
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   

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