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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

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 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 > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: