[BioC] biomaRt problem

[James W. MacDonald]

   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
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