[Bioc-devel] how can I declare that a package doesn't/can't fully support Windows

Hervé Pagès hp@ge@ @ending from fredhutch@org
Thu Oct 11 07:41:48 CEST 2018

And of course: the whole trick I described below only makes sense
if MTseeker doesn't rely on gmapR for its core functionality, that
is, if not having gmapR installed still allows the user to accomplish
something meaningful with MTseeker.

Otherwise the trick below will make MTseeker available on Windows
but Windows users won't be able to accomplish anything meaningful
with it. In that case, marking the package as unsupported on Windows
would be preferable.

Hope this makes sense,


On 10/10/2018 10:26 PM, Hervé Pagès wrote:
> Hi Tim,
> No platform-specific dontrun capabilities AFAIK but you can use
> something like:
>    if (requireNamespace("gmapR", quietly=TRUE)) {
>        ...
>        ...
>    }
> in your man pages.
> You would also need to move gmapR from Imports to Suggests.
> Then make sure that MTseeker passes 'R CMD check' **without**
> the gmapR package being installed. You'll need to define and set
> environment variable _R_CHECK_FORCE_SUGGESTS_ to 0 for this.
> Do it with:
>    export _R_CHECK_FORCE_SUGGESTS_=0
> on Linux or Mac, or with:
> on Windows.
> Once MTseeker is accepted, we'll add a .BBSoptions file with special
> directive:
>    CHECKprepend.win: set _R_CHECK_FORCE_SUGGESTS_=0&&
> This will have the effect to set the environment variable on the
> Windows build machines before running 'R CMD check' there.
> So MTseeker will be supported and available on all platforms.
> For MTseekerData: the package doesn't seem to make any use of gmapR
> so you can probably remove gmapR from its Suggests field.
> Hope this helps,
> H.
> On 10/10/2018 07:46 AM, Tim Triche, Jr. wrote:
>> it looks like gmapR does not support Windows, and as a result, my 
>> MTseeker
>> package cannot build on tokay1, so the Data package which requires it 
>> also
>> cannot build on tokay1.  Are there platform-specific dontrun 
>> capabilities?
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_spb-5Freports_MTseekerData-5Fbuildreport-5F20181010103212.html&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=x8fxgyra6DmetOzKCh1Zm1X25BwPM7TDr8UUNYwgV18&s=QNKSsmQnfEAQOTI0r8dDuW_d01XzL_cL1cb5QIElLxw&e= 
>> Short of somehow forcing gmapR to build on Windows, which I believe is
>> beyond my control, is there a way to declare that parts of the MTseeker
>> package are unsupported/unsupportable on Windows?
>> I suppose I could cleave off the variant-recalling portions but that 
>> seems
>> a little ridiculous. The original goal was to take the non-NuMT reads 
>> from
>> a given alignment, realign (only) those to rCRS/RSRS, and call against
>> that, for better mitochondrial haplogroup inference. We're still working
>> towards the full version, but even just calling variants against rCRS 
>> with
>> indels is hugely useful, and the ability to screen out 
>> haplogroup-specific
>> variants while retaining indels, SNVs, etc. turns out to be VERY handy.
>> More generally, there isn't any equivalent (AFAIK) in BioC, at all.
>> --t
>>     [[alternative HTML version deleted]]
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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

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