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!
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