[Bioc-devel] memory exhausted on tokay2

Aaron Taudt @@ron@t@udt @end|ng |rom gm@||@com
Thu Apr 11 20:53:42 CEST 2019

Dear Hervé,

thank you for your reply and the explanations. I have checked the R CMD
check on my system (MacOS Mojave) and the whole check does not exceed 1Gb
of RAM. I am also surprised why it would need that much, because all the
examples are pretty slim, so even if all objects are kept, I am wondering
why it needs that much RAM on Windows/Linux.
If you can give me some more hints I'd be glad.


Am So., 7. Apr. 2019 um 00:03 Uhr schrieb Pages, Herve <hpages using fredhutch.org

> Hi Aaron,
> Maybe the particular example (plotting) where the "memory exhausted"
> error occurs is not particularly memory-intensive. However keep in mind
> 2 important things:
>    1) 'R CMD check' runs all the examples from all the man pages in the
> same R session. This means that memory used (and not released) by other
> examples will reduce the memory available for the example being
> currently run. So even though your plotting examples use less than 1 Gb
> of RAM, the 'top' command on my Linux laptop indicates that a full 'R
> CMD check' on the methimpute package uses about 6 Gb of RAM!
>    2) We use the --force-multiarch option when running 'R CMD check' on
> the Windows build machines. This forces 'R CMD check' to run all the
> examples from all the man pages twice: once in 32-bit mode and once in
> 64-bit mode. Note that 32-bit Windows limits the amount of memory that a
> single process can use to about 3Gb. This would explain why the plotting
> examples fail only when run in 32-bit mode (i386 arch). All the examples
> run ok in 64-bit mode (x64 arch).
> The solution is to try to reduce the memory footprint of your examples
> in general, not just the plotting examples. Maybe there is an example
> somewhere that creates a big object. Note that because all the examples
> are run in the same session, this object will persist when other
> examples are run. Removing the object (with 'rm(object)') might help.
> The very last resort would be to mark the package as not supported on
> 32-bit Windows but hopefully we won't need to do that.
> Hope this helps,
> H.
> On 4/6/19 04:10, Aaron Taudt wrote:
> > Dear bioconductor-devel,
> >
> > I am trying to fix an "Error: memory exhausted (limit reached?)" error
> that
> > arises during Rcheck on tokay2 (Windows Server 2012 R2 Standard / x64) .
> > The package builds and passes Rcheck just fine on all other hosts. Is
> this
> > something I can fix? The function in question is not particularly
> > memory-intensive.
> >
> > Regards,
> > Aaron Taudt
> >
> >       [[alternative HTML version deleted]]
> >
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> >
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> --
> Hervé Pagès
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
> E-mail: hpages using fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319

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