Last updated on 2022-03-27 07:54:25 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.0.9 | 9.77 | 369.68 | 379.45 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.0.9 | 8.02 | 266.53 | 274.55 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.0.9 | 429.75 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.0.9 | 434.78 | ERROR | |||
| r-devel-windows-x86_64-new-UL | 0.0.9 | 31.00 | 443.00 | 474.00 | OK | |
| r-devel-windows-x86_64-new-TK | 0.0.9 | ERROR | ||||
| r-patched-linux-x86_64 | 0.0.9 | 7.54 | 342.99 | 350.53 | ERROR | |
| r-release-linux-x86_64 | 0.0.9 | 6.09 | 345.84 | 351.93 | ERROR | |
| r-release-macos-arm64 | 0.0.9 | OK | ||||
| r-release-macos-x86_64 | 0.0.9 | OK | ||||
| r-release-windows-ix86+x86_64 | 0.0.9 | 31.00 | 442.00 | 473.00 | OK | |
| r-oldrel-macos-x86_64 | 0.0.9 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 0.0.9 | 19.00 | 454.00 | 473.00 | OK |
Version: 0.0.9
Check: package dependencies
Result: NOTE
Package suggested but not available for checking: 'psychometric'
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.0.9
Check: examples
Result: ERROR
Running examples in 'aba-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: stat_ancova
> ### Title: Create an ancova stat object.
> ### Aliases: stat_ancova
>
> ### ** Examples
>
> # filter to 24 month visit; calculate change in cognition to use as outcome;
> # assume abeta status as "treatment" variable.
> # The goal is to see if "treatment" has an effect on 2y cognitive decline
> data <- adnimerge %>%
+ dplyr::filter(
+ VISCODE == 'm24',
+ DX_bl %in% c('MCI', 'AD'),
+ !is.na(CSF_ABETA_STATUS_bl)
+ ) %>%
+ dplyr::mutate(
+ CDRSB = CDRSB - CDRSB_bl,
+ ADAS13 = ADAS13 - ADAS13_bl,
+ TREATMENT = factor(CSF_ABETA_STATUS_bl, levels=c(1,0),
+ labels=c('Placebo','Treatment'))
+ )
>
> # fit model. note that baseline outcome will be added based on the suffix.
> # e.g., fits with "CDRSB" as outcome will also add "CDRSB_bl" to the formula.
> ancova_model <- data %>% aba_model() %>%
+ set_outcomes(CDRSB, ADAS13) %>%
+ set_covariates(AGE, GENDER, EDUCATION) %>%
+ set_stats(
+ stat_ancova(treatment = 'TREATMENT', baseline_suffix = 'bl')
+ ) %>%
+ fit()
>
> # summarise model. treatment effect will be shown in the treatment coefficient
> ancova_summary <- ancova_model %>% summary()
Error in `mutate()`:
! Problem while computing `metrics = purrr::map2(...)`.
Caused by error in `loadNamespace()`:
! there is no package called 'psychometric'
Backtrace:
x
1. +-ancova_model %>% summary()
2. +-base::summary(.)
3. +-aba:::summary.abaModel(.)
4. | \-object %>% aba_summary(...)
5. +-aba::aba_summary(., ...)
6. | \-object %>% calculate_metrics(control)
7. +-aba:::calculate_metrics(., control)
8. | \-r %>% ...
9. +-dplyr::mutate(...)
10. +-dplyr:::mutate.data.frame(...)
11. | \-dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
12. | +-base::withCallingHandlers(...)
13. | \-mask$eval_all_mutate(quo)
14. +-purrr::map2(...)
15. | \-aba .f(.x[[i]], .y[[i]], ...)
16. | +-... %>% mutate(term = tolower(term))
17. | +-aba:::aba_glance(model, basic_model)
18. | \-aba:::aba_glance.lm(model, basic_model)
19. +-dplyr::mutate(., term = tolower(term))
20. +-dplyr::arrange(., match(term, metric_vars))
21. +-dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
22. +-dplyr::filter(., term %in% metric_vars)
23. +-base::loadNamespace(x)
24. | +-base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
25. | | \-base withOneRestart(expr, restarts[[1L]])
26. | | \-base doWithOneRestart(return(expr), restart)
27. | \-base::stop(cond)
28. \-dplyr `<fn>`(`<pckgNtFE>`)
29. \-rlang::abort(...)
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.0.9
Check: tests
Result: ERROR
Running 'testthat.R' [164s/193s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> library(testthat)
> library(aba)
>
>
> test_check("aba")
Stratified by DX_bl
level Overall
n 2347 24
AGE (mean (SD)) 73.07 (7.43) 68.85 (8.30)
GENDER (mean (SD)) 0.53 (0.50) 0.38 (0.49)
EDUCATION (mean (SD)) 16.05 (2.75) 15.83 (2.16)
ConvertedToAlzheimers (mean (SD)) 0.20 (0.40) NaN (NA)
CSF_ABETA_STATUS_bl (mean (SD)) 0.62 (0.49) NaN (NA)
PLASMA_PTAU181_bl (mean (SD)) 2.71 (0.64) NaN (NA)
PLASMA_NFL_bl (mean (SD)) 3.54 (0.46) NaN (NA)
Stratified by DX_bl
AD CU MCI
n 405 846 1072
AGE (mean (SD)) 74.80 (7.92) 72.69 (6.34) 72.80 (7.89)
GENDER (mean (SD)) 0.57 (0.50) 0.44 (0.50) 0.59 (0.49)
EDUCATION (mean (SD)) 15.20 (2.91) 16.54 (2.53) 15.99 (2.78)
ConvertedToAlzheimers (mean (SD)) 0.00 (NA) 0.03 (0.18) 0.33 (0.47)
CSF_ABETA_STATUS_bl (mean (SD)) 0.88 (0.33) 0.39 (0.49) 0.63 (0.48)
PLASMA_PTAU181_bl (mean (SD)) 3.05 (0.41) 2.54 (0.67) 2.70 (0.64)
PLASMA_NFL_bl (mean (SD)) 3.77 (0.42) 3.45 (0.42) 3.52 (0.47)
Stratified by DX_bl
p test
n
AGE (mean (SD)) <0.001
GENDER (mean (SD)) <0.001
EDUCATION (mean (SD)) <0.001
ConvertedToAlzheimers (mean (SD)) NA
CSF_ABETA_STATUS_bl (mean (SD)) <0.001
PLASMA_PTAU181_bl (mean (SD)) <0.001
PLASMA_NFL_bl (mean (SD)) <0.001
[ FAIL 5 | WARN 0 | SKIP 2 | PASS 127 ]
== Skipped tests ===============================================================
* On CRAN (2)
== Failed tests ================================================================
-- Failure (test-stat_ancova.R:28:3): example works ----------------------------
`ancova_summary <- ancova_model %>% summary()` threw an unexpected error.
Message: Problem while computing `metrics = purrr::map2(...)`.
Caused by error in `loadNamespace()`:
! there is no package called 'psychometric'
Class: dplyr:::mutate_error/rlang_error/error/condition
Backtrace:
x
1. +-testthat::expect_error(...) at test-stat_ancova.R:28:2
2. | \-testthat:::expect_condition_matching(...)
3. | \-testthat:::quasi_capture(...)
4. | +-testthat .capture(...)
5. | | \-base::withCallingHandlers(...)
6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. +-ancova_model %>% summary()
8. +-base::summary(.)
9. +-aba:::summary.abaModel(.)
10. | \-object %>% aba_summary(...)
11. +-aba::aba_summary(., ...)
12. | \-object %>% calculate_metrics(control)
13. +-aba:::calculate_metrics(., control)
14. | \-r %>% ...
15. +-dplyr::mutate(...)
16. +-dplyr:::mutate.data.frame(...)
17. | \-dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
18. | +-base::withCallingHandlers(...)
19. | \-mask$eval_all_mutate(quo)
20. +-purrr::map2(...)
21. | \-aba .f(.x[[i]], .y[[i]], ...)
22. | +-... %>% mutate(term = tolower(term))
23. | +-aba:::aba_glance(model, basic_model)
24. | \-aba:::aba_glance.lm(model, basic_model)
25. +-dplyr::mutate(., term = tolower(term))
26. +-dplyr::arrange(., match(term, metric_vars))
27. +-dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
28. +-dplyr::filter(., term %in% metric_vars)
29. +-base::loadNamespace(x)
30. | +-base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
31. | | \-base withOneRestart(expr, restarts[[1L]])
32. | | \-base doWithOneRestart(return(expr), restart)
33. | \-base::stop(cond)
34. \-dplyr `<fn>`(`<pckgNtFE>`)
35. \-rlang::abort(...)
-- Failure (test-stat_lm.R:6:3): complete.cases=F for lm works -----------------
`... <- NULL` threw an unexpected error.
Message: Problem while computing `metrics = purrr::map2(...)`.
Caused by error in `loadNamespace()`:
! there is no package called 'psychometric'
Class: dplyr:::mutate_error/rlang_error/error/condition
Backtrace:
x
1. +-testthat::expect_error(...) at test-stat_lm.R:6:2
2. | \-testthat:::expect_condition_matching(...)
3. | \-testthat:::quasi_capture(...)
4. | +-testthat .capture(...)
5. | | \-base::withCallingHandlers(...)
6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. +-... %>% aba_summary()
8. +-aba::aba_summary(.)
9. | \-object %>% calculate_metrics(control)
10. +-aba:::calculate_metrics(., control)
11. | \-r %>% ...
12. +-dplyr::mutate(...)
13. +-dplyr:::mutate.data.frame(...)
14. | \-dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
15. | +-base::withCallingHandlers(...)
16. | \-mask$eval_all_mutate(quo)
17. +-purrr::map2(...)
18. | \-aba .f(.x[[i]], .y[[i]], ...)
19. | +-... %>% mutate(term = tolower(term))
20. | +-aba:::aba_glance(model, basic_model)
21. | \-aba:::aba_glance.lm(model, basic_model)
22. +-dplyr::mutate(., term = tolower(term))
23. +-dplyr::arrange(., match(term, metric_vars))
24. +-dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
25. +-dplyr::filter(., term %in% metric_vars)
26. +-base::loadNamespace(x)
27. | +-base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
28. | | \-base withOneRestart(expr, restarts[[1L]])
29. | | \-base doWithOneRestart(return(expr), restart)
30. | \-base::stop(cond)
31. \-dplyr `<fn>`(`<pckgNtFE>`)
32. \-rlang::abort(...)
-- Failure (test-stat_lm.R:41:3): std.beta works as intended for stat_lm -------
`... <- NULL` threw an unexpected error.
Message: Problem while computing `metrics = purrr::map2(...)`.
Caused by error in `loadNamespace()`:
! there is no package called 'psychometric'
Class: dplyr:::mutate_error/rlang_error/error/condition
Backtrace:
x
1. +-testthat::expect_error(...) at test-stat_lm.R:41:2
2. | \-testthat:::expect_condition_matching(...)
3. | \-testthat:::quasi_capture(...)
4. | +-testthat .capture(...)
5. | | \-base::withCallingHandlers(...)
6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. +-model %>% set_stats(stat_lm(std.beta = T)) %>% fit() %>% ...
8. +-base::summary(.)
9. +-aba:::summary.abaModel(.)
10. | \-object %>% aba_summary(...)
11. +-aba::aba_summary(., ...)
12. | \-object %>% calculate_metrics(control)
13. +-aba:::calculate_metrics(., control)
14. | \-r %>% ...
15. +-dplyr::mutate(...)
16. +-dplyr:::mutate.data.frame(...)
17. | \-dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
18. | +-base::withCallingHandlers(...)
19. | \-mask$eval_all_mutate(quo)
20. +-purrr::map2(...)
21. | \-aba .f(.x[[i]], .y[[i]], ...)
22. | +-... %>% mutate(term = tolower(term))
23. | +-aba:::aba_glance(model, basic_model)
24. | \-aba:::aba_glance.lm(model, basic_model)
25. +-dplyr::mutate(., term = tolower(term))
26. +-dplyr::arrange(., match(term, metric_vars))
27. +-dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
28. +-dplyr::filter(., term %in% metric_vars)
29. +-base::loadNamespace(x)
30. | +-base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
31. | | \-base withOneRestart(expr, restarts[[1L]])
32. | | \-base doWithOneRestart(return(expr), restart)
33. | \-base::stop(cond)
34. \-dplyr `<fn>`(`<pckgNtFE>`)
35. \-rlang::abort(...)
-- Failure (test-stat_lm.R:51:3): std.beta works as intended for stat_lm -------
`... <- NULL` threw an unexpected error.
Message: Problem while computing `metrics = purrr::map2(...)`.
Caused by error in `loadNamespace()`:
! there is no package called 'psychometric'
Class: dplyr:::mutate_error/rlang_error/error/condition
Backtrace:
x
1. +-testthat::expect_error(...) at test-stat_lm.R:51:2
2. | \-testthat:::expect_condition_matching(...)
3. | \-testthat:::quasi_capture(...)
4. | +-testthat .capture(...)
5. | | \-base::withCallingHandlers(...)
6. | \-rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. +-model %>% set_stats(stat_lm(std.beta = F)) %>% fit() %>% ...
8. +-base::summary(.)
9. +-aba:::summary.abaModel(.)
10. | \-object %>% aba_summary(...)
11. +-aba::aba_summary(., ...)
12. | \-object %>% calculate_metrics(control)
13. +-aba:::calculate_metrics(., control)
14. | \-r %>% ...
15. +-dplyr::mutate(...)
16. +-dplyr:::mutate.data.frame(...)
17. | \-dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
18. | +-base::withCallingHandlers(...)
19. | \-mask$eval_all_mutate(quo)
20. +-purrr::map2(...)
21. | \-aba .f(.x[[i]], .y[[i]], ...)
22. | +-... %>% mutate(term = tolower(term))
23. | +-aba:::aba_glance(model, basic_model)
24. | \-aba:::aba_glance.lm(model, basic_model)
25. +-dplyr::mutate(., term = tolower(term))
26. +-dplyr::arrange(., match(term, metric_vars))
27. +-dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
28. +-dplyr::filter(., term %in% metric_vars)
29. +-base::loadNamespace(x)
30. | +-base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
31. | | \-base withOneRestart(expr, restarts[[1L]])
32. | | \-base doWithOneRestart(return(expr), restart)
33. | \-base::stop(cond)
34. \-dplyr `<fn>`(`<pckgNtFE>`)
35. \-rlang::abort(...)
-- Error (test-stat_lm.R:61:3): std.beta works as intended for stat_lm ---------
Error in `all.equal(m1$results$coefs$estimate, m2$results$coefs$estimate)`: object 'm1' not found
Backtrace:
x
1. +-testthat::expect_false(...) at test-stat_lm.R:61:2
2. | \-testthat::quasi_label(enquo(object), label, arg = "object")
3. | \-rlang::eval_bare(expr, quo_get_env(quo))
4. +-base::isTRUE(all.equal(m1$results$coefs$estimate, m2$results$coefs$estimate))
5. \-base::all.equal(m1$results$coefs$estimate, m2$results$coefs$estimate)
[ FAIL 5 | WARN 0 | SKIP 2 | PASS 127 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.0.9
Check: examples
Result: ERROR
Running examples in ‘aba-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: stat_ancova
> ### Title: Create an ancova stat object.
> ### Aliases: stat_ancova
>
> ### ** Examples
>
> # filter to 24 month visit; calculate change in cognition to use as outcome;
> # assume abeta status as "treatment" variable.
> # The goal is to see if "treatment" has an effect on 2y cognitive decline
> data <- adnimerge %>%
+ dplyr::filter(
+ VISCODE == 'm24',
+ DX_bl %in% c('MCI', 'AD'),
+ !is.na(CSF_ABETA_STATUS_bl)
+ ) %>%
+ dplyr::mutate(
+ CDRSB = CDRSB - CDRSB_bl,
+ ADAS13 = ADAS13 - ADAS13_bl,
+ TREATMENT = factor(CSF_ABETA_STATUS_bl, levels=c(1,0),
+ labels=c('Placebo','Treatment'))
+ )
>
> # fit model. note that baseline outcome will be added based on the suffix.
> # e.g., fits with "CDRSB" as outcome will also add "CDRSB_bl" to the formula.
> ancova_model <- data %>% aba_model() %>%
+ set_outcomes(CDRSB, ADAS13) %>%
+ set_covariates(AGE, GENDER, EDUCATION) %>%
+ set_stats(
+ stat_ancova(treatment = 'TREATMENT', baseline_suffix = 'bl')
+ ) %>%
+ fit()
>
> # summarise model. treatment effect will be shown in the treatment coefficient
> ancova_summary <- ancova_model %>% summary()
Error in `mutate()`:
! Problem while computing `metrics = purrr::map2(...)`.
Caused by error in `loadNamespace()`:
! there is no package called ‘psychometric’
Backtrace:
▆
1. ├─ancova_model %>% summary()
2. ├─base::summary(.)
3. ├─aba:::summary.abaModel(.)
4. │ └─object %>% aba_summary(...)
5. ├─aba::aba_summary(., ...)
6. │ └─object %>% calculate_metrics(control)
7. ├─aba:::calculate_metrics(., control)
8. │ └─r %>% ...
9. ├─dplyr::mutate(...)
10. ├─dplyr:::mutate.data.frame(...)
11. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
12. │ ├─base::withCallingHandlers(...)
13. │ └─mask$eval_all_mutate(quo)
14. ├─purrr::map2(...)
15. │ └─aba .f(.x[[i]], .y[[i]], ...)
16. │ ├─... %>% mutate(term = tolower(term))
17. │ ├─aba:::aba_glance(model, basic_model)
18. │ └─aba:::aba_glance.lm(model, basic_model)
19. ├─dplyr::mutate(., term = tolower(term))
20. ├─dplyr::arrange(., match(term, metric_vars))
21. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
22. ├─dplyr::filter(., term %in% metric_vars)
23. ├─base::loadNamespace(x)
24. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
25. │ │ └─base withOneRestart(expr, restarts[[1L]])
26. │ │ └─base doWithOneRestart(return(expr), restart)
27. │ └─base::stop(cond)
28. └─dplyr `<fn>`(`<pckgNtFE>`)
29. └─rlang::abort(...)
Execution halted
Flavors: r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64, r-release-linux-x86_64
Version: 0.0.9
Check: tests
Result: ERROR
Running ‘testthat.R’ [119s/188s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(aba)
>
>
> test_check("aba")
Stratified by DX_bl
level Overall
n 2347 24
AGE (mean (SD)) 73.07 (7.43) 68.85 (8.30)
GENDER (mean (SD)) 0.53 (0.50) 0.38 (0.49)
EDUCATION (mean (SD)) 16.05 (2.75) 15.83 (2.16)
ConvertedToAlzheimers (mean (SD)) 0.20 (0.40) NaN (NA)
CSF_ABETA_STATUS_bl (mean (SD)) 0.62 (0.49) NaN (NA)
PLASMA_PTAU181_bl (mean (SD)) 2.71 (0.64) NaN (NA)
PLASMA_NFL_bl (mean (SD)) 3.54 (0.46) NaN (NA)
Stratified by DX_bl
AD CU MCI
n 405 846 1072
AGE (mean (SD)) 74.80 (7.92) 72.69 (6.34) 72.80 (7.89)
GENDER (mean (SD)) 0.57 (0.50) 0.44 (0.50) 0.59 (0.49)
EDUCATION (mean (SD)) 15.20 (2.91) 16.54 (2.53) 15.99 (2.78)
ConvertedToAlzheimers (mean (SD)) 0.00 (NA) 0.03 (0.18) 0.33 (0.47)
CSF_ABETA_STATUS_bl (mean (SD)) 0.88 (0.33) 0.39 (0.49) 0.63 (0.48)
PLASMA_PTAU181_bl (mean (SD)) 3.05 (0.41) 2.54 (0.67) 2.70 (0.64)
PLASMA_NFL_bl (mean (SD)) 3.77 (0.42) 3.45 (0.42) 3.52 (0.47)
Stratified by DX_bl
p test
n
AGE (mean (SD)) <0.001
GENDER (mean (SD)) <0.001
EDUCATION (mean (SD)) <0.001
ConvertedToAlzheimers (mean (SD)) NA
CSF_ABETA_STATUS_bl (mean (SD)) <0.001
PLASMA_PTAU181_bl (mean (SD)) <0.001
PLASMA_NFL_bl (mean (SD)) <0.001
[ FAIL 5 | WARN 0 | SKIP 2 | PASS 127 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On CRAN (2)
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure (test-stat_ancova.R:28:3): example works ────────────────────────────
`ancova_summary <- ancova_model %>% summary()` threw an unexpected error.
Message: Problem while computing `metrics = purrr::map2(...)`.
Caused by error in `loadNamespace()`:
! there is no package called 'psychometric'
Class: dplyr:::mutate_error/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-stat_ancova.R:28:2
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─ancova_model %>% summary()
8. ├─base::summary(.)
9. ├─aba:::summary.abaModel(.)
10. │ └─object %>% aba_summary(...)
11. ├─aba::aba_summary(., ...)
12. │ └─object %>% calculate_metrics(control)
13. ├─aba:::calculate_metrics(., control)
14. │ └─r %>% ...
15. ├─dplyr::mutate(...)
16. ├─dplyr:::mutate.data.frame(...)
17. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
18. │ ├─base::withCallingHandlers(...)
19. │ └─mask$eval_all_mutate(quo)
20. ├─purrr::map2(...)
21. │ └─aba .f(.x[[i]], .y[[i]], ...)
22. │ ├─... %>% mutate(term = tolower(term))
23. │ ├─aba:::aba_glance(model, basic_model)
24. │ └─aba:::aba_glance.lm(model, basic_model)
25. ├─dplyr::mutate(., term = tolower(term))
26. ├─dplyr::arrange(., match(term, metric_vars))
27. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
28. ├─dplyr::filter(., term %in% metric_vars)
29. ├─base::loadNamespace(x)
30. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
31. │ │ └─base withOneRestart(expr, restarts[[1L]])
32. │ │ └─base doWithOneRestart(return(expr), restart)
33. │ └─base::stop(cond)
34. └─dplyr `<fn>`(`<pckgNtFE>`)
35. └─rlang::abort(...)
── Failure (test-stat_lm.R:6:3): complete.cases=F for lm works ─────────────────
`... <- NULL` threw an unexpected error.
Message: Problem while computing `metrics = purrr::map2(...)`.
Caused by error in `loadNamespace()`:
! there is no package called 'psychometric'
Class: dplyr:::mutate_error/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-stat_lm.R:6:2
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─... %>% aba_summary()
8. ├─aba::aba_summary(.)
9. │ └─object %>% calculate_metrics(control)
10. ├─aba:::calculate_metrics(., control)
11. │ └─r %>% ...
12. ├─dplyr::mutate(...)
13. ├─dplyr:::mutate.data.frame(...)
14. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
15. │ ├─base::withCallingHandlers(...)
16. │ └─mask$eval_all_mutate(quo)
17. ├─purrr::map2(...)
18. │ └─aba .f(.x[[i]], .y[[i]], ...)
19. │ ├─... %>% mutate(term = tolower(term))
20. │ ├─aba:::aba_glance(model, basic_model)
21. │ └─aba:::aba_glance.lm(model, basic_model)
22. ├─dplyr::mutate(., term = tolower(term))
23. ├─dplyr::arrange(., match(term, metric_vars))
24. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
25. ├─dplyr::filter(., term %in% metric_vars)
26. ├─base::loadNamespace(x)
27. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
28. │ │ └─base withOneRestart(expr, restarts[[1L]])
29. │ │ └─base doWithOneRestart(return(expr), restart)
30. │ └─base::stop(cond)
31. └─dplyr `<fn>`(`<pckgNtFE>`)
32. └─rlang::abort(...)
── Failure (test-stat_lm.R:41:3): std.beta works as intended for stat_lm ───────
`... <- NULL` threw an unexpected error.
Message: Problem while computing `metrics = purrr::map2(...)`.
Caused by error in `loadNamespace()`:
! there is no package called 'psychometric'
Class: dplyr:::mutate_error/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-stat_lm.R:41:2
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─model %>% set_stats(stat_lm(std.beta = T)) %>% fit() %>% ...
8. ├─base::summary(.)
9. ├─aba:::summary.abaModel(.)
10. │ └─object %>% aba_summary(...)
11. ├─aba::aba_summary(., ...)
12. │ └─object %>% calculate_metrics(control)
13. ├─aba:::calculate_metrics(., control)
14. │ └─r %>% ...
15. ├─dplyr::mutate(...)
16. ├─dplyr:::mutate.data.frame(...)
17. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
18. │ ├─base::withCallingHandlers(...)
19. │ └─mask$eval_all_mutate(quo)
20. ├─purrr::map2(...)
21. │ └─aba .f(.x[[i]], .y[[i]], ...)
22. │ ├─... %>% mutate(term = tolower(term))
23. │ ├─aba:::aba_glance(model, basic_model)
24. │ └─aba:::aba_glance.lm(model, basic_model)
25. ├─dplyr::mutate(., term = tolower(term))
26. ├─dplyr::arrange(., match(term, metric_vars))
27. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
28. ├─dplyr::filter(., term %in% metric_vars)
29. ├─base::loadNamespace(x)
30. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
31. │ │ └─base withOneRestart(expr, restarts[[1L]])
32. │ │ └─base doWithOneRestart(return(expr), restart)
33. │ └─base::stop(cond)
34. └─dplyr `<fn>`(`<pckgNtFE>`)
35. └─rlang::abort(...)
── Failure (test-stat_lm.R:51:3): std.beta works as intended for stat_lm ───────
`... <- NULL` threw an unexpected error.
Message: Problem while computing `metrics = purrr::map2(...)`.
Caused by error in `loadNamespace()`:
! there is no package called 'psychometric'
Class: dplyr:::mutate_error/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-stat_lm.R:51:2
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─model %>% set_stats(stat_lm(std.beta = F)) %>% fit() %>% ...
8. ├─base::summary(.)
9. ├─aba:::summary.abaModel(.)
10. │ └─object %>% aba_summary(...)
11. ├─aba::aba_summary(., ...)
12. │ └─object %>% calculate_metrics(control)
13. ├─aba:::calculate_metrics(., control)
14. │ └─r %>% ...
15. ├─dplyr::mutate(...)
16. ├─dplyr:::mutate.data.frame(...)
17. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
18. │ ├─base::withCallingHandlers(...)
19. │ └─mask$eval_all_mutate(quo)
20. ├─purrr::map2(...)
21. │ └─aba .f(.x[[i]], .y[[i]], ...)
22. │ ├─... %>% mutate(term = tolower(term))
23. │ ├─aba:::aba_glance(model, basic_model)
24. │ └─aba:::aba_glance.lm(model, basic_model)
25. ├─dplyr::mutate(., term = tolower(term))
26. ├─dplyr::arrange(., match(term, metric_vars))
27. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
28. ├─dplyr::filter(., term %in% metric_vars)
29. ├─base::loadNamespace(x)
30. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
31. │ │ └─base withOneRestart(expr, restarts[[1L]])
32. │ │ └─base doWithOneRestart(return(expr), restart)
33. │ └─base::stop(cond)
34. └─dplyr `<fn>`(`<pckgNtFE>`)
35. └─rlang::abort(...)
── Error (test-stat_lm.R:61:3): std.beta works as intended for stat_lm ─────────
Error in `all.equal(m1$results$coefs$estimate, m2$results$coefs$estimate)`: object 'm1' not found
Backtrace:
▆
1. ├─testthat::expect_false(...) at test-stat_lm.R:61:2
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::isTRUE(all.equal(m1$results$coefs$estimate, m2$results$coefs$estimate))
5. └─base::all.equal(m1$results$coefs$estimate, m2$results$coefs$estimate)
[ FAIL 5 | WARN 0 | SKIP 2 | PASS 127 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.0.9
Check: examples
Result: ERROR
Running examples in ‘aba-Ex.R’ failed
The error most likely occurred in:
> ### Name: stat_ancova
> ### Title: Create an ancova stat object.
> ### Aliases: stat_ancova
>
> ### ** Examples
>
> # filter to 24 month visit; calculate change in cognition to use as outcome;
> # assume abeta status as "treatment" variable.
> # The goal is to see if "treatment" has an effect on 2y cognitive decline
> data <- adnimerge %>%
+ dplyr::filter(
+ VISCODE == 'm24',
+ DX_bl %in% c('MCI', 'AD'),
+ !is.na(CSF_ABETA_STATUS_bl)
+ ) %>%
+ dplyr::mutate(
+ CDRSB = CDRSB - CDRSB_bl,
+ ADAS13 = ADAS13 - ADAS13_bl,
+ TREATMENT = factor(CSF_ABETA_STATUS_bl, levels=c(1,0),
+ labels=c('Placebo','Treatment'))
+ )
>
> # fit model. note that baseline outcome will be added based on the suffix.
> # e.g., fits with "CDRSB" as outcome will also add "CDRSB_bl" to the formula.
> ancova_model <- data %>% aba_model() %>%
+ set_outcomes(CDRSB, ADAS13) %>%
+ set_covariates(AGE, GENDER, EDUCATION) %>%
+ set_stats(
+ stat_ancova(treatment = 'TREATMENT', baseline_suffix = 'bl')
+ ) %>%
+ fit()
>
> # summarise model. treatment effect will be shown in the treatment coefficient
> ancova_summary <- ancova_model %>% summary()
Error in `mutate()`:
! Problem while computing `metrics = purrr::map2(...)`.
Caused by error in `loadNamespace()`:
! there is no package called ‘psychometric’
Backtrace:
▆
1. ├─ancova_model %>% summary()
2. ├─base::summary(.)
3. ├─aba:::summary.abaModel(.)
4. │ └─object %>% aba_summary(...)
5. ├─aba::aba_summary(., ...)
6. │ └─object %>% calculate_metrics(control)
7. ├─aba:::calculate_metrics(., control)
8. │ └─r %>% ...
9. ├─dplyr::mutate(...)
10. ├─dplyr:::mutate.data.frame(...)
11. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
12. │ ├─base::withCallingHandlers(...)
13. │ └─mask$eval_all_mutate(quo)
14. ├─purrr::map2(...)
15. │ └─aba .f(.x[[i]], .y[[i]], ...)
16. │ ├─... %>% mutate(term = tolower(term))
17. │ ├─aba:::aba_glance(model, basic_model)
18. │ └─aba:::aba_glance.lm(model, basic_model)
19. ├─dplyr::mutate(., term = tolower(term))
20. ├─dplyr::arrange(., match(term, metric_vars))
21. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
22. ├─dplyr::filter(., term %in% metric_vars)
23. ├─base::loadNamespace(x)
24. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
25. │ │ └─base withOneRestart(expr, restarts[[1L]])
26. │ │ └─base doWithOneRestart(return(expr), restart)
27. │ └─base::stop(cond)
28. └─dplyr `<fn>`(`<pckgNtFE>`)
29. └─rlang::abort(...)
Execution halted
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc
Version: 0.0.9
Check: tests
Result: ERROR
Running ‘testthat.R’ [186s/232s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(aba)
>
>
> test_check("aba")
Stratified by DX_bl
level Overall
n 2347 24
AGE (mean (SD)) 73.07 (7.43) 68.85 (8.30)
GENDER (mean (SD)) 0.53 (0.50) 0.38 (0.49)
EDUCATION (mean (SD)) 16.05 (2.75) 15.83 (2.16)
ConvertedToAlzheimers (mean (SD)) 0.20 (0.40) NaN (NA)
CSF_ABETA_STATUS_bl (mean (SD)) 0.62 (0.49) NaN (NA)
PLASMA_PTAU181_bl (mean (SD)) 2.71 (0.64) NaN (NA)
PLASMA_NFL_bl (mean (SD)) 3.54 (0.46) NaN (NA)
Stratified by DX_bl
AD CU MCI
n 405 846 1072
AGE (mean (SD)) 74.80 (7.92) 72.69 (6.34) 72.80 (7.89)
GENDER (mean (SD)) 0.57 (0.50) 0.44 (0.50) 0.59 (0.49)
EDUCATION (mean (SD)) 15.20 (2.91) 16.54 (2.53) 15.99 (2.78)
ConvertedToAlzheimers (mean (SD)) 0.00 (NA) 0.03 (0.18) 0.33 (0.47)
CSF_ABETA_STATUS_bl (mean (SD)) 0.88 (0.33) 0.39 (0.49) 0.63 (0.48)
PLASMA_PTAU181_bl (mean (SD)) 3.05 (0.41) 2.54 (0.67) 2.70 (0.64)
PLASMA_NFL_bl (mean (SD)) 3.77 (0.42) 3.45 (0.42) 3.52 (0.47)
Stratified by DX_bl
p test
n
AGE (mean (SD)) <0.001
GENDER (mean (SD)) <0.001
EDUCATION (mean (SD)) <0.001
ConvertedToAlzheimers (mean (SD)) NA
CSF_ABETA_STATUS_bl (mean (SD)) <0.001
PLASMA_PTAU181_bl (mean (SD)) <0.001
PLASMA_NFL_bl (mean (SD)) <0.001
[ FAIL 5 | WARN 0 | SKIP 2 | PASS 127 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On CRAN (2)
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure (test-stat_ancova.R:28:3): example works ────────────────────────────
`ancova_summary <- ancova_model %>% summary()` threw an unexpected error.
Message: Problem while computing `metrics = purrr::map2(...)`.
Caused by error in `loadNamespace()`:
! there is no package called 'psychometric'
Class: dplyr:::mutate_error/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-stat_ancova.R:28:2
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─ancova_model %>% summary()
8. ├─base::summary(.)
9. ├─aba:::summary.abaModel(.)
10. │ └─object %>% aba_summary(...)
11. ├─aba::aba_summary(., ...)
12. │ └─object %>% calculate_metrics(control)
13. ├─aba:::calculate_metrics(., control)
14. │ └─r %>% ...
15. ├─dplyr::mutate(...)
16. ├─dplyr:::mutate.data.frame(...)
17. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
18. │ ├─base::withCallingHandlers(...)
19. │ └─mask$eval_all_mutate(quo)
20. ├─purrr::map2(...)
21. │ └─aba .f(.x[[i]], .y[[i]], ...)
22. │ ├─... %>% mutate(term = tolower(term))
23. │ ├─aba:::aba_glance(model, basic_model)
24. │ └─aba:::aba_glance.lm(model, basic_model)
25. ├─dplyr::mutate(., term = tolower(term))
26. ├─dplyr::arrange(., match(term, metric_vars))
27. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
28. ├─dplyr::filter(., term %in% metric_vars)
29. ├─base::loadNamespace(x)
30. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
31. │ │ └─base withOneRestart(expr, restarts[[1L]])
32. │ │ └─base doWithOneRestart(return(expr), restart)
33. │ └─base::stop(cond)
34. └─dplyr `<fn>`(`<pckgNtFE>`)
35. └─rlang::abort(...)
── Failure (test-stat_lm.R:6:3): complete.cases=F for lm works ─────────────────
`... <- NULL` threw an unexpected error.
Message: Problem while computing `metrics = purrr::map2(...)`.
Caused by error in `loadNamespace()`:
! there is no package called 'psychometric'
Class: dplyr:::mutate_error/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-stat_lm.R:6:2
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─... %>% aba_summary()
8. ├─aba::aba_summary(.)
9. │ └─object %>% calculate_metrics(control)
10. ├─aba:::calculate_metrics(., control)
11. │ └─r %>% ...
12. ├─dplyr::mutate(...)
13. ├─dplyr:::mutate.data.frame(...)
14. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
15. │ ├─base::withCallingHandlers(...)
16. │ └─mask$eval_all_mutate(quo)
17. ├─purrr::map2(...)
18. │ └─aba .f(.x[[i]], .y[[i]], ...)
19. │ ├─... %>% mutate(term = tolower(term))
20. │ ├─aba:::aba_glance(model, basic_model)
21. │ └─aba:::aba_glance.lm(model, basic_model)
22. ├─dplyr::mutate(., term = tolower(term))
23. ├─dplyr::arrange(., match(term, metric_vars))
24. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
25. ├─dplyr::filter(., term %in% metric_vars)
26. ├─base::loadNamespace(x)
27. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
28. │ │ └─base withOneRestart(expr, restarts[[1L]])
29. │ │ └─base doWithOneRestart(return(expr), restart)
30. │ └─base::stop(cond)
31. └─dplyr `<fn>`(`<pckgNtFE>`)
32. └─rlang::abort(...)
── Failure (test-stat_lm.R:41:3): std.beta works as intended for stat_lm ───────
`... <- NULL` threw an unexpected error.
Message: Problem while computing `metrics = purrr::map2(...)`.
Caused by error in `loadNamespace()`:
! there is no package called 'psychometric'
Class: dplyr:::mutate_error/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-stat_lm.R:41:2
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─model %>% set_stats(stat_lm(std.beta = T)) %>% fit() %>% ...
8. ├─base::summary(.)
9. ├─aba:::summary.abaModel(.)
10. │ └─object %>% aba_summary(...)
11. ├─aba::aba_summary(., ...)
12. │ └─object %>% calculate_metrics(control)
13. ├─aba:::calculate_metrics(., control)
14. │ └─r %>% ...
15. ├─dplyr::mutate(...)
16. ├─dplyr:::mutate.data.frame(...)
17. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
18. │ ├─base::withCallingHandlers(...)
19. │ └─mask$eval_all_mutate(quo)
20. ├─purrr::map2(...)
21. │ └─aba .f(.x[[i]], .y[[i]], ...)
22. │ ├─... %>% mutate(term = tolower(term))
23. │ ├─aba:::aba_glance(model, basic_model)
24. │ └─aba:::aba_glance.lm(model, basic_model)
25. ├─dplyr::mutate(., term = tolower(term))
26. ├─dplyr::arrange(., match(term, metric_vars))
27. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
28. ├─dplyr::filter(., term %in% metric_vars)
29. ├─base::loadNamespace(x)
30. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
31. │ │ └─base withOneRestart(expr, restarts[[1L]])
32. │ │ └─base doWithOneRestart(return(expr), restart)
33. │ └─base::stop(cond)
34. └─dplyr `<fn>`(`<pckgNtFE>`)
35. └─rlang::abort(...)
── Failure (test-stat_lm.R:51:3): std.beta works as intended for stat_lm ───────
`... <- NULL` threw an unexpected error.
Message: Problem while computing `metrics = purrr::map2(...)`.
Caused by error in `loadNamespace()`:
! there is no package called 'psychometric'
Class: dplyr:::mutate_error/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-stat_lm.R:51:2
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─model %>% set_stats(stat_lm(std.beta = F)) %>% fit() %>% ...
8. ├─base::summary(.)
9. ├─aba:::summary.abaModel(.)
10. │ └─object %>% aba_summary(...)
11. ├─aba::aba_summary(., ...)
12. │ └─object %>% calculate_metrics(control)
13. ├─aba:::calculate_metrics(., control)
14. │ └─r %>% ...
15. ├─dplyr::mutate(...)
16. ├─dplyr:::mutate.data.frame(...)
17. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
18. │ ├─base::withCallingHandlers(...)
19. │ └─mask$eval_all_mutate(quo)
20. ├─purrr::map2(...)
21. │ └─aba .f(.x[[i]], .y[[i]], ...)
22. │ ├─... %>% mutate(term = tolower(term))
23. │ ├─aba:::aba_glance(model, basic_model)
24. │ └─aba:::aba_glance.lm(model, basic_model)
25. ├─dplyr::mutate(., term = tolower(term))
26. ├─dplyr::arrange(., match(term, metric_vars))
27. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
28. ├─dplyr::filter(., term %in% metric_vars)
29. ├─base::loadNamespace(x)
30. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
31. │ │ └─base withOneRestart(expr, restarts[[1L]])
32. │ │ └─base doWithOneRestart(return(expr), restart)
33. │ └─base::stop(cond)
34. └─dplyr `<fn>`(`<pckgNtFE>`)
35. └─rlang::abort(...)
── Error (test-stat_lm.R:61:3): std.beta works as intended for stat_lm ─────────
Error in `all.equal(m1$results$coefs$estimate, m2$results$coefs$estimate)`: object 'm1' not found
Backtrace:
▆
1. ├─testthat::expect_false(...) at test-stat_lm.R:61:2
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::isTRUE(all.equal(m1$results$coefs$estimate, m2$results$coefs$estimate))
5. └─base::all.equal(m1$results$coefs$estimate, m2$results$coefs$estimate)
[ FAIL 5 | WARN 0 | SKIP 2 | PASS 127 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.0.9
Check: tests
Result: ERROR
Running ‘testthat.R’ [193s/265s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(aba)
>
>
> test_check("aba")
Stratified by DX_bl
level Overall
n 2347 24
AGE (mean (SD)) 73.07 (7.43) 68.85 (8.30)
GENDER (mean (SD)) 0.53 (0.50) 0.38 (0.49)
EDUCATION (mean (SD)) 16.05 (2.75) 15.83 (2.16)
ConvertedToAlzheimers (mean (SD)) 0.20 (0.40) NaN (NA)
CSF_ABETA_STATUS_bl (mean (SD)) 0.62 (0.49) NaN (NA)
PLASMA_PTAU181_bl (mean (SD)) 2.71 (0.64) NaN (NA)
PLASMA_NFL_bl (mean (SD)) 3.54 (0.46) NaN (NA)
Stratified by DX_bl
AD CU MCI
n 405 846 1072
AGE (mean (SD)) 74.80 (7.92) 72.69 (6.34) 72.80 (7.89)
GENDER (mean (SD)) 0.57 (0.50) 0.44 (0.50) 0.59 (0.49)
EDUCATION (mean (SD)) 15.20 (2.91) 16.54 (2.53) 15.99 (2.78)
ConvertedToAlzheimers (mean (SD)) 0.00 (NA) 0.03 (0.18) 0.33 (0.47)
CSF_ABETA_STATUS_bl (mean (SD)) 0.88 (0.33) 0.39 (0.49) 0.63 (0.48)
PLASMA_PTAU181_bl (mean (SD)) 3.05 (0.41) 2.54 (0.67) 2.70 (0.64)
PLASMA_NFL_bl (mean (SD)) 3.77 (0.42) 3.45 (0.42) 3.52 (0.47)
Stratified by DX_bl
p test
n
AGE (mean (SD)) <0.001
GENDER (mean (SD)) <0.001
EDUCATION (mean (SD)) <0.001
ConvertedToAlzheimers (mean (SD)) NA
CSF_ABETA_STATUS_bl (mean (SD)) <0.001
PLASMA_PTAU181_bl (mean (SD)) <0.001
PLASMA_NFL_bl (mean (SD)) <0.001
[ FAIL 5 | WARN 0 | SKIP 2 | PASS 127 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On CRAN (2)
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure (test-stat_ancova.R:28:3): example works ────────────────────────────
`ancova_summary <- ancova_model %>% summary()` threw an unexpected error.
Message: Problem while computing `metrics = purrr::map2(...)`.
Caused by error in `loadNamespace()`:
! there is no package called 'psychometric'
Class: dplyr:::mutate_error/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-stat_ancova.R:28:2
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─ancova_model %>% summary()
8. ├─base::summary(.)
9. ├─aba:::summary.abaModel(.)
10. │ └─object %>% aba_summary(...)
11. ├─aba::aba_summary(., ...)
12. │ └─object %>% calculate_metrics(control)
13. ├─aba:::calculate_metrics(., control)
14. │ └─r %>% ...
15. ├─dplyr::mutate(...)
16. ├─dplyr:::mutate.data.frame(...)
17. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
18. │ ├─base::withCallingHandlers(...)
19. │ └─mask$eval_all_mutate(quo)
20. ├─purrr::map2(...)
21. │ └─aba .f(.x[[i]], .y[[i]], ...)
22. │ ├─... %>% mutate(term = tolower(term))
23. │ ├─aba:::aba_glance(model, basic_model)
24. │ └─aba:::aba_glance.lm(model, basic_model)
25. ├─dplyr::mutate(., term = tolower(term))
26. ├─dplyr::arrange(., match(term, metric_vars))
27. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
28. ├─dplyr::filter(., term %in% metric_vars)
29. ├─base::loadNamespace(x)
30. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
31. │ │ └─base withOneRestart(expr, restarts[[1L]])
32. │ │ └─base doWithOneRestart(return(expr), restart)
33. │ └─base::stop(cond)
34. └─dplyr `<fn>`(`<pckgNtFE>`)
35. └─rlang::abort(...)
── Failure (test-stat_lm.R:6:3): complete.cases=F for lm works ─────────────────
`... <- NULL` threw an unexpected error.
Message: Problem while computing `metrics = purrr::map2(...)`.
Caused by error in `loadNamespace()`:
! there is no package called 'psychometric'
Class: dplyr:::mutate_error/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-stat_lm.R:6:2
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─... %>% aba_summary()
8. ├─aba::aba_summary(.)
9. │ └─object %>% calculate_metrics(control)
10. ├─aba:::calculate_metrics(., control)
11. │ └─r %>% ...
12. ├─dplyr::mutate(...)
13. ├─dplyr:::mutate.data.frame(...)
14. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
15. │ ├─base::withCallingHandlers(...)
16. │ └─mask$eval_all_mutate(quo)
17. ├─purrr::map2(...)
18. │ └─aba .f(.x[[i]], .y[[i]], ...)
19. │ ├─... %>% mutate(term = tolower(term))
20. │ ├─aba:::aba_glance(model, basic_model)
21. │ └─aba:::aba_glance.lm(model, basic_model)
22. ├─dplyr::mutate(., term = tolower(term))
23. ├─dplyr::arrange(., match(term, metric_vars))
24. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
25. ├─dplyr::filter(., term %in% metric_vars)
26. ├─base::loadNamespace(x)
27. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
28. │ │ └─base withOneRestart(expr, restarts[[1L]])
29. │ │ └─base doWithOneRestart(return(expr), restart)
30. │ └─base::stop(cond)
31. └─dplyr `<fn>`(`<pckgNtFE>`)
32. └─rlang::abort(...)
── Failure (test-stat_lm.R:41:3): std.beta works as intended for stat_lm ───────
`... <- NULL` threw an unexpected error.
Message: Problem while computing `metrics = purrr::map2(...)`.
Caused by error in `loadNamespace()`:
! there is no package called 'psychometric'
Class: dplyr:::mutate_error/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-stat_lm.R:41:2
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─model %>% set_stats(stat_lm(std.beta = T)) %>% fit() %>% ...
8. ├─base::summary(.)
9. ├─aba:::summary.abaModel(.)
10. │ └─object %>% aba_summary(...)
11. ├─aba::aba_summary(., ...)
12. │ └─object %>% calculate_metrics(control)
13. ├─aba:::calculate_metrics(., control)
14. │ └─r %>% ...
15. ├─dplyr::mutate(...)
16. ├─dplyr:::mutate.data.frame(...)
17. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
18. │ ├─base::withCallingHandlers(...)
19. │ └─mask$eval_all_mutate(quo)
20. ├─purrr::map2(...)
21. │ └─aba .f(.x[[i]], .y[[i]], ...)
22. │ ├─... %>% mutate(term = tolower(term))
23. │ ├─aba:::aba_glance(model, basic_model)
24. │ └─aba:::aba_glance.lm(model, basic_model)
25. ├─dplyr::mutate(., term = tolower(term))
26. ├─dplyr::arrange(., match(term, metric_vars))
27. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
28. ├─dplyr::filter(., term %in% metric_vars)
29. ├─base::loadNamespace(x)
30. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
31. │ │ └─base withOneRestart(expr, restarts[[1L]])
32. │ │ └─base doWithOneRestart(return(expr), restart)
33. │ └─base::stop(cond)
34. └─dplyr `<fn>`(`<pckgNtFE>`)
35. └─rlang::abort(...)
── Failure (test-stat_lm.R:51:3): std.beta works as intended for stat_lm ───────
`... <- NULL` threw an unexpected error.
Message: Problem while computing `metrics = purrr::map2(...)`.
Caused by error in `loadNamespace()`:
! there is no package called 'psychometric'
Class: dplyr:::mutate_error/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-stat_lm.R:51:2
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─model %>% set_stats(stat_lm(std.beta = F)) %>% fit() %>% ...
8. ├─base::summary(.)
9. ├─aba:::summary.abaModel(.)
10. │ └─object %>% aba_summary(...)
11. ├─aba::aba_summary(., ...)
12. │ └─object %>% calculate_metrics(control)
13. ├─aba:::calculate_metrics(., control)
14. │ └─r %>% ...
15. ├─dplyr::mutate(...)
16. ├─dplyr:::mutate.data.frame(...)
17. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
18. │ ├─base::withCallingHandlers(...)
19. │ └─mask$eval_all_mutate(quo)
20. ├─purrr::map2(...)
21. │ └─aba .f(.x[[i]], .y[[i]], ...)
22. │ ├─... %>% mutate(term = tolower(term))
23. │ ├─aba:::aba_glance(model, basic_model)
24. │ └─aba:::aba_glance.lm(model, basic_model)
25. ├─dplyr::mutate(., term = tolower(term))
26. ├─dplyr::arrange(., match(term, metric_vars))
27. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
28. ├─dplyr::filter(., term %in% metric_vars)
29. ├─base::loadNamespace(x)
30. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
31. │ │ └─base withOneRestart(expr, restarts[[1L]])
32. │ │ └─base doWithOneRestart(return(expr), restart)
33. │ └─base::stop(cond)
34. └─dplyr `<fn>`(`<pckgNtFE>`)
35. └─rlang::abort(...)
── Error (test-stat_lm.R:61:3): std.beta works as intended for stat_lm ─────────
Error in `all.equal(m1$results$coefs$estimate, m2$results$coefs$estimate)`: object 'm1' not found
Backtrace:
▆
1. ├─testthat::expect_false(...) at test-stat_lm.R:61:2
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::isTRUE(all.equal(m1$results$coefs$estimate, m2$results$coefs$estimate))
5. └─base::all.equal(m1$results$coefs$estimate, m2$results$coefs$estimate)
[ FAIL 5 | WARN 0 | SKIP 2 | PASS 127 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.0.9
Check: package dependencies
Result: ERROR
Packages required but not available:
'purrr', 'dplyr', 'broom', 'tibble', 'ggplot2', 'glue', 'magrittr',
'stringr', 'rlang', 'tidyr', 'generics'
Packages suggested but not available for checking:
'covr', 'knitr', 'plotly', 'rmarkdown', 'testthat', 'tidyselect',
'yardstick', 'pins', 'MuMIn', 'broom.mixed', 'emmeans', 'ggpubr',
'pROC', 'progress', 'OptimalCutpoints', 'tableone', 'longpower',
'withr', 'reactable', 'psychometric', 'readr', 'writexl'
VignetteBuilder package required for checking but not installed: 'knitr'
See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Flavor: r-devel-windows-x86_64-new-TK
Version: 0.0.9
Check: tests
Result: ERROR
Running ‘testthat.R’ [152s/172s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(aba)
>
>
> test_check("aba")
Stratified by DX_bl
level Overall
n 2347 24
AGE (mean (SD)) 73.07 (7.43) 68.85 (8.30)
GENDER (mean (SD)) 0.53 (0.50) 0.38 (0.49)
EDUCATION (mean (SD)) 16.05 (2.75) 15.83 (2.16)
ConvertedToAlzheimers (mean (SD)) 0.20 (0.40) NaN (NA)
CSF_ABETA_STATUS_bl (mean (SD)) 0.62 (0.49) NaN (NA)
PLASMA_PTAU181_bl (mean (SD)) 2.71 (0.64) NaN (NA)
PLASMA_NFL_bl (mean (SD)) 3.54 (0.46) NaN (NA)
Stratified by DX_bl
AD CU MCI
n 405 846 1072
AGE (mean (SD)) 74.80 (7.92) 72.69 (6.34) 72.80 (7.89)
GENDER (mean (SD)) 0.57 (0.50) 0.44 (0.50) 0.59 (0.49)
EDUCATION (mean (SD)) 15.20 (2.91) 16.54 (2.53) 15.99 (2.78)
ConvertedToAlzheimers (mean (SD)) 0.00 (NA) 0.03 (0.18) 0.33 (0.47)
CSF_ABETA_STATUS_bl (mean (SD)) 0.88 (0.33) 0.39 (0.49) 0.63 (0.48)
PLASMA_PTAU181_bl (mean (SD)) 3.05 (0.41) 2.54 (0.67) 2.70 (0.64)
PLASMA_NFL_bl (mean (SD)) 3.77 (0.42) 3.45 (0.42) 3.52 (0.47)
Stratified by DX_bl
p test
n
AGE (mean (SD)) <0.001
GENDER (mean (SD)) <0.001
EDUCATION (mean (SD)) <0.001
ConvertedToAlzheimers (mean (SD)) NA
CSF_ABETA_STATUS_bl (mean (SD)) <0.001
PLASMA_PTAU181_bl (mean (SD)) <0.001
PLASMA_NFL_bl (mean (SD)) <0.001
[ FAIL 5 | WARN 0 | SKIP 2 | PASS 127 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On CRAN (2)
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure (test-stat_ancova.R:28:3): example works ────────────────────────────
`ancova_summary <- ancova_model %>% summary()` threw an unexpected error.
Message: Problem while computing `metrics = purrr::map2(...)`.
Caused by error in `loadNamespace()`:
! there is no package called 'psychometric'
Class: dplyr:::mutate_error/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-stat_ancova.R:28:2
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─ancova_model %>% summary()
8. ├─base::summary(.)
9. ├─aba:::summary.abaModel(.)
10. │ └─object %>% aba_summary(...)
11. ├─aba::aba_summary(., ...)
12. │ └─object %>% calculate_metrics(control)
13. ├─aba:::calculate_metrics(., control)
14. │ └─r %>% ...
15. ├─dplyr::mutate(...)
16. ├─dplyr:::mutate.data.frame(...)
17. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
18. │ ├─base::withCallingHandlers(...)
19. │ └─mask$eval_all_mutate(quo)
20. ├─purrr::map2(...)
21. │ └─aba .f(.x[[i]], .y[[i]], ...)
22. │ ├─... %>% mutate(term = tolower(term))
23. │ ├─aba:::aba_glance(model, basic_model)
24. │ └─aba:::aba_glance.lm(model, basic_model)
25. ├─dplyr::mutate(., term = tolower(term))
26. ├─dplyr::arrange(., match(term, metric_vars))
27. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
28. ├─dplyr::filter(., term %in% metric_vars)
29. ├─base::loadNamespace(x)
30. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
31. │ │ └─base withOneRestart(expr, restarts[[1L]])
32. │ │ └─base doWithOneRestart(return(expr), restart)
33. │ └─base::stop(cond)
34. └─dplyr `<fn>`(`<pckgNtFE>`)
35. └─rlang::abort(...)
── Failure (test-stat_lm.R:6:3): complete.cases=F for lm works ─────────────────
`... <- NULL` threw an unexpected error.
Message: Problem while computing `metrics = purrr::map2(...)`.
Caused by error in `loadNamespace()`:
! there is no package called 'psychometric'
Class: dplyr:::mutate_error/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-stat_lm.R:6:2
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─... %>% aba_summary()
8. ├─aba::aba_summary(.)
9. │ └─object %>% calculate_metrics(control)
10. ├─aba:::calculate_metrics(., control)
11. │ └─r %>% ...
12. ├─dplyr::mutate(...)
13. ├─dplyr:::mutate.data.frame(...)
14. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
15. │ ├─base::withCallingHandlers(...)
16. │ └─mask$eval_all_mutate(quo)
17. ├─purrr::map2(...)
18. │ └─aba .f(.x[[i]], .y[[i]], ...)
19. │ ├─... %>% mutate(term = tolower(term))
20. │ ├─aba:::aba_glance(model, basic_model)
21. │ └─aba:::aba_glance.lm(model, basic_model)
22. ├─dplyr::mutate(., term = tolower(term))
23. ├─dplyr::arrange(., match(term, metric_vars))
24. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
25. ├─dplyr::filter(., term %in% metric_vars)
26. ├─base::loadNamespace(x)
27. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
28. │ │ └─base withOneRestart(expr, restarts[[1L]])
29. │ │ └─base doWithOneRestart(return(expr), restart)
30. │ └─base::stop(cond)
31. └─dplyr `<fn>`(`<pckgNtFE>`)
32. └─rlang::abort(...)
── Failure (test-stat_lm.R:41:3): std.beta works as intended for stat_lm ───────
`... <- NULL` threw an unexpected error.
Message: Problem while computing `metrics = purrr::map2(...)`.
Caused by error in `loadNamespace()`:
! there is no package called 'psychometric'
Class: dplyr:::mutate_error/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-stat_lm.R:41:2
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─model %>% set_stats(stat_lm(std.beta = T)) %>% fit() %>% ...
8. ├─base::summary(.)
9. ├─aba:::summary.abaModel(.)
10. │ └─object %>% aba_summary(...)
11. ├─aba::aba_summary(., ...)
12. │ └─object %>% calculate_metrics(control)
13. ├─aba:::calculate_metrics(., control)
14. │ └─r %>% ...
15. ├─dplyr::mutate(...)
16. ├─dplyr:::mutate.data.frame(...)
17. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
18. │ ├─base::withCallingHandlers(...)
19. │ └─mask$eval_all_mutate(quo)
20. ├─purrr::map2(...)
21. │ └─aba .f(.x[[i]], .y[[i]], ...)
22. │ ├─... %>% mutate(term = tolower(term))
23. │ ├─aba:::aba_glance(model, basic_model)
24. │ └─aba:::aba_glance.lm(model, basic_model)
25. ├─dplyr::mutate(., term = tolower(term))
26. ├─dplyr::arrange(., match(term, metric_vars))
27. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
28. ├─dplyr::filter(., term %in% metric_vars)
29. ├─base::loadNamespace(x)
30. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
31. │ │ └─base withOneRestart(expr, restarts[[1L]])
32. │ │ └─base doWithOneRestart(return(expr), restart)
33. │ └─base::stop(cond)
34. └─dplyr `<fn>`(`<pckgNtFE>`)
35. └─rlang::abort(...)
── Failure (test-stat_lm.R:51:3): std.beta works as intended for stat_lm ───────
`... <- NULL` threw an unexpected error.
Message: Problem while computing `metrics = purrr::map2(...)`.
Caused by error in `loadNamespace()`:
! there is no package called 'psychometric'
Class: dplyr:::mutate_error/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-stat_lm.R:51:2
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─model %>% set_stats(stat_lm(std.beta = F)) %>% fit() %>% ...
8. ├─base::summary(.)
9. ├─aba:::summary.abaModel(.)
10. │ └─object %>% aba_summary(...)
11. ├─aba::aba_summary(., ...)
12. │ └─object %>% calculate_metrics(control)
13. ├─aba:::calculate_metrics(., control)
14. │ └─r %>% ...
15. ├─dplyr::mutate(...)
16. ├─dplyr:::mutate.data.frame(...)
17. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
18. │ ├─base::withCallingHandlers(...)
19. │ └─mask$eval_all_mutate(quo)
20. ├─purrr::map2(...)
21. │ └─aba .f(.x[[i]], .y[[i]], ...)
22. │ ├─... %>% mutate(term = tolower(term))
23. │ ├─aba:::aba_glance(model, basic_model)
24. │ └─aba:::aba_glance.lm(model, basic_model)
25. ├─dplyr::mutate(., term = tolower(term))
26. ├─dplyr::arrange(., match(term, metric_vars))
27. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
28. ├─dplyr::filter(., term %in% metric_vars)
29. ├─base::loadNamespace(x)
30. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
31. │ │ └─base withOneRestart(expr, restarts[[1L]])
32. │ │ └─base doWithOneRestart(return(expr), restart)
33. │ └─base::stop(cond)
34. └─dplyr `<fn>`(`<pckgNtFE>`)
35. └─rlang::abort(...)
── Error (test-stat_lm.R:61:3): std.beta works as intended for stat_lm ─────────
Error in `all.equal(m1$results$coefs$estimate, m2$results$coefs$estimate)`: object 'm1' not found
Backtrace:
▆
1. ├─testthat::expect_false(...) at test-stat_lm.R:61:2
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::isTRUE(all.equal(m1$results$coefs$estimate, m2$results$coefs$estimate))
5. └─base::all.equal(m1$results$coefs$estimate, m2$results$coefs$estimate)
[ FAIL 5 | WARN 0 | SKIP 2 | PASS 127 ]
Error: Test failures
Execution halted
Flavor: r-patched-linux-x86_64
Version: 0.0.9
Check: tests
Result: ERROR
Running ‘testthat.R’ [156s/187s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(aba)
>
>
> test_check("aba")
Stratified by DX_bl
level Overall
n 2347 24
AGE (mean (SD)) 73.07 (7.43) 68.85 (8.30)
GENDER (mean (SD)) 0.53 (0.50) 0.38 (0.49)
EDUCATION (mean (SD)) 16.05 (2.75) 15.83 (2.16)
ConvertedToAlzheimers (mean (SD)) 0.20 (0.40) NaN (NA)
CSF_ABETA_STATUS_bl (mean (SD)) 0.62 (0.49) NaN (NA)
PLASMA_PTAU181_bl (mean (SD)) 2.71 (0.64) NaN (NA)
PLASMA_NFL_bl (mean (SD)) 3.54 (0.46) NaN (NA)
Stratified by DX_bl
AD CU MCI
n 405 846 1072
AGE (mean (SD)) 74.80 (7.92) 72.69 (6.34) 72.80 (7.89)
GENDER (mean (SD)) 0.57 (0.50) 0.44 (0.50) 0.59 (0.49)
EDUCATION (mean (SD)) 15.20 (2.91) 16.54 (2.53) 15.99 (2.78)
ConvertedToAlzheimers (mean (SD)) 0.00 (NA) 0.03 (0.18) 0.33 (0.47)
CSF_ABETA_STATUS_bl (mean (SD)) 0.88 (0.33) 0.39 (0.49) 0.63 (0.48)
PLASMA_PTAU181_bl (mean (SD)) 3.05 (0.41) 2.54 (0.67) 2.70 (0.64)
PLASMA_NFL_bl (mean (SD)) 3.77 (0.42) 3.45 (0.42) 3.52 (0.47)
Stratified by DX_bl
p test
n
AGE (mean (SD)) <0.001
GENDER (mean (SD)) <0.001
EDUCATION (mean (SD)) <0.001
ConvertedToAlzheimers (mean (SD)) NA
CSF_ABETA_STATUS_bl (mean (SD)) <0.001
PLASMA_PTAU181_bl (mean (SD)) <0.001
PLASMA_NFL_bl (mean (SD)) <0.001
[ FAIL 5 | WARN 0 | SKIP 2 | PASS 127 ]
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On CRAN (2)
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure (test-stat_ancova.R:28:3): example works ────────────────────────────
`ancova_summary <- ancova_model %>% summary()` threw an unexpected error.
Message: Problem while computing `metrics = purrr::map2(...)`.
Caused by error in `loadNamespace()`:
! there is no package called 'psychometric'
Class: dplyr:::mutate_error/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-stat_ancova.R:28:2
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─ancova_model %>% summary()
8. ├─base::summary(.)
9. ├─aba:::summary.abaModel(.)
10. │ └─object %>% aba_summary(...)
11. ├─aba::aba_summary(., ...)
12. │ └─object %>% calculate_metrics(control)
13. ├─aba:::calculate_metrics(., control)
14. │ └─r %>% ...
15. ├─dplyr::mutate(...)
16. ├─dplyr:::mutate.data.frame(...)
17. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
18. │ ├─base::withCallingHandlers(...)
19. │ └─mask$eval_all_mutate(quo)
20. ├─purrr::map2(...)
21. │ └─aba .f(.x[[i]], .y[[i]], ...)
22. │ ├─... %>% mutate(term = tolower(term))
23. │ ├─aba:::aba_glance(model, basic_model)
24. │ └─aba:::aba_glance.lm(model, basic_model)
25. ├─dplyr::mutate(., term = tolower(term))
26. ├─dplyr::arrange(., match(term, metric_vars))
27. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
28. ├─dplyr::filter(., term %in% metric_vars)
29. ├─base::loadNamespace(x)
30. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
31. │ │ └─base withOneRestart(expr, restarts[[1L]])
32. │ │ └─base doWithOneRestart(return(expr), restart)
33. │ └─base::stop(cond)
34. └─dplyr `<fn>`(`<pckgNtFE>`)
35. └─rlang::abort(...)
── Failure (test-stat_lm.R:6:3): complete.cases=F for lm works ─────────────────
`... <- NULL` threw an unexpected error.
Message: Problem while computing `metrics = purrr::map2(...)`.
Caused by error in `loadNamespace()`:
! there is no package called 'psychometric'
Class: dplyr:::mutate_error/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-stat_lm.R:6:2
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─... %>% aba_summary()
8. ├─aba::aba_summary(.)
9. │ └─object %>% calculate_metrics(control)
10. ├─aba:::calculate_metrics(., control)
11. │ └─r %>% ...
12. ├─dplyr::mutate(...)
13. ├─dplyr:::mutate.data.frame(...)
14. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
15. │ ├─base::withCallingHandlers(...)
16. │ └─mask$eval_all_mutate(quo)
17. ├─purrr::map2(...)
18. │ └─aba .f(.x[[i]], .y[[i]], ...)
19. │ ├─... %>% mutate(term = tolower(term))
20. │ ├─aba:::aba_glance(model, basic_model)
21. │ └─aba:::aba_glance.lm(model, basic_model)
22. ├─dplyr::mutate(., term = tolower(term))
23. ├─dplyr::arrange(., match(term, metric_vars))
24. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
25. ├─dplyr::filter(., term %in% metric_vars)
26. ├─base::loadNamespace(x)
27. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
28. │ │ └─base withOneRestart(expr, restarts[[1L]])
29. │ │ └─base doWithOneRestart(return(expr), restart)
30. │ └─base::stop(cond)
31. └─dplyr `<fn>`(`<pckgNtFE>`)
32. └─rlang::abort(...)
── Failure (test-stat_lm.R:41:3): std.beta works as intended for stat_lm ───────
`... <- NULL` threw an unexpected error.
Message: Problem while computing `metrics = purrr::map2(...)`.
Caused by error in `loadNamespace()`:
! there is no package called 'psychometric'
Class: dplyr:::mutate_error/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-stat_lm.R:41:2
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─model %>% set_stats(stat_lm(std.beta = T)) %>% fit() %>% ...
8. ├─base::summary(.)
9. ├─aba:::summary.abaModel(.)
10. │ └─object %>% aba_summary(...)
11. ├─aba::aba_summary(., ...)
12. │ └─object %>% calculate_metrics(control)
13. ├─aba:::calculate_metrics(., control)
14. │ └─r %>% ...
15. ├─dplyr::mutate(...)
16. ├─dplyr:::mutate.data.frame(...)
17. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
18. │ ├─base::withCallingHandlers(...)
19. │ └─mask$eval_all_mutate(quo)
20. ├─purrr::map2(...)
21. │ └─aba .f(.x[[i]], .y[[i]], ...)
22. │ ├─... %>% mutate(term = tolower(term))
23. │ ├─aba:::aba_glance(model, basic_model)
24. │ └─aba:::aba_glance.lm(model, basic_model)
25. ├─dplyr::mutate(., term = tolower(term))
26. ├─dplyr::arrange(., match(term, metric_vars))
27. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
28. ├─dplyr::filter(., term %in% metric_vars)
29. ├─base::loadNamespace(x)
30. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
31. │ │ └─base withOneRestart(expr, restarts[[1L]])
32. │ │ └─base doWithOneRestart(return(expr), restart)
33. │ └─base::stop(cond)
34. └─dplyr `<fn>`(`<pckgNtFE>`)
35. └─rlang::abort(...)
── Failure (test-stat_lm.R:51:3): std.beta works as intended for stat_lm ───────
`... <- NULL` threw an unexpected error.
Message: Problem while computing `metrics = purrr::map2(...)`.
Caused by error in `loadNamespace()`:
! there is no package called 'psychometric'
Class: dplyr:::mutate_error/rlang_error/error/condition
Backtrace:
▆
1. ├─testthat::expect_error(...) at test-stat_lm.R:51:2
2. │ └─testthat:::expect_condition_matching(...)
3. │ └─testthat:::quasi_capture(...)
4. │ ├─testthat .capture(...)
5. │ │ └─base::withCallingHandlers(...)
6. │ └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
7. ├─model %>% set_stats(stat_lm(std.beta = F)) %>% fit() %>% ...
8. ├─base::summary(.)
9. ├─aba:::summary.abaModel(.)
10. │ └─object %>% aba_summary(...)
11. ├─aba::aba_summary(., ...)
12. │ └─object %>% calculate_metrics(control)
13. ├─aba:::calculate_metrics(., control)
14. │ └─r %>% ...
15. ├─dplyr::mutate(...)
16. ├─dplyr:::mutate.data.frame(...)
17. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), caller_env = caller_env())
18. │ ├─base::withCallingHandlers(...)
19. │ └─mask$eval_all_mutate(quo)
20. ├─purrr::map2(...)
21. │ └─aba .f(.x[[i]], .y[[i]], ...)
22. │ ├─... %>% mutate(term = tolower(term))
23. │ ├─aba:::aba_glance(model, basic_model)
24. │ └─aba:::aba_glance.lm(model, basic_model)
25. ├─dplyr::mutate(., term = tolower(term))
26. ├─dplyr::arrange(., match(term, metric_vars))
27. ├─dplyr::rename(., conf_low = conf.low, conf_high = conf.high)
28. ├─dplyr::filter(., term %in% metric_vars)
29. ├─base::loadNamespace(x)
30. │ ├─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
31. │ │ └─base withOneRestart(expr, restarts[[1L]])
32. │ │ └─base doWithOneRestart(return(expr), restart)
33. │ └─base::stop(cond)
34. └─dplyr `<fn>`(`<pckgNtFE>`)
35. └─rlang::abort(...)
── Error (test-stat_lm.R:61:3): std.beta works as intended for stat_lm ─────────
Error in `all.equal(m1$results$coefs$estimate, m2$results$coefs$estimate)`: object 'm1' not found
Backtrace:
▆
1. ├─testthat::expect_false(...) at test-stat_lm.R:61:2
2. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
3. │ └─rlang::eval_bare(expr, quo_get_env(quo))
4. ├─base::isTRUE(all.equal(m1$results$coefs$estimate, m2$results$coefs$estimate))
5. └─base::all.equal(m1$results$coefs$estimate, m2$results$coefs$estimate)
[ FAIL 5 | WARN 0 | SKIP 2 | PASS 127 ]
Error: Test failures
Execution halted
Flavor: r-release-linux-x86_64