Package: afex Check: tests New result: ERROR Running ‘testthat.R’ [36s/36s] 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) ``(...) 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 Package: simr Check: tests New result: ERROR Running ‘test-all.R’ [30s/30s] Running the tests in ‘tests/test-all.R’ failed. Complete output: > if(require(testthat)) { + + test_check("simr") + } Loading required package: testthat Loading required package: simr Loading required package: lme4 Loading required package: Matrix Attaching package: 'simr' The following object is masked from 'package:lme4': getData The following object is masked from 'package:testthat': compare boundary (singular) fit: see help('isSingular') [ FAIL 1 | WARN 0 | SKIP 0 | PASS 112 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_testLibrary.R:31:5'): tests run ──────────────────────────────── Error in `glmer(formula = z ~ x + (1 | g), data = dd, family = poisson, REML = FALSE, control = ctrl)`: unused argument (REML = FALSE) Backtrace: ▆ 1. ├─base::suppressWarnings(doTest(fm3, rcompare(~(1 | g), "pb"))) at test_testLibrary.R:31:5 2. │ └─base::withCallingHandlers(...) 3. ├─simr::doTest(fm3, rcompare(~(1 | g), "pb")) 4. └─simr:::doTest.default(fm3, rcompare(~(1 | g), "pb")) 5. └─simr (local) test(object) 6. └─simr (local) test(fit1, fit2) 7. ├─pbkrtest::PBmodcomp(model1, model2, nsim = getSimrOption("pbnsim")) 8. └─pbkrtest:::PBmodcomp.merMod(model1, model2, nsim = getSimrOption("pbnsim")) 9. ├─pbkrtest::PBrefdist(...) 10. └─pbkrtest:::PBrefdist.merMod(...) 11. └─pbkrtest:::do_sampling(largeModel, smallModel, nsim, cl, details) 12. ├─base::unlist(...) 13. └─parallel::mclapply(...) 14. └─base::lapply(X = X, FUN = FUN, ...) 15. └─pbkrtest (local) FUN(X[[i]], ...) 16. └─pbkrtest (local) get_fun(largeModel, smallModel, nsim = nsim.cl) 17. ├─base::unname(...) 18. ├─base::unlist(...) 19. └─base::lapply(...) 20. └─pbkrtest (local) FUN(X[[i]], ...) 21. ├─base::suppressMessages(refit_safe(sm, yyy, ctrl)) 22. │ └─base::withCallingHandlers(...) 23. └─pbkrtest (local) refit_safe(sm, yyy, ctrl) [ FAIL 1 | WARN 0 | SKIP 0 | PASS 112 ] Error: Test failures Execution halted