Update to Eigen 5.0.1 (#150)

* Synchronized with upstream 5.0.1 release (via git tag in 5.0 branch)

* Applied (and documented) diff carried over from 5.0.0

* Additional one-line change, added to diff as well

* Set release to 0.4.9.9-2 for upstream 5.0.1

Author: eddelbuettel

.Rbuildignore

@@ -13,3 +13,4 @@ debian
 ^\.github
 ^\.codecov.yml
 ^\.covrignore
+^local

ChangeLog

@@ -1,3 +1,14 @@
+2026-06-04  Dirk Eddelbuettel  <edd@debian.org>
+
+	* inst/include/Eigen/: Sync with upstream Eigen 5.0.1
+	* inst/include/unsupported/Eigen/: Idem
+
+	* inst/include/Eigen/CholmodSupport: Apply previous patch
+	* inst/include/Eigen/src/CholmodSupport/CholmodSupport.h: Idem
+	* inst/include/Eigen/src/Core/util/DisableStupidWarnings.h: Idem
+	* inst/include/unsupported/Eigen/src/SparseExtra/MatrixMarketIterator.h: Idem
+	* inst/include/Eigen/src/Core/arch/AltiVec/PacketMath.h: New one-line patch
+
 2026-05-03  Dirk Eddelbuettel  <edd@debian.org>
 
 	* vignettes/rnw/RcppEigen-Introduction.Rnw: Moved, also update three

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: RcppEigen
 Type: Package
 Title: 'Rcpp' Integration for the 'Eigen' Templated Linear Algebra Library
-Version: 0.4.9.9-1
-Date: 2025-12-29
+Version: 0.4.9.9-2
+Date: 2026-06-04
 Authors@R: c(person("Doug", "Bates", role = "aut",
                     comment = c(ORCID = "0000-0001-8316-9503")),
              person("Dirk", "Eddelbuettel", role = c("aut", "cre"), email = "edd@debian.org",

inst/include/Eigen/Core

@@ -106,6 +106,11 @@
 #include <thread>
 #endif
 
+// for __cpp_lib feature test macros
+#if defined(__has_include) && __has_include(<version>)
+#include <version>
+#endif
+
 // for std::bit_cast()
 #if defined(__cpp_lib_bit_cast) && __cpp_lib_bit_cast >= 201806L
 #include <bit>

inst/include/Eigen/Version

@@ -6,9 +6,9 @@
 // As of Eigen3 5.0.0, we have moved to Semantic Versioning (semver.org).
 #define EIGEN_MAJOR_VERSION 5
 #define EIGEN_MINOR_VERSION 0
-#define EIGEN_PATCH_VERSION 0
+#define EIGEN_PATCH_VERSION 1
 #define EIGEN_PRERELEASE_VERSION ""
 #define EIGEN_BUILD_VERSION ""
-#define EIGEN_VERSION_STRING "5.0.0"
+#define EIGEN_VERSION_STRING "5.0.1"
 
 #endif  // EIGEN_VERSION_H

inst/include/Eigen/src/CholmodSupport/CholmodSupport.h

@@ -177,13 +177,13 @@ namespace internal {
   template <typename StorageIndex_>                                 \
   inline ret cm_##name(cholmod_common& Common) {                    \
     return R_MATRIX_CHOLMOD(name)(&Common);			    \
-  }                                                                 
+  }
 
 #define EIGEN_CHOLMOD_SPECIALIZE1(ret, name, t1, a1)                    \
   template <typename StorageIndex_>                                     \
   inline ret cm_##name(t1& a1, cholmod_common& Common) {                \
     return R_MATRIX_CHOLMOD(name) (&a1, &Common);			\
-  }                                                                          
+  }
 
 EIGEN_CHOLMOD_SPECIALIZE0(int, start)
 EIGEN_CHOLMOD_SPECIALIZE0(int, finish)

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

@@ -56,11 +56,11 @@ class vml_assign_traits {
                                                    : int(Dst::MaxRowsAtCompileTime),
     MaxSizeAtCompileTime = Dst::SizeAtCompileTime,
 
-    MightEnableVml = StorageOrdersAgree && DstHasDirectAccess && SrcHasDirectAccess &&
+    MightEnableVml = bool(StorageOrdersAgree) && bool(DstHasDirectAccess) && bool(SrcHasDirectAccess) &&
                      Src::InnerStrideAtCompileTime == 1 && Dst::InnerStrideAtCompileTime == 1,
-    MightLinearize = MightEnableVml && (int(Dst::Flags) & int(Src::Flags) & LinearAccessBit),
-    VmlSize = MightLinearize ? MaxSizeAtCompileTime : InnerMaxSize,
-    LargeEnough = VmlSize == Dynamic || VmlSize >= EIGEN_MKL_VML_THRESHOLD
+    MightLinearize = bool(MightEnableVml) && (int(Dst::Flags) & int(Src::Flags) & LinearAccessBit),
+    VmlSize = bool(MightLinearize) ? MaxSizeAtCompileTime : InnerMaxSize,
+    LargeEnough = (VmlSize == Dynamic) || VmlSize >= EIGEN_MKL_VML_THRESHOLD
   };
 
  public:

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

@@ -94,7 +94,7 @@ class CwiseNullaryOp : public internal::dense_xpr_base<CwiseNullaryOp<NullaryOp,
  * the returned matrix. Must be compatible with this MatrixBase type.
  *
  * This variant is meant to be used for dynamic-size matrix types. For fixed-size types,
- * it is redundant to pass \a rows and \a cols as arguments, so Zero() should be used
+ * it is redundant to pass \a rows and \a cols as arguments, so NullaryExpr(const CustomNullaryOp&) should be used
  * instead.
  *
  * The template parameter \a CustomNullaryOp is the type of the functor.
@@ -121,7 +121,7 @@ EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
  * \only_for_vectors
  *
  * This variant is meant to be used for dynamic-size vector types. For fixed-size types,
- * it is redundant to pass \a size as argument, so Zero() should be used
+ * it is redundant to pass \a size as argument, so NullaryExpr(const CustomNullaryOp&) should be used
  * instead.
  *
  * The template parameter \a CustomNullaryOp is the type of the functor.
@@ -174,7 +174,7 @@ EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE
  * the returned matrix. Must be compatible with this DenseBase type.
  *
  * This variant is meant to be used for dynamic-size matrix types. For fixed-size types,
- * it is redundant to pass \a rows and \a cols as arguments, so Zero() should be used
+ * it is redundant to pass \a rows and \a cols as arguments, so Constant(const Scalar&) should be used
  * instead.
  *
  * The template parameter \a CustomNullaryOp is the type of the functor.
@@ -195,7 +195,7 @@ DenseBase<Derived>::Constant(Index rows, Index cols, const Scalar& value) {
  * \only_for_vectors
  *
  * This variant is meant to be used for dynamic-size vector types. For fixed-size types,
- * it is redundant to pass \a size as argument, so Zero() should be used
+ * it is redundant to pass \a size as argument, so Constant(const Scalar&) should be used
  * instead.
  *
  * The template parameter \a CustomNullaryOp is the type of the functor.

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

@@ -65,20 +65,15 @@ struct plain_array {
 
 template <typename T, int Size, int MatrixOrArrayOptions>
 struct plain_array<T, Size, MatrixOrArrayOptions, 0> {
-  T array[Size];
+  // on some 32-bit platforms, stack-allocated arrays are aligned to 4 bytes, not the preferred alignment of T
+  EIGEN_ALIGN_TO_BOUNDARY(alignof(T)) T array[Size];
 #if defined(EIGEN_NO_DEBUG) || defined(EIGEN_TESTING_PLAINOBJECT_CTOR)
   EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE constexpr plain_array() = default;
 #else
   EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE constexpr plain_array() { EIGEN_MAKE_STACK_ALLOCATION_ASSERT(Size * sizeof(T)) }
 #endif
 };
 
-template <typename T, int MatrixOrArrayOptions, int Alignment>
-struct plain_array<T, 0, MatrixOrArrayOptions, Alignment> {
-  T array[1];
-  EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE constexpr plain_array() = default;
-};
-
 template <typename T, int Size, int Options, int Alignment>
 EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE constexpr void swap_plain_array(plain_array<T, Size, Options, Alignment>& a,
                                                                       plain_array<T, Size, Options, Alignment>& b,

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

@@ -115,17 +115,15 @@ struct eigen_zero_impl<Xpr, /*use_memset*/ false> {
 template <typename Xpr>
 struct eigen_zero_impl<Xpr, /*use_memset*/ true> {
   using Scalar = typename Xpr::Scalar;
-  static constexpr size_t max_bytes = (std::numeric_limits<std::ptrdiff_t>::max)();
   static EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void run(Xpr& dst) {
-    const size_t num_bytes = dst.size() * sizeof(Scalar);
-    if (num_bytes == 0) return;
+    const std::ptrdiff_t num_bytes = dst.size() * static_cast<std::ptrdiff_t>(sizeof(Scalar));
+    if (num_bytes <= 0) return;
     void* dst_ptr = static_cast<void*>(dst.data());
 #ifndef EIGEN_NO_DEBUG
-    if (num_bytes > max_bytes) throw_std_bad_alloc();
     eigen_assert((dst_ptr != nullptr) && "null pointer dereference error!");
 #endif
     EIGEN_USING_STD(memset);
-    memset(dst_ptr, 0, num_bytes);
+    memset(dst_ptr, 0, static_cast<std::size_t>(num_bytes));
   }
   template <typename SrcXpr>
   static EIGEN_DEVICE_FUNC EIGEN_STRONG_INLINE void run(Xpr& dst, const SrcXpr& src) {