Last updated on 2024-07-26 08:51:10 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.0.0 | 11.85 | 139.13 | 150.98 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.0.0 | 10.06 | 90.43 | 100.49 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 1.0.0 | 171.07 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.0.0 | 183.61 | OK | |||
| r-devel-windows-x86_64 | 1.0.0 | 12.00 | 114.00 | 126.00 | OK | |
| r-patched-linux-x86_64 | 1.0.0 | ERROR | ||||
| r-release-linux-x86_64 | 1.0.0 | 9.10 | 134.38 | 143.48 | OK | |
| r-release-macos-arm64 | 1.0.0 | 54.00 | OK | |||
| r-release-macos-x86_64 | 1.0.0 | 79.00 | OK | |||
| r-release-windows-x86_64 | 1.0.0 | 13.00 | 114.00 | 127.00 | OK | |
| r-oldrel-macos-arm64 | 1.0.0 | 87.00 | OK | |||
| r-oldrel-macos-x86_64 | 1.0.0 | 114.00 | OK | |||
| r-oldrel-windows-x86_64 | 1.0.0 | 14.00 | 123.00 | 137.00 | ERROR |
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/1s]
Running ‘testthat.R’ [13s/21s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(tidycmprsk)
>
> test_check("tidycmprsk")
11 cases omitted due to missing values
-- crr() -----------------------------------------------------------------------
* Call Surv(ttdeath, death_cr) ~ age
* Failure type of interest "death from cancer"
Variable Coef SE HR 95% CI p-value
age 0.006 0.010 1.01 0.99, 1.03 0.55
11 cases omitted due to missing values
11 cases omitted due to missing values
11 cases omitted due to missing values
11 cases omitted due to missing values
11 cases omitted due to missing values
x There was an error evaluating the LHS of the formula.
-- cuminc() --------------------------------------------------------------------
* Failure type "death from cancer"
strata time n.risk estimate std.error 95% CI
Drug A 5.00 97 0.000 0.000 NA, NA
Drug A 10.0 94 0.020 0.014 0.004, 0.065
Drug A 15.0 83 0.071 0.026 0.031, 0.134
Drug A 20.0 61 0.173 0.039 0.106, 0.255
Drug B 5.00 102 0.000 0.000 NA, NA
Drug B 10.0 95 0.039 0.019 0.013, 0.090
Drug B 15.0 75 0.167 0.037 0.102, 0.246
Drug B 20.0 55 0.255 0.043 0.175, 0.343
* Failure type "death other causes"
strata time n.risk estimate std.error 95% CI
Drug A 5.00 97 0.010 0.010 0.001, 0.050
Drug A 10.0 94 0.020 0.014 0.004, 0.065
Drug A 15.0 83 0.082 0.028 0.038, 0.147
Drug A 20.0 61 0.204 0.041 0.131, 0.289
Drug B 5.00 102 0.000 0.000 NA, NA
Drug B 10.0 95 0.029 0.017 0.008, 0.077
Drug B 15.0 75 0.098 0.030 0.050, 0.165
Drug B 20.0 55 0.206 0.040 0.133, 0.289
* Tests
outcome statistic df p.value
death from cancer 1.99 1.00 0.16
death other causes 0.089 1.00 0.77
Attaching package: 'dplyr'
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
[ FAIL 6 | WARN 0 | SKIP 1 | PASS 92 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test-tbl_cuminc.R:30:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-gtsummary.R:2:3'): gtsummary tables work with crr() output ───
`crr(Surv(ttdeath, death_cr) ~ age + trt, trial) %>% gtsummary::tbl_regression()` threw an unexpected error.
Message: The package "broom.helpers" (>= 1.15.0) is required.
Class: rlib_error_package_not_found/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-gtsummary.R:2:3
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─crr(Surv(ttdeath, death_cr) ~ age + trt, trial) %>% ...
8. └─gtsummary::tbl_regression(.)
9. └─gtsummary:::check_pkg_installed(...)
10. ├─base::suppressWarnings(...)
11. │ └─base::withCallingHandlers(...)
12. └─rlang::check_installed(...)
── Failure ('test-gtsummary.R:7:3'): gtsummary tables work with crr() output ───
``%>%`(...)` threw an unexpected error.
Message: The package "broom.helpers" (>= 1.15.0) is required.
Class: rlib_error_package_not_found/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-gtsummary.R:7:3
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─... %>% gtsummary::tbl_regression()
8. └─gtsummary::tbl_regression(.)
9. └─gtsummary:::check_pkg_installed(...)
10. ├─base::suppressWarnings(...)
11. │ └─base::withCallingHandlers(...)
12. └─rlang::check_installed(...)
── Failure ('test-gtsummary.R:12:3'): gtsummary tables work with crr() output ──
`crr(Surv(ttdeath, death_cr) ~ age, trial) %>% gtsummary::tbl_regression()` threw an unexpected error.
Message: The package "broom.helpers" (>= 1.15.0) is required.
Class: rlib_error_package_not_found/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-gtsummary.R:12:3
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─crr(Surv(ttdeath, death_cr) ~ age, trial) %>% gtsummary::tbl_regression()
8. └─gtsummary::tbl_regression(.)
9. └─gtsummary:::check_pkg_installed(...)
10. ├─base::suppressWarnings(...)
11. │ └─base::withCallingHandlers(...)
12. └─rlang::check_installed(...)
── Failure ('test-gtsummary.R:17:3'): gtsummary tables work with crr() output ──
`crr(Surv(ttdeath, death_cr) ~ trt, trial) %>% gtsummary::tbl_regression()` threw an unexpected error.
Message: The package "broom.helpers" (>= 1.15.0) is required.
Class: rlib_error_package_not_found/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-gtsummary.R:17:3
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─crr(Surv(ttdeath, death_cr) ~ trt, trial) %>% gtsummary::tbl_regression()
8. └─gtsummary::tbl_regression(.)
9. └─gtsummary:::check_pkg_installed(...)
10. ├─base::suppressWarnings(...)
11. │ └─base::withCallingHandlers(...)
12. └─rlang::check_installed(...)
── Failure ('test-gtsummary.R:29:3'): gtsummary tables work with crr() output ──
`... <- NULL` threw an unexpected error.
Message: The package "broom.helpers" (>= 1.15.0) is required.
Class: rlib_error_package_not_found/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-gtsummary.R:29:3
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─crr(Surv(ttdeath, death_cr) ~ grade, trial_contr) %>% ...
8. └─gtsummary::tbl_regression(.)
9. └─gtsummary:::check_pkg_installed(...)
10. ├─base::suppressWarnings(...)
11. │ └─base::withCallingHandlers(...)
12. └─rlang::check_installed(...)
── Error ('test-gtsummary.R:35:3'): gtsummary tables work with crr() output ────
Error in `eval(code, test_env)`: object 'contr_sum' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-gtsummary.R:35:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─base::unique(contr_sum$table_body$contrasts_type)
[ FAIL 6 | WARN 0 | SKIP 1 | PASS 92 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘spelling.R’
Running ‘testthat.R’ [22s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(tidycmprsk)
>
> test_check("tidycmprsk")
11 cases omitted due to missing values
-- crr() -----------------------------------------------------------------------
* Call Surv(ttdeath, death_cr) ~ age
* Failure type of interest "death from cancer"
Variable Coef SE HR 95% CI p-value
age 0.006 0.010 1.01 0.99, 1.03 0.55
11 cases omitted due to missing values
11 cases omitted due to missing values
11 cases omitted due to missing values
11 cases omitted due to missing values
11 cases omitted due to missing values
x There was an error evaluating the LHS of the formula.
-- cuminc() --------------------------------------------------------------------
* Failure type "death from cancer"
strata time n.risk estimate std.error 95% CI
Drug A 5.00 97 0.000 0.000 NA, NA
Drug A 10.0 94 0.020 0.014 0.004, 0.065
Drug A 15.0 83 0.071 0.026 0.031, 0.134
Drug A 20.0 61 0.173 0.039 0.106, 0.255
Drug B 5.00 102 0.000 0.000 NA, NA
Drug B 10.0 95 0.039 0.019 0.013, 0.090
Drug B 15.0 75 0.167 0.037 0.102, 0.246
Drug B 20.0 55 0.255 0.043 0.175, 0.343
* Failure type "death other causes"
strata time n.risk estimate std.error 95% CI
Drug A 5.00 97 0.010 0.010 0.001, 0.050
Drug A 10.0 94 0.020 0.014 0.004, 0.065
Drug A 15.0 83 0.082 0.028 0.038, 0.147
Drug A 20.0 61 0.204 0.041 0.131, 0.289
Drug B 5.00 102 0.000 0.000 NA, NA
Drug B 10.0 95 0.029 0.017 0.008, 0.077
Drug B 15.0 75 0.098 0.030 0.050, 0.165
Drug B 20.0 55 0.206 0.040 0.133, 0.289
* Tests
outcome statistic df p.value
death from cancer 1.99 1.00 0.16
death other causes 0.089 1.00 0.77
Attaching package: 'dplyr'
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
[ FAIL 6 | WARN 0 | SKIP 1 | PASS 92 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test-tbl_cuminc.R:30:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-gtsummary.R:2:3'): gtsummary tables work with crr() output ───
`crr(Surv(ttdeath, death_cr) ~ age + trt, trial) %>% gtsummary::tbl_regression()` threw an unexpected error.
Message: The package "broom.helpers" (>= 1.15.0) is required.
Class: rlib_error_package_not_found/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-gtsummary.R:2:3
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─crr(Surv(ttdeath, death_cr) ~ age + trt, trial) %>% ...
8. └─gtsummary::tbl_regression(.)
9. └─gtsummary:::check_pkg_installed(...)
10. ├─base::suppressWarnings(...)
11. │ └─base::withCallingHandlers(...)
12. └─rlang::check_installed(...)
── Failure ('test-gtsummary.R:7:3'): gtsummary tables work with crr() output ───
``%>%`(...)` threw an unexpected error.
Message: The package "broom.helpers" (>= 1.15.0) is required.
Class: rlib_error_package_not_found/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-gtsummary.R:7:3
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─... %>% gtsummary::tbl_regression()
8. └─gtsummary::tbl_regression(.)
9. └─gtsummary:::check_pkg_installed(...)
10. ├─base::suppressWarnings(...)
11. │ └─base::withCallingHandlers(...)
12. └─rlang::check_installed(...)
── Failure ('test-gtsummary.R:12:3'): gtsummary tables work with crr() output ──
`crr(Surv(ttdeath, death_cr) ~ age, trial) %>% gtsummary::tbl_regression()` threw an unexpected error.
Message: The package "broom.helpers" (>= 1.15.0) is required.
Class: rlib_error_package_not_found/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-gtsummary.R:12:3
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─crr(Surv(ttdeath, death_cr) ~ age, trial) %>% gtsummary::tbl_regression()
8. └─gtsummary::tbl_regression(.)
9. └─gtsummary:::check_pkg_installed(...)
10. ├─base::suppressWarnings(...)
11. │ └─base::withCallingHandlers(...)
12. └─rlang::check_installed(...)
── Failure ('test-gtsummary.R:17:3'): gtsummary tables work with crr() output ──
`crr(Surv(ttdeath, death_cr) ~ trt, trial) %>% gtsummary::tbl_regression()` threw an unexpected error.
Message: The package "broom.helpers" (>= 1.15.0) is required.
Class: rlib_error_package_not_found/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-gtsummary.R:17:3
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─crr(Surv(ttdeath, death_cr) ~ trt, trial) %>% gtsummary::tbl_regression()
8. └─gtsummary::tbl_regression(.)
9. └─gtsummary:::check_pkg_installed(...)
10. ├─base::suppressWarnings(...)
11. │ └─base::withCallingHandlers(...)
12. └─rlang::check_installed(...)
── Failure ('test-gtsummary.R:29:3'): gtsummary tables work with crr() output ──
`... <- NULL` threw an unexpected error.
Message: The package "broom.helpers" (>= 1.15.0) is required.
Class: rlib_error_package_not_found/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-gtsummary.R:29:3
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─crr(Surv(ttdeath, death_cr) ~ grade, trial_contr) %>% ...
8. └─gtsummary::tbl_regression(.)
9. └─gtsummary:::check_pkg_installed(...)
10. ├─base::suppressWarnings(...)
11. │ └─base::withCallingHandlers(...)
12. └─rlang::check_installed(...)
── Error ('test-gtsummary.R:35:3'): gtsummary tables work with crr() output ────
Error in `eval(code, test_env)`: object 'contr_sum' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-gtsummary.R:35:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─base::unique(contr_sum$table_body$contrasts_type)
[ FAIL 6 | WARN 0 | SKIP 1 | PASS 92 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.0.0
Check: tests
Result: ERROR
Running ‘spelling.R’ [0s/1s]
Running ‘testthat.R’ [17s/21s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(tidycmprsk)
>
> test_check("tidycmprsk")
11 cases omitted due to missing values
-- crr() -----------------------------------------------------------------------
* Call Surv(ttdeath, death_cr) ~ age
* Failure type of interest "death from cancer"
Variable Coef SE HR 95% CI p-value
age 0.006 0.010 1.01 0.99, 1.03 0.55
11 cases omitted due to missing values
11 cases omitted due to missing values
11 cases omitted due to missing values
11 cases omitted due to missing values
11 cases omitted due to missing values
x There was an error evaluating the LHS of the formula.
-- cuminc() --------------------------------------------------------------------
* Failure type "death from cancer"
strata time n.risk estimate std.error 95% CI
Drug A 5.00 97 0.000 0.000 NA, NA
Drug A 10.0 94 0.020 0.014 0.004, 0.065
Drug A 15.0 83 0.071 0.026 0.031, 0.134
Drug A 20.0 61 0.173 0.039 0.106, 0.255
Drug B 5.00 102 0.000 0.000 NA, NA
Drug B 10.0 95 0.039 0.019 0.013, 0.090
Drug B 15.0 75 0.167 0.037 0.102, 0.246
Drug B 20.0 55 0.255 0.043 0.175, 0.343
* Failure type "death other causes"
strata time n.risk estimate std.error 95% CI
Drug A 5.00 97 0.010 0.010 0.001, 0.050
Drug A 10.0 94 0.020 0.014 0.004, 0.065
Drug A 15.0 83 0.082 0.028 0.038, 0.147
Drug A 20.0 61 0.204 0.041 0.131, 0.289
Drug B 5.00 102 0.000 0.000 NA, NA
Drug B 10.0 95 0.029 0.017 0.008, 0.077
Drug B 15.0 75 0.098 0.030 0.050, 0.165
Drug B 20.0 55 0.206 0.040 0.133, 0.289
* Tests
outcome statistic df p.value
death from cancer 1.99 1.00 0.16
death other causes 0.089 1.00 0.77
Attaching package: 'dplyr'
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
[ FAIL 6 | WARN 0 | SKIP 1 | PASS 92 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test-tbl_cuminc.R:30:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-gtsummary.R:2:3'): gtsummary tables work with crr() output ───
`crr(Surv(ttdeath, death_cr) ~ age + trt, trial) %>% gtsummary::tbl_regression()` threw an unexpected error.
Message: The package "broom.helpers" (>= 1.15.0) is required.
Class: rlib_error_package_not_found/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-gtsummary.R:2:3
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─crr(Surv(ttdeath, death_cr) ~ age + trt, trial) %>% ...
8. └─gtsummary::tbl_regression(.)
9. └─gtsummary:::check_pkg_installed(...)
10. ├─base::suppressWarnings(...)
11. │ └─base::withCallingHandlers(...)
12. └─rlang::check_installed(...)
── Failure ('test-gtsummary.R:7:3'): gtsummary tables work with crr() output ───
``%>%`(...)` threw an unexpected error.
Message: The package "broom.helpers" (>= 1.15.0) is required.
Class: rlib_error_package_not_found/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-gtsummary.R:7:3
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─... %>% gtsummary::tbl_regression()
8. └─gtsummary::tbl_regression(.)
9. └─gtsummary:::check_pkg_installed(...)
10. ├─base::suppressWarnings(...)
11. │ └─base::withCallingHandlers(...)
12. └─rlang::check_installed(...)
── Failure ('test-gtsummary.R:12:3'): gtsummary tables work with crr() output ──
`crr(Surv(ttdeath, death_cr) ~ age, trial) %>% gtsummary::tbl_regression()` threw an unexpected error.
Message: The package "broom.helpers" (>= 1.15.0) is required.
Class: rlib_error_package_not_found/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-gtsummary.R:12:3
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─crr(Surv(ttdeath, death_cr) ~ age, trial) %>% gtsummary::tbl_regression()
8. └─gtsummary::tbl_regression(.)
9. └─gtsummary:::check_pkg_installed(...)
10. ├─base::suppressWarnings(...)
11. │ └─base::withCallingHandlers(...)
12. └─rlang::check_installed(...)
── Failure ('test-gtsummary.R:17:3'): gtsummary tables work with crr() output ──
`crr(Surv(ttdeath, death_cr) ~ trt, trial) %>% gtsummary::tbl_regression()` threw an unexpected error.
Message: The package "broom.helpers" (>= 1.15.0) is required.
Class: rlib_error_package_not_found/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-gtsummary.R:17:3
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─crr(Surv(ttdeath, death_cr) ~ trt, trial) %>% gtsummary::tbl_regression()
8. └─gtsummary::tbl_regression(.)
9. └─gtsummary:::check_pkg_installed(...)
10. ├─base::suppressWarnings(...)
11. │ └─base::withCallingHandlers(...)
12. └─rlang::check_installed(...)
── Failure ('test-gtsummary.R:29:3'): gtsummary tables work with crr() output ──
`... <- NULL` threw an unexpected error.
Message: The package "broom.helpers" (>= 1.15.0) is required.
Class: rlib_error_package_not_found/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-gtsummary.R:29:3
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─crr(Surv(ttdeath, death_cr) ~ grade, trial_contr) %>% ...
8. └─gtsummary::tbl_regression(.)
9. └─gtsummary:::check_pkg_installed(...)
10. ├─base::suppressWarnings(...)
11. │ └─base::withCallingHandlers(...)
12. └─rlang::check_installed(...)
── Error ('test-gtsummary.R:35:3'): gtsummary tables work with crr() output ────
Error in `eval(code, test_env)`: object 'contr_sum' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-gtsummary.R:35:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─base::unique(contr_sum$table_body$contrasts_type)
[ FAIL 6 | WARN 0 | SKIP 1 | PASS 92 ]
Error: Test failures
Execution halted
Flavor: r-patched-linux-x86_64
Version: 1.0.0
Check: tests
Result: ERROR
Running 'spelling.R' [0s]
Running 'testthat.R' [16s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(tidycmprsk)
>
> test_check("tidycmprsk")
11 cases omitted due to missing values
-- crr() -----------------------------------------------------------------------
* Call Surv(ttdeath, death_cr) ~ age
* Failure type of interest "death from cancer"
Variable Coef SE HR 95% CI p-value
age 0.006 0.010 1.01 0.99, 1.03 0.55
11 cases omitted due to missing values
11 cases omitted due to missing values
11 cases omitted due to missing values
11 cases omitted due to missing values
11 cases omitted due to missing values
x There was an error evaluating the LHS of the formula.
-- cuminc() --------------------------------------------------------------------
* Failure type "death from cancer"
strata time n.risk estimate std.error 95% CI
Drug A 5.00 97 0.000 0.000 NA, NA
Drug A 10.0 94 0.020 0.014 0.004, 0.065
Drug A 15.0 83 0.071 0.026 0.031, 0.134
Drug A 20.0 61 0.173 0.039 0.106, 0.255
Drug B 5.00 102 0.000 0.000 NA, NA
Drug B 10.0 95 0.039 0.019 0.013, 0.090
Drug B 15.0 75 0.167 0.037 0.102, 0.246
Drug B 20.0 55 0.255 0.043 0.175, 0.343
* Failure type "death other causes"
strata time n.risk estimate std.error 95% CI
Drug A 5.00 97 0.010 0.010 0.001, 0.050
Drug A 10.0 94 0.020 0.014 0.004, 0.065
Drug A 15.0 83 0.082 0.028 0.038, 0.147
Drug A 20.0 61 0.204 0.041 0.131, 0.289
Drug B 5.00 102 0.000 0.000 NA, NA
Drug B 10.0 95 0.029 0.017 0.008, 0.077
Drug B 15.0 75 0.098 0.030 0.050, 0.165
Drug B 20.0 55 0.206 0.040 0.133, 0.289
* Tests
outcome statistic df p.value
death from cancer 1.99 1.00 0.16
death other causes 0.089 1.00 0.77
Attaching package: 'dplyr'
The following object is masked from 'package:testthat':
matches
The following objects are masked from 'package:stats':
filter, lag
The following objects are masked from 'package:base':
intersect, setdiff, setequal, union
[ FAIL 6 | WARN 0 | SKIP 1 | PASS 92 ]
══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On CRAN (1): 'test-tbl_cuminc.R:30:3'
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-gtsummary.R:2:3'): gtsummary tables work with crr() output ───
`crr(Surv(ttdeath, death_cr) ~ age + trt, trial) %>% gtsummary::tbl_regression()` threw an unexpected error.
Message: The package "broom.helpers" (>= 1.15.0) is required.
Class: rlib_error_package_not_found/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-gtsummary.R:2:3
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─crr(Surv(ttdeath, death_cr) ~ age + trt, trial) %>% ...
8. └─gtsummary::tbl_regression(.)
9. └─gtsummary:::check_pkg_installed(...)
10. ├─base::suppressWarnings(...)
11. │ └─base::withCallingHandlers(...)
12. └─rlang::check_installed(...)
── Failure ('test-gtsummary.R:7:3'): gtsummary tables work with crr() output ───
``%>%`(...)` threw an unexpected error.
Message: The package "broom.helpers" (>= 1.15.0) is required.
Class: rlib_error_package_not_found/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-gtsummary.R:7:3
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─... %>% gtsummary::tbl_regression()
8. └─gtsummary::tbl_regression(.)
9. └─gtsummary:::check_pkg_installed(...)
10. ├─base::suppressWarnings(...)
11. │ └─base::withCallingHandlers(...)
12. └─rlang::check_installed(...)
── Failure ('test-gtsummary.R:12:3'): gtsummary tables work with crr() output ──
`crr(Surv(ttdeath, death_cr) ~ age, trial) %>% gtsummary::tbl_regression()` threw an unexpected error.
Message: The package "broom.helpers" (>= 1.15.0) is required.
Class: rlib_error_package_not_found/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-gtsummary.R:12:3
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─crr(Surv(ttdeath, death_cr) ~ age, trial) %>% gtsummary::tbl_regression()
8. └─gtsummary::tbl_regression(.)
9. └─gtsummary:::check_pkg_installed(...)
10. ├─base::suppressWarnings(...)
11. │ └─base::withCallingHandlers(...)
12. └─rlang::check_installed(...)
── Failure ('test-gtsummary.R:17:3'): gtsummary tables work with crr() output ──
`crr(Surv(ttdeath, death_cr) ~ trt, trial) %>% gtsummary::tbl_regression()` threw an unexpected error.
Message: The package "broom.helpers" (>= 1.15.0) is required.
Class: rlib_error_package_not_found/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-gtsummary.R:17:3
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─crr(Surv(ttdeath, death_cr) ~ trt, trial) %>% gtsummary::tbl_regression()
8. └─gtsummary::tbl_regression(.)
9. └─gtsummary:::check_pkg_installed(...)
10. ├─base::suppressWarnings(...)
11. │ └─base::withCallingHandlers(...)
12. └─rlang::check_installed(...)
── Failure ('test-gtsummary.R:29:3'): gtsummary tables work with crr() output ──
`... <- NULL` threw an unexpected error.
Message: The package "broom.helpers" (>= 1.15.0) is required.
Class: rlib_error_package_not_found/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-gtsummary.R:29:3
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat (local) .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─crr(Surv(ttdeath, death_cr) ~ grade, trial_contr) %>% ...
8. └─gtsummary::tbl_regression(.)
9. └─gtsummary:::check_pkg_installed(...)
10. ├─base::suppressWarnings(...)
11. │ └─base::withCallingHandlers(...)
12. └─rlang::check_installed(...)
── Error ('test-gtsummary.R:35:3'): gtsummary tables work with crr() output ────
Error in `eval(code, test_env)`: object 'contr_sum' not found
Backtrace:
▆
1. ├─testthat::expect_equal(...) at test-gtsummary.R:35:3
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. └─base::unique(contr_sum$table_body$contrasts_type)
[ FAIL 6 | WARN 0 | SKIP 1 | PASS 92 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-windows-x86_64