[R] how to avoid a script from hanging up

Carlos J. Gil Bellosta cgb at datanalytics.com
Mon Aug 3 00:33:10 CEST 2009


Something you can do is saving your strings in a external text file
(using cat, for instance). In this way, you would not require much
memory while extracting your data.

Once you have extracted it, you can always have a look at your external
file to see if it is too big, what to do with it, etc.

You can even consider saving your data into a database if need be.

Best regards,

Carlos J. Gil Bellosta

On Sun, 2009-08-02 at 20:02 +0200, mauede at alice.it wrote:
> I am submitting this problem to the  R forum , rather than the Bioconductor forum, because its nature is closer to programming style than any  Bioinformatic contents.
> I have implemented an R script to extracts many strings  through querying 3 Bioinformatic databases in the same loop cycle. Ideally, the script should perform as many cycles as necessary to extract all available data of interest.
> Inevitably it triggers a BioMart exception after running many cycles in a row. The exception seems to be independent of the script instructions because if I restart the script from the point where it got interrupted then it runs for another while, extracting also the data where the exception occurred with no problem at all.
> Sometimes, though, the script does not respond any more, it hangs up, even if no exception has apparently occurred, and the only way to regain control is to kill the R process. This way I lose memory of how many data have been processed and stored to disk files (unless I manually count them ... there are thousands ..). If I restart the script then it restarts processing the data strings from scratch. I guess it may be a memory problem as the task manager (Windows/XP) shows that the hung-up R script is taking more than 70% of the available RAM.
> I wonder whether there is any system command to make the script self-aware of its memory requirements and running time.
> Ideally the script should be able to trap the exception and be sensitive to its current RAM / CPU time requirements, self-exit after freezing and saving the current program status so that when rerun it would not restart from scratch but rather pick up from where it exited.
> Maybe this is asking too much from a non-compiled language ?
> Thank you in advance,
> Maura 
> tutti i telefonini TIM!
> 	[[alternative HTML version deleted]]
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