thank you very much Steffen!!!

On Mon, Mar 3, 2008 at 11:21 PM, Steffen Durinck <SDurinck@lbl.gov> wrote:

> Hi Jo,
>
> The Ensembl team moved their latest release (Ensembl 48) to be accessed
> through another port.  This explains why we couldn't see it anymore with
> biomaRt in MySQL mode.  I've updated the biomaRt code and committed the
> changes to the svn devel branch.  If you're not using svn, you should be
> able to download the package from the devel  packages link on the
> Bioconductor website within the next 24h.
> You'll need biomaRt 1.13.9
>
> Cheers,
> Steffen
>
>
> >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@tcri.at>
> Date: Monday, March 3, 2008 6:03 am
> Subject: Re: [BioC] biomaRt, mysql ensembl db not available, again
> To: Sean Davis <sdavis2@mail.nih.gov>
> Cc: bioconductor@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@mail.nih.gov>
> > > wrote:
> >> > > On Mon, Mar 3, 2008 at 2:15 AM, Johannes Rainer
> > > <johannes.rainer@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@tcri.at
> > >           johannes.rainer@i-med.ac.at
> > >
> > >     [[alternative HTML version deleted]]
> > >
> > > _______________________________________________
> > > Bioconductor mailing list
> > > Bioconductor@stat.math.ethz.ch
> > > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > > Search the archives:
> > > http://news.gmane.org/gmane.science.biology.informatics.conductor
>
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-- 
Johannes Rainer, PhD
Tyrolean Cancer Research Institute
Innrain 66, 6020 Innsbruck, Austria
Tel.: +43 512 570485 33
Email: johannes.rainer@tcri.at
           johannes.rainer@i-med.ac.at

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