[BioC] GenomeGraphs error

Wolfgang Huber huber at ebi.ac.uk
Thu Jan 8 14:30:24 CET 2009

Dear Arnaud

thank you for reporting this! There were two issues:

1. GenomeGraphs tries to use the BioMart webservices at Ensembl to query 
for a property called "biotype" (a.k.a. "structure_biotype"?), which 
perhaps existed in the past but doesn't seem to be there any more. 
Steffen Durinck, the author of the GenomeGraphs package, or Rhoda might 
be able to know better what's going on here.

2. The getBM function produced a slightly obscure error message, which 
made it difficult to diagnose the error. I have fixed that in the devel 
version of the biomaRt package.

  Thank you and best wishes

Droit Arnaud ha scritto:
> Dear BioC,
> For many months, I have used the GenomeGraphs package without any problems.
> But since a few days, the following code from the documentation :
> mart <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> gene <- makeGene(id = "ENSG00000095203",type = "ensembl_gene_id", biomart = mart)
> Gives the following error message :
> error in getBM(c("structure_gene_stable_id", "structure_transcript_stable_id",  :
> Number of columns in the query result doesn't equal number of attributes in query.  This is probably an internal error, please report.
> I have the following version of R on 64 bit : R version 2.8.1 RC (2008-12-20 r47269)
> Also, I have installed the release version and development version of GenomeGraphs.
> Does anyone know what is the problem ?
> Thanks
> Arnaud.

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