Ndtyjky

I have some running c++ code using the Lapacke version that comes with OpenBlas. I would like to include this code into an R package and transfer data between that function and R using the Rcpp package. But somehow the two seem not to like each other. As soon as I have #include <lapacke.h> and #include <Rcpp.h> in one source file it isn't compiling anymore. Both separately work fine. There is a whole bunch off error messages which as far as I can tell say that Rcpp is broken (e.g /home/Alex/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include/Rcpp/traits/traits.h:32:15: error: expected ‘)’ before ‘__extension__’).

I have no idea why this happens. Is there a way to use both at same time?
Or should I do something completely different?

Here is a minimal example that gives me the error:

1. 
   

   I created a package using

   
   
   

   Rcpp::Rcpp.package.skeleton("LT", example_code = FALSE)
   
   

   
   


2. 
   

   I added a .cpp file to /src containing

   
   
   

   #include <lapacke.h>
   
   #include <Rcpp.h>
   
   
   
   int test_LAPACK(){
   
     return(1);
   
   }
   
   

   
   


3. 
   

   I added a Makvars file to /src containing

   
   
   

   PKG_CXXFLAGS = -I/opt/OpenBLAS/include
   
   PKG_LIBS =  -L/opt/OpenBLAS/lib -lopenblas -lpthread -lgfortran
   
   CXX_STD = CXX11
   
   

   
   


4. 
   

   Compile and install

   
   
   

   Rcpp::compileAttributes("LT")
   
   devtools::install("LT")
   
   

   
   

It actually works on my system following a standard sudo apt install liblapacke-dev provided I also change the include order.

Witness:

Source

rob:/tmp/lapacke/LT$ cat src/lt.cpp 

#include <Rcpp.h>

#include <lapacke.h>



int test_LAPACK(){

          return(1);

}

rob:/tmp/lapacke/LT$ ls src/      ## no Makevars needed

lt.cpp

rob:/tmp/lapacke/LT$ 

Build

rob:/tmp/lapacke/LT$ build.r 

* checking for file ‘./DESCRIPTION’ ... OK

* preparing ‘LT’:

* checking DESCRIPTION meta-information ... OK

* cleaning src

* installing the package to process help pages

* saving partial Rd database

* cleaning src

* checking for LF line-endings in source and make files and shell scripts

* checking for empty or unneeded directories

Removed empty directory ‘LT/R’

* building ‘LT_1.0.tar.gz’



rob:/tmp/lapacke/LT$

Install

rob:/tmp/lapacke/LT$ install.r LT_1.0.tar.gz 

* installing *source* package ‘LT’ ...

** libs

ccache g++ -I"/usr/share/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include"    -fpic  -g -O3 -Wall -pipe   -march=native -c lt.cpp -o lt.o

ccache g++ -Wl,-S -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o LT.so lt.o -L/usr/lib/R/lib -lR

installing to /usr/local/lib/R/site-library/LT/libs

** help

*** installing help indices

** building package indices

** testing if installed package can be loaded

* DONE (LT)

rob:/tmp/lapacke/LT$ 

Run

(After I added a line // [[Rcpp::export]], ran compileAtttributes() and rebuilt and installed.)

rob:/tmp/lapacke/LT$ r -lLT -p -e'test_LAPACK()'

[1] 1

rob:/tmp/lapacke/LT$ 

Summary

Check your compiler. There is no fundamental reason this should not work, and it works here (Ubuntu 18.04).