Cannot Run BlueprintEncodeData()

[taraeicher]

I am trying to run the following line of code after installing celldex.

ref <- BlueprintEncodeData()

However, I get 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?

Here is the stack trace:

1. ├─celldex::BlueprintEncodeData(rm.NA = "none", cell.ont = "all")
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::tryCatch(...)
17. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
18. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
19. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
20. └─dbplyr::db_collect(x$src$con, sql, n = n, warn_incomplete = warn_incomplete, ...)

[lichtobergo]

I have a very similiar error when trying to
ref <- celldex::MouseRNAseqData()
with error message being

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::MouseRNAseqData()
2. dbplyr:::collect.tbl_sql(., Inf)
3. dbplyr::db_collect(x$src$con, sql, n = n, warn_incomplete = warn_incomplete, ...)

Here is the traceback

Backtrace:
▆

1. ├─celldex::MouseRNAseqData()
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::tryCatch(...)
17. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
18. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
19. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
20. └─dbplyr::db_collect(x$src$con, sql, n = n, warn_incomplete = warn_incomplete, ...)

For completeness the session info

R version 4.3.1 (2023-06-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

locale:
 [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C               LC_TIME=de_DE.UTF-8       
 [4] LC_COLLATE=de_DE.UTF-8     LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=de_DE.UTF-8   
 [7] LC_PAPER=de_DE.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       

time zone: Europe/Berlin
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
  [1] RColorBrewer_1.1-3            rstudioapi_0.15.0             magrittr_2.0.3               
  [4] ggbeeswarm_0.7.2              rmarkdown_2.25                zlibbioc_1.46.0              
  [7] vctrs_0.6.4                   memoise_2.0.1                 DelayedMatrixStats_1.22.6    
 [10] RCurl_1.98-1.12               webshot_0.5.5                 htmltools_0.5.6.1            
 [13] S4Arrays_1.0.6                AnnotationHub_3.8.0           curl_5.1.0                   
 [16] BiocNeighbors_1.18.0          tictoc_1.2                    cachem_1.0.8                 
 [19] igraph_1.5.1                  mime_0.12                     lifecycle_1.0.3              
 [22] pkgconfig_2.0.3               rsvd_1.0.5                    Matrix_1.6-1.1               
 [25] R6_2.5.1                      fastmap_1.1.1                 shiny_1.7.5.1                
 [28] GenomeInfoDbData_1.2.10       MatrixGenerics_1.12.3         digest_0.6.33                
 [31] colorspace_2.1-0              AnnotationDbi_1.62.2          S4Vectors_0.38.2             
 [34] scater_1.28.0                 dqrng_0.3.1                   irlba_2.3.5.1                
 [37] ExperimentHub_2.8.1           GenomicRanges_1.52.1          RSQLite_2.3.1                
 [40] beachmat_2.16.0               filelock_1.0.2                fansi_1.0.5                  
 [43] httr_1.4.7                    abind_1.4-5                   compiler_4.3.1               
 [46] bit64_4.0.5                   BiocParallel_1.34.2           viridis_0.6.4                
 [49] DBI_1.1.3                     rappdirs_0.3.3                DelayedArray_0.26.7          
 [52] bluster_1.10.0                tools_4.3.1                   vipor_0.4.5                  
 [55] interactiveDisplayBase_1.38.0 beeswarm_0.4.0                httpuv_1.6.12                
 [58] glue_1.6.2                    promises_1.2.1                grid_4.3.1                   
 [61] cluster_2.1.4                 generics_0.1.3                gtable_0.3.4                 
 [64] tidyr_1.3.0                   BiocSingular_1.16.0           ScaledMatrix_1.8.1           
 [67] metapod_1.8.0                 xml2_1.3.5                    utf8_1.2.4                   
 [70] XVector_0.40.0                BiocGenerics_0.46.0           ggrepel_0.9.4                
 [73] BiocVersion_3.17.1            pillar_1.9.0                  stringr_1.5.0                
 [76] limma_3.56.2                  later_1.3.1                   dplyr_1.1.3                  
 [79] BiocFileCache_2.8.0           lattice_0.21-9                bit_4.0.5                    
 [82] tidyselect_1.2.0              SingleCellExperiment_1.22.0   locfit_1.5-9.8               
 [85] Biostrings_2.68.1             scuttle_1.10.3                knitr_1.44                   
 [88] gridExtra_2.3                 IRanges_2.34.1                edgeR_3.42.4                 
 [91] SummarizedExperiment_1.30.2   svglite_2.1.2                 stats4_4.3.1                 
 [94] xfun_0.40                     dittoSeq_1.12.2               Biobase_2.60.0               
 [97] statmod_1.5.0                 matrixStats_1.0.0             pheatmap_1.0.12              
[100] stringi_1.7.12                yaml_2.3.7                    kableExtra_1.3.4             
[103] evaluate_0.22                 codetools_0.2-19              tibble_3.2.1                 
[106] BiocManager_1.30.22           cli_3.6.1                     xtable_1.8-4                 
[109] systemfonts_1.0.5             munsell_0.5.0                 Rcpp_1.0.11                  
[112] GenomeInfoDb_1.36.4           dbplyr_2.4.0                  png_0.1-8                    
[115] parallel_4.3.1                ellipsis_0.3.2                ggplot2_3.4.4                
[118] blob_1.2.4                    SingleR_2.2.0                 scran_1.28.2                 
[121] sparseMatrixStats_1.12.2      bitops_1.0-7                  viridisLite_0.4.2            
[124] scales_1.2.1                  ggridges_0.5.4                writexl_1.4.2                
[127] purrr_1.0.2                   crayon_1.5.2                  rlang_1.1.1                  
[130] cowplot_1.1.1                 KEGGREST_1.40.1               rvest_1.0.3                  
[133] celldex_1.10.1               

[LTLA]

Nothing comes to mind, I haven't changed anything. I'd speculate you'd get the same error if you just did

ExperimentHub::ExperimentHub()

which suggests it's a problem with the ExperimentHub package rather than celldex.

[lichtobergo]

I dont't know where exactly the problem was, but I encountered it also using biomaRt and the found a solution in that repository's issue section:
grimbough/biomaRt#89 (comment)

[anaarsenijevic]

Hello,

I am getting the same error, and others have suggested downgrading dplyr but this causes problems when I'm running some Seurat functions. Did you manage to fix it? Thanks!

[LTLA]

Before investigating further, I would advise making sure all your packages are up to date, in particular BiocFileCache. Run BiocManager::valid() and follow the prompts to fix any problems, restart your R session, and then try again.