- using R Under development (unstable) (2024-04-14 r86421)
- using platform: x86_64-pc-linux-gnu
- R was compiled by
Debian clang version 18.1.0 (rc4-1)
Debian flang-new version 18.1.0 (rc4-1)
- running under: Debian GNU/Linux trixie/sid
- using session charset: UTF-8
- checking for file ‘ggeffects/DESCRIPTION’ ... OK
- checking extension type ... Package
- this is package ‘ggeffects’ version ‘1.5.1’
- package encoding: UTF-8
- checking package namespace information ... OK
- checking package dependencies ... NOTE
Package suggested but not available for checking: ‘margins’
- 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 ‘ggeffects’ can be installed ... OK
See the install log for details.
- checking package directory ... OK
- checking for future file timestamps ... 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 ... [0s/1s] OK
- checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
- checking whether the package can be unloaded cleanly ... [0s/1s] OK
- checking whether the namespace can be loaded with stated dependencies ... [0s/1s] OK
- checking whether the namespace can be unloaded cleanly ... [0s/1s] OK
- checking loading without being on the library search path ... [0s/1s] 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 ... [48s/59s] OK
- checking Rd files ... [1s/1s] 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 ... [0s/1s] OK
- checking data for ASCII and uncompressed saves ... OK
- checking installed files from ‘inst/doc’ ... OK
- checking files in ‘vignettes’ ... OK
- checking examples ... [18s/22s] OK
- checking for unstated dependencies in ‘tests’ ... OK
- checking tests ... [143s/172s] ERROR
Running ‘testthat.R’ [142s/172s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(ggeffects)
> test_check("ggeffects")
(Intercept) tensionM tensionH
36.38889 -10.00000 -14.72222
Not all rows are shown in the output. Use `print(..., n = Inf)` to show
all rows.
Not all rows are shown in the output. Use `print(..., n = Inf)` to show
all rows.
NOTE: Results may be misleading due to involvement in interactions
NOTE: Results may be misleading due to involvement in interactions
Data points may overlap. Use the `jitter` argument to add some amount of
random variation to the location of data points and avoid overplotting.
Data points may overlap. Use the `jitter` argument to add some amount of
random variation to the location of data points and avoid overplotting.
Data points may overlap. Use the `jitter` argument to add some amount of
random variation to the location of data points and avoid overplotting.
Data points may overlap. Use the `jitter` argument to add some amount of
random variation to the location of data points and avoid overplotting.
Re-fitting to get Hessian
Re-fitting to get Hessian
Model contains splines or polynomial terms. Consider using `terms="mined
[all]"` to get smooth plots. See also package-vignette 'Adjusted
Predictions at Specific Values'.
Model contains splines or polynomial terms. Consider using `terms="cover
[all]"` to get smooth plots. See also package-vignette 'Adjusted
Predictions at Specific Values'.
Model contains splines or polynomial terms. Consider using `terms="mined
[all]"` to get smooth plots. See also package-vignette 'Adjusted
Predictions at Specific Values'.
Model contains splines or polynomial terms. Consider using `terms="cover
[all]"` to get smooth plots. See also package-vignette 'Adjusted
Predictions at Specific Values'.
Can't compute adjusted predictions, `effects::Effect()` returned an error.
Reason: Invalid operation on a survival time
You may try `ggpredict()` or `ggemmeans()`.
Can't compute adjusted predictions, `effects::Effect()` returned an error.
Reason: non-conformable arguments
You may try `ggpredict()` or `ggemmeans()`.
[ FAIL 1 | WARN 16 | SKIP 48 | PASS 556 ]
══ Skipped tests (48) ══════════════════════════════════════════════════════════
• On CRAN (40): 'test-MCMCglmm.R:1:1', 'test-MixMod.R:1:1',
'test-avg_predictions.R:24:3', 'test-avg_predictions.R:79:5',
'test-brms-categ-cum.R:1:1', 'test-brms-ppd.R:1:1', 'test-brms-trial.R:1:1',
'test-clean_vars.R:1:1', 'test-clm.R:1:1', 'test-clm2.R:1:1',
'test-clmm.R:1:1', 'test-correct_se_sorting.R:1:1', 'test-decimals.R:1:1',
'test-fixest.R:1:1', 'test-format.R:1:1', 'test-gamlss.R:1:1',
'test-gamm4.R:1:1', 'test-glmer.R:2:1', 'test-glmmTMB.R:1:1',
'test-interval_re.R:1:1', 'test-ivreg.R:1:1',
'test-johnson_neyman_numcat.R:1:1', 'test-list_terms.R:36:3',
'test-lmer.R:1:1', 'test-mgcv.R:1:1', 'test-polr.R:21:7', 'test-polr.R:60:7',
'test-pool_comparisons.R:1:1', 'test-print.R:1:1', 'test-print_digits.R:1:1',
'test-print_md.R:1:1', 'test-resid_over_grid.R:33:5',
'test-rstanarm-ppd.R:1:1', 'test-rstanarm.R:1:1', 'test-sdmTMB.R:1:1',
'test-simulate.R:1:1', 'test-vcov.R:1:1', 'test-vglm.R:1:1',
'test-zeroinfl.R:27:3', 'test-zi_prob.R:1:1'
• On Linux (5): 'test-ordinal.R:1:1', 'test-parsnip.R:94:3',
'test-print_subsets.R:1:1', 'test-print_test_predictions-ordinal.R:1:1',
'test-print_test_predictions.R:1:1'
• empty test (3): 'test-plot.R:11:1', 'test-polr.R:136:5', 'test-polr.R:142:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-test_predictions.R:289:3'): test_predictions, works with glmmTMB and w/o vcov ──
Error: For this model type, `vcov` must be `TRUE` or `FALSE`.
Backtrace:
▆
1. ├─ggeffects::test_predictions(predictions, vcov = vcov(m_null)$cond) at test-test_predictions.R:289:3
2. └─ggeffects:::test_predictions.ggeffects(predictions, vcov = vcov(m_null)$cond)
3. ├─base::do.call(test_predictions.default, c(my_args, dot_args))
4. └─ggeffects (local) `<fn>`(...)
5. ├─base::do.call(...)
6. └─marginaleffects (local) `<fn>`(...)
7. └─marginaleffects::predictions(...)
8. └─marginaleffects:::sanitize_model(...)
9. ├─marginaleffects:::sanitize_model_specific(...)
10. └─marginaleffects:::sanitize_model_specific.glmmTMB(...)
11. └─insight::format_error(msg)
12. └─insight::format_alert(..., type = "error")
[ FAIL 1 | WARN 16 | SKIP 48 | PASS 556 ]
Error: Test failures
Execution halted
- checking for unstated dependencies in vignettes ... OK
- checking package vignettes ... OK
- checking re-building of vignette outputs ... [1s/2s] OK
- checking PDF version of manual ... [9s/13s] OK
- checking HTML version of manual ... [3s/4s] OK
- checking for non-standard things in the check directory ... OK
- DONE
Status: 1 ERROR, 1 NOTE