sampling without replacement in C for use in R code

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 #include 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)); ... } ```

Accepted Answer

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
```

sampling without replacement in C for use in R code

Solution

Problem