[Bioc-devel] Importing classes into NAMESPACE

On Wed, Feb 25, 2015 at 9:02 AM, Karolis Uziela <

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.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

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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

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[Bioc-devel] Importing classes into NAMESPACE

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