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

From: Ramon Diaz-Uriarte <rdiaz02_at_gmail.com>
Date: Wed, 05 Mar 2008 22:00:30 +0100

Dear Prof. Ripley,

Yes, of course! You are right. What a silly mistake on my part! I was using a standalone program for development of functions, debugging, etc, of what is part of a package.

Thanks,

R.

On Wed, Mar 5, 2008 at 8:45 PM, Prof Brian Ripley <ripley_at_stats.ox.ac.uk> wrote:
> 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
> >
> > ______________________________________________
> > R-help_at_r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
> --
> 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
>

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

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Received on Wed 05 Mar 2008 - 21:03:54 GMT

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