[Bioc-devel] Error on Windows when selecting a single chromosome from a BSgenome

[Dan Tenenbaum]

----- Original Message -----
> From: "Bernat Gel" <bgel at imppc.org>
> To: bioc-devel at r-project.org
> Sent: Friday, March 20, 2015 8:06:59 AM
> Subject: [Bioc-devel] Error on Windows when selecting a single chromosome	from a BSgenome
> 
> Hi all,
> 
> We are trying to get our first package (regioneR) included into
> Bioconductor. A couple of months ago it passed all the automatic
> checks
> but now, without code changes from our part fails on windows.
> 
> I've been digging and it seems the problem arises when selecting a
> single chromosome from a BSgenome object.
> 
> library("BSgenome.Hsapiens.UCSC.hg19.masked")
> BSgenome.Hsapiens.UCSC.hg19.masked[["chr1"]]
> 
> This works in linux and mac but in windows it kills R without any
> error
> message. Any idea of what's going on?
> 
> Our final aim when doing that is to have a data.frame with the
> genomic
> coordinates of the masked regions, so if there's an alternative
> approach
> we could use it as a workaround.
> 

I can't reproduce this. Can you send the output of sessionInfo() (run after loading BSgenome.Hsapiens.UCSC.hg19.masked but before the line that causes the crash)?

Dan


> Thanks a lot!
> 
> Bernat
> 
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