[BioC] biomaRt, mysql ensembl db not available, again

Sean Davis 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:

> library(biomaRt)
Loading required package: RCurl
> listMarts(mysql=TRUE)
Loading required package: RMySQL
Loading required package: DBI
[1] "ensembl_mart_47"           "vega_mart_47"
[3] "snp_mart_47"               "sequence_mart_47"
[5] "ensembl_expressionmart_48" "danio_snp_mart"
[7] "msd_mart_4"                "uniprot_mart_17"
> mart <- useMart('ensembl_mart_47',mysql=TRUE)
connected to:  ensembl_mart_47

> sessionInfo()
R version 2.7.0 Under development (unstable) (2008-01-15 r44010)


attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] RMySQL_0.6-0   DBI_0.2-4      biomaRt_1.13.6 RCurl_0.8-3

loaded via a namespace (and not attached):
[1] XML_1.93-2

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