Hi everyone,

I am trying to annotate ensembl gene IDs. I have used the following code to load and select a biomaRt dataset:

ensembl <- useEnsembl(biomart="ensembl", dataset="mmusculus_gene_ensembl", mirror="www")  

This returns the error

Error in `collect()`:
! Failed to collect lazy table.
Caused by error in `db_collect()`:
! Arguments in `...` must be used.
Problematic argument:
 ..1 = Inf
 Did you misspell an argument name?
Run `rlang::last_trace()` to see where the error occurred.

This did not happen before and I have tried reinstall and reload biomaRt, dplyr, and tidyverse but none of that helps. I have also tried using other mirrors such as useast, uswest, and asia.

Because of this, getBM()... does not work either. Any help would be appreciated!

-shasabhi1

As James alluded to, this is actually an incompatibility between dbplyr and BiocFileCache, and biomaRt is an innocent bystander!

The problem in BiocFileCache should already have been fixed if you update to version 2.10.1 or greater (see BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR for more details).

This might necessitate updating to Bioconductor 3.18 if you aren't using that already. You can do that via:

BiocManager::install(version = "3.18")

library(BiocManager)
install("BiocFileCache")

Then try again.