On Wed, Feb 25, 2015 at 9:02 AM, Karolis Uziela < karolis.uzi...@scilifelab.se> wrote:
> Thank you for your help everyone! Importing constructors separately (as > Thomas suggested), has solved the problem. > > @Gabe: I am not using any methods from Biobase, GenomicRanges > and S4Vectors. I am only using their constructors. Does it mean that I can > skip importing the classes and only import the constructors? Or did you > have something else in your mind? > So the code in your package never uses the objects, only returning them directly to the user for their use? If so, I think that's actually a case where Depends is called for, since that functionality is not useful to the user if they don't have those classes and methods available. > I thought it is better to avoid importing whole packages, especially if > they are large. Or do you have some arguments, why I should do that? > I haven't seen timings that tell me that targeted importing is worth the extra maintenance cost when methods move around between packages, functions change names, etc. It's largely a preference thing AFAIK, but I like to make sure I get everything I will need without worrying about when I do an import, rather than needing to be sure of the exact subset of symbols I want to use before hand. This, of course, is less compelling when you really do only need one thing, but I don't find that to be particularly common situation myself. ~G > > Regards, > Karolis > > On Wed, Feb 25, 2015 at 3:31 PM, Gabe Becker <becker.g...@gene.com> wrote: > >> Karolis, >> >> Do you really not need any of the methods for GRanges and ExpressionSet >> objects? import(GenomicRanges) might be better, even though the package >> isn't exactly small. >> >> ~G >> >> On Wed, Feb 25, 2015 at 6:27 AM, Thomas Sandmann < >> sandmann.tho...@gene.com> wrote: >> >>> Hi Karolis, >>> >>> These classes have constructor functions of the same name as the class. >>> For >>> example, the constructor function for GRanges is called GRanges(). >>> >>> If you use the constructors you need to import them separately, e.g. >>> >>> importFrom GenomicRanges GRanges >>> >>> Best, >>> Thomas >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioc-devel@r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> >> >> >> >> -- >> Gabriel Becker, Ph.D >> Computational Biologist >> Genentech Research >> > > > > -- > > Karolis Uziela > > PhD student > Science for Life Laboratory > Box 1031 > 17121 Solna, Sweden > Mob. +46 729 120 395 > -- Gabriel Becker, Ph.D Computational Biologist Genentech Research [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
