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)) : error in evaluating the argument 'x' in selecting a method for function 'bsgenomeName': no method or default for coercing "BSgenome" to "GenomeDescription" # 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-boun...@r-project.org] on behalf of Bhagwat, Aditya [aditya.bhag...@mpi-bn.mpg.de] Sent: Tuesday, July 07, 2020 10:22 AM To: bioc-devel@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 [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel