dbplyr update is breaking AnnotationHub #46
Description
Hi Bioconductor team, I'm now seeing this error with the new dbplyr 2.4.0 update:
> packageVersion("AnnotationHub")
[1] ‘3.8.0’
> packageVersion("dbplyr")
[1] ‘2.4.0’
> AnnotationHub::AnnotationHub()
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. ├─AnnotationHub::AnnotationHub()
2. │ └─AnnotationHub::.Hub(...)
3. │ └─AnnotationHub:::.create_cache(...)
4. │ └─BiocFileCache::BiocFileCache(cache = cache, ask = ask)
5. │ └─BiocFileCache:::.sql_create_db(bfc)
6. │ └─BiocFileCache:::.sql_validate_version(bfc)
7. │ └─BiocFileCache:::.sql_schema_version(bfc)
8. │ ├─base::tryCatch(...)
9. │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
10. │ └─tbl(src, "metadata") %>% collect(Inf)
11. ├─dplyr::collect(., Inf)
12. └─dbplyr:::collect.tbl_sql(., Inf)
13. ├─base::tryCatch(...)
14. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
15. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
16. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
17. └─dbplyr::db_collect(x$src$con, sql, n = n, warn_incomplete = warn_incomplete, ...)
18. └─rlang (local) `<fn>`()
19. └─rlang:::check_dots(env, error, action, call)
20. └─rlang:::action_dots(...)
21. ├─base (local) try_dots(...)
22. └─rlang (local) action(...)
Best,
Mike