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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)
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‎ChangeLog‎

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -20,6 +20,8 @@
2020
* inst/include/Eigen/src/CholmodSupport/CholmodSupport.h: Comment-out
2121
another SuiteSparse reference
2222

23+
* patches/eigen-5.0.0.diff: Updated against git commit of Eigen 5.0.0 sync
24+
2325
2025-12-25 Dirk Eddelbuettel <[email protected]>
2426

2527
* inst/include/Eigen/: Sync with upstream Eigen 5.0.0 (aka 3.5.0)

‎patches/eigen-5.0.0.diff‎

Lines changed: 199 additions & 61 deletions
Original file line numberDiff line numberDiff line change
@@ -1,36 +1,56 @@
1-
diff --git c/inst/include/Eigen/CholmodSupport i/inst/include/Eigen/CholmodSupport
1+
diff --git c/inst/include/Eigen/CholmodSupport w/inst/include/Eigen/CholmodSupport
22
index adc5f8d..bff39e6 100644
33
--- c/inst/include/Eigen/CholmodSupport
4-
+++ i/inst/include/Eigen/CholmodSupport
4+
+++ w/inst/include/Eigen/CholmodSupport
55
@@ -12,7 +12,7 @@
6-
6+
77
#include "src/Core/util/DisableStupidWarnings.h"
8-
8+
99
-#include <cholmod.h>
1010
+#include <RcppEigenCholmod.h>
11-
11+
1212
/** \ingroup Support_modules
1313
* \defgroup CholmodSupport_Module CholmodSupport module
14-
diff --git c/inst/include/Eigen/src/CholmodSupport/CholmodSupport.h i/inst/include/Eigen/src/CholmodSupport/CholmodSupport.h
15-
index 7e3c881..cf0059f 100644
14+
diff --git c/inst/include/Eigen/src/CholmodSupport/CholmodSupport.h w/inst/include/Eigen/src/CholmodSupport/CholmodSupport.h
15+
index 7e3c881..758fb5a 100644
1616
--- c/inst/include/Eigen/src/CholmodSupport/CholmodSupport.h
17-
+++ i/inst/include/Eigen/src/CholmodSupport/CholmodSupport.h
18-
@@ -170,24 +170,12 @@ namespace internal {
19-
// template specializations for int and long that call the correct cholmod method
20-
17+
+++ w/inst/include/Eigen/src/CholmodSupport/CholmodSupport.h
18+
@@ -13,6 +13,10 @@
19+
// IWYU pragma: private
20+
#include "./InternalHeaderCheck.h"
21+
22+
+#ifndef R_MATRIX_CHOLMOD
23+
+# define R_MATRIX_CHOLMOD(_NAME_) cholmod_ ## _NAME_
24+
+#endif
25+
+
26+
namespace Eigen {
27+
28+
namespace internal {
29+
@@ -84,8 +88,8 @@ cholmod_sparse viewAsCholmod(Ref<SparseMatrix<Scalar_, Options_, StorageIndex_>
30+
31+
if (internal::is_same<StorageIndex_, int>::value) {
32+
res.itype = CHOLMOD_INT;
33+
- } else if (internal::is_same<StorageIndex_, SuiteSparse_long>::value) {
34+
- res.itype = CHOLMOD_LONG;
35+
+ // } else if (internal::is_same<StorageIndex_, SuiteSparse_long>::value) {
36+
+ // res.itype = CHOLMOD_LONG;
37+
} else {
38+
eigen_assert(false && "Index type not supported yet");
39+
}
40+
@@ -172,22 +176,14 @@ namespace internal {
2141
#define EIGEN_CHOLMOD_SPECIALIZE0(ret, name) \
22-
- template <typename StorageIndex_> \
23-
- inline ret cm_##name(cholmod_common& Common) { \
42+
template <typename StorageIndex_> \
43+
inline ret cm_##name(cholmod_common& Common) { \
2444
- return cholmod_##name(&Common); \
2545
- } \
2646
- template <> \
2747
- inline ret cm_##name<SuiteSparse_long>(cholmod_common & Common) { \
2848
- return cholmod_l_##name(&Common); \
2949
- }
30-
+ template<typename _StorageIndex> inline ret cm_ ## name \
31-
+ (cholmod_common &Common) { return cholmod_ ## name (&Common); }
32-
33-
#define EIGEN_CHOLMOD_SPECIALIZE1(ret, name, t1, a1) \
50+
+ return R_MATRIX_CHOLMOD(name)(&Common); \
51+
+ }
52+
53+
-#define EIGEN_CHOLMOD_SPECIALIZE1(ret, name, t1, a1) \
3454
- template <typename StorageIndex_> \
3555
- inline ret cm_##name(t1& a1, cholmod_common& Common) { \
3656
- return cholmod_##name(&a1, &Common); \
@@ -39,64 +59,72 @@ index 7e3c881..cf0059f 100644
3959
- inline ret cm_##name<SuiteSparse_long>(t1 & a1, cholmod_common & Common) { \
4060
- return cholmod_l_##name(&a1, &Common); \
4161
- }
42-
+ template<typename _StorageIndex> inline ret cm_ ## name \
43-
+ (t1& a1, cholmod_common &Common) { return cholmod_ ## name (&a1, &Common); }
44-
62+
+#define EIGEN_CHOLMOD_SPECIALIZE1(ret, name, t1, a1) \
63+
+ template <typename StorageIndex_> \
64+
+ inline ret cm_##name(t1& a1, cholmod_common& Common) { \
65+
+ return R_MATRIX_CHOLMOD(name) (&a1, &Common); \
66+
+ }
67+
4568
EIGEN_CHOLMOD_SPECIALIZE0(int, start)
4669
EIGEN_CHOLMOD_SPECIALIZE0(int, finish)
47-
@@ -203,31 +191,31 @@ template <typename StorageIndex_>
70+
@@ -201,33 +197,33 @@ EIGEN_CHOLMOD_SPECIALIZE1(cholmod_sparse*, factor_to_sparse, cholmod_factor, L)
71+
72+
template <typename StorageIndex_>
4873
inline cholmod_dense* cm_solve(int sys, cholmod_factor& L, cholmod_dense& B, cholmod_common& Common) {
49-
return cholmod_solve(sys, &L, &B, &Common);
50-
}
74+
- return cholmod_solve(sys, &L, &B, &Common);
75+
-}
5176
-template <>
5277
-inline cholmod_dense* cm_solve<SuiteSparse_long>(int sys, cholmod_factor& L, cholmod_dense& B, cholmod_common& Common) {
5378
- return cholmod_l_solve(sys, &L, &B, &Common);
54-
-}
55-
+//template <>
56-
+//inline cholmod_dense* cm_solve<SuiteSparse_long>(int sys, cholmod_factor& L, cholmod_dense& B, cholmod_common& Common) {
57-
+// return cholmod_l_solve(sys, &L, &B, &Common);
58-
+//}
59-
79+
+ return R_MATRIX_CHOLMOD(solve) (sys, &L, &B, &Common);
80+
}
81+
+// template <>
82+
+// inline cholmod_dense* cm_solve<SuiteSparse_long>(int sys, cholmod_factor& L, cholmod_dense& B, cholmod_common& Common) {
83+
+// return cholmod_l_solve(sys, &L, &B, &Common);
84+
+// }
85+
6086
template <typename StorageIndex_>
6187
inline cholmod_sparse* cm_spsolve(int sys, cholmod_factor& L, cholmod_sparse& B, cholmod_common& Common) {
62-
return cholmod_spsolve(sys, &L, &B, &Common);
63-
}
88+
- return cholmod_spsolve(sys, &L, &B, &Common);
89+
-}
6490
-template <>
6591
-inline cholmod_sparse* cm_spsolve<SuiteSparse_long>(int sys, cholmod_factor& L, cholmod_sparse& B,
6692
- cholmod_common& Common) {
6793
- return cholmod_l_spsolve(sys, &L, &B, &Common);
68-
-}
69-
+//template <>
70-
+//inline cholmod_sparse* cm_spsolve<SuiteSparse_long>(int sys, cholmod_factor& L, cholmod_sparse& B,
71-
+// cholmod_common& Common) {
72-
+// return cholmod_l_spsolve(sys, &L, &B, &Common);
73-
+//}
74-
94+
+ return R_MATRIX_CHOLMOD(spsolve) (sys, &L, &B, &Common);
95+
}
96+
+// template <>
97+
+// inline cholmod_sparse* cm_spsolve<SuiteSparse_long>(int sys, cholmod_factor& L, cholmod_sparse& B,
98+
+// cholmod_common& Common) {
99+
+// return cholmod_l_spsolve(sys, &L, &B, &Common);
100+
+// }
101+
75102
template <typename StorageIndex_>
76103
inline int cm_factorize_p(cholmod_sparse* A, double beta[2], StorageIndex_* fset, std::size_t fsize, cholmod_factor* L,
77104
cholmod_common& Common) {
78-
return cholmod_factorize_p(A, beta, fset, fsize, L, &Common);
79-
}
105+
- return cholmod_factorize_p(A, beta, fset, fsize, L, &Common);
106+
-}
80107
-template <>
81108
-inline int cm_factorize_p<SuiteSparse_long>(cholmod_sparse* A, double beta[2], SuiteSparse_long* fset,
82109
- std::size_t fsize, cholmod_factor* L, cholmod_common& Common) {
83110
- return cholmod_l_factorize_p(A, beta, fset, fsize, L, &Common);
84-
-}
85-
+//template <>
86-
+//inline int cm_factorize_p<SuiteSparse_long>(cholmod_sparse* A, double beta[2], SuiteSparse_long* fset,
87-
+// std::size_t fsize, cholmod_factor* L, cholmod_common& Common) {
88-
+// return cholmod_l_factorize_p(A, beta, fset, fsize, L, &Common);
89-
+//}
90-
111+
+ return R_MATRIX_CHOLMOD(factorize_p) (A, beta, fset, fsize, L, &Common);
112+
}
113+
+// template <>
114+
+// inline int cm_factorize_p<SuiteSparse_long>(cholmod_sparse* A, double beta[2], SuiteSparse_long* fset,
115+
+// std::size_t fsize, cholmod_factor* L, cholmod_common& Common) {
116+
+// return cholmod_l_factorize_p(A, beta, fset, fsize, L, &Common);
117+
+// }
118+
91119
#undef EIGEN_CHOLMOD_SPECIALIZE0
92120
#undef EIGEN_CHOLMOD_SPECIALIZE1
93-
diff --git c/inst/include/Eigen/src/Core/util/DisableStupidWarnings.h i/inst/include/Eigen/src/Core/util/DisableStupidWarnings.h
121+
diff --git c/inst/include/Eigen/src/Core/util/DisableStupidWarnings.h w/inst/include/Eigen/src/Core/util/DisableStupidWarnings.h
94122
index ab0c542..8c27b14 100644
95123
--- c/inst/include/Eigen/src/Core/util/DisableStupidWarnings.h
96-
+++ i/inst/include/Eigen/src/Core/util/DisableStupidWarnings.h
124+
+++ w/inst/include/Eigen/src/Core/util/DisableStupidWarnings.h
97125
@@ -42,45 +42,45 @@
98126
#pragma warning disable 2196 279 1684 2259
99-
127+
100128
#elif defined __clang__
101129
-#ifndef EIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS
102130
-#pragma clang diagnostic push
@@ -138,9 +166,9 @@ index ab0c542..8c27b14 100644
138166
+// #endif
139167
+// #endif
140168
+// #endif
141-
169+
142170
#elif defined __GNUC__ && !defined(__FUJITSU)
143-
171+
144172
-#if (!defined(EIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS)) && (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 6))
145173
-#pragma GCC diagnostic push
146174
-#endif
@@ -174,19 +202,129 @@ index ab0c542..8c27b14 100644
174202
+// #pragma GCC diagnostic ignored "-Wattributes"
175203
+// #endif
176204
#endif
177-
205+
178206
#if defined __NVCC__ && defined __CUDACC__
179-
diff --git c/inst/include/unsupported/Eigen/src/SparseExtra/MatrixMarketIterator.h i/inst/include/unsupported/Eigen/src/SparseExtra/MatrixMarketIterator.h
180-
index 15d7fb2..0ccb566 100644
207+
diff --git c/inst/include/RcppEigenForward.h w/inst/include/RcppEigenForward.h
208+
index ef347e4..a41212c 100644
209+
--- c/inst/include/RcppEigenForward.h
210+
+++ w/inst/include/RcppEigenForward.h
211+
@@ -54,10 +54,10 @@ namespace Rcpp {
212+
template<typename T> class Exporter< Eigen::Array<T, Eigen::Dynamic, 1> >;
213+
template<typename T> class Exporter< Eigen::Array<T, 1, Eigen::Dynamic> >;
214+
template<typename T> class Exporter< Eigen::Map<Eigen::SparseMatrix<T> > >;
215+
- template<typename T> class Exporter< Eigen::MappedSparseMatrix<T> >; // Deprecated
216+
+ //template<typename T> class Exporter< Eigen::MappedSparseMatrix<T> >; // Deprecated
217+
template<typename T> class Exporter< Eigen::SparseMatrix<T> >;
218+
template<typename T> class Exporter< Eigen::Map<Eigen::SparseMatrix<T, Eigen::RowMajor> > >;
219+
- template<typename T> class Exporter< Eigen::MappedSparseMatrix<T, Eigen::RowMajor> >; // Deprecated
220+
+ //template<typename T> class Exporter< Eigen::MappedSparseMatrix<T, Eigen::RowMajor> >; // Deprecated
221+
template<typename T> class Exporter< Eigen::SparseMatrix<T, Eigen::RowMajor> >;
222+
223+
} // namespace traits
224+
diff --git c/inst/include/RcppEigenWrap.h w/inst/include/RcppEigenWrap.h
225+
index 3c0e04e..4750b61 100644
226+
--- c/inst/include/RcppEigenWrap.h
227+
+++ w/inst/include/RcppEigenWrap.h
228+
@@ -310,24 +310,24 @@ namespace Rcpp{
229+
IntegerVector d_dims, d_i, d_p;
230+
Vector<RTYPE> xx ;
231+
};
232+
- // Deprecated
233+
- template<typename T>
234+
- class Exporter<Eigen::MappedSparseMatrix<T> > {
235+
- public:
236+
- const static int RTYPE = ::Rcpp::traits::r_sexptype_traits<T>::rtype ;
237+
- Exporter(SEXP x) : d_x(x), d_dims(d_x.slot("Dim")), d_i(d_x.slot("i")), d_p(d_x.slot("p")), xx( d_x.slot("x") ) {
238+
- if (!d_x.is("dgCMatrix"))
239+
- throw std::invalid_argument("Need S4 class dgCMatrix for a mapped sparse matrix");
240+
- }
241+
- Eigen::MappedSparseMatrix<T> get() {
242+
- return Eigen::MappedSparseMatrix<T>(d_dims[0], d_dims[1], d_p[d_dims[1]],
243+
- d_p.begin(), d_i.begin(), xx.begin() );
244+
- }
245+
- protected:
246+
- S4 d_x;
247+
- IntegerVector d_dims, d_i, d_p;
248+
- Vector<RTYPE> xx ;
249+
- };
250+
+ // // Deprecated
251+
+ // template<typename T>
252+
+ // class Exporter<Eigen::MappedSparseMatrix<T> > {
253+
+ // public:
254+
+ // const static int RTYPE = ::Rcpp::traits::r_sexptype_traits<T>::rtype ;
255+
+ // Exporter(SEXP x) : d_x(x), d_dims(d_x.slot("Dim")), d_i(d_x.slot("i")), d_p(d_x.slot("p")), xx( d_x.slot("x") ) {
256+
+ // if (!d_x.is("dgCMatrix"))
257+
+ // throw std::invalid_argument("Need S4 class dgCMatrix for a mapped sparse matrix");
258+
+ // }
259+
+ // Eigen::MappedSparseMatrix<T> get() {
260+
+ // return Eigen::MappedSparseMatrix<T>(d_dims[0], d_dims[1], d_p[d_dims[1]],
261+
+ // d_p.begin(), d_i.begin(), xx.begin() );
262+
+ // }
263+
+ // protected:
264+
+ // S4 d_x;
265+
+ // IntegerVector d_dims, d_i, d_p;
266+
+ // Vector<RTYPE> xx ;
267+
+ // };
268+
269+
// Starting from Eigen 3.3 MappedSparseMatrix was deprecated.
270+
// The new type is Map<SparseMatrix>.
271+
@@ -348,24 +348,24 @@ namespace Rcpp{
272+
IntegerVector d_dims, d_j, d_p;
273+
Vector<RTYPE> xx ;
274+
};
275+
- // Deprecated
276+
- template<typename T>
277+
- class Exporter<Eigen::MappedSparseMatrix<T, Eigen::RowMajor> > {
278+
- public:
279+
- const static int RTYPE = ::Rcpp::traits::r_sexptype_traits<T>::rtype ;
280+
- Exporter(SEXP x) : d_x(x), d_dims(d_x.slot("Dim")), d_j(d_x.slot("j")), d_p(d_x.slot("p")), xx( d_x.slot("x") ) {
281+
- if (!d_x.is("dgRMatrix"))
282+
- throw std::invalid_argument("Need S4 class dgRMatrix for a mapped sparse matrix");
283+
- }
284+
- Eigen::MappedSparseMatrix<T, Eigen::RowMajor> get() {
285+
- return Eigen::MappedSparseMatrix<T, Eigen::RowMajor>(d_dims[0], d_dims[1], d_p[d_dims[1]],
286+
- d_p.begin(), d_j.begin(), xx.begin() );
287+
- }
288+
- protected:
289+
- S4 d_x;
290+
- IntegerVector d_dims, d_j, d_p;
291+
- Vector<RTYPE> xx ;
292+
- };
293+
+ // // Deprecated
294+
+ // template<typename T>
295+
+ // class Exporter<Eigen::MappedSparseMatrix<T, Eigen::RowMajor> > {
296+
+ // public:
297+
+ // const static int RTYPE = ::Rcpp::traits::r_sexptype_traits<T>::rtype ;
298+
+ // Exporter(SEXP x) : d_x(x), d_dims(d_x.slot("Dim")), d_j(d_x.slot("j")), d_p(d_x.slot("p")), xx( d_x.slot("x") ) {
299+
+ // if (!d_x.is("dgRMatrix"))
300+
+ // throw std::invalid_argument("Need S4 class dgRMatrix for a mapped sparse matrix");
301+
+ // }
302+
+ // Eigen::MappedSparseMatrix<T, Eigen::RowMajor> get() {
303+
+ // return Eigen::MappedSparseMatrix<T, Eigen::RowMajor>(d_dims[0], d_dims[1], d_p[d_dims[1]],
304+
+ // d_p.begin(), d_j.begin(), xx.begin() );
305+
+ // }
306+
+ // protected:
307+
+ // S4 d_x;
308+
+ // IntegerVector d_dims, d_j, d_p;
309+
+ // Vector<RTYPE> xx ;
310+
+ // };
311+
312+
template<typename T>
313+
class Exporter<Eigen::SparseMatrix<T> > {
314+
diff --git c/inst/include/unsupported/Eigen/src/SparseExtra/MatrixMarketIterator.h w/inst/include/unsupported/Eigen/src/SparseExtra/MatrixMarketIterator.h
315+
index 21b62f6..0ccb566 100644
181316
--- c/inst/include/unsupported/Eigen/src/SparseExtra/MatrixMarketIterator.h
182-
+++ i/inst/include/unsupported/Eigen/src/SparseExtra/MatrixMarketIterator.h
183-
@@ -170,7 +170,9 @@ class MatrixMarketIterator {
317+
+++ w/inst/include/unsupported/Eigen/src/SparseExtra/MatrixMarketIterator.h
318+
@@ -170,10 +170,10 @@ class MatrixMarketIterator {
184319
m_isvalid = false;
185320
std::string curfile;
186321
curfile = m_folder + "/" + m_curs_id->d_name;
187-
+#if !(defined(__sun) || defined(_AIX) || defined(__hpux) || defined(__sgi) || defined(__HAIKU__))
188-
// Discard if it is a folder
189-
+#endif
190-
if (m_curs_id->d_type == DT_DIR) continue; // FIXME This may not be available on non BSD systems
322+
- // Discard if it is a folder
323+
#if !(defined(__sun) || defined(_AIX) || defined(__hpux) || defined(__sgi) || defined(__HAIKU__))
324+
- if (m_curs_id->d_type == DT_DIR) continue; // FIXME This may not be available on non BSD systems
325+
+ // Discard if it is a folder
326+
#endif
327+
+ if (m_curs_id->d_type == DT_DIR) continue; // FIXME This may not be available on non BSD systems
191328
// struct stat st_buf;
192329
// stat (curfile.c_str(), &st_buf);
330+
// if (S_ISDIR(st_buf.st_mode)) continue;

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