RcppArmadillo and arma namespace

Question

Begin experienced in R but a complete newbie to C++, I wrote some functions with RcppArmadillo and am pretty enthusiastic about both its usability and speed. I'd now like to turn the functions into a package, using the function RcppArmadillo.package.skeleton().

This works okay as long as I explicitly use the arma:: prefix before every Armadillo object (mat, colvec etc). However, if I put using namespace arma; at the beginning of my cpp file, and omit the arma:: afterwards, I cannot load the newly created package and get tons of errors which make clear that the Armadillo namespace is not being recognized.

Any help/advice on how to fix this greatly appreciated. Thanks,

Fabian

PS: I tried the above on both Windows 7 and Ubuntu 12.04, using R 3.0.2 and RcppArmadillo_0.4.000.4 in each case.

PS2: The attached cpp file (loosely following http://gallery.rcpp.org/articles/simulate-multivariate-normal/) illustrates my point. It works nicely if I source it into R via sourceCpp (from the Rcpp package), but leads to the problems mentioned above when I try to include it in a new package.

// [[Rcpp::depends(RcppArmadillo)]]
#include <RcppArmadillo.h>
using namespace Rcpp;
using namespace arma;

// [[Rcpp::export]]
colvec mvndrawC(colvec mu, mat sig) {

double k = mu.size();
colvec aux = as<colvec>(rnorm(k));
mat csig = chol(sig).t();
colvec out = mu + csig*aux;
return(out);

}

EDIT: Details

Here's the error output I get when I do the following:

1. Run the command RcppArmadillo.package.skeleton("test2"), thus creating folders for a new package "test2"
2. Paste the above code into a .cpp file, and copy it into the new test2/src folder
3. Trying to load the new test2 package, by calling load_all("test2") from the devtools package

Error messages (in Rstudio)

Loading test2
Re-compiling test2
'/usr/lib/R/bin/R' --vanilla CMD INSTALL '/home/fabian/test2' --library='/tmp    
/RtmplfAET0'  \
--no-R --no-data --no-help --no-demo --no-inst --no-docs --no-exec --no-multiarch  \
--no-test-load --preclean 

* installing *source* package 'test2' ...
** libs
g++ -I/usr/share/R/include -DNDEBUG   -I"/home/fabian/R/x86_64-pc-linux-gnu-library   
/3.0/Rcpp/include" -I"/home/fabian/R/x86_64-pc-linux-gnu-library/3.0/RcppArmadillo  
/include"  -UNDEBUG -Wall -pedantic -g -O0 -fpic  -O3 -pipe  -g  -c RcppExports.cpp -o 
RcppExports.o
RcppExports.cpp:10:1: error: 'colvec' does not name a type
RcppExports.cpp: In function 'SEXPREC* test2_mvndrawC(SEXP, SEXP)':
RcppExports.cpp:16:40: error: 'colvec' was not declared in this scope
RcppExports.cpp:16:40: note: suggested alternative:
/home/fabian/R/x86_64-pc-linux-gnu-library/3.0/RcppArmadillo/include/armadillo_bits   
/typedef_mat.hpp:65:22: note:   'arma::colvec'
RcppExports.cpp:16:47: error: template argument 1 is invalid
RcppExports.cpp:16:55: error: expected initializer before 'mu'
RcppExports.cpp:17:40: error: 'mat' was not declared in this scope
RcppExports.cpp:17:40: note: suggested alternative:
/home/fabian/R/x86_64-pc-linux-gnu-library/3.0/RcppArmadillo/include/armadillo_bits   
/typedef_mat.hpp:63:22: note:   'arma::mat'
RcppExports.cpp:17:44: error: template argument 1 is invalid
RcppExports.cpp:17:52: error: expected initializer before 'sig'
RcppExports.cpp:18:16: error: expected ';' before '__result'
RcppExports.cpp:19:9: error: '__result' was not declared in this scope
make: *** [RcppExports.o] Error 1
ERROR: compilation failed for package 'test2'
* removing '/tmp/RtmplfAET0/test2'
Error: Command failed (1)
In addition: Warning message:
The following packages are referenced using Rcpp::depends attributes however are  
not listed in the Depends and LinkingTo fields of the package DESCRIPTION file: 
RcppArmadillo 

PS3: The warning message at the end disappears if I drop the // [[Rcpp... line at the beginning of the file (but then I cannot source it via sourceCpp, so I let it in).

Answer 1

I believe this is because Rcpp attributes, which compiles the C++ source files you make into RcppExports.cpp, does not copy over the using namespace arma; statements into there.

This is tricky, since different files might use different namespaces, so the attributes parser can't just copy all the using namespace ... statements into RcppExports.cpp -- it just defaults to using the Rcpp namespace. If we just copied all the using namespace statements willy nilly into RcppExports.cpp there could surely be conflicts.

Anyway, the fix is either to explicitly prefix arma:: or you can modify the RcppExports.cpp file to have the using namespace arma; at the top (but you'd have to do this each time after calling compileAttributes()).