[BioC] BiomaRt error

[Steffen at stat.Berkeley.EDU]

It looks like the central repository at www.biomart.org doesn't work at the
moment.  This is what biomaRt uses as default server.

You could reroute and use www.ensembl.org as webservice until the central
service is fixed. Below an example to reroute:


> listMarts(host="www.ensembl.org")
               biomart                        version
1 ENSEMBL_MART_ENSEMBL                     Ensembl 55
2     ENSEMBL_MART_SNP           Ensembl variation 55
3 ENSEMBL_MART_FUNCGEN Ensembl functional genomics 55
4    ENSEMBL_MART_VEGA                        Vega 35
5             REACTOME            Reactome (CSHL US)
6     wormbase_current             WormBase (CSHL US)
7                pride                 PRIDE (EBI UK)
> mart =
useMart("ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl",host="www.ensembl.org")
Checking attributes ... ok
Checking filters ... ok


Once you're connected you via www.ensembl.org you should be able to do
your queries.

Cheers,
Steffen

> I am getting a biomaRt error. it works last night, but is failing today.
>
>  > library(biomaRt)
>  > example(getBM)
>
> getBM> if(interactive()){
> getBM+ mart <- useMart("ensembl")
> getBM+ datasets <- listDatasets(mart)
> getBM+ mart<-useDataset("hsapiens_gene_ensembl",mart)
> getBM+
> getBM(attributes=c("affy_hg_u95av2","hgnc_symbol","chromosome_name","band"),filters="affy_hg_u95av2",values=c("1939_at","1503_at","1454_at"),
> mart=mart)
> getBM+
> getBM+ }
> Checking attributes and filters ... ok
>
> V1
> 1 Query ERROR: caught BioMart::Exception::Database: Error during query
> execution: Can't find file:
> './ensembl_mart_55/hsapiens_gene_ensembl__ox_AFFY_HG_U95Av2__dm.frm'
> (errno: 13)
> Error in getBM(attributes = c("affy_hg_u95av2", "hgnc_symbol",
> "chromosome_name",  :
>   Number of columns in the query result doesn't equal number of
> attributes in query.  This is probably an internal error, please report.
>
>  > sessionInfo()
> R version 2.9.0 (2009-04-17)
> i486-pc-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=C;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] biomaRt_1.16.0
>
> loaded via a namespace (and not attached):
> [1] RCurl_0.94-1 XML_1.93-2
>
> --
> Aedín Culhane,
> Research Associate
> Computational Biology and Functional Genomics Laboratory
> Harvard School of Public Health, Dana-Farber Cancer Institute
>
> 44 Binney Street, SM822C
> Department of Biostatistics and Computational Biology,
> Dana-Farber Cancer Institute
> Boston, MA 02115
> USA
>
> Phone: +1 (617) 632 2468
> Fax:   +1 (617) 582 7760
> Email: aedin at jimmy.harvard.edu
> Web URL: http://www.hsph.harvard.edu/research/aedin-culhane/
>
> _______________________________________________
> 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
>