[Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?

[Kasper Daniel Hansen]

There are
  importMethodsFrom(PACKAGE, NAME_OF_METHODS)
  importClassesFrom(PACKAGE, NAME_OF_METHODS)
to help with selective importing S4 methods/classes.  See section 1.5.6 of
WRE.

On Fri, Sep 6, 2019 at 9:24 AM Michael Lawrence via Bioc-devel <
bioc-devel using r-project.org> wrote:

> It sounds like you are trying to defer loading of namespaces in order
> to save time when they are unnecessary? That's probably going to end
> up a losing battle.
>
> On Fri, Sep 6, 2019 at 5:47 AM Bhagwat, Aditya
> <Aditya.Bhagwat using mpi-bn.mpg.de> wrote:
> >
> > Thank you Michael,
> >
> > Appreciate your time for helping me fill the gaps in my understanding of
> the S4 flow :-).
> >
> > It all started when I defined (in my multicrispr package) the S4 coercer
> :
> > methods::setAs( "BSgenome",
> >
> > "GRanges",
> > function(from) as(GenomeInfoDb::seqinfo(from), "GRanges")
> >
> > When building, I noticed the message
> > in method for 'coerce' with signature '"BSgenome","GRanges"': no
> definition for class "BSgenome"
> >
> > So, I added
> > BSgenome <- methods::getClassDef('BSgenome', package = 'BSgenome')
> >
> > That loads all these dependencies.
> > From your answer, I understand that there is currently no alternative to
> loading all these dependencies.
> > I guess because these dependencies are needed to provide for all
> required S4 methods for the BSgenome class, am I right?
> >
> > Is there a way to define a methods::setAs without loading the class
> definition?
> >
> > Aditya
> >
> >
> >
> >
> > ________________________________________
> > From: Michael Lawrence [lawrence.michael using gene.com]
> > Sent: Friday, September 06, 2019 1:09 PM
> > To: Bhagwat, Aditya
> > Cc: bioc-devel using r-project.org
> > Subject: Re: [Bioc-devel] Import BSgenome class without attaching
> BiocGenerics (and others)?
> >
> > The way to keep a "clean namespace" is to selectively import symbols
> > into your namespace, not to import _nothing_ into your namespace.
> > Otherwise, your code will fill with namespace qualifications that
> > distract from what is more important to communicate: the intent of the
> > code. And no, there's no way to define method signatures using
> > anything other than simple class names.
> >
> > It would be interesting to explore alternative ways of specifying
> > method signatures. One way would be if every package exported a "class
> > reference" (class name with package attribute, at least) for each of
> > its classes. Those could be treated like any other exported object,
> > and referenced via namespace qualification. It would require major
> > changes to the methods package but that should probably happen anyway
> > to support disambiguation when two packages define a class of the same
> > name. It would be nice to get away from the exportClasses() and
> > importClasses() stuff. File that under the "rainy year" category.
> >
> > Michael
> >
> > On Fri, Sep 6, 2019 at 3:39 AM Bhagwat, Aditya
> > <Aditya.Bhagwat using mpi-bn.mpg.de> wrote:
> > >
> > > Dear Bioc devel,
> > >
> > > Is it possible to import the BSgenome class without attaching
> BiocGenerics (to keep a clean namespace during the development of
> multicrispr<https://gitlab.gwdg.de/loosolab/software/multicrispr>).
> > >
> > > BSgenome <- methods::getClassDef('BSgenome', package = 'BSgenome')
> > >
> > > (Posted earlier on BioC support<
> https://support.bioconductor.org/p/124442/> and redirected here following
> Martin's suggestion)
> > >
> > > Thankyou :-)
> > >
> > > Aditya
> > >
> > > [[alternative HTML version deleted]]
> > >
> > > _______________________________________________
> > > Bioc-devel using r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >
> >
> >
> > --
> > Michael Lawrence
> > Scientist, Bioinformatics and Computational Biology
> > Genentech, A Member of the Roche Group
> > Office +1 (650) 225-7760
> > michafla using gene.com
> >
> > Join Genentech on LinkedIn | Twitter | Facebook | Instagram | YouTube
>
>
>
> --
> Michael Lawrence
> Scientist, Bioinformatics and Computational Biology
> Genentech, A Member of the Roche Group
> Office +1 (650) 225-7760
> michafla using gene.com
>
> Join Genentech on LinkedIn | Twitter | Facebook | Instagram | YouTube
>
> _______________________________________________
> Bioc-devel using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>


-- 
Best,
Kasper

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