Last updated on 2025-07-18 18:51:08 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.4-1 | 16.03 | 350.19 | 366.22 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.4-1 | 8.94 | 243.27 | 252.21 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.4-1 | 552.29 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 1.4-1 | 573.16 | ERROR | |||
| r-devel-windows-x86_64 | 1.4-1 | 17.00 | 336.00 | 353.00 | OK | |
| r-patched-linux-x86_64 | 1.4-1 | 16.21 | 333.69 | 349.90 | OK | |
| r-release-linux-x86_64 | 1.4-1 | 13.88 | 334.01 | 347.89 | OK | |
| r-release-macos-arm64 | 1.4-1 | 163.00 | OK | |||
| r-release-macos-x86_64 | 1.4-1 | 279.00 | OK | |||
| r-release-windows-x86_64 | 1.4-1 | 17.00 | 335.00 | 352.00 | OK | |
| r-oldrel-macos-arm64 | 1.4-1 | 126.00 | OK | |||
| r-oldrel-macos-x86_64 | 1.4-1 | 259.00 | OK | |||
| r-oldrel-windows-x86_64 | 1.4-1 | 23.00 | 441.00 | 464.00 | OK |
Version: 1.4-1
Check: tests
Result: ERROR
Running ‘testthat.R’ [92s/145s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(afex)
Loading required package: lme4
Loading required package: Matrix
************
Welcome to afex. For support visit: http://afex.singmann.science/
- Functions for ANOVAs: aov_car(), aov_ez(), and aov_4()
- Methods for calculating p-values with mixed(): 'S', 'KR', 'LRT', and 'PB'
- 'afex_aov' and 'mixed' objects can be passed to emmeans() for follow-up tests
- Get and set global package options with: afex_options()
- Set sum-to-zero contrasts globally: set_sum_contrasts()
- For example analyses see: browseVignettes("afex")
************
Attaching package: 'afex'
The following object is masked from 'package:lme4':
lmer
>
> test_check("afex")
Mixed Model Anova Table (Type 3 tests, S-method)
Model: value ~ treatment + (1 | id)
Data: obk.long
Effect df F p.value
1 treatment 2, 13.00 2.91 + .090
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '+' 0.1 ' ' 1
Mixed Model Anova Table (Type 3 tests, S-method)
Model: value ~ treatment + phase + (1 | id)
Data: obk.long
Effect df F p.value
1 treatment 2, 13.00 2.91 + .090
2 phase 2, 222.00 38.48 *** <.001
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '+' 0.1 ' ' 1
Mixed Model Anova Table (Type 3 tests, LRT-method)
Model: value ~ treatment + (1 | id)
Data: obk.long
Df full model: 5
Effect df Chisq p.value
1 treatment 2 5.93 + .052
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '+' 0.1 ' ' 1
Mixed Model Anova Table (Type 3 tests, LRT-method)
Model: value ~ treatment + phase + (1 | id)
Data: obk.long
Df full model: 7
Effect df Chisq p.value
1 treatment 2 5.93 + .052
2 phase 2 66.67 *** <.001
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '+' 0.1 ' ' 1
[ FAIL 1 | WARN 1 | SKIP 29 | PASS 339 ]
══ Skipped tests (29) ══════════════════════════════════════════════════════════
• On CRAN (28): 'test-afex_plot-basics.R:11:3', 'test-afex_plot-basics.R:76:3',
'test-afex_plot-basics.R:111:3', 'test-afex_plot-basics.R:140:3',
'test-afex_plot-basics.R:346:3', 'test-afex_plot-basics.R:360:3',
'test-afex_plot-bugs.R:6:3', 'test-afex_plot-bugs.R:21:3',
'test-afex_plot-bugs.R:43:3', 'test-afex_plot-bugs.R:79:3',
'test-afex_plot-default-support.R:11:3',
'test-afex_plot-default-support.R:20:3',
'test-afex_plot-default-support.R:38:3',
'test-afex_plot-default-support.R:66:3', 'test-afex_plot-vignette.R:4:3',
'test-afex_plot-vignette.R:38:3', 'test-afex_plot-vignette.R:114:3',
'test-aov_car-bugs.R:253:3', 'test-emmeans-interface.R:144:3',
'test-emmeans-interface.R:209:3', 'test-mixed-bugs.R:6:3',
'test-mixed-bugs.R:19:3', 'test-mixed-structure.R:214:5',
'test-mixed-structure.R:242:3', 'test-mixed-structure.R:264:3',
'test-mixed-structure.R:305:3', 'test-mixed-structure.R:349:3',
'test-mixed-structure.R:369:3'
• empty test (1): 'test-mixed-structure.R:86:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-mixed-structure.R:120:3'): print(mixed) works: only 1 or 2 fixed effects with all methods ──
Error in `glmer(formula = use ~ m.matrix[, -2] + (1 | district) - 1, data = dd,
family = binomial, REML = FALSE, control = ctrl)`: unused argument (REML = FALSE)
Backtrace:
▆
1. ├─testthat::expect_that(...) at test-mixed-structure.R:120:3
2. │ └─testthat (local) condition(object)
3. │ └─testthat::expect_is(x, class)
4. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
5. │ └─rlang::eval_bare(expr, quo_get_env(quo))
6. ├─base::print(...)
7. └─afex::mixed(...)
8. ├─base::do.call(...)
9. ├─pbkrtest (local) `<fn>`(...)
10. └─pbkrtest:::PBmodcomp.merMod(...)
11. ├─pbkrtest::PBrefdist(...)
12. └─pbkrtest:::PBrefdist.merMod(...)
13. └─pbkrtest:::do_sampling(largeModel, smallModel, nsim, cl, details)
14. ├─base::unlist(...)
15. └─parallel::mclapply(...)
16. └─base::lapply(X = X, FUN = FUN, ...)
17. └─pbkrtest (local) FUN(X[[i]], ...)
18. └─pbkrtest (local) get_fun(largeModel, smallModel, nsim = nsim.cl)
19. ├─base::unname(...)
20. ├─base::unlist(...)
21. └─base::lapply(...)
22. └─pbkrtest (local) FUN(X[[i]], ...)
23. ├─base::suppressMessages(refit_safe(sm, yyy, ctrl))
24. │ └─base::withCallingHandlers(...)
25. └─pbkrtest (local) refit_safe(sm, yyy, ctrl)
[ FAIL 1 | WARN 1 | SKIP 29 | PASS 339 ]
Deleting unused snapshots:
• afex_plot-basics/afex-plot-connecting-individual-points-works.svg
• afex_plot-basics/geoms-work-box-plot.svg
• afex_plot-basics/geoms-work-boxjitter-1.svg
• afex_plot-basics/geoms-work-boxjitter-2.svg
• afex_plot-basics/geoms-work-boxjitter-3.svg
• afex_plot-basics/geoms-work-geom-count.svg
• afex_plot-basics/geoms-work-ggbeeswarm-geom-beeswarm.svg
• afex_plot-basics/geoms-work-ggbeeswarm-geom-quasirandom.svg
• afex_plot-basics/geoms-work-jitterdodge.svg
• afex_plot-basics/geoms-work-violin-with-colour.svg
• afex_plot-basics/geoms-work-violin.svg
• afex_plot-basics/lme4-mermod-plot-2.svg
• afex_plot-basics/lme4-mermod-plot-3.svg
• afex_plot-basics/mixed-model-1.svg
• afex_plot-basics/mixed-model-2.svg
• afex_plot-basics/mixed-model-3.svg
• afex_plot-basics/mixed-model-4.svg
• afex_plot-basics/multiple-geoms-work-1.svg
• afex_plot-basics/multiple-geoms-work-2.svg
• afex_plot-basics/one-way-within.svg
• afex_plot-basics/plot-first-for-afex-plot-works-1.svg
• afex_plot-basics/plot-first-for-afex-plot-works-2.svg
• afex_plot-basics/plot-first-for-afex-plot-works-3.svg
• afex_plot-basics/plot-first-for-afex-plot-works-4.svg
• afex_plot-basics/two-way.svg
• afex_plot-basics/x-trace-panel.svg
• afex_plot-bugs/afex-plot-binomial-glm-with-factor-2.svg
• afex_plot-bugs/afex-plot-dv-y-works.svg
• afex_plot-bugs/afex-plot-lmm-type-2.svg
• afex_plot-bugs/afex-plot-mermod-objects-with-missing-data.svg
• afex_plot-default-support/afex-plots-binomial-glm-1.svg
• afex_plot-default-support/afex-plots-binomial-glm-2.svg
• afex_plot-default-support/afex-plots-lm-model-2.svg
• afex_plot-default-support/afex-plots-nlme-2.svg
• afex_plot-default-support/afex-plots-nlme-3.svg
• afex_plot-default-support/afex-plots-nlme-4.svg
• afex_plot-default-support/afex-plots-nlme-5.svg
• afex_plot-default-support/afex-plots-poisson-glm-1.svg
• afex_plot-default-support/afex-plots-poisson-glm-2.svg
• afex_plot-vignette/afex-plot-glmmtmb-1.svg
• afex_plot-vignette/afex-plot-glmmtmb-2.svg
• afex_plot-vignette/afex-plot-glmmtmb-3.svg
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 1.4-1
Check: tests
Result: ERROR
Running ‘testthat.R’ [94s/111s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(afex)
Loading required package: lme4
Loading required package: Matrix
************
Welcome to afex. For support visit: http://afex.singmann.science/
- Functions for ANOVAs: aov_car(), aov_ez(), and aov_4()
- Methods for calculating p-values with mixed(): 'S', 'KR', 'LRT', and 'PB'
- 'afex_aov' and 'mixed' objects can be passed to emmeans() for follow-up tests
- Get and set global package options with: afex_options()
- Set sum-to-zero contrasts globally: set_sum_contrasts()
- For example analyses see: browseVignettes("afex")
************
Attaching package: 'afex'
The following object is masked from 'package:lme4':
lmer
>
> test_check("afex")
Mixed Model Anova Table (Type 3 tests, S-method)
Model: value ~ treatment + (1 | id)
Data: obk.long
Effect df F p.value
1 treatment 2, 13.00 2.91 + .090
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '+' 0.1 ' ' 1
Mixed Model Anova Table (Type 3 tests, S-method)
Model: value ~ treatment + phase + (1 | id)
Data: obk.long
Effect df F p.value
1 treatment 2, 13.00 2.91 + .090
2 phase 2, 222.00 38.48 *** <.001
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '+' 0.1 ' ' 1
Mixed Model Anova Table (Type 3 tests, LRT-method)
Model: value ~ treatment + (1 | id)
Data: obk.long
Df full model: 5
Effect df Chisq p.value
1 treatment 2 5.93 + .052
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '+' 0.1 ' ' 1
Mixed Model Anova Table (Type 3 tests, LRT-method)
Model: value ~ treatment + phase + (1 | id)
Data: obk.long
Df full model: 7
Effect df Chisq p.value
1 treatment 2 5.93 + .052
2 phase 2 66.67 *** <.001
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '+' 0.1 ' ' 1
[ FAIL 1 | WARN 1 | SKIP 29 | PASS 339 ]
══ Skipped tests (29) ══════════════════════════════════════════════════════════
• On CRAN (28): 'test-afex_plot-basics.R:11:3', 'test-afex_plot-basics.R:76:3',
'test-afex_plot-basics.R:111:3', 'test-afex_plot-basics.R:140:3',
'test-afex_plot-basics.R:346:3', 'test-afex_plot-basics.R:360:3',
'test-afex_plot-bugs.R:6:3', 'test-afex_plot-bugs.R:21:3',
'test-afex_plot-bugs.R:43:3', 'test-afex_plot-bugs.R:79:3',
'test-afex_plot-default-support.R:11:3',
'test-afex_plot-default-support.R:20:3',
'test-afex_plot-default-support.R:38:3',
'test-afex_plot-default-support.R:66:3', 'test-afex_plot-vignette.R:4:3',
'test-afex_plot-vignette.R:38:3', 'test-afex_plot-vignette.R:114:3',
'test-aov_car-bugs.R:253:3', 'test-emmeans-interface.R:144:3',
'test-emmeans-interface.R:209:3', 'test-mixed-bugs.R:6:3',
'test-mixed-bugs.R:19:3', 'test-mixed-structure.R:214:5',
'test-mixed-structure.R:242:3', 'test-mixed-structure.R:264:3',
'test-mixed-structure.R:305:3', 'test-mixed-structure.R:349:3',
'test-mixed-structure.R:369:3'
• empty test (1): 'test-mixed-structure.R:86:1'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-mixed-structure.R:120:3'): print(mixed) works: only 1 or 2 fixed effects with all methods ──
Error in `glmer(formula = use ~ m.matrix[, -2] + (1 | district) - 1, data = dd,
family = binomial, REML = FALSE, control = ctrl)`: unused argument (REML = FALSE)
Backtrace:
▆
1. ├─testthat::expect_that(...) at test-mixed-structure.R:120:3
2. │ └─testthat (local) condition(object)
3. │ └─testthat::expect_is(x, class)
4. │ └─testthat::quasi_label(enquo(object), label, arg = "object")
5. │ └─rlang::eval_bare(expr, quo_get_env(quo))
6. ├─base::print(...)
7. └─afex::mixed(...)
8. ├─base::do.call(...)
9. ├─pbkrtest (local) `<fn>`(...)
10. └─pbkrtest:::PBmodcomp.merMod(...)
11. ├─pbkrtest::PBrefdist(...)
12. └─pbkrtest:::PBrefdist.merMod(...)
13. └─pbkrtest:::do_sampling(largeModel, smallModel, nsim, cl, details)
14. ├─base::unlist(...)
15. └─parallel::mclapply(...)
16. └─base::lapply(X = X, FUN = FUN, ...)
17. └─pbkrtest (local) FUN(X[[i]], ...)
18. └─pbkrtest (local) get_fun(largeModel, smallModel, nsim = nsim.cl)
19. ├─base::unname(...)
20. ├─base::unlist(...)
21. └─base::lapply(...)
22. └─pbkrtest (local) FUN(X[[i]], ...)
23. ├─base::suppressMessages(refit_safe(sm, yyy, ctrl))
24. │ └─base::withCallingHandlers(...)
25. └─pbkrtest (local) refit_safe(sm, yyy, ctrl)
[ FAIL 1 | WARN 1 | SKIP 29 | PASS 339 ]
Deleting unused snapshots:
• afex_plot-basics/afex-plot-connecting-individual-points-works.svg
• afex_plot-basics/geoms-work-box-plot.svg
• afex_plot-basics/geoms-work-boxjitter-1.svg
• afex_plot-basics/geoms-work-boxjitter-2.svg
• afex_plot-basics/geoms-work-boxjitter-3.svg
• afex_plot-basics/geoms-work-geom-count.svg
• afex_plot-basics/geoms-work-ggbeeswarm-geom-beeswarm.svg
• afex_plot-basics/geoms-work-ggbeeswarm-geom-quasirandom.svg
• afex_plot-basics/geoms-work-jitterdodge.svg
• afex_plot-basics/geoms-work-violin-with-colour.svg
• afex_plot-basics/geoms-work-violin.svg
• afex_plot-basics/lme4-mermod-plot-2.svg
• afex_plot-basics/lme4-mermod-plot-3.svg
• afex_plot-basics/mixed-model-1.svg
• afex_plot-basics/mixed-model-2.svg
• afex_plot-basics/mixed-model-3.svg
• afex_plot-basics/mixed-model-4.svg
• afex_plot-basics/multiple-geoms-work-1.svg
• afex_plot-basics/multiple-geoms-work-2.svg
• afex_plot-basics/one-way-within.svg
• afex_plot-basics/plot-first-for-afex-plot-works-1.svg
• afex_plot-basics/plot-first-for-afex-plot-works-2.svg
• afex_plot-basics/plot-first-for-afex-plot-works-3.svg
• afex_plot-basics/plot-first-for-afex-plot-works-4.svg
• afex_plot-basics/two-way.svg
• afex_plot-basics/x-trace-panel.svg
• afex_plot-bugs/afex-plot-binomial-glm-with-factor-2.svg
• afex_plot-bugs/afex-plot-dv-y-works.svg
• afex_plot-bugs/afex-plot-lmm-type-2.svg
• afex_plot-bugs/afex-plot-mermod-objects-with-missing-data.svg
• afex_plot-default-support/afex-plots-binomial-glm-1.svg
• afex_plot-default-support/afex-plots-binomial-glm-2.svg
• afex_plot-default-support/afex-plots-lm-model-2.svg
• afex_plot-default-support/afex-plots-nlme-2.svg
• afex_plot-default-support/afex-plots-nlme-3.svg
• afex_plot-default-support/afex-plots-nlme-4.svg
• afex_plot-default-support/afex-plots-nlme-5.svg
• afex_plot-default-support/afex-plots-poisson-glm-1.svg
• afex_plot-default-support/afex-plots-poisson-glm-2.svg
• afex_plot-vignette/afex-plot-glmmtmb-1.svg
• afex_plot-vignette/afex-plot-glmmtmb-2.svg
• afex_plot-vignette/afex-plot-glmmtmb-3.svg
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc