[BioC] biomaRt, mysql ensembl db not available, again
sdavis2 at mail.nih.gov
Mon Mar 3 11:36:52 CET 2008
On Mon, Mar 3, 2008 at 2:15 AM, Johannes Rainer <johannes.rainer at tcri.at> wrote:
> sorry guys,
> somehow i sent the mail without finishing to write it... sorry
> so, again, i can no longer connect to the ensembl biomart via mysql:
> mart <- useMart("ensembl", mysql=TRUE)
> returns me an error "Requested BioMart database is not available..."
> this is strange since it worked until the end of last week.
> listMarts(mysql=TRUE) returns me only older ensembl versions (besides that
> the getSequence function does not work with these databases). is there some
> update in progress at ensembl, that the mysql database is currently not
> available or do they have changed the port number?
Hi, Jo. This is what I get this morning:
Loading required package: RCurl
Loading required package: RMySQL
Loading required package: DBI
 "ensembl_mart_47" "vega_mart_47"
 "snp_mart_47" "sequence_mart_47"
 "ensembl_expressionmart_48" "danio_snp_mart"
 "msd_mart_4" "uniprot_mart_17"
> mart <- useMart('ensembl_mart_47',mysql=TRUE)
connected to: ensembl_mart_47
R version 2.7.0 Under development (unstable) (2008-01-15 r44010)
attached base packages:
 stats graphics grDevices utils datasets methods base
other attached packages:
 RMySQL_0.6-0 DBI_0.2-4 biomaRt_1.13.6 RCurl_0.8-3
loaded via a namespace (and not attached):
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