fix Makevars for abort .so warning from devtools::check()

Author: cmjt

R/plots.r

@@ -113,7 +113,7 @@ show_multivariate_hawkes <- function(obj, type = c("fitted", "data", "both")){
                       lam = unlist(lam.p),
                       stream = rep(names(table(stream)), each = length(p)))
 
-    line <- ggplot2::ggplot(dat, ggplot2::aes(x = x, y = lam, col = stream, group = stream)) +
+    line <- ggplot2::ggplot(dat, ggplot2::aes(x = .data$x, y = .data$lam, col = .data$stream, group = .data$stream)) +
         ggplot2::geom_line() +
         ggplot2::xlab("") +
         ggplot2::ylab(expression(lambda(t))) +  ggplot2::theme_minimal()

src/Makevars

@@ -1,12 +1,3 @@
-CXX_STD = CXX17
-
-PKG_CXXFLAGS = $(SHLIB_OPENMP_CXXFLAGS)
-PKG_CPPFLAGS = -I../inst/include -I../inst/include/boost
-PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS) $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)
-
-ifeq ($(OS),Windows_NT)
-PKG_LIBS += -lgfortran
-endif
-
-# Add additional compiler flags here
-PKG_CXXFLAGS += -DTMB_SAFEBOUNDS -DTMB_EIGEN_DISABLE_WARNINGS
+PKG_CPPFLAGS = -DTMBAD_FRAMEWORK
+PKG_LIBS = $(SHLIB_OPENMP_CXXFLAGS)
+PKG_CXXFLAGS=$(SHLIB_OPENMP_CXXFLAGS)

src/spatial_hawkes.h

@@ -175,7 +175,6 @@ Type spatial_hawkes(objective_function<Type>* obj) {
   vector<Type> A(times.size());
   A.setZero();
   if (simple == 0) {
-    // std::cout << "[SIMULATE] SIMPLE == 0" << std::endl;
     for (int j = 1; j < times.size(); ++j)
       for (int i = 0; i < j; ++i){
         Q2 = Qbase * (times[j] - times[i]);
@@ -222,7 +221,6 @@ Type spatial_hawkes(objective_function<Type>* obj) {
     // Only for constant background without covariates
     // This simulation process follows Algorithm 4 in Section 3.3 of Reinhart (2018).
     DATA_IMATRIX(tv);
-    // std::cout << "[SIMULATE] tv dimensions: " << tv.rows() << " x " << tv.cols() << std::endl;
     /*
       Need the triangulation to check whether points generated are in the area of interest.
 

src/spde_hawkes.h

@@ -261,7 +261,6 @@ Type spde_hawkes(objective_function<Type>* obj) {
     loci = rpoisplane_sp(xyloc, tv, x, w);
     locs.row(0) = loci;
     // Step 10 for the first time.
-    // std::cout<<times[i]<<" "<<locs(i, 0)<<" "<<locs(i, 1)<<" "<<gammac<<std::endl;
     i++;
     // Repeat from Step 3
     while (i < times.size()){
@@ -293,7 +292,6 @@ Type spde_hawkes(objective_function<Type>* obj) {
             if (pointinSP_sp(loci, xyloc, tv)){
               // Step 10
               locs.row(i) = loci;
-              // std::cout<<times[i]<<" "<<locs(i, 0)<<" "<<locs(i, 1)<<" "<<gammac<<std::endl;
               i++;
             }
             break;
@@ -305,7 +303,6 @@ Type spde_hawkes(objective_function<Type>* obj) {
         loci = rpoisplane_sp(xyloc, tv, x, w);
         locs.row(i) = loci;
         // Step 10.
-        // std::cout<<times[i]<<" "<<locs(i, 0)<<" "<<locs(i, 1)<<" "<<gammac<<std::endl;
         i++;
       }
       gammac = D + sum(lambdaXsasep);

src/stelfi.cpp

@@ -52,3 +52,9 @@ Type objective_function<Type>::operator() ()
 }
 
 
+// RegisteringDynamic Symbols
+
+void R_init_stelfi(DllInfo* info) {
+  R_registerRoutines(info, NULL, NULL, NULL, NULL);
+  R_useDynamicSymbols(info, TRUE);
+}