Hi folks,
I'm trying to call an R function (fisher.test) in my program for like a
billion times! Though my program is in Python and I feel that using rpy2 to
interface R to python doesn't give me satisfactory performance. So I looked
into R code and found out that fisher.test is actually a wrapper around
another function called fexact which is implemented in C. Using Cython I
managed to directly call the function and get the desired results.
But the weird problem is that after calling the function for like 4000
times (with same parameters) a segmentation fault occurs! Eliminating the
possibility that my interfacing code has any problem, I wrote a piece of
code in C to call the fexact multiple times:
int main(){
int nr = 3, nc = 2;
int x[6] = {3, 1, 5, 1, 3, 6};
double expect = -1, percnt = 100, emin = 0, prt = 1;
double p;
int workspace = 200000, mult = 30;
int i;
for (i=0; i<100000; i++){
fexact(&nr, &nc, x, &nr, &expect,
&percnt, &emin, &prt, &p, &workspace, &mult);
printf("%d %f\n", i, p);
}
return 0;
}
I statically linked the program to libRmath, which I don't suppose has
anything to do with problem. I also dynamically linked to libRmath.so which
yielded the same problem.
nima@nima-laptop:~/BioProject/fet$ gcc -I/usr/share/R/include -lm fexact.c
/usr/lib/libRmath.a
nima@nima-laptop:~/BioProject/fet$ ./a.out
0 0.408431
1 0.408431
2 0.408431
3 0.408431
4 0.408431
....
....
4003 0.408431
4004 0.408431
4005 0.408431
Segmentation fault
Any help would be highly appreciated :)
*-- **Nima Mohammadi*
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