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

[Prof Brian Ripley]

On Wed, 5 Mar 2008, Ramon Diaz-Uriarte wrote:

> 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).

You can't use R_alloc in a standalone program without initializing R, 
which has not been done here.

You said 'in a package', but this is not in a package.

>
>
> 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
>
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>

-- 
Brian D. Ripley,                  ripley at stats.ox.ac.uk
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595