Hello,

I'm having trouble connecting to ensembl with biomaRt package. I'm using this code

useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl", verbose = TRUE)

About 50% of the time I get the following error. It is impossible to reproduce consistently

Ensembl site unresponsive, trying uswest mirror
Attempting web service request:
https://www.ensembl.org:443/biomart/martservice?type=version&requestid=biomaRt&mart=ENSEMBL_MART_ENSEMBL
Ensembl site unresponsive, trying asia mirror
Error in textConnection(BioMartVersion) : invalid 'text' argument
In addition: Warning message:
In if (BioMartVersion == "\n" | BioMartVersion == "") { :
  the condition has length > 1 and only the first element will be used

What am I doing wrong? How to make it more consistent so that I can trust my scripts to run without problems?

I'm running R 4.1.1 and biomaRt 2.50.3

Thank you,

Paul

Hi Paul,

I was getting the exact same error with biomaRt 2.50.3 under R 4.1.3, running:

mart <- useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl")

(while this command was working ok a few days back!).

I fixed it by explicitely stating the host, as mentioned in this post:

mart <- useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl", host="https://uswest.ensembl.org")

so it might be an issue with the current host useMart is using by default (Defaults to www.ensembl.org)?