Namespace declarations to enable Eigen/Tensor in TMB models

TMB/DESCRIPTION

@@ -1,8 +1,8 @@
 Package: TMB
 Type: Package
 Title: Template Model Builder: A General Random Effect Tool Inspired by 'ADMB'
-Version: 1.7.22
-Date: 2021-09-28
+Version: 1.7.22-2
+Date: 2022-02-12
 Authors@R: c(person("Kasper","Kristensen",role=c("aut","cre","cph"),email="kaskr@dtu.dk"),
              person("Brad","Bell",role="cph"),
              person("Hans","Skaug",role="ctb"),

TMB/NEWS

@@ -1,3 +1,30 @@
+------------------------------------------------------------------------
+TMB 1.7.22-2 (2022-02-13)
+*** FORKED PATCH VERSION ***
+------------------------------------------------------------------------
+
+o Explicitly reference tmbutils::array in tmbutils/density.hpp and
+  tmbutils/R_inla.hpp. This avoids a namespace clash between
+  Eigen:: and tmbutils:: when Eigen/Tensor headers are included:
+
+  > TMB/include/tmbutils/density.hpp:106:3: error: 
+  >    reference to 'array' is ambiguous
+
+o Add `#define R_NO_REMAP` before `#include <Rinternals.h>` in TMB.hpp. This
+  avoids a compiler error when including <TMB.hpp> is included before <Tensor>
+  (compiler Apple clang version 13.0.0):
+
+   >  unsupported/Eigen/CXX11/src/Tensor/TensorTraits.h:122:8: error: 
+   >    explicit specialization of non-template struct 'Rf_eval'
+
+o Specify Rf_ prefix in a few locations in tmb_core.hpp and dynamic_data.hpp
+  where it was omitted (Rf_findVar, Rf_install, Rf_setAttrib, Rf_mkString,
+  Rf_ScalarLogical).
+
+o Update `inst/include/unsupported/` headers to Eigen 3.4.0 for consistency
+  with updated headers in `inst/include/Eigen`.
+
+
 ------------------------------------------------------------------------
 TMB 1.7.22 (2021-09-28)
 ------------------------------------------------------------------------

TMB/inst/include/TMB.hpp

@@ -140,6 +140,8 @@ namespace TMBad {
    macros can cause conflicts (as they do not respect the Eigen and
    CppAD namespace limits). E.g., the 'length' macro conflicts with
    CppAD when compiling with '-std=c++11'. */
+
+#define R_NO_REMAP  // avoid Eigen clashes with eval(), length(), 
 #include <R.h>
 #include <Rinternals.h>
 #include "toggle_thread_safe_R.hpp"

TMB/inst/include/dynamic_data.hpp

@@ -87,7 +87,7 @@ namespace dynamic_data {
                              // forward double
                              SEXP envir = double_to_sexp( tx[0] );
                              const char* nam = double_to_charptr( tx[1] );
-                             SEXP res = findVar(install(nam), envir);
+                             SEXP res = Rf_findVar(Rf_install(nam), envir);
                              ty[0] = sexp_to_double( res );
                              ,
                              // reverse

TMB/inst/include/tmb_core.hpp

@@ -711,7 +711,7 @@ class objective_function
   /** \brief Syncronize user's data object. It could be changed between calls to e.g. EvalDoubleFunObject */
   void sync_data() {
     SEXP env = ENCLOS(this->report);
-    this->data = findVar(install("data"), env);
+    this->data = Rf_findVar(Rf_install("data"), env);
   }
 
   /** \brief Extract theta vector from objetive function object */
@@ -1452,7 +1452,7 @@ extern "C"
 
 #ifdef TMBAD_FRAMEWORK
 inline int get_num_tapes(SEXP f) {
-  if (isNull(f))
+  if (Rf_isNull(f))
     return 0;
   SEXP tag = R_ExternalPtrTag(f);
   if (tag != Rf_install("parallelADFun"))
@@ -1488,7 +1488,7 @@ SEXP TMBAD_TransformADFunObjectTemplate(TMBad::ADFun<TMBad::ad_aug>* pf, SEXP co
     return R_NilValue;
   }
   SEXP random_order = getListElement(control, "random_order");
-  int nr = (isNull(random_order) ? 0 : LENGTH(random_order));
+  int nr = (Rf_isNull(random_order) ? 0 : LENGTH(random_order));
   std::vector<TMBad::Index> random;
   if (nr != 0) {
     random = std::vector<TMBad::Index>(INTEGER(random_order),
@@ -1823,7 +1823,7 @@ SEXP CPPAD_TransformADFunObject(SEXP f, SEXP control)
     std::string method =
       CHAR(STRING_ELT(getListElement(control, "method"), 0));
     if (method == "num_tapes") { // Get number of tapes
-      return ScalarInteger(num_tapes);
+      return Rf_ScalarInteger(num_tapes);
     }
     else if (method == "tape") { // Print tape
       int depth = getListInteger(control, "depth", 1);
@@ -1862,15 +1862,15 @@ SEXP CPPAD_TransformADFunObject(SEXP f, SEXP control)
       int input_size = getListInteger(control, "input_size", 0);
       int output_size = getListInteger(control, "output_size", 0);
       size_t n = pf->glob.opstack.size();
-      SEXP ans = PROTECT(allocVector(STRSXP, n));
+      SEXP ans = PROTECT(Rf_allocVector(STRSXP, n));
       for (size_t i=0; i<n; i++) {
         std::stringstream strm;
         if (address)     strm << (void*) pf->glob.opstack[i] << " ";
         if (name)        strm << pf->glob.opstack[i]->op_name() << " ";
         if (input_size)  strm << pf->glob.opstack[i]->input_size();
         if (output_size) strm << pf->glob.opstack[i]->output_size();
         const std::string& tmp = strm.str();
-        SET_STRING_ELT(ans, i, mkChar(tmp.c_str()));
+        SET_STRING_ELT(ans, i, Rf_mkChar(tmp.c_str()));
       }
       UNPROTECT(1);
       return ans;
@@ -1952,7 +1952,7 @@ extern "C"
       if(get_reportdims) {
         SEXP reportdims;
         PROTECT( reportdims = pf -> reportvector.reportdims() );
-        setAttrib( res, install("reportdims"), reportdims);
+        Rf_setAttrib( res, Rf_install("reportdims"), reportdims);
         UNPROTECT(1);
       }
       UNPROTECT(2);
@@ -2516,20 +2516,20 @@ extern "C"
     SEXP ans;
     PROTECT(ans = R_NilValue);
 #ifdef TMBAD_FRAMEWORK
-    ans = mkString("TMBad");
+    ans = Rf_mkString("TMBad");
 #elif  CPPAD_FRAMEWORK
-    ans = mkString("CppAD");
+    ans = Rf_mkString("CppAD");
 #else
-    ans = mkString("Unknown");
+    ans = Rf_mkString("Unknown");
 #endif
     SEXP openmp_sym, openmp_res;
     PROTECT(openmp_sym = R_NilValue);
     PROTECT(openmp_res = R_NilValue);
     openmp_sym = Rf_install("openmp");
 #ifdef _OPENMP
-    openmp_res = ScalarLogical(1);
+    openmp_res = Rf_ScalarLogical(1);
 #else
-    openmp_res = ScalarLogical(0);
+    openmp_res = Rf_ScalarLogical(0);
 #endif
     Rf_setAttrib(ans, openmp_sym, openmp_res);
     UNPROTECT(3);

TMB/inst/include/tmbutils/R_inla.hpp

@@ -97,7 +97,7 @@ template<class Type>
   // Calculate new SPDE matrices
 
   // Calculate G1 - pt. 1
-  array<Type> Gtmp(n_tri,3,3);
+  tmbutils::array<Type> Gtmp(n_tri,3,3);
   for(i=0; i<n_tri; i++){    
     // 1st line: E0(i,) %*% adjH %*% t(E0(i,)), etc.    
     Gtmp(i,0,0) = (E0(i,0)*(E0(i,0)*adj_H(0,0)+E0(i,1)*adj_H(1,0)) + E0(i,1)*(E0(i,0)*adj_H(0,1)+E0(i,1)*adj_H(1,1))) / (4*Tri_Area(i));  

TMB/inst/include/tmbutils/density.hpp

@@ -12,7 +12,7 @@ public:						\
 typedef scalartype_ scalartype;			\
 typedef vector<scalartype> vectortype;		\
 typedef matrix<scalartype> matrixtype;		\
-typedef array<scalartype> arraytype
+typedef tmbutils::array<scalartype> arraytype
 
 #define VARIANCE_NOT_YET_IMPLEMENTED            \
 private:                                        \
@@ -730,7 +730,7 @@ class contAR2_t{
   scalartype operator()(vectortype x){ /* x.dim=[2,n] */
     vector<int> dim(2);
     dim << 2 , x.size()/2 ;
-    array<scalartype> y(x,dim);
+    tmbutils::array<scalartype> y(x,dim);
     y=y.transpose();
     return this->operator()(y.col(0),y.col(1));
   }

TMB/inst/include/unsupported/CMakeLists.txt

@@ -1,7 +1,11 @@
 add_subdirectory(Eigen)
-add_subdirectory(doc EXCLUDE_FROM_ALL)
-if(EIGEN_LEAVE_TEST_IN_ALL_TARGET)
-  add_subdirectory(test) # can't do EXCLUDE_FROM_ALL here, breaks CTest
-else()
-  add_subdirectory(test EXCLUDE_FROM_ALL)
+if(EIGEN_BUILD_DOC)
+  add_subdirectory(doc EXCLUDE_FROM_ALL)
+endif()
+if(BUILD_TESTING)
+  if(EIGEN_LEAVE_TEST_IN_ALL_TARGET)
+    add_subdirectory(test) # can't do EXCLUDE_FROM_ALL here, breaks CTest
+  else()
+    add_subdirectory(test EXCLUDE_FROM_ALL)
+  endif()
 endif()

