[Bioc-sig-seq] Combining 2 GRangesList Objects Error

[mtmorgan at fhcrc.org]

Hi Dario --

Quoting Dario Strbenac <D.Strbenac at garvan.org.au>:

> Hello,
>
> I'm trying to create a longer list out of two GRangesList objects   
> and am getting an unusual error. I think it should work out OK from   
> the information in the package reference manual.
>
>> summary(grl)
>      Length       Class        Mode
>           3 GRangesList          S4
>> summary(grl2)
>      Length       Class        Mode
>           3 GRangesList          S4
>> g <- append(grl, grl2)
> Error in `rownames<-`(`*tmp*`, value = c("gr1", "gr2", "gr3", "gr1",  
>  "gr2",  :
>   invalid rownames length
>> g <- c(grl, grl2)
> Error in `rownames<-`(`*tmp*`, value = c("gr1", "gr2", "gr3", "gr1",  
>  "gr2",  :
>   invalid rownames length
>
> I'm using GenomicRanges 1.09 and R 2.11.1.

This should be fixed in IRanges 1.6.17. Try updating your IRanges,  
e.g., in a new R session

   source('http://bioconductor.org/biocLite.R')
   biocLite('IRanges')

you should end up with

> sessionInfo()
R version 2.11.1 Patched (2010-08-30 r52862)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages:
[1] GenomicRanges_1.0.9 IRanges_1.6.17

Martin
>
> --------------------------------------
> Dario Strbenac
> Research Assistant
> Cancer Epigenetics
> Garvan Institute of Medical Research
> Darlinghurst NSW 2010
> Australia
>
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