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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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Error with getBM with certain attributes ("go_id") #69

Open licmn opened 1 year ago

licmn commented 1 year ago

Hi!

I've been trying to pull 3 attributes with getBM() function

sapiens_mart = useEnsembl("ensembl", dataset = "hsapiens_gene_ensembl")
   anno_mart_go <- getBM(mart = sapiens_mart, attributes = c('ensembl_gene_id', 'external_gene_name', 'go_id'))

But keep getting this error:

Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [www.ensembl.org:443] Operation timed out after 300000 milliseconds with 9869172 bytes received

Any thoughts on how to fix? It works fine when I remove go_id attribute, but really need this one.

Thanks!

github-actions[bot] commented 1 year ago

Thank you for opening this issue.

Please note that the repository maintainer (@grimbough) is currently on parental leave until October 2022 and any response will take longer than usual.