I'd like to recommend that you attempt this export with the smallest
sessionInfo you can muster -- after just library(rtracklayer) if possible.
i have run into this recursion error in connection with symbol collisions
related to update() methods and it "goes away" if i get rid of certain
packages.  a full diagnosis awaits....

On Sat, Feb 19, 2011 at 3:21 PM, Michael Dondrup <michael.dondrup@uni.no>wrote:

> Hi,
> I am trying to use export in the rtracklayer package on R 2.12.1 on MacOS
> but already the example fails, see below:
>
> Best
> Michael
>
> > example(export)
>
> export>   track <- import(system.file("tests", "v1.gff", package =
> "rtracklayer"))
>
> export>   ## Not run: export(track, "my.gff", version = "3")
> export>   ## equivalently,
> export>   ## Not run: export(track, "my.gff3")
> export>   ## or
> export>   ## Not run:
> export> ##D   con <- file("my.gff3")
> export> ##D   export(track, con, "gff3")
> export> ##D   close(con)
> export> ##D
> export> ## End(Not run)
> export>   ## or as a string
> export>   export(track, format = "gff3")
> Error: evaluation nested too deeply: infinite recursion /
> options(expressions=)?
> > sessionInfo()
> R version 2.12.1 (2010-12-16)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> 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_1.10.6 RCurl_1.4-3        bitops_1.0-4.1     IRanges_1.8.9
>
> loaded via a namespace (and not attached):
>  [1] annotate_1.28.0      AnnotationDbi_1.12.0 Biobase_2.10.0
> Biostrings_2.18.2
>  [5] BSgenome_1.18.0      DBI_0.2-5            DESeq_1.2.1
>  genefilter_1.32.0
>  [9] geneplotter_1.28.0   GenomicRanges_1.2.0  grid_2.12.1
>  RColorBrewer_1.0-2
> [13] RSQLite_0.9-2        splines_2.12.1       survival_2.36-2
>  tools_2.12.1
> [17] XML_3.2-0            xtable_1.5-6
> >
>
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