[BioC] bioMart 1.6.3 missing mysql=TRUE in useMart

[mkeehan at lic.co.nz]

Hello,

I'd like to report a missing mysql=TRUE in the useMart method for version 
1.6.3 of biomaRt.

I am attempting to connect to a local MYSQL database using MySQL not the 
webservice.

I get the following error:

> mart <- useMart(biomart="ensembl_mart_40",host="somehost",user = 
"someuser", local=TRUE, 
dataset="btaurus_gene_ensembl",password="somepassword",mysql=TRUE)
Error in curlPerform(curl = curl, .opts = opts) : 
        couldn't connect to host

When I call the following: 

> listMarts(mart="ensembl_mart_40", host="somehost", user = "someuser", 
password="somepassword")
Error in curlPerform(curl = curl, .opts = opts) : 
        couldn't connect to host
> 

But when I add the mysql=TRUE parameter to listMarts
 
> listMarts(mart="ensembl_mart_40", host="somehost", user = "someuser", 
password="somepassword",mysql=TRUE)
[1] "ensembl_mart_40"

So I would suggest that line 14 of the useMart function be changed to add 
the missing mysql=TRUE parameter

        database <- listMarts(mart = biomart, host = host, 
                  user = user, password = password)

be changed to 
        database <- listMarts(mart = biomart, host = host, 
                  user = user, password = password, mysql=TRUE )

> packageDescription("biomaRt")
Package: biomaRt
Version: 1.6.3
Date: 2006-07-17
Title: Interface to BioMart databases (e.g. Ensembl)
Author: Steffen Durinck <steffen.durinck at esat.kuleuven.ac.be>, Wolfgang 
Huber <huber at ebi.ac.uk>, Sean Davis <sdavis2 at mail.nih.gov>
Maintainer: Steffen Durinck <steffen.durinck at mail.nih.gov>
Depends: methods, XML, RCurl
Suggests: annotate
biocViews: Annotation
Description: The package provides and API in R to query BioMart databases 
such as Ensembl (http://www.ensembl.org), a software system
              which produces and maintains automatic annotation on 
metazoan genomes.  Two sets of functions are currently
              implemented.  A first set of functions aims to mimic 
functionality of other BioMart APIs such as Martshell, Martview,
              etc. (see http://www.biomart.org for more information). 
These functions are very general, and can be used with any
              BioMart system.  They allow retrieval of all information 
that other BioMart APIs provide.  A Second set of functions
              are tailored towards Ensembl and are a set of commonly used 
queries in microarray data analysis.  With these two sets
              of functions, one can for example annotate the features on 
your array with the latest annotations starting from
              identifiers such as affy ids, locuslink, RefSeq, 
entrezgene,.. Annotation includes gene names, GO, OMIM annotation,
              etc. The package also provides homology mappings between 
these identifiers across all species present in Ensembl.
              Genes can be pre-selected such that they fulfill a certain 
requirement e.g. give all human refseq ids of genes known
              to be involved in diabetes.On top of this, biomaRt enables 
you to retrieve any type of information available from the
              BioMart databases from R.
License: LGPL version
URL: http://www.esat.kuleuven.ac.be/~sdurinck
SaveImage: yes
Packaged: Tue Jul 25 18:36:48 2006; biocbuild
Built: R 2.3.1; ; 2006-07-25 23:07:57; windows

-- File: C:/PROGRA~1/R/R-23~1.1/library/biomaRt/DESCRIPTION 


Mike Keehan
Programmer
Research and Development
Livestock Improvement Corporation
www.lic.co.nz

"Our mice are big, black and white"