[Bioc-devel] depends on packages providing classes
James W. MacDonald
jmacdon at uw.edu
Tue Oct 28 16:14:31 CET 2014
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
On Tue, Oct 28, 2014 at 11:04 AM, Vincent Carey <stvjc at channing.harvard.edu>
> 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
> > now.
> I've wondered about this as well. It seems the principle is that the user
> take care of attaching additional packages when needed. It might be
> to give a hint in the package startup message, if having some other package
> would typically be of great utility.
> Given your list above, I would think that depending on GenomicRanges would
> be sufficient, and IRanges/S4Vectors would not require dependency
> assertion. I would
> think that GenomeInfoDb should be a voluntary attachment for a specific
> 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
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James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
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