[Bioc-devel] Error when relying on biomaRt function due to Ensembl server being down

[Hugo Gruson]

Hi Peter,

I don't know of a great solution right now. We're dependent on the 
upstream service availability and stability.

We're aware of the issue though and currently working on a solution for 
the next Bioconductor release (3.24 in ~6 months). I added minor changes 
in the very experimental remart package 
(https://github.com/Huber-group-EMBL/remart) which should address your 
use case as far as I can tell.

It still needs to be improved, better tested, go through review, etc. 
but if all goes according to plan, it should provide a much more stable 
and faster drop-in alternative to biomaRt.

Best wishes,

Hugo

On 07/04/2026 12:04, Peter Blattmann wrote:
> Does anyone knows a good way to deal with the error when using the biomaRt function (such as useMart see below) that relies on the Ensembl server working? Because it then throws an error that makes the whole package fail.
> 'useMart()' failed: error: HTTP 500 Internal Server Error.
>
> Error:https://bioconductor.org/checkResults/3.23/bioc-LATEST/DominoEffect/nebbiolo1-buildsrc.html
> As it worked on kjohnson3 and this problem persisted since years, I assume the server was just temporarily down while buiding the package on linux and that this is not related to the OS.
>
> Thanks a lot. Peter
>
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