Entering edit mode
I seem to be unable to use biomaRt today (working fine Friday) but I
don't see anything on the Biomart website wbout downtime, so I am not
sure if the problem lies at my end. Any ideas?
Jose
example:
library(biomaRt)
ensembl=useMart("ensembl")
dataset="hsapiens_gene_ensembl"
ensembl=useDataset(dataset, mart=ensembl)
getBM(attributes="hgnc_curated_gene_name", filters="entrezgene",
values=c(1,33), mart=ensembl)
I get:
Error in getBM(attributes = "hgnc_curated_gene_name", filters =
"entrezgene", :
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
>
my sessionInfo()
R version 2.11.0 (2010-04-22)
i386-pc-mingw32
locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United
Kingdom.1252 LC_MONETARY=English_United Kingdom.1252
[4] LC_NUMERIC=C LC_TIME=English_United
Kingdom.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] xtable_1.5-6 GO.db_2.4.1 org.Hs.eg.db_2.4.1
annotate_1.26.0 GOstats_2.14.0
[6] RSQLite_0.9-0 DBI_0.2-5 graph_1.28.0
Category_2.14.0 AnnotationDbi_1.10.1
[11] Biobase_2.8.0 biomaRt_2.4.0
loaded via a namespace (and not attached):
[1] genefilter_1.30.0 GSEABase_1.10.0 RBGL_1.26.0 RCurl_1.4-2
splines_2.11.0 survival_2.35-9
[7] tools_2.11.0 XML_3.1-0
--
Dr. Jose I. de las Heras Email: J.delasHeras at
ed.ac.uk
The Wellcome Trust Centre for Cell Biology Phone: +44 (0)131
6507095
Institute for Cell & Molecular Biology Fax: +44 (0)131
6507360
Swann Building, Mayfield Road
University of Edinburgh
Edinburgh EH9 3JR
UK
--
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Scotland, with registration number SC005336.