Re: [Bioc-devel] How to import a setAs method in one's package?

2020-05-08 Thread Michael Lawrence via Bioc-devel
setAs() defines methods on the coerce() generic, so you could write importMethodsFrom(pkg, coerce). However, as() searches the namespace associated with class(from) for coerce() methods. As long as that namespace hasn't selectively imported methods on coerce(), it should end up using the global

Re: [Bioc-devel] How to import a setAs method in one's package?

2020-05-08 Thread Hervé Pagès
Hi Aditya, It is very hard to get selective imports from the methods package right and there is no real benefit in doing so. I would strongly recommend that you just import its full namespace with: import(methods) Best, H. On 5/8/20 02:48, Bhagwat, Aditya wrote: Looks like this can be

Re: [Bioc-devel] Issues with annotation packages

2020-05-08 Thread Interdonato, Kayla
Hello again Bioconductor community, There is now a fixed version (3.11.1) of the GO.db package available. We will continue working on integrating the new OBO file format, but due to time constraints we decided to resort back to using the sql files that Gene Ontology provides. The fixed version

Re: [Bioc-devel] Docker images for RELEASE_3_11 and devel on R-4.0.0

2020-05-08 Thread Nitesh Turaga
Hi Vinh, According the the bioconda community, they have just finished rebuilding the CRAN binaries today and they will start the bioconductor packages now. They should be ready tomorrow or day after most likely. For more bioconda related questions, I will refer you to

Re: [Bioc-devel] How to import a setAs method in one's package?

2020-05-08 Thread Bhagwat, Aditya
Looks like this can be successfully done by @importFrom methods as @importFrom S4Vectors DataFrame Cheers, Aditya From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Bhagwat, Aditya [aditya.bhag...@mpi-bn.mpg.de] Sent:

[Bioc-devel] How to import a setAs method in one's package?

2020-05-08 Thread Bhagwat, Aditya
Dear BioC compatriots, How does one import a setAs method (which is generally not exported)? I in particular need to import as(., DataFrame) and am a bit puzzled on how to do this. Thank you! Aditya [[alternative HTML version deleted]] ___

[Bioc-devel] BiocCheck-a-thon!

2020-05-08 Thread Martin Morgan
Join us for 'BiocCheck-a-thon', a week-long virtual hackathon to improve BiocCheck and the consistency and quality of Bioconductor packages! See https://github.com/Bioconductor/BiocCheck/wiki for details; starting May 18. Martin Morgan Bioconductor