This sounds like you need to reinstall rtracklayer and/or one of its
dependencies.

Michael

On Thu, Apr 8, 2010 at 8:15 PM, Paul Shannon <pshannon@systemsbiology.org>wrote:

> Dear Bioc,
>
> Following the rtracklayer documentation, section 2.2.4, 'A Shortcut', I
> encounter the following error
>
> > browseGenome (subTargetTrack)
> Error in validObject(.Object) :
>  invalid class "ucscCart" object: superclass "ANYTHING" not defined in the
> environment of the object's class
>
> > traceback ()
> 13: stop(msg, " ", errors, domain = NA)
> 12: validObject(.Object)
> 11: initialize(value, ...)
> 10: initialize(value, ...)
> 9: new("ucscCart", vals)
> 8: .local(object, ...)
> 7: ucscCart(x)
> 6: ucscCart(x)
> 5: range(<S4 object of class "UCSCSession">, na.rm = FALSE)
> 4: mergeRange(range(session), range)
> 3: .local(object, ...)
> 2: browseGenome(subTargetTrack)
> 1: browseGenome(subTargetTrack)
>
> > summary (subTargetTrack)
>    Length      Class       Mode
>        23 RangedData         S4
>
> > sessionInfo ()
> R version 2.10.1 (2009-12-14)
> x86_64-apple-darwin9.8.0
>
> locale:
> [1] en_US.utf-8/en_US.utf-8/C/C/en_US.utf-8/en_US.utf-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] rtracklayer_1.6.0    microRNA_1.4.0       Rlibstree_0.3-2
>  Biostrings_2.14.12   IRanges_1.4.8        limma_3.2.1
>  genefilter_1.28.2
>  [8] humanStemCell_0.2.3  hgu133plus2.db_2.3.5 org.Hs.eg.db_2.3.6
> RSQLite_0.7-3        DBI_0.2-4            AnnotationDbi_1.8.0  Biobase_2.6.1
> [15] RCurl_1.2-0          bitops_1.0-4.1       RUnit_0.4.22
>
> loaded via a namespace (and not attached):
> [1] annotate_1.24.1 BSgenome_1.14.2 splines_2.10.1  survival_2.35-8
> tools_2.10.1    XML_2.6-0       xtable_1.5-6
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