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

From: Thomas Lumley <tlumley_at_u.washington.edu>
Date: Mon 25 Dec 2006 - 03:52:49 GMT

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

This allocates memory for one k x k C array wherever C allocates temporary storage. You need to allocate n vectors of length k*k on the R heap to create a list of n matrices in R. So you need to use allocVector(k*k, REALSXP) to allocate space for each element of the list, inside the loop, and then copy the data into that rather than into rm.

SET_VECTOR_ELT is giving a warning about incompatible pointer types, but the more important issue is that you need to return pointers to n different blocks of memory that are not going to go away after your function finishes.

         -thomas

>
>
> 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
>

Thomas Lumley			Assoc. Professor, Biostatistics
tlumley@u.washington.edu	University of Washington, Seattle

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https://stat.ethz.ch/mailman/listinfo/r-devel Received on Mon Dec 25 14:56:44 2006

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