On Tue, Oct 28, 2014 at 10:19 AM, Kasper Daniel Hansen < [email protected]> 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]] > > _______________________________________________ > [email protected] mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
