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

[Hervé Pagès]

Hi Aditya,

This change was not intended, sorry. Should be fixed in BSgenome 1.57.4.

Cheers,
H.

On 7/7/20 01:53, Bhagwat, Aditya wrote:
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__bioconductor.org_checkResults_3.12_bioc-2DLATEST_multicrispr_malbec1-2Dchecksrc.html&d=DwIFAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=_1eFc4UGidLaNS3zXQqjaaIUIU5zu68VT0g6PN0b24E&s=N-MGRsB-Th9-Po32CSpim6CogpSSPciuLCjci-Uuh8g&e= >, 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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-- 
Hervé Pagès

Program in Computational Biology
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