[Bioc-devel] Importing classes into NAMESPACE

[Michael Lawrence]

On Wed, Feb 25, 2015 at 9:13 AM, Gabe Becker <becker.gabe at gene.com> wrote:

> On Wed, Feb 25, 2015 at 9:02 AM, Karolis Uziela <
> karolis.uziela at 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.
>
>
Have them listed in Depends, but still import in the NAMESPACE, of course.


>
>
> > 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?
> >
>
>
If GenomicRanges forms the foundation of your package, then it's more
practical to import(GenomicRanges). If you're only cherry-picking a few key
functions from a package, then individual importFrom() declarations better
describe the specifics of that dependency.


> 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.gabe at 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.thomas at 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 at 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 at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

	[[alternative HTML version deleted]]