* using log directory 'd:/Rcompile/CRANpkg/local/4.3/IPDFileCheck.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 'IPDFileCheck/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'IPDFileCheck' version '0.8.1'
* 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 'IPDFileCheck' 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 ... [4s] OK
* checking whether the package can be loaded with stated dependencies ... [3s] OK
* checking whether the package can be unloaded cleanly ... [3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [4s] OK
* checking whether the namespace can be unloaded cleanly ... [4s] OK
* checking loading without being on the library search path ... [4s] 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 ... [11s] 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 ... [13s] ERROR
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")
The following errors were returned during `::()`, `gtsummary()`, and
`modify_header()`:
✖ For variable `age` (`trt`) and "estimate" statistic: The package "cardx" (>=
  0.2.0) is required.
✖ For variable `grade` (`trt`) and "estimate" statistic: The package "cardx"
  (>= 0.2.0) is required.
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
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [13s] ERROR
  Running 'testthat.R' [12s]
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
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking re-building of vignette outputs ... [7s] OK
* checking PDF version of manual ... [17s] OK
* checking HTML version of manual ... [6s] OK
* DONE
Status: 2 ERRORs