TMB/inst/include/unsupported/Eigen/AdolcForward

@@ -40,7 +40,7 @@
 # undef realloc
 #endif
 
-#include <Eigen/Core>
+#include "../../Eigen/Core"
 
 namespace Eigen {
 
@@ -74,6 +74,9 @@ inline adouble imag(const adouble&)    { return 0.; }
 inline adouble abs(const adouble&  x)  { return fabs(x); }
 inline adouble abs2(const adouble& x)  { return x*x; }
 
+inline bool (isinf)(const adouble& x) { return (Eigen::numext::isinf)(x.getValue()); }
+inline bool (isnan)(const adouble& x) { return (Eigen::numext::isnan)(x.getValue()); }
+
 }
 
 namespace Eigen {

TMB/inst/include/unsupported/Eigen/AlignedVector3

@@ -10,7 +10,9 @@
 #ifndef EIGEN_ALIGNED_VECTOR3
 #define EIGEN_ALIGNED_VECTOR3
 
-#include <Eigen/Geometry>
+#include "../../Eigen/Geometry"
+
+#include "../../Eigen/src/Core/util/DisableStupidWarnings.h"
 
 namespace Eigen {
 
@@ -76,6 +78,9 @@ template<typename _Scalar> class AlignedVector3
     { return m_coeffs.coeffRef(index);}
 
 
+    inline AlignedVector3()
+    {}
+
     inline AlignedVector3(const Scalar& x, const Scalar& y, const Scalar& z)
       : m_coeffs(x, y, z, Scalar(0))
     {}
@@ -129,6 +134,9 @@ template<typename _Scalar> class AlignedVector3
     inline AlignedVector3 operator-(const AlignedVector3& other) const
     { return AlignedVector3(m_coeffs - other.m_coeffs); }
 
+    inline AlignedVector3 operator-() const
+    { return AlignedVector3(-m_coeffs); }
+
     inline AlignedVector3 operator-=(const AlignedVector3& other)
     { m_coeffs -= other.m_coeffs; return *this; }
 
@@ -221,4 +229,6 @@ struct evaluator<AlignedVector3<Scalar> >
 
 }
 
+#include "../../Eigen/src/Core/util/ReenableStupidWarnings.h"
+
 #endif // EIGEN_ALIGNED_VECTOR3

TMB/inst/include/unsupported/Eigen/ArpackSupport

@@ -9,9 +9,7 @@
 #ifndef EIGEN_ARPACKSUPPORT_MODULE_H
 #define EIGEN_ARPACKSUPPORT_MODULE_H
 
-#include <Eigen/Core>
-
-#include <Eigen/src/Core/util/DisableStupidWarnings.h>
+#include "../../Eigen/Core"
 
 /** \defgroup ArpackSupport_Module Arpack support module
   *
@@ -22,10 +20,11 @@
   * \endcode
   */
 
-#include <Eigen/SparseCholesky>
+#include "../../Eigen/SparseCholesky"
+
+#include "../../Eigen/src/Core/util/DisableStupidWarnings.h"
 #include "src/Eigenvalues/ArpackSelfAdjointEigenSolver.h"
 
-#include <Eigen/src/Core/util/ReenableStupidWarnings.h>
+#include "../../Eigen/src/Core/util/ReenableStupidWarnings.h"
 
 #endif // EIGEN_ARPACKSUPPORT_MODULE_H
-/* vim: set filetype=cpp et sw=2 ts=2 ai: */

TMB/inst/include/unsupported/Eigen/AutoDiff

@@ -28,11 +28,17 @@ namespace Eigen {
 //@{
 
 }
+#include "../../Eigen/src/Core/util/DisableStupidWarnings.h"
+
 
 #include "src/AutoDiff/AutoDiffScalar.h"
 // #include "src/AutoDiff/AutoDiffVector.h"
 #include "src/AutoDiff/AutoDiffJacobian.h"
 
+#include "../../Eigen/src/Core/util/ReenableStupidWarnings.h"
+
+
+
 namespace Eigen {
 //@}
 }

TMB/inst/include/unsupported/Eigen/BVH

@@ -10,9 +10,9 @@
 #ifndef EIGEN_BVH_MODULE_H
 #define EIGEN_BVH_MODULE_H
 
-#include <Eigen/Core>
-#include <Eigen/Geometry>
-#include <Eigen/StdVector>
+#include "../../Eigen/Core"
+#include "../../Eigen/Geometry"
+#include "../../Eigen/StdVector"
 #include <algorithm>
 #include <queue>