[Bioc-devel] depends on packages providing classes

[James W. MacDonald]

I agree with Vince. It's your job as a package developer to make available
to your package all the functions necessary for the package to work. But I
am not sure it is your job to load all the packages that your end user
might need.

Best,

Jim



On Tue, Oct 28, 2014 at 11:04 AM, Vincent Carey <stvjc at channing.harvard.edu>
wrote:

> On Tue, Oct 28, 2014 at 10:19 AM, Kasper Daniel Hansen <
> kasperdanielhansen at gmail.com> wrote:
>
> > What is the current best paradigm for using all the classes in
> > S4Vectors/GenomeInfoDb/GenomicRanges/IRanges
> >
> > I obviously import methods and classes from the relevant packages.
> >
> > But shouldn't I depend on these packages as well?  Since I basically want
> > the user to have this functionality at the command line? That is what I
> do
> > now.
> >
> >
> I've wondered about this as well.  It seems the principle is that the user
> should
> take care of attaching additional packages when needed.  It might be
> appropriate
> to give a hint in the package startup message, if having some other package
> attached
> would typically be of great utility.
>
> Given your list above, I would think that depending on GenomicRanges would
> often
> be sufficient, and IRanges/S4Vectors would not require dependency
> assertion.  I would
> think that GenomeInfoDb should be a voluntary attachment for a specific
> session.
>
> These are just my guesses -- I doubt there will be complete consensus, but
> I have
> started to think very critically about using Depends, and I think it is
> better when its
> use is minimized.
>
>
> > That of course leads to the R CMD check NOTE on depending on too many
> > packages.... I guess I should ignore that one.
> >
> > Best,
> > Kasper
> >
> >         [[alternative HTML version deleted]]
> >
> > _______________________________________________
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> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
>
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>
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>



-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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