[BioC] rtracklayer 1.6: invalid class "ucscCart" object
Paul Shannon
pshannon at systemsbiology.org
Fri Apr 9 05:15:59 CEST 2010
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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