biomaRt still in trouble
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John Lande ▴ 280
@john-lande-2357
Last seen 9.6 years ago
dear BioC I still have problem regarding biomart if I run > ensembl <- useMart("ensembl") > ensembl_human <- useDataset("hsapiens_gene_ensembl", mart=ensembl) > EnsTS <- getGene(id = as.vector(TS[,1]), type="entrezgene", mart=ensembl_human) Error in getBM(attributes = attrib, filters = type, values = id, mart = mart) : Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_61: DBI connect('database=ensembl_mart_61;host= dcc-qa-db.oicr.on.ca;port=3306','bm_web',...) failed: Can't connect to MySQL server on 'dcc-qa-db.oicr.on.ca' (113) at /srv/biomart_server/ biomart.org/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98 I retrieve this error. how can I solve this??? [[alternative HTML version deleted]]
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@steffen-durinck-4465
Last seen 9.6 years ago
Hi John, This is a problem at the central BioMart service and needs to be fixed at their site. I've contacted them to see what is going on and will let you know as soon as this is fixed. Cheers, Steffen On Tue, Feb 22, 2011 at 11:20 PM, John Lande <john.lande77@gmail.com> wrote: > dear BioC > > I still have problem regarding biomart > > if I run > > > ensembl <- useMart("ensembl") > > ensembl_human <- useDataset("hsapiens_gene_ensembl", mart=ensembl) > > EnsTS <- getGene(id = as.vector(TS[,1]), type="entrezgene", > mart=ensembl_human) > Error in getBM(attributes = attrib, filters = type, values = id, mart = > mart) : > Query ERROR: caught BioMart::Exception::Database: Could not connect to > mysql database ensembl_mart_61: DBI connect('database=ensembl_mart_61;host= > dcc-qa-db.oicr.on.ca;port=3306','bm_web',...) failed: Can't connect to > MySQL > server on 'dcc-qa-db.oicr.on.ca' (113) at /srv/biomart_server/ > biomart.org/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98 > > > I retrieve this error. how can I solve this??? > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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Hi John, I just got an email that saying that the BioMart service should be restored now so everything should work at this time. Cheers, Steffen On Wed, Feb 23, 2011 at 11:51 AM, Steffen Durinck <durincks@gene.com> wrote: > Hi John, > > This is a problem at the central BioMart service and needs to be fixed at > their site. > I've contacted them to see what is going on and will let you know as soon > as this is fixed. > > Cheers, > Steffen > > > On Tue, Feb 22, 2011 at 11:20 PM, John Lande <john.lande77@gmail.com>wrote: > >> dear BioC >> >> I still have problem regarding biomart >> >> if I run >> >> > ensembl <- useMart("ensembl") >> > ensembl_human <- useDataset("hsapiens_gene_ensembl", mart=ensembl) >> > EnsTS <- getGene(id = as.vector(TS[,1]), type="entrezgene", >> mart=ensembl_human) >> Error in getBM(attributes = attrib, filters = type, values = id, mart = >> mart) : >> Query ERROR: caught BioMart::Exception::Database: Could not connect to >> mysql database ensembl_mart_61: DBI >> connect('database=ensembl_mart_61;host= >> dcc-qa-db.oicr.on.ca;port=3306','bm_web',...) failed: Can't connect to >> MySQL >> server on 'dcc-qa-db.oicr.on.ca' (113) at /srv/biomart_server/ >> biomart.org/biomart-perl/lib/BioMart/Configuration/DBLocation.pm line 98 >> >> >> I retrieve this error. how can I solve this??? >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]
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