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

[Valerie Obenchain]

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
>
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>
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