[Bioc-devel] What are the R CMD check settings (env vars) that Bioc uses?

Pages, Herve hp@ge@ @end|ng |rom |redhutch@org
Tue Dec 3 18:23:28 CET 2019

Hi Henrik,

On 12/3/19 09:13, Henrik Bengtsson wrote:
> I'm interested in finding out what customization Bioconductor servers
> do to R CMD check, e.g. _R_CHECK_***_ settings.  I think someone
> pointed me to some location in the past, but I cannot locate it.

The settings on the Linux/Mac builders are:


and on the Windows builder they are:


We just moved those settings to their own files yesterday (good timing) 
to make it easier to re-use them for the devel docker image (see

>  I
> think a natural place to document those would be on the 'Node Info'
> pages together with the existing platform and compiler information,
> e.g. https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_malbec2-2DNodeInfo.html&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=vTnT-DDbyP899v1VHljMc9jEcFqcbhXe6Dk3aTtU_YA&s=AFrilsJa2FP3Gk7trNjD2KuWa0WegOBq6ig8SHl0-sI&e= .

Exactly. That's the plan.


> Thanks,
> Henrik
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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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