The R script below worked several days ago, for the past two days it hangs or occasionally returns
Error in value[[3L]](cond) :
Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web service is temporarily down.
R libraries and biconductor libraries updated with no effect.
Suggestions?
library(biomaRt)
variation = useEnsembl(biomart="snp", dataset="hsapiens_snp")
px <- c("rs11432677","rs632952","rs60178352","rs174686","rs201456215")
ppx <- getBM(attributes=c('refsnp_id','chr_name','chrom_start','chrom_end',"ensembl_peptide_allele",
'ensembl_gene_stable_id','ensembl_transcript_stable_id'),
filters = 'snp_filter', values =px, mart = variation)
I can confirm I'm experiencing the same issues. I see the same problem if I use one the Ensembl mirror sites, or the web interface to carry out the query, which suggests to me that it's an issue with the databae, rather than the web interface. If that's the case then there isn't really anything we can 'fix' in biomaRt, but I'll keep look at the issue.