[BioC] Problem using useMart with local DB

[Steffen Durinck]

Hi Alessandro,

 From biomaRt 1.10.0 you have to specify the port as well.  Default for 
MySQL is 3306 so try:

ensembl=useMart("ensembl_mart_44", 
dataset="hsapiens_gene_ensembl",host="localhost", user="*****", 
password="******", local = TRUE,mysql = TRUE, port="3306")

That should work.

Cheers,
Steffen

Alessandro Bruselles wrote:
> Hi, I'm trying to use Biomart with a local version of db: ensembl_mart_44;
> Since a week ago, before upgrading to R 2.5 and bioconductor 1.10, I was
> using the command:
> /ensembl=useMart("ensembl_mart_44", dataset="hsapiens_gene_ensembl",
> host="localhost", user="*****", password="******", local = TRUE,
> mysql = TRUE)/" and it worked...
> Now, with the same command I get the following error:
> /Errore in useMart("ensembl_mart_44", dataset = "hsapiens_gene_ensembl",  :
>         Please provide host, user, password and port for using local 
> database 'ensembl_mart_44'.
> /
> I'm using R v2.5 and bioconductor v.1.10/
> /Any help will be appreciated/
> /
> _________________________________________
>
> Alessandro Bruselles
> University of Rome "Tor Vergata"
> **
>
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>   


-- 
Steffen Durinck, Ph.D.

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

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