Last updated on 2024-05-02 01:57:46 CEST.
| Package | ERROR | OK |
|---|---|---|
| visOmopResults | 3 | 10 |
Current CRAN status: ERROR: 3, OK: 10
Version: 0.2.1
Check: examples
Result: 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
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-oldrel-windows-x86_64
Version: 0.2.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [67s/40s]
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
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.2.1
Check: re-building of vignette outputs
Result: 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
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-oldrel-windows-x86_64
Version: 0.2.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [43s/22s]
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
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.2.1
Check: tests
Result: 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
Flavor: r-oldrel-windows-x86_64
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