On Sun, Feb 20, 2011 at 8:58 AM, Michael Dondrup <Michael.Dondrup@uni.no>wrote:

> So here is the example where export fails:
>
> $ R --vanilla
>
> > library(rtracklayer)
> Loading required package: RCurl
> Loading required package: bitops
> > library(IRanges)
>
> Attaching package: 'IRanges'
>
> The following object(s) are masked from 'package:base':
>
>    cbind, eval, Map, mapply, order, paste, pmax, pmax.int, pmin,
>    pmin.int, rbind, rep.int, table
>
> > example(RangedData)
> ....
> > rd2
> RangedData with 3 rows and 1 value column across 1 space
>        space    ranges |     score
>  <character> <IRanges> | <integer>
> 1           1    [1, 4] |        10
> 2           1    [2, 5] |         2
> 3           1    [3, 6] |        NA
> > export.gff2(rd2, con=stdout())
> Error: evaluation nested too deeply: infinite recursion /
> options(expressions=)?
>
> My best guess is that the RangedData object is missing something, but then
> the error message and the documentation is wrong,
> because the documentation says it can handle any RangedData object.
>
>
No, as Vince said, this infinite recursion usually results from weird
dispatching on the update generic. Thanks for the report and simple example.
I'll look into it some more.

Michael



> Best
> Michael
>
>
>
>
>
>
>
>
> On Feb 20, 2011, at 5:47 PM, Michael Dondrup wrote:
>
> > 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@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@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
> >>>>
> >>>
> >>> _______________________________________________
> >>> Bioconductor mailing list
> >>> Bioconductor@r-project.org
> >>> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >>> Search the archives:
> >>> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>>
> >>
> >>       [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor@r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>

	[[alternative HTML version deleted]]

