Running ‘testthat.R’ [12s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(IPDFileCheck)
  > 
  > test_check("IPDFileCheck")
  The following errors were returned during `::()`, `gtsummary()`, and `modify_header()`:
  x For variable `age` (`trt`) and "estimate" statistic: The package "cardx" (>= 0.2.0) is required.
  x For variable `marker` (`trt`) and "estimate" statistic: The package "cardx" (>= 0.2.0) is required.
  x For variable `response` (`trt`) and "estimate" statistic: The package "cardx" (>= 0.2.0) is required.
  [ FAIL 2 | WARN 8 | SKIP 0 | PASS 162 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-IPDFilecheck.R:948:3'): testing getting summary from gtsummary ──
  summary_tempdata$N (`actual`) not equal to 4 (`expected`).
  
  `actual` is NULL
  `expected` is a double vector (4)
  ── Error ('test-IPDFilecheck.R:951:3'): testing getting summary from gtsummary ──
  <dplyr:::mutate_error/rlang_error/error/condition>
  Error in `dplyr::mutate(dplyr::tibble(variable = names(fns)), summary_type = map_chr(.data$variable, 
      ~x$inputs$type[[.x]]), row_type = map_chr(.data$variable, 
      ~location[[.x]]), label = map2(.data$variable, .data$row_type, 
      ~dplyr::filter(x$table_body, .data$variable == .x, .data$row_type == 
          .y)$label))`: i In argument: `summary_type = map_chr(.data$variable, ~x$inputs$type[[.x]])`.
  Caused by error in `.data$variable`:
  ! Column `variable` not found in `.data`.
  
  [ FAIL 2 | WARN 8 | SKIP 0 | PASS 162 ]
  Error: Test failures
  Execution halted
Running ‘testthat.R’ [7s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(IPDFileCheck)
  > 
  > test_check("IPDFileCheck")
  The following errors were returned during `::()`, `gtsummary()`, and `modify_header()`:
  x For variable `age` (`trt`) and "estimate" statistic: The package "cardx" (>= 0.2.0) is required.
  x For variable `marker` (`trt`) and "estimate" statistic: The package "cardx" (>= 0.2.0) is required.
  x For variable `response` (`trt`) and "estimate" statistic: The package "cardx" (>= 0.2.0) is required.
  [ FAIL 2 | WARN 8 | SKIP 0 | PASS 162 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-IPDFilecheck.R:948:3'): testing getting summary from gtsummary ──
  summary_tempdata$N (`actual`) not equal to 4 (`expected`).
  
  `actual` is NULL
  `expected` is a double vector (4)
  ── Error ('test-IPDFilecheck.R:951:3'): testing getting summary from gtsummary ──
  <dplyr:::mutate_error/rlang_error/error/condition>
  Error in `dplyr::mutate(dplyr::tibble(variable = names(fns)), summary_type = map_chr(.data$variable, 
      ~x$inputs$type[[.x]]), row_type = map_chr(.data$variable, 
      ~location[[.x]]), label = map2(.data$variable, .data$row_type, 
      ~dplyr::filter(x$table_body, .data$variable == .x, .data$row_type == 
          .y)$label))`: i In argument: `summary_type = map_chr(.data$variable, ~x$inputs$type[[.x]])`.
  Caused by error in `.data$variable`:
  ! Column `variable` not found in `.data`.
  
  [ FAIL 2 | WARN 8 | SKIP 0 | PASS 162 ]
  Error: Test failures
  Execution halted
Running ‘testthat.R’ [19s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(IPDFileCheck)
  > 
  > test_check("IPDFileCheck")
  The following errors were returned during `::()`, `gtsummary()`, and `modify_header()`:
  x For variable `age` (`trt`) and "estimate" statistic: The package "cardx" (>= 0.2.0) is required.
  x For variable `marker` (`trt`) and "estimate" statistic: The package "cardx" (>= 0.2.0) is required.
  x For variable `response` (`trt`) and "estimate" statistic: The package "cardx" (>= 0.2.0) is required.
  [ FAIL 2 | WARN 8 | SKIP 0 | PASS 162 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-IPDFilecheck.R:948:3'): testing getting summary from gtsummary ──
  summary_tempdata$N (`actual`) not equal to 4 (`expected`).
  
  `actual` is NULL
  `expected` is a double vector (4)
  ── Error ('test-IPDFilecheck.R:951:3'): testing getting summary from gtsummary ──
  <dplyr:::mutate_error/rlang_error/error/condition>
  Error in `dplyr::mutate(dplyr::tibble(variable = names(fns)), summary_type = map_chr(.data$variable, 
      ~x$inputs$type[[.x]]), row_type = map_chr(.data$variable, 
      ~location[[.x]]), label = map2(.data$variable, .data$row_type, 
      ~dplyr::filter(x$table_body, .data$variable == .x, .data$row_type == 
          .y)$label))`: i In argument: `summary_type = map_chr(.data$variable, ~x$inputs$type[[.x]])`.
  Caused by error in `.data$variable`:
  ! Column `variable` not found in `.data`.
  
  [ FAIL 2 | WARN 8 | SKIP 0 | PASS 162 ]
  Error: Test failures
  Execution halted
Running examples in ‘IPDFileCheck-Ex.R’ failed
The error most likely occurred in:

> ### Name: get_summary_gtsummary
> ### Title: Function to return the summary table using gtsummary package
> ### Aliases: get_summary_gtsummary
> 
> ### ** Examples
> 
> trial <- gtsummary::trial
> table1 <- get_summary_gtsummary(trial, c("trt", "age", "grade"),
+ byvar = "trt")
Error in `dplyr::mutate()`:
ℹ In argument: `summary_type = map_chr(.data$variable,
  ~x$inputs$type[[.x]])`.
Caused by error in `.data$variable`:
! Column `variable` not found in `.data`.
Backtrace:
     ▆
  1. ├─IPDFileCheck::get_summary_gtsummary(...)
  2. │ └─... %>% gtsummary::bold_labels()
  3. ├─gtsummary::bold_labels(.)
  4. ├─gtsummary::modify_header(., label = "**Variable**")
  5. ├─gtsummary::modify_header(., add_stat_2 ~ "**p value (Wilcox rank sum test for equal median)**")
  6. ├─gtsummary::add_stat(., where(is.numeric) ~ wilcoxtest)
  7. ├─gtsummary::modify_header(., add_stat_1 ~ "**Difference in mean**")
  8. ├─gtsummary::add_stat(., fns = where(is.numeric) ~ get_effect_size)
  9. │ ├─dplyr::select(...)
 10. │ ├─dplyr::mutate(...)
 11. │ ├─dplyr::mutate(...)
 12. │ └─dplyr:::mutate.data.frame(...)
 13. │   └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
 14. │     ├─base::withCallingHandlers(...)
 15. │     └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
 16. │       └─mask$eval_all_mutate(quo)
 17. │         └─dplyr (local) eval()
 18. ├─gtsummary:::map_chr(.data$variable, ~x$inputs$type[[.x]])
 19. │ └─gtsummary:::.rlang_purrr_map_mold(.x, .f, character(1), ...)
 20. │   └─base::vapply(.x, .f, .mold, ..., USE.NAMES = FALSE)
 21. ├─variable
 22. ├─rlang:::`$.rlang_data_pronoun`(.data, variable)
 23. │ └─rlang:::data_pronoun_get(...)
 24. └─rlang:::abort_data_pronoun(x, call = y)
 25.   └─rlang::abort(msg, "rlang_error_data_pronoun_not_found", call = call)
Execution halted
Running ‘testthat.R’ [19s/50s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(IPDFileCheck)
  > 
  > test_check("IPDFileCheck")
  [ FAIL 2 | WARN 8 | SKIP 0 | PASS 162 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-IPDFilecheck.R:948:3'): testing getting summary from gtsummary ──
  summary_tempdata$N (`actual`) not equal to 4 (`expected`).
  
  `actual` is NULL
  `expected` is a double vector (4)
  ── Error ('test-IPDFilecheck.R:951:3'): testing getting summary from gtsummary ──
  <dplyr:::mutate_error/rlang_error/error/condition>
  Error in `dplyr::mutate(dplyr::tibble(variable = names(fns)), summary_type = map_chr(.data$variable, 
      ~x$inputs$type[[.x]]), row_type = map_chr(.data$variable, 
      ~location[[.x]]), label = map2(.data$variable, .data$row_type, 
      ~dplyr::filter(x$table_body, .data$variable == .x, .data$row_type == 
          .y)$label))`: i In argument: `summary_type = map_chr(.data$variable, ~x$inputs$type[[.x]])`.
  Caused by error in `.data$variable`:
  ! Column `variable` not found in `.data`.
  
  [ FAIL 2 | WARN 8 | SKIP 0 | PASS 162 ]
  Error: Test failures
  Execution halted
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(IPDFileCheck)
  > 
  > test_check("IPDFileCheck")
  The following errors were returned during `::()`, `gtsummary()`, and `modify_header()`:
  x For variable `age` (`trt`) and "estimate" statistic: The package "cardx" (>= 0.2.0) is required.
  x For variable `marker` (`trt`) and "estimate" statistic: The package "cardx" (>= 0.2.0) is required.
  x For variable `response` (`trt`) and "estimate" statistic: The package "cardx" (>= 0.2.0) is required.
  [ FAIL 2 | WARN 8 | SKIP 0 | PASS 162 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-IPDFilecheck.R:948:3'): testing getting summary from gtsummary ──
  summary_tempdata$N (`actual`) not equal to 4 (`expected`).
  
  `actual` is NULL
  `expected` is a double vector (4)
  ── Error ('test-IPDFilecheck.R:951:3'): testing getting summary from gtsummary ──
  <dplyr:::mutate_error/rlang_error/error/condition>
  Error in `dplyr::mutate(dplyr::tibble(variable = names(fns)), summary_type = map_chr(.data$variable, 
      ~x$inputs$type[[.x]]), row_type = map_chr(.data$variable, 
      ~location[[.x]]), label = map2(.data$variable, .data$row_type, 
      ~dplyr::filter(x$table_body, .data$variable == .x, .data$row_type == 
          .y)$label))`: i In argument: `summary_type = map_chr(.data$variable, ~x$inputs$type[[.x]])`.
  Caused by error in `.data$variable`:
  ! Column `variable` not found in `.data`.
  
  [ FAIL 2 | WARN 8 | SKIP 0 | PASS 162 ]
  Error: Test failures
  Execution halted
Running ‘testthat.R’ [12s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(IPDFileCheck)
  > 
  > test_check("IPDFileCheck")
  The following errors were returned during `::()`, `gtsummary()`, and `modify_header()`:
  x For variable `age` (`trt`) and "estimate" statistic: The package "cardx" (>= 0.2.0) is required.
  x For variable `marker` (`trt`) and "estimate" statistic: The package "cardx" (>= 0.2.0) is required.
  x For variable `response` (`trt`) and "estimate" statistic: The package "cardx" (>= 0.2.0) is required.
  [ FAIL 2 | WARN 8 | SKIP 0 | PASS 162 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-IPDFilecheck.R:948:3'): testing getting summary from gtsummary ──
  summary_tempdata$N (`actual`) not equal to 4 (`expected`).
  
  `actual` is NULL
  `expected` is a double vector (4)
  ── Error ('test-IPDFilecheck.R:951:3'): testing getting summary from gtsummary ──
  <dplyr:::mutate_error/rlang_error/error/condition>
  Error in `dplyr::mutate(dplyr::tibble(variable = names(fns)), summary_type = map_chr(.data$variable, 
      ~x$inputs$type[[.x]]), row_type = map_chr(.data$variable, 
      ~location[[.x]]), label = map2(.data$variable, .data$row_type, 
      ~dplyr::filter(x$table_body, .data$variable == .x, .data$row_type == 
          .y)$label))`: i In argument: `summary_type = map_chr(.data$variable, ~x$inputs$type[[.x]])`.
  Caused by error in `.data$variable`:
  ! Column `variable` not found in `.data`.
  
  [ FAIL 2 | WARN 8 | SKIP 0 | PASS 162 ]
  Error: Test failures
  Execution halted
Running ‘testthat.R’ [11s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(IPDFileCheck)
  > 
  > test_check("IPDFileCheck")
  The following errors were returned during `::()`, `gtsummary()`, and `modify_header()`:
  x For variable `age` (`trt`) and "estimate" statistic: The package "cardx" (>= 0.2.0) is required.
  x For variable `marker` (`trt`) and "estimate" statistic: The package "cardx" (>= 0.2.0) is required.
  x For variable `response` (`trt`) and "estimate" statistic: The package "cardx" (>= 0.2.0) is required.
  [ FAIL 2 | WARN 8 | SKIP 0 | PASS 162 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-IPDFilecheck.R:948:3'): testing getting summary from gtsummary ──
  summary_tempdata$N (`actual`) not equal to 4 (`expected`).
  
