[ensembl-dev] biomaRt ListEnsemblArchives

[Steffen Möller]

Hello,


On 16.12.19 14:55, ARMANT Olivier wrote:
>
> Dear Ensembl dev list,
>
> First thanx for you great job !
>
> I use the R package biomaRt R version 3.6.1 (2019-07-05) -- "Action of
> the Toes"
>
> to query ensembl on a debian system Ubuntu 18.04.3 LTS
>
> I can sucessfully connect to the current version of the assembly :
>
> > listMarts()
>
> biomart               version
>
> 1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 98
>
> 2 ENSEMBL_MART_MOUSE      Mouse strains 98
>
> 3 ENSEMBL_MART_SNP  Ensembl Variation 98
>
> 4 ENSEMBL_MART_FUNCGEN Ensembl Regulation 98
>
> But this fail when I try to connect to archives :
>
> > listEnsemblArchives()
>
> Error: failed to load HTTP resource
>
> Your help and suggestion would be very much appreciated
>
I tried it on two Debian systems with that package where this works just
fine. But I can confirm that error for a system with a very strict
firewall - and a self-compiled biomaRt installation. My hunch is that
the HTTP proxy settings are not forwarded to/used by curl. The way I
help myself is that I execute what I want to execute with biomaRt with
very lose filters on another machine and then read that file in the HPC
environment where I apply the filters within R. This may not be
applicable for your problem, though.


Cheers,

Steffen



>
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