Question: Problem using useMart with local DB
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gravatar for Alessandro Bruselles
12.4 years ago by
Alessandro Bruselles100 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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ADD COMMENTlink modified 12.4 years ago by Steffen Durinck580 • written 12.4 years ago by Alessandro Bruselles100
Answer: Problem using useMart with local DB
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gravatar for Steffen Durinck
12.4 years ago by
Steffen Durinck580 wrote:
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" > ** > > _______________________________________________ > 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 > -- Steffen Durinck, Ph.D. Oncogenomics Section Pediatric Oncology Branch National Cancer Institute, National Institutes of Health URL: http://home.ccr.cancer.gov/oncology/oncogenomics/ Phone: 301-402-8103 Address: Advanced Technology Center, 8717 Grovemont Circle Gaithersburg, MD 20877
ADD COMMENTlink written 12.4 years ago by Steffen Durinck580
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