When executing R commands with the biomaRt package, I often get the error "Internal Server Error (HTTP 500)." with basic commands like
ensembl<-useMart("ensembl")
ensembl <- useMart("ensembl", dataset="hsapiens_gene_ensembl")
These commands occasionally work however. I'm not sure if this is an issue on the Biomart server's end, or if there's something that could be causing it on my end, like an old package (I tried reinstalling Biomart). Has anyone dealt with a similar issue?
I circumvented this by setting mirror argument to "useast". Valid mirror options are 'www', 'uswest', 'useast', 'asia'. If no mirror is specified the primary site at www.ensembl.org will be used (it appears they are overloaded on the primary).
ensembl = useEnsembl(biomart = "ensembl", dataset = "hsapiens_gene_ensembl", mirror = "useast")