grimbough / biomaRt

R package providing query functionality to BioMart instances like Ensembl
https://bioconductor.org/packages/biomaRt/
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useMart Timeout reached #25

Closed rlittman16 closed 3 years ago

rlittman16 commented 3 years ago

Hello,

When using this function: human = useMart("ensembl", dataset = "hsapiens_gene_ensembl", host = "uswest.ensembl.org")

I get the following error: Error in curl::curl_fetch_memory(url, handle = handle): Timeout was reached: Resolving timed out after 10000 milliseconds

Thanks in advanced!

grimbough commented 3 years ago

It's likely that the Ensembl site is being slow, and this is intermittent. You can try using useEnsembl() instead of useMart(). It should try to use an alternative mirror if the first site it tries doesn't respond, which hopefully makes things easier for you.

rlittman16 commented 3 years ago

Thanks! It may have been my connection as well. I got it to work on a server (not on my internet).