I'm getting a
curl error when using the
ensembl@host  "https://useast.ensembl.org:443/biomart/martservice?redirect=no" ensembl@biomart "ENSEMBL_MART_ENSEMBL" getBM(attributes = c('ensembl_transcript_id','transcript_tsl'), filters = 'external_gene_name', values = my_fav_gene_of_interest, mart = ensembl, verbose = F, uniqueRows = T, quote = "\'")
Error in curl::curl_fetch_memory(url, handle = handle) : Timeout was reached: [useast.ensembl.org:8443] Connection timed out after 10005 milliseconds
I am using
getBM in a loop and I saw that one of the options of this function is
An optional 'CURLHandle' object, that can be used to speed up getBM when used in a loop.
In the reference vignette I cannot really find info on how to properly use this option. I assume I should create a new handle and set some longer timeout options like:
h_long <- new_handle() handle_option(h_long, timeout = 99999)
But I'm not really sure if this would help or if the syntax is right. Any suggestion or help would be greatly appreciated!
curl version 4.3 and
biomaRt version 2.42
Thanks a lot! Nicco