Package check result: OK Changes to worse in reverse depends: Package: catregs Check: examples New result: ERROR Running examples in ‘catregs-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: compare.margins > ### Title: Compares two marginal effects (MEMs or AMEs). Estimate of > ### uncertainty is from a simulated draw from a normal distribution. > ### Aliases: compare.margins > > ### ** Examples > > data("essUK") > m1 <- glm(safe ~ religious + minority*female + age,data=essUK,family="binomial") > des<-margins.des(m1,expand.grid(minority=c(0,1),female=c(0,1))) > des minority female religious age 1 0 0 3.602404 53.14563 2 1 0 3.602404 53.14563 3 0 1 3.602404 53.14563 4 1 1 3.602404 53.14563 > ma1<-suppressWarnings(as.data.frame(marginaleffects::avg_slopes(m1, + variables="female",newdata=data.frame(minority=0,religious=3.6024,age=53.146)))) Error: There is no valid predictor variable. Please change the `variables` argument or supply an alternative data frame to the `newdata` argument. Execution halted Package: catregs Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘compare.margins.Rmd’ using rmarkdown Quitting from compare.margins.Rmd:15-25 [unnamed-chunk-1] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! There is no valid predictor variable. Please change the `variables` argument or supply an alternative data frame to the `newdata` argument. --- Backtrace: ▆ 1. └─marginaleffects::comparisons(...) 2. └─marginaleffects:::add_variables(variables = variables, mfx = mfx) 3. └─marginaleffects:::get_predictors(variables, mfx) 4. └─marginaleffects (local) stop_zero(predictors) 5. └─marginaleffects:::stop_sprintf(msg) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'compare.margins.Rmd' failed with diagnostics: There is no valid predictor variable. Please change the `variables` argument or supply an alternative data frame to the `newdata` argument. --- failed re-building ‘compare.margins.Rmd’ --- re-building ‘count.fit.Rmd’ using rmarkdown --- finished re-building ‘count.fit.Rmd’ --- re-building ‘daign.Rmd’ using rmarkdown --- finished re-building ‘daign.Rmd’ --- re-building ‘first.diff.fitted.Rmd’ using rmarkdown --- finished re-building ‘first.diff.fitted.Rmd’ --- re-building ‘list.coef.Rmd’ using rmarkdown --- finished re-building ‘list.coef.Rmd’ --- re-building ‘margins.dat.Rmd’ using rmarkdown --- finished re-building ‘margins.dat.Rmd’ --- re-building ‘margins.dat.clogit.Rmd’ using rmarkdown --- finished re-building ‘margins.dat.clogit.Rmd’ --- re-building ‘margins.des.Rmd’ using rmarkdown --- finished re-building ‘margins.des.Rmd’ --- re-building ‘rubins.rule.Rmd’ using rmarkdown --- finished re-building ‘rubins.rule.Rmd’ --- re-building ‘second.diff.fitted.Rmd’ using rmarkdown --- finished re-building ‘second.diff.fitted.Rmd’ SUMMARY: processing the following file failed: ‘compare.margins.Rmd’ Error: Vignette re-building failed. Execution halted Package: clarify Check: tests New result: ERROR Running ‘testthat.R’ [41s/41s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(clarify) > > test_check("clarify") [ FAIL 3 | WARN 1 | SKIP 7 | PASS 4759 ] ══ Skipped tests (7) ═══════════════════════════════════════════════════════════ • !file.exists(test_path("fixtures", "mimira.rds")) is TRUE (1): 'test-misim.R:124:3' • 'estimatr' has problems with model.frame.iv_robust(), which causes an error with insight::get_data(). (1): 'test-sim_ame.R:594:3' • On CRAN (4): 'test-sim.R:659:3', 'test-sim.R:729:3', 'test-sim_ame.R:671:3', 'test-sim_ame.R:750:3' • predict() is bugged for glmRob() (1): 'test-sim_ame.R:1390:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-sim.R:231:3'): sim() works with betareg::betareg() ─────────── colnames(s$sim.coefs) (`actual`) not equal to c(...) (`expected`). actual | expected [5] "racehispan" | "racehispan" [5] [6] "racewhite" | "racewhite" [6] [7] "re74" | "re74" [7] [8] "(Intercept)" - "(phi)_(Intercept)" [8] [9] "treat" - "(phi)_treat" [9] [10] "age" - "(phi)_age" [10] ── Error ('test-sim_ame.R:317:3'): sim_ame() works with MASS::polr() ─────────── Error in `sim_ame(s, "treat", contrast = "diff", type = "mean", verbose = FALSE)`: Not all units received a predicted value, suggesting a bug. Backtrace: ▆ 1. └─clarify::sim_ame(...) at test-sim_ame.R:317:3 2. └─clarify:::.err("not all units received a predicted value, suggesting a bug") 3. └─chk::err(..., call = pkg_caller_call(start = 2)) 4. └─rlang::abort(msg, class = class, !!!args[named], call = call) ── Error ('test-sim_ame.R:369:3'): sim_ame() works with betareg::betareg() ───── Error in `sim_ame(s, "treat", verbose = FALSE)`: `FUN` failed to run on an initial check with the following error: Predicted values could not be extracted from the model. Backtrace: ▆ 1. └─clarify::sim_ame(s, "treat", verbose = FALSE) at test-sim_ame.R:369:3 2. └─clarify::sim_apply(sim, FUN = FUN, verbose = verbose, cl = cl) 3. └─clarify:::.err(...) 4. └─chk::err(..., call = pkg_caller_call(start = 2)) 5. └─rlang::abort(msg, class = class, !!!args[named], call = call) [ FAIL 3 | WARN 1 | SKIP 7 | PASS 4759 ] Error: Test failures Execution halted Package: insight Check: tests New result: ERROR Running ‘testthat.R’ [208s/104s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(insight) > test_check("insight") Starting 2 test processes [ FAIL 2 | WARN 0 | SKIP 90 | PASS 3436 ] ══ Skipped tests (90) ══════════════════════════════════════════════════════════ • On CRAN (82): 'test-GLMMadaptive.R:2:1', 'test-averaging.R:3:1', 'test-bias_correction.R:1:1', 'test-blmer.R:249:3', 'test-brms.R:1:1', 'test-brms_aterms.R:1:1', 'test-brms_gr_random_effects.R:1:1', 'test-brms_missing.R:1:1', 'test-brms_mm.R:1:1', 'test-brms_von_mises.R:1:1', 'test-clean_names.R:103:3', 'test-clean_parameters.R:1:1', 'test-coxme.R:7:1', 'test-cpglmm.R:145:3', 'test-clmm.R:165:3', 'test-display.R:10:3', 'test-display.R:32:3', 'test-export_table.R:4:3', 'test-export_table.R:8:3', 'test-export_table.R:106:3', 'test-export_table.R:133:3', 'test-export_table.R:164:3', 'test-export_table.R:192:3', 'test-export_table.R:204:3', 'test-export_table.R:232:3', 'test-export_table.R:292:3', 'test-export_table.R:309:3', 'test-export_table.R:372:3', 'test-find_smooth.R:31:3', 'test-format_table.R:2:1', 'test-format_table_ci.R:71:3', 'test-find_random.R:27:3', 'test-gam.R:2:1', 'test-get_data.R:385:1', 'test-get_loglikelihood.R:94:3', 'test-get_loglikelihood.R:159:3', 'test-get_predicted.R:2:1', 'test-get_priors.R:3:3', 'test-get_priors.R:18:3', 'test-get_varcov.R:40:3', 'test-get_datagrid.R:692:3', 'test-is_converged.R:28:1', 'test-iv_robust.R:120:3', 'test-lavaan.R:1:1', 'test-lme.R:34:3', 'test-lme.R:210:3', 'test-glmmTMB.R:71:3', 'test-glmmTMB.R:755:3', 'test-glmmTMB.R:787:3', 'test-glmmTMB.R:1095:3', 'test-marginaleffects.R:1:1', 'test-mgcv.R:1:1', 'test-mipo.R:1:1', 'test-mlogit.R:2:1', 'test-model_info.R:110:3', 'test-mvrstanarm.R:1:1', 'test-null_model.R:71:3', 'test-panelr-asym.R:142:3', 'test-panelr.R:272:3', 'test-phylolm.R:5:1', 'test-print_parameters.R:1:1', 'test-r2_nakagawa_bernoulli.R:1:1', 'test-r2_nakagawa_beta.R:1:1', 'test-r2_nakagawa_binomial.R:1:1', 'test-r2_nakagawa_gamma.R:1:1', 'test-r2_nakagawa_linear.R:1:1', 'test-r2_nakagawa_negbin.R:1:1', 'test-r2_nakagawa_negbin_zi.R:1:1', 'test-r2_nakagawa_ordered_beta.R:1:1', 'test-r2_nakagawa_poisson.R:1:1', 'test-r2_nakagawa_poisson_zi.R:1:1', 'test-r2_nakagawa_truncated_poisson.R:1:1', 'test-r2_nakagawa_tweedie.R:1:1', 'test-rlmer.R:259:3', 'test-rqss.R:1:1', 'test-rstanarm.R:1:1', 'test-sdmTMB.R:1:1', 'test-selection.R:2:1', 'test-spatial.R:2:1', 'test-svylme.R:1:1', 'test-vgam.R:2:1', 