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

Patrick Aboyoun paboyoun at fhcrc.org
Mon Jan 11 21:36:26 CET 2010

We have been silent on when to add R_CheckUserInterrupt calls at the C 
level for long running operations and only around 20 BioC packages use 
it. I added calls to R_CheckUserInterrupt in coverage, run*, and view* 
methods in IRanges, but more can certainly be added to the interval 

For the developer wiki how does the following general rule sound:

C level for loops should include a call to R_CheckUserInterrupt when the 
total loop time exceeds 10 seconds for a "reasonably sized" job on 
"reasonable" hardware AND the method is intended for interactive use.



Wolfgang Huber wrote:
> Hi all,
> I noted that some functions in IRanges, e.g. 'runq', can take a long 
> time to terminate; that interrupting the evaluation e.g. by Ctrl-C 
> does not seem to be possible; and that in the C code of that package, 
> the function R_CheckUserInterrupt is never used.
> Are these conscious design decisions? Are there (should there be) 
> general recommendations from the project regarding use of that 
> function (or possibly equivalent functionality)?
> Various other packages (Biostrings, Biobase, ShortRead, vsn, puma, 
> limma) do use it in various places.
> Best wishes
>      Wolfgang
> -- 
> Wolfgang Huber
> http://www.embl.de/research/units/genome_biology/huber/contact
> _______________________________________________
> Bioc-devel at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

More information about the Bioc-devel mailing list