Building package with Rcpp, generated .h file missing header - r

Question

I am currently building a package in RStudio that uses Rcpp. I have defined the following .cpp file, which works with Rcpp::sourceCpp.
// [[Rcpp::plugins(cpp11)]]
// [[Rcpp::interfaces(r, cpp)]]
#include <Rcpp.h>
#include <unordered_set>
using namespace Rcpp;
// [[Rcpp::export]]
std::unordered_set<int> traverse_cor(NumericMatrix x, float maxcor) {
std::unordered_set<int> elements;
int ncol = x.ncol();
for(int i = 0; i < ncol; i++) {
for(int j = 0; j < ncol; j++) {
if(i < j) {
if(x(i, j) > maxcor && x(i, j) < 1){
elements.insert(i + 1);
}
}
}
}
return elements;
}
I am following the directions from here and here. Next I call Rcpp::compileAttributes(). This produces the following files:
src/RcppExports.cpp
R/RcppExports.R
inst/include/mypackage.h
inst/include/mypackage_RcppExports.h
The generated mypackage_RcppExports.h file looks as follows:
// This file was generated by Rcpp::compileAttributes
// Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
#ifndef __gwassim_RcppExports_h__
#define __gwassim_RcppExports_h__
#include <Rcpp.h>
namespace gwassim {
using namespace Rcpp;
namespace {
void validateSignature(const char* sig) {
Rcpp::Function require = Rcpp::Environment::base_env()["require"];
require("gwassim", Rcpp::Named("quietly") = true);
typedef int(*Ptr_validate)(const char*);
static Ptr_validate p_validate = (Ptr_validate)
R_GetCCallable("gwassim", "gwassim_RcppExport_validate");
if (!p_validate(sig)) {
throw Rcpp::function_not_exported(
"C++ function with signature '" + std::string(sig) + "' not found in gwassim");
}
}
}
inline std::unordered_set<int> traverse_cor(NumericMatrix x, float maxcor) {
typedef SEXP(*Ptr_traverse_cor)(SEXP,SEXP);
static Ptr_traverse_cor p_traverse_cor = NULL;
if (p_traverse_cor == NULL) {
validateSignature("std::unordered_set<int>(*traverse_cor)(NumericMatrix,float)");
p_traverse_cor = (Ptr_traverse_cor)R_GetCCallable("gwassim", "gwassim_traverse_cor");
}
RObject __result;
{
RNGScope __rngScope;
__result = p_traverse_cor(Rcpp::wrap(x), Rcpp::wrap(maxcor));
}
if (__result.inherits("interrupted-error"))
throw Rcpp::internal::InterruptedException();
if (__result.inherits("try-error"))
throw Rcpp::exception(as<std::string>(__result).c_str());
return Rcpp::as<std::unordered_set<int> >(__result);
}
}
#endif // __gwassim_RcppExports_h__
After attempting to build and reload the package, I receive the following errors (1):
../inst/include/gwassim_RcppExports.h:27:12: error: 'unordered_set' in
namespace 'std' does not name a type
And (2)
RcppExports.cpp:12:1: error: 'unordered_set' in namespace 'std' does
not name a type
I have limited C++ experience, but my sense is that these errors occur due to #include <unordered_set> being omitted. How do I get these automatically generated files to have the correct headers?
My sessionInfo is the following:
Session info ----------------------------------------------------------------------
setting value
version R version 3.1.0 (2014-04-10)
system x86_64, mingw32
ui RStudio (0.99.235)
language (EN)
collate English_United States.1252
tz America/New_York
Packages --------------------------------------------------------------------------
package * version date source
devtools 1.7.0.9000 2015-02-11 Github (hadley/devtools#9415a8a)
digest * 0.6.4 2013-12-03 CRAN (R 3.1.0)
memoise * 0.2.1 2014-04-22 CRAN (R 3.1.0)
mvtnorm 1.0-2 2014-12-18 CRAN (R 3.1.2)
Rcpp 0.11.4 2015-01-24 CRAN (R 3.1.2)
roxygen2 * 4.1.0 2014-12-13 CRAN (R 3.1.2)
rstudioapi * 0.2 2014-12-31 CRAN (R 3.1.2)
stringr * 0.6.2 2012-12-06 CRAN (R 3.0.0)
And my version of g++ is 4.6.3, as included in the RTools package for Windows. I have enabled C++11 features with the following:
Sys.setenv("PKG_CXXFLAGS"="-std=c++0x").

Answer 1

That is a finicky one. I think you want Section 3.5.2 of the Rcpp Attributes vignette and this trick:
The Package.h file does nothing other than include the
Package_RcppExports.h header. This is done so that package
authors can replace the Package.h header with a custom one
and still be able to include the automatically generated exports
(details on doing this are provided in the next section).
In passing, I think I also convinced you to create a package rather than to rely just on sourceCpp() :)
Edit: Doh!! I overlooked the part that
std::unordered_set<int> traverse_cor(NumericMatrix x, float maxcor)
is probably not an automatically wrappable function. You may need to convert your set into a vector (or list or ...) to get one of the types that matches naturally into R.