[Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in bioc-devel?

[Bhagwat, Aditya]

Sorry, my earlier email had a copy/paste error - corrected now
________________________________________
From: Bioc-devel [bioc-devel-bounces using r-project.org] on behalf of Bhagwat, Aditya [Aditya.Bhagwat using mpi-bn.mpg.de]
Sent: Tuesday, July 07, 2020 10:50 AM
To: bioc-devel using r-project.org
Subject: Re: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in bioc-devel?

It's the BSgenome to GenomeDescription coercer that seems to be missing - is this on purpose?

# bsgenomeName(BSgenomeObj) FAILS
#-------------------------------------------
bsname <- GenomeInfoDb::bsgenomeName(bsgenome)
index_genome(bsgenome, indexedgenomesdir = tempdir())
Error in h(simpleError(msg, call)) :
  unable to find an inherited method for function 'bsgenomeName' for signature '"BSgenome"

# as(bsgenome, 'GenomeDescription') also FAILS
#----------------------------------------------------
bsname <- GenomeInfoDb::bsgenomeName(as(bsgenome, 'GenomeDescription')) # ALSO FAILS
index_genome(bsgenome, indexedgenomesdir = tempdir())
Error in h(simpleError(msg, call)) :
  error in evaluating the argument 'x' in selecting a method for function 'bsgenomeName': no method or default for coercing "BSgenome" to "GenomeDescription"

Aditya

________________________________________
From: Bioc-devel [bioc-devel-bounces using r-project.org] on behalf of Bhagwat, Aditya [Aditya.Bhagwat using mpi-bn.mpg.de]
Sent: Tuesday, July 07, 2020 10:22 AM
To: bioc-devel using r-project.org
Subject: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in bioc-devel?

Dear bioc-devel,

multicrispr is having an error on the bioc-devel build machines<https://bioconductor.org/checkResults/3.12/bioc-LATEST/multicrispr/malbec1-checksrc.html>, caused by:

unable to find an inherited method for function 'bsgenomeName' for signature '"BSgenome"

This is a bit strange, because normally a BSgenome object gets automatically converted to a GenomeDescription object before being sent to the method bsgenomeName. In bioc-devel, for some reason this mechanism seems to be broken. Is it on purpose? What would be the best fix/patch?

Right now, I'm checking whether explicitation fixes things:
bsname <- GenomeInfoDb::bsgenomeName(bsgenome)                                     # FAILS
bsname <- GenomeInfoDb::bsgenomeName(as(bsgenome, 'GenomeDescription')) # WORKS ? (VERIFYING)

Thank you for feedback :-)

Aditya

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