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

Pages, Herve hp@ge@ @end|ng |rom |redhutch@org
Mon Oct 14 19:34:15 CEST 2019

Hi Toth,

Not clear to me what's going on but I kind of suspect this might have 
something to do with the use of data.table.

A few things to keep in mind:

- 'R CMD check' runs all the example in the same R session. This means 
that the outcome of the examples of a given man page can be affected by 
the examples from other man pages.

- A process cannot allocate more than 3 Gb of memory on 32-bit Windows. 
There is no such limit on 64-bit Windows or on the other platforms we 
support (Linux and Mac). On these platforms the maximum amount of memory 
a process can allocate only depends on what's available on the system.

- Generally speaking, sticking to the Bioconductor way of doing things 
(e.g use of GRanges objects instead of data.table objects, use of 
findOverlaps() instead of data.table::foverlaps()) will lead to faster 
code and reduced memory usage. Therefore I would strongly encourage you 
to consider switching to GRanges/findOverlaps() and to avoid the use of 
data.table in methrix.


On 10/11/19 09:36, Toth, Reka wrote:
> Dear BioC developers,
> The most recent build of methrix fails on Tokay1 server:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_spb-5Freports_methrix-5Fbuildreport-5F20191009174210.html&d=DwIF-g&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=doO3ej8vD58ZBQWVxkHTaCLk-xipbskav8uofJL2syI&s=zs3uDnFqyAl-hr_7StB3Yr-tGZW8VPfclbPY_JKtSt8&e=
> 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!
> Best,
> Reka
> 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
> Germany
> r.toth using dkfz-heidelberg.de
> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.dkfz.de&d=DwIF-g&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=doO3ej8vD58ZBQWVxkHTaCLk-xipbskav8uofJL2syI&s=U7YGBonX7WmBqfyEneCtEsuRUKl1fbTS6Esi3e9XGAI&e=
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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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P.O. Box 19024
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