[Bioc-devel] R_CheckUserInterrupt guidelines (was Re: R_CheckUserInterrupt in IRanges)

[Wolfgang Huber]

Hi Seth

Yes. I would hope that someone who goes to the trouble of writing C code 
understands that.

	Best wishes
	Wolfgang


Seth Falcon wrote:
> On 1/11/10 1:31 PM, Patrick Aboyoun wrote:
>> I just modified the C or Fortran code section of package guidelines to
>> reflect this new entry:
>>
>> http://wiki.fhcrc.org/bioc/Package_Guidelines#c-or-fortran-code
> 
> This looks reasonable.
> 
> It is worth noting, however, that calling R_CheckUserInterrupt is not 
> entirely free.  If you have a tight loop it might make more sense to 
> check at intervals rather than each time through and the choice of when 
> to check will depend very much on the computation.
> 
> Here's an example using the inline package (code is at the bottom) with 
> a silly double loop to compare checking vs not:
> 
> With R_CheckUserInterrupt inner loop:
> 
>  > system.time(z <- funx(10000L, TRUE))
>    user  system elapsed
>   1.310   0.001   1.313
> 
> No checking:
> 
> system.time(z <- funx(10000L, FALSE))
>    user  system elapsed
>    0.08    0.00    0.08
> 
> Now this may be completely unrealistic, but I suspect that a sensible 
> take away message is that we should be making sure our C code that loops 
> does call R_CheckUserInterrupt, but depending on the computation, not at 
> every loop iteration.
> 
> + seth
> 
> 
> ## example code is below.
> 
> library("inline")
> 
> code <- "
> int i, j, sum = 0, int n = INTEGER(max)[0];
> int check_inter = LOGICAL(do_check)[0];
> SEXP ans;
> PROTECT(ans = allocVector(INTSXP, n));
> for (i = 0; i < n; i++) {
>     INTEGER(ans)[i] = i;
>     for (j = 0; j < n; j++) {
>         sum = i + j;
>         if (check_inter) {
>             R_CheckUserInterrupt();
>         }
>     }
> }
> UNPROTECT(1);
> return ans;
> "
> 
> funx <- cfunction(signature(max="integer", do_check="logical"), code)
> 
> system.time(z <- funx(10000L, TRUE))
> system.time(z <- funx(10000L, FALSE))
> 
> 

-- 

Best wishes
      Wolfgang


--
Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber/contact