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"