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

Toth, Reka r@toth @end|ng |rom dk|z-he|de|berg@de
Tue Oct 15 15:18:02 CEST 2019

Thank you Herve, 

I finally was able to reproduce the error and solve it. You are right, it was most probably due to the data.table package.
Interestingly, the problem occurs randomly, with different error messages (sometimes it is complaining about negative vector size...). I will open an issue for data.table, because on these small datasets it shouldn't happen that it needs those big vector sizes. 

Thanks again. 


-----Original Message-----
From: Pages, Herve [mailto:hpages using fredhutch.org] 
Sent: Monday, October 14, 2019 7:34 PM
To: Toth, Reka; bioc-devel using r-project.org
Subject: Re: [Bioc-devel] check fails on arch 'i386'

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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