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 <sandmat1@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
>



-- 
Thomas Sandmann, PhD
Computational biologist

Genentech, Inc.
1 DNA Way
South San Francisco, CA 94080
USA

Phone: +1 650 225 6273
Fax: +1 650 225 5389
Email: sandmat1@gene.com

"Computational biology is no more about computers than astronomy is about
telescopes."

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