When specifying the current version of Ensembl (97) to the biomaRt package in the same way that you would specify the archive version I’m getting the following error message and the script fails.
I should note that this does not occur on my work computer which has a slightly older version of R installed via conda, but does happen on my personal computer which has the latest version of R installed directly from CRAN.
Any guidance for resolving this error would be greatly appreciated, the code (with the version swapped for a user prompt) is going in a script that will be user-facing, so having it fail under unknown circumstances is a bit of a problem.
> species <- "hsapiens_gene_ensembl"
> ensemblversion <- "97"
> ensmart <- useEnsembl(biomart = "ensembl", dataset = species, version = ensemblversion)
Note: requested houst was redirected from
http://jul2019.archive.ensembl.org to https://www.ensembl.org:80/biomart/martservice
This often occurs when connecting to the archive URL for the current Ensembl release
You can check the current version number using listEnsemblArchives()
Error in curl::curl_fetch_memory(url, handle = handle) :
error:1400410B:SSL routines:CONNECT_CT_SRVR_HELLO:wrong version number
I initially reached out to ENSEMBL about the error and they believe that it is a biomaRt error and not on their end.
Thanks for any assistance
Can you provide the output of
sessionInfo()
so we can see which version of biomaRt you are using?There's definitely something odd going on as it's specify
https
and port 80 which is probably incompatible, and will be due to a bug in trying to match up the 'current version' URL with the fact this is automatically redirected towww
Here's that output: