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

[Hervé Pagès]

Hi Bernat,

Sorry for the delay in getting back to you. Like Dan, I cannot
reproduce this either. Without more input from you (e.g. sessionInfo()),
there is not much we can do.

Note that an easy way to get the coordinates of the masked regions in
a data.frame is with something like this:

   path <- system.file("extdata", "chr1.masks.rda",
                     package="BSgenome.Hsapiens.UCSC.hg19.masked")
   load(path)
   as.data.frame(chr1.masks[["AGAPS"]])

This is for the assembly gaps on chr1. You can do the same for any
of the 3 other types of masks (intra-contig ambiguities, RepeatMasker,
Tandem Repeats Finder) on any other chromosome/scaffold.

Cheers,
H.


On 03/20/2015 02:50 PM, Dan Tenenbaum wrote:
>
>
> ----- 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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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
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>

-- 
Hervé Pagès

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