[Bioc-devel] GenomeData Constructor

[Dario Strbenac]

Hello,

The example in the manual doesn't work for me, and I have all of the current release packages.

The code I try it with is:

library(BSgenome)
gd <- GenomeData(list(chr1 = IRanges(1, 10), chrX = IRanges(2, 5)))

I get:

Error in validObject(.Object) : 
  invalid class "GenomeData" object: superclass "Vector" not defined in the environment of the object's class

> sessionInfo()
R version 2.12.2 (2011-02-25)
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] BSgenome_1.18.3     Biostrings_2.18.4   GenomicRanges_1.2.3
[4] IRanges_1.8.9      

loaded via a namespace (and not attached):
[1] Biobase_2.10.0

What can I do to get it running ?

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