biomaRt error message: Error in textConnection(bmResult) : invalid 'text' argument
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bd2000 ▴ 30
@5d657c1d
Last seen 9 months ago
United Kingdom

Hi everyone, I'm having issues with my code below:

 ensembl <- useEnsembl(biomart = "ensembl",
                        host = "www.ensembl.org",
                        dataset = "hsapiens_gene_ensembl"
                        )

This is the error message I keep getting:

Error in textConnection(bmResult) : invalid 'text' argument

I've looked through a couple of other queries on this website and I've tried to change the host/mirror but unfortunately nothing has worked for me. I've checked and it works when I use "grch37.ensembl.org" as a host, however, I do need GRCh38 and not 37. Has anyone else experienced this and know how to fix it?

biomaRt • 1.0k views
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Is this still the case today? Running you code example works for me.

I think it might have been a transient issue. Unfortunately, the Ensembl BioMart server is notoriously slow and can be unreliable at busy times.

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It seems to be working today! Thank you for your help, I wasn't sure if it was just an issue with me or with biomaRt in general

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