[BioC] problem connecting to bioMart - NOT proxy error
James F. Reid
james.reid at ifom-ieo-campus.it
Thu Nov 19 00:36:10 CET 2009
I don't see this on my side and I have the set-up as you so I guess it
must some connection issue. I can also open the web page
Can you confirm that this is happening in a 'fresh' session i.e. with
not many previous open connections?
Here is my session:
R version 2.10.0 (2009-10-26)
 LC_COLLATE=English_United Kingdom.1252
 LC_CTYPE=English_United Kingdom.1252
 LC_MONETARY=English_United Kingdom.1252
 LC_TIME=English_United Kingdom.1252
attached base packages:
 stats graphics grDevices utils datasets methods base
other attached packages:
loaded via a namespace (and not attached):
 RCurl_1.2-1 XML_2.6-0
> ensembl = useMart("ensembl")
> ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl)
Checking attributes ... ok
Checking filters ... ok
Jenny Drnevich wrote:
> 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/.
> > library(biomaRt)
> > sessionInfo()
> R version 2.10.0 (2009-10-26)
>  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:
>  stats graphics grDevices utils datasets methods base
> other attached packages:
>  biomaRt_2.2.0
> loaded via a namespace (and not attached):
>  RCurl_1.2-1 XML_2.6-0
> > Sys.time()
>  "2009-11-18 16:08:44 CST"
> > ensembl = useMart("ensembl")
> > Sys.time()
>  "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
> ph: 217-244-7355
> fax: 217-265-5066
> e-mail: drnevich at illinois.edu
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
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