[Rd] FW: Passing lists from R to C, extracting elements, and sending lists back again

From: Michael Braun <braunm_at_MIT.EDU>
Date: Sun 24 Dec 2006 - 23:58:50 GMT


Thank you to everyone who responded to my previous post regarding the integration into R of C programs that use external libraries. I have another issue that I simply have not been able to figure out using documentation, list archives, and so forth.

I have data that is stored in R lists. I would like to pass the list to C code using the .Call function, perform mathematical operations on the elements of the lists (which might be other lists), and return results in a new list.

As a simple example, suppose I have a list of n matrices (dimension k-by-k) that I want to invert, and return the result in another list. I wrote the C code below that reads the list as a SEXP. Then, for each of the i=1..n matrices, I convert the R vector to a gsl matrix, perform the linear algebra operations and populate the new list with the inverted matrix.

The problem is that I can't figure out the best way to get the real elements into the list SEXP to return it to R. When I run the code below, the compiler (R CMD SHLIB sexp1.c) gives me:

-bash-3.00$ R CMD SHLIB sexp1.c
gcc -I/usr/lib64/R/include -I/usr/lib64/R/include -I/usr/include -I/usr/local/include -fpic -O2 -g -c sexp1.c -o sexp1.o sexp1.c: In function `invMatList':
sexp1.c:37: warning: passing arg 3 of `SET_VECTOR_ELT' from incompatible pointer type gcc -shared -L/usr/local/lib64 -o sexp1.so sexp1.o -L/usr/lib64 -lgsl -lgslcblas -L/usr/lib -L/usr/lib64/R/lib -lR

So, not only would it be helpful to understand how to solve this specific problem, but I would greatly appreciate some general guidance on how to best more data from lists or C datatypes and back again (especially arrays). Also, are the functions and macros described in the Rinternals header documented anywhere? I can't seem to find the source code, or a description of what these functions actually do.

Thanks again for any help you can provide.

Best wishes,

Michael Braun
MIT Sloan School of Management

	SEXP r = PROTECT(allocVector(VECSXP,n));
	double rm[k][k];

	for (i=0; i<n; i=i+1) {

		for (a=0; a<k; ++a){ // convert to gsl matrix
			for (b=0; b<k; ++b){
				ind = b*k + a;
				m = REAL(VECTOR_ELT(list,i))[ind];
				gsl_matrix_set(mat, b, a, m);

} // end conversion loops gsl_linalg_LU_decomp(mat, p, &s); gsl_linalg_LU_invert(mat, p, inv); for (a=0; a<k; ++a){ // convert from gsl matrix for (b=0; b<k; ++b){ rm[b][a] = gsl_matrix_get(inv,b,a);
} SET_VECTOR_ELT(r, i, rm); } UNPROTECT(1); return (r);


R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel Received on Mon Dec 25 11:03:47 2006

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.1.8, at Mon 25 Dec 2006 - 04:30:57 GMT.

Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-devel. Please read the posting guide before posting to the list.