Hello,

I am trying to use a local biomaRt .

 > library(biomaRt)

# It works with remote biomart:

 > mart <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")
Checking attributes ... ok
Checking filters ... ok

# But not with our local biomart:

 > listMarts(host="ubio.bioinfo.cnio.es", port="9002",  path="/biomart/ 
martview/")
Space required after the Public Identifier
SystemLiteral " or ' expected
SYSTEM or PUBLIC, the URI is missing
Error: 1: Space required after the Public Identifier
2: SystemLiteral " or ' expected
3: SYSTEM or PUBLIC, the URI is missing


Latest version of biomaRt does not support 'mysql' anymore (which  
worked!) and we can't make it work through the web service (our local  
biomart url is http://ubio.bioinfo.cnio.es:9002/biomart/martview, and  
the web interface works).

We are following "The biomaRt user’s guide" the example (which in the  
pdf is incomplete):

listMarts(host="www.myLocalHost.org", path="/myPathToWebservice/ 
martservice")
mart=useMart("nameOfMyMart",dataset="nameOfMyDataset",host="www.myLocalHost.org 
", path="/myPathToWebservice/martser <<<< HERE IS CUT!!!


So maybe we are missing something!

Thanks for any help.
Best,
Daniel

 > sessionInfo()
R version 2.9.0 (2009-04-17)
i386-apple-darwin8.11.1

locale:
C/UTF-8/C/C/C/C

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] GenomeGraphs_1.4.1 biomaRt_2.0.0

loaded via a namespace (and not attached):
[1] RCurl_0.94-1 XML_2.3-0    tools_2.9.0


********************************************

Daniel Rico Rodriguez, PhD.
Structural Computational Biology Group
& Bioinformatics Unit
Spanish National Cancer Research Center, CNIO
Melchor Fernandez Almagro, 3.
28029 Madrid, Spain.
Phone: +34 91 224 69 00 #3015
drico@cnio.es
http://www.cnio.es

********************************************






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