Try explicitly deleting large data objects by calling `rm`, then `gc`.
On Mon, Nov 23, 2020 at 6:15 AM Tomas Kalibera <tomas.kalib...@gmail.com>
wrote:
> On 11/21/20 6:51 PM, Jan Gorecki wrote:
> > Dear R-developers,
> >
> > Some of the more fat scripts (50+ GB mem used by R) that I am running,
> > when they finish they do quit with q("no", status=0)
> > Quite often it happens that there is an extra stderr output produced
> > at the very end which looks like this:
> >
> > Warning message:
> > In .Internal(quit(save, status, runLast)) :
> > system call failed: Cannot allocate memory
> >
> > Is there any way to avoid this kind of warnings? I am using stderr
> > output for detecting failures in scripts and this warning is a false
> > positive of a failure.
> >
> > Maybe quit function could wait little bit longer trying to allocate
> > before it raises this warning?
>
> If you see this warning, some call to system() or system2() or similar,
> which executes an external program, failed to even run a shell to run
> that external program, because there was not enough memory. You should
> be able to find out where it happens by checking the exit status of
> system().
>
> Tomas
>
>
> >
> > Best regards,
> > Jan Gorecki
> >
> > ______________________________________________
> > R-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
>
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