Running ‘testthat.R’ [17s/25s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tidyseurat)
  Loading required package: ttservice
  Loading required package: SeuratObject
  Loading required package: sp
  The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
  which was just loaded, will retire in October 2023.
  Please refer to R-spatial evolution reports for details, especially
  https://r-spatial.org/r/2023/05/15/evolution4.html.
  It may be desirable to make the sf package available;
  package maintainers should consider adding sf to Suggests:.
  The sp package is now running under evolution status 2
       (status 2 uses the sf package in place of rgdal)
  ========================================
  tidyseurat version 0.6.1
  If you use TIDYSEURAT in published research, please cite:
  
  Mangiola et al. Interfacing Seurat with the R tidy universe. Bioinformatics 2021.
  
  This message can be suppressed by:
    suppressPackageStartupMessages(library(tidyseurat))
    
  To restore the Seurat default display use options("restore_Seurat_show" = TRUE) 
  ========================================
  
  
  Attaching package: 'tidyseurat'
  
  The following object is masked from 'package:stats':
  
      filter
  
  > 
  > test_check("tidyseurat")
  
    |                                                                            
    |                                                                      |   0%
    |                                                                            
    |======================================================================| 100%
  Calculating gene variances
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  Calculating feature variances of standardized and clipped values
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  
    |                                                                            
    |                                                                      |   0%
    |                                                                            
    |======================================================================| 100%
  Calculating gene variances
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  Calculating feature variances of standardized and clipped values
  0%   10   20   30   40   50   60   70   80   90   100%
  [----|----|----|----|----|----|----|----|----|----|
  **************************************************|
  [ FAIL 1 | WARN 13 | SKIP 1 | PASS 29 ]
  
  ══ Skipped tests (1) ═══════════════════════════════════════════════════════════
  • empty test (1): 'test-tidyr.R:33:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-methods.R:20:3'): aggregate_cells() returns expected values ────
  Error in `tidyr::nest(., ...)`: In expression named `data`:
  Caused by error:
  ! object 'groups' not found
  Backtrace:
       ▆
    1. ├─ttservice::aggregate_cells(...) at test-methods.R:20:2
    2. ├─tidyseurat::aggregate_cells(...)
    3. │ └─tidyseurat (local) .local(.data, .sample, slot, assays, aggregation_function, ...)
    4. │   ├─tidyseurat:::drop_class(...)
    5. │   ├─dplyr::select(...)
    6. │   └─... %>% ...
    7. ├─tidyr::unite(., ".sample", !!.sample, sep = "___", remove = FALSE)
    8. ├─tidyseurat::unnest(., data)
    9. ├─dplyr::left_join(., .data %>% tidyseurat::as_tibble() %>% subset_tidyseurat(!!.sample))
   10. ├─dplyr::mutate(...)
   11. ├─dplyr::mutate(., .aggregated_cells = map_int(data, ~ncol(.x)))
   12. ├─tidyseurat::nest(., data = -!!.sample)
   13. ├─tidyseurat:::nest.Seurat(., data = -!!.sample)
   14. │ └─to_tib(my_data__[1, ]) %>% tidyr::nest(...)
   15. ├─tidyr::nest(., ...)
   16. ├─tidyr:::nest.tbl_df(., ...)
   17. │ └─tidyr:::nest_info(...)
   18. │   ├─tidyr:::with_indexed_errors(...)
   19. │   │ └─rlang::try_fetch(...)
   20. │   │   └─base::withCallingHandlers(...)
   21. │   └─purrr::map(...)
   22. │     └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
   23. │       ├─purrr:::with_indexed_errors(...)
   24. │       │ └─base::withCallingHandlers(...)
   25. │       ├─purrr:::call_with_cleanup(...)
   26. │       └─tidyr (local) .f(.x[[i]], ...)
   27. │         └─tidyselect::eval_select(...)
   28. │           └─tidyselect:::eval_select_impl(...)
   29. │             ├─tidyselect:::with_subscript_errors(...)
   30. │             │ └─rlang::try_fetch(...)
   31. │             │   └─base::withCallingHandlers(...)
   32. │             └─tidyselect:::vars_select_eval(...)
   33. │               └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
   34. │                 └─tidyselect:::eval_minus(expr, data_mask, context_mask, error_call)
   35. │                   └─tidyselect:::eval_bang(expr, data_mask, context_mask)
   36. │                     └─tidyselect:::walk_data_tree(expr[[2]], data_mask, context_mask)
   37. │                       └─tidyselect:::eval_sym(expr, data_mask, context_mask)
   38. │                         └─rlang::env_get(env, name, default = missing_arg(), inherit = TRUE)
   39. ├─base::.handleSimpleError(...)
   40. │ └─purrr (local) h(simpleError(msg, call))
   41. │   └─cli::cli_abort(...)
   42. │     └─rlang::abort(...)
   43. │       └─rlang:::signal_abort(cnd, .file)
   44. │         └─base::signalCondition(cnd)
   45. └─rlang (local) `<fn>`(`<prrr_rr_>`)
   46.   └─handlers[[1L]](cnd)
   47.     └─rlang::abort(...)
  
  [ FAIL 1 | WARN 13 | SKIP 1 | PASS 29 ]
  Error: Test failures
  Execution halted