Error in `collect()`: ! Failed to collect lazy table.

[Shi-YuZhang]

When run hsapathway <- downloadPathways("hsa")

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?
Traceback:

1. downloadPathways("hsa")
2. .getResourceFromCache(pwys.name)
3. BiocFileCache::BiocFileCache(cache.dir)
4. .sql_create_db(bfc)
5. .sql_validate_version(bfc)
6. .sql_schema_version(bfc)
7. tryCatch({
 .     info <- .sql_connect_RO(.sql_dbfile(bfc))
 .     con <- info$con
 .     src <- src_dbi(con)
 .     tbl <- tbl(src, "metadata") %>% collect(Inf)
 . }, finally = {
 .     .sql_disconnect(info)
 . })
8. tryCatchList(expr, classes, parentenv, handlers)
9. tbl(src, "metadata") %>% collect(Inf)
10. collect(., Inf)
11. collect.tbl_sql(., Inf)
12. tryCatch(out <- db_collect(x$src$con, sql, n = n, warn_incomplete = warn_incomplete, 
  .     ...), error = function(cnd) {
  .     cli_abort("Failed to collect lazy table.", parent = cnd)
  . })
13. tryCatchList(expr, classes, parentenv, handlers)
14. tryCatchOne(expr, names, parentenv, handlers[[1L]])
15. value[[3L]](cond)
16. cli_abort("Failed to collect lazy table.", parent = cnd)
17. rlang::abort(message, ..., call = call, use_cli_format = TRUE, 
  .     .frame = .frame)
18. signal_abort(cnd, .file)

R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.0

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] zh_CN.UTF-8/zh_CN.UTF-8/zh_CN.UTF-8/C/zh_CN.UTF-8/C

time zone: Asia/Shanghai
tzcode source: internal

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] EnrichmentBrowser_2.32.0    graph_1.80.0               
 [3] SummarizedExperiment_1.32.0 Biobase_2.62.0             
 [5] GenomicRanges_1.54.0        GenomeInfoDb_1.38.0        
 [7] IRanges_2.36.0              S4Vectors_0.40.0           
 [9] BiocGenerics_0.48.0         MatrixGenerics_1.14.0      
[11] matrixStats_1.0.0           KEGGREST_1.42.0            

loaded via a namespace (and not attached):
 [1] lattice_0.22-5          vctrs_0.6.4             tools_4.3.1            
 [4] bitops_1.0-7            generics_0.1.3          curl_5.1.0             
 [7] tibble_3.2.1            fansi_1.0.5             AnnotationDbi_1.64.0   
[10] RSQLite_2.3.1           blob_1.2.4              pkgconfig_2.0.3        
[13] Matrix_1.6-1.1          dbplyr_2.4.0            uuid_1.1-1             
[16] lifecycle_1.0.3         GenomeInfoDbData_1.2.11 compiler_4.3.1         
[19] Biostrings_2.70.1       repr_1.1.6              htmltools_0.5.6.1      
[22] RCurl_1.98-1.12         pillar_1.9.0            crayon_1.5.2           
[25] DelayedArray_0.28.0     cachem_1.0.8            abind_1.4-5            
[28] tidyselect_1.2.0        digest_0.6.33           purrr_1.0.2            
[31] dplyr_1.1.3             fastmap_1.1.1           grid_4.3.1             
[34] cli_3.6.1               SparseArray_1.2.0       magrittr_2.0.3         
[37] S4Arrays_1.2.0          base64enc_0.1-3         XML_3.99-0.14          
[40] utf8_1.2.4              IRdisplay_1.1           GSEABase_1.64.0        
[43] filelock_1.0.2          IRkernel_1.3.2          bit64_4.0.5            
[46] XVector_0.42.0          httr_1.4.7              bit_4.0.5              
[49] pbdZMQ_0.3-10           png_0.1-8               memoise_2.0.1          
[52] evaluate_0.22           BiocFileCache_2.10.0    rlang_1.1.1            
[55] xtable_1.8-4            glue_1.6.2              DBI_1.1.3              
[58] Rgraphviz_2.46.0        KEGGgraph_1.62.0        annotate_1.80.0        
[61] jsonlite_1.8.7          R6_2.5.1                zlibbioc_1.48.0 

[lgeistlinger]

Thanks for reporting this. It looks like your local cache is corrupt. Can you try:

hsapathway <- downloadPathways("hsa", cache = FALSE)

and let me know how that goes. Thanks!

[Shi-YuZhang]

Thank you for your quick reply, and it helps me solve the problem.