[BioC] Problems with biomaRt

john seers (IFR) john.seers at bbsrc.ac.uk
Mon Jul 13 16:59:49 CEST 2009


I had similar problems which I raised in this forum a month or so ago.

The solution was, I think, to specify both the "--internet2" and the
"http_proxy" options on the command line.

It appears that just the one option is not sufficient for bioMart and
one of the packages it uses (RCurl?). The two packages must handle the
proxy slightly differently.    



-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of michael
watson (IAH-C)
Sent: 13 July 2009 14:11
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] Problems with biomaRt

I'm having problems connecting to biomaRt through R.


useMart reports an error and claims either the service is down or I am
not connected to the internet:


> mart <- useMart(biomart="ensembl", dataset="ggallus_gene_ensembl")

Error in value[[3L]](cond) : 

  Request to BioMart web service failed. Verify if you are still
connected to the internet.  Alternatively the BioMart web service is
temporarily down.


But R can connect to martservice just fine:


> download.file(url="http://www.biomart.org/biomart/martservice",

trying URL 'http://www.biomart.org/biomart/martservice'

Content type 'text/plain' length 200 bytes

opened URL

downloaded 5810 bytes


So the problem is not R, it is biomaRt.


Any help appreciated




> sessionInfo()

R version 2.9.1 (2009-06-26) 




LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252


attached base packages:

[1] tools     stats     graphics  grDevices utils     datasets  methods


other attached packages:

[1] CORNA_1.1      XML_2.5-3      GEOquery_2.8.0 RCurl_0.98-1
bitops_1.0-4.1 biomaRt_2.0.0  Biobase_2.4.1


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