[BioC] biomaRt problem
James W. MacDonald
jmacdon at med.umich.edu
Wed Aug 23 16:21:17 CEST 2006
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@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.
More information about the Bioconductor
mailing list