Hi everyone !

I know that sometimes it's difficult to connect to Ensembl server and it's pretty instable but I have weird errors that change depending on the function or the mirror I'm using:

mart <- useEnsembl(biomart = "ensembl",dataset = "hsapiens_gene_ensembl", mirror = "asia")
Error in bmRequest(request = request, httr_config = httr_config, verbose = verbose) : 
   Not Found (HTTP 404).

mart <- useEnsembl(biomart = "ensembl",dataset = "hsapiens_gene_ensembl", mirror = "www")
Error in checkDataset(dataset = dataset, mart = mart) : 
   The given dataset:  hsapiens_gene_ensembl , is not valid.  Correct dataset names can be obtained with the listDatasets() function.

mart <- useEnsembl(biomart = "ensembl",dataset = "hsapiens_gene_ensembl", mirror = "useast")
Ensembl site unresponsive, trying asia mirror
Error in bmRequest(request = request, httr_config = httr_config, verbose = verbose) : 
   Not Found (HTTP 404).

I tried to use useMart but again different results for different mirrors:

mart <- useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl",host = "https://asia.ensembl.org/")
Error in bmRequest(request = request, httr_config = httr_config, verbose = verbose) : 
  Not Found (HTTP 404).

mart <- useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl",host = "https://ensembl.org/")
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [www.ensembl.org] Operation timed out after 60001 milliseconds with 0 bytes received

mart <- useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl",host = "https://useast.ensembl.org/")
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [useast.ensembl.org:443] Operation timed out after 60000 milliseconds with 0 bytes received

Do you have any idea why I have these different errors ? Is there a way to get around ? Like increasing the time out limit ?

Thanks in advance !

The acid test is trying to load https://ensembl.org/biomart/martview in a browser. Which isn't happening right now, so you know for sure that there are problems on their end. It is unfortunate that this service is so intermittent. It's one reason that I generally use NCBI/UCSC instead, because I can't have work stoppages because I can't get data from Ensembl.

That said, you can get most of the information you might want from biomaRt by using an EnsDb. And you can find an EnsDb for Ensembl builds from 80-112 on the AnnotationHub.