add RcppEigen patches

Author: eddelbuettel

ChangeLog

@@ -1,3 +1,9 @@
+2020-12-05  Dirk Eddelbuettel  <edd@debian.org>
+
+	* inst/include/Eigen: Upgraded to Eigen 3.3.9
+	* inst/include/unsupported/Eigen: Idem
+	* patches/eigen-3.3.9.diff: Carried local CRAN patches forward
+
 2020-08-16  Dirk Eddelbuettel  <edd@debian.org>
 
 	* README.md: Add JSS badge

inst/include/Eigen/CholmodSupport

@@ -13,7 +13,7 @@
 #include "src/Core/util/DisableStupidWarnings.h"
 
 extern "C" {
-  #include <cholmod.h>
+  #include <RcppEigenCholmod.h>
 }
 
 /** \ingroup Support_modules
@@ -45,4 +45,3 @@ extern "C" {
 #include "src/Core/util/ReenableStupidWarnings.h"
 
 #endif // EIGEN_CHOLMODSUPPORT_MODULE_H
-

inst/include/Eigen/src/Core/arch/CUDA/Half.h

@@ -127,12 +127,14 @@ struct half : public half_impl::half_base {
   EIGEN_DEVICE_FUNC EIGEN_EXPLICIT_CAST(unsigned long) const {
     return static_cast<unsigned long>(half_impl::half_to_float(*this));
   }
+#if EIGEN_HAS_CXX11
   EIGEN_DEVICE_FUNC EIGEN_EXPLICIT_CAST(long long) const {
     return static_cast<long long>(half_impl::half_to_float(*this));
   }
   EIGEN_DEVICE_FUNC EIGEN_EXPLICIT_CAST(unsigned long long) const {
     return static_cast<unsigned long long>(half_to_float(*this));
   }
+#endif
   EIGEN_DEVICE_FUNC EIGEN_EXPLICIT_CAST(float) const {
     return half_impl::half_to_float(*this);
   }

inst/include/Eigen/src/Core/arch/SSE/Complex.h

@@ -98,10 +98,10 @@ template<> EIGEN_STRONG_INLINE Packet2cf pset1<Packet2cf>(const std::complex<flo
   res.v = _mm_loadl_pi(_mm_set1_ps(0.0f), reinterpret_cast<const __m64*>(&from));
 #elif EIGEN_GNUC_AT_LEAST(4,6)
   // Suppress annoying "may be used uninitialized in this function" warning with gcc >= 4.6
-  #pragma GCC diagnostic push
-  #pragma GCC diagnostic ignored "-Wuninitialized"
+  //#pragma GCC diagnostic push
+  //#pragma GCC diagnostic ignored "-Wuninitialized"
   res.v = _mm_loadl_pi(res.v, (const __m64*)&from);
-  #pragma GCC diagnostic pop
+  //#pragma GCC diagnostic pop
 #else
   res.v = _mm_loadl_pi(res.v, (const __m64*)&from);
 #endif

inst/include/Eigen/src/Core/util/DisableStupidWarnings.h

@@ -4,7 +4,6 @@
 #ifdef _MSC_VER
   // 4100 - unreferenced formal parameter (occurred e.g. in aligned_allocator::destroy(pointer p))
   // 4101 - unreferenced local variable
-  // 4127 - conditional expression is constant
   // 4181 - qualifier applied to reference type ignored
   // 4211 - nonstandard extension used : redefined extern to static
   // 4244 - 'argument' : conversion from 'type1' to 'type2', possible loss of data
@@ -20,7 +19,7 @@
   #ifndef EIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS
     #pragma warning( push )
   #endif
-  #pragma warning( disable : 4100 4101 4127 4181 4211 4244 4273 4324 4503 4512 4522 4700 4714 4717 4800)
+  #pragma warning( disable : 4100 4101 4181 4211 4244 4273 4324 4503 4512 4522 4700 4714 4717 4800)
 
 #elif defined __INTEL_COMPILER
   // 2196 - routine is both "inline" and "noinline" ("noinline" assumed)
@@ -38,32 +37,33 @@
 #elif defined __clang__
   // -Wconstant-logical-operand - warning: use of logical && with constant operand; switch to bitwise & or remove constant
   //     this is really a stupid warning as it warns on compile-time expressions involving enums
-  #ifndef EIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS
-    #pragma clang diagnostic push
-  #endif
-  #pragma clang diagnostic ignored "-Wconstant-logical-operand"
+  //#ifndef EIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS
+  //  #pragma clang diagnostic push
+  //#endif
+  //#pragma clang diagnostic ignored "-Wconstant-logical-operand"
 
 #elif defined __GNUC__
 
-  #if (!defined(EIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS)) &&  (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 6))
-    #pragma GCC diagnostic push
-  #endif
-  // g++ warns about local variables shadowing member functions, which is too strict
-  #pragma GCC diagnostic ignored "-Wshadow"
-  #if __GNUC__ == 4 && __GNUC_MINOR__ < 8
-    // Until g++-4.7 there are warnings when comparing unsigned int vs 0, even in templated functions:
-    #pragma GCC diagnostic ignored "-Wtype-limits"
-  #endif
-  #if __GNUC__>=6
-    #pragma GCC diagnostic ignored "-Wignored-attributes"
-  #endif
-  #if __GNUC__==7
-    // See: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=89325
-    #pragma GCC diagnostic ignored "-Wattributes"
-  #endif
+  // #if (!defined(EIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS)) &&  (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 6))
+  //   #pragma GCC diagnostic push
+  // #endif
+  // // g++ warns about local variables shadowing member functions, which is too strict
+  // #pragma GCC diagnostic ignored "-Wshadow"
+  // #if __GNUC__ == 4 && __GNUC_MINOR__ < 8
+  //   // Until g++-4.7 there are warnings when comparing unsigned int vs 0, even in templated functions:
+  //   #pragma GCC diagnostic ignored "-Wtype-limits"
+  // #endif
+  // #if __GNUC__>=6
+  //   #pragma GCC diagnostic ignored "-Wignored-attributes"
+  // #endif
+  // #if __GNUC__==7
+  //   // See: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=89325
+  //   #pragma GCC diagnostic ignored "-Wattributes"
+  // #endif
 #endif
 
 #if defined __NVCC__
+  #pragma diag_suppress boolean_controlling_expr_is_constant
   // Disable the "statement is unreachable" message
   #pragma diag_suppress code_is_unreachable
   // Disable the "dynamic initialization in unreachable code" message
@@ -81,6 +81,7 @@
   #pragma diag_suppress 2671
   #pragma diag_suppress 2735
   #pragma diag_suppress 2737
+  #pragma diag_suppress 2739
 #endif
 
 #else