Hello, 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 http://www.datanalytics.com On Sun, 2009-08-02 at 20:02 +0200, mau...@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]] > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
