[BioC] problems when trying to use biomaRt

[Martin Morgan]

On 03/17/2010 04:00 AM, Juan Pablo Fededa wrote:
> Dear bioconductor-help contributors,
> 
> 
> I'm trying to use biomaRt package in R, and when I run the next line, the R
> GUI crashes:
> 
> ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> 
> Theres is no error message at all, simply R is not responding anymore.
> when loading library(biomaRt) the prompt sign appears again, and you can
> already run basic things like:
> listMarts()

This is unusual, because the only part of useMart that might end up with
real trouble is a call to listMarts() ! Start R with the --vanilla
argument, e.g., from the DOS shell

  Rgui --vanilla

try to place a debugger on useMart, and step through until R stops
responding. Restart R, get to a similar place, and look at the arguments
to the function that causes problems. Any hints?

  > debug(useMart)
  > ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
  Browser[2]> n

('n' is for 'next', see ?browser)

Martin

> 
> When I run sessionInfo() I get this:
> 
> R version 2.10.1 (2009-12-14)
> i386-pc-mingw32
> 
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
> States.1252
> [3] LC_MONETARY=English_United States.1252
> LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] biomaRt_2.2.0
> 
> loaded via a namespace (and not attached):
> [1] RCurl_1.3-1 XML_2.6-0
> 
> Do you have any idea of what can I change to make it work?
> Thanks in advance,
> 
> 	[[alternative HTML version deleted]]
> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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