Thank you very much.
The instructions you suggested allow the script itself to decide whether to
exit spontaneously.
What I am still missing is how to prevent the script from restarting from
scratch.
I'll try to explain my problem a little bit better.
Please, assume I have 3 huge data.frames called d1,d2,d3
My script searched d1 first and d2, d3 looking for matching fields with d1.
A very simplified version of my script looks like the following:
while (length(d1) > 0) {#............................ LOOP ON MirBase miRNAs
LIST ........................
if (length (which (d2[] == d1[1])) > 0) {
tmp <- d2[which(d2[] == d1[1])]
FromWhere <- "d2"
<PROCESS ALL DATA in tmp>
}else if (length(which (d2[] == d1[1])) > 0) {
tmp <- d3[which(d3[] == d1[1])]
FromWhere <- "d3"
<PROCESS ALL DATA in tmp>
}else {
missing_miRNA <- d1[1]
cat("\n miRNA: ",missing_miRNA," NOT FOUND IN d2 OR IN d3 \n")
flush(stdout())
d1 <- d1[-c(which(d1[] == d1[1]))]
next
}
Please, notice also the sub-session <PROCESS ALL DATA in tmp> ends with the
instructions that remove from d1
all the entries whose name is the same. Maybe it is not clear from my concise
version. In reality d1,d2,d3 have many fields.
d1 can have many rows whose field "miRNA_ID" is the same, but the other fields
contain different pointers.
For the sake of freeing some memory, I remove all the rows that pertain to the
same miRNA_ID regardless whether the current
miRNA has been found in d2 or d3 or not.
Actually, perhaps I can operate a similar dynamic data pruning on d2 .. but I
have first to check all the links carefully to avoid deleting data
that may pertain to different miRNAs.
In short, if the script handles its own exit through the instructions you
suggested, even saving the environment variables, when the script is
run again it will restart processing d1,d2,d3 from scratch.
I am dreaming of a re-entrant process. Maybe I should use some environment
(system) variables, not just the program variables, to save the necessary
information to make next run a process resumption rather than a re-run
Is it possible to access / create environment variables from inside an R script
?
Regards,
Maura
-----Messaggio originale-----
Da: jim holtman [mailto:jholt...@gmail.com]
Inviato: dom 02/08/2009 21.54
A: mau...@alice.it
Cc: r-h...@stat.math.ethz.ch
Oggetto: Re: [R] how to avoid a script from hanging up
You can use 'try' to catch errors and take corrective action.
'memory.size' and 'proc.time' will give you information on the memory
usage of your application and the CPU time that has been used.
On Sun, Aug 2, 2009 at 2:02 PM, <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.
>
--
Jim Holtman
Cincinnati, OH
+1 513 646 9390
What is the problem that you are trying to solve?
tutti i telefonini TIM!
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