[BioC] rtracklayer export fails

[Michael Dondrup]

Yes, it's totally strange
it seemed to be something in my session. If I start R --vanilla the simple example works,
however I am still struggling with exporting real-size data because it yields the same error message.

I will post an example later.

Thanks for your help

On Feb 19, 2011, at 11:02 PM, Michael Lawrence wrote:

> I've managed to correct this for certain combinations of packages, don't really remember how. But haven't found a solution to the underlying problem.
> 
> On Sat, Feb 19, 2011 at 1:49 PM, Vincent Carey <stvjc at channing.harvard.edu> wrote:
> 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 at 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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