[Bioc-devel] bsGenomeName(BSgenomeObject) disappeared in bioc-devel?
On 7/7/20 02:50, Herv? Pag?s 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: 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 ????????? [[alternative HTML version deleted]] _______________________________________________ Bioc-devel at r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=_1eFc4UGidLaNS3zXQqjaaIUIU5zu68VT0g6PN0b24E&s=aAOK1NFWIMal4FrsocE13hvo95BTk3RL18eVMCncRzk&e= _______________________________________________ Bioc-devel at r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=_1eFc4UGidLaNS3zXQqjaaIUIU5zu68VT0g6PN0b24E&s=aAOK1NFWIMal4FrsocE13hvo95BTk3RL18eVMCncRzk&e= _______________________________________________ Bioc-devel at r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=_1eFc4UGidLaNS3zXQqjaaIUIU5zu68VT0g6PN0b24E&s=aAOK1NFWIMal4FrsocE13hvo95BTk3RL18eVMCncRzk&e= -- Herv? Pag?s 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 at fredhutch.org Phone:? (206) 667-5791 Fax:??? (206) 667-1319
Herv? Pag?s 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 at fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319