[R] Mediation analysis takes up all RAM, then all swap, and then RStudio/terminal suddenly closes

Phillips Rogfield thebudget72 @end|ng |rom gm@||@com
Wed Jun 23 17:01:45 CEST 2021

Hello Bert,

thank you for your kinds answer.

No I didn't contact the maintainer of the package first, that's my fault :)

I have come to the conclusion that the problem is that I don't have 
enough resources on my PC (RAM) for the task at hand.

I have tried to run it on a remote VM with more RAM and seems to work.

Best regards

On 22/06/2021 17:50, Bert Gunter wrote:
> Please read and follow the posting guide, linked below, which says:
> "For questions about functions in standard packages distributed with R 
> (see the FAQ Add-on packages in R 
> <https://cran.r-project.org/doc/FAQ/R-FAQ.html#Add-on-packages-in-R>), 
> ask questions on R-help.
> If the question relates to a /contributed package/ , e.g., one 
> downloaded from CRAN, try contacting the package maintainer first. You 
> can also use |find("functionname")| and 
> |packageDescription("packagename")| to find this information. *Only* 
> send such questions to R-help or R-devel if you get no reply or need 
> further assistance. This applies to both requests for help and to bug 
> reports."
> So, while you *may* get a useful response here, you should contact the 
> maintainer. If you have already done so, please say so.
> Another possibility that may be helpful is the Fedora SIG, 
> https://stat.ethz.ch/mailman/listinfo/r-sig-fedora 
> <https://stat.ethz.ch/mailman/listinfo/r-sig-fedora> , though of 
> course I have no idea whether your problem is OS specific.
> Bert Gunter
> "The trouble with having an open mind is that people keep coming along 
> and sticking things into it."
> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )
> On Tue, Jun 22, 2021 at 8:38 AM Philips Roger <thebudget72 using gmail.com 
> <mailto:thebudget72 using gmail.com>> wrote:
>     I am using the mediation
>     <https://cran.r-project.org/package=mediation
>     <https://cran.r-project.org/package=mediation>>
>     package to run a mediation analysis.
>     But when I call the `mediate` function, R eats up all RAM, then it
>     eats
>     up all swap, and then RStudio suddenly closes.
>     The same happens if I call `Rscript` from the terminal, and the
>     terminal
>     suddenly closes.
>     Here is measures for RAM and swap. Notice the peaks:
>     RAM diagnostics
>     I have Fedora Worstation 24.
>     This happens BOTH with the R 4.0.5 that uses Open BLAS provided in
>     the
>     Fedora repository, and a custom R 4.1.0 I compiled from source linked
>     against Intel MKL.
>     It doesn't seem to happen every time, some times (rarely), the RAM
>     stays
>     constant (around 40/50%) and it works (it takes a long time through).
>     What is the cause of this? How can I debug?
>     ______________________________________________
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>     PLEASE do read the posting guide
>     http://www.R-project.org/posting-guide.html
>     <http://www.R-project.org/posting-guide.html>
>     and provide commented, minimal, self-contained, reproducible code.

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