[Bioc-devel] Importing classes into NAMESPACE

Gabe Becker becker.gabe at gene.com
Wed Feb 25 18:13:30 CET 2015

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.

> 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.


> 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]]

More information about the Bioc-devel mailing list