'test-weightit.R:1:1' • On Linux (3): 'test-BayesFactorBF.R:1:1', 'test-MCMCglmm.R:1:1', 'test-get_data.R:150:3' • Package `logistf` is loaded and breaks `mmrm::mmrm()` (1): 'test-mmrm.R:4:1' • TRUE is TRUE (1): 'test-fixest.R:2:1' • works interactively (2): 'test-coxph-panel.R:34:3', 'test-coxph.R:38:3' • {bigglm} is not installed (1): 'test-model_info.R:24:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-get_datagrid.R:352:3'): get_datagrid - marginaleffects ─────── dim(res) (`actual`) not identical to c(6L, 2L) (`expected`). `actual`: 6 0 `expected`: 6 2 ── Error ('test-get_datagrid.R:353:3'): get_datagrid - marginaleffects ───────── Error in `.subset2(x, i, exact = exact)`: subscript out of bounds Backtrace: ▆ 1. ├─testthat::expect_true(all(c(4, 6, 8) %in% res[[1]])) at test-get_datagrid.R:353:3 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. ├─c(4, 6, 8) %in% res[[1]] 5. ├─res[[1]] 6. └─base::`[[.data.frame`(res, 1) 7. └─(function(x, i, exact) if (is.matrix(i)) as.matrix(x)[[i]] else .subset2(x, ... [ FAIL 2 | WARN 0 | SKIP 90 | PASS 3436 ] Error: Test failures Execution halted Package: modelbased Check: tests New result: ERROR Running ‘testthat.R’ [54s/30s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > library(testthat) > library(modelbased) > > test_check("modelbased") Starting 2 test processes [ FAIL 2 | WARN 0 | SKIP 46 | PASS 224 ] ══ Skipped tests (46) ══════════════════════════════════════════════════════════ • .Platform$OS.type == "windows" is not TRUE (1): 'test-estimate_predicted.R:58:3' • On CRAN (38): 'test-backtransform_invlink.R:1:1', 'test-betareg.R:1:1', 'test-bias_correction.R:1:1', 'test-brms-marginaleffects.R:1:1', 'test-brms.R:1:1', 'test-estimate_contrasts-average.R:1:1', 'test-estimate_contrasts.R:1:1', 'test-estimate_contrasts_bookexamples.R:1:1', 'test-estimate_contrasts_effectsize.R:1:1', 'test-estimate_contrasts_methods.R:1:1', 'test-estimate_filter.R:1:1', 'test-estimate_means-average.R:1:1', 'test-estimate_means.R:1:1', 'test-estimate_means_ci.R:1:1', 'test-estimate_means_counterfactuals.R:1:1', 'test-estimate_grouplevel.R:54:3', 'test-estimate_grouplevel.R:72:3', 'test-estimate_grouplevel.R:93:3', 'test-estimate_grouplevel.R:123:3', 'test-estimate_means_dotargs.R:1:1', 'test-estimate_means_marginalization.R:1:1', 'test-estimate_means_mixed.R:1:1', 'test-estimate_slopes.R:129:1', 'test-g_computation.R:1:1', 'test-get_marginaltrends.R:1:1', 'test-glmmTMB.R:1:1', 'test-joint_test.R:1:1', 'test-keep_iterations.R:1:1', 'test-maihda.R:1:1', 'test-mice.R:1:1', 'test-ordinal.R:1:1', 'test-plot-grouplevel.R:1:1', 'test-predict-dpar.R:1:1', 'test-standardize.R:1:1', 'test-summary_estimate_slopes.R:3:1', 'test-transform_response.R:16:3', 'test-vcov.R:1:1', 'test-zeroinfl.R:1:1' • On Linux (7): 'test-plot-facet.R:1:1', 'test-plot-flexible_numeric.R:1:1', 'test-plot-ordinal.R:1:1', 'test-plot-slopes.R:1:1', 'test-plot.R:1:1', 'test-print.R:1:1', 'test-scoping_issues.R:1:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-attributes_estimatefun.R:93:3'): attributes_means, slopes ──── Names of attributes(estim) ('names', 'class', 'row.names', 'trend', 'p_adjust', 'transform', 'coef_name', 'slope', 'ci', 'model_info', 'keep_iterations', 'vcov', 'table_title', 'table_footer', 'model', 'response') don't match 'names', 'class', 'row.names', 'trend', 'comparison', 'p_adjust', 'transform', 'coef_name', 'slope', 'ci', 'model_info', 'keep_iterations', 'vcov', 'table_title', 'table_footer', 'model', 'response' ── Error ('test-estimate_slopes.R:81:3'): estimate_slopes, johnson-neyman p-adjust ── Error: The entered object is not a model object. Backtrace: ▆ 1. └─modelbased::estimate_slopes(...) at test-estimate_slopes.R:81:3 2. └─modelbased::get_marginaltrends(...) 3. └─modelbased:::.p_adjust(model, estimated, p_adjust, verbose, