[Bioc-devel] memory exhausted on tokay2

Pages, Herve hp@ge@ @end|ng |rom |redhutch@org
Sun Apr 7 00:03:49 CEST 2019

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,


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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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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