[BioC] Problem with GenomicRanges 1.14.3, as(from, \"GRanges\") not working for RleViewsList

Giorgos Baskozos [guest] guest at bioconductor.org
Mon Nov 4 14:45:45 CET 2013

I thik I have found a recently introduced bug in the newer version of Bioconductor and of the GenomicRanges package. I cannot turn an RleViewsList object into a GRanges object using the function as(from, "GRanges"). Specifficaly I et the following error: "Error in normalizeSingleBracketSubscript(i, x) : invalid subscript type
". The code example illustrating the problem is below:

> example(GRanges)
> mycov = coverage(longGR)
> rle.i = slice(mycov, lower=3)
> gr = as (rle.i, "GRanges")
Error in normalizeSingleBracketSubscript(i, x) : invalid subscript type
> traceback()
10: stop("invalid subscript type")
9: normalizeSingleBracketSubscript(i, x)
8: extractROWS(subject, from_ranges)
7: extractROWS(subject, from_ranges)
6: asMethod(object)
5: as(from, "RangedData")
4: .class1(object)
3: as(as(from, "RangedData"), "GRanges")
2: asMethod(object)
1: as(rle.i, "GRanges")

All best,

 -- output of sessionInfo(): 

R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-linux-gnu (64-bit)

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] GenomicRanges_1.14.3 XVector_0.2.0        IRanges_1.20.4      
[4] BiocGenerics_0.8.0  

loaded via a namespace (and not attached):
[1] bitops_1.0-6   stats4_3.0.2   tools_3.0.2    zlibbioc_1.8.0

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