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 <[EMAIL PROTECTED]> 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 >> > <[EMAIL PROTECTED]> 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@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, [EMAIL PROTECTED] >> 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 ______________________________________________ R-help@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.