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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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Unable to use biomaRt #94

Open NTherrien93 opened 5 months ago

NTherrien93 commented 5 months ago

When trying to view databases with biomaRt::listEnsembl() I receive the following error:

Error in collect(): ! Failed to collect lazy table. Caused by error in db_collect(): ! Arguments in ... must be used. ✖ Problematic argument: • ..1 = Inf ℹ Did you misspell an argument name? Backtrace:

  1. biomaRt::useEnsembl(biomart = "genes", dataset = "hsapiens_gene_ensembl")
    1. dbplyr:::collect.tbl_sql(., Inf)
    2. dbplyr::db_collect(x$src$con, sql, n = n, warn_incomplete = warn_incomplete, ...) Error in collect(., Inf) : Caused by error in db_collect(): ! Arguments in ... must be used. ✖ Problematic argument: • ..1 = Inf ℹ Did you misspell an argument name?

Do you have recommendations on how to resolve this issue?

grimbough commented 5 months ago

This is caused by having an out-of-date version of BiocFileCache. There's some more details and suggested solutions in this support site post: https://support.bioconductor.org/p/9154901/#9154924