I noticed the unfriendly indentation and formatting of my response , so I updated my original question on BioC support (with a much more eye-friendly formatting):
https://support.bioconductor.org/p/124442 ________________________________ From: Bhagwat, Aditya Sent: Friday, September 06, 2019 2:47 PM To: Michael Lawrence Cc: bioc-devel@r-project.org Subject: RE: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)? 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.mich...@gene.com] Sent: Friday, September 06, 2019 1:09 PM To: Bhagwat, Aditya Cc: bioc-devel@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.bhag...@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@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 micha...@gene.com Join Genentech on LinkedIn | Twitter | Facebook | Instagram | YouTube [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
