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

[Hervé Pagès]

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:

   set _R_CHECK_FORCE_SUGGESTS_=0

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
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