* using log directory ‘/data/gannet/ripley/R/packages/tests-clang/afex.Rcheck’
* using R Under development (unstable) (2025-02-28 r87848)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
clang version 20.1.0-rc3
flang version 20.1.0-rc3
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘afex’ can be installed ... [25s/30s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-clang/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 ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... 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 ... [40s/51s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 ... 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 ... [38s/46s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [122s/151s] ERROR
Running ‘testthat.R’ [121s/151s]
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, 8.24 2.19 .173
---
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, 12.78 2.88 + .093
2 phase 2, 222.08 38.51 *** <.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 NaN <NA>
---
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 NaN <NA>
2 phase 2 NaN <NA>
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '+' 0.1 ' ' 1
Mixed Model Anova Table (Type 3 tests, PB-method)
Model: use ~ urban + (1 | district)
Data: Contraception
Effect df Chisq p.value
1 urban 1 31.28 .333
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '+' 0.1 ' ' 1
Mixed Model Anova Table (Type 3 tests, PB-method)
Model: use ~ urban + livch + (1 | district)
Data: Contraception
Effect df Chisq p.value
1 urban 1 36.33 .333
2 livch 3 77.91 .333
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '+' 0.1 ' ' 1
[ FAIL 9 | WARN 496 | SKIP 29 | PASS 332 ]
â•â• Skipped tests (29) â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•
• 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'
â•â• Failed tests â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•
── Failure ('test-mixed-mw.R:10:3'): mixed: Maxell & Delaney (2004), Table 16.3, p. 837 ──
`x` not equal to `expected`.
1/1 mismatches
[1] 3.28 - 9.97 == -6.69
Backtrace:
â–†
1. └─testthat::expect_that(round(anova(mixed1_orig)[1, "F"], 2), equals(9.97)) at test-mixed-mw.R:10:3
2. └─testthat (local) condition(object)
3. └─testthat::expect_equal(x, expected, ..., expected.label = label)
── Failure ('test-mixed-mw.R:11:3'): mixed: Maxell & Delaney (2004), Table 16.3, p. 837 ──
`x` not equal to `expected`.
1/1 mismatches
[1] 0.83 - 0.03 == 0.8
Backtrace:
â–†
1. └─testthat::expect_that(...) at test-mixed-mw.R:11:3
2. └─testthat (local) condition(object)
3. └─testthat::expect_equal(x, expected, ..., expected.label = label)
── Failure ('test-mixed-mw.R:20:3'): mixed: Maxell & Delaney (2004), Table 16.6, p. 845 ──
unname(round(fixef(mixed2_orig$full_model), 4)) not equivalent to c(35.6261, -8.1485).
2/2 mismatches (average diff: 0.0848)
[1] 35.54 - 35.63 == -0.0821
[2] -8.06 - -8.15 == 0.0875
── Failure ('test-mixed-mw.R:23:3'): mixed: Maxell & Delaney (2004), Table 16.6, p. 845 ──
`x` not equal to `expected`.
2/2 mismatches (average diff: 1.12)
[1] 4.16 - 3.23 == 0.927
[2] 5.86 - 4.55 == 1.315
Backtrace:
â–†
1. └─testthat::expect_that(...) at test-mixed-mw.R:23:3
2. └─testthat (local) condition(object)
3. └─testthat::expect_equal(x, expected, ..., expected.label = label)
── Failure ('test-mixed-mw.R:27:3'): mixed: Maxell & Delaney (2004), Table 16.6, p. 845 ──
`x` not equal to `expected`.
1/1 mismatches
[1] 1.9 - 3.2 == -1.3
Backtrace:
â–†
1. └─testthat::expect_that(round(mixed2_orig[[1]]$F, 1), equals(3.2)) at test-mixed-mw.R:27:3
2. └─testthat (local) condition(object)
3. └─testthat::expect_equal(x, expected, ..., expected.label = label)
── Failure ('test-mixed-mw.R:39:3'): mixed: Maxell & Delaney (2004), Table 16.7, p. 851 (uses simple F!) ──
`x` not equivalent to `expected`.
2/3 mismatches (average diff: 0.26)
[1] 20.05 - 20.25 == -0.20
[2] -7.25 - -7.57 == 0.32
Backtrace:
â–†
1. └─testthat::expect_that(...) at test-mixed-mw.R:39:3
2. └─testthat (local) condition(object)
3. └─testthat::expect_equivalent(x, expected, expected.label = label)
── Failure ('test-mixed-mw.R:41:3'): mixed: Maxell & Delaney (2004), Table 16.7, p. 851 (uses simple F!) ──
`x` not equal to `expected`.
3/3 mismatches (average diff: 3.42)
[1] 12.1 - 5.82 == 6.30
[2] 5.8 - 2.72 == 3.08
[3] 1.7 - 0.81 == 0.89
Backtrace:
â–†
1. └─testthat::expect_that(...) at test-mixed-mw.R:41:3
2. └─testthat (local) condition(object)
3. └─testthat::expect_equal(x, expected, ..., expected.label = label)
── Failure ('test-mixed-mw.R:45:3'): mixed: Maxell & Delaney (2004), Table 16.7, p. 851 (uses simple F!) ──
`x` not equal to `expected`.
2/2 mismatches (average diff: 6)
[1] 2 - 8 == -6
[2] 2 - 8 == -6
Backtrace:
â–†
1. └─testthat::expect_that(...) at test-mixed-mw.R:45:3
2. └─testthat (local) condition(object)
3. └─testthat::expect_equal(x, expected, ..., expected.label = label)
── Failure ('test-mixed-mw.R:58:3'): mixed: Maxell & Delaney (2004), Table 16.10, p. 862 (does not replicate the table!) ──
`x` not equivalent to `expected`.
4/4 mismatches (average diff: 0.153)
[1] 35.90 - 36.10 == -0.20
[2] -8.87 - -9.07 == 0.20
[3] 0.72 - 0.64 == 0.08
[4] -0.10 - 0.03 == -0.13
Backtrace:
â–†
1. └─testthat::expect_that(...) at test-mixed-mw.R:58:3
2. └─testthat (local) condition(object)
3. └─testthat::expect_equivalent(x, expected, expected.label = label)
[ FAIL 9 | WARN 496 | SKIP 29 | PASS 332 ]
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 ... [212s/263s] OK
* checking PDF version of manual ... [10s/13s] OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR