[BioC] viewApply Bug

[Martin Morgan]

On 02/10/2011 11:00 PM, Dario Strbenac wrote:
> Hello,
> 
> viewApply seems to not properly iterate over the views, but rather return the last view repeatedly.
> 
> Minimal example :
> 
> r <- Rle(1:1000)
> v <- Views(r, start=c(10, 100, 500), width = 1)
>> viewApply(v, function(x) x)
> [[1]]
> 'integer' Rle of length 1 with 1 run
>   Lengths:   1
>   Values : 500

Thank you for the report; this bug, which would only be manifest when
FUN returns the Rle in the view (not, e..g, viewApply(v, mean)), is
fixed in IRanges v. 1.8.9 (release) / 1.9.22 (devel), which should be
propagating to biocLite() in the next day or so.

Martin

> [[2]]
> 'integer' Rle of length 1 with 1 run
>   Lengths:   1
>   Values : 500
> 
> [[3]]
> 'integer' Rle of length 1 with 1 run
>   Lengths:   1
>   Values : 500
> 
>> sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: x86_64-unknown-linux-gnu (64-bit)
> 
> locale:
>  [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C              
>  [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8    
>  [5] LC_MONETARY=C              LC_MESSAGES=en_AU.UTF-8   
>  [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C                 
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
> [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C       
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
> 
> other attached packages:
> [1] GenomicRanges_1.2.3 IRanges_1.8.8      
> 
> loaded via a namespace (and not attached):
> [1] tools_2.12.0
> 
> --------------------------------------
> Dario Strbenac
> Research Assistant
> Cancer Epigenetics
> Garvan Institute of Medical Research
> Darlinghurst NSW 2010
> Australia
> 
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