Have you tried reinstalling rtracklayer?

Michael

On Wed, Sep 16, 2009 at 8:14 PM, LiGang <luzifer.li@gmail.com> wrote:

>
> 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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