[BioC] biomaRt problem

[Steffen Durinck]

Hi Jim, Dario,

There is a typo here:
mart <- useMart("ensembl","hsapiens_gene_ensembl", mart=TRUE)

Should be:
mart <- useMart("ensembl","hsapiens_gene_ensembl", mysql=TRUE)

Also the EBI BioMart web service is on again. It looks like the BioMart 
developers shut it down for a while as they where investigating a problem.
This is what they mailed me:

> there have been problems with people hammering the central server with 
> martservice requests. We are investigating how to solve this - probably IP 
> banning I think.

> I think the problem below is with the proxy - hopefully I will restart the 
> server with the correct settings in a few minutes

> thanks
> Damian

This highlights the looping issue:  When using the biomaRt package in 
web service mode we should try not to loop over vectors of identifiers 
to annotate them but query for the annotation of all these identifiers 
at once. Alternatively if you can't resist to loop, one should use 
biomaRt in RMySQL mode.

best,
Steffen

James W. MacDonald wrote:
> Hi Dario, Note that if you use the RMySQL interface it doesn't matter 
> if the BioMart webservice is available or not. biocLite("RMySQL") mart 
> <- useMart("ensembl","hsapiens_gene_ensembl", mart=TRUE) HTH, Jim 
> Dario Greco wrote: > hi Steffen, > thanks for your help. > now 
> biomart.org is up, but there are still some problems. > > >>mart <- 
> useMart("ensembl", dataset = "hsapiens_gene_ensembl") > > Error in 
> file(file, "r") : unable to open connection > In addition: Warning 
> message: > unable to resolve 'web50-node4.ebi.ac.uk'. > > and in fact, 
> if i try to open in browser the address > 
> http://www.biomart.org/biomart/martservice > > i get this internal 
> error message: > > > > >
>
>
>   OK
>
> > The server encountered an internal error or > misconfiguration and 
> was unable to complete > your request.
>
> > Please contact the server administrator, > 
> webmaster&#064;mydomain.org and inform them of the time the error > 
> occurred, > and anything you might have done that may have > caused 
> the error.
>
> > More information about this error may be available > in the server 
> error log.
>
> > > > > what to do? > > thanks again for your kind help > sincerely > 
> Dario > > > > On Tuesday 22 August 2006 15:58, Durinck, Steffen 
> (NIH/NCI) [F] wrote: > >>Hi Dario, >> >>Yes it looks like the website 
> has been down for a few days which explains >>why useMart fails. I've 
> CC'd Arek (BioMart developer) maybe he can shed >>more light on what 
> is happening. >> >>best. >>Steffen >> >> >>-----Original Message----- 
> >>From: Dario Greco [mailto:dario.greco at helsinki.fi] >>Sent: Tue 
> 8/22/2006 4:59 AM >>To: bioconductor at stat.math.ethz.ch >>Subject: 
> [BioC] biomaRt problem >> >>dear list, >>i am trying to annotate some 
> genes using biomaRt, but i am running in the >> >>following problem: 
> >> >>>library(biomaRt) >> >>Loading required package: XML >>Loading 
> required package: RCurl >> >> >>>mart <- useMart("ensembl") >> >>Error 
> in curlPerform(curl = curl, .opts = opts) : >> Couldn't resolve host 
> 'www.biomart.org' >> >>i have also updated to the 1.7.6 version of 
> biomaRt, but no change in the >>result. >> >> >>>sessionInfo() >> 
> >>Version 2.3.1 (2006-06-01) >>i686-redhat-linux-gnu >> >>attached 
> base packages: >>[1] "methods" "stats" "graphics" "grDevices" "utils" 
> "datasets" >>[7] "base" >> >>other attached packages: >> biomaRt RCurl 
> XML >> "1.7.6" "0.6-2" "0.99-8" >> >>i am pretty sure my computer 
> doesn't have any proxy issues. moreover, if i >>try to open the 
> www.biomart.org website in my browser, it appears down. is >>there 
> some problem with the biomart mirror? should i use an alternative 
> >>host? if yes, which? >>do you have any other suggestions? >>thanks 
> in advance for your kind help. >>sincerely >>Dario > > -- James W. 
> MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core 
> University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 
> CCGC Ann Arbor MI 48109 734-647-5623 
> ********************************************************** Electronic 
> Mail is not secure, may not be read every day, and should not be used 
> for urgent or sensitive issues.
>


-- 
Steffen Durinck, Ph.D.

Oncogenomics Section
Pediatric Oncology Branch
National Cancer Institute, National Institutes of Health
URL: http://home.ccr.cancer.gov/oncology/oncogenomics/

Phone: 301-402-8103
Address:
Advanced Technology Center,
8717 Grovemont Circle
Gaithersburg, MD 20877