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

[Wolfgang Huber]

Hi Patrick

I suggest:

> 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 
> operations.
> 
> 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.

C level loops should include a call to R_CheckUserInterrupt when there 
is any chance that they may not terminate for certain parameter 
constellations, or when their run time exceeds 10 seconds with typical 
parameters and the method is intended for interactive use.

/*
The notion "reasonable hardware" is difficult, since it may just be on 
unreasonable hardware (like a netbook) where people experience the 
greatest need for interrupting a carelessly called function. Also, even
reasonable hardware can become unreasonable when there is competition 
for memory and it starts swapping. Unless there is a substantial cost 
for calling R_CheckUserInterrupt, I don't see why not to be liberal with it.
*/


	Best wishes
	Wolfgang

> Thoughts?
> 
> 
> Patrick
> 
> 
> 
> 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
>> EMBL
>> 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
> 


-- 

Best wishes
      Wolfgang


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