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

From: Jeffrey Horner <jeff.horner_at_vanderbilt.edu>
Date: Wed, 05 Mar 2008 15:38:29 -0600

Ramon Diaz-Uriarte wrote on 03/05/2008 03:00 PM:

> 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.

Aha! The lesson I take away from this then is question everything, assume nothing.

Jeff

> 
> 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


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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. Received on Wed 05 Mar 2008 - 21:43:34 GMT

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