It is for me now, only I had to add: Sys.setenv("http_proxy"="http://wwwcache.bbsrc.ac.uk:8080") I didn't have to do this previously, and obviously R knows about my proxy as it can use download.file (I am using the --internet2 switch to get connection settings from IE). Does biomaRt not use the proxy settings in some way that download.file does? Clearly this is not a huge problem as I can simply add "Sys.setenv("http_proxy"="http://wwwcache.bbsrc.ac.uk:8080")" to all my scripts, but this wasn't the case previously and I expect biomaRt should be smart enough to pick up my proxy settings... -----Original Message----- From: James W. MacDonald [mailto:jmacdon@med.umich.edu] Sent: 13 July 2009 14:19 To: michael watson (IAH-C) Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Problems with biomaRt It's working for me: > library(biomaRt) > mart <- useMart("ensembl","hsapiens_gene_ensembl") Checking attributes ... ok Checking filters ... ok > sessionInfo() R version 2.9.0 (2009-04-17) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices datasets utils methods base other attached packages: [1] biomaRt_2.0.0 loaded via a namespace (and not attached): [1] RCurl_0.98-1 XML_2.5-1 > Sys.time() [1] "2009-07-13 09:17:58 EDT" Maybe try again? Best, Jim michael watson (IAH-C) wrote: > 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", > destfile="test.html") > > 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 > > > > Mick > > > >> sessionInfo() > > R version 2.9.1 (2009-06-26) > > i386-pc-mingw32 > > > > locale: > > LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United > Kingdom.1252;LC_MONETARY=English_United > Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 > > > > attached base packages: > > [1] tools stats graphics grDevices utils datasets methods > base > > > > 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 > > > > Head of Bioinformatics > Institute for Animal Health > Compton > Berks > RG20 7NN > 01635 578411 > > > > Please consider the environment and don't print this e-mail unless you > really need to. > > The information contained in this message may be confide...{{dropped:26}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826