Last updated on 2024-07-24 12:21:32 CEST.
| Package | ERROR | NOTE | OK |
|---|---|---|---|
| IPDFileCheck | 2 | 11 | |
| packDAMipd | 1 | 7 | 5 |
| valueEQ5D | 2 | 11 |
Current CRAN status: ERROR: 2, OK: 11
Version: 0.8.1
Check: examples
Result: 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:::`$.rlang_data_pronoun`(.data, variable)
23. │ └─rlang:::data_pronoun_get(...)
24. └─rlang:::abort_data_pronoun(x, call = y)
25. └─rlang::abort(msg, "rlang_error_data_pronoun_not_found", call = call)
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.8.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [20s/50s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(IPDFileCheck)
>
> test_check("IPDFileCheck")
The following errors were returned during `::()`, `gtsummary()`, and `modify_header()`:
x For variable `age` (`trt`) and "estimate" statistic: The package "cardx" (>= 0.2.0) is required.
x For variable `marker` (`trt`) and "estimate" statistic: The package "cardx" (>= 0.2.0) is required.
x For variable `response` (`trt`) and "estimate" statistic: The package "cardx" (>= 0.2.0) is required.
[ FAIL 2 | WARN 8 | SKIP 0 | PASS 162 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-IPDFilecheck.R:948:3'): testing getting summary from gtsummary ──
summary_tempdata$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
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.8.1
Check: examples
Result: 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")
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:::`$.rlang_data_pronoun`(.data, variable)
23. │ └─rlang:::data_pronoun_get(...)
24. └─rlang:::abort_data_pronoun(x, call = y)
25. └─rlang::abort(msg, "rlang_error_data_pronoun_not_found", call = call)
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.8.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [19s/47s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(IPDFileCheck)
>
> test_check("IPDFileCheck")
[ FAIL 2 | WARN 8 | SKIP 0 | PASS 162 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-IPDFilecheck.R:948:3'): testing getting summary from gtsummary ──
summary_tempdata$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
Flavor: r-devel-linux-x86_64-fedora-gcc
Current CRAN status: ERROR: 1, NOTE: 7, OK: 5
Version: 1.1.0
Check: package dependencies
Result: NOTE
Imports includes 29 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.1.0
Check: installed package size
Result: NOTE
installed size is 5.8Mb
sub-directories of 1Mb or more:
extdata 4.3Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-x86_64, r-release-macos-arm64, r-release-macos-x86_64, r-release-windows-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 1.1.0
Check: examples
Result: ERROR
Running examples in ‘packDAMipd-Ex.R’ failed
The error most likely occurred in:
> ### 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
Flavor: r-devel-linux-x86_64-fedora-clang
Current CRAN status: NOTE: 2, OK: 11
Version: 0.7.2
Check: dependencies in R code
Result: NOTE
Namespace in Imports field not imported from: ‘testthat’
All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc