatrix.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/Block.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/BooleanRedux.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/CMakeLists.txt
   pkg/RcppEigen/inst/include/Eigen/src/Core/CommaInitializer.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/CwiseBinaryOp.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/CwiseNullaryOp.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/CwiseUnaryOp.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/CwiseUnaryView.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/DenseBase.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/DenseCoeffsBase.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/DenseStorage.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/Diagonal.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/DiagonalMatrix.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/DiagonalProduct.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/Dot.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/EigenBase.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/Flagged.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/ForceAlignedAccess.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/Functors.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/Fuzzy.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/GenericPacketMath.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/GlobalFunctions.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/IO.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/Map.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/MapBase.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/MathFunctions.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/Matrix.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/MatrixBase.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/NestByValue.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/NoAlias.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/NumTraits.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/PermutationMatrix.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/PlainObjectBase.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/Product.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/ProductBase.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/Random.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/Redux.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/Replicate.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/ReturnByValue.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/Reverse.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/Select.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/SelfAdjointView.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/SelfCwiseBinaryOp.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/SolveTriangular.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/StableNorm.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/Stride.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/Swap.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/Transpose.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/Transpositions.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/TriangularMatrix.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/VectorBlock.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/VectorwiseOp.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/Visitor.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/arch/
   pkg/RcppEigen/inst/include/Eigen/src/Core/arch/AltiVec/
   pkg/RcppEigen/inst/include/Eigen/src/Core/arch/AltiVec/CMakeLists.txt
   pkg/RcppEigen/inst/include/Eigen/src/Core/arch/AltiVec/Complex.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/arch/AltiVec/PacketMath.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/arch/CMakeLists.txt
   pkg/RcppEigen/inst/include/Eigen/src/Core/arch/Default/
   pkg/RcppEigen/inst/include/Eigen/src/Core/arch/Default/CMakeLists.txt
   pkg/RcppEigen/inst/include/Eigen/src/Core/arch/Default/Settings.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/arch/NEON/
   pkg/RcppEigen/inst/include/Eigen/src/Core/arch/NEON/CMakeLists.txt
   pkg/RcppEigen/inst/include/Eigen/src/Core/arch/NEON/Complex.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/arch/NEON/PacketMath.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/arch/SSE/
   pkg/RcppEigen/inst/include/Eigen/src/Core/arch/SSE/CMakeLists.txt
   pkg/RcppEigen/inst/include/Eigen/src/Core/arch/SSE/Complex.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/arch/SSE/MathFunctions.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/arch/SSE/PacketMath.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/products/
   pkg/RcppEigen/inst/include/Eigen/src/Core/products/CMakeLists.txt
   pkg/RcppEigen/inst/include/Eigen/src/Core/products/CoeffBasedProduct.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/products/GeneralBlockPanelKernel.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/products/GeneralMatrixMatrix.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/products/GeneralMatrixMatrixTriangular.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/products/GeneralMatrixVector.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/products/Parallelizer.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/products/SelfadjointMatrixMatrix.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/products/SelfadjointMatrixVector.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/products/SelfadjointProduct.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/products/SelfadjointRank2Update.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/products/TriangularMatrixMatrix.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/products/TriangularMatrixVector.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/products/TriangularSolverMatrix.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/products/TriangularSolverVector.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/util/
   pkg/RcppEigen/inst/include/Eigen/src/Core/util/BlasUtil.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/util/CMakeLists.txt
   pkg/RcppEigen/inst/include/Eigen/src/Core/util/Constants.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/util/DisableStupidWarnings.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/util/ForwardDeclarations.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/util/Macros.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/util/Memory.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/util/Meta.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/util/StaticAssert.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/util/XprHelper.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigen2Support/
   pkg/RcppEigen/inst/include/Eigen/src/Eigen2Support/Block.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigen2Support/CMakeLists.txt
   pkg/RcppEigen/inst/include/Eigen/src/Eigen2Support/Cwise.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigen2Support/CwiseOperators.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigen2Support/Geometry/
   pkg/RcppEigen/inst/include/Eigen/src/Eigen2Support/Geometry/AlignedBox.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigen2Support/Geometry/All.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigen2Support/Geometry/AngleAxis.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigen2Support/Geometry/CMakeLists.txt
