[Bioc-devel] modify _R_CHECK_FORCE_SUGGESTS_ ?

[Hervé Pagès]

Hi Vivek,

I'd say don't worry about R CMD check failing with the Single Package
Builder on Windows for now. When your package gets accepted, we'll
set _R_CHECK_FORCE_SUGGESTS_ to FALSE on Windows so your package will
be supported on this platform despite having Rsubread in Suggests.

Note that this not unprecedented: we're already doing this for
VariantTools (suggests gmapR, which is no supported on Windows
either) and singleCellTK (suggests Rsubread).

The way we do this is by adding a .BBSoptions file to the package
source tree with the following line in it:

   CHECKprepend.win: set _R_CHECK_FORCE_SUGGESTS_=0&&

Of course, you'll have to make sure that the code in the man pages,
vignettes and unit tests can run without Rsubread being installed.

Cheers,
H.


On 05/19/2018 02:49 AM, Bhardwaj, Vivek wrote:
> ??I think one option for me would be to switch to RBowtie instead of Rsubread, since this seems to have a windows binary. I would try this as soon as I have access to a windows system.
> 
> 
> --------
> 
> Vivek Bhardwaj
> PhD Candidate | International Max Planck Research School
> Max Planck Institute of Immunobiology and Epigenetics
> Stübeweg 51, Freiburg
> ________________________________
> From: Bhardwaj, Vivek
> Sent: Saturday, May 19, 2018 10:35 AM
> To: Michael Lawrence; Martin Morgan
> Cc: bioc-devel at r-project.org
> Subject: Re: [Bioc-devel] modify _R_CHECK_FORCE_SUGGESTS_ ?
> 
> 
> @All thanks for your comments
> 
> I have provided Rsubread mapping wrapper as an optional step in the pipeline. Users can continue the analysis after mapping with their tool of choice as well. Therefore I added it in "suggests" and skip running it in the example and don't evaluate that chunk in the vignette.
> 
> I wouldn't want to skip supporting windows only because of an optional step, but I also prefer to keep that function as it allows users to perform end-to-end analysis in R if they wish to.
> 
> What would be the best option for me for now?
> 
> 
> 
> On 5/19/18 12:00 AM, Michael Lawrence wrote:
> 
> On Fri, May 18, 2018 at 2:26 PM, Martin Morgan
> <martin.morgan at roswellpark.org><mailto:martin.morgan at roswellpark.org> wrote:
> 
> 
> You can create a plain text file in the root directory of your package
> .BBSoptions with the line
> 
>    UnsupportedPlatform: win
> 
> Your package will not be available on Windows, losing about 1/2 your
> potential audience.
> 
> 
> I'm not sure how many people will endeavor to run that part of the
> icetea pipeline on their Windows laptop. What about separating the
> preprocessing and downstream exploratory stuff into two packages?
> 
> 
> 
> A better strategy is to figure out why you are
> Suggests:'ing Rsubread, and find alternative cross-platform solutions.
> 
> I would not hesitate to add your voice to mine in asking the Rsubread
> maintainer to make their package cross-platform compatible. While this
> requires considerable work, it would benefit the Bioconductor community in
> this and subsequent years.
> 
> Martin
> 
> On 05/18/2018 04:55 PM, Bhardwaj, Vivek wrote:
> 
> 
> Hi All
> 
> 
> My package is in review and the build is failing since a suggested package
> (Rsubread) is not available on windows. Is there a way for me to instruct
> the build machine on bioc to use: _R_CHECK_FORCE_SUGGESTS_ = FALSE ??
> 
> 
> 
> Best,
> 
> Vivek
> 
> --------
> 
> Vivek Bhardwaj
> PhD Candidate | International Max Planck Research School
> Max Planck Institute of Immunobiology and Epigenetics
> St?beweg 51, Freiburg
> 
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-- 
Hervé Pagès

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