[Bioc-devel] octad.db check windows i386 not enough memory

Hervé Pagès hp@ge@@on@g|thub @end|ng |rom gm@||@com
Fri Nov 12 05:01:58 CET 2021

Hi Evgenii,

A process cannot allocate more than 3Gb of memory on 32-bit Windows so 
it looks like the process running the runsRGES() examples is hitting 
that limit. What doesn't help is that 'R CMD check' concatenates all the 
examples from all the man pages into a single file before running the 
code from this file so even if a particular example doesn't require a 
lot of memory it could fail because other examples before it created big 
objects that are sticking around.

The good news is that you're submitting a package for inclusion to the 
next version of Bioconductor (BioC 3.15) and we're going to drop support 
for 32-bit Windows for this new version. That's because BioC 3.15 will 
be based on R 4.2 which will also drop support for 32-bit Windows.

In the mean time, you should be able to disable the 32-bit checks by 
adding a .BBSoptions file in the top-level folder of your package. With 
the following line in it:

UnsupportedPlatforms: win32

I don't know if the SPB (Single Package Builder) will recognize this but 
it's worth the try.


On 11/11/2021 13:33, Evgenii Chekalin wrote:
> Hi,
> As a part of the pipeline function example for runsRGES() have to load
> several additional files and during examples check for the i386 win server
> the automatic check encounters an error.
> Any ideas on how to address this?
> Oddly enough, during the vignette building, a similar example seems to run
> smoothly.
> Thank you in advance.
> ** running examples for arch 'i386' ... [179s] ERROR
> Running examples in 'octad-Ex.R' failed
> The error most likely occurred in:
>> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
>> ### Name: runsRGES
>> ### Title: Compute sRGES
>> ### Aliases: runsRGES
>> ### Keywords: sRGES
>> ### ** Examples
>> #load differential expression example for HCC vs adjacent liver tissue computed in diffExp() function
>> res=ExperimentHub()[["EH7278"]]
> snapshotDate(): 2021-10-19
> see ?octad.db and browseVignettes('octad.db') for documentation
> loading from cache
>> res=subset(res,abs(log2FoldChange)>1&padj<0.001)
>> #run sRGES computation
>> runsRGES(dz_signature=res,choose_fda_drugs = FALSE,max_gene_size=100,permutations=1000)
> snapshotDate(): 2021-10-19
> see ?octad.db and browseVignettes('octad.db') for documentation
> loading from cache
> see ?octad.db and browseVignettes('octad.db') for documentation
> loading from cache
> Started sRGES computation. Average computation time ~1-3mins.
> mem check 1
> mem check 2
> Error: cannot allocate vector of size 260 Kb
> Execution halted
> ** running examples for arch 'x64' ... [268s] OK
> Kind regards,
> Evgenii Chekalin, PhD,
> Research associate,
> Michigan State University, College of Human Medicine
> Department of Pediatrics and Human Development
> Secchia Center, room 732
> 15 Michigan St. NE
> Grand Rapids, MI 49503
> +1(616) 617-1746
> 	[[alternative HTML version deleted]]
> _______________________________________________
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Hervé Pagès

Bioconductor Core Team
hpages.on.github using gmail.com

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