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

[Hervé Pagès]

On 7/7/20 02:50, Hervé Pagès wrote:
> 
> 
> On 7/7/20 02:46, Bhagwat, Aditya wrote:
>> Thankyou Herve!
>>
>> I guess that means that I can pull the fix in a day or two, is that 
>> right?
> 
> Yes, as soon as BSgenome 1.57.4 propagates, which should take between 
> 24h and 48h.

To be clear: BSgenome 1.57.4 will become available for installation with 
BiocManager::install("BSgenome") only in a couple of days but you can 
get it now by installing directly from GitHub with 
BiocManager::install("Bioconductor/BSgenome").

H.

> 
> H.
> 
>>
>> Aditya
>> ________________________________________
>> From: Hervé Pagès [hpages using fredhutch.org]
>> Sent: Tuesday, July 07, 2020 11:45 AM
>> To: Bhagwat, Aditya; bioc-devel using 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 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
>>>
>>>           [[alternative HTML version deleted]]
>>>
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>>>
>>
>> -- 
>> Hervé Pagès
>>
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N, M1-B514
>> P.O. Box 19024
>> Seattle, WA 98109-1024
>>
>> E-mail: hpages using fredhutch.org
>> Phone:  (206) 667-5791
>> Fax:    (206) 667-1319
>>
> 

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages using fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319