RcppCore · eddelbuettel · Mar 3, 2026 · Dec 25, 2025 · Dec 25, 2025 · Dec 25, 2025
diff --git a/ChangeLog b/ChangeLog
@@ -2,6 +2,11 @@
 
 	* .github/workflows/ci.yaml: Switch to actions/checkout@v6
 
+2026-01-07  Dirk Eddelbuettel  <edd@debian.org>
+
+	* README.md: Another pair of URL updates for Eigen
+	* man/fastLm.Rd: Idem
+
 2025-12-30  Dirk Eddelbuettel  <edd@debian.org>
 
 	* inst/tinytest/test_misc.R: Additional tests predicate
@@ -29,6 +34,28 @@
 	* man/RcppEigen_throttle_cores.Rd: Document additional helpers
 	* cleanup: Minor extension
 
+2025-12-26  Dirk Eddelbuettel  <edd@debian.org>
+
+	* inst/include/Eigen/src/CholmodSupport/CholmodSupport.h: Comment-out
+	another SuiteSparse reference
+
+	* patches/eigen-5.0.0.diff: Updated against git commit of Eigen 5.0.0 sync
+
+2025-12-25  Dirk Eddelbuettel  <edd@debian.org>
+
+	* inst/include/Eigen/: Sync with upstream Eigen 5.0.0 (aka 3.5.0)
+	* inst/include/unsupported/Eigen/: Idem
+
+	* patches/eigen-5.0.0.diff: Summary of changes applied
+
+	* inst/include/RcppEigenForward.h: No longer use deprecated type
+	* inst/include/RcppEigenWrap.h: Idem
+	* inst/tinytest/cpp/rcppeigen.cpp: Adjust test to non-deprecated map
+	* inst/tinytest/cpp/sparse.cpp: Skip test of deprecated type
+	* inst/tinytest/test_sparse.R: Idem
+
+	* src/fastLm.cpp (SVD::SVD): Update to current form of option setting
+
 2025-08-26  Dirk Eddelbuettel  <edd@debian.org>
 
 	* inst/tinytest/test_misc.R: Add minimal test for EigenNbThreads()

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: RcppEigen
 Type: Package
 Title: 'Rcpp' Integration for the 'Eigen' Templated Linear Algebra Library
-Version: 0.3.4.0.2-1
+Version: 0.4.9.9-1
 Date: 2025-12-29
 Authors@R: c(person("Doug", "Bates", role = "aut",
                     comment = c(ORCID = "0000-0001-8316-9503")),

diff --git a/README.md b/README.md
@@ -18,13 +18,13 @@
 
 ### Synopsis
 
-[Eigen](http://eigen.tuxfamily.org/index.php?title=Main_Page) is a C++ template library for linear algebra:
+[Eigen](https://libeigen.gitlab.io/) is a C++ 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, decompositions of such matrices,
 and solutions of linear systems. Its performance on many algorithms is comparable with
 some of the best implementations based on `Lapack` and level-3 `BLAS`.
 
-RcppEigen provides an interface from R to and from [Eigen](http://eigen.tuxfamily.org/index.php?title=Main_Page) by
+RcppEigen provides an interface from R to and from [Eigen](https://libeigen.gitlab.io/) by
 using the facilities offered by the [Rcpp](http://dirk.eddelbuettel.com/code/rcpp.html)
 package for seamless R and C++ integration.
 
@@ -62,8 +62,8 @@ post](https://gallery.rcpp.org/articles/eigen-eigenvalues/) for details.
 
 ### Status
 
-The package is mature and under active development, following the
-[Eigen](http://eigen.tuxfamily.org/index.php?title=Main_Page) release cycle.
+The package is mature and under acthttps://libeigen.gitlab.io/ive development, following the
+[Eigen](https://libeigen.gitlab.io/) release cycle.
 
