> void dnk_c(double *sortedFsample, unsigned long int n, unsigned
long int k, double *dKol)
All arguments to C functions called by .C() must be pointers. Also, R
integers are C ints, not unsigned long ints.
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Mon, Mar 20, 2017 at 5:55 AM, Hristo Inouzhe Valdes
wrote:
> Hello,
>
> I'm trying to calculate a certain distance estimator for my thesis. I have a
> program in C that works fine when I call it with .C() in R, but since
> I'm dealing with big matrices like 3x2 it was getting a stack
> overflow. Now I have the same program but more efficeintly coded using
> malloc, and it works perfectlry in C, compiles well with R CMD SHLIB
> but when I call it with .C() my pc basicly stops working independantly
> of the size of the matrices involved.
>
> The C code is the following (sorry it is a bit long):
>
> #include
> #include
> #include
> #include
> #ifdef NAN
> /* NAN is supported */
> #endif
> #ifdef INFINITY
> /* INFINITY is supported */
> #endif
>
> void dnk_c(double *sortedFsample, unsigned long int n, unsigned
> long int k, double *dKol){
>
> double min(double a, double b) {
> return (a < b) ? a : b;
> }
>
> double max(double a, double b) {
> return (a > b) ? a : b;
> }
>
> double r_abs(double a){
> return (a < 0) ? -a : a;
> }
>
> int cmp(const void *a, const void *b) {
> return (*(double*)a - *(double*)b);
> }
>
> double superior(double x, double i, double m){
> double op1 = r_abs(x-(i)/(m));
> double op2 = r_abs(x-(i-1)/(m));
> return max(op1,op2);
> }
>
> double termino1, termino2, f, g, t, h1, h2, l=1.0, m=n-k;
> unsigned long int i, j, filas;
>
> double **matrixA, **matrixB;
>
> matrixA = (double **) malloc((k+1)*sizeof(double *));
> matrixB = (double **) malloc((k+1)*sizeof(double *));
>
> for (i=0; i <= k; i++) {
> matrixA[i] = (double *) malloc(n*sizeof(double));
> matrixB[i] = (double *) malloc(n*sizeof(double));
>
> for (j=0; j < n; j++) {
> matrixA[i][j] = 0;
> matrixB[i][j] = 0;
> }
> }
>
> for (i=0; i j = k;
> f = i-m+1;
> l = 0;
> h2 = min(i,j);
> h1 = max(l,f);
>
> for(; h1 <= h2; h1++) {
> t = i-h1+1;
> filas = (unsigned long int) h1;
> matrixA[filas][i] = superior(sortedFsample[i], t, m);
> }
> }
>
> for (i=0; i j = n-m-1;
> f = i-m;
> g = 0;
> h2 = min(i,j);
> h1 = max(g,f);
>
> for(; h1 <= h2; h1++) {
> t = i-h1+1;
> filas = (unsigned long int) h1;
> matrixB[filas][i] = r_abs(sortedFsample[i] - (i-h1)/m);
> }
> }
>
>
> i = 1;
> j = n-m;
>
> for(; i< n; i++) {
> f = i-m+1;
> g = 1;
> h2 = min(i,j);
> h1 = max(g,f);
>
> matrixA[0][i] = max(matrixA[0][i], matrixA[0][i-1]);
>
> for(; h1 <= h2; h1++) {
> filas = (unsigned long int) h1;
> termino1 = max(matrixA[filas][i], matrixA[filas][i-1]);
> termino2 = max(matrixA[filas][i], matrixB[filas-1][i-1]);
>
> matrixA[filas][i] = min(termino1, termino2);
> }
>
> t = n-m-1;
> f = i-m;
> g = 0;
> h2 = min(i,t);
> h1 = max(g,f);
>
> filas = (unsigned long int) h1;
> matrixB[0][i] = max(matrixB[0][i], matrixA[0][i-1]);
>
> for(; h1 <= h2; h1++) {
> filas = (unsigned long int) h1;
> termino1 = max(matrixB[filas][i], matrixA[filas][i-1]);
>
> if (filas == 0) {
> termino2 = max(matrixB[filas][i], - INFINITY);
> }
> else{
> termino2 = max(matrixB[filas][i], matrixB[filas-1][i-1]);
> }
> matrixB[filas][i] = min(termino1, termino2);
> }
> }
>
> filas = (unsigned long int) t;
> unsigned long int n_int = (unsigned long int) (n-1);
> double result = min(matrixA[filas+1][n_int], matrixB[filas][n_int]);
>
> for (i=0; i <= k; i++) {
> free(matrixA[i]);
> free(matrixB[i]);
> }
>
> free(matrixA);
> free(matrixB);
>
> dKol[0] = result;
> }
>
> The R CMD SHLIB returns:
>
> gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2
> -fstack-protector --param=ssp-buffer-size=4 -Wformat
> -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c
> /home/hristo/pCloudDrive/R/dnk_c.c -o
> /home/hristo/pCloudDrive/R/dnk_c.o
> gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions
> -Wl,-z,relro -o /home/hristo/pCloudDrive/R/dnk_c.so
> /home/hristo/pCloudDrive/R/dnk_c.o -L/usr/lib/R/lib -lR
>
> My call in R to the function is:
>
> dyn.load("dnk_c.so")
> .C("dnk_c", as.double(sortedFs
