Hi Thomas,
Thanks for the report. I'm looking at this. Will let you know
when the problem is fixed.
H.
On 10/25/2013 11:33 AM, Thomas Sandmann wrote:
Sorry, forgot that attachments don't make it through.
Here's how to generate the example objects and reproduce the error:
library(IRanges)
keep_ranges <- IRangesList( IRanges( start=20, end=108), IRanges( start=41,
end=131), IRanges( start=21, end=105))
return_rles <- RleList( Rle(values=TRUE,lengths=151),
Rle(values=TRUE,lengths=151), Rle(values=TRUE,lengths=151))
return_rles[ keep_ranges ] <- TRUE
return_rles[ keep_ranges ] ## subsetting works
return_rles[ keep_ranges ] <- TRUE ## assignment doesn't work
Error in callNextMethod() :
in processing 'callNextMethod', found a '...' in the matched call, but no
corresponding '...' argument
On Fri, Oct 25, 2013 at 11:23 AM, Thomas Sandmann <sandm...@gene.com> wrote:
Dear BioC developers,
I am trying to subset an RleList with an IRangesList (see attached rdata
object). Unfortunately, the following line fails with IRanges 1.20.0:
return_rles[keep_ranges] <- TRUE
Error in subsetListByList_replace(x, i, value) :
cannot subscript an unnamed list-like object by a named list-like object
Unnaming the IRangesList doesn't help, either:
return_rles[unname(keep_ranges)] <- TRUE
Error in callNextMethod() :
in processing 'callNextMethod', found a '...' in the matched call, but
no corresponding '...' argument
The same operation worked with IRanges 1.18.2 using the (now deprecated)
seqselect method:
seqselect( return_rles, keep_ranges ) <- TRUE
Any hints ?
Thanks,
Thomas
SessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (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
base
other attached packages:
[1] BiocInstaller_1.12.0 IRanges_1.20.0 BiocGenerics_0.8.0
devtools_1.3
loaded via a namespace (and not attached):
[1] digest_0.6.3 evaluate_0.5.1 httr_0.2 memoise_0.1
RCurl_1.95-4.1 stats4_3.0.2 stringr_0.6.2
[8] tools_3.0.2 whisker_0.3-2
--
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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