Re: [R] R_alloc with structures with "flexible array members"

From: Jeffrey Horner <jeff.horner_at_vanderbilt.edu>
Date: Wed, 05 Mar 2008 10:23:29 -0600

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

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Received on Wed 05 Mar 2008 - 16:27:35 GMT

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