[Bioc-devel] How to declare optional system requirement for package

[Kasper Daniel Hansen]

To me, whether or not this is a good idea depends a bit on the degree to
which these functions are generally useful.

Best,
Kasper

On Wed, Nov 29, 2023 at 5:41 PM Hervé Pagès <hpages.on.github using gmail.com>
wrote:

> Hi Alex,
>
> On 11/28/23 22:47, Alex Wong via Bioc-devel wrote:
>
> > Hi there,
> >
> > I am the author of SpliceWiz. My package contains several wrapper
> functions
> > that run the STAR aligner on systems where it is installed. If STAR is
> not
> > found, these functions do nothing other than return a helpful message
> that
> > says STAR is not available. The vast majority of the functions in the
> > package does not depend on STAR, thus STAR is a highly optional
> requirement
> > for my package.
> >
> > What is the best way to convey this in the DESCRIPTION file? Is it
> > acceptable to add the following line?
> >
> >> SystemRequirements: STAR (optional)
>
> That works but it's hard to know what functionality is lost by not
> having STAR on the machine.
>
> Would it make sense to put all the STAR-related stuff in their own
> package and have SpliceWiz suggest that package?
>
> STAR would now be a hard requirement for the package that contains the
> STAR-related stuff.
>
> This kind of separation might help with maintenance and quality control.
> It might also help making things less confusing for the end user.
>
> Best,
>
> H.
>
> > Kind Regards,
> >
> > Alex
> >
> --
> Hervé Pagès
>
> Bioconductor Core Team
> hpages.on.github using gmail.com
>
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>
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-- 
Best,
Kasper

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