Error: ! Failed to collect lazy table. Caused by error in `db_collect()` - using biomaRt package in R

I'm currently working on a bioinformatics project using R, and I'm encountering an error when trying to use the biomaRt package. After installing the package and loading it into R, I tried to select a biomaRt database to use in my analysis.

Here's the code I ran when I received an error:

library(biomaRt)
ensembl <- useEnsembl(biomart = "ensembl", dataset = "hsapiens_gene_ensembl")

The error message:

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")
  2. │ └─biomaRt:::.getEnsemblSSL()
  3. │   └─BiocFileCache::BiocFileCache(cache, ask = FALSE)
  4. │     └─BiocFileCache:::.sql_create_db(bfc)
  5. │       └─BiocFileCache:::.sql_validate_version(bfc)
  6. │         └─BiocFileCache:::.sql_schema_version(bfc)
  7. │           ├─base::tryCatch(...)
  8. │           │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
  9. │           └─tbl(src, "metadata") %>% collect(Inf)
 10. ├─dplyr::collect(., Inf)
 11. └─dbplyr:::collect.tbl_sql(., Inf)
 12.   ├─base::tryCatch(...)
 13.   │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 14.   │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 15.   │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 16.   └─dbplyr::db_collect(x$src$con, sql, n = n, warn_incomplete = warn_incomplete, ...)`

R Version: 4.3.1 (2023-06-16 ucrt)
BiomaRt Version: 2.58.0
Operating System: Windows

I tried updating all the packages (biomaRt and dbplyr) and restarting R, but nothing helped.

I would greatly appreciate any guidance or insights on how to resolve this error. Thank you in advance for your help!

Solution

This is probably due to the dbplyr upgrade, there is already a merged PR in BiocFileCache to solve this.

Somehow the Inf argument in tbl(src, "metadata") %>% collect(Inf) got into the ... of dbplyr::db_collect <- function(con, sql, n = -1, warn_incomplete = TRUE, ...) instead of the n argument.

While BiocFileCache 2.10.1 is waiting to be built on the Bioconductor servers, downgrading dbplyr solves this issue for me (devtools::install_version("dbplyr", version = "2.3.4")).

I suppose installing the latest BiocFileCache from their Github repo would work as well.