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grimbough / biomaRt

R package providing query functionality to BioMart instances like Ensembl
https://bioconductor.org/packages/biomaRt/
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Ensembl redirection issues in Release 91 #1

Closed grimbough closed 6 years ago

grimbough commented 6 years ago

Multiple people have reported issues that seem to stem from being redirect to local Ensembl mirrors e.g. https://support.bioconductor.org/p/104069/, https://support.bioconductor.org/p/104025/, https://support.bioconductor.org/p/104185/, https://www.biostars.org/p/289145/.

If you continue to have problems, please report them here. Please include a minimally reproducible example, the output of packageVersion(biomaRt) and your location (since this determines the mirror you are redirected to).

Here's an example that is currently working for me:

Sys.timezone()
[1] "Europe/Berlin"
packageVersion('biomaRt')
[1] ‘2.35.3’
library(biomaRt)
human <- useMart(mart = "ensembl", 
                 dataset = "mmusculus_gene_ensembl", 
                 host = "www.ensembl.org",
                  ensemblRedirect = FALSE)

genes <- c("Zfp286", "Tmx2")

getBM(attributes = "mgi_symbol", 
           filters = "mgi_symbol", 
           values = genes, 
           mart = mouse)
  mgi_symbol
1       Tmx2
2     Zfp286