  `actual` is NULL
  `expected` is a double vector (4)
  ── Error ('test-IPDFilecheck.R:951:3'): testing getting summary from gtsummary ──
  <dplyr:::mutate_error/rlang_error/error/condition>
  Error in `dplyr::mutate(dplyr::tibble(variable = names(fns)), summary_type = map_chr(.data$variable, 
      ~x$inputs$type[[.x]]), row_type = map_chr(.data$variable, 
      ~location[[.x]]), label = map2(.data$variable, .data$row_type, 
      ~dplyr::filter(x$table_body, .data$variable == .x, .data$row_type == 
          .y)$label))`: i In argument: `summary_type = map_chr(.data$variable, ~x$inputs$type[[.x]])`.
  Caused by error in `.data$variable`:
  ! Column `variable` not found in `.data`.
  
  [ FAIL 2 | WARN 8 | SKIP 0 | PASS 162 ]
  Error: Test failures
  Execution halted
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(IPDFileCheck)
  > 
  > test_check("IPDFileCheck")
  The following errors were returned during `::()`, `gtsummary()`, and `modify_header()`:
  x For variable `age` (`trt`) and "estimate" statistic: The package "cardx" (>= 0.2.0) is required.
  x For variable `marker` (`trt`) and "estimate" statistic: The package "cardx" (>= 0.2.0) is required.
  x For variable `response` (`trt`) and "estimate" statistic: The package "cardx" (>= 0.2.0) is required.
  [ FAIL 2 | WARN 8 | SKIP 0 | PASS 162 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-IPDFilecheck.R:948:3'): testing getting summary from gtsummary ──
  summary_tempdata$N (`actual`) not equal to 4 (`expected`).
  
  `actual` is NULL
  `expected` is a double vector (4)
  ── Error ('test-IPDFilecheck.R:951:3'): testing getting summary from gtsummary ──
  <dplyr:::mutate_error/rlang_error/error/condition>
  Error in `dplyr::mutate(dplyr::tibble(variable = names(fns)), summary_type = map_chr(.data$variable, 
      ~x$inputs$type[[.x]]), row_type = map_chr(.data$variable, 
      ~location[[.x]]), label = map2(.data$variable, .data$row_type, 
      ~dplyr::filter(x$table_body, .data$variable == .x, .data$row_type == 
          .y)$label))`: i In argument: `summary_type = map_chr(.data$variable, ~x$inputs$type[[.x]])`.
  Caused by error in `.data$variable`:
  ! Column `variable` not found in `.data`.
  
  [ FAIL 2 | WARN 8 | SKIP 0 | PASS 162 ]
  Error: Test failures
  Execution halted
Running 'testthat.R' [13s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(IPDFileCheck)
  > 
  > test_check("IPDFileCheck")
  The following errors were returned during `::()`, `gtsummary()`, and `modify_header()`:
  x For variable `age` (`trt`) and "estimate" statistic: The package "cardx" (>= 0.2.0) is required.
  x For variable `marker` (`trt`) and "estimate" statistic: The package "cardx" (>= 0.2.0) is required.
  x For variable `response` (`trt`) and "estimate" statistic: The package "cardx" (>= 0.2.0) is required.
  [ FAIL 2 | WARN 8 | SKIP 0 | PASS 162 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-IPDFilecheck.R:948:3'): testing getting summary from gtsummary ──
  summary_tempdata$N (`actual`) not equal to 4 (`expected`).
  
  `actual` is NULL
  `expected` is a double vector (4)
  ── Error ('test-IPDFilecheck.R:951:3'): testing getting summary from gtsummary ──
  <dplyr:::mutate_error/rlang_error/error/condition>
  Error in `dplyr::mutate(dplyr::tibble(variable = names(fns)), summary_type = map_chr(.data$variable, 
      ~x$inputs$type[[.x]]), row_type = map_chr(.data$variable, 
      ~location[[.x]]), label = map2(.data$variable, .data$row_type, 
      ~dplyr::filter(x$table_body, .data$variable == .x, .data$row_type == 
          .y)$label))`: i In argument: `summary_type = map_chr(.data$variable, ~x$inputs$type[[.x]])`.
  Caused by error in `.data$variable`:
  ! Column `variable` not found in `.data`.
  
  [ FAIL 2 | WARN 8 | SKIP 0 | PASS 162 ]
  Error: Test failures
  Execution halted