[BioC] problem connecting to bioMart - NOT proxy error

[Jenny Drnevich]

Hi,

I've been trying to use biomaRt to connect to BioMart for the last 
week, and I've been running into a weird problem. I'm not getting any 
"proxy" errors, so I don't think it's that problem that's mentioned 
in the vignette and almost all BioC posts on biomaRt connection 
problems. Here's a quick explanation of the problem, and the code and 
sessionInfo are below. ensembl = useMart("ensembl") seems to run 
fine, although it takes 20 seconds or so to get the prompt back. When 
I put in ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl), 
R seems to freeze up, or at least the prompt never comes back. I've 
left it running for 2 hours over lunch one time! This has happened 
every time I've tried it since last week. I hadn't used biomaRt in 
about year before then, but I never had this problem before. I don't 
know if this is related, but I can't get http://www.biomart.org/ to 
come up on my browser, either, although I have no trouble with 
http://www.ensembl.org/biomart/martview/.

Thanks,
Jenny


 > library(biomaRt)
 > sessionInfo()
R version 2.10.0 (2009-10-26)
i386-pc-mingw32

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] 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_1.2-1 XML_2.6-0
 > Sys.time()
[1] "2009-11-18 16:08:44 CST"
 > ensembl = useMart("ensembl")
 > Sys.time()
[1] "2009-11-18 16:09:07 CST"
 >
 > ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl)

... and then nothing!!!


Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at illinois.edu