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

[Henrik Bengtsson]

To 2nd what Seth's says, I think it is worth showing an explicit
example of how to check at regular intervals, e.g.  for (i = 0; i < n;
i++) { if (i %% 100 == 0) R_CheckUserInterrupt(); ... }

/Henrik

On Mon, Jan 11, 2010 at 3:50 PM, Seth Falcon <sfalcon at fhcrc.org> 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))
>
>
> --
> Seth Falcon
> Bioconductor Core Team | FHCRC
>
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