I am currently trying to run biomaRt as a qsub job on a node, and I keep getting the error below:
> library(biomaRt) > ensembl = useMart("ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl", host="http://useast.ensembl.org") Ensembl site unresponsive, trying useast mirror Error in curl::curl_fetch_memory(url, handle = handle) : Timeout was reached: [useast.ensembl.org:80] Connection timed out after 10000 milliseconds Calls: useMart ... request_fetch -> request_fetch.write_memory -> <Anonymous> Execution halted
The code works fine on RStudio on my local computer, but on the node in the cluster, I get the error above. Is there any way I can fix this? Is this because the node has no internet connection so it cannot retrieve data from http://useast.ensembl.org?