R_alloc with structures with "flexible array members"

Wed, Mar 5, 2008 9:52 AM

Dear Jeff,

Thanks for the suggestion. However, something is still not working.
This is a simple example:

***************************  start C ************
#include <R.h>

struct Sequence {
  int len;
  unsigned int state_count[];
};


int main(void) {

  struct Sequence *A;
  int n = 4;

  // First line segfaults. Second doesn't
    A = (struct Sequence *) R_alloc(1,  sizeof(struct Sequence) + n *
sizeof(unsigned int));
  //  A = malloc(sizeof(struct Sequence) + n * sizeof(unsigned int));

  return(0);
}

***********  end C  **********


I then do
gcc -std=gnu99 -Wall -I/usr/share/R/include -I/usr/share/R/include
-L/usr/lib/R/lib -lR ex7.c

and the ./a.out segfaults when I use R_alloc (not with malloc).


Best,

R.

On Wed, Mar 5, 2008 at 5:23 PM, Jeffrey Horner

<jeff.horner at vanderbilt.edu> wrote:

Ramon Diaz-Uriarte wrote on 03/05/2008 04:25 AM:

Dear All,
 >
 > In a package, I want to use some C code where I am using a structure
 > (as the basic element of a linked list) with flexible array members.
 > Basically, this is a structure where the last component is an
 > incomplete array type  (e.g., Harbison & Steel, "C, a reference
 > manual, 5th ed.", p. 159) such as:
 >
 > struct Sequence {
 >   struct Sequence *next;
 >   int len;
 >   unsigned int state_count[];
 > };
 >
 >
 > To create one such sequence, I allocate storage (following Harbison
 > and Steel) in a C program as follows:
 >
 > struct Sequence *A;
 > int n = 4;
 > A = malloc( sizeof(struct Sequence) + n * sizeof(unsigned int));
 >
 >
 > If I understand correctly, however, it would be better to use R_alloc
 > instead of malloc (memory automagically freed on exit and error;
 > error-checking). But I do not know how to make the call to R_alloc
 > here, since R_alloc allocates n units of size bytes each.
 >
 >
 > I've tried, without success, the following two:
 >
 > int to_add_for_R_alloc =
 >     (int) ceil((float) sizeof(struct sequence) / sizeof(unsigned int));
 >
 >   A = (struct sequence *) R_alloc(to_add_for_R_alloc + n,
 > sizeof(unsigned int));
 >
 > or even a brute force attempt as:
 >
 >  A = (struct sequence *) R_alloc( 100,  sizeof(struct sequence));
 >
 >
 > but both result in segmentation faults.
 >
 >
 > Should I just keep using malloc (and free at end)?

 Hi Ramon,

 You should be able to use R_alloc without seg faults, so there's
 something wrong with your code somewhere. R_alloc multiplies its
 arguments together to come up with the total number of bytes to allocate
 then it allocates a raw vector and returns the data portion.

 So you can just treat R_alloc similarly to malloc by calling
 R_alloc(1,sizeof(struct Sequence) + n * sizeof(unsigned int)).

 Best,

 Jeff
 --
 http://biostat.mc.vanderbilt.edu/JeffreyHorner

Ramon Diaz-Uriarte
Statistical Computing Team
Structural Biology and Biocomputing Programme
Spanish National Cancer Centre (CNIO)
http://ligarto.org/rdiaz

R_alloc with structures with "flexible array members"

Thread (9 messages)