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 <[email protected]> wrote: > 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 > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099 [[alternative HTML version deleted]] _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
