Yes sorry to Mike, Michael, Kasper, Julian, and all those that
have been hit by the refactoring of the subsetting code in
IRanges/GenomicRanges. The main bulk of this refactoring is over
now and things should be much more stable. The major goals of this
refactoring were to simplifiy the code, fix old standing bugs, and
bring more consistency across Vector derivatives (e.g. they should
all support subsetting by a Ranges or Rle object now). There are
also some speed improvements. No known regression but of course
there might be some (which should be easy to fix now that the code
is much simpler).
Please let me know if you still see problems in your packages that
could be related to this refactoring. Thanks!
H.
On 09/18/2013 12:07 PM, Mike Love wrote:
Yes, works for me now.
Thanks,
Mike
On Sep 18, 2013, at 8:47 PM, Valerie Obenchain <voben...@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@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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--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpa...@fhcrc.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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