* using log directory 'd:/Rcompile/CRANpkg/local/4.3/visOmopResults.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 12.3.0
    GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* checking for file 'visOmopResults/DESCRIPTION' ... OK
* this is package 'visOmopResults' version '0.2.1'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'visOmopResults' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s] OK
* checking whether the package can be unloaded cleanly ... [1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s] OK
* checking loading without being on the library search path ... [1s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [8s] OK
* checking Rd files ... [1s] OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... [7s] ERROR
Running examples in 'visOmopResults-Ex.R' failed
The error most likely occurred in:

> ### Name: formatTable
> ### Title: Format a summarised_result object into a gt, flextable or tibble
> ###   object
> ### Aliases: formatTable
> 
> ### ** Examples
> 
> mockSummarisedResult() |> formatTable(
+   formatEstimateName = c("N%" = "<count> (<percentage>)",
+                          "N" = "<count>",
+                          "Mean (SD)" = "<mean> (<sd>)"),
+   header = c("group"),
+   split = c("group","strata",  "additional")
+ )
! The following variables: result_type, package_name, package_version; were added to `settings`
Error in `dplyr::select()`:
ℹ In argument: `dplyr::all_of(excludeColumns)`.
Caused by error in `dplyr::all_of()`:
! Can't subset elements that don't exist.
✖ Elements `result_type`, `package_name`, and `package_version` don't exist.
Backtrace:
     ▆
  1. ├─visOmopResults::formatTable(...)
  2. │ ├─dplyr::rename_with(...)
  3. │ ├─dplyr::select(...)
  4. │ └─dplyr:::select.data.frame(...)
  5. │   └─tidyselect::eval_select(expr(c(...)), data = .data, error_call = error_call)
  6. │     └─tidyselect:::eval_select_impl(...)
  7. │       ├─tidyselect:::with_subscript_errors(...)
  8. │       │ └─base::withCallingHandlers(...)
  9. │       └─tidyselect:::vars_select_eval(...)
 10. │         └─tidyselect:::walk_data_tree(expr, data_mask, context_mask)
 11. │           └─tidyselect:::eval_c(expr, data_mask, context_mask)
 12. │             └─tidyselect:::reduce_sels(node, data_mask, context_mask, init = init)
 13. │               └─tidyselect:::walk_data_tree(new, data_mask, context_mask)
 14. │                 └─tidyselect:::eval_bang(expr, data_mask, context_mask)
 15. │                   └─tidyselect:::walk_data_tree(expr[[2]], data_mask, context_mask)
 16. │                     └─tidyselect:::eval_context(expr, context_mask, call = error_call)
 17. │                       ├─tidyselect:::with_chained_errors(...)
 18. │                       │ └─base::withCallingHandlers(...)
 19. │                       └─rlang::eval_tidy(as_quosure(expr, env), context_mask)
 20. ├─dplyr::all_of(excludeColumns)
 21. │ └─tidyselect:::as_indices_impl(x, vars = vars, strict = TRUE)
 22. │   └─tidyselect:::chr_as_locations(x, vars, call = call, arg = arg)
 23. │     └─vctrs::vec_as_location(...)
 24. └─vctrs (local) `<fn>`()
 25.   └─vctrs:::stop_subscript_oob(...)
 26.     └─vctrs:::stop_subscript(...)
 27.       └─rlang::abort(...)
Execution halted
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [28s] ERROR
  Running 'testthat.R' [28s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
  > # * https://testthat.r-lib.org/articles/special-files.html
  > 
  > library(testthat)
  > library(visOmopResults)
  > 
  > test_check("visOmopResults")
  Starting 2 test processes
  [ FAIL 20 | WARN 5 | SKIP 0 | PASS 255 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-appendSettings.R:34:3'): appendSettings ────────────────────────
  Error in `dplyr::union_all(result, dplyr::mutate(result, result_id = as.integer(2), 
      package_name = "testing"))`: `x` and `y` are not compatible.
  x Different number of columns: 15 vs 16.
  Backtrace:
      ▆
   1. ├─dplyr::union_all(...) at test-appendSettings.R:34:3
   2. └─dplyr:::union_all.data.frame(result, dplyr::mutate(result, result_id = as.integer(2), package_name = "testing"))
   3.   └─dplyr:::check_compatible(x, y)
   4.     └─rlang::abort(c("`x` and `y` are not compatible.", compat), call = error_call)
  ── Error ('test-formatEstimateValue.R:209:5'): formatEstimateValue ─────────────
  Error in `dplyr::union_all(mockSummarisedResult(), dplyr::tibble(result_id = as.integer(1), 
      cdm_name = "mock", result_type = NA_character_, package_name = "visOmopResults", 
      package_version = as.character(utils::packageVersion("visOmopResults")), 
      group_name = "cohort_name", group_level = "cohort3", strata_name = rep(c("overall", 
          rep("age_group &&& sex", 4), rep("sex", 2), rep("age_group", 
              2)), 2), strata_level = rep(c("overall", "<40 &&& Male", 
          ">=40 &&& Male", "<40 &&& Female", ">=40 &&& Female", 
          "Male", "Female", "<40", ">=40"), 2), variable_name = "number subjects", 
      variable_level = NA_character_, estimate_name = "count", 
      estimate_type = "integer", estimate_value = NA_character_, 
      additional_name = "overall", additional_level = "overall"))`: `x` and `y` are not compatible.
  x Different number of columns: 13 vs 16.
  Backtrace:
      ▆
   1. ├─dplyr::union_all(...) at test-formatEstimateValue.R:209:5
   2. └─dplyr:::union_all.data.frame(...)
   3.   └─dplyr:::check_compatible(x, y)
   4.     └─rlang::abort(c("`x` and `y` are not compatible.", compat), call = error_call)
  ── Failure ('test-formatTable.R:4:3'): formatTable ─────────────────────────────
  Expected `... <- NULL` to run without any errors.
  i Actually got a <rlang_error> with text:
    i In argument: `dplyr::all_of(excludeColumns)`.
    Caused by error in `dplyr::all_of()`:
    ! Can't subset elements that don't exist.
    x Elements `result_type`, `package_name`, and `package_version` don't exist.
  ── Error ('test-formatTable.R:17:3'): formatTable ──────────────────────────────
  Error in `eval(code, test_env)`: object 'gt1' not found
  Backtrace:
      ▆
   1. ├─testthat::expect_true("gt_tbl" %in% class(gt1)) at test-formatTable.R:17:3
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─"gt_tbl" %in% class(gt1)
  ── Failure ('test-fxTable.R:45:3'): fxTable ────────────────────────────────────
  unique(fxResult$body$dataset$result_type) (`actual`) not equal to "mock_summarised_result" (`expected`).
  
  `actual` is NULL
  `expected` is a character vector ('mock_summarised_result')
  ── Error ('test-fxTable.R:56:3'): fxTable ──────────────────────────────────────
  <subscriptOutOfBoundsError/error/condition>
  Error in `fxResult$body$styles$pars$text.align$data[1, 12:29]`: subscript out of bounds
  Backtrace:
      ▆
   1. ├─testthat::expect_equal(...) at test-fxTable.R:56:3
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. └─base::unique(fxResult$body$styles$pars$text.align$data[1, 12:29])
  ── Failure ('test-fxTable.R:284:3'): fxTable, test colsToMergeRows ─────────────
  fxResult$body$styles$cells$border.color.top$data[, 7] (`actual`) not equal to c(...) (`expected`).
  
       actual | expected               
   [1] "gray" | "gray"   [1]           
   [2] "gray" | "gray"   [2]           
   [3] "gray" | "gray"   [3]           
   [4] "gray" - "black"  [4]           
   [5] "gray" | "gray"   [5]           
   [6] "gray" - "black"  [6]           
   [7] "gray" - "black"  [7]           
   [8] "gray" - "black"  [8]           
   [9] "gray" | "gray"   [9]           
  [10] "gray" | "gray"   [10]          
   ... ...      ...      and 6 more ...
  ── Failure ('test-fxTable.R:287:3'): fxTable, test colsToMergeRows ─────────────
  fxResult$body$styles$cells$border.color.top$data[, 8] (`actual`) not equal to c(...) (`expected`).
  
       actual | expected               
   [1] "gray" | "gray"   [1]           
   [2] "gray" | "gray"   [2]           
   [3] "gray" | "gray"   [3]           
   [4] "gray" - "black"  [4]           
   [5] "gray" | "gray"   [5]           
   [6] "gray" - "black"  [6]           
   [7] "gray" | "gray"   [7]           
   [8] "gray" - "black"  [8]           
   [9] "gray" | "gray"   [9]           
  [10] "gray" | "gray"   [10]          
   ... ...      ...      and 6 more ...
  ── Error ('test-fxTable.R:290:3'): fxTable, test colsToMergeRows ───────────────
  <subscriptOutOfBoundsError/error/condition>
  Error in `fxResult$body$styles$cells$border.color.top$data[, 19]`: subscript out of bounds
  Backtrace:
      ▆
   1. └─testthat::expect_equal(...) at test-fxTable.R:290:3
   2.   └─testthat::quasi_label(enquo(object), label, arg = "object")
   3.     └─rlang::eval_bare(expr, quo_get_env(quo))
  ── Failure ('test-gtTable.R:57:3'): gtTable ────────────────────────────────────
  ... == "bold" is not TRUE
  
  `actual`:   TRUE <NA>
  `expected`: TRUE     
  ── Failure ('test-gtTable.R:111:3'): gtTable ───────────────────────────────────
  ... == 11 is not TRUE
  
  `actual`:   FALSE
  `expected`: TRUE 
  ── Failure ('test-gtTable.R:193:3'): gtTable, test default styles and NULL ─────
  gtResult$`_styles`$styles[203][[1]]$cell_text$align == "left" is not TRUE
  
  `actual`:       
  `expected`: TRUE
  ── Failure ('test-gtTable.R:232:3'): gtTable, test default styles and NULL ─────
  unique(...) (`actual`) not equal to c("center", "bold") (`expected`).
  
  `actual`:   "center" "bold" NA
  `expected`: "center" "bold"   
  ── Failure ('test-gtTable.R:276:3'): gtTable, test colsToMergeRows ─────────────
  gtResult$`_data`$result_type (`actual`) not equal to c(...) (`expected`).
  
  `actual` is NULL
  `expected` is a character vector ('mock_summarised_result', '', '', '', '', ...)
  ── Failure ('test-gtTable.R:299:3'): gtTable, test colsToMergeRows ─────────────
  gtResult$`_data`$result_type (`actual`) not equal to rep("mock_summarised_result", 14) (`expected`).
  
  `actual` is NULL
  `expected` is a character vector ('mock_summarised_result', 'mock_summarised_result', 'mock_summarised_result', 'mock_summarised_result', 'mock_summarised_result', ...)
  ── Failure ('test-gtTable.R:322:3'): gtTable, test colsToMergeRows ─────────────
  gtResult$`_data`$result_type (`actual`) not equal to c(...) (`expected`).
  
