[Bioc-devel] check fails on arch 'i386'

Toth, Reka r@toth @end|ng |rom dk|z-he|de|berg@de
Fri Oct 11 18:36:11 CEST 2019

Dear BioC developers,

The most recent build of methrix fails on Tokay1 server:
The error message is the following:

** running examples for arch 'i386' ... ERROR
Running examples in 'methrix-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_region_summary
> ### Title: Extract and summarize methylation or coverage info by regions of
> ###   interest
> ### Aliases: get_region_summary
> ### ** Examples
> data("methrix_data")
> get_region_summary(m = methrix_data, regions = data.table(chr = "chr21", start = 27867971, end =  27868103), type = "M", how = "mean")
-Checking for overlaps..
Error: cannot allocate vector of size 1.4 Gb
Execution halted

I am a bit puzzled what the reasons could be, since it passed this step during the previous builds and I didn’t change any of the functions in my last commit.
When I run the check on our local Windows, I don’t get any error. We use a very small dataset as example, it definitely should not use a vector of size 1.4 Gb.

I would appreciate every input or idea on how to tackle this error.
Thanks a lot!


Dr. Reka Toth
Computational Epigenomics Group
Division of Epigenomics and Cancer Risk Factors /C010
Postdoctoral Fellow

German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 280
69120 Heidelberg

r.toth using dkfz-heidelberg.de

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