Hi Steffen I have solved the problem by specifically installing RMySQL: >biocLite(RMySQL) And then using the "mysql=T" option to useMart. I now have another problem. I want to retrieve ensembl stable ids for genes, along with chromosomal location. The documentation says I can do this, however, it does not work as advertised. > ychrom <- getFeature(chromosome = "Y", mart = mart, type="entrezgene") > ychrom An object of class "martTable" Slot "id": [1] "6736" "6192" "7544" etc Slot "table": $chromosome [1] "Y" "Y" "Y" "Y etc $start [1] 2714896 2769527 2863322 etc $end [1] 2715740 2794997 2910547 etc I took this code from the biomaRt.pdf document, and in there the above code returns ensembl stable ids. At the end, I want a list of ensembl gene or transcript stable ids, along with start and end chromosomal location: is this possible? Many thanks Mick -----Original Message----- From: Steffen Durinck [mailto:durincks@mail.nih.gov] Sent: 06 July 2006 15:17 To: michael watson (IAH-C) Cc: Bioconductor Subject: Re: [BioC] biomaRt error: useMart fails Hi Mick, This should only happen when you do not have an internet connection or the Ensembl website goes down. Make sure you are online and try again. best, Steffen michael watson (IAH-C) wrote: > Hi > > Sorry if this has been covered before, I did search the archives but I > didn't find a solution. > > I'm using R 2.3.1 on windows and bioMart 1.6.0 (the BioC 1.8 release > version) > > >> library(biomaRt) >> > Loading required package: XML > Loading required package: RCurl > Warning message: > use of NULL environment is deprecated > > >> mart <- useMart("ensembl") >> > Error in curlPerform(curl = curl, .opts = opts) : > couldn't connect to host > > >> mart <- useMart("ensembl", dataset = "hsapiens_gene_ensembl") >> > Error in curlPerform(curl = curl, .opts = opts) : > couldn't connect to host > > I know some people have been getting this "couldn't connect to host" > error before, but I didn't find a solution. > > Many thanks > > Mick > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >