Last updated on 2024-03-12 07:50:11 CET.
Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
---|---|---|---|---|---|---|
r-devel-linux-x86_64-debian-clang | 0.4.0 | 13.42 | 330.69 | 344.11 | ERROR | |
r-devel-linux-x86_64-debian-gcc | 0.4.0 | 10.66 | 249.86 | 260.52 | ERROR | |
r-devel-linux-x86_64-fedora-clang | 0.4.0 | 419.12 | ERROR | |||
r-devel-linux-x86_64-fedora-gcc | 0.4.0 | 443.38 | ERROR | |||
r-devel-windows-x86_64 | 0.4.0 | 13.00 | 238.00 | 251.00 | ERROR | |
r-patched-linux-x86_64 | 0.4.0 | 12.17 | 329.02 | 341.19 | ERROR | |
r-release-linux-x86_64 | 0.4.0 | 10.82 | 332.14 | 342.96 | ERROR | |
r-release-macos-arm64 | 0.4.0 | 102.00 | OK | |||
r-release-macos-x86_64 | 0.4.0 | 206.00 | OK | |||
r-release-windows-x86_64 | 0.4.0 | 16.00 | 308.00 | 324.00 | ERROR | |
r-oldrel-macos-arm64 | 0.4.0 | 110.00 | OK | |||
r-oldrel-windows-x86_64 | 0.4.0 | 17.00 | 315.00 | 332.00 | ERROR |
Version: 0.4.0
Check: examples
Result: ERROR
Running examples in ‘visR-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_highlight
> ### Title: Highlight a specific strata
> ### Aliases: add_highlight add_highlight.ggsurvfit
>
> ### ** Examples
>
>
> adtte %>%
+ visR::estimate_KM(strata = "SEX") %>%
+ visR::visr() %>%
+ visR::add_CI(alpha = 0.4) %>%
+ visR::add_highlight(strata = "M", bg_alpha = 0.2)
Error in FUN(X[[i]], ...) :
The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL
Please adjust and rerun.
Calls: %>% ... add_highlight.ggsurvfit -> <Anonymous> -> lapply -> FUN
Execution halted
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.4.0
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/1s]
Running ‘testthat.R’ [178s/198s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(visR)
> library(vdiffr)
> library(survival)
>
> test_check("visR")
[ FAIL 12 | WARN 28 | SKIP 27 | PASS 988 ]
══ Skipped tests (27) ══════════════════════════════════════════════════════════
• On CRAN (27): 'test-add_CI.R:30:3', 'test-add_CI.R:45:3',
'test-add_CI.R:65:3', 'test-add_CI.R:95:3', 'test-add_CI.R:124:3',
'test-add_CI.R:144:3', 'test-add_CNSR.R:34:3', 'test-add_CNSR.R:47:3',
'test-add_CNSR.R:60:3', 'test-add_CNSR.R:78:3', 'test-add_CNSR.R:95:3',
'test-add_CNSR.R:112:3', 'test-add_highlight.R:107:3',
'test-add_highlight.R:151:3', 'test-add_highlight.R:281:3',
'test-add_risktable.R:81:3', 'test-add_risktable.R:93:3',
'test-add_risktable.R:204:3', 'test-add_risktable.R:214:3',
'test-stat_stepribbon.R:32:3', 'test-stat_stepribbon.R:60:3',
'test-stat_stepribbon.R:94:3', 'test-stat_stepribbon.R:117:3',
'test-utils_visR.R:135:3', 'test-utils_visR.R:146:3',
'test-visr_survfit.R:528:3', 'test-watchdog_testfiles.R:14:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-add_highlight.R:41:3'): T1.1 No error when `add_highlight` is called on a `ggsurvfit` object. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "Placebo") %>% ... at test-add_highlight.R:41:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = "Placebo")
8. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo")
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Error ('test-add_highlight.R:87:3'): T1.5 The function returns a modified object of type `ggsurvfit`. ──
Error in `FUN(X[[i]], ...)`: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Backtrace:
▆
1. ├─gg %>% add_highlight("Placebo") at test-add_highlight.R:87:3
2. ├─visR::add_highlight(., "Placebo")
3. └─visR:::add_highlight.ggsurvfit(., "Placebo")
4. └─base::sapply(...)
5. └─base::lapply(X = X, FUN = FUN, ...)
6. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:103:3'): T2.1 No error when `strata` is a character string found in the plot strata. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "Placebo") %>% ... at test-add_highlight.R:103:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = "Placebo")
8. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo")
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:120:3'): T2.2 An error when `strata` is a character string not found in the plot strata. ──
`.` threw an error with unexpected message.
Expected match: "The strata you specified has not been found in the provided plot.\n Available strata: Placebo, Xanomeline High Dose, Xanomeline Low Dose\n Please adjust and rerun."
Actual message: "The strata you specified has not been found in the provided plot.\n Available strata: NULL, NULL, NULL\n Please adjust and rerun."
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "visR") %>% ... at test-add_highlight.R:120:3
2. ├─testthat::expect_error(., expected_error)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = "visR")
8. └─visR:::add_highlight.ggsurvfit(., strata = "visR")
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:143:3'): T2.4 No error when `strata` is a `list` or `vector` of character strings found in the plot strata. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = strata_list) %>% ... at test-add_highlight.R:143:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = strata_list)
8. └─visR:::add_highlight.ggsurvfit(., strata = strata_list)
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:147:3'): T2.4 No error when `strata` is a `list` or `vector` of character strings found in the plot strata. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = strata_vector) %>% ... at test-add_highlight.R:147:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = strata_vector)
8. └─visR:::add_highlight.ggsurvfit(., strata = strata_vector)
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:231:3'): T3.1 No error when `bg_alpha` is a `numberic`. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─... %>% testthat::expect_error(NA) at test-add_highlight.R:231:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = "Placebo", bg_alpha = 0.2)
8. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo", bg_alpha = 0.2)
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Error ('test-add_highlight.R:314:3'): T4.1 The function adds the alpha channel to the hex-encoded colour. ──
Error in `FUN(X[[i]], ...)`: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "Placebo") at test-add_highlight.R:314:3
2. ├─visR::add_highlight(., strata = "Placebo")
3. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo")
4. └─base::sapply(...)
5. └─base::lapply(X = X, FUN = FUN, ...)
6. └─visR (local) FUN(X[[i]], ...)
── Error ('test-add_highlight.R:339:3'): T4.2 The function also reduces the alpha value of the confidence intervals introduced by `add_CI`. ──
Error in `FUN(X[[i]], ...)`: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "Placebo", bg_alpha = bg_alpha) at test-add_highlight.R:339:3
2. ├─visR::add_highlight(., strata = "Placebo", bg_alpha = bg_alpha)
3. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo", bg_alpha = bg_alpha)
4. └─base::sapply(...)
5. └─base::lapply(X = X, FUN = FUN, ...)
6. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-apply_theme.R:539:3'): T1.19 The named list is used in the legend title. ──
get_legend_title(gg) not equal to "SEX".
target is NULL, current is character
── Failure ('test-apply_theme.R:559:3'): T1.19 The named list is used in the legend title. ──
get_legend_title(gg) not equal to "Sex, ph.ecog".
target is NULL, current is character
── Failure ('test-utils_visR.R:109:3'): T2.1 Columns are added to the grob-converted plot. ──
dim(grob_orig)[2] == dim(pltlist[[2]])[2] is not FALSE
`actual`: TRUE
`expected`: FALSE
[ FAIL 12 | WARN 28 | SKIP 27 | PASS 988 ]
Error: Test failures
In addition: Warning message:
closing unused connection 4 (https://raw.githubusercontent.com/vntkumar8/covid-survival/main/data/final.csv)
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.4.0
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/1s]
Running ‘testthat.R’ [133s/209s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(visR)
> library(vdiffr)
> library(survival)
>
> test_check("visR")
[ FAIL 12 | WARN 28 | SKIP 27 | PASS 988 ]
══ Skipped tests (27) ══════════════════════════════════════════════════════════
• On CRAN (27): 'test-add_CI.R:30:3', 'test-add_CI.R:45:3',
'test-add_CI.R:65:3', 'test-add_CI.R:95:3', 'test-add_CI.R:124:3',
'test-add_CI.R:144:3', 'test-add_CNSR.R:34:3', 'test-add_CNSR.R:47:3',
'test-add_CNSR.R:60:3', 'test-add_CNSR.R:78:3', 'test-add_CNSR.R:95:3',
'test-add_CNSR.R:112:3', 'test-add_highlight.R:107:3',
'test-add_highlight.R:151:3', 'test-add_highlight.R:281:3',
'test-add_risktable.R:81:3', 'test-add_risktable.R:93:3',
'test-add_risktable.R:204:3', 'test-add_risktable.R:214:3',
'test-stat_stepribbon.R:32:3', 'test-stat_stepribbon.R:60:3',
'test-stat_stepribbon.R:94:3', 'test-stat_stepribbon.R:117:3',
'test-utils_visR.R:135:3', 'test-utils_visR.R:146:3',
'test-visr_survfit.R:528:3', 'test-watchdog_testfiles.R:14:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-add_highlight.R:41:3'): T1.1 No error when `add_highlight` is called on a `ggsurvfit` object. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "Placebo") %>% ... at test-add_highlight.R:41:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = "Placebo")
8. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo")
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Error ('test-add_highlight.R:87:3'): T1.5 The function returns a modified object of type `ggsurvfit`. ──
Error in `FUN(X[[i]], ...)`: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Backtrace:
▆
1. ├─gg %>% add_highlight("Placebo") at test-add_highlight.R:87:3
2. ├─visR::add_highlight(., "Placebo")
3. └─visR:::add_highlight.ggsurvfit(., "Placebo")
4. └─base::sapply(...)
5. └─base::lapply(X = X, FUN = FUN, ...)
6. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:103:3'): T2.1 No error when `strata` is a character string found in the plot strata. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "Placebo") %>% ... at test-add_highlight.R:103:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = "Placebo")
8. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo")
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:120:3'): T2.2 An error when `strata` is a character string not found in the plot strata. ──
`.` threw an error with unexpected message.
Expected match: "The strata you specified has not been found in the provided plot.\n Available strata: Placebo, Xanomeline High Dose, Xanomeline Low Dose\n Please adjust and rerun."
Actual message: "The strata you specified has not been found in the provided plot.\n Available strata: NULL, NULL, NULL\n Please adjust and rerun."
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "visR") %>% ... at test-add_highlight.R:120:3
2. ├─testthat::expect_error(., expected_error)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = "visR")
8. └─visR:::add_highlight.ggsurvfit(., strata = "visR")
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:143:3'): T2.4 No error when `strata` is a `list` or `vector` of character strings found in the plot strata. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = strata_list) %>% ... at test-add_highlight.R:143:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = strata_list)
8. └─visR:::add_highlight.ggsurvfit(., strata = strata_list)
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:147:3'): T2.4 No error when `strata` is a `list` or `vector` of character strings found in the plot strata. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = strata_vector) %>% ... at test-add_highlight.R:147:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = strata_vector)
8. └─visR:::add_highlight.ggsurvfit(., strata = strata_vector)
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:231:3'): T3.1 No error when `bg_alpha` is a `numberic`. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─... %>% testthat::expect_error(NA) at test-add_highlight.R:231:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = "Placebo", bg_alpha = 0.2)
8. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo", bg_alpha = 0.2)
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Error ('test-add_highlight.R:314:3'): T4.1 The function adds the alpha channel to the hex-encoded colour. ──
Error in `FUN(X[[i]], ...)`: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "Placebo") at test-add_highlight.R:314:3
2. ├─visR::add_highlight(., strata = "Placebo")
3. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo")
4. └─base::sapply(...)
5. └─base::lapply(X = X, FUN = FUN, ...)
6. └─visR (local) FUN(X[[i]], ...)
── Error ('test-add_highlight.R:339:3'): T4.2 The function also reduces the alpha value of the confidence intervals introduced by `add_CI`. ──
Error in `FUN(X[[i]], ...)`: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "Placebo", bg_alpha = bg_alpha) at test-add_highlight.R:339:3
2. ├─visR::add_highlight(., strata = "Placebo", bg_alpha = bg_alpha)
3. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo", bg_alpha = bg_alpha)
4. └─base::sapply(...)
5. └─base::lapply(X = X, FUN = FUN, ...)
6. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-apply_theme.R:539:3'): T1.19 The named list is used in the legend title. ──
get_legend_title(gg) not equal to "SEX".
target is NULL, current is character
── Failure ('test-apply_theme.R:559:3'): T1.19 The named list is used in the legend title. ──
get_legend_title(gg) not equal to "Sex, ph.ecog".
target is NULL, current is character
── Failure ('test-utils_visR.R:109:3'): T2.1 Columns are added to the grob-converted plot. ──
dim(grob_orig)[2] == dim(pltlist[[2]])[2] is not FALSE
`actual`: TRUE
`expected`: FALSE
[ FAIL 12 | WARN 28 | SKIP 27 | PASS 988 ]
Error: Test failures
In addition: Warning message:
In for (name in names(public_methods)) lockBinding(name, public_bind_env) :
closing unused connection 4 (https://raw.githubusercontent.com/vntkumar8/covid-survival/main/data/final.csv)
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.4.0
Check: examples
Result: ERROR
Running examples in ‘visR-Ex.R’ failed
The error most likely occurred in:
> ### Name: add_highlight
> ### Title: Highlight a specific strata
> ### Aliases: add_highlight add_highlight.ggsurvfit
>
> ### ** Examples
>
>
> adtte %>%
+ visR::estimate_KM(strata = "SEX") %>%
+ visR::visr() %>%
+ visR::add_CI(alpha = 0.4) %>%
+ visR::add_highlight(strata = "M", bg_alpha = 0.2)
Error in FUN(X[[i]], ...) :
The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL
Please adjust and rerun.
Calls: %>% ... add_highlight.ggsurvfit -> <Anonymous> -> lapply -> FUN
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64, r-release-windows-x86_64, r-oldrel-windows-x86_64
Version: 0.4.0
Check: tests
Result: ERROR
Running ‘spelling.R’
Running ‘testthat.R’ [208s/229s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(visR)
> library(vdiffr)
> library(survival)
>
> test_check("visR")
[ FAIL 12 | WARN 28 | SKIP 27 | PASS 988 ]
══ Skipped tests (27) ══════════════════════════════════════════════════════════
• On CRAN (27): 'test-add_CI.R:30:3', 'test-add_CI.R:45:3',
'test-add_CI.R:65:3', 'test-add_CI.R:95:3', 'test-add_CI.R:124:3',
'test-add_CI.R:144:3', 'test-add_CNSR.R:34:3', 'test-add_CNSR.R:47:3',
'test-add_CNSR.R:60:3', 'test-add_CNSR.R:78:3', 'test-add_CNSR.R:95:3',
'test-add_CNSR.R:112:3', 'test-add_highlight.R:107:3',
'test-add_highlight.R:151:3', 'test-add_highlight.R:281:3',
'test-add_risktable.R:81:3', 'test-add_risktable.R:93:3',
'test-add_risktable.R:204:3', 'test-add_risktable.R:214:3',
'test-stat_stepribbon.R:32:3', 'test-stat_stepribbon.R:60:3',
'test-stat_stepribbon.R:94:3', 'test-stat_stepribbon.R:117:3',
'test-utils_visR.R:135:3', 'test-utils_visR.R:146:3',
'test-visr_survfit.R:528:3', 'test-watchdog_testfiles.R:14:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-add_highlight.R:41:3'): T1.1 No error when `add_highlight` is called on a `ggsurvfit` object. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "Placebo") %>% ... at test-add_highlight.R:41:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = "Placebo")
8. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo")
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Error ('test-add_highlight.R:87:3'): T1.5 The function returns a modified object of type `ggsurvfit`. ──
Error in `FUN(X[[i]], ...)`: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Backtrace:
▆
1. ├─gg %>% add_highlight("Placebo") at test-add_highlight.R:87:3
2. ├─visR::add_highlight(., "Placebo")
3. └─visR:::add_highlight.ggsurvfit(., "Placebo")
4. └─base::sapply(...)
5. └─base::lapply(X = X, FUN = FUN, ...)
6. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:103:3'): T2.1 No error when `strata` is a character string found in the plot strata. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "Placebo") %>% ... at test-add_highlight.R:103:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = "Placebo")
8. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo")
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:120:3'): T2.2 An error when `strata` is a character string not found in the plot strata. ──
`.` threw an error with unexpected message.
Expected match: "The strata you specified has not been found in the provided plot.\n Available strata: Placebo, Xanomeline High Dose, Xanomeline Low Dose\n Please adjust and rerun."
Actual message: "The strata you specified has not been found in the provided plot.\n Available strata: NULL, NULL, NULL\n Please adjust and rerun."
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "visR") %>% ... at test-add_highlight.R:120:3
2. ├─testthat::expect_error(., expected_error)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = "visR")
8. └─visR:::add_highlight.ggsurvfit(., strata = "visR")
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:143:3'): T2.4 No error when `strata` is a `list` or `vector` of character strings found in the plot strata. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = strata_list) %>% ... at test-add_highlight.R:143:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = strata_list)
8. └─visR:::add_highlight.ggsurvfit(., strata = strata_list)
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:147:3'): T2.4 No error when `strata` is a `list` or `vector` of character strings found in the plot strata. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = strata_vector) %>% ... at test-add_highlight.R:147:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = strata_vector)
8. └─visR:::add_highlight.ggsurvfit(., strata = strata_vector)
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:231:3'): T3.1 No error when `bg_alpha` is a `numberic`. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─... %>% testthat::expect_error(NA) at test-add_highlight.R:231:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = "Placebo", bg_alpha = 0.2)
8. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo", bg_alpha = 0.2)
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Error ('test-add_highlight.R:314:3'): T4.1 The function adds the alpha channel to the hex-encoded colour. ──
Error in `FUN(X[[i]], ...)`: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "Placebo") at test-add_highlight.R:314:3
2. ├─visR::add_highlight(., strata = "Placebo")
3. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo")
4. └─base::sapply(...)
5. └─base::lapply(X = X, FUN = FUN, ...)
6. └─visR (local) FUN(X[[i]], ...)
── Error ('test-add_highlight.R:339:3'): T4.2 The function also reduces the alpha value of the confidence intervals introduced by `add_CI`. ──
Error in `FUN(X[[i]], ...)`: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "Placebo", bg_alpha = bg_alpha) at test-add_highlight.R:339:3
2. ├─visR::add_highlight(., strata = "Placebo", bg_alpha = bg_alpha)
3. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo", bg_alpha = bg_alpha)
4. └─base::sapply(...)
5. └─base::lapply(X = X, FUN = FUN, ...)
6. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-apply_theme.R:539:3'): T1.19 The named list is used in the legend title. ──
get_legend_title(gg) not equal to "SEX".
target is NULL, current is character
── Failure ('test-apply_theme.R:559:3'): T1.19 The named list is used in the legend title. ──
get_legend_title(gg) not equal to "Sex, ph.ecog".
target is NULL, current is character
── Failure ('test-utils_visR.R:109:3'): T2.1 Columns are added to the grob-converted plot. ──
dim(grob_orig)[2] == dim(pltlist[[2]])[2] is not FALSE
`actual`: TRUE
`expected`: FALSE
[ FAIL 12 | WARN 28 | SKIP 27 | PASS 988 ]
Error: Test failures
In addition: Warning message:
In fetch_ggproto(x, name) :
closing unused connection 4 (https://raw.githubusercontent.com/vntkumar8/covid-survival/main/data/final.csv)
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.4.0
Check: tests
Result: ERROR
Running ‘spelling.R’
Running ‘testthat.R’ [223s/271s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(visR)
> library(vdiffr)
> library(survival)
>
> test_check("visR")
[ FAIL 12 | WARN 28 | SKIP 27 | PASS 988 ]
══ Skipped tests (27) ══════════════════════════════════════════════════════════
• On CRAN (27): 'test-add_CI.R:30:3', 'test-add_CI.R:45:3',
'test-add_CI.R:65:3', 'test-add_CI.R:95:3', 'test-add_CI.R:124:3',
'test-add_CI.R:144:3', 'test-add_CNSR.R:34:3', 'test-add_CNSR.R:47:3',
'test-add_CNSR.R:60:3', 'test-add_CNSR.R:78:3', 'test-add_CNSR.R:95:3',
'test-add_CNSR.R:112:3', 'test-add_highlight.R:107:3',
'test-add_highlight.R:151:3', 'test-add_highlight.R:281:3',
'test-add_risktable.R:81:3', 'test-add_risktable.R:93:3',
'test-add_risktable.R:204:3', 'test-add_risktable.R:214:3',
'test-stat_stepribbon.R:32:3', 'test-stat_stepribbon.R:60:3',
'test-stat_stepribbon.R:94:3', 'test-stat_stepribbon.R:117:3',
'test-utils_visR.R:135:3', 'test-utils_visR.R:146:3',
'test-visr_survfit.R:528:3', 'test-watchdog_testfiles.R:14:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-add_highlight.R:41:3'): T1.1 No error when `add_highlight` is called on a `ggsurvfit` object. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "Placebo") %>% ... at test-add_highlight.R:41:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = "Placebo")
8. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo")
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Error ('test-add_highlight.R:87:3'): T1.5 The function returns a modified object of type `ggsurvfit`. ──
Error in `FUN(X[[i]], ...)`: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Backtrace:
▆
1. ├─gg %>% add_highlight("Placebo") at test-add_highlight.R:87:3
2. ├─visR::add_highlight(., "Placebo")
3. └─visR:::add_highlight.ggsurvfit(., "Placebo")
4. └─base::sapply(...)
5. └─base::lapply(X = X, FUN = FUN, ...)
6. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:103:3'): T2.1 No error when `strata` is a character string found in the plot strata. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "Placebo") %>% ... at test-add_highlight.R:103:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = "Placebo")
8. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo")
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:120:3'): T2.2 An error when `strata` is a character string not found in the plot strata. ──
`.` threw an error with unexpected message.
Expected match: "The strata you specified has not been found in the provided plot.\n Available strata: Placebo, Xanomeline High Dose, Xanomeline Low Dose\n Please adjust and rerun."
Actual message: "The strata you specified has not been found in the provided plot.\n Available strata: NULL, NULL, NULL\n Please adjust and rerun."
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "visR") %>% ... at test-add_highlight.R:120:3
2. ├─testthat::expect_error(., expected_error)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = "visR")
8. └─visR:::add_highlight.ggsurvfit(., strata = "visR")
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:143:3'): T2.4 No error when `strata` is a `list` or `vector` of character strings found in the plot strata. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = strata_list) %>% ... at test-add_highlight.R:143:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = strata_list)
8. └─visR:::add_highlight.ggsurvfit(., strata = strata_list)
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:147:3'): T2.4 No error when `strata` is a `list` or `vector` of character strings found in the plot strata. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = strata_vector) %>% ... at test-add_highlight.R:147:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = strata_vector)
8. └─visR:::add_highlight.ggsurvfit(., strata = strata_vector)
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:231:3'): T3.1 No error when `bg_alpha` is a `numberic`. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─... %>% testthat::expect_error(NA) at test-add_highlight.R:231:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = "Placebo", bg_alpha = 0.2)
8. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo", bg_alpha = 0.2)
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Error ('test-add_highlight.R:314:3'): T4.1 The function adds the alpha channel to the hex-encoded colour. ──
Error in `FUN(X[[i]], ...)`: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "Placebo") at test-add_highlight.R:314:3
2. ├─visR::add_highlight(., strata = "Placebo")
3. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo")
4. └─base::sapply(...)
5. └─base::lapply(X = X, FUN = FUN, ...)
6. └─visR (local) FUN(X[[i]], ...)
── Error ('test-add_highlight.R:339:3'): T4.2 The function also reduces the alpha value of the confidence intervals introduced by `add_CI`. ──
Error in `FUN(X[[i]], ...)`: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "Placebo", bg_alpha = bg_alpha) at test-add_highlight.R:339:3
2. ├─visR::add_highlight(., strata = "Placebo", bg_alpha = bg_alpha)
3. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo", bg_alpha = bg_alpha)
4. └─base::sapply(...)
5. └─base::lapply(X = X, FUN = FUN, ...)
6. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-apply_theme.R:539:3'): T1.19 The named list is used in the legend title. ──
get_legend_title(gg) not equal to "SEX".
target is NULL, current is character
── Failure ('test-apply_theme.R:559:3'): T1.19 The named list is used in the legend title. ──
get_legend_title(gg) not equal to "Sex, ph.ecog".
target is NULL, current is character
── Failure ('test-utils_visR.R:109:3'): T2.1 Columns are added to the grob-converted plot. ──
dim(grob_orig)[2] == dim(pltlist[[2]])[2] is not FALSE
`actual`: TRUE
`expected`: FALSE
[ FAIL 12 | WARN 28 | SKIP 27 | PASS 988 ]
Error: Test failures
In addition: Warning message:
closing unused connection 4 (https://raw.githubusercontent.com/vntkumar8/covid-survival/main/data/final.csv)
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.4.0
Check: tests
Result: ERROR
Running 'spelling.R' [0s]
Running 'testthat.R' [110s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(visR)
> library(vdiffr)
> library(survival)
>
> test_check("visR")
[ FAIL 12 | WARN 28 | SKIP 27 | PASS 988 ]
══ Skipped tests (27) ══════════════════════════════════════════════════════════
• On CRAN (27): 'test-add_CI.R:30:3', 'test-add_CI.R:45:3',
'test-add_CI.R:65:3', 'test-add_CI.R:95:3', 'test-add_CI.R:124:3',
'test-add_CI.R:144:3', 'test-add_CNSR.R:34:3', 'test-add_CNSR.R:47:3',
'test-add_CNSR.R:60:3', 'test-add_CNSR.R:78:3', 'test-add_CNSR.R:95:3',
'test-add_CNSR.R:112:3', 'test-add_highlight.R:107:3',
'test-add_highlight.R:151:3', 'test-add_highlight.R:281:3',
'test-add_risktable.R:81:3', 'test-add_risktable.R:93:3',
'test-add_risktable.R:204:3', 'test-add_risktable.R:214:3',
'test-stat_stepribbon.R:32:3', 'test-stat_stepribbon.R:60:3',
'test-stat_stepribbon.R:94:3', 'test-stat_stepribbon.R:117:3',
'test-utils_visR.R:135:3', 'test-utils_visR.R:146:3',
'test-visr_survfit.R:528:3', 'test-watchdog_testfiles.R:14:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-add_highlight.R:41:3'): T1.1 No error when `add_highlight` is called on a `ggsurvfit` object. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "Placebo") %>% ... at test-add_highlight.R:41:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = "Placebo")
8. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo")
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Error ('test-add_highlight.R:87:3'): T1.5 The function returns a modified object of type `ggsurvfit`. ──
Error in `FUN(X[[i]], ...)`: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Backtrace:
▆
1. ├─gg %>% add_highlight("Placebo") at test-add_highlight.R:87:3
2. ├─visR::add_highlight(., "Placebo")
3. └─visR:::add_highlight.ggsurvfit(., "Placebo")
4. └─base::sapply(...)
5. └─base::lapply(X = X, FUN = FUN, ...)
6. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:103:3'): T2.1 No error when `strata` is a character string found in the plot strata. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "Placebo") %>% ... at test-add_highlight.R:103:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = "Placebo")
8. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo")
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:120:3'): T2.2 An error when `strata` is a character string not found in the plot strata. ──
`.` threw an error with unexpected message.
Expected match: "The strata you specified has not been found in the provided plot.\n Available strata: Placebo, Xanomeline High Dose, Xanomeline Low Dose\n Please adjust and rerun."
Actual message: "The strata you specified has not been found in the provided plot.\n Available strata: NULL, NULL, NULL\n Please adjust and rerun."
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "visR") %>% ... at test-add_highlight.R:120:3
2. ├─testthat::expect_error(., expected_error)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = "visR")
8. └─visR:::add_highlight.ggsurvfit(., strata = "visR")
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:143:3'): T2.4 No error when `strata` is a `list` or `vector` of character strings found in the plot strata. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = strata_list) %>% ... at test-add_highlight.R:143:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = strata_list)
8. └─visR:::add_highlight.ggsurvfit(., strata = strata_list)
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:147:3'): T2.4 No error when `strata` is a `list` or `vector` of character strings found in the plot strata. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = strata_vector) %>% ... at test-add_highlight.R:147:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = strata_vector)
8. └─visR:::add_highlight.ggsurvfit(., strata = strata_vector)
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:231:3'): T3.1 No error when `bg_alpha` is a `numberic`. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─... %>% testthat::expect_error(NA) at test-add_highlight.R:231:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = "Placebo", bg_alpha = 0.2)
8. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo", bg_alpha = 0.2)
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Error ('test-add_highlight.R:314:3'): T4.1 The function adds the alpha channel to the hex-encoded colour. ──
Error in `FUN(X[[i]], ...)`: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "Placebo") at test-add_highlight.R:314:3
2. ├─visR::add_highlight(., strata = "Placebo")
3. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo")
4. └─base::sapply(...)
5. └─base::lapply(X = X, FUN = FUN, ...)
6. └─visR (local) FUN(X[[i]], ...)
── Error ('test-add_highlight.R:339:3'): T4.2 The function also reduces the alpha value of the confidence intervals introduced by `add_CI`. ──
Error in `FUN(X[[i]], ...)`: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "Placebo", bg_alpha = bg_alpha) at test-add_highlight.R:339:3
2. ├─visR::add_highlight(., strata = "Placebo", bg_alpha = bg_alpha)
3. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo", bg_alpha = bg_alpha)
4. └─base::sapply(...)
5. └─base::lapply(X = X, FUN = FUN, ...)
6. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-apply_theme.R:539:3'): T1.19 The named list is used in the legend title. ──
get_legend_title(gg) not equal to "SEX".
target is NULL, current is character
── Failure ('test-apply_theme.R:559:3'): T1.19 The named list is used in the legend title. ──
get_legend_title(gg) not equal to "Sex, ph.ecog".
target is NULL, current is character
── Failure ('test-utils_visR.R:109:3'): T2.1 Columns are added to the grob-converted plot. ──
dim(grob_orig)[2] == dim(pltlist[[2]])[2] is not FALSE
`actual`: TRUE
`expected`: FALSE
[ FAIL 12 | WARN 28 | SKIP 27 | PASS 988 ]
Error: Test failures
In addition: Warning message:
In inherits(x, "factor") :
closing unused connection 4 (https://raw.githubusercontent.com/vntkumar8/covid-survival/main/data/final.csv)
Execution halted
Flavor: r-devel-windows-x86_64
Version: 0.4.0
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/1s]
Running ‘testthat.R’ [177s/204s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(visR)
> library(vdiffr)
> library(survival)
>
> test_check("visR")
[ FAIL 12 | WARN 28 | SKIP 27 | PASS 988 ]
══ Skipped tests (27) ══════════════════════════════════════════════════════════
• On CRAN (27): 'test-add_CI.R:30:3', 'test-add_CI.R:45:3',
'test-add_CI.R:65:3', 'test-add_CI.R:95:3', 'test-add_CI.R:124:3',
'test-add_CI.R:144:3', 'test-add_CNSR.R:34:3', 'test-add_CNSR.R:47:3',
'test-add_CNSR.R:60:3', 'test-add_CNSR.R:78:3', 'test-add_CNSR.R:95:3',
'test-add_CNSR.R:112:3', 'test-add_highlight.R:107:3',
'test-add_highlight.R:151:3', 'test-add_highlight.R:281:3',
'test-add_risktable.R:81:3', 'test-add_risktable.R:93:3',
'test-add_risktable.R:204:3', 'test-add_risktable.R:214:3',
'test-stat_stepribbon.R:32:3', 'test-stat_stepribbon.R:60:3',
'test-stat_stepribbon.R:94:3', 'test-stat_stepribbon.R:117:3',
'test-utils_visR.R:135:3', 'test-utils_visR.R:146:3',
'test-visr_survfit.R:528:3', 'test-watchdog_testfiles.R:14:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-add_highlight.R:41:3'): T1.1 No error when `add_highlight` is called on a `ggsurvfit` object. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "Placebo") %>% ... at test-add_highlight.R:41:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = "Placebo")
8. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo")
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Error ('test-add_highlight.R:87:3'): T1.5 The function returns a modified object of type `ggsurvfit`. ──
Error in `FUN(X[[i]], ...)`: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Backtrace:
▆
1. ├─gg %>% add_highlight("Placebo") at test-add_highlight.R:87:3
2. ├─visR::add_highlight(., "Placebo")
3. └─visR:::add_highlight.ggsurvfit(., "Placebo")
4. └─base::sapply(...)
5. └─base::lapply(X = X, FUN = FUN, ...)
6. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:103:3'): T2.1 No error when `strata` is a character string found in the plot strata. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "Placebo") %>% ... at test-add_highlight.R:103:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = "Placebo")
8. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo")
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:120:3'): T2.2 An error when `strata` is a character string not found in the plot strata. ──
`.` threw an error with unexpected message.
Expected match: "The strata you specified has not been found in the provided plot.\n Available strata: Placebo, Xanomeline High Dose, Xanomeline Low Dose\n Please adjust and rerun."
Actual message: "The strata you specified has not been found in the provided plot.\n Available strata: NULL, NULL, NULL\n Please adjust and rerun."
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "visR") %>% ... at test-add_highlight.R:120:3
2. ├─testthat::expect_error(., expected_error)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = "visR")
8. └─visR:::add_highlight.ggsurvfit(., strata = "visR")
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:143:3'): T2.4 No error when `strata` is a `list` or `vector` of character strings found in the plot strata. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = strata_list) %>% ... at test-add_highlight.R:143:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = strata_list)
8. └─visR:::add_highlight.ggsurvfit(., strata = strata_list)
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:147:3'): T2.4 No error when `strata` is a `list` or `vector` of character strings found in the plot strata. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = strata_vector) %>% ... at test-add_highlight.R:147:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = strata_vector)
8. └─visR:::add_highlight.ggsurvfit(., strata = strata_vector)
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:231:3'): T3.1 No error when `bg_alpha` is a `numberic`. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─... %>% testthat::expect_error(NA) at test-add_highlight.R:231:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = "Placebo", bg_alpha = 0.2)
8. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo", bg_alpha = 0.2)
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Error ('test-add_highlight.R:314:3'): T4.1 The function adds the alpha channel to the hex-encoded colour. ──
Error in `FUN(X[[i]], ...)`: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "Placebo") at test-add_highlight.R:314:3
2. ├─visR::add_highlight(., strata = "Placebo")
3. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo")
4. └─base::sapply(...)
5. └─base::lapply(X = X, FUN = FUN, ...)
6. └─visR (local) FUN(X[[i]], ...)
── Error ('test-add_highlight.R:339:3'): T4.2 The function also reduces the alpha value of the confidence intervals introduced by `add_CI`. ──
Error in `FUN(X[[i]], ...)`: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "Placebo", bg_alpha = bg_alpha) at test-add_highlight.R:339:3
2. ├─visR::add_highlight(., strata = "Placebo", bg_alpha = bg_alpha)
3. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo", bg_alpha = bg_alpha)
4. └─base::sapply(...)
5. └─base::lapply(X = X, FUN = FUN, ...)
6. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-apply_theme.R:539:3'): T1.19 The named list is used in the legend title. ──
get_legend_title(gg) not equal to "SEX".
target is NULL, current is character
── Failure ('test-apply_theme.R:559:3'): T1.19 The named list is used in the legend title. ──
get_legend_title(gg) not equal to "Sex, ph.ecog".
target is NULL, current is character
── Failure ('test-utils_visR.R:109:3'): T2.1 Columns are added to the grob-converted plot. ──
dim(grob_orig)[2] == dim(pltlist[[2]])[2] is not FALSE
`actual`: TRUE
`expected`: FALSE
[ FAIL 12 | WARN 28 | SKIP 27 | PASS 988 ]
Error: Test failures
In addition: Warning message:
In for (i in seq_len(n)) { :
closing unused connection 4 (https://raw.githubusercontent.com/vntkumar8/covid-survival/main/data/final.csv)
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.4.0
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/1s]
Running ‘testthat.R’ [180s/202s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(visR)
> library(vdiffr)
> library(survival)
>
> test_check("visR")
[ FAIL 12 | WARN 28 | SKIP 27 | PASS 988 ]
══ Skipped tests (27) ══════════════════════════════════════════════════════════
• On CRAN (27): 'test-add_CI.R:30:3', 'test-add_CI.R:45:3',
'test-add_CI.R:65:3', 'test-add_CI.R:95:3', 'test-add_CI.R:124:3',
'test-add_CI.R:144:3', 'test-add_CNSR.R:34:3', 'test-add_CNSR.R:47:3',
'test-add_CNSR.R:60:3', 'test-add_CNSR.R:78:3', 'test-add_CNSR.R:95:3',
'test-add_CNSR.R:112:3', 'test-add_highlight.R:107:3',
'test-add_highlight.R:151:3', 'test-add_highlight.R:281:3',
'test-add_risktable.R:81:3', 'test-add_risktable.R:93:3',
'test-add_risktable.R:204:3', 'test-add_risktable.R:214:3',
'test-stat_stepribbon.R:32:3', 'test-stat_stepribbon.R:60:3',
'test-stat_stepribbon.R:94:3', 'test-stat_stepribbon.R:117:3',
'test-utils_visR.R:135:3', 'test-utils_visR.R:146:3',
'test-visr_survfit.R:528:3', 'test-watchdog_testfiles.R:14:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-add_highlight.R:41:3'): T1.1 No error when `add_highlight` is called on a `ggsurvfit` object. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "Placebo") %>% ... at test-add_highlight.R:41:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = "Placebo")
8. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo")
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Error ('test-add_highlight.R:87:3'): T1.5 The function returns a modified object of type `ggsurvfit`. ──
Error in `FUN(X[[i]], ...)`: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Backtrace:
▆
1. ├─gg %>% add_highlight("Placebo") at test-add_highlight.R:87:3
2. ├─visR::add_highlight(., "Placebo")
3. └─visR:::add_highlight.ggsurvfit(., "Placebo")
4. └─base::sapply(...)
5. └─base::lapply(X = X, FUN = FUN, ...)
6. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:103:3'): T2.1 No error when `strata` is a character string found in the plot strata. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "Placebo") %>% ... at test-add_highlight.R:103:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = "Placebo")
8. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo")
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:120:3'): T2.2 An error when `strata` is a character string not found in the plot strata. ──
`.` threw an error with unexpected message.
Expected match: "The strata you specified has not been found in the provided plot.\n Available strata: Placebo, Xanomeline High Dose, Xanomeline Low Dose\n Please adjust and rerun."
Actual message: "The strata you specified has not been found in the provided plot.\n Available strata: NULL, NULL, NULL\n Please adjust and rerun."
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "visR") %>% ... at test-add_highlight.R:120:3
2. ├─testthat::expect_error(., expected_error)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = "visR")
8. └─visR:::add_highlight.ggsurvfit(., strata = "visR")
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:143:3'): T2.4 No error when `strata` is a `list` or `vector` of character strings found in the plot strata. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = strata_list) %>% ... at test-add_highlight.R:143:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = strata_list)
8. └─visR:::add_highlight.ggsurvfit(., strata = strata_list)
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:147:3'): T2.4 No error when `strata` is a `list` or `vector` of character strings found in the plot strata. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = strata_vector) %>% ... at test-add_highlight.R:147:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = strata_vector)
8. └─visR:::add_highlight.ggsurvfit(., strata = strata_vector)
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:231:3'): T3.1 No error when `bg_alpha` is a `numberic`. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─... %>% testthat::expect_error(NA) at test-add_highlight.R:231:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = "Placebo", bg_alpha = 0.2)
8. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo", bg_alpha = 0.2)
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Error ('test-add_highlight.R:314:3'): T4.1 The function adds the alpha channel to the hex-encoded colour. ──
Error in `FUN(X[[i]], ...)`: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "Placebo") at test-add_highlight.R:314:3
2. ├─visR::add_highlight(., strata = "Placebo")
3. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo")
4. └─base::sapply(...)
5. └─base::lapply(X = X, FUN = FUN, ...)
6. └─visR (local) FUN(X[[i]], ...)
── Error ('test-add_highlight.R:339:3'): T4.2 The function also reduces the alpha value of the confidence intervals introduced by `add_CI`. ──
Error in `FUN(X[[i]], ...)`: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "Placebo", bg_alpha = bg_alpha) at test-add_highlight.R:339:3
2. ├─visR::add_highlight(., strata = "Placebo", bg_alpha = bg_alpha)
3. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo", bg_alpha = bg_alpha)
4. └─base::sapply(...)
5. └─base::lapply(X = X, FUN = FUN, ...)
6. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-apply_theme.R:539:3'): T1.19 The named list is used in the legend title. ──
get_legend_title(gg) not equal to "SEX".
target is NULL, current is character
── Failure ('test-apply_theme.R:559:3'): T1.19 The named list is used in the legend title. ──
get_legend_title(gg) not equal to "Sex, ph.ecog".
target is NULL, current is character
── Failure ('test-utils_visR.R:109:3'): T2.1 Columns are added to the grob-converted plot. ──
dim(grob_orig)[2] == dim(pltlist[[2]])[2] is not FALSE
`actual`: TRUE
`expected`: FALSE
[ FAIL 12 | WARN 28 | SKIP 27 | PASS 988 ]
Error: Test failures
In addition: Warning message:
In for (i in seq_along(quosures)) { :
closing unused connection 4 (https://raw.githubusercontent.com/vntkumar8/covid-survival/main/data/final.csv)
Execution halted
Flavor: r-release-linux-x86_64
Version: 0.4.0
Check: tests
Result: ERROR
Running 'spelling.R' [0s]
Running 'testthat.R' [157s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(visR)
> library(vdiffr)
> library(survival)
>
> test_check("visR")
[ FAIL 12 | WARN 28 | SKIP 27 | PASS 988 ]
══ Skipped tests (27) ══════════════════════════════════════════════════════════
• On CRAN (27): 'test-add_CI.R:30:3', 'test-add_CI.R:45:3',
'test-add_CI.R:65:3', 'test-add_CI.R:95:3', 'test-add_CI.R:124:3',
'test-add_CI.R:144:3', 'test-add_CNSR.R:34:3', 'test-add_CNSR.R:47:3',
'test-add_CNSR.R:60:3', 'test-add_CNSR.R:78:3', 'test-add_CNSR.R:95:3',
'test-add_CNSR.R:112:3', 'test-add_highlight.R:107:3',
'test-add_highlight.R:151:3', 'test-add_highlight.R:281:3',
'test-add_risktable.R:81:3', 'test-add_risktable.R:93:3',
'test-add_risktable.R:204:3', 'test-add_risktable.R:214:3',
'test-stat_stepribbon.R:32:3', 'test-stat_stepribbon.R:60:3',
'test-stat_stepribbon.R:94:3', 'test-stat_stepribbon.R:117:3',
'test-utils_visR.R:135:3', 'test-utils_visR.R:146:3',
'test-visr_survfit.R:528:3', 'test-watchdog_testfiles.R:14:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-add_highlight.R:41:3'): T1.1 No error when `add_highlight` is called on a `ggsurvfit` object. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "Placebo") %>% ... at test-add_highlight.R:41:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = "Placebo")
8. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo")
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Error ('test-add_highlight.R:87:3'): T1.5 The function returns a modified object of type `ggsurvfit`. ──
Error in `FUN(X[[i]], ...)`: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Backtrace:
▆
1. ├─gg %>% add_highlight("Placebo") at test-add_highlight.R:87:3
2. ├─visR::add_highlight(., "Placebo")
3. └─visR:::add_highlight.ggsurvfit(., "Placebo")
4. └─base::sapply(...)
5. └─base::lapply(X = X, FUN = FUN, ...)
6. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:103:3'): T2.1 No error when `strata` is a character string found in the plot strata. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "Placebo") %>% ... at test-add_highlight.R:103:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = "Placebo")
8. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo")
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:120:3'): T2.2 An error when `strata` is a character string not found in the plot strata. ──
`.` threw an error with unexpected message.
Expected match: "The strata you specified has not been found in the provided plot.\n Available strata: Placebo, Xanomeline High Dose, Xanomeline Low Dose\n Please adjust and rerun."
Actual message: "The strata you specified has not been found in the provided plot.\n Available strata: NULL, NULL, NULL\n Please adjust and rerun."
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "visR") %>% ... at test-add_highlight.R:120:3
2. ├─testthat::expect_error(., expected_error)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = "visR")
8. └─visR:::add_highlight.ggsurvfit(., strata = "visR")
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:143:3'): T2.4 No error when `strata` is a `list` or `vector` of character strings found in the plot strata. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = strata_list) %>% ... at test-add_highlight.R:143:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = strata_list)
8. └─visR:::add_highlight.ggsurvfit(., strata = strata_list)
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:147:3'): T2.4 No error when `strata` is a `list` or `vector` of character strings found in the plot strata. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = strata_vector) %>% ... at test-add_highlight.R:147:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = strata_vector)
8. └─visR:::add_highlight.ggsurvfit(., strata = strata_vector)
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:231:3'): T3.1 No error when `bg_alpha` is a `numberic`. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─... %>% testthat::expect_error(NA) at test-add_highlight.R:231:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = "Placebo", bg_alpha = 0.2)
8. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo", bg_alpha = 0.2)
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Error ('test-add_highlight.R:314:3'): T4.1 The function adds the alpha channel to the hex-encoded colour. ──
Error in `FUN(X[[i]], ...)`: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "Placebo") at test-add_highlight.R:314:3
2. ├─visR::add_highlight(., strata = "Placebo")
3. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo")
4. └─base::sapply(...)
5. └─base::lapply(X = X, FUN = FUN, ...)
6. └─visR (local) FUN(X[[i]], ...)
── Error ('test-add_highlight.R:339:3'): T4.2 The function also reduces the alpha value of the confidence intervals introduced by `add_CI`. ──
Error in `FUN(X[[i]], ...)`: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "Placebo", bg_alpha = bg_alpha) at test-add_highlight.R:339:3
2. ├─visR::add_highlight(., strata = "Placebo", bg_alpha = bg_alpha)
3. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo", bg_alpha = bg_alpha)
4. └─base::sapply(...)
5. └─base::lapply(X = X, FUN = FUN, ...)
6. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-apply_theme.R:539:3'): T1.19 The named list is used in the legend title. ──
get_legend_title(gg) not equal to "SEX".
target is NULL, current is character
── Failure ('test-apply_theme.R:559:3'): T1.19 The named list is used in the legend title. ──
get_legend_title(gg) not equal to "Sex, ph.ecog".
target is NULL, current is character
── Failure ('test-utils_visR.R:109:3'): T2.1 Columns are added to the grob-converted plot. ──
dim(grob_orig)[2] == dim(pltlist[[2]])[2] is not FALSE
`actual`: TRUE
`expected`: FALSE
[ FAIL 12 | WARN 28 | SKIP 27 | PASS 988 ]
Error: Test failures
In addition: Warning message:
In .Call(ffi_env_bind, env = .env, values = exprs(...), needs_old = TRUE, :
closing unused connection 4 (https://raw.githubusercontent.com/vntkumar8/covid-survival/main/data/final.csv)
Execution halted
Flavor: r-release-windows-x86_64
Version: 0.4.0
Check: tests
Result: ERROR
Running 'spelling.R' [0s]
Running 'testthat.R' [162s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(visR)
> library(vdiffr)
> library(survival)
>
> test_check("visR")
[ FAIL 12 | WARN 28 | SKIP 27 | PASS 988 ]
══ Skipped tests (27) ══════════════════════════════════════════════════════════
• On CRAN (27): 'test-add_CI.R:30:3', 'test-add_CI.R:45:3',
'test-add_CI.R:65:3', 'test-add_CI.R:95:3', 'test-add_CI.R:124:3',
'test-add_CI.R:144:3', 'test-add_CNSR.R:34:3', 'test-add_CNSR.R:47:3',
'test-add_CNSR.R:60:3', 'test-add_CNSR.R:78:3', 'test-add_CNSR.R:95:3',
'test-add_CNSR.R:112:3', 'test-add_highlight.R:107:3',
'test-add_highlight.R:151:3', 'test-add_highlight.R:281:3',
'test-add_risktable.R:81:3', 'test-add_risktable.R:93:3',
'test-add_risktable.R:204:3', 'test-add_risktable.R:214:3',
'test-stat_stepribbon.R:32:3', 'test-stat_stepribbon.R:60:3',
'test-stat_stepribbon.R:94:3', 'test-stat_stepribbon.R:117:3',
'test-utils_visR.R:135:3', 'test-utils_visR.R:146:3',
'test-visr_survfit.R:528:3', 'test-watchdog_testfiles.R:14:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-add_highlight.R:41:3'): T1.1 No error when `add_highlight` is called on a `ggsurvfit` object. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "Placebo") %>% ... at test-add_highlight.R:41:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = "Placebo")
8. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo")
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Error ('test-add_highlight.R:87:3'): T1.5 The function returns a modified object of type `ggsurvfit`. ──
Error in `FUN(X[[i]], ...)`: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Backtrace:
▆
1. ├─gg %>% add_highlight("Placebo") at test-add_highlight.R:87:3
2. ├─visR::add_highlight(., "Placebo")
3. └─visR:::add_highlight.ggsurvfit(., "Placebo")
4. └─base::sapply(...)
5. └─base::lapply(X = X, FUN = FUN, ...)
6. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:103:3'): T2.1 No error when `strata` is a character string found in the plot strata. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "Placebo") %>% ... at test-add_highlight.R:103:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = "Placebo")
8. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo")
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:120:3'): T2.2 An error when `strata` is a character string not found in the plot strata. ──
`.` threw an error with unexpected message.
Expected match: "The strata you specified has not been found in the provided plot.\n Available strata: Placebo, Xanomeline High Dose, Xanomeline Low Dose\n Please adjust and rerun."
Actual message: "The strata you specified has not been found in the provided plot.\n Available strata: NULL, NULL, NULL\n Please adjust and rerun."
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "visR") %>% ... at test-add_highlight.R:120:3
2. ├─testthat::expect_error(., expected_error)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = "visR")
8. └─visR:::add_highlight.ggsurvfit(., strata = "visR")
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:143:3'): T2.4 No error when `strata` is a `list` or `vector` of character strings found in the plot strata. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = strata_list) %>% ... at test-add_highlight.R:143:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = strata_list)
8. └─visR:::add_highlight.ggsurvfit(., strata = strata_list)
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:147:3'): T2.4 No error when `strata` is a `list` or `vector` of character strings found in the plot strata. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = strata_vector) %>% ... at test-add_highlight.R:147:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = strata_vector)
8. └─visR:::add_highlight.ggsurvfit(., strata = strata_vector)
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-add_highlight.R:231:3'): T3.1 No error when `bg_alpha` is a `numberic`. ──
`.` threw an error.
Message: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Class: simpleError/error/condition
Backtrace:
▆
1. ├─... %>% testthat::expect_error(NA) at test-add_highlight.R:231:3
2. ├─testthat::expect_error(., NA)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─visR::add_highlight(., strata = "Placebo", bg_alpha = 0.2)
8. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo", bg_alpha = 0.2)
9. └─base::sapply(...)
10. └─base::lapply(X = X, FUN = FUN, ...)
11. └─visR (local) FUN(X[[i]], ...)
── Error ('test-add_highlight.R:314:3'): T4.1 The function adds the alpha channel to the hex-encoded colour. ──
Error in `FUN(X[[i]], ...)`: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "Placebo") at test-add_highlight.R:314:3
2. ├─visR::add_highlight(., strata = "Placebo")
3. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo")
4. └─base::sapply(...)
5. └─base::lapply(X = X, FUN = FUN, ...)
6. └─visR (local) FUN(X[[i]], ...)
── Error ('test-add_highlight.R:339:3'): T4.2 The function also reduces the alpha value of the confidence intervals introduced by `add_CI`. ──
Error in `FUN(X[[i]], ...)`: The strata you specified has not been found in the provided plot.
Available strata: NULL, NULL, NULL
Please adjust and rerun.
Backtrace:
▆
1. ├─gg %>% visR::add_highlight(strata = "Placebo", bg_alpha = bg_alpha) at test-add_highlight.R:339:3
2. ├─visR::add_highlight(., strata = "Placebo", bg_alpha = bg_alpha)
3. └─visR:::add_highlight.ggsurvfit(., strata = "Placebo", bg_alpha = bg_alpha)
4. └─base::sapply(...)
5. └─base::lapply(X = X, FUN = FUN, ...)
6. └─visR (local) FUN(X[[i]], ...)
── Failure ('test-apply_theme.R:539:3'): T1.19 The named list is used in the legend title. ──
get_legend_title(gg) not equal to "SEX".
target is NULL, current is character
── Failure ('test-apply_theme.R:559:3'): T1.19 The named list is used in the legend title. ──
get_legend_title(gg) not equal to "Sex, ph.ecog".
target is NULL, current is character
── Failure ('test-utils_visR.R:109:3'): T2.1 Columns are added to the grob-converted plot. ──
dim(grob_orig)[2] == dim(pltlist[[2]])[2] is not FALSE
`actual`: TRUE
`expected`: FALSE
[ FAIL 12 | WARN 28 | SKIP 27 | PASS 988 ]
Error: Test failures
In addition: Warning message:
closing unused connection 4 (https://raw.githubusercontent.com/vntkumar8/covid-survival/main/data/final.csv)
Execution halted
Flavor: r-oldrel-windows-x86_64