apply patches

Author: yixuan

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

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

@@ -37,40 +37,40 @@
 #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"
-  #if __clang_major__ >= 3 && __clang_minor__ >= 5
-    #pragma clang diagnostic ignored "-Wabsolute-value"
-  #endif
-  #if __clang_major__ >= 10
-    #pragma clang diagnostic ignored "-Wimplicit-int-float-conversion"
-  #endif
-  #if ( defined(__ALTIVEC__) || defined(__VSX__) ) && __cplusplus < 201103L
-    // warning: generic selections are a C11-specific feature
-    // ignoring warnings thrown at vec_ctf in Altivec/PacketMath.h
-    #pragma clang diagnostic ignored "-Wc11-extensions"
-  #endif
+  // #ifndef EIGEN_PERMANENTLY_DISABLE_STUPID_WARNINGS
+  //   #pragma clang diagnostic push
+  // #endif
+  // #pragma clang diagnostic ignored "-Wconstant-logical-operand"
+  // #if __clang_major__ >= 3 && __clang_minor__ >= 5
+  //   #pragma clang diagnostic ignored "-Wabsolute-value"
+  // #endif
+  // #if __clang_major__ >= 10
+  //   #pragma clang diagnostic ignored "-Wimplicit-int-float-conversion"
+  // #endif
+  // #if ( defined(__ALTIVEC__) || defined(__VSX__) ) && __cplusplus < 201103L
+  //   // warning: generic selections are a C11-specific feature
+  //   // ignoring warnings thrown at vec_ctf in Altivec/PacketMath.h
+  //   #pragma clang diagnostic ignored "-Wc11-extensions"
+  // #endif
 
 #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__

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

@@ -11,9 +11,9 @@
   #elif defined __INTEL_COMPILER
     #pragma warning pop
   #elif defined __clang__
-    #pragma clang diagnostic pop
+    // #pragma clang diagnostic pop
   #elif defined __GNUC__  &&  (__GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 6))
-    #pragma GCC diagnostic pop
+    // #pragma GCC diagnostic pop
   #endif
 
   #if defined __NVCC__

inst/include/unsupported/Eigen/src/SparseExtra/MatrixMarketIterator.h

@@ -193,7 +193,9 @@ class MatrixMarketIterator
         std::string curfile;
         curfile = m_folder + "/" + m_curs_id->d_name;
         // Discard if it is a folder
+#if !(defined(__sun) || defined(_AIX) || defined(__hpux) || defined(__sgi) || defined(__HAIKU__))
         if (m_curs_id->d_type == DT_DIR) continue; //FIXME This may not be available on non BSD systems
+#endif
 //         struct stat st_buf; 
 //         stat (curfile.c_str(), &st_buf);
 //         if (S_ISDIR(st_buf.st_mode)) continue;