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

[Evgenii Chekalin]

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

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