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

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