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Update to Eigen 5.0.0 (#148)
* Sync with Eigen 5.0.0 (aka 3.5.0) * Small touchup removing patch that should not have in past commit * Patches for RcppEigen applied to Eigen 5.0.0 files * Commit patch file * Adjust tests and example to deprecations * Comment-out another SuiteSparse reference in CholmodSupport * Partial revert to (updated) previous CholModSupport.h * Updated CholmodSupport.h * Roll micro-release and date following rebase * Additional ChangeLog entry * Refresh patch against Eigen 5.0.0 Uses git commit hash, excludes non-Eigen files (as we do not have to patch them again when we patch again) * Update Eigen URLs in three more places
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‎ChangeLog‎

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* .github/workflows/ci.yaml: Switch to actions/checkout@v6
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2026-01-07 Dirk Eddelbuettel <edd@debian.org>
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* README.md: Another pair of URL updates for Eigen
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* man/fastLm.Rd: Idem
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2025-12-30 Dirk Eddelbuettel <edd@debian.org>
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* inst/tinytest/test_misc.R: Additional tests predicate
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* man/RcppEigen_throttle_cores.Rd: Document additional helpers
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* cleanup: Minor extension
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2025-12-26 Dirk Eddelbuettel <edd@debian.org>
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* inst/include/Eigen/src/CholmodSupport/CholmodSupport.h: Comment-out
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another SuiteSparse reference
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* patches/eigen-5.0.0.diff: Updated against git commit of Eigen 5.0.0 sync
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2025-12-25 Dirk Eddelbuettel <edd@debian.org>
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* inst/include/Eigen/: Sync with upstream Eigen 5.0.0 (aka 3.5.0)
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* inst/include/unsupported/Eigen/: Idem
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* patches/eigen-5.0.0.diff: Summary of changes applied
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* inst/include/RcppEigenForward.h: No longer use deprecated type
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* inst/include/RcppEigenWrap.h: Idem
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* inst/tinytest/cpp/rcppeigen.cpp: Adjust test to non-deprecated map
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* inst/tinytest/cpp/sparse.cpp: Skip test of deprecated type
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* inst/tinytest/test_sparse.R: Idem
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* src/fastLm.cpp (SVD::SVD): Update to current form of option setting
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2025-08-26 Dirk Eddelbuettel <edd@debian.org>
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* inst/tinytest/test_misc.R: Add minimal test for EigenNbThreads()

‎DESCRIPTION‎

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Package: RcppEigen
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Type: Package
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Title: 'Rcpp' Integration for the 'Eigen' Templated Linear Algebra Library
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Version: 0.3.4.0.2-1
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Version: 0.4.9.9-1
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Date: 2025-12-29
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Authors@R: c(person("Doug", "Bates", role = "aut",
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comment = c(ORCID = "0000-0001-8316-9503")),

‎README.md‎

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### Synopsis
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[Eigen](http://eigen.tuxfamily.org/index.php?title=Main_Page) is a C++ template library for linear algebra:
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[Eigen](https://libeigen.gitlab.io/) is a C++ template library for linear algebra:
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matrices, vectors, numerical solvers and related algorithms. It supports dense and sparse
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matrices on integer, floating point and complex numbers, decompositions of such matrices,
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and solutions of linear systems. Its performance on many algorithms is comparable with
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some of the best implementations based on `Lapack` and level-3 `BLAS`.
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RcppEigen provides an interface from R to and from [Eigen](http://eigen.tuxfamily.org/index.php?title=Main_Page) by
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RcppEigen provides an interface from R to and from [Eigen](https://libeigen.gitlab.io/) by
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using the facilities offered by the [Rcpp](http://dirk.eddelbuettel.com/code/rcpp.html)
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package for seamless R and C++ integration.
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### Status
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The package is mature and under active development, following the
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[Eigen](http://eigen.tuxfamily.org/index.php?title=Main_Page) release cycle.
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The package is mature and under acthttps://libeigen.gitlab.io/ive development, following the
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[Eigen](https://libeigen.gitlab.io/) release cycle.
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### Documentation
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‎inst/include/Eigen/AccelerateSupport‎

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// This file is part of Eigen, a lightweight C++ template library
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// for linear algebra.
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//
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// This Source Code Form is subject to the terms of the Mozilla
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// Public License v. 2.0. If a copy of the MPL was not distributed
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// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
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#ifndef EIGEN_ACCELERATESUPPORT_MODULE_H
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#define EIGEN_ACCELERATESUPPORT_MODULE_H
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#include "SparseCore"
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#include "src/Core/util/DisableStupidWarnings.h"
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/** \ingroup Support_modules
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* \defgroup AccelerateSupport_Module AccelerateSupport module
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*
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* This module provides an interface to the Apple Accelerate library.
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* It provides the seven following main factorization classes:
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* - class AccelerateLLT: a Cholesky (LL^T) factorization.
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* - class AccelerateLDLT: the default LDL^T factorization.
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* - class AccelerateLDLTUnpivoted: a Cholesky-like LDL^T factorization with only 1x1 pivots and no pivoting
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* - class AccelerateLDLTSBK: an LDL^T factorization with Supernode Bunch-Kaufman and static pivoting
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* - class AccelerateLDLTTPP: an LDL^T factorization with full threshold partial pivoting
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* - class AccelerateQR: a QR factorization
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* - class AccelerateCholeskyAtA: a QR factorization without storing Q (equivalent to A^TA = R^T R)
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*
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* \code
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* #include <Eigen/AccelerateSupport>
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* \endcode
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*
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* In order to use this module, the Accelerate headers must be accessible from
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* the include paths, and your binary must be linked to the Accelerate framework.
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* The Accelerate library is only available on Apple hardware.
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*
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* Note that many of the algorithms can be influenced by the UpLo template
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* argument. All matrices are assumed to be symmetric. For example, the following
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* creates an LDLT factorization where your matrix is symmetric (implicit) and
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* uses the lower triangle:
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*
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* \code
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* AccelerateLDLT<SparseMatrix<float>, Lower> ldlt;
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* \endcode
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*/
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// IWYU pragma: begin_exports
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#include "src/AccelerateSupport/AccelerateSupport.h"
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// IWYU pragma: end_exports
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#include "src/Core/util/ReenableStupidWarnings.h"
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#endif // EIGEN_ACCELERATESUPPORT_MODULE_H

‎inst/include/Eigen/Cholesky‎

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#include "src/Core/util/DisableStupidWarnings.h"
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/** \defgroup Cholesky_Module Cholesky module
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*
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*
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*
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* This module provides two variants of the Cholesky decomposition for selfadjoint (hermitian) matrices.
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* Those decompositions are also accessible via the following methods:
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* - MatrixBase::llt()
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* - MatrixBase::ldlt()
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* - SelfAdjointView::llt()
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* - SelfAdjointView::ldlt()
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*
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* \code
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* #include <Eigen/Cholesky>
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* \endcode
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*/
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*
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*
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*
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* This module provides two variants of the Cholesky decomposition for selfadjoint (hermitian) matrices.
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* Those decompositions are also accessible via the following methods:
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* - MatrixBase::llt()
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* - MatrixBase::ldlt()
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* - SelfAdjointView::llt()
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* - SelfAdjointView::ldlt()
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*
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* \code
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* #include <Eigen/Cholesky>
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* \endcode
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*/
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// IWYU pragma: begin_exports
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#include "src/Cholesky/LLT.h"
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#include "src/Cholesky/LDLT.h"
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#ifdef EIGEN_USE_LAPACKE
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#ifdef EIGEN_USE_MKL
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#include "mkl_lapacke.h"
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#else
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#include "src/misc/lapacke.h"
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#endif
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#include "src/misc/lapacke_helpers.h"
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#include "src/Cholesky/LLT_LAPACKE.h"
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#endif
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// IWYU pragma: end_exports
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#include "src/Core/util/ReenableStupidWarnings.h"
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#endif // EIGEN_CHOLESKY_MODULE_H
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#endif // EIGEN_CHOLESKY_MODULE_H

‎inst/include/Eigen/CholmodSupport‎

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#include "src/Core/util/DisableStupidWarnings.h"
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/** \ingroup Support_modules
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* \defgroup CholmodSupport_Module CholmodSupport module
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*
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* This module provides an interface to the Cholmod library which is part of the <a href="http://www.suitesparse.com">suitesparse</a> package.
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* It provides the two following main factorization classes:
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* - class CholmodSupernodalLLT: a supernodal LLT Cholesky factorization.
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* - class CholmodDecomposiiton: a general L(D)LT Cholesky factorization with automatic or explicit runtime selection of the underlying factorization method (supernodal or simplicial).
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*
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* For the sake of completeness, this module also propose the two following classes:
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* - class CholmodSimplicialLLT
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* - class CholmodSimplicialLDLT
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* Note that these classes does not bring any particular advantage compared to the built-in
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* SimplicialLLT and SimplicialLDLT factorization classes.
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*
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* \code
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* #include <Eigen/CholmodSupport>
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* \endcode
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*
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* 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.
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* The dependencies depend on how cholmod has been compiled.
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* For a cmake based project, you can use our FindCholmod.cmake module to help you in this task.
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#include <RcppEigenCholmod.h>
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/** \ingroup Support_modules
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* \defgroup CholmodSupport_Module CholmodSupport module
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*
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* This module provides an interface to the Cholmod library which is part of the <a
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* href="http://www.suitesparse.com">suitesparse</a> package. It provides the two following main factorization classes:
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* - class CholmodSupernodalLLT: a supernodal LLT Cholesky factorization.
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* - class CholmodDecomposition: a general L(D)LT Cholesky factorization with automatic or explicit runtime selection of
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* the underlying factorization method (supernodal or simplicial).
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*
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* For the sake of completeness, this module also propose the two following classes:
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* - class CholmodSimplicialLLT
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* - class CholmodSimplicialLDLT
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* Note that these classes does not bring any particular advantage compared to the built-in
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* SimplicialLLT and SimplicialLDLT factorization classes.
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*
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* \code
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* #include <Eigen/CholmodSupport>
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* \endcode
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*
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* In order to use this module, the cholmod headers must be accessible from the include paths, and your binary must be
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* linked to the cholmod library and its dependencies. The dependencies depend on how cholmod has been compiled. For a
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* cmake based project, you can use our FindCholmod.cmake module to help you in this task.
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*
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*/
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// IWYU pragma: begin_exports
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#include "src/CholmodSupport/CholmodSupport.h"
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// IWYU pragma: end_exports
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#include "src/Core/util/ReenableStupidWarnings.h"
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#endif // EIGEN_CHOLMODSUPPORT_MODULE_H
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#endif // EIGEN_CHOLMODSUPPORT_MODULE_H

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