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

[Alex Wong via Bioc-devel]

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)

Kind Regards,

Alex

-- 

*Alex Wong BSc(Med)/MBBS FRACP FRCPA PhD*
Research Officer, Gene and Stem Cell Therapy Program, Centenary Institute

-- 
 

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

[Hervé Pagès]

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.git...@gmail.com

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Re: [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 
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.git...@gmail.com
>
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>
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>


-- 
Best,
Kasper

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