   pkg/RcppEigen/inst/include/Eigen/src/Eigen2Support/Geometry/Hyperplane.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigen2Support/Geometry/ParametrizedLine.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigen2Support/Geometry/Quaternion.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigen2Support/Geometry/Rotation2D.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigen2Support/Geometry/RotationBase.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigen2Support/Geometry/Scaling.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigen2Support/Geometry/Transform.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigen2Support/Geometry/Translation.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigen2Support/LU.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigen2Support/Lazy.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigen2Support/LeastSquares.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigen2Support/Macros.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigen2Support/MathFunctions.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigen2Support/Memory.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigen2Support/Meta.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigen2Support/Minor.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigen2Support/QR.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigen2Support/SVD.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigen2Support/TriangularSolver.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigen2Support/VectorBlock.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigenvalues/
   pkg/RcppEigen/inst/include/Eigen/src/Eigenvalues/CMakeLists.txt
   pkg/RcppEigen/inst/include/Eigen/src/Eigenvalues/ComplexEigenSolver.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigenvalues/ComplexSchur.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigenvalues/EigenSolver.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigenvalues/EigenvaluesCommon.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigenvalues/HessenbergDecomposition.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigenvalues/RealSchur.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigenvalues/Tridiagonalization.h
   pkg/RcppEigen/inst/include/Eigen/src/Geometry/
   pkg/RcppEigen/inst/include/Eigen/src/Geometry/AlignedBox.h
   pkg/RcppEigen/inst/include/Eigen/src/Geometry/AngleAxis.h
   pkg/RcppEigen/inst/include/Eigen/src/Geometry/CMakeLists.txt
   pkg/RcppEigen/inst/include/Eigen/src/Geometry/EulerAngles.h
   pkg/RcppEigen/inst/include/Eigen/src/Geometry/Homogeneous.h
   pkg/RcppEigen/inst/include/Eigen/src/Geometry/Hyperplane.h
   pkg/RcppEigen/inst/include/Eigen/src/Geometry/OrthoMethods.h
   pkg/RcppEigen/inst/include/Eigen/src/Geometry/ParametrizedLine.h
   pkg/RcppEigen/inst/include/Eigen/src/Geometry/Quaternion.h
   pkg/RcppEigen/inst/include/Eigen/src/Geometry/Rotation2D.h
   pkg/RcppEigen/inst/include/Eigen/src/Geometry/RotationBase.h
   pkg/RcppEigen/inst/include/Eigen/src/Geometry/Scaling.h
   pkg/RcppEigen/inst/include/Eigen/src/Geometry/Transform.h
   pkg/RcppEigen/inst/include/Eigen/src/Geometry/Translation.h
   pkg/RcppEigen/inst/include/Eigen/src/Geometry/Umeyama.h
   pkg/RcppEigen/inst/include/Eigen/src/Geometry/arch/
   pkg/RcppEigen/inst/include/Eigen/src/Geometry/arch/CMakeLists.txt
   pkg/RcppEigen/inst/include/Eigen/src/Geometry/arch/Geometry_SSE.h
   pkg/RcppEigen/inst/include/Eigen/src/Householder/
   pkg/RcppEigen/inst/include/Eigen/src/Householder/BlockHouseholder.h
   pkg/RcppEigen/inst/include/Eigen/src/Householder/CMakeLists.txt
   pkg/RcppEigen/inst/include/Eigen/src/Householder/Householder.h
   pkg/RcppEigen/inst/include/Eigen/src/Householder/HouseholderSequence.h
   pkg/RcppEigen/inst/include/Eigen/src/Jacobi/
   pkg/RcppEigen/inst/include/Eigen/src/Jacobi/CMakeLists.txt
   pkg/RcppEigen/inst/include/Eigen/src/Jacobi/Jacobi.h
   pkg/RcppEigen/inst/include/Eigen/src/LU/
   pkg/RcppEigen/inst/include/Eigen/src/LU/CMakeLists.txt
   pkg/RcppEigen/inst/include/Eigen/src/LU/Determinant.h
   pkg/RcppEigen/inst/include/Eigen/src/LU/FullPivLU.h
   pkg/RcppEigen/inst/include/Eigen/src/LU/Inverse.h
   pkg/RcppEigen/inst/include/Eigen/src/LU/PartialPivLU.h
   pkg/RcppEigen/inst/include/Eigen/src/LU/arch/
   pkg/RcppEigen/inst/include/Eigen/src/LU/arch/CMakeLists.txt
   pkg/RcppEigen/inst/include/Eigen/src/LU/arch/Inverse_SSE.h
   pkg/RcppEigen/inst/include/Eigen/src/QR/
   pkg/RcppEigen/inst/include/Eigen/src/QR/CMakeLists.txt
   pkg/RcppEigen/inst/include/Eigen/src/QR/ColPivHouseholderQR.h
   pkg/RcppEigen/inst/include/Eigen/src/QR/FullPivHouseholderQR.h
   pkg/RcppEigen/inst/include/Eigen/src/QR/HouseholderQR.h
   pkg/RcppEigen/inst/include/Eigen/src/SVD/
   pkg/RcppEigen/inst/include/Eigen/src/SVD/CMakeLists.txt
   pkg/RcppEigen/inst/include/Eigen/src/SVD/JacobiSVD.h
   pkg/RcppEigen/inst/include/Eigen/src/SVD/UpperBidiagonalization.h
   pkg/RcppEigen/inst/include/Eigen/src/Sparse/
   pkg/RcppEigen/inst/include/Eigen/src/Sparse/AmbiVector.h
   pkg/RcppEigen/inst/include/Eigen/src/Sparse/CMakeLists.txt
   pkg/RcppEigen/inst/include/Eigen/src/Sparse/CompressedStorage.h
   pkg/RcppEigen/inst/include/Eigen/src/Sparse/CoreIterators.h
   pkg/RcppEigen/inst/include/Eigen/src/Sparse/DynamicSparseMatrix.h
   pkg/RcppEigen/inst/include/Eigen/src/Sparse/MappedSparseMatrix.h
   pkg/RcppEigen/inst/include/Eigen/src/Sparse/SparseAssign.h
   pkg/RcppEigen/inst/include/Eigen/src/Sparse/SparseBlock.h
   pkg/RcppEigen/inst/include/Eigen/src/Sparse/SparseCwiseBinaryOp.h
   pkg/RcppEigen/inst/include/Eigen/src/Sparse/SparseCwiseUnaryOp.h
   pkg/RcppEigen/inst/include/Eigen/src/Sparse/SparseDenseProduct.h
   pkg/RcppEigen/inst/include/Eigen/src/Sparse/SparseDiagonalProduct.h
   pkg/RcppEigen/inst/include/Eigen/src/Sparse/SparseDot.h
   pkg/RcppEigen/inst/include/Eigen/src/Sparse/SparseFuzzy.h
   pkg/RcppEigen/inst/include/Eigen/src/Sparse/SparseMatrix.h
   pkg/RcppEigen/inst/include/Eigen/src/Sparse/SparseMatrixBase.h
   pkg/RcppEigen/inst/include/Eigen/src/Sparse/SparseProduct.h
   pkg/RcppEigen/inst/include/Eigen/src/Sparse/SparseRedux.h
   pkg/RcppEigen/inst/include/Eigen/src/Sparse/SparseSelfAdjointView.h
   pkg/RcppEigen/inst/include/Eigen/src/Sparse/SparseSparseProduct.h
   pkg/RcppEigen/inst/include/Eigen/src/Sparse/SparseTranspose.h
   pkg/RcppEigen/inst/include/Eigen/src/Sparse/SparseTriangularView.h
   pkg/RcppEigen/inst/include/Eigen/src/Sparse/SparseUtil.h
   pkg/RcppEigen/inst/include/Eigen/src/Sparse/SparseVector.h
   pkg/RcppEigen/inst/include/Eigen/src/Sparse/SparseView.h
   pkg/RcppEigen/inst/include/Eigen/src/Sparse/TriangularSolver.h
   pkg/RcppEigen/inst/include/Eigen/src/StlSupport/
   pkg/RcppEigen/inst/include/Eigen/src/StlSupport/CMakeLists.txt
   pkg/RcppEigen/inst/include/Eigen/src/StlSupport/StdDeque.h
   pkg/RcppEigen/inst/include/Eigen/src/StlSupport/StdList.h
   pkg/RcppEigen/inst/include/Eigen/src/StlSupport/StdVector.h
   pkg/RcppEigen/inst/include/Eigen/src/StlSupport/details.h
   pkg/RcppEigen/inst/include/Eigen/src/misc/
   pkg/RcppEigen/inst/include/Eigen/src/misc/CMakeLists.txt
   pkg/RcppEigen/inst/include/Eigen/src/misc/Image.h
   pkg/RcppEigen/inst/include/Eigen/src/misc/Kernel.h
   pkg/RcppEigen/inst/include/Eigen/src/misc/Solve.h
   pkg/RcppEigen/inst/include/Eigen/src/plugins/
   pkg/RcppEigen/inst/include/Eigen/src/plugins/ArrayCwiseBinaryOps.h
   pkg/RcppEigen/inst/include/Eigen/src/plugins/ArrayCwiseUnaryOps.h
   pkg/RcppEigen/inst/include/Eigen/src/plugins/BlockMethods.h
   pkg/RcppEigen/inst/include/Eigen/src/plugins/CMakeLists.txt
   pkg/RcppEigen/inst/include/Eigen/src/plugins/CommonCwiseBinaryOps.h
   pkg/RcppEigen/inst/include/Eigen/src/plugins/CommonCwiseUnaryOps.h
   pkg/RcppEigen/inst/include/Eigen/src/plugins/MatrixCwiseBinaryOps.h
   pkg/RcppEigen/inst/include/Eigen/src/plugins/MatrixCwiseUnaryOps.h
   pkg/RcppEigen/inst/include/RcppEigen.h
   pkg/RcppEigen/inst/include/RcppEigenConfig.h
   pkg/RcppEigen/inst/include/RcppEigenForward.h
   pkg/RcppEigen/inst/include/RcppEigenWrap.h
   pkg/RcppEigen/man/
   pkg/RcppEigen/man/RcppEigen-package.Rd
   pkg/RcppEigen/man/fastLm.Rd
   pkg/RcppEigen/src/
   pkg/RcppEigen/src/Makevars
   pkg/RcppEigen/src/Makevars.win
   pkg/RcppEigen/src/RcppEigen.cpp
   pkg/RcppEigen/src/fastLm.cpp
Log:


Added: pkg/RcppEigen/DESCRIPTION
===================================================================

--- pkg/RcppEigen/DESCRIPTION	                        (rev 0)
+++ pkg/RcppEigen/DESCRIPTION	2011-06-12 00:22:33 UTC (rev 3053)
@@ -0,0 +1,32 @@
+Package: RcppEigen
+Type: Package
+Title: Rcpp integration for the Eigen templated linear algebra library.
+Version: 0.1.0
+Date: 2011-06-13
+Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
+Maintainer: Romain Francois, Dirk Eddelbuettel and Doug Bates <RcppArmadillo-authors at r-enthusiasts.com>
+Description: R and Eigen integration using Rcpp
+ Eigen is a C++ linear template library for linear algebra: matrices,
+ vectors, numerical solvers and related algorithms.  It supports dense
+ and sparse matrices on integer, floating point and complex numbers.
+ The performance on many algorithms is comparable with some of the
+ best implementations based on Lapack and level-3 BLAS.
+ .
+ This library is useful if C++ has been decided as the language of
+ choice for linear algebra (due to speed and/or integration
+ capabilities), rather than another language.
+ .
+ The RcppEigen package includes the header files from the Eigen C++
+ template library (currently version 3.0.1). Thus users do not need to
+ install Eigen itself in order to use RcppEigen.
+ .
+ Eigen is licensed under the GNU LGPL version 3 or later, and also
+ under the GNU GPL version 2 or later.  RcppEigen (the Rcpp
+ bindings/bridge to Eigen) is licensed under the GNU GPL version 2 or
+ later, as is the rest of Rcpp.
+License: GPL (>= 2)
+Depends: Rcpp (>= 0.9.4.2), methods
+LazyLoad: yes
+LinkingTo: Rcpp
+Suggests: inline, RUnit
+URL: http://eigen.tuxfamily.org

Added: pkg/RcppEigen/NAMESPACE
===================================================================
--- pkg/RcppEigen/NAMESPACE	                        (rev 0)
+++ pkg/RcppEigen/NAMESPACE	2011-06-12 00:22:33 UTC (rev 3053)
@@ -0,0 +1,14 @@
+useDynLib(RcppEigen)
+import(Rcpp)
+
+#exportPattern("^[[:alpha:]]+")
+export(fastLm,
+       fastLmPure
+       )
+
+S3method(fastLm, default)
+S3method(fastLm, formula)
+S3method(predict, fastLm)
+S3method(print, fastLm)
+S3method(summary, fastLm)
+S3method(print, summary.fastLm)

Added: pkg/RcppEigen/R/fastLm.R
===================================================================
--- pkg/RcppEigen/R/fastLm.R	                        (rev 0)
+++ pkg/RcppEigen/R/fastLm.R	2011-06-12 00:22:33 UTC (rev 3053)
@@ -0,0 +1,118 @@
+## fastLm.R: Rcpp/Eigen implementation of lm()
+##
+## Copyright (C)  2011 Dirk Eddelbuettel, Romain Francois and Douglas Bates
+##
+## This file is part of RcppEigen.
+##
+## RcppEigen is free software: you can redistribute it and/or modify it
+## under the terms of the GNU General Public License as published by
+## the Free Software Foundation, either version 2 of the License, or
+## (at your option) any later version.
+##
+## RcppEigen is distributed in the hope that it will be useful, but
+## WITHOUT ANY WARRANTY; without even the implied warranty of
+## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+## GNU General Public License for more details.
+##
+## You should have received a copy of the GNU General Public License
+## along with RcppEigen.  If not, see <http://www.gnu.org/licenses/>.
+
+fastLmPure <- function(y, X) {
+
+    stopifnot(is.matrix(X), is.numeric(y), NROW(y)==nrow(X))
+
+    .Call("fastLm", y, X, package="RcppEigen")
+}
+
+fastLm <- function(X, ...) UseMethod("fastLm")
+
+fastLm.default <- function(X, y, ...) {
+
+    X <- as.matrix(X)
+    y <- as.numeric(y)
+
+    res <- fastLmPure(y, X)
+    res$call <- match.call()
+
+    class(res) <- "fastLm"
+    res
+}
+
+print.fastLm <- function(x, ...) {
+    cat("\nCall:\n")
+    print(x$call)
+    cat("\nCoefficients:\n")
+    print(x$coefficients, digits=5)
+}
+
+summary.fastLm <- function(object, ...) {
+    se <- object$stderr
+    tval <- coef(object)/se
+
+    TAB <- cbind(Estimate = coef(object),
+                 StdErr = se,
+                 t.value = tval,
+                 p.value = 2*pt(-abs(tval), df=object$df))
+
+    # why do I need this here?
+    rownames(TAB) <- names(object$coefficients)
+    colnames(TAB) <- c("Estimate", "StdErr", "t.value", "p.value")
+
+    ## cf src/stats/R/lm.R and case with no weights and an intercept
+    f <- object$fitted.values
+    r <- object$residuals
+    mss <- sum((f - mean(f))^2)
+    rss <- sum(r^2)
+
+    r.squared <- mss/(mss + rss)
+    df.int <- 1 		# case of intercept
+    n <- length(f)
+    rdf <- object$df
+    adj.r.squared <- 1 - (1 - r.squared) * ((n - df.int)/rdf)
+
+    res <- list(call=object$call,
+                coefficients=TAB,
+                r.squared=r.squared,
+                adj.r.squared=adj.r.squared)
+
+    class(res) <- "summary.fastLm"
+    res
+}
+
+print.summary.fastLm <- function(x, ...) {
+    cat("\nCall:\n")
+    print(x$call)
+    cat("\n")
+
+    printCoefmat(x$coefficients, P.values=TRUE, has.Pvalue=TRUE)
+    digits <- max(3, getOption("digits") - 3)
+    cat("Multiple R-squared: ", formatC(x$r.squared, digits=digits),
+        ",\tAdjusted R-squared: ",formatC(x$adj.r.squared, digits=digits),
+        "\n", sep="")
+    invisible(x)
+}
+
+fastLm.formula <- function(formula, data=list(), ...) {
+    mf <- model.frame(formula=formula, data=data)
+    x <- model.matrix(attr(mf, "terms"), data=mf)
+    y <- model.response(mf)
+
+    res <- fastLm.default(x, y, ...)
+    res$call <- match.call()
+    res$formula <- formula
+    res
+}
+
+predict.fastLm <- function(object, newdata=NULL, ...) {
+    if (is.null(newdata)) {
+        y <- fitted(object)
+    } else {
+        if (!is.null(object$formula)) {
+            x <- model.matrix(object$formula, newdata)
+        } else {
+            x <- newdata
+        }
+        y <- as.vector(x %*% coef(object))
+    }
+    y
+}

Added: pkg/RcppEigen/R/zzz.R
===================================================================
--- pkg/RcppEigen/R/zzz.R	                        (rev 0)
+++ pkg/RcppEigen/R/zzz.R	2011-06-12 00:22:33 UTC (rev 3053)
@@ -0,0 +1,4 @@
+## .onLoad <- function(libname, pkgname) {
+##     require(methods, quietly=TRUE)
+##     loadRcppModules()
+## }

Added: pkg/RcppEigen/inst/include/Eigen/Array
===================================================================
--- pkg/RcppEigen/inst/include/Eigen/Array	                        (rev 0)
+++ pkg/RcppEigen/inst/include/Eigen/Array	2011-06-12 00:22:33 UTC (rev 3053)
@@ -0,0 +1,11 @@
+#ifndef EIGEN_ARRAY_MODULE_H
+#define EIGEN_ARRAY_MODULE_H
+
+// include Core first to handle Eigen2 support macros
+#include "Core"
+
+#ifndef EIGEN2_SUPPORT
+  #error The Eigen/Array header does no longer exist in Eigen3. All that functionality has moved to Eigen/Core.
+#endif
+
+#endif // EIGEN_ARRAY_MODULE_H

Added: pkg/RcppEigen/inst/include/Eigen/CMakeLists.txt
===================================================================
--- pkg/RcppEigen/inst/include/Eigen/CMakeLists.txt	                        (rev 0)
+++ pkg/RcppEigen/inst/include/Eigen/CMakeLists.txt	2011-06-12 00:22:33 UTC (rev 3053)
@@ -0,0 +1,19 @@
+include(RegexUtils)
+test_escape_string_as_regex()
+
+file(GLOB Eigen_directory_files "*")
+
+escape_string_as_regex(ESCAPED_CMAKE_CURRENT_SOURCE_DIR "${CMAKE_CURRENT_SOURCE_DIR}")
+
+foreach(f ${Eigen_directory_files})
+  if(NOT f MATCHES "\\.txt" AND NOT f MATCHES "${ESCAPED_CMAKE_CURRENT_SOURCE_DIR}/[.].+" AND NOT f MATCHES "${ESCAPED_CMAKE_CURRENT_SOURCE_DIR}/src")
+    list(APPEND Eigen_directory_files_to_install ${f})
+  endif()
+endforeach(f ${Eigen_directory_files})
+
+install(FILES
+  ${Eigen_directory_files_to_install}
+  DESTINATION ${INCLUDE_INSTALL_DIR}/Eigen COMPONENT Devel
+  )
+
+add_subdirectory(src)

Added: pkg/RcppEigen/inst/include/Eigen/Cholesky
===================================================================
--- pkg/RcppEigen/inst/include/Eigen/Cholesky	                        (rev 0)
+++ pkg/RcppEigen/inst/include/Eigen/Cholesky	2011-06-12 00:22:33 UTC (rev 3053)
@@ -0,0 +1,33 @@
+#ifndef EIGEN_CHOLESKY_MODULE_H
+#define EIGEN_CHOLESKY_MODULE_H
+
+#include "Core"
+
+#include "src/Core/util/DisableStupidWarnings.h"
+
+namespace Eigen {
+
+/** \defgroup Cholesky_Module Cholesky module
+  *
+  *
+  *
+  * This module provides two variants of the Cholesky decomposition for selfadjoint (hermitian) matrices.
+  * Those decompositions are accessible via the following MatrixBase methods:
+  *  - MatrixBase::llt(),
+  *  - MatrixBase::ldlt()
+  *
+  * \code
+  * #include <Eigen/Cholesky>
+  * \endcode
+  */
+
+#include "src/misc/Solve.h"
+#include "src/Cholesky/LLT.h"
+#include "src/Cholesky/LDLT.h"
+
+} // namespace Eigen
+
+#include "src/Core/util/ReenableStupidWarnings.h"
+
+#endif // EIGEN_CHOLESKY_MODULE_H
+/* vim: set filetype=cpp et sw=2 ts=2 ai: */

Added: pkg/RcppEigen/inst/include/Eigen/Core
===================================================================
--- pkg/RcppEigen/inst/include/Eigen/Core	                        (rev 0)
+++ pkg/RcppEigen/inst/include/Eigen/Core	2011-06-12 00:22:33 UTC (rev 3053)
@@ -0,0 +1,367 @@
+// This file is part of Eigen, a lightweight C++ template library
+// for linear algebra.
+//
+// Copyright (C) 2008 Gael Guennebaud <gael.guennebaud at inria.fr>
+// Copyright (C) 2007-2011 Benoit Jacob <jacob.benoit.1 at gmail.com>
+//
+// Eigen is free software; you can redistribute it and/or
+// modify it under the terms of the GNU Lesser General Public
+// License as published by the Free Software Foundation; either
+// version 3 of the License, or (at your option) any later version.
+//
+// Alternatively, you can redistribute it and/or
+// modify it under the terms of the GNU General Public License as
+// published by the Free Software Foundation; either version 2 of
+// the License, or (at your option) any later version.
+//
+// Eigen is distributed in the hope that it will be useful, but WITHOUT ANY
+// WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License or the
+// GNU General Public License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public
+// License and a copy of the GNU General Public License along with
+// Eigen. If not, see <http://www.gnu.org/licenses/>.
+
+#ifndef EIGEN_CORE_H
+#define EIGEN_CORE_H
+
+// first thing Eigen does: stop the compiler from committing suicide
+#include "src/Core/util/DisableStupidWarnings.h"
+
+// then include this file where all our macros are defined. It's really important to do it first because
+// it's where we do all the alignment settings (platform detection and honoring the user's will if he
+// defined e.g. EIGEN_DONT_ALIGN) so it needs to be done before we do anything with vectorization.
+#include "src/Core/util/Macros.h"
+
+// if alignment is disabled, then disable vectorization. Note: EIGEN_ALIGN is the proper check, it takes into
+// account both the user's will (EIGEN_DONT_ALIGN) and our own platform checks
+#if !EIGEN_ALIGN
+  #ifndef EIGEN_DONT_VECTORIZE
+    #define EIGEN_DONT_VECTORIZE
+  #endif
+#endif
+
+#ifdef _MSC_VER
+  #include <malloc.h> // for _aligned_malloc -- need it regardless of whether vectorization is enabled
+  #if (_MSC_VER >= 1500) // 2008 or later
+    // Remember that usage of defined() in a #define is undefined by the standard.
+    // a user reported that in 64-bit mode, MSVC doesn't care to define _M_IX86_FP.
+    #if (defined(_M_IX86_FP) && (_M_IX86_FP >= 2)) || defined(_M_X64)
+      #define EIGEN_SSE2_ON_MSVC_2008_OR_LATER
+    #endif
+  #endif
+#else
+  // Remember that usage of defined() in a #define is undefined by the standard
+  #if (defined __SSE2__) && ( (!defined __GNUC__) || EIGEN_GNUC_AT_LEAST(4,2) )
+    #define EIGEN_SSE2_ON_NON_MSVC_BUT_NOT_OLD_GCC
+  #endif
+#endif
+
+#ifndef EIGEN_DONT_VECTORIZE
+
+  #if defined (EIGEN_SSE2_ON_NON_MSVC_BUT_NOT_OLD_GCC) || defined(EIGEN_SSE2_ON_MSVC_2008_OR_LATER)
+
+    // Defines symbols for compile-time detection of which instructions are
+    // used.
+    // EIGEN_VECTORIZE_YY is defined if and only if the instruction set YY is used
+    #define EIGEN_VECTORIZE
+    #define EIGEN_VECTORIZE_SSE
+    #define EIGEN_VECTORIZE_SSE2
+
+    // Detect sse3/ssse3/sse4:
+    // gcc and icc defines __SSE3__, ...
+    // there is no way to know about this on msvc. You can define EIGEN_VECTORIZE_SSE* if you
+    // want to force the use of those instructions with msvc.
+    #ifdef __SSE3__
+      #define EIGEN_VECTORIZE_SSE3
+    #endif
+    #ifdef __SSSE3__
+      #define EIGEN_VECTORIZE_SSSE3
+    #endif
+    #ifdef __SSE4_1__
+      #define EIGEN_VECTORIZE_SSE4_1
+    #endif
+    #ifdef __SSE4_2__
+      #define EIGEN_VECTORIZE_SSE4_2
+    #endif
+
+    // include files
+
+    // This extern "C" works around a MINGW-w64 compilation issue
+    // https://sourceforge.net/tracker/index.php?func=detail&aid=3018394&group_id=202880&atid=983354
+    // In essence, intrin.h is included by windows.h and also declares intrinsics (just as emmintrin.h etc. below do).
+    // However, intrin.h uses an extern "C" declaration, and g++ thus complains of duplicate declarations
+    // with conflicting linkage.  The linkage for intrinsics doesn't matter, but at that stage the compiler doesn't know;
+    // so, to avoid compile errors when windows.h is included after Eigen/Core, ensure intrinsics are extern "C" here too.
+    // notice that since these are C headers, the extern "C" is theoretically needed anyways.
+    extern "C" {
+      #include <emmintrin.h>
+      #include <xmmintrin.h>
+      #ifdef  EIGEN_VECTORIZE_SSE3
+      #include <pmmintrin.h>
+      #endif
+      #ifdef EIGEN_VECTORIZE_SSSE3
+      #include <tmmintrin.h>
+      #endif
+      #ifdef EIGEN_VECTORIZE_SSE4_1
+      #include <smmintrin.h>
+      #endif
+      #ifdef EIGEN_VECTORIZE_SSE4_2
+      #include <nmmintrin.h>
+      #endif
+    } // end extern "C"
+  #elif defined __ALTIVEC__
+    #define EIGEN_VECTORIZE
+    #define EIGEN_VECTORIZE_ALTIVEC
+    #include <altivec.h>
+    // We need to #undef all these ugly tokens defined in <altivec.h>
+    // => use __vector instead of vector
+    #undef bool
+    #undef vector
+    #undef pixel
+  #elif defined  __ARM_NEON__
+    #define EIGEN_VECTORIZE
+    #define EIGEN_VECTORIZE_NEON
+    #include <arm_neon.h>
+  #endif
+#endif
+
+#if (defined _OPENMP) && (!defined EIGEN_DONT_PARALLELIZE)
+  #define EIGEN_HAS_OPENMP
+#endif
+
+#ifdef EIGEN_HAS_OPENMP
+#include <omp.h>
+#endif
+
+// MSVC for windows mobile does not have the errno.h file
+#if !(defined(_MSC_VER) && defined(_WIN32_WCE))
+#define EIGEN_HAS_ERRNO
+#endif
+
+#ifdef EIGEN_HAS_ERRNO
+#include <cerrno>
+#endif
+#include <cstddef>
+#include <cstdlib>
+#include <cmath>
+#include <complex>
+#include <cassert>
+#include <functional>
+#include <iosfwd>
+#include <cstring>
+#include <string>
+#include <limits>
+#include <climits> // for CHAR_BIT
+// for min/max:
+#include <algorithm>
+
+// for outputting debug info
+#ifdef EIGEN_DEBUG_ASSIGN
+#include <iostream>
+#endif
+
+// required for __cpuid, needs to be included after cmath
+#if defined(_MSC_VER) && (defined(_M_IX86)||defined(_M_X64))
+  #include <intrin.h>
+#endif
+
+#if (defined(_CPPUNWIND) || defined(__EXCEPTIONS)) && !defined(EIGEN_NO_EXCEPTIONS)
+  #define EIGEN_EXCEPTIONS
+#endif
+
+#ifdef EIGEN_EXCEPTIONS
+  #include <new>
+#endif
+
+// this needs to be done after all possible windows C header includes and before any Eigen source includes
+// (system C++ includes are supposed to be able to deal with this already):
+// windows.h defines min and max macros which would make Eigen fail to compile.
+#if defined(min) || defined(max)
+#error The preprocessor symbols 'min' or 'max' are defined. If you are compiling on Windows, do #define NOMINMAX to prevent windows.h from defining these symbols.
+#endif
+
+// defined in bits/termios.h
+#undef B0
+
+/** \brief Namespace containing all symbols from the %Eigen library. */
+namespace Eigen {
+
+inline static const char *SimdInstructionSetsInUse(void) {
+#if defined(EIGEN_VECTORIZE_SSE4_2)
+  return "SSE, SSE2, SSE3, SSSE3, SSE4.1, SSE4.2";
+#elif defined(EIGEN_VECTORIZE_SSE4_1)
+  return "SSE, SSE2, SSE3, SSSE3, SSE4.1";
+#elif defined(EIGEN_VECTORIZE_SSSE3)
+  return "SSE, SSE2, SSE3, SSSE3";
+#elif defined(EIGEN_VECTORIZE_SSE3)
+  return "SSE, SSE2, SSE3";
+#elif defined(EIGEN_VECTORIZE_SSE2)
+  return "SSE, SSE2";
+#elif defined(EIGEN_VECTORIZE_ALTIVEC)
+  return "AltiVec";
+#elif defined(EIGEN_VECTORIZE_NEON)
+  return "ARM NEON";
+#else
+  return "None";
+#endif
+}
+
+#define STAGE10_FULL_EIGEN2_API             10
+#define STAGE20_RESOLVE_API_CONFLICTS       20
+#define STAGE30_FULL_EIGEN3_API             30
+#define STAGE40_FULL_EIGEN3_STRICTNESS      40
+#define STAGE99_NO_EIGEN2_SUPPORT           99
+
+#if   defined EIGEN2_SUPPORT_STAGE40_FULL_EIGEN3_STRICTNESS
+  #define EIGEN2_SUPPORT
+  #define EIGEN2_SUPPORT_STAGE STAGE40_FULL_EIGEN3_STRICTNESS
+#elif defined EIGEN2_SUPPORT_STAGE30_FULL_EIGEN3_API
+  #define EIGEN2_SUPPORT
+  #define EIGEN2_SUPPORT_STAGE STAGE30_FULL_EIGEN3_API
+#elif defined EIGEN2_SUPPORT_STAGE20_RESOLVE_API_CONFLICTS
+  #define EIGEN2_SUPPORT
+  #define EIGEN2_SUPPORT_STAGE STAGE20_RESOLVE_API_CONFLICTS
+#elif defined EIGEN2_SUPPORT_STAGE10_FULL_EIGEN2_API
+  #define EIGEN2_SUPPORT
+  #define EIGEN2_SUPPORT_STAGE STAGE10_FULL_EIGEN2_API
+#elif defined EIGEN2_SUPPORT
+  // default to stage 3, that's what it's always meant
+  #define EIGEN2_SUPPORT_STAGE30_FULL_EIGEN3_API
+  #define EIGEN2_SUPPORT_STAGE STAGE30_FULL_EIGEN3_API
+#else
+  #define EIGEN2_SUPPORT_STAGE STAGE99_NO_EIGEN2_SUPPORT
+#endif
+
+#ifdef EIGEN2_SUPPORT
+#undef minor
+#endif
+
+// we use size_t frequently and we'll never remember to prepend it with std:: everytime just to
+// ensure QNX/QCC support
+using std::size_t;
+// gcc 4.6.0 wants std:: for ptrdiff_t 
+using std::ptrdiff_t;
+
+/** \defgroup Core_Module Core module
+  * This is the main module of Eigen providing dense matrix and vector support
+  * (both fixed and dynamic size) with all the features corresponding to a BLAS library
+  * and much more...
+  *
+  * \code
+  * #include <Eigen/Core>
+  * \endcode
+  */
+
+#include "src/Core/util/Constants.h"
+#include "src/Core/util/ForwardDeclarations.h"
+#include "src/Core/util/Meta.h"
+#include "src/Core/util/XprHelper.h"
+#include "src/Core/util/StaticAssert.h"
+#include "src/Core/util/Memory.h"
+
+#include "src/Core/NumTraits.h"
+#include "src/Core/MathFunctions.h"
+#include "src/Core/GenericPacketMath.h"
+
+#if defined EIGEN_VECTORIZE_SSE
+  #include "src/Core/arch/SSE/PacketMath.h"
+  #include "src/Core/arch/SSE/MathFunctions.h"
+  #include "src/Core/arch/SSE/Complex.h"
+#elif defined EIGEN_VECTORIZE_ALTIVEC
+  #include "src/Core/arch/AltiVec/PacketMath.h"
+  #include "src/Core/arch/AltiVec/Complex.h"
+#elif defined EIGEN_VECTORIZE_NEON
+  #include "src/Core/arch/NEON/PacketMath.h"
+  #include "src/Core/arch/NEON/Complex.h"
+#endif
+
+#include "src/Core/arch/Default/Settings.h"
+
+#include "src/Core/Functors.h"
+#include "src/Core/DenseCoeffsBase.h"
+#include "src/Core/DenseBase.h"
+#include "src/Core/MatrixBase.h"
+#include "src/Core/EigenBase.h"
+
+#ifndef EIGEN_PARSED_BY_DOXYGEN // work around Doxygen bug triggered by Assign.h r814874
+                                // at least confirmed with Doxygen 1.5.5 and 1.5.6
+  #include "src/Core/Assign.h"
+#endif
+
+#include "src/Core/util/BlasUtil.h"
+#include "src/Core/DenseStorage.h"
+#include "src/Core/NestByValue.h"
+#include "src/Core/ForceAlignedAccess.h"
+#include "src/Core/ReturnByValue.h"
+#include "src/Core/NoAlias.h"
+#include "src/Core/PlainObjectBase.h"
+#include "src/Core/Matrix.h"
+#include "src/Core/Array.h"
+#include "src/Core/CwiseBinaryOp.h"
+#include "src/Core/CwiseUnaryOp.h"
+#include "src/Core/CwiseNullaryOp.h"
+#include "src/Core/CwiseUnaryView.h"
+#include "src/Core/SelfCwiseBinaryOp.h"
+#include "src/Core/Dot.h"
+#include "src/Core/StableNorm.h"
+#include "src/Core/MapBase.h"
+#include "src/Core/Stride.h"
+#include "src/Core/Map.h"
+#include "src/Core/Block.h"
+#include "src/Core/VectorBlock.h"
+#include "src/Core/Transpose.h"
+#include "src/Core/DiagonalMatrix.h"
+#include "src/Core/Diagonal.h"
+#include "src/Core/DiagonalProduct.h"
+#include "src/Core/PermutationMatrix.h"
+#include "src/Core/Transpositions.h"
+#include "src/Core/Redux.h"
+#include "src/Core/Visitor.h"
+#include "src/Core/Fuzzy.h"
+#include "src/Core/IO.h"
+#include "src/Core/Swap.h"
+#include "src/Core/CommaInitializer.h"
+#include "src/Core/Flagged.h"
+#include "src/Core/ProductBase.h"
+#include "src/Core/Product.h"
+#include "src/Core/TriangularMatrix.h"
+#include "src/Core/SelfAdjointView.h"
+#include "src/Core/SolveTriangular.h"
+#include "src/Core/products/Parallelizer.h"
+#include "src/Core/products/CoeffBasedProduct.h"
+#include "src/Core/products/GeneralBlockPanelKernel.h"
+#include "src/Core/products/GeneralMatrixVector.h"
+#include "src/Core/products/GeneralMatrixMatrix.h"
+#include "src/Core/products/GeneralMatrixMatrixTriangular.h"
+#include "src/Core/products/SelfadjointMatrixVector.h"
+#include "src/Core/products/SelfadjointMatrixMatrix.h"
+#include "src/Core/products/SelfadjointProduct.h"
+#include "src/Core/products/SelfadjointRank2Update.h"
+#include "src/Core/products/TriangularMatrixVector.h"
+#include "src/Core/products/TriangularMatrixMatrix.h"
+#include "src/Core/products/TriangularSolverMatrix.h"
+#include "src/Core/products/TriangularSolverVector.h"
+#include "src/Core/BandMatrix.h"
+
+#include "src/Core/BooleanRedux.h"
+#include "src/Core/Select.h"
+#include "src/Core/VectorwiseOp.h"
+#include "src/Core/Random.h"
+#include "src/Core/Replicate.h"
+#include "src/Core/Reverse.h"
+#include "src/Core/ArrayBase.h"
+#include "src/Core/ArrayWrapper.h"
+
+} // namespace Eigen
+
+#include "src/Core/GlobalFunctions.h"
+
+#include "src/Core/util/ReenableStupidWarnings.h"
+
+#ifdef EIGEN2_SUPPORT
+#include "Eigen2Support"
+#endif
+
+#endif // EIGEN_CORE_H

Added: pkg/RcppEigen/inst/include/Eigen/Dense
===================================================================
--- pkg/RcppEigen/inst/include/Eigen/Dense	                        (rev 0)
+++ pkg/RcppEigen/inst/include/Eigen/Dense	2011-06-12 00:22:33 UTC (rev 3053)
@@ -0,0 +1,7 @@
+#include "Core"
+#include "LU"
+#include "Cholesky"
+#include "QR"
+#include "SVD"
+#include "Geometry"
+#include "Eigenvalues"

Added: pkg/RcppEigen/inst/include/Eigen/Eigen
===================================================================
--- pkg/RcppEigen/inst/include/Eigen/Eigen	                        (rev 0)
+++ pkg/RcppEigen/inst/include/Eigen/Eigen	2011-06-12 00:22:33 UTC (rev 3053)
@@ -0,0 +1,2 @@
+#include "Dense"
+//#include "Sparse"

Added: pkg/RcppEigen/inst/include/Eigen/Eigen2Support
===================================================================
--- pkg/RcppEigen/inst/include/Eigen/Eigen2Support	                        (rev 0)
+++ pkg/RcppEigen/inst/include/Eigen/Eigen2Support	2011-06-12 00:22:33 UTC (rev 3053)
@@ -0,0 +1,82 @@
+// This file is part of Eigen, a lightweight C++ template library
+// for linear algebra.
+//
+// Copyright (C) 2009 Gael Guennebaud <gael.guennebaud at inria.fr>
+//
+// Eigen is free software; you can redistribute it and/or
+// modify it under the terms of the GNU Lesser General Public
+// License as published by the Free Software Foundation; either
+// version 3 of the License, or (at your option) any later version.
+//
+// Alternatively, you can redistribute it and/or
+// modify it under the terms of the GNU General Public License as
+// published by the Free Software Foundation; either version 2 of
+// the License, or (at your option) any later version.
+//
+// Eigen is distributed in the hope that it will be useful, but WITHOUT ANY
+// WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License or the
+// GNU General Public License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public
+// License and a copy of the GNU General Public License along with
+// Eigen. If not, see <http://www.gnu.org/licenses/>.
+
+#ifndef EIGEN2SUPPORT_H
+#define EIGEN2SUPPORT_H
+
+#if (!defined(EIGEN2_SUPPORT)) || (!defined(EIGEN_CORE_H))
+#error Eigen2 support must be enabled by defining EIGEN2_SUPPORT before including any Eigen header
+#endif
+
+#include "src/Core/util/DisableStupidWarnings.h"
+
+namespace Eigen {
+
+/** \defgroup Eigen2Support_Module Eigen2 support module
+  * This module provides a couple of deprecated functions improving the compatibility with Eigen2.
+  *
+  * To use it, define EIGEN2_SUPPORT before including any Eigen header
+  * \code
+  * #define EIGEN2_SUPPORT
+  * \endcode
+  *
+  */
+
+#include "src/Eigen2Support/Macros.h"
+#include "src/Eigen2Support/Memory.h"
+#include "src/Eigen2Support/Meta.h"
+#include "src/Eigen2Support/Lazy.h"
+#include "src/Eigen2Support/Cwise.h"
+#include "src/Eigen2Support/CwiseOperators.h"
+#include "src/Eigen2Support/TriangularSolver.h"
+#include "src/Eigen2Support/Block.h"
+#include "src/Eigen2Support/VectorBlock.h"
+#include "src/Eigen2Support/Minor.h"
+#include "src/Eigen2Support/MathFunctions.h"
+
+
+} // namespace Eigen
+
+#include "src/Core/util/ReenableStupidWarnings.h"
+
+// Eigen2 used to include iostream
+#include<iostream>
+
+#define USING_PART_OF_NAMESPACE_EIGEN \
+EIGEN_USING_MATRIX_TYPEDEFS \
+using Eigen::Matrix; \
+using Eigen::MatrixBase; \
+using Eigen::ei_random; \
+using Eigen::ei_real; \
+using Eigen::ei_imag; \
+using Eigen::ei_conj; \
+using Eigen::ei_abs; \
+using Eigen::ei_abs2; \
+using Eigen::ei_sqrt; \
+using Eigen::ei_exp; \
+using Eigen::ei_log; \
+using Eigen::ei_sin; \
+using Eigen::ei_cos;
+
+#endif // EIGEN2SUPPORT_H

Added: pkg/RcppEigen/inst/include/Eigen/Eigenvalues
===================================================================
--- pkg/RcppEigen/inst/include/Eigen/Eigenvalues	                        (rev 0)
+++ pkg/RcppEigen/inst/include/Eigen/Eigenvalues	2011-06-12 00:22:33 UTC (rev 3053)
@@ -0,0 +1,44 @@
+#ifndef EIGEN_EIGENVALUES_MODULE_H
+#define EIGEN_EIGENVALUES_MODULE_H
+
+#include "Core"
+
+#include "src/Core/util/DisableStupidWarnings.h"
+
+#include "Cholesky"
+#include "Jacobi"
+#include "Householder"
+#include "LU"
+
+namespace Eigen {
+
+/** \defgroup Eigenvalues_Module Eigenvalues module
+  *
+  *
+  *
+  * This module mainly provides various eigenvalue solvers.
+  * This module also provides some MatrixBase methods, including:
+  *  - MatrixBase::eigenvalues(),
+  *  - MatrixBase::operatorNorm()
+  *
+  * \code
+  * #include <Eigen/Eigenvalues>
+  * \endcode
+  */
+
+#include "src/Eigenvalues/Tridiagonalization.h"
+#include "src/Eigenvalues/RealSchur.h"
+#include "src/Eigenvalues/EigenSolver.h"
+#include "src/Eigenvalues/SelfAdjointEigenSolver.h"
+#include "src/Eigenvalues/GeneralizedSelfAdjointEigenSolver.h"
+#include "src/Eigenvalues/HessenbergDecomposition.h"
+#include "src/Eigenvalues/ComplexSchur.h"
+#include "src/Eigenvalues/ComplexEigenSolver.h"
+#include "src/Eigenvalues/MatrixBaseEigenvalues.h"
+
+} // namespace Eigen
+
+#include "src/Core/util/ReenableStupidWarnings.h"
+
+#endif // EIGEN_EIGENVALUES_MODULE_H
+/* vim: set filetype=cpp et sw=2 ts=2 ai: */

Added: pkg/RcppEigen/inst/include/Eigen/Geometry
===================================================================
--- pkg/RcppEigen/inst/include/Eigen/Geometry	                        (rev 0)
+++ pkg/RcppEigen/inst/include/Eigen/Geometry	2011-06-12 00:22:33 UTC (rev 3053)
@@ -0,0 +1,67 @@
+#ifndef EIGEN_GEOMETRY_MODULE_H
+#define EIGEN_GEOMETRY_MODULE_H
+
+#include "Core"
+
+#include "src/Core/util/DisableStupidWarnings.h"
+
+#include "SVD"
+#include "LU"
+#include <limits>
+
+#ifndef M_PI
+#define M_PI 3.14159265358979323846
+#endif
+
+namespace Eigen {
+
+/** \defgroup Geometry_Module Geometry module
+  *
+  *
+  *
+  * This module provides support for:
+  *  - fixed-size homogeneous transformations
+  *  - translation, scaling, 2D and 3D rotations
+  *  - quaternions
+  *  - \ref MatrixBase::cross() "cross product"
+  *  - \ref MatrixBase::unitOrthogonal() "orthognal vector generation"
+  *  - some linear components: parametrized-lines and hyperplanes
+  *
+  * \code
+  * #include <Eigen/Geometry>
+  * \endcode
+  */
+
+#include "src/Geometry/OrthoMethods.h"
+#include "src/Geometry/EulerAngles.h"
+
+#if EIGEN2_SUPPORT_STAGE > STAGE20_RESOLVE_API_CONFLICTS
+  #include "src/Geometry/Homogeneous.h"
+  #include "src/Geometry/RotationBase.h"
+  #include "src/Geometry/Rotation2D.h"
+  #include "src/Geometry/Quaternion.h"
+  #include "src/Geometry/AngleAxis.h"
+  #include "src/Geometry/Transform.h"
+  #include "src/Geometry/Translation.h"
+  #include "src/Geometry/Scaling.h"
+  #include "src/Geometry/Hyperplane.h"
+  #include "src/Geometry/ParametrizedLine.h"
+  #include "src/Geometry/AlignedBox.h"
+  #include "src/Geometry/Umeyama.h"
+
+  #if defined EIGEN_VECTORIZE_SSE
+    #include "src/Geometry/arch/Geometry_SSE.h"
+  #endif
+#endif
+
+#ifdef EIGEN2_SUPPORT
+#include "src/Eigen2Support/Geometry/All.h"
+#endif
+
+} // namespace Eigen
+
+#include "src/Core/util/ReenableStupidWarnings.h"
+
+#endif // EIGEN_GEOMETRY_MODULE_H
+/* vim: set filetype=cpp et sw=2 ts=2 ai: */
+

Added: pkg/RcppEigen/inst/include/Eigen/Householder
===================================================================
--- pkg/RcppEigen/inst/include/Eigen/Householder	                        (rev 0)
+++ pkg/RcppEigen/inst/include/Eigen/Householder	2011-06-12 00:22:33 UTC (rev 3053)
@@ -0,0 +1,27 @@
+#ifndef EIGEN_HOUSEHOLDER_MODULE_H
+#define EIGEN_HOUSEHOLDER_MODULE_H
+
+#include "Core"
+
+#include "src/Core/util/DisableStupidWarnings.h"
+
+namespace Eigen {
+
+/** \defgroup Householder_Module Householder module
+  * This module provides Householder transformations.
+  *
+  * \code
+  * #include <Eigen/Householder>
+  * \endcode
+  */
+
+#include "src/Householder/Householder.h"
+#include "src/Householder/HouseholderSequence.h"
+#include "src/Householder/BlockHouseholder.h"
+
+} // namespace Eigen
+
+#include "src/Core/util/ReenableStupidWarnings.h"
+
+#endif // EIGEN_HOUSEHOLDER_MODULE_H
+/* vim: set filetype=cpp et sw=2 ts=2 ai: */

Added: pkg/RcppEigen/inst/include/Eigen/Jacobi
===================================================================
--- pkg/RcppEigen/inst/include/Eigen/Jacobi	                        (rev 0)
+++ pkg/RcppEigen/inst/include/Eigen/Jacobi	2011-06-12 00:22:33 UTC (rev 3053)
@@ -0,0 +1,30 @@
+#ifndef EIGEN_JACOBI_MODULE_H
+#define EIGEN_JACOBI_MODULE_H
+
+#include "Core"
+
+#include "src/Core/util/DisableStupidWarnings.h"
+
+namespace Eigen {
+
+/** \defgroup Jacobi_Module Jacobi module
+  * This module provides Jacobi and Givens rotations.
+  *
+  * \code
+  * #include <Eigen/Jacobi>
+  * \endcode
+  *
+  * In addition to listed classes, it defines the two following MatrixBase methods to apply a Jacobi or Givens rotation:
+  *  - MatrixBase::applyOnTheLeft()
+  *  - MatrixBase::applyOnTheRight().
+  */
+
+#include "src/Jacobi/Jacobi.h"
+
+} // namespace Eigen
+
+#include "src/Core/util/ReenableStupidWarnings.h"
+
+#endif // EIGEN_JACOBI_MODULE_H
+/* vim: set filetype=cpp et sw=2 ts=2 ai: */
+

Added: pkg/RcppEigen/inst/include/Eigen/LU
===================================================================
--- pkg/RcppEigen/inst/include/Eigen/LU	                        (rev 0)
+++ pkg/RcppEigen/inst/include/Eigen/LU	2011-06-12 00:22:33 UTC (rev 3053)
@@ -0,0 +1,42 @@
+#ifndef EIGEN_LU_MODULE_H
+#define EIGEN_LU_MODULE_H
+
+#include "Core"
+
+#include "src/Core/util/DisableStupidWarnings.h"
+
+namespace Eigen {
+
+/** \defgroup LU_Module LU module
+  * This module includes %LU decomposition and related notions such as matrix inversion and determinant.
+  * This module defines the following MatrixBase methods:
+  *  - MatrixBase::inverse()
+  *  - MatrixBase::determinant()
+  *
+  * \code
+  * #include <Eigen/LU>
+  * \endcode
+  */
+
+#include "src/misc/Solve.h"
+#include "src/misc/Kernel.h"
+#include "src/misc/Image.h"
+#include "src/LU/FullPivLU.h"
+#include "src/LU/PartialPivLU.h"
+#include "src/LU/Determinant.h"
+#include "src/LU/Inverse.h"
+
+#if defined EIGEN_VECTORIZE_SSE
+  #include "src/LU/arch/Inverse_SSE.h"
+#endif
+
+#ifdef EIGEN2_SUPPORT
+  #include "src/Eigen2Support/LU.h"
+#endif
+
+} // namespace Eigen
+
+#include "src/Core/util/ReenableStupidWarnings.h"
+
+#endif // EIGEN_LU_MODULE_H
+/* vim: set filetype=cpp et sw=2 ts=2 ai: */

Added: pkg/RcppEigen/inst/include/Eigen/LeastSquares
===================================================================
--- pkg/RcppEigen/inst/include/Eigen/LeastSquares	                        (rev 0)
+++ pkg/RcppEigen/inst/include/Eigen/LeastSquares	2011-06-12 00:22:33 UTC (rev 3053)
@@ -0,0 +1,36 @@
+#ifndef EIGEN_REGRESSION_MODULE_H
+#define EIGEN_REGRESSION_MODULE_H
+
+#ifndef EIGEN2_SUPPORT
+#error LeastSquares is only available in Eigen2 support mode (define EIGEN2_SUPPORT)
+#endif
+
+// exclude from normal eigen3-only documentation
+#ifdef EIGEN2_SUPPORT
+
+#include "Core"
+
+#include "src/Core/util/DisableStupidWarnings.h"
+
+#include "Eigenvalues"
+#include "Geometry"
+
+namespace Eigen {
+
+/** \defgroup LeastSquares_Module LeastSquares module
+  * This module provides linear regression and related features.
+  *
+  * \code
+  * #include <Eigen/LeastSquares>
+  * \endcode
+  */
+
+#include "src/Eigen2Support/LeastSquares.h"
+
+} // namespace Eigen
+
+#include "src/Core/util/ReenableStupidWarnings.h"
+
+#endif // EIGEN2_SUPPORT
+
+#endif // EIGEN_REGRESSION_MODULE_H

Added: pkg/RcppEigen/inst/include/Eigen/QR
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/rcpp -r 3053
