[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


Hi Jenny,

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 
http://www.biomart.org/.
Can you confirm that this is happening in a 'fresh' session i.e. with 
not many previous open connections?

Best,
James.

Here is my session:

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

locale:
[1] LC_COLLATE=English_United Kingdom.1252
[2] LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.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
 > ensembl = useMart("ensembl")
 > ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl)
Checking attributes ... ok
Checking filters ... ok
 >



Jenny Drnevich wrote:
> 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
> 
> _______________________________________________
> 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
>



More information about the Bioconductor mailing list