  `actual` is NULL
  `expected` is a character vector ('mock_summarised_result', '', '', '', '', ...)
  ── Error ('test-pivotSettings.R:2:3'): pivotSettings ───────────────────────────
  Error in `dplyr::union_all(mockSummarisedResult()[1, ], dplyr::tibble(result_id = as.integer(1), 
      cdm_name = "mock", result_type = "mock_summarised_result", 
      package_name = "visOmopResults", package_version = as.character(utils::packageVersion("visOmopResults")), 
      group_name = "overall", group_level = "overall", strata_name = "overall", 
      strata_level = "overall", variable_name = "settings", variable_level = NA_character_, 
      estimate_name = "mock_default", estimate_type = "logical", 
      estimate_value = "TRUE", additional_name = "overall", additional_level = "overall"))`: `x` and `y` are not compatible.
  x Different number of columns: 13 vs 16.
  Backtrace:
      ▆
   1. ├─dplyr::union_all(...) at test-pivotSettings.R:2:3
   2. └─dplyr:::union_all.data.frame(...)
   3.   └─dplyr:::check_compatible(x, y)
   4.     └─rlang::abort(c("`x` and `y` are not compatible.", compat), call = error_call)
  ── Error ('test-tidy.R:2:3'): tidy ─────────────────────────────────────────────
  Error in `dplyr::union_all(mockSummarisedResult(), dplyr::tibble(result_id = as.integer(1), 
      cdm_name = "mock", result_type = "mock_summarised_result", 
      package_name = "visOmopResults", package_version = as.character(utils::packageVersion("visOmopResults")), 
      group_name = "overall", group_level = "overall", strata_name = "overall", 
      strata_level = "overall", variable_name = "settings", variable_level = NA_character_, 
      estimate_name = "mock_default", estimate_type = "logical", 
      estimate_value = "TRUE", additional_name = "overall", additional_level = "overall"))`: `x` and `y` are not compatible.
  x Different number of columns: 13 vs 16.
  Backtrace:
      ▆
   1. ├─dplyr::union_all(...) at test-tidy.R:2:3
   2. └─dplyr:::union_all.data.frame(...)
   3.   └─dplyr:::check_compatible(x, y)
   4.     └─rlang::abort(c("`x` and `y` are not compatible.", compat), call = error_call)
  ── Failure ('test-tidy.R:118:3'): tidy, dates ──────────────────────────────────
  Expected `result_out <- tidy(result)` to run without any errors.
  i Actually got a <rlang_error> with text:
    Join columns in `x` must be present in the data.
    x Problem with `result_type`.
  ── Error ('test-tidy.R:119:3'): tidy, dates ────────────────────────────────────
  Error in `eval(code, test_env)`: object 'result_out' not found
  Backtrace:
      ▆
   1. ├─testthat::expect_true(...) at test-tidy.R:119:3
   2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
   3. │   └─rlang::eval_bare(expr, quo_get_env(quo))
   4. ├─base::as.Date(dplyr::pull(result_out, date))
   5. └─dplyr::pull(result_out, date)
  
  [ FAIL 20 | WARN 5 | SKIP 0 | PASS 255 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking re-building of vignette outputs ... [12s] ERROR
Error(s) in re-building vignettes:
--- re-building 'formatFunctions.Rmd' using rmarkdown

Quitting from lines  at lines 121-128 [unnamed-chunk-6] (formatFunctions.Rmd)
Error: processing vignette 'formatFunctions.Rmd' failed with diagnostics:
ℹ In argument: `all_of(...)`.
Caused by error in `all_of()`:
! Can't subset elements that don't exist.
✖ Elements `result_type`, `package_name`, and `package_version` don't exist.
--- failed re-building 'formatFunctions.Rmd'

--- re-building 'splitAndUnite.Rmd' using rmarkdown
--- finished re-building 'splitAndUnite.Rmd'

--- re-building 'tidy.Rmd' using rmarkdown

Quitting from lines  at lines 55-58 [unnamed-chunk-5] (tidy.Rmd)
Error: processing vignette 'tidy.Rmd' failed with diagnostics:
Join columns in `x` must be present in the data.
✖ Problem with `result_type`.
--- failed re-building 'tidy.Rmd'

SUMMARY: processing the following files failed:
  'formatFunctions.Rmd' 'tidy.Rmd'

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... [17s] OK
* checking HTML version of manual ... [4s] OK
* DONE
Status: 3 ERRORs