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

________________________________________
From: Herv? Pag?s [hpages at fredhutch.org]
Sent: Tuesday, July 07, 2020 11:45 AM
To: Bhagwat, Aditya; bioc-devel at r-project.org
Subject: Re: [Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in bioc-devel?

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 at r-project.org] on behalf of Bhagwat, Aditya [Aditya.Bhagwat at mpi-bn.mpg.de]
Sent: Tuesday, July 07, 2020 10:50 AM
To: bioc-devel at 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 at r-project.org] on behalf of Bhagwat, Aditya [Aditya.Bhagwat at mpi-bn.mpg.de]
Sent: Tuesday, July 07, 2020 10:22 AM
To: bioc-devel at 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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--
Herv? Pag?s

Program in Computational Biology
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