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.myLoca lHost.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 ******************************************** **NOTA DE CONFIDENCIALIDAD** Este correo electrÿnico, ...{{dropped:18}}