[BioC] "rtracklayer" is not compatible with the lateset "IRanges" package

LiGang luzifer.li at gmail.com
Thu Sep 17 05:14:25 CEST 2009


the newest "rtracklayer" and "IRanges" packages are not compatible, is it
because class "ANYTHING" is not defined in package "IRanges" since version
1.3.73 anymore?

library(rtracklayer)

Loading required package: RCurl
Loading required package: bitops

browserSession("UCSC")->inter
range(inter)


###error!
#Error in validObject(.Object) : 
#  invalid class "ucscCart" object: superclass "ANYTHING" not defined in the
#environment of the object's class

rtracklayer:::ucscCart(inter)

###error!
#Error in validObject(.Object) : 
#  invalid class "ucscCart" object: superclass "ANYTHING" not defined in the
#environment of the object's class
  
getClass("ANYTHING",where=getNamespace("IRanges"))

##error!  "ANYTHING" is not defined in package "IRanges" since version 1.3.75
#anymore

#Error in getClass("ANYTHING", where = getNamespace("IRanges")) : 
#  "ANYTHING" is not a defined class
  
sessionInfo()
R version 2.10.0 Under development (unstable) (2009-09-14 r49685) 
i386-pc-mingw32 

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252 
  LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
[1] rtracklayer_1.5.13 RCurl_1.2-0        bitops_1.0-4.1    

loaded via a namespace (and not attached):
[1] Biobase_2.5.6      Biostrings_2.13.39 BSgenome_1.13.11   IRanges_1.3.75    
Rcompression_0.6-0 XML_2.6-0



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