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

[Henrik Bengtsson]

Thank you - sounds great. /Henrik

On Tue, Dec 3, 2019 at 9:23 AM Pages, Herve <hpages using fredhutch.org> wrote:
>
> 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:
>
>    https://github.com/Bioconductor/BBS/blob/master/3.11/R_env_vars.sh
>
> and on the Windows builder they are:
>
>    https://github.com/Bioconductor/BBS/blob/master/3.11/R_env_vars.bat
>
> 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
> https://github.com/Bioconductor/bioconductor_full/pull/20#issuecomment-560546981).
>
> >  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.
>
> Cheers,
> H.
>
> >
> > Thanks,
> >
> > Henrik
> >
> > _______________________________________________
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> > https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=vTnT-DDbyP899v1VHljMc9jEcFqcbhXe6Dk3aTtU_YA&s=Cc5slvLV6zlwGr9LwvWDwH44Dc5_zv-CoLF6Q83l9bE&e=
> >
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
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