[Bioc-devel] depends on packages providing classes

Vincent Carey stvjc at channing.harvard.edu
Tue Oct 28 16:04:50 CET 2014

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
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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