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.
Cheers,
H.
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
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