[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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