[BioC] Interrupting an R command

Kasper Daniel Hansen kasperdanielhansen at gmail.com
Wed Oct 6 16:05:09 CEST 2010

There is no other way.

How effective C-c is depends a lot on the code you are running.  In C
code for example the author has to place a command like
once in a while.  Some packages don't do this, making them impossible
to interrupt.  Some packages do this inside a for loop, only checking
for example every 1000 iterations.  In that case you have to wait
until the code reaches the interrupt check, which may take forever if
the system is starting to swap a lot.

I don't know which category randomForest belongs to.


On Wed, Oct 6, 2010 at 9:06 AM, January Weiner
<january.weiner at mpiib-berlin.mpg.de> wrote:
> Dear all,
> I have recklessly started an R command (randomForest from the
> randomForest library) and I was foolish enough not to save my
> workspace earlier (a typo and rf runs on a data set of 1000 x 100
> instead of 100 x 10).
> I don't want to kill R -- I don't want to lose the changes to the workspace.
> I would like to interrupt the random forests command only without
> killing the session; however, it does not react to ^C (control-C).
> Are there any other options available? Killing R, but with forcing it
> to save the workspace first would be fine as well.
> The platform: Linux / Ubuntu 10.04; R version 2.10.1 (2009-12-14);
> randomForest library version: randomForest 4.5-36
> Best regards,
> j.
> --
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

More information about the Bioconductor mailing list