BioMart connection problem
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Paul Leo ▴ 970
@paul-leo-2092
Last seen 7.1 years ago
I've never actually seen this error, though it appears benign .. I assume someone is flogging in poor BioMart server? If there a alternative mirror site? This has persisted for a few hours ... > library(biomaRt) > mart <- useMart("ensembl", dataset="hsapiens_gene_ensembl") > ann.refseq<-getBM(attributes = c( "ensembl_gene_id","hgnc_symbol","gene_biotype","entrezgene","descri ption"), filters = "hgnc_symbol", values=gene.names, mart = mart) Error in getBM(attributes = c("ensembl_gene_id", "hgnc_symbol", "gene_biotype", : Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_60: DBI connect('database=ensembl_mart_60;host=dcc-qa- db.oicr.on.ca;port=3306','bm_web',...) failed: Too many connections at /srv/biomart_server/biomart.org/biomart- perl/lib/BioMart/Configuration/DBLocation.pm line 98 > sessionInfo() R version 2.13.0 Under development (unstable) (2010-11-03 r53517) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_AU.UTF-8 [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.7.1 loaded via a namespace (and not attached): [1] RCurl_1.5-0 XML_3.2-0 [[alternative HTML version deleted]]
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@rhoda-kinsella-3200
Last seen 7.1 years ago
Hi Paul You can set your host to www.ensembl.org rather than accessing the www.biomart.org server. I hope that helps Regards Rhoda > listMarts(host="www.ensembl.org") biomart version 1 ENSEMBL_MART_ENSEMBL Ensembl Genes 60 2 ENSEMBL_MART_SNP Ensembl Variation 60 3 ENSEMBL_MART_FUNCGEN Ensembl Regulation 60 4 ENSEMBL_MART_VEGA Vega 40 5 REACTOME Reactome 6 wormbase215 WormBase 215 (CSHL US) 7 pride PRIDE (EBI UK) On 14 Dec 2010, at 07:44, Paul Leo wrote: > I've never actually seen this error, though it appears benign .. I > assume someone is flogging in poor BioMart server? > > If there a alternative mirror site? This has persisted for a few > hours ... > > > >> library(biomaRt) >> mart <- useMart("ensembl", dataset="hsapiens_gene_ensembl") >> ann.refseq<-getBM(attributes = > c > ( "ensembl_gene_id > ","hgnc_symbol","gene_biotype","entrezgene","description"), filters > = "hgnc_symbol", values=gene.names, mart = mart) > Error in getBM(attributes = c("ensembl_gene_id", "hgnc_symbol", > "gene_biotype", : > Query ERROR: caught BioMart::Exception::Database: Could not connect > to > mysql database ensembl_mart_60: DBI > connect('database=ensembl_mart_60;host=dcc-qa- > db.oicr.on.ca;port=3306','bm_web',...) failed: Too many connections > at /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/ > Configuration/DBLocation.pm line 98 >> sessionInfo() > R version 2.13.0 Under development (unstable) (2010-11-03 r53517) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_AU.UTF-8 > [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] biomaRt_2.7.1 > > loaded via a namespace (and not attached): > [1] RCurl_1.5-0 XML_3.2-0 > > > > > > [[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 Rhoda Kinsella Ph.D. Ensembl Bioinformatician, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK. [[alternative HTML version deleted]]
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Thanks Rhoda, That's what I was looking for. Cheers Paul -----Original Message----- From: Rhoda Kinsella <rhoda@ebi.ac.uk> To: Paul Leo <p.leo@uq.edu.au> Cc: bioconductor <bioconductor@stat.math.ethz.ch> Subject: Re: [BioC] BioMart connection problem Date: Tue, 21 Dec 2010 09:24:47 +0000 Hi Paul You can set your host to www.ensembl.org rather than accessing the www.biomart.org server. I hope that helps Regards Rhoda > listMarts(host="www.ensembl.org") biomart version 1 ENSEMBL_MART_ENSEMBL Ensembl Genes 60 2 ENSEMBL_MART_SNP Ensembl Variation 60 3 ENSEMBL_MART_FUNCGEN Ensembl Regulation 60 4 ENSEMBL_MART_VEGA Vega 40 5 REACTOME Reactome 6 wormbase215 WormBase 215 (CSHL US) 7 pride PRIDE (EBI UK) On 14 Dec 2010, at 07:44, Paul Leo wrote: > I've never actually seen this error, though it appears benign .. I > assume someone is flogging in poor BioMart server? > > If there a alternative mirror site? This has persisted for a few > hours ... > > > > > > library(biomaRt) > > mart <- useMart("ensembl", dataset="hsapiens_gene_ensembl") > > ann.refseq<-getBM(attributes = > > c( "ensembl_gene_id","hgnc_symbol","gene_biotype","entrezgene","desc ription"), filters = "hgnc_symbol", values=gene.names, mart = mart) > Error in getBM(attributes = c("ensembl_gene_id", "hgnc_symbol", > "gene_biotype", : > Query ERROR: caught BioMart::Exception::Database: Could not connect > to > mysql database ensembl_mart_60: DBI > connect('database=ensembl_mart_60;host=dcc-qa- db.oicr.on.ca;port=3306','bm_web',...) failed: Too many connections at /srv/biomart_server/biomart.org/biomart- perl/lib/BioMart/Configuration/DBLocation.pm line 98 > > > sessionInfo() > > R version 2.13.0 Under development (unstable) (2010-11-03 r53517) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_AU.UTF-8 > [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] biomaRt_2.7.1 > > loaded via a namespace (and not attached): > [1] RCurl_1.5-0 XML_3.2-0 > > > > > > [[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 > Rhoda Kinsella Ph.D. Ensembl Bioinformatician, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK. [[alternative HTML version deleted]]
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Paul Leo ▴ 970
@paul-leo-2092
Last seen 7.1 years ago
A new record ! my most arrives at BioC 7 days after I posted it... (on the 14 of DEC). Electrons must move slowly form Australia. -----Original Message----- From: Paul Leo <p.leo@uq.edu.au> To: bioconductor <bioconductor@stat.math.ethz.ch> Subject: [BioC] BioMart connection problem Date: Tue, 14 Dec 2010 17:44:29 +1000 I've never actually seen this error, though it appears benign .. I assume someone is flogging in poor BioMart server? If there a alternative mirror site? This has persisted for a few hours ... > library(biomaRt) > mart <- useMart("ensembl", dataset="hsapiens_gene_ensembl") > ann.refseq<-getBM(attributes = c( "ensembl_gene_id","hgnc_symbol","gene_biotype","entrezgene","descri ption"), filters = "hgnc_symbol", values=gene.names, mart = mart) Error in getBM(attributes = c("ensembl_gene_id", "hgnc_symbol", "gene_biotype", : Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_60: DBI connect('database=ensembl_mart_60;host=dcc-qa- db.oicr.on.ca;port=3306','bm_web',...) failed: Too many connections at /srv/biomart_server/biomart.org/biomart- perl/lib/BioMart/Configuration/DBLocation.pm line 98 > sessionInfo() R version 2.13.0 Under development (unstable) (2010-11-03 r53517) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_AU.UTF-8 [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.7.1 loaded via a namespace (and not attached): [1] RCurl_1.5-0 XML_3.2-0 [[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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On 12/20/2010 05:04 PM, Paul Leo wrote: > > A new record ! my most arrives at BioC 7 days after I posted it... (on > the 14 of DEC). > Electrons must move slowly form Australia. The mailing list is 'subscriber only', solely in an effort to reduce spam. Messages from unsubscribed members (or, in your case, members posting from email addresses not associated with their subscription) are queued for moderator approval (rather than being discarded outright) which under normal circumstances is on a daily basis. So subscribe, and post from your subscribed address. Martin > > > > > -----Original Message----- > From: Paul Leo <p.leo at="" uq.edu.au=""> > To: bioconductor <bioconductor at="" stat.math.ethz.ch=""> > Subject: [BioC] BioMart connection problem > Date: Tue, 14 Dec 2010 17:44:29 +1000 > > > I've never actually seen this error, though it appears benign .. I > assume someone is flogging in poor BioMart server? > > If there a alternative mirror site? This has persisted for a few > hours ... > > > >> library(biomaRt) >> mart <- useMart("ensembl", dataset="hsapiens_gene_ensembl") >> ann.refseq<-getBM(attributes = > c( "ensembl_gene_id","hgnc_symbol","gene_biotype","entrezgene","desc ription"), filters = "hgnc_symbol", values=gene.names, mart = mart) > Error in getBM(attributes = c("ensembl_gene_id", "hgnc_symbol", > "gene_biotype", : > Query ERROR: caught BioMart::Exception::Database: Could not connect to > mysql database ensembl_mart_60: DBI > connect('database=ensembl_mart_60;host=dcc-qa- db.oicr.on.ca;port=3306','bm_web',...) failed: Too many connections at /srv/biomart_server/biomart.org/biomart- perl/lib/BioMart/Configuration/DBLocation.pm line 98 >> sessionInfo() > R version 2.13.0 Under development (unstable) (2010-11-03 r53517) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_AU.UTF-8 > [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] biomaRt_2.7.1 > > loaded via a namespace (and not attached): > [1] RCurl_1.5-0 XML_3.2-0 > > > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at 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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793
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@arnemuellernovartiscom-2205
Last seen 6.0 years ago
Switzerland
Hi, I had the same error some days ago - but it seems ok now. Arne Paul Leo <p.leo@uq.edu.au> Sent by: bioconductor-bounces@r-project.org 12/21/2010 01:55 AM To bioconductor <bioconductor@stat.math.ethz.ch> cc Subject [BioC] BioMart connection problem I've never actually seen this error, though it appears benign .. I assume someone is flogging in poor BioMart server? If there a alternative mirror site? This has persisted for a few hours ... > library(biomaRt) > mart <- useMart("ensembl", dataset="hsapiens_gene_ensembl") > ann.refseq<-getBM(attributes = c( "ensembl_gene_id","hgnc_symbol","gene_biotype","entrezgene","descripti on"), filters = "hgnc_symbol", values=gene.names, mart = mart) Error in getBM(attributes = c("ensembl_gene_id", "hgnc_symbol", "gene_biotype", : Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql database ensembl_mart_60: DBI connect('database=ensembl_mart_60;host=dcc-qa- db.oicr.on.ca;port=3306','bm_web',...) failed: Too many connections at /srv/biomart_server/biomart.org/biomart- perl/lib/BioMart/Configuration/DBLocation.pm line 98 > sessionInfo() R version 2.13.0 Under development (unstable) (2010-11-03 r53517) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_AU.UTF-8 [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.7.1 loaded via a namespace (and not attached): [1] RCurl_1.5-0 XML_3.2-0 [[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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