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@elementMetadata, i)
15: extractROWS(x@elementMetadata, i)
14: extractROWS(x@elementMetadata, i)
13: extractROWS(x@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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