 ### Documentation
 

diff --git a/inst/include/Eigen/AccelerateSupport b/inst/include/Eigen/AccelerateSupport
@@ -0,0 +1,52 @@
+// This file is part of Eigen, a lightweight C++ template library
+// for linear algebra.
+//
+// This Source Code Form is subject to the terms of the Mozilla
+// Public License v. 2.0. If a copy of the MPL was not distributed
+// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
+#ifndef EIGEN_ACCELERATESUPPORT_MODULE_H
+#define EIGEN_ACCELERATESUPPORT_MODULE_H
+
+#include "SparseCore"
+
+#include "src/Core/util/DisableStupidWarnings.h"
+
+/** \ingroup Support_modules
+ * \defgroup AccelerateSupport_Module AccelerateSupport module
+ *
+ * This module provides an interface to the Apple Accelerate library.
+ * It provides the seven following main factorization classes:
+ * - class AccelerateLLT: a Cholesky (LL^T) factorization.
+ * - class AccelerateLDLT: the default LDL^T factorization.
+ * - class AccelerateLDLTUnpivoted: a Cholesky-like LDL^T factorization with only 1x1 pivots and no pivoting
+ * - class AccelerateLDLTSBK: an LDL^T factorization with Supernode Bunch-Kaufman and static pivoting
+ * - class AccelerateLDLTTPP: an LDL^T factorization with full threshold partial pivoting
+ * - class AccelerateQR: a QR factorization
+ * - class AccelerateCholeskyAtA: a QR factorization without storing Q (equivalent to A^TA = R^T R)
+ *
+ * \code
+ * #include <Eigen/AccelerateSupport>
+ * \endcode
+ *
+ * In order to use this module, the Accelerate headers must be accessible from
+ * the include paths, and your binary must be linked to the Accelerate framework.
+ * The Accelerate library is only available on Apple hardware.
+ *
+ * Note that many of the algorithms can be influenced by the UpLo template
+ * argument. All matrices are assumed to be symmetric. For example, the following
+ * creates an LDLT factorization where your matrix is symmetric (implicit) and
+ * uses the lower triangle:
+ *
+ * \code
+ * AccelerateLDLT<SparseMatrix<float>, Lower> ldlt;
+ * \endcode
+ */
+
+// IWYU pragma: begin_exports
+#include "src/AccelerateSupport/AccelerateSupport.h"
+// IWYU pragma: end_exports
+
+#include "src/Core/util/ReenableStupidWarnings.h"
+
+#endif  // EIGEN_ACCELERATESUPPORT_MODULE_H
diff --git a/inst/include/Eigen/Cholesky b/inst/include/Eigen/Cholesky
@@ -14,32 +14,30 @@
 #include "src/Core/util/DisableStupidWarnings.h"
 
 /** \defgroup Cholesky_Module Cholesky module
-  *
-  *
-  *
-  * This module provides two variants of the Cholesky decomposition for selfadjoint (hermitian) matrices.
-  * Those decompositions are also accessible via the following methods:
-  *  - MatrixBase::llt()
-  *  - MatrixBase::ldlt()
-  *  - SelfAdjointView::llt()
-  *  - SelfAdjointView::ldlt()
-  *
-  * \code
-  * #include <Eigen/Cholesky>
-  * \endcode
-  */
+ *
+ *
+ *
+ * This module provides two variants of the Cholesky decomposition for selfadjoint (hermitian) matrices.
+ * Those decompositions are also accessible via the following methods:
+ *  - MatrixBase::llt()
+ *  - MatrixBase::ldlt()
+ *  - SelfAdjointView::llt()
+ *  - SelfAdjointView::ldlt()
+ *
+ * \code
+ * #include <Eigen/Cholesky>
+ * \endcode
+ */
 
+// IWYU pragma: begin_exports
 #include "src/Cholesky/LLT.h"
 #include "src/Cholesky/LDLT.h"
 #ifdef EIGEN_USE_LAPACKE
-#ifdef EIGEN_USE_MKL
-#include "mkl_lapacke.h"
-#else
-#include "src/misc/lapacke.h"
-#endif
+#include "src/misc/lapacke_helpers.h"
 #include "src/Cholesky/LLT_LAPACKE.h"
 #endif
+// IWYU pragma: end_exports
 
 #include "src/Core/util/ReenableStupidWarnings.h"
 
-#endif // EIGEN_CHOLESKY_MODULE_H
+#endif  // EIGEN_CHOLESKY_MODULE_H
diff --git a/inst/include/Eigen/CholmodSupport b/inst/include/Eigen/CholmodSupport
@@ -12,33 +12,37 @@
 
 #include "src/Core/util/DisableStupidWarnings.h"
 
-/** \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.suitesparse.com">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 <RcppEigenCholmod.h>
 
+/** \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.suitesparse.com">suitesparse</a> package. It provides the two following main factorization classes:
+ * - class CholmodSupernodalLLT: a supernodal LLT Cholesky factorization.
+ * - class CholmodDecomposition: 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.
+ *
+ */
+
+// IWYU pragma: begin_exports
 #include "src/CholmodSupport/CholmodSupport.h"
+// IWYU pragma: end_exports
 
 #include "src/Core/util/ReenableStupidWarnings.h"
 
-#endif // EIGEN_CHOLMODSUPPORT_MODULE_H
-
+#endif  // EIGEN_CHOLMODSUPPORT_MODULE_H