[BioC] biomaRt error

[Rhoda Kinsella]

Hi Juerg,
We appear to be having some server issues at the moment which is why  
you got this error. Hopefully we will be able to resume normal service  
soon. Many apologies for any inconvenience.
Regards,
Rhoda


On 29 Apr 2009, at 15:23, Straubhaar, Juerg wrote:

>
> Running example(getSequence) returns an error. See below.
>
> Juerg, UMass Med School
>
>
>> library(biomaRt)
>> example(getSequence)
>
> gtSqnc> if(interactive()){
> gtSqnc+ mart <- useMart("ensembl",dataset="hsapiens_gene_ensembl")
> gtSqnc+
> gtSqnc+ seq = getSequence(id="BRCA1", type="hgnc_symbol",  
> seqType="peptide", mart = mart)
> gtSqnc+ show(seq)
> gtSqnc+
> gtSqnc+ seq = getSequence(id="1939_at", type="affy_hg_u95av2",  
> seqType="gene_flank",upstream = 20, mart = mart)
> gtSqnc+ show(seq)
> gtSqnc+
> gtSqnc+ }
> Checking attributes ... ok
> Checking filters ... ok
> Error in getBM(c(seqType, type), filters = type, values = id, mart =  
> mart,  :
>  Query ERROR: caught BioMart::Exception: non-BioMart die():  
> DBD::mysql::st execute failed: File './sequence_mart_53/ 
> hsapiens_genomic_sequence__dna_chunks__main.MYD' not found (Errcode:  
> 27) at /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/ 
> Dataset/GenomicSequence/DNAAdaptor.pm line 209.
>
>> sessionInfo()
> R version 2.9.0 (2009-04-17)
> x86_64-pc-linux-gnu
>
> locale:
> C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] biomaRt_2.0.0
>
> loaded via a namespace (and not attached):
> [1] RCurl_0.94-1 XML_2.3-0
>
> 	[[alternative HTML version deleted]]
>
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Rhoda Kinsella Ph.D.
Ensembl Bioinformatician,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.