[BioC] biomaRt does not like flies

[Wolfgang Huber]

Hi Simon

the following code just worked for me. One way to further diagnose the 
"hanging" would be to use R's debugger (see e.g. function "debug") to 
step through the "useMart" code and see where the hanging occurs.

library(biomaRt)
mart <- useMart( "ensembl", dataset="dmelanogaster_gene_ensembl" )
mart
#Object of class 'Mart':
# Using the ensembl BioMart database
# Using the dmelanogaster_gene_ensembl dataset

 > sessionInfo()
R version 2.10.0 Under development (unstable) (2009-07-16 r48943)
x86_64-unknown-linux-gnu

locale:
  [1] LC_CTYPE=C              LC_NUMERIC=C            LC_TIME=C 

  [4] LC_COLLATE=C            LC_MONETARY=C 
LC_MESSAGES=la_AU.UTF-8
  [7] LC_PAPER=C              LC_NAME=C               LC_ADDRESS=C 

[10] LC_TELEPHONE=C          LC_MEASUREMENT=C        LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base

other attached packages:
[1] biomaRt_2.1.0  fortunes_1.3-6

loaded via a namespace (and not attached):
[1] RCurl_0.98-1 XML_2.5-3    tools_2.10.0



> Hi,
> 
> I'm trying to access Ensembl's D. melanogaster dataset via biomaRt.
> 
> This here works fine:
> 
> mart <- useMart( "ensembl", dataset="hsapiens_gene_ensembl" )
> 
> This command here, however, causes the R process to hang:
> 
> mart <- useMart( "ensembl", dataset="dmelanogaster_gene_ensembl" )
> 
> If I use Ensembl's web interface to Biomart, I can access both datasets 
> just fine.
> 
> Any idea what the reason might be, and how I could find out whether the 
> fault is local or on the web server? Is there any way to let biomaRt be 
> a bit more verbose with diagnostic messages?
> 
> Cheers
>   Simon
> 
> 
>  > sessionInfo()
> R version 2.9.0 (2009-04-17)
> x86_64-unknown-linux-gnu
> 
> locale:
> LC_CTYPE=en_GB.UTF-8;LC_NUMERIC=C;LC_TIME=en_GB.UTF-8;LC_COLLATE=en_GB.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_GB.UTF-8;LC_PAPER=en_GB.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_GB.UTF-8;LC_IDENTIFICATION=C 
> 
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] biomaRt_2.0.0
> 
> loaded via a namespace (and not attached):
> [1] RCurl_0.97-3 XML_2.3-0
> 
> 
> +---
> | Dr. Simon Anders, Dipl. Phys.
> | European Bioinformatics Institute (EMBL-EBI)
> | Hinxton, Cambridgeshire, UK
> | office phone +44-1223-492680, mobile phone +44-7505-841692
> | preferred (permanent) e-mail: sanders at fs.tum.de
> 
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-- 

Best wishes
      Wolfgang

-------------------------------------------------------
Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber