useMart and listEnsembl : Timeout was reached. Unable to query any Ensembl site

[corinabioinformatic]

I cannot run any query using BiomaRt package:

listEnsembl()

or

 useMart("ensembl", version=versionEnsembl_raw , host = "https://www.ensembl.org")

I get:

> df_ensembls <- listEnsembl()
Error in `req_perform()`:
! Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [www.ensembl.org]: Connection timed out after 10002 milliseconds
Run `rlang::last_trace()` to see where the error occurred.
> ensembl <- useEnsembl(biomart = "genes", dataset = "hsapiens_gene_ensembl")
Ensembl site unresponsive, trying asia mirror
Ensembl site unresponsive, trying useast mirror
Error in .chooseEnsemblMirror(mirror = mirror, http_config = http_config) : 
  Unable to query any Ensembl site
> rlang::last_trace()
<error/httr2_failure>
Error in `req_perform()`:
! Failed to perform HTTP request.
Caused by error in `curl::curl_fetch_memory()`:
! Timeout was reached [www.ensembl.org]: Connection timed out after 10002 milliseconds
---
Backtrace:
    ▆
 1. └─biomaRt::listEnsembl()
 2.   └─biomaRt:::.listEnsembl(...)
 3.     └─biomaRt:::.currentEnsemblVersion()
 4.       └─biomaRt::listEnsemblArchives()
 5.         └─biomaRt:::.listEnsemblArchives(https = https, http_config = list())
 6.           └─biomaRt:::.checkArchiveList(https, http_config)
 7.             └─biomaRt:::.getArchiveList(https = https, http_config = http_config)
 8.               └─httr2::req_perform(html_request)
Run rlang::last_trace(drop = FALSE) to see 2 hidden frames.
> 

Related to:
#25

[MikeWLloyd]

    Possible SSL connectivity problems detected.
    Please report this issue at https://github.com/grimbough/biomaRt/issues
    Error in curl::curl_fetch_memory(url, handle = handle) :
      SSL peer certificate or SSH remote key was not OK: [uswest.ensembl.org] SSL certificate problem: certificate has expired

    Error in curl::curl_fetch_memory(url, handle = handle) :
      Timeout was reached: [dec2021.archive.ensembl.org:443] Operation timed out after 10000 milliseconds with 0 bytes received
    Calls: useEnsembl ... request_fetch -> request_fetch.write_memory -> <Anonymous>

[MeriamOs]

I've been having the same issue as well since last week or so. I've tried multiple times over several days. Is there anything else I can try? I use:

ensembl <- useEnsembl(
  biomart = "genes",
  dataset = "clfamiliaris_gene_ensembl",
  host = "https://may2021.archive.ensembl.org",
  version = "CanFam3.1")

This was working fine before.

[grimbough]

I think there are some slightly different issues here, although already related to conectivity / server status:

@corinabioinformatic I suspect your issue is simply that the Ensembl BioMart server was not performing very well at the time you were tryign to connect. This unfortunately happens and there's little that can be done.

@MikeWLloyd if you're getting errors about connecting to uswest.ensembl.org you're probably using a fairly outdated version of biomaRt. That particular mirror was retired several years ago, and more recent versions of biomaRt should not try to contact it anymore. Specifying the host argument in useEnsembl() should also prevent this happening in older versions.

@MeriamOs You're code should in theory work, but there seem to be some persistent issues with the Ensembl archives. I can occasionally connect to that archive, sometimes I get a status page, and sometimes a 500 error. This seems the case for several of the archive, not just May 2021. You can connect Ensembl at https://www.ensembl.org/Help/Contact incase they aren't aware of the issues, or simply wait until the service is restored.