Question

I am trying to write a function in C that will be called by R. Within it I need to take a random sample without replacement from a vector. Is it possible with Rmath.h to use something like sample() in R? If not, does anyone know why I might be getting

    Symbol not found: _gsl_rng_mt19937

When I try to dyn.load() code that calls that includes (with the appropriate headers):

      #include <gsl/gsl_randist.h>
      #include <gsl/gsl_rng.h>

     void update_infs (int *inds,
      int *inf_times,
      int *n,
      int *n_inf,
      int *locs,
      int *Rinds,
      double *logmean,
      double *logsd,
      double *alpha,
      double *wts,
      int *indices  /* a vector 1:n */
      ) { 
    ...

   /* set up GSL RNG */
   gsl_rng * rng = gsl_rng_alloc(gsl_rng_mt19937);
   /* end of GSL setup */
    ...
   gsl_ran_choose(rng, tmp_inf_me, Rinds[i], indices, *n, sizeof (double));
    ... }

Answer 1

Likely the shared object needs to be compiled with a command like

export PKG_CFLAGS=`gsl-config --cflags`
export PKG_LIBS=`gsl-config --libs`

and then

R CMD SHLIB gsl.c

or alternatively

PKG_CFLAGS=`gsl-config --cflags` PKG_LIBS=`gsl-config --libs` R CMD SHLIB gsl.c

This is telling the compiler where to look for headers, and the linker where to find libraries to link against. During compilation and linking the commands should contain the output of gsl-config --cflags and gsl-config --libs, along the lines of

gcc -std=gnu99 -I/home/mtmorgan/bin/R-devel/include -I/usr/local/include -I/usr/include -fpi -c gsl.c -o gsl.o

during compilatoin and

gcc -std=gnu99 -shared -L/usr/local/lib64 -o gsl.so gsl.o -L/usr/lib -lgsl -lgslcblas -lm -L/home/mtmorgan/bin/R-devel/lib -lR

during linking. A test of success is

R -e 'dyn.load("gsl.so")'

In a package one would have a file src/Makevars with

PKG_CFLAGS = `gsl-config --cflags`
PKG_LIBS = `gsl-config --libs`

and, for Windows where gsl-config might not be available but the user has managed to install gsl and set an environment variable LIB_GSL, a file src/Makevars.win

PKG_LIBS += -L$(LIB_GSL)$(R_ARCH)/lib -lgsl -lgslcblas -lm
PKG_CPPFLAGS += -I$(RHOME)/src/include -I$(LIB_GSL)$(R_ARCH)/include