cannot load references

[sdwien]

Dear colleagues,

I have not used SingleR and celldex in a while, it worked for me well before and I was hoping to use it again for a new project.

However, loading the references seems to cause an error:

ref <- celldex::BlueprintEncodeData()

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?
Run `rlang::last_trace()` to see where the error occurred.

I am in R 4.3.3 on Ubuntu 24.
The backtrace says the following:

rlang::last_trace()
<error/rlang_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. ├─celldex::BlueprintEncodeData()
  2. │ └─celldex:::.create_se(...)
  3. │   └─celldex:::.ExperimentHub()
  4. │     └─ExperimentHub::ExperimentHub()
  5. │       └─AnnotationHub::.Hub(...)
  6. │         └─AnnotationHub:::.create_cache(...)
  7. │           └─BiocFileCache::BiocFileCache(cache = cache, ask = ask)
  8. │             └─BiocFileCache:::.sql_create_db(bfc)
  9. │               └─BiocFileCache:::.sql_validate_version(bfc)
 10. │                 └─BiocFileCache:::.sql_schema_version(bfc)
 11. │                   ├─base::tryCatch(...)
 12. │                   │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 13. │                   └─tbl(src, "metadata") %>% collect(Inf)
 14. ├─dplyr::collect(., Inf)
 15. └─dbplyr:::collect.tbl_sql(., Inf)
 16.   ├─base::withCallingHandlers(...)
 17.   └─dbplyr::db_collect(x$src$con, sql, n = n, warn_incomplete = warn_incomplete, ...)

I also tried with other references.
I would be very happy to get it to run again, otherwise I will have to look for another workflow for cell type annotation.

Many thanks for your help and suggestions,
best regards from Vienna,
Sophia

[LTLA]

Apparently this is due to some changes to dbplyr that breaks BiocFileCache, see here for details.

If you update to the indicated version of BiocFileCache, perhaps that might solve your problem. Note that you are running on R 4.3, which is several years old. Fortunately for you, BioC 3.18 still runs on 4.3 so you can still update to the fixed version of BiocFileCache. However, unless you have a real need to stay on 4.3, I'd recommend getting onto the latest version of R and using the latest versions of all Bioconductor.