Passing lists from R to C, extracting elements, and sending lists back again
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);
}
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Thomas Lumley Assoc. Professor, Biostatistics tlumley at u.washington.edu University of Washington, Seattle