R: Interactive RcppGSL use

Question

I am trying to use RcppGSL on a 64-bit Windows machine, but feel that there are some nuances of the make variables that I am not understanding.

Here is what I tried:
1. Installed GSL from binaries available here in a new directory I created in the top-level R installation directory.
2. Updated the environment variables to include a new variable LIB_GSL to point to the folder where I unzipped GSL.
3. Create a set of files in a new directory:
- example1.cpp
- Makevars.win

Here is what each of the files looks like.

example1.cpp

The example1.cpp file is the basic column norms function that is included as an example in the RcppGSL package itself:

// [[Rcpp::depends(RcppGSL)]]
#include <RcppGSL.h>
#include <gsl/gsl_matrix.h>
#include <gsl/gsl_blas.h>

// [[Rcpp::export]]
Rcpp::NumericVector colNorm(Rcpp::NumericMatrix sM) {

    RcppGSL::matrix<double> M(sM);   // create gsl data structures from SEXP
    int k = M.ncol();
    Rcpp::NumericVector n(k);       // to store results 

    for (int j = 0; j < k; j++) {
        RcppGSL::vector_view<double> colview = gsl_matrix_column (M, j);
        n[j] = gsl_blas_dnrm2(colview);
    }

    M.free();       // important: GSL wrappers use C structure
    return n;               // return vector  
}

Makevars.win

PKG_CPPFLAGS=-I$(LIB_GSL)/include -I../inst/include 
PKG_LIBS=-L$(LIB_GSL)/lib/x64 -lgsl -lgslcblas

Question:

However, when I sourceCpp the example1.cpp file, it gives me the following output:

> Rcpp::sourceCpp('example53[RcppGSL].cpp')
g++ -m64 -I"F:/PROGRA~1/r/R-31~1.1/include" -DNDEBUG -IF:/programming/r/R-3.1.1/GSL/include     -I"F:/programming/r/R-3.1.1/library/Rcpp/include" -I"F:/programming/r/R-3.1.1/library/RcppGSL/include"  -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c example53[RcppGSL].cpp -o example53[RcppGSL].o
g++ -m64 -shared -s -static-libgcc -o sourceCpp_9705.dll tmp.def example53[RcppGSL].o -LF:/programming/r/R-3.1.1/GSL/lib -lgsl -lgslcblas -LF:/PROGRA~1/r/R-31~1.1/bin/x64 -lRlapack -LF:/PROGRA~1/r/R-31~1.1/bin/x64 -lRblas -lgfortran -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LF:/PROGRA~1/r/R-31~1.1/bin/x64 -lR
f:/programming/r/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/bin/ld.exe: cannot find -lgsl
f:/programming/r/rtools/gcc-4.6.3/bin/../lib/gcc/i686-w64-mingw32/4.6.3/../../../../i686-w64-mingw32/bin/ld.exe: cannot find -lgslcblas
collect2: ld returned 1 exit status
Error in Rcpp::sourceCpp("example53[RcppGSL].cpp") : 
  Error occurred building shared library.

Now, I know that my files are actually in -L$(LIB_GSL)/lib/x64, but the linker is looking in -L$(LIB_GSL)/lib (this is reflected in my Makevars.win as well), hence is not able to find libgsl or libgslcblas. How can I enforce that this is the PKG_LIBS passed to cppSource instead of whatever the default is.

My current workaround is to copy everything from -L$(LIB_GSL)/lib/x64 to -L$(LIB_GSL)/lib but not happy with that solution.

Answer 1

The Makevars.win is not used by sourceCpp().

When I do this here on Linux, things just work as expected:

R> sourceCpp("/tmp/coln.cpp")   # where coln.cpp is what you have above
R> colNorm(matrix(1:16,4,4))
[1]  5.47723 13.19091 21.11871 29.08608
R> 

What is used for you on Windows is determined at package load time via the file R/inline.R in the package sources, and it reflects what the LIB_GSL has.

Maybe the line gsl_libs <- sprintf( "-L%s/lib -lgsl -lgslcblas", LIB_GSL ) needs a correction and we need to append /x64 for you? Could you debug that?