- using R version 4.4.1 Patched (2024-07-08 r86915)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
gcc-13 (Debian 13.3.0-3) 13.3.0
GNU Fortran (Debian 13.3.0-3) 13.3.0
- running under: Debian GNU/Linux trixie/sid
- using session charset: UTF-8
- checking for file ‘packDAMipd/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘packDAMipd’ version ‘1.1.0’
- 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 ‘packDAMipd’ can be installed ... OK
See the install log for details.
- checking package directory ... OK
- checking for future file timestamps ... 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/7s] OK
- checking whether the package can be loaded with stated dependencies ... [4s/5s] OK
- checking whether the package can be unloaded cleanly ... [5s/5s] OK
- checking whether the namespace can be loaded with stated dependencies ... [5s/5s] OK
- checking whether the namespace can be unloaded cleanly ... [5s/6s] OK
- checking loading without being on the library search path ... [5s/7s] 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 ... [68s/81s] OK
- checking Rd files ... [1s/2s] 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 contents of ‘data’ directory ... OK
- checking data for non-ASCII characters ... [0s/0s] OK
- checking LazyData ... OK
- checking data for ASCII and uncompressed saves ... OK
- checking R/sysdata.rda ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [12s/16s] ERROR
Running examples in ‘packDAMipd-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: create_shorttable_from_gtsummary_compare_twogroups_timpoints
> ### Title: Create a table to compare the descriptive analysis (short) from
> ### gtsummary of two groups, but at different timepoints
> ### Aliases: create_shorttable_from_gtsummary_compare_twogroups_timpoints
>
> ### ** Examples
>
> eg_data <- as.data.frame(list(no = c(1, 2, 3, 4),
+ mark_at_1 = c(12, 34, 23, 45), gender = c("M", "F", "M", "F"),
+ mark_at_2 = c(12, 34, 23, 45)))
> outcome_summary <- IPDFileCheck::get_summary_gtsummary(eg_data,
+ c("gender", "mark_at_1", "mark_at_2"), byvar = "gender")
The following errors were returned during `::()`, `gtsummary()`, and
`modify_header()`:
✖ For variable `mark_at_1` (`gender`) and "estimate" statistic: The package
"cardx" (>= 0.2.0) is required.
✖ For variable `mark_at_2` (`gender`) 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 vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [11m/13m] OK
- checking PDF version of manual ... [12s/15s] OK
- checking HTML version of manual ... [6s/11s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 1 ERROR