[Bioc-devel] Subsetting GRangesList with mcols on the mcols: Error in normalizeSingleBracketSubscript

[Mike Love]

Yes, works for me now.

Thanks,

Mike

On Sep 18, 2013, at 8:47 PM, Valerie Obenchain <vobencha at fhcrc.org> wrote:

> Hi Michael,
> 
> This looks like an artifact from reorganizing the subsetting code in IRanges/XVector. The operation works for me with the most recent versions from devel. I'm assuming it now works for you?
> 
> Valerie
> 
> On 09/13/2013 02:33 AM, Michael Love wrote:
>> hi,
>> 
>> I came across an error in trying to subset a GRangesList with metadata
>> columns on the metadata columns:
>> 
>>> library(GenomicRanges)
>> 
>>> grl <- GRangesList(GRanges(),GRanges())
>> 
>>> mcols(grl) <- DataFrame(a=1:2)
>> 
>>> mcols(mcols(grl)) <- DataFrame(type="z")
>> 
>>> grl[1:2]
>> 
>> Error in normalizeSingleBracketSubscript(i, x, byrow = TRUE) :
>>   subscript contains NAs or out of bounds indices
>> Calls: [ ... extractROWS -> extractROWS -> normalizeSingleBracketSubscript
>> 
>> Also grl[2] produces the same error, while grl[1] does not.  traceback and
>> sessionInfo below.
>> 
>> thanks,
>> 
>> Mike
>> 
>> 
>>> grl[2]
>> Error in normalizeSingleBracketSubscript(i, x, byrow = TRUE) :
>>   subscript contains NAs or out of bounds indices
>> Calls: [ ... extractROWS -> extractROWS -> normalizeSingleBracketSubscript
>>> traceback()
>> 18: stop("subscript contains NAs or out of bounds indices")
>> 17: normalizeSingleBracketSubscript(i, x, byrow = TRUE)
>> 16: extractROWS(x at elementMetadata, i)
>> 15: extractROWS(x at elementMetadata, i)
>> 14: extractROWS(x at elementMetadata, i)
>> 13: extractROWS(x at elementMetadata, i)
>> 12: extractROWS(x, i)
>> 11: extractROWS(x, i)
>> 10: .nextMethod(x, i)
>> 9: eval(expr, envir, enclos)
>> 8: eval(call, callEnv)
>> 7: callNextMethod(x, i)
>> 6: .nextMethod(x = x, i = i)
>> 5: eval(expr, envir, enclos)
>> 4: eval(call, callEnv)
>> 3: callNextMethod(x = x, i = i)
>> 2: grl[2]
>> 1: grl[2]
>> 
>>> sessionInfo()
>> R Under development (unstable) (2013-09-12 r63919)
>> Platform: x86_64-apple-darwin12.3.0 (64-bit)
>> 
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>> 
>> attached base packages:
>> [1] parallel  stats     graphics  grDevices utils     datasets  methods
>> [8] base
>> 
>> other attached packages:
>> [1] GenomicRanges_1.13.42 XVector_0.1.2         IRanges_1.19.33
>> [4] BiocGenerics_0.7.5    knitr_1.2             BiocInstaller_1.11.4
>> [7] Defaults_1.1-1
>> 
>> loaded via a namespace (and not attached):
>> [1] digest_0.6.3   evaluate_0.4.3 formatR_0.7    stats4_3.1.0
>> stringr_0.6.2
>> [6] tools_3.1.0
>> 
>>    [[alternative HTML version deleted]]
>> 
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