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

[Tim Triche, Jr.]

This makes sense. Windows users won’t be easily able to call variants across thousands of samples but at least the plotting, impact prediction, etc will work fine for them. 

I will need to define things such that the variant calling is optional, which is not too absurd — I’ll add loading of MVRanges/MVRangesList objects from VCFs and move gmapR to suggests. 

Personally I use the variant calling functionality regularly, but I have my doubts as to whether someone on Windows would even have enough RAM to call variants across 2000+ samples in a shot, so this is a good compromise.  Everything else is, I believe, platform agnostic. This should work. 

--t

> On Oct 11, 2018, at 1:41 AM, Hervé Pagès <hpages using fredhutch.org> wrote:
> 
> 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,
> 
> H.
> 
>> 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:
>>   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]]
>>> 
>>> _______________________________________________
>>> Bioc-devel using r-project.org mailing list
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=x8fxgyra6DmetOzKCh1Zm1X25BwPM7TDr8UUNYwgV18&s=rzPUqLBge6xE1TymeYxIxJxkiiOHefbSgzPOLYEhvrM&e= 
>>> 
> 
> -- 
> 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
> 
> E-mail: hpages using fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319