<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Dear Julien,<div class=""><br class=""></div><div class="">Yes, this is the right place to post this since you are querying the Ensembl marts on <a href="http://ensembl.org" class="">ensembl.org</a> ;-)</div><div class="">There is nothing wrong with your code, I’ve just tried your query and got the result in few minutes:</div><blockquote style="margin: 0 0 0 40px; border: none; padding: 0px;" class=""><div class=""><div class="">> library("biomaRt")</div></div><div class=""><div class="">> ensembl71 <- useMart(host='<a href="http://apr2013.archive.ensembl.org" class="">apr2013.archive.ensembl.org</a>', biomart='ENSEMBL_MART_ENSEMBL', dataset='hsapiens_gene_ensembl')</div></div><div class=""><div class="">> GO <- getBM(attributes=c(‘go_id', 'name_1006', 'namespace_1003'), mart = ensembl71)</div></div><div class="">> head(GO)</div><div class=""> go_id name_1006 namespace_1003</div><div class="">1 GO:0007186 G-protein coupled receptor signaling pathway biological_process</div><div class="">2 GO:0016021 integral to membrane cellular_component</div><div class="">3 GO:0005886 plasma membrane cellular_component</div><div class="">4 GO:0004930 G-protein coupled receptor activity molecular_function</div><div class="">5 GO:0004984 olfactory receptor activity molecular_function</div><div class="">6 GO:0008150 biological_process biological_process</div></blockquote><div class=""><br class=""></div><div class="">It could be that our website our your internet connection had a glitch. Could you please try again?</div><div class="">You could also try to update the BiomaRt package to the current 2.20 version (<a href="http://www.bioconductor.org/packages/release/bioc/html/biomaRt.html" class="">http://www.bioconductor.org/packages/release/bioc/html/biomaRt.html</a>) and update your R software version.</div><div class="">It’s also good practice to refrain yourself from running full genome queries with BioMart, an easy way around this is to us filters to break down your query in smaller pieces (e.g: to filter on chromosome names).</div><div class=""><br class=""></div><div class="">Hope this helps,</div><div class="">Regards,</div><div class="">Thomas</div><div class=""><div><blockquote type="cite" class=""><div class="">On 15 Apr 2015, at 15:34, Julien Roux <<a href="mailto:julien.roux@unil.ch" class="">julien.roux@unil.ch</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">Hi all,<br class="">Not sure this is the right place to post this, please redirect me if not.<br class=""><br class="">I'm having troubles retrieving data with biomaRt (2.18) from Ensembl 71<br class="">> library("biomaRt")<br class="">> ensembl71 <- useMart(host='<a href="http://apr2013.archive.ensembl.org" class="">apr2013.archive.ensembl.org</a>', biomart='ENSEMBL_MART_ENSEMBL', dataset='hsapiens_gene_ensembl')<br class="">> GO <- getBM(attributes=c('go_id', 'name_1006', 'namespace_1003'), mart = ensembl71)<br class="">Error in value[[3L]](cond) :<br class=""> Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web service is temporarily down.<br class=""><br class="">However the fwollowing commands work well, so I wonder if the service is really down or if there is some other issue<br class="">> listFilters(ensembl71)<br class="">> listAttributes(ensembl71)<br class=""><br class="">Best<br class="">Julien<br class=""><br class="">-- <br class="">Julien Roux<br class="">Marie-Curie postdoctoral fellow<br class="">Department of Ecology and Evolution, University of Lausanne, Switzerland<br class=""><a href="http://www.unil.ch/dee/home/menuinst/people/post-docs--associates/dr-julien-roux.html" class="">http://www.unil.ch/dee/home/menuinst/people/post-docs--associates/dr-julien-roux.html</a><br class="">Tel: +41 78 700 2931<br class=""><br class=""><br class="">_______________________________________________<br class="">Dev mailing list Dev@ensembl.org<br class="">Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev<br class="">Ensembl Blog: http://www.ensembl.info/<br class=""></div></blockquote></div><br class=""><div class="">
<div class=""><div class="" style="orphans: 2; widows: 2;">--</div><div class="" style="orphans: 2; widows: 2;">Thomas Maurel<br class="">Bioinformatician - Ensembl Production Team<br class="">European Bioinformatics Institute (EMBL-EBI)<br class="">European Molecular Biology Laboratory<br class="">Wellcome Trust Genome Campus<br class="">Hinxton<br class="">Cambridge CB10 1SD<br class="">United Kingdom</div></div>
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