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

[Steffen Durinck]

Hi Jo,

It looks indeed like the 48 version of Ensembl is not the MySQL database anymore..
I'll drop a mail to the ensembl helpdesk to figure out what happened.

Cheers,
Steffen


----- Original Message -----
From: Johannes Rainer <johannes.rainer at tcri.at>
Date: Monday, March 3, 2008 6:03 am
Subject: Re: [BioC] biomaRt, mysql ensembl db not available, again
To: Sean Davis <sdavis2 at mail.nih.gov>
Cc: bioconductor at stat.math.ethz.ch

> thanks Sean,
> 
> yes, it works with the "old" ensembl version.
> i was just wondering what happened since last week, that i can't 
> connect to
> the ensembl mart directly using mysql.
> 
> thanks, jo
> 
> On Mon, Mar 3, 2008 at 11:36 AM, Sean Davis <sdavis2 at mail.nih.gov> 
> wrote:
> > 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)
> > x86_64-unknown-linux-gnu
> >
> > locale:
> >
> > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-
> 8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-
> 8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-
> 8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> >
> > 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
> >
> 
> 
> 
> -- 
> Johannes Rainer, PhD
> Tyrolean Cancer Research Institute
> Innrain 66, 6020 Innsbruck, Austria
> Tel.: +43 512 570485 33
> Email: johannes.rainer at tcri.at
>           johannes.rainer at i-med.ac.at
> 
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> 
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