- using R Under development (unstable) (2024-07-24 r86924)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
clang version 18.1.8
flang-new version 18.1.8
- running under: Fedora Linux 36 (Workstation Edition)
- using session charset: UTF-8
- using option ‘--no-stop-on-test-error’
- 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 executable files ... OK
- checking for hidden files and directories ... OK
- checking for portable file names ... OK
- checking for sufficient/correct file permissions ... OK
- checking whether package ‘IPDFileCheck’ can be installed ... [21s/42s] OK
See the install log for details.
- 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 code files for non-ASCII characters ... OK
- checking R files for syntax errors ... OK
- checking whether the package can be loaded ... [5s/11s] OK
- checking whether the package can be loaded with stated dependencies ... OK
- checking whether the package can be unloaded cleanly ... OK
- checking whether the namespace can be loaded with stated dependencies ... OK
- checking whether the namespace can be unloaded cleanly ... OK
- checking loading without being on the library search path ... 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 ... [30s/58s] OK
- checking Rd files ... OK
- checking Rd metadata ... OK
- checking Rd line widths ... 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/21s] 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:::`$.rlang_data_pronoun`(.data, variable)
23. │ └─rlang:::data_pronoun_get(...)
24. └─rlang:::abort_data_pronoun(x, call = y)
25. └─rlang::abort(msg, "rlang_error_data_pronoun_not_found", call = call)
Execution halted
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [18s/28s] ERROR
Running ‘testthat.R’ [18s/27s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(IPDFileCheck)
>
> test_check("IPDFileCheck")
The following errors were returned during `::()`, `gtsummary()`, and `modify_header()`:
x For variable `age` (`trt`) and "estimate" statistic: The package "cardx" (>= 0.2.0) is required.
x For variable `marker` (`trt`) and "estimate" statistic: The package "cardx" (>= 0.2.0) is required.
x For variable `response` (`trt`) and "estimate" statistic: The package "cardx" (>= 0.2.0) is required.
[ FAIL 2 | WARN 8 | SKIP 0 | PASS 162 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-IPDFilecheck.R:948:3'): testing getting summary from gtsummary ──
summary_tempdata$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 ... OK
- checking re-building of vignette outputs ... [10s/17s] OK
- checking PDF version of manual ... [8s/14s] OK
- checking HTML version of manual ... OK
- checking for non-standard things in the check directory ... OK
- checking for detritus in the temp directory ... OK
- DONE
Status: 2 ERRORs