* using log directory 'd:/Rcompile/CRANpkg/local/4.5/afex.Rcheck' * using R version 4.5.1 (2025-06-13 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * checking for file 'afex/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'afex' version '1.4-1' * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking whether package 'afex' can be installed ... OK See 'https://www.r-project.org/nosvn/R.check/r-release-windows-x86_64/afex-00install.html' for details. * checking installed package size ... OK * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... [3s] OK * checking whether the package can be loaded with stated dependencies ... [3s] OK * checking whether the package can be unloaded cleanly ... [3s] OK * checking whether the namespace can be loaded with stated dependencies ... [3s] OK * checking whether the namespace can be unloaded cleanly ... [3s] OK * checking loading without being on the library search path ... [3s] OK * checking whether startup messages can be suppressed ... [3s] OK * checking use of S3 registration ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... [13s] OK * checking Rd files ... [1s] OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of 'data' directory ... OK * checking data for non-ASCII characters ... [1s] OK * checking LazyData ... OK * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under 'inst/doc' ... OK * checking installed files from 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... [21s] OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... [52s] ERROR Running 'testthat.R' [52s] 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, 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 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... [116s] OK * checking PDF version of manual ... [23s] OK * checking HTML version of manual ... [7s] OK * DONE Status: 1 ERROR