[BioC] biomaRt error
Rhoda Kinsella
rhoda at ebi.ac.uk
Wed Apr 29 16:45:21 CEST 2009
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.
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