Tue Jun 26 19:06:43 CEST 2012

Author: dmbates
Date: 2012-06-26 19:06:43 +0200 (Tue, 26 Jun 2012)
New Revision: 3644

Added:
   pkg/RcppEigen/inst/include/Eigen/PaStiXSupport
   pkg/RcppEigen/inst/include/Eigen/src/PaStiXSupport/
   pkg/RcppEigen/inst/include/Eigen/src/PaStiXSupport/PaStiXSupport.h
   pkg/RcppEigen/inst/include/Eigen/src/SparseCore/SparsePermutation.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/BVH
   pkg/RcppEigen/inst/include/unsupported/Eigen/FFT
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/FFT/
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/FFT/ei_fftw_impl.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/FFT/ei_kissfft_impl.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/IterativeSolvers/GMRES.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/IterativeSolvers/Scaling.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/SparseExtra/MatrixMarketIterator.h
Modified:
   pkg/RcppEigen/ChangeLog
   pkg/RcppEigen/DESCRIPTION
   pkg/RcppEigen/NEWS
   pkg/RcppEigen/NEWS.org
   pkg/RcppEigen/inst/include/Eigen/Cholesky
   pkg/RcppEigen/inst/include/Eigen/CholmodSupport
   pkg/RcppEigen/inst/include/Eigen/Core
   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/IterativeLinearSolvers
   pkg/RcppEigen/inst/include/Eigen/Jacobi
   pkg/RcppEigen/inst/include/Eigen/LU
   pkg/RcppEigen/inst/include/Eigen/LeastSquares
   pkg/RcppEigen/inst/include/Eigen/OrderingMethods
   pkg/RcppEigen/inst/include/Eigen/PardisoSupport
   pkg/RcppEigen/inst/include/Eigen/QR
   pkg/RcppEigen/inst/include/Eigen/SVD
   pkg/RcppEigen/inst/include/Eigen/Sparse
   pkg/RcppEigen/inst/include/Eigen/SparseCholesky
   pkg/RcppEigen/inst/include/Eigen/SparseCore
   pkg/RcppEigen/inst/include/Eigen/SuperLUSupport
   pkg/RcppEigen/inst/include/Eigen/UmfPackSupport
   pkg/RcppEigen/inst/include/Eigen/src/Cholesky/LDLT.h
   pkg/RcppEigen/inst/include/Eigen/src/Cholesky/LLT.h
   pkg/RcppEigen/inst/include/Eigen/src/Cholesky/LLT_MKL.h
   pkg/RcppEigen/inst/include/Eigen/src/CholmodSupport/CholmodSupport.h
   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/Assign_MKL.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/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/GeneralProduct.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/GenericPacketMath.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/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/AltiVec/Complex.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/arch/AltiVec/PacketMath.h
   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/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/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/GeneralMatrixMatrixTriangular_MKL.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/products/GeneralMatrixMatrix_MKL.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/products/GeneralMatrixVector.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/products/GeneralMatrixVector_MKL.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/SelfadjointMatrixMatrix_MKL.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/products/SelfadjointMatrixVector.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/products/SelfadjointMatrixVector_MKL.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/TriangularMatrixMatrix_MKL.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/products/TriangularMatrixVector.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/products/TriangularMatrixVector_MKL.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/products/TriangularSolverMatrix.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/products/TriangularSolverMatrix_MKL.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/products/TriangularSolverVector.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/util/BlasUtil.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/util/Constants.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/StaticAssert.h
   pkg/RcppEigen/inst/include/Eigen/src/Core/util/XprHelper.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigen2Support/Block.h
   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/AlignedBox.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigen2Support/Geometry/AngleAxis.h
   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/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/ComplexEigenSolver.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigenvalues/ComplexSchur.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigenvalues/ComplexSchur_MKL.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigenvalues/EigenSolver.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/RealSchur_MKL.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_MKL.h
   pkg/RcppEigen/inst/include/Eigen/src/Eigenvalues/Tridiagonalization.h
   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/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/Geometry_SSE.h
   pkg/RcppEigen/inst/include/Eigen/src/Householder/BlockHouseholder.h
   pkg/RcppEigen/inst/include/Eigen/src/Householder/Householder.h
   pkg/RcppEigen/inst/include/Eigen/src/Householder/HouseholderSequence.h
   pkg/RcppEigen/inst/include/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h
   pkg/RcppEigen/inst/include/Eigen/src/IterativeLinearSolvers/BiCGSTAB.h
   pkg/RcppEigen/inst/include/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h
   pkg/RcppEigen/inst/include/Eigen/src/IterativeLinearSolvers/IncompleteLUT.h
   pkg/RcppEigen/inst/include/Eigen/src/IterativeLinearSolvers/IterativeSolverBase.h
   pkg/RcppEigen/inst/include/Eigen/src/Jacobi/Jacobi.h
   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/PartialPivLU_MKL.h
   pkg/RcppEigen/inst/include/Eigen/src/LU/arch/Inverse_SSE.h
   pkg/RcppEigen/inst/include/Eigen/src/OrderingMethods/Amd.h
   pkg/RcppEigen/inst/include/Eigen/src/PardisoSupport/PardisoSupport.h
   pkg/RcppEigen/inst/include/Eigen/src/QR/ColPivHouseholderQR.h
   pkg/RcppEigen/inst/include/Eigen/src/QR/ColPivHouseholderQR_MKL.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/QR/HouseholderQR_MKL.h
   pkg/RcppEigen/inst/include/Eigen/src/SVD/JacobiSVD.h
   pkg/RcppEigen/inst/include/Eigen/src/SVD/JacobiSVD_MKL.h
   pkg/RcppEigen/inst/include/Eigen/src/SVD/UpperBidiagonalization.h
   pkg/RcppEigen/inst/include/Eigen/src/SparseCholesky/SimplicialCholesky.h
   pkg/RcppEigen/inst/include/Eigen/src/SparseCore/AmbiVector.h
   pkg/RcppEigen/inst/include/Eigen/src/SparseCore/CompressedStorage.h
   pkg/RcppEigen/inst/include/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h
   pkg/RcppEigen/inst/include/Eigen/src/SparseCore/CoreIterators.h
   pkg/RcppEigen/inst/include/Eigen/src/SparseCore/SparseBlock.h
   pkg/RcppEigen/inst/include/Eigen/src/SparseCore/SparseCwiseBinaryOp.h
   pkg/RcppEigen/inst/include/Eigen/src/SparseCore/SparseCwiseUnaryOp.h
   pkg/RcppEigen/inst/include/Eigen/src/SparseCore/SparseDenseProduct.h
   pkg/RcppEigen/inst/include/Eigen/src/SparseCore/SparseDiagonalProduct.h
   pkg/RcppEigen/inst/include/Eigen/src/SparseCore/SparseDot.h
   pkg/RcppEigen/inst/include/Eigen/src/SparseCore/SparseMatrix.h
   pkg/RcppEigen/inst/include/Eigen/src/SparseCore/SparseMatrixBase.h
   pkg/RcppEigen/inst/include/Eigen/src/SparseCore/SparseProduct.h
   pkg/RcppEigen/inst/include/Eigen/src/SparseCore/SparseRedux.h
   pkg/RcppEigen/inst/include/Eigen/src/SparseCore/SparseSelfAdjointView.h
   pkg/RcppEigen/inst/include/Eigen/src/SparseCore/SparseSparseProductWithPruning.h
   pkg/RcppEigen/inst/include/Eigen/src/SparseCore/SparseTranspose.h
   pkg/RcppEigen/inst/include/Eigen/src/SparseCore/SparseTriangularView.h
   pkg/RcppEigen/inst/include/Eigen/src/SparseCore/SparseUtil.h
   pkg/RcppEigen/inst/include/Eigen/src/SparseCore/SparseVector.h
   pkg/RcppEigen/inst/include/Eigen/src/SparseCore/SparseView.h
   pkg/RcppEigen/inst/include/Eigen/src/SparseCore/TriangularSolver.h
   pkg/RcppEigen/inst/include/Eigen/src/SuperLUSupport/SuperLUSupport.h
   pkg/RcppEigen/inst/include/Eigen/src/UmfPackSupport/UmfPackSupport.h
   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/misc/SparseSolve.h
   pkg/RcppEigen/inst/include/RcppEigenForward.h
   pkg/RcppEigen/inst/include/RcppEigenWrap.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/IterativeSolvers
   pkg/RcppEigen/inst/include/unsupported/Eigen/KroneckerProduct
   pkg/RcppEigen/inst/include/unsupported/Eigen/MatrixFunctions
   pkg/RcppEigen/inst/include/unsupported/Eigen/NonLinearOptimization
   pkg/RcppEigen/inst/include/unsupported/Eigen/NumericalDiff
   pkg/RcppEigen/inst/include/unsupported/Eigen/Polynomials
   pkg/RcppEigen/inst/include/unsupported/Eigen/Skyline
   pkg/RcppEigen/inst/include/unsupported/Eigen/SparseExtra
   pkg/RcppEigen/inst/include/unsupported/Eigen/Splines
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/AutoDiff/AutoDiffScalar.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/BVH/BVAlgorithms.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/BVH/KdBVH.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/IterativeSolvers/ConstrainedConjGrad.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/IterativeSolvers/IncompleteLU.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/IterativeSolvers/IterationController.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/KroneckerProduct/KroneckerTensorProduct.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/MatrixFunctions/MatrixExponential.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/MatrixFunctions/MatrixFunction.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/MatrixFunctions/MatrixFunctionAtomic.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/MatrixFunctions/MatrixLogarithm.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/MatrixFunctions/MatrixSquareRoot.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/MatrixFunctions/StemFunction.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/NonLinearOptimization/HybridNonLinearSolver.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/NonLinearOptimization/LevenbergMarquardt.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/NonLinearOptimization/chkder.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/NonLinearOptimization/covar.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/NonLinearOptimization/dogleg.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/NonLinearOptimization/fdjac1.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/NonLinearOptimization/lmpar.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/NonLinearOptimization/qrsolv.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/NonLinearOptimization/r1mpyq.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/NonLinearOptimization/r1updt.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/NonLinearOptimization/rwupdt.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/NumericalDiff/NumericalDiff.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/Polynomials/Companion.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/Polynomials/PolynomialSolver.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/Polynomials/PolynomialUtils.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/Skyline/SkylineInplaceLU.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/Skyline/SkylineMatrix.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/Skyline/SkylineMatrixBase.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/Skyline/SkylineProduct.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/Skyline/SkylineStorage.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/Skyline/SkylineUtil.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/SparseExtra/BlockOfDynamicSparseMatrix.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/SparseExtra/DynamicSparseMatrix.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/SparseExtra/MarketIO.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/SparseExtra/RandomSetter.h
   pkg/RcppEigen/inst/include/unsupported/Eigen/src/Splines/SplineFitting.h
   pkg/RcppEigen/inst/unitTests/runit.RcppEigen.R
   pkg/RcppEigen/inst/unitTests/runit.sparse.R
Log:
Version 0.3.0 with upgrade of Eigen to Eigen 3.1


Modified: pkg/RcppEigen/ChangeLog
===================================================================

--- pkg/RcppEigen/ChangeLog	2012-06-26 16:59:05 UTC (rev 3643)
+++ pkg/RcppEigen/ChangeLog	2012-06-26 17:06:43 UTC (rev 3644)
@@ -1,3 +1,8 @@
+2012-06-26  Douglas Bates  <bates at stat.wisc.edu>
+
+	* DESCRIPTION, R/unit.test.R, inst/include/Eigen/*: Massive
+	changes related to upgrade to Eigen-3.1.0
+
 2012-03-08  Douglas Bates <bates at stat.wisc.edu>
 
 	* inst/tests/test-solutions.R, inst/tests/test-transform.R,

Modified: pkg/RcppEigen/DESCRIPTION
===================================================================
--- pkg/RcppEigen/DESCRIPTION	2012-06-26 16:59:05 UTC (rev 3643)
+++ pkg/RcppEigen/DESCRIPTION	2012-06-26 17:06:43 UTC (rev 3644)
@@ -1,8 +1,8 @@
 Package: RcppEigen
 Type: Package
 Title: Rcpp integration for the Eigen templated linear algebra library.
-Version: 0.2.0
-Date: 2012-03-08
+Version: 0.3.0
+Date: 2012-06-25
 Author: Douglas Bates, Romain Francois and Dirk Eddelbuettel
 Maintainer: Douglas Bates, Romain Francois and Dirk Eddelbuettel <RcppArmadillo-authors at r-enthusiasts.com>
 Description: R and Eigen integration using Rcpp.
@@ -15,7 +15,7 @@
  implementations based on Lapack and level-3 BLAS.
  .
  The RcppEigen package includes the header files from the Eigen C++
- template library (currently version 3.0.3). Thus users do not need to
+ template library (currently version 3.1.0). 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

Modified: pkg/RcppEigen/NEWS
===================================================================
--- pkg/RcppEigen/NEWS	2012-06-26 16:59:05 UTC (rev 3643)
+++ pkg/RcppEigen/NEWS	2012-06-26 17:06:43 UTC (rev 3644)
@@ -1,18 +1,31 @@
-                       NEWS for RcppEigen-0.2.0
+                       NEWS for RcppEigen-0.3.0
                        ========================
 
 Author: Douglas Bates
-Date: 2012-03-08 Thu
+Date: 2012-06-26 Tue
 
 
 Table of Contents
 =================
 1 New features visible to users
-2 New features not visible to users
+2 New features visible to users in RcppEigen-0.2.0
+3 New features not visible to users in RcppEigen-0.2.0
 
 
 1 New features visible to users 
 --------------------------------
+  + Upgraded to Eigen 3.1.0
+  + Removed the "unsupported" Eigen module AutoDiff which defined a
+    macro "sign" that conflicted with a function in the R API (which
+    really should be visible as "Rf_sign", not sure why it shows up as
+    "sign" and don't have time to investigate)
+  + Commented out several tests involving complex vectors and
+    matrices.  Again there are compilation problems related to
+    conflicting definitions in the std:: namespace and the R API and
+    Eigen, which I don't have time to investigate.
+
+2 New features visible to users in RcppEigen-0.2.0 
+---------------------------------------------------
   + Upgraded the version of Eigen to 3.1.0-alpha2, in which the sparse
     matrix modules are now in the "supported" tree.
   + Added several "unsupported" Eigen modules including
@@ -32,14 +45,14 @@
       Market I/O functions)
     - Splines (multidimensional spline representations and spline
       interpolation)
-  + At present the MatrixFunctions module is included with
-    RcppEigen.h but that may change if too many people get
-    unexpected results from A.exp()
+  + At present all these modules, including the MatrixFunctions
+    module, are included with RcppEigen.h but that may change if too
+    many people get unexpected results from A.exp()
   + The ability to wrap RowMajor sparse matrices and to use
     as<Eigen::ArrayXd> etc.
 
-2 New features not visible to users 
-------------------------------------
+3 New features not visible to users in RcppEigen-0.2.0 
+-------------------------------------------------------
   + Migrated some tests to the testthat package.  Currently there is
     some difficulty with combining testthat, inline and R CMD check.
     These checks are available as
@@ -50,4 +63,4 @@
 
 
  
-
+  

Modified: pkg/RcppEigen/NEWS.org
===================================================================
--- pkg/RcppEigen/NEWS.org	2012-06-26 16:59:05 UTC (rev 3643)
+++ pkg/RcppEigen/NEWS.org	2012-06-26 17:06:43 UTC (rev 3644)
@@ -1,12 +1,23 @@
-#+TITLE:     NEWS for RcppEigen-0.2.0
+#+TITLE:     NEWS for RcppEigen-0.3.0
 #+AUTHOR:    Douglas Bates
 #+EMAIL:     bates at stat.wisc.edu
-#+DATE:      2012-03-08 Thu
+#+DATE:      2012-06-26 Tue
 #+DESCRIPTION: News regarding the latest version of RcppEigen
 #+KEYWORDS:
 #+LANGUAGE:  en
 
 * New features visible to users
+  + Upgraded to Eigen 3.1.0
+  + Removed the "unsupported" Eigen module AutoDiff which defined a
+    macro "sign" that conflicted with a function in the R API (which
+    really should be visible as "Rf_sign", not sure why it shows up as
+    "sign" and don't have time to investigate)
+  + Commented out several tests involving complex vectors and
+    matrices.  Again there are compilation problems related to
+    conflicting definitions in the std:: namespace and the R API and
+    Eigen, which I don't have time to investigate.
+
+* New features visible to users in RcppEigen-0.2.0
   + Upgraded the version of Eigen to 3.1.0-alpha2, in which the sparse
     matrix modules are now in the "supported" tree.
   + Added several "unsupported" Eigen modules including
@@ -32,7 +43,7 @@
   + The ability to wrap RowMajor sparse matrices and to use
     as<Eigen::ArrayXd> etc.
 
-* New features not visible to users
+* New features not visible to users in RcppEigen-0.2.0
   + Migrated some tests to the testthat package.  Currently there is
     some difficulty with combining testthat, inline and R CMD check.
     These checks are available as
@@ -42,4 +53,4 @@
 #+END_EXAMPLE
 
  
-
+  

Modified: pkg/RcppEigen/inst/include/Eigen/Cholesky
===================================================================
--- pkg/RcppEigen/inst/include/Eigen/Cholesky	2012-06-26 16:59:05 UTC (rev 3643)
+++ pkg/RcppEigen/inst/include/Eigen/Cholesky	2012-06-26 17:06:43 UTC (rev 3644)
@@ -5,8 +5,6 @@
 
 #include "src/Core/util/DisableStupidWarnings.h"
 
-namespace Eigen {
-
 /** \defgroup Cholesky_Module Cholesky module
   *
   *
@@ -28,8 +26,6 @@
 #include "src/Cholesky/LLT_MKL.h"
 #endif
 
-} // namespace Eigen
-
 #include "src/Core/util/ReenableStupidWarnings.h"
 
 #endif // EIGEN_CHOLESKY_MODULE_H

Modified: pkg/RcppEigen/inst/include/Eigen/CholmodSupport
===================================================================
--- pkg/RcppEigen/inst/include/Eigen/CholmodSupport	2012-06-26 16:59:05 UTC (rev 3643)
+++ pkg/RcppEigen/inst/include/Eigen/CholmodSupport	2012-06-26 17:06:43 UTC (rev 3644)
@@ -9,15 +9,28 @@
   #include <RcppEigenCholmod.h>
 }
 
-namespace Eigen {
-
 /** \ingroup Support_modules
   * \defgroup CholmodSupport_Module CholmodSupport module
   *
+  * This module provides an interface to the Cholmod library which is part of the <a href="http://www.cise.ufl.edu/research/sparse/SuiteSparse/">suitesparse</a> package.
+  * It provides the two following main factorization classes:
+  * - class CholmodSupernodalLLT: a supernodal LLT Cholesky factorization.
+  * - class CholmodDecomposiiton: a general L(D)LT Cholesky factorization with automatic or explicit runtime selection of the underlying factorization method (supernodal or simplicial).
   *
+  * For the sake of completeness, this module also propose the two following classes:
+  * - class CholmodSimplicialLLT
+  * - class CholmodSimplicialLDLT
+  * Note that these classes does not bring any particular advantage compared to the built-in
+  * SimplicialLLT and SimplicialLDLT factorization classes.
+  *
   * \code
   * #include <Eigen/CholmodSupport>
   * \endcode
+  *
+  * In order to use this module, the cholmod headers must be accessible from the include paths, and your binary must be linked to the cholmod library and its dependencies.
+  * The dependencies depend on how cholmod has been compiled.
+  * For a cmake based project, you can use our FindCholmod.cmake module to help you in this task.
+  *
   */
 
 #include "src/misc/Solve.h"
@@ -26,8 +39,6 @@
 #include "src/CholmodSupport/CholmodSupport.h"
 
 
-} // namespace Eigen
-
 #include "src/Core/util/ReenableStupidWarnings.h"
 
 #endif // EIGEN_CHOLMODSUPPORT_MODULE_H

Modified: pkg/RcppEigen/inst/include/Eigen/Core
===================================================================
--- pkg/RcppEigen/inst/include/Eigen/Core	2012-06-26 16:59:05 UTC (rev 3643)
+++ pkg/RcppEigen/inst/include/Eigen/Core	2012-06-26 17:06:43 UTC (rev 3644)
@@ -142,7 +142,7 @@
 #endif
 
 // MSVC for windows mobile does not have the errno.h file
-#if !(defined(_MSC_VER) && defined(_WIN32_WCE))
+#if !(defined(_MSC_VER) && defined(_WIN32_WCE)) && !defined(__ARMCC_VERSION)
 #define EIGEN_HAS_ERRNO
 #endif
 
@@ -203,6 +203,8 @@
 #endif
 }
 
+} // end namespace Eigen
+
 #define STAGE10_FULL_EIGEN2_API             10
 #define STAGE20_RESOLVE_API_CONFLICTS       20
 #define STAGE30_FULL_EIGEN3_API             30
@@ -327,12 +329,12 @@
 #include "src/Core/GeneralProduct.h"
 #include "src/Core/TriangularMatrix.h"
 #include "src/Core/SelfAdjointView.h"
-#include "src/Core/SolveTriangular.h"
+#include "src/Core/products/GeneralBlockPanelKernel.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/SolveTriangular.h"
 #include "src/Core/products/GeneralMatrixMatrixTriangular.h"
 #include "src/Core/products/SelfadjointMatrixVector.h"
 #include "src/Core/products/SelfadjointMatrixMatrix.h"
@@ -368,8 +370,6 @@
 #include "src/Core/Assign_MKL.h"
 #endif
 
-} // namespace Eigen
-
 #include "src/Core/GlobalFunctions.h"
 
 #include "src/Core/util/ReenableStupidWarnings.h"

Modified: pkg/RcppEigen/inst/include/Eigen/Eigen2Support
===================================================================
--- pkg/RcppEigen/inst/include/Eigen/Eigen2Support	2012-06-26 16:59:05 UTC (rev 3643)
+++ pkg/RcppEigen/inst/include/Eigen/Eigen2Support	2012-06-26 17:06:43 UTC (rev 3644)
@@ -31,8 +31,6 @@
 
 #include "src/Core/util/DisableStupidWarnings.h"
 
-namespace Eigen {
-
 /** \ingroup Support_modules
   * \defgroup Eigen2Support_Module Eigen2 support module
   * This module provides a couple of deprecated functions improving the compatibility with Eigen2.
@@ -57,8 +55,6 @@
 #include "src/Eigen2Support/MathFunctions.h"
 
 
-} // namespace Eigen
-
 #include "src/Core/util/ReenableStupidWarnings.h"
 
 // Eigen2 used to include iostream

Modified: pkg/RcppEigen/inst/include/Eigen/Eigenvalues
===================================================================
--- pkg/RcppEigen/inst/include/Eigen/Eigenvalues	2012-06-26 16:59:05 UTC (rev 3643)
+++ pkg/RcppEigen/inst/include/Eigen/Eigenvalues	2012-06-26 17:06:43 UTC (rev 3644)
@@ -11,8 +11,6 @@
 #include "LU"
 #include "Geometry"
 
-namespace Eigen {
-
 /** \defgroup Eigenvalues_Module Eigenvalues module
   *
   *
@@ -42,8 +40,6 @@
 #include "src/Eigenvalues/SelfAdjointEigenSolver_MKL.h"
 #endif
 
-} // namespace Eigen
-
 #include "src/Core/util/ReenableStupidWarnings.h"
 
 #endif // EIGEN_EIGENVALUES_MODULE_H

Modified: pkg/RcppEigen/inst/include/Eigen/Geometry
===================================================================
--- pkg/RcppEigen/inst/include/Eigen/Geometry	2012-06-26 16:59:05 UTC (rev 3643)
+++ pkg/RcppEigen/inst/include/Eigen/Geometry	2012-06-26 17:06:43 UTC (rev 3644)
@@ -13,8 +13,6 @@
 #define M_PI 3.14159265358979323846
 #endif
 
-namespace Eigen {
-
 /** \defgroup Geometry_Module Geometry module
   *
   *
@@ -58,8 +56,6 @@
 #include "src/Eigen2Support/Geometry/All.h"
 #endif
 
-} // namespace Eigen
-
 #include "src/Core/util/ReenableStupidWarnings.h"
 
 #endif // EIGEN_GEOMETRY_MODULE_H

Modified: pkg/RcppEigen/inst/include/Eigen/Householder
===================================================================
--- pkg/RcppEigen/inst/include/Eigen/Householder	2012-06-26 16:59:05 UTC (rev 3643)
+++ pkg/RcppEigen/inst/include/Eigen/Householder	2012-06-26 17:06:43 UTC (rev 3644)
@@ -5,8 +5,6 @@
 
 #include "src/Core/util/DisableStupidWarnings.h"
 
-namespace Eigen {
-
 /** \defgroup Householder_Module Householder module
   * This module provides Householder transformations.
   *
@@ -19,8 +17,6 @@
 #include "src/Householder/HouseholderSequence.h"
 #include "src/Householder/BlockHouseholder.h"
 
-} // namespace Eigen
-
 #include "src/Core/util/ReenableStupidWarnings.h"
 
 #endif // EIGEN_HOUSEHOLDER_MODULE_H

Modified: pkg/RcppEigen/inst/include/Eigen/IterativeLinearSolvers
===================================================================
--- pkg/RcppEigen/inst/include/Eigen/IterativeLinearSolvers	2012-06-26 16:59:05 UTC (rev 3643)
+++ pkg/RcppEigen/inst/include/Eigen/IterativeLinearSolvers	2012-06-26 17:06:43 UTC (rev 3644)
@@ -6,8 +6,6 @@
 
 #include "src/Core/util/DisableStupidWarnings.h"
 
-namespace Eigen {
-
 /** \ingroup Sparse_modules
   * \defgroup IterativeLinearSolvers_Module IterativeLinearSolvers module
   *
@@ -37,8 +35,6 @@
 #include "src/IterativeLinearSolvers/BiCGSTAB.h"
 #include "src/IterativeLinearSolvers/IncompleteLUT.h"
 
-} // namespace Eigen
-
 #include "src/Core/util/ReenableStupidWarnings.h"
 
 #endif // EIGEN_ITERATIVELINEARSOLVERS_MODULE_H

Modified: pkg/RcppEigen/inst/include/Eigen/Jacobi
===================================================================
--- pkg/RcppEigen/inst/include/Eigen/Jacobi	2012-06-26 16:59:05 UTC (rev 3643)
+++ pkg/RcppEigen/inst/include/Eigen/Jacobi	2012-06-26 17:06:43 UTC (rev 3644)
@@ -5,8 +5,6 @@
 
 #include "src/Core/util/DisableStupidWarnings.h"
 
-namespace Eigen {
-
 /** \defgroup Jacobi_Module Jacobi module
   * This module provides Jacobi and Givens rotations.
   *
@@ -21,8 +19,6 @@
 
 #include "src/Jacobi/Jacobi.h"
 
-} // namespace Eigen
-
 #include "src/Core/util/ReenableStupidWarnings.h"
 
 #endif // EIGEN_JACOBI_MODULE_H

Modified: pkg/RcppEigen/inst/include/Eigen/LU
===================================================================
--- pkg/RcppEigen/inst/include/Eigen/LU	2012-06-26 16:59:05 UTC (rev 3643)
+++ pkg/RcppEigen/inst/include/Eigen/LU	2012-06-26 17:06:43 UTC (rev 3644)
@@ -5,8 +5,6 @@
 
 #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:
@@ -37,8 +35,6 @@
   #include "src/Eigen2Support/LU.h"
 #endif
 
-} // namespace Eigen
-
 #include "src/Core/util/ReenableStupidWarnings.h"
 
 #endif // EIGEN_LU_MODULE_H

Modified: pkg/RcppEigen/inst/include/Eigen/LeastSquares
===================================================================
--- pkg/RcppEigen/inst/include/Eigen/LeastSquares	2012-06-26 16:59:05 UTC (rev 3643)
+++ pkg/RcppEigen/inst/include/Eigen/LeastSquares	2012-06-26 17:06:43 UTC (rev 3644)
@@ -15,8 +15,6 @@
 #include "Eigenvalues"
 #include "Geometry"
 
-namespace Eigen {
-
 /** \defgroup LeastSquares_Module LeastSquares module
   * This module provides linear regression and related features.
   *
@@ -27,8 +25,6 @@
 
 #include "src/Eigen2Support/LeastSquares.h"
 
-} // namespace Eigen
-
 #include "src/Core/util/ReenableStupidWarnings.h"
 
 #endif // EIGEN2_SUPPORT

Modified: pkg/RcppEigen/inst/include/Eigen/OrderingMethods
===================================================================
--- pkg/RcppEigen/inst/include/Eigen/OrderingMethods	2012-06-26 16:59:05 UTC (rev 3643)
+++ pkg/RcppEigen/inst/include/Eigen/OrderingMethods	2012-06-26 17:06:43 UTC (rev 3644)
@@ -5,8 +5,6 @@
 
 #include "src/Core/util/DisableStupidWarnings.h"
 
-namespace Eigen {
-
 /** \ingroup Sparse_modules
   * \defgroup OrderingMethods_Module OrderingMethods module
   *
@@ -20,8 +18,6 @@
 
 #include "src/OrderingMethods/Amd.h"
 
-} // namespace Eigen
-
 #include "src/Core/util/ReenableStupidWarnings.h"
 
 #endif // EIGEN_ORDERINGMETHODS_MODULE_H

Added: pkg/RcppEigen/inst/include/Eigen/PaStiXSupport
===================================================================
--- pkg/RcppEigen/inst/include/Eigen/PaStiXSupport	                        (rev 0)
+++ pkg/RcppEigen/inst/include/Eigen/PaStiXSupport	2012-06-26 17:06:43 UTC (rev 3644)
@@ -0,0 +1,46 @@
+#ifndef EIGEN_PASTIXSUPPORT_MODULE_H
+#define EIGEN_PASTIXSUPPORT_MODULE_H
+
+#include "SparseCore"
+
+#include "src/Core/util/DisableStupidWarnings.h"
+
+#include <complex.h>
+extern "C" {
+#include <pastix_nompi.h>
+#include <pastix.h>
+}
+
+#ifdef complex
+#undef complex
+#endif
+
+/** \ingroup Support_modules
+  * \defgroup PaStiXSupport_Module PaStiXSupport module
+  * 
+  * This module provides an interface to the <a href="http://pastix.gforge.inria.fr/">PaSTiX</a> library.
+  * PaSTiX is a general \b supernodal, \b parallel and \b opensource sparse solver.
+  * It provides the two following main factorization classes:
+  * - class PastixLLT : a supernodal, parallel LLt Cholesky factorization.
+  * - class PastixLDLT: a supernodal, parallel LDLt Cholesky factorization.
+  * - class PastixLU : a supernodal, parallel LU factorization (optimized for a symmetric pattern).
+  * 
+  * \code
+  * #include <Eigen/PaStiXSupport>
+  * \endcode
+  *
+  * In order to use this module, the PaSTiX headers must be accessible from the include paths, and your binary must be linked to the PaSTiX library and its dependencies.
+  * The dependencies depend on how PaSTiX has been compiled.
+  * For a cmake based project, you can use our FindPaSTiX.cmake module to help you in this task.
+  *
+  */
+
+#include "src/misc/Solve.h"
+#include "src/misc/SparseSolve.h"
+
+#include "src/PaStiXSupport/PaStiXSupport.h"
+
+
+#include "src/Core/util/ReenableStupidWarnings.h"
+
+#endif // EIGEN_PASTIXSUPPORT_MODULE_H

Modified: pkg/RcppEigen/inst/include/Eigen/PardisoSupport
===================================================================
--- pkg/RcppEigen/inst/include/Eigen/PardisoSupport	2012-06-26 16:59:05 UTC (rev 3643)
+++ pkg/RcppEigen/inst/include/Eigen/PardisoSupport	2012-06-26 17:06:43 UTC (rev 3644)
@@ -9,22 +9,22 @@
 
 #include <unsupported/Eigen/SparseExtra>
 
-namespace Eigen {
-
 /** \ingroup Support_modules
   * \defgroup PardisoSupport_Module PardisoSupport module
   *
-  * This module brings support for the Intel(R) MKL PARDISO direct sparse solvers
+  * This module brings support for the Intel(R) MKL PARDISO direct sparse solvers.
   *
   * \code
   * #include <Eigen/PardisoSupport>
   * \endcode
+  *
+  * In order to use this module, the MKL headers must be accessible from the include paths, and your binary must be linked to the MKL library and its dependencies.
+  * See this \ref TopicUsingIntelMKL "page" for more information on MKL-Eigen integration.
+  * 
   */
 
 #include "src/PardisoSupport/PardisoSupport.h"
 
-} // namespace Eigen
-
 #include "src/Core/util/ReenableStupidWarnings.h"
 
 #endif // EIGEN_PARDISOSUPPORT_MODULE_H

Modified: pkg/RcppEigen/inst/include/Eigen/QR
===================================================================
--- pkg/RcppEigen/inst/include/Eigen/QR	2012-06-26 16:59:05 UTC (rev 3643)
+++ pkg/RcppEigen/inst/include/Eigen/QR	2012-06-26 17:06:43 UTC (rev 3644)
@@ -9,8 +9,6 @@
 #include "Jacobi"
 #include "Householder"
 
-namespace Eigen {
-
 /** \defgroup QR_Module QR module
   *
   *
@@ -37,8 +35,6 @@
 #include "src/Eigen2Support/QR.h"
 #endif
 
-} // namespace Eigen
-
 #include "src/Core/util/ReenableStupidWarnings.h"
 
 #ifdef EIGEN2_SUPPORT

Modified: pkg/RcppEigen/inst/include/Eigen/SVD
===================================================================
--- pkg/RcppEigen/inst/include/Eigen/SVD	2012-06-26 16:59:05 UTC (rev 3643)
+++ pkg/RcppEigen/inst/include/Eigen/SVD	2012-06-26 17:06:43 UTC (rev 3644)
@@ -7,8 +7,6 @@
 
 #include "src/Core/util/DisableStupidWarnings.h"
 
-namespace Eigen {
-
 /** \defgroup SVD_Module SVD module
   *
   *
@@ -33,8 +31,6 @@
 #include "src/Eigen2Support/SVD.h"
 #endif
 
-} // namespace Eigen
-
 #include "src/Core/util/ReenableStupidWarnings.h"
 
 #endif // EIGEN_SVD_MODULE_H

Modified: pkg/RcppEigen/inst/include/Eigen/Sparse
===================================================================
--- pkg/RcppEigen/inst/include/Eigen/Sparse	2012-06-26 16:59:05 UTC (rev 3643)
+++ pkg/RcppEigen/inst/include/Eigen/Sparse	2012-06-26 17:06:43 UTC (rev 3644)
@@ -1,8 +1,6 @@
 #ifndef EIGEN_SPARSE_MODULE_H
 #define EIGEN_SPARSE_MODULE_H
 
-namespace Eigen {
-
 /** \defgroup Sparse_modules Sparse modules
   *
   * Meta-module including all related modules:
@@ -16,8 +14,6 @@
   * \endcode
   */
 
-} // namespace Eigen
-
 #include "SparseCore"
 #include "OrderingMethods"
 #include "SparseCholesky"

Modified: pkg/RcppEigen/inst/include/Eigen/SparseCholesky
===================================================================
--- pkg/RcppEigen/inst/include/Eigen/SparseCholesky	2012-06-26 16:59:05 UTC (rev 3643)
+++ pkg/RcppEigen/inst/include/Eigen/SparseCholesky	2012-06-26 17:06:43 UTC (rev 3644)
@@ -5,8 +5,6 @@
 
 #include "src/Core/util/DisableStupidWarnings.h"
 
-namespace Eigen {
-
 /** \ingroup Sparse_modules
   * \defgroup SparseCholesky_Module SparseCholesky module
   *
@@ -27,8 +25,6 @@
 
 #include "src/SparseCholesky/SimplicialCholesky.h"
 
-} // namespace Eigen
-
 #include "src/Core/util/ReenableStupidWarnings.h"
 
 #endif // EIGEN_SPARSECHOLESKY_MODULE_H

Modified: pkg/RcppEigen/inst/include/Eigen/SparseCore
===================================================================
--- pkg/RcppEigen/inst/include/Eigen/SparseCore	2012-06-26 16:59:05 UTC (rev 3643)
+++ pkg/RcppEigen/inst/include/Eigen/SparseCore	2012-06-26 17:06:43 UTC (rev 3644)
@@ -11,8 +11,6 @@
 #include <cstring>
 #include <algorithm>
 
-namespace Eigen {
-
 /** \ingroup Sparse_modules
   * \defgroup SparseCore_Module SparseCore module
   *
@@ -28,9 +26,13 @@
   * This module depends on: Core.
   */
 
+namespace Eigen {
+
 /** The type used to identify a general sparse storage. */
 struct Sparse {};
 
+}
+
 #include "src/SparseCore/SparseUtil.h"
 #include "src/SparseCore/SparseMatrixBase.h"
 #include "src/SparseCore/CompressedStorage.h"
@@ -44,6 +46,7 @@
 #include "src/SparseCore/SparseCwiseUnaryOp.h"
 #include "src/SparseCore/SparseCwiseBinaryOp.h"
 #include "src/SparseCore/SparseDot.h"
+#include "src/SparseCore/SparsePermutation.h"
 #include "src/SparseCore/SparseAssign.h"
 #include "src/SparseCore/SparseRedux.h"
 #include "src/SparseCore/SparseFuzzy.h"
@@ -57,8 +60,6 @@
 #include "src/SparseCore/TriangularSolver.h"
 #include "src/SparseCore/SparseView.h"
 
-} // namespace Eigen
-
 #include "src/Core/util/ReenableStupidWarnings.h"
 
 #endif // EIGEN_SPARSECORE_MODULE_H

Modified: pkg/RcppEigen/inst/include/Eigen/SuperLUSupport
===================================================================
--- pkg/RcppEigen/inst/include/Eigen/SuperLUSupport	2012-06-26 16:59:05 UTC (rev 3643)
+++ pkg/RcppEigen/inst/include/Eigen/SuperLUSupport	2012-06-26 17:06:43 UTC (rev 3644)
@@ -16,7 +16,7 @@
 
 // slu_util.h defines a preprocessor token named EMPTY which is really polluting,
 // so we remove it in favor of a SUPERLU_EMPTY token.
-// If EMPTY was already, defined then we don't undef it.
+// If EMPTY was already defined then we don't undef it.
 
 #if defined(EIGEN_EMPTY_WAS_ALREADY_DEFINED)
 # undef EIGEN_EMPTY_WAS_ALREADY_DEFINED
@@ -28,16 +28,24 @@
 
 namespace Eigen { struct SluMatrix; }
 
-namespace Eigen {
-
 /** \ingroup Support_modules
   * \defgroup SuperLUSupport_Module SuperLUSupport module
   *
+  * This module provides an interface to the <a href="http://crd-legacy.lbl.gov/~xiaoye/SuperLU/">SuperLU</a> library.
+  * It provides the following factorization class:
+  * - class SuperLU: a supernodal sequential LU factorization.
+  * - class SuperILU: a supernodal sequential incomplete LU factorization (to be used as a preconditioner for iterative methods).
+  *
   * \warning When including this module, you have to use SUPERLU_EMPTY instead of EMPTY which is no longer defined because it is too polluting.
   *
   * \code
   * #include <Eigen/SuperLUSupport>
   * \endcode
+  *
+  * In order to use this module, the superlu headers must be accessible from the include paths, and your binary must be linked to the superlu library and its dependencies.
+  * The dependencies depend on how superlu has been compiled.
+  * For a cmake based project, you can use our FindSuperLU.cmake module to help you in this task.
+  *
   */
 
 #include "src/misc/Solve.h"
@@ -46,8 +54,6 @@
 #include "src/SuperLUSupport/SuperLUSupport.h"
 
 
-} // namespace Eigen
-
 #include "src/Core/util/ReenableStupidWarnings.h"
 
 #endif // EIGEN_SUPERLUSUPPORT_MODULE_H

Modified: pkg/RcppEigen/inst/include/Eigen/UmfPackSupport
===================================================================
--- pkg/RcppEigen/inst/include/Eigen/UmfPackSupport	2012-06-26 16:59:05 UTC (rev 3643)
+++ pkg/RcppEigen/inst/include/Eigen/UmfPackSupport	2012-06-26 17:06:43 UTC (rev 3644)
@@ -9,17 +9,21 @@
 #include <umfpack.h>
 }
 
-namespace Eigen {
-
 /** \ingroup Support_modules
   * \defgroup UmfPackSupport_Module UmfPackSupport module
   *
+  * This module provides an interface to the UmfPack library which is part of the <a href="http://www.cise.ufl.edu/research/sparse/SuiteSparse/">suitesparse</a> package.
+  * It provides the following factorization class:
+  * - class UmfPackLU: a multifrontal sequential LU factorization.
   *
-  *
-  *
   * \code
   * #include <Eigen/UmfPackSupport>
   * \endcode
+  *
+  * In order to use this module, the umfpack headers must be accessible from the include paths, and your binary must be linked to the umfpack library and its dependencies.
+  * The dependencies depend on how umfpack has been compiled.
+  * For a cmake based project, you can use our FindUmfPack.cmake module to help you in this task.
+  *
   */
 
 #include "src/misc/Solve.h"
@@ -27,8 +31,6 @@
 
 #include "src/UmfPackSupport/UmfPackSupport.h"
 
-} // namespace Eigen
-
 #include "src/Core/util/ReenableStupidWarnings.h"
 
 #endif // EIGEN_UMFPACKSUPPORT_MODULE_H

Modified: pkg/RcppEigen/inst/include/Eigen/src/Cholesky/LDLT.h
===================================================================
--- pkg/RcppEigen/inst/include/Eigen/src/Cholesky/LDLT.h	2012-06-26 16:59:05 UTC (rev 3643)
+++ pkg/RcppEigen/inst/include/Eigen/src/Cholesky/LDLT.h	2012-06-26 17:06:43 UTC (rev 3644)
@@ -28,6 +28,8 @@
 #ifndef EIGEN_LDLT_H
 #define EIGEN_LDLT_H
 
+namespace Eigen { 
+
 namespace internal {
 template<typename MatrixType, int UpLo> struct LDLT_Traits;
 }
@@ -419,16 +421,16 @@
 
 template<typename MatrixType> struct LDLT_Traits<MatrixType,Lower>
 {
-  typedef TriangularView<const MatrixType, UnitLower> MatrixL;
-  typedef TriangularView<const typename MatrixType::AdjointReturnType, UnitUpper> MatrixU;
+  typedef const TriangularView<const MatrixType, UnitLower> MatrixL;
+  typedef const TriangularView<const typename MatrixType::AdjointReturnType, UnitUpper> MatrixU;
   static inline MatrixL getL(const MatrixType& m) { return m; }
   static inline MatrixU getU(const MatrixType& m) { return m.adjoint(); }
 };
 
 template<typename MatrixType> struct LDLT_Traits<MatrixType,Upper>
 {
-  typedef TriangularView<const typename MatrixType::AdjointReturnType, UnitLower> MatrixL;
-  typedef TriangularView<const MatrixType, UnitUpper> MatrixU;
+  typedef const TriangularView<const typename MatrixType::AdjointReturnType, UnitLower> MatrixL;
+  typedef const TriangularView<const MatrixType, UnitUpper> MatrixU;
   static inline MatrixL getL(const MatrixType& m) { return m.adjoint(); }
   static inline MatrixU getU(const MatrixType& m) { return m; }
 };
@@ -477,7 +479,7 @@
     for (Index i = 0; i < size; i++)
       m_transpositions.coeffRef(i) = i;
     m_temporary.resize(size);
-    m_sign = sigma;
+    m_sign = sigma>=0 ? 1 : -1;
     m_isInitialized = true;
   }
 
@@ -600,4 +602,6 @@
   return LDLT<PlainObject>(derived());
 }
 
+} // end namespace Eigen
+
 #endif // EIGEN_LDLT_H

Modified: pkg/RcppEigen/inst/include/Eigen/src/Cholesky/LLT.h
===================================================================
--- pkg/RcppEigen/inst/include/Eigen/src/Cholesky/LLT.h	2012-06-26 16:59:05 UTC (rev 3643)
+++ pkg/RcppEigen/inst/include/Eigen/src/Cholesky/LLT.h	2012-06-26 17:06:43 UTC (rev 3644)
@@ -25,6 +25,8 @@
 #ifndef EIGEN_LLT_H
 #define EIGEN_LLT_H
 
+namespace Eigen { 
+
 namespace internal{
 template<typename MatrixType, int UpLo> struct LLT_Traits;
 }
@@ -335,7 +337,7 @@
   template<typename MatrixType, typename VectorType>
   static typename MatrixType::Index rankUpdate(MatrixType& mat, const VectorType& vec, const RealScalar& sigma)
   {
-    return llt_rank_update_lower(mat, vec, sigma);
+    return Eigen::internal::llt_rank_update_lower(mat, vec, sigma);
   }
 };
   
@@ -365,8 +367,8 @@
 
 template<typename MatrixType> struct LLT_Traits<MatrixType,Lower>
 {
-  typedef TriangularView<const MatrixType, Lower> MatrixL;
-  typedef TriangularView<const typename MatrixType::AdjointReturnType, Upper> MatrixU;
+  typedef const TriangularView<const MatrixType, Lower> MatrixL;
+  typedef const TriangularView<const typename MatrixType::AdjointReturnType, Upper> MatrixU;
   static inline MatrixL getL(const MatrixType& m) { return m; }
   static inline MatrixU getU(const MatrixType& m) { return m.adjoint(); }
   static bool inplace_decomposition(MatrixType& m)
@@ -375,8 +377,8 @@
 
 template<typename MatrixType> struct LLT_Traits<MatrixType,Upper>
 {
-  typedef TriangularView<const typename MatrixType::AdjointReturnType, Lower> MatrixL;
-  typedef TriangularView<const MatrixType, Upper> MatrixU;
+  typedef const TriangularView<const typename MatrixType::AdjointReturnType, Lower> MatrixL;
+  typedef const TriangularView<const MatrixType, Upper> MatrixU;
   static inline MatrixL getL(const MatrixType& m) { return m.adjoint(); }
   static inline MatrixU getU(const MatrixType& m) { return m; }
   static bool inplace_decomposition(MatrixType& m)
@@ -496,5 +498,6 @@
   return LLT<PlainObject,UpLo>(m_matrix);
 }
 
+} // end namespace Eigen
+
 #endif // EIGEN_LLT_H
-

Modified: pkg/RcppEigen/inst/include/Eigen/src/Cholesky/LLT_MKL.h
===================================================================
--- pkg/RcppEigen/inst/include/Eigen/src/Cholesky/LLT_MKL.h	2012-06-26 16:59:05 UTC (rev 3643)
+++ pkg/RcppEigen/inst/include/Eigen/src/Cholesky/LLT_MKL.h	2012-06-26 17:06:43 UTC (rev 3644)
@@ -36,6 +36,8 @@
 #include "Eigen/src/Core/util/MKL_support.h"
 #include <iostream>
 
+namespace Eigen { 
+
 namespace internal {
 
 template<typename Scalar> struct mkl_llt;
@@ -71,7 +73,7 @@
   } \
   template<typename MatrixType, typename VectorType> \
   static typename MatrixType::Index rankUpdate(MatrixType& mat, const VectorType& vec, const typename MatrixType::RealScalar& sigma) \
-  { return llt_rank_update_lower(mat, vec, sigma); } \
+  { return Eigen::internal::llt_rank_update_lower(mat, vec, sigma); } \
 }; \
 template<> struct llt_inplace<EIGTYPE, Upper> \
 { \
@@ -93,6 +95,8 @@
 EIGEN_MKL_LLT(dcomplex, MKL_Complex16, z)
 EIGEN_MKL_LLT(scomplex, MKL_Complex8, c)
 
-}
+} // end namespace internal
 
+} // end namespace Eigen
+
 #endif // EIGEN_LLT_MKL_H

Modified: pkg/RcppEigen/inst/include/Eigen/src/CholmodSupport/CholmodSupport.h
===================================================================
--- pkg/RcppEigen/inst/include/Eigen/src/CholmodSupport/CholmodSupport.h	2012-06-26 16:59:05 UTC (rev 3643)
+++ pkg/RcppEigen/inst/include/Eigen/src/CholmodSupport/CholmodSupport.h	2012-06-26 17:06:43 UTC (rev 3644)
@@ -25,6 +25,8 @@
 #ifndef EIGEN_CHOLMODSUPPORT_H
 #define EIGEN_CHOLMODSUPPORT_H
 
+namespace Eigen { 
+
 namespace internal {
 
 template<typename Scalar, typename CholmodType>
@@ -158,24 +160,14 @@
   CholmodAuto, CholmodSimplicialLLt, CholmodSupernodalLLt, CholmodLDLt
 };
 
+
 /** \ingroup CholmodSupport_Module
-  * \class CholmodDecomposition
-  * \brief A Cholesky factorization and solver based on Cholmod
-  *
-  * This class allows to solve for A.X = B sparse linear problems via a LL^T or LDL^T Cholesky factorization
-  * using the Cholmod library. The sparse matrix A must be selfajoint and positive definite. The vectors or matrices
-  * X and B can be either dense or sparse.
-  *
-  * \tparam _MatrixType the type of the sparse matrix A, it must be a SparseMatrix<>
-  * \tparam _UpLo the triangular part that will be used for the computations. It can be Lower
-  *               or Upper. Default is Lower.
-  *
-  * This class supports all kind of SparseMatrix<>: row or column major; upper, lower, or both; isCompressed() or unisCompressed().
-  *
-  * \sa \ref TutorialSparseDirectSolvers
+  * \class CholmodBase
+  * \brief The base class for the direct Cholesky factorization of Cholmod
+  * \sa class CholmodSupernodalLLT, class CholmodSimplicialLDLT, class CholmodSimplicialLLT
   */
-template<typename _MatrixType, int _UpLo = Lower>
-class CholmodDecomposition
+template<typename _MatrixType, int _UpLo, typename Derived>
+class CholmodBase : internal::noncopyable
 {
   public:
     typedef _MatrixType MatrixType;
@@ -187,21 +179,20 @@
 
   public:
 
-    CholmodDecomposition()
+    CholmodBase()
       : m_cholmodFactor(0), m_info(Success), m_isInitialized(false)
     {
       cholmod_start(&m_cholmod);
-      setMode(CholmodLDLt);
     }
 
-    CholmodDecomposition(const MatrixType& matrix)
+    CholmodBase(const MatrixType& matrix)
[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/rcpp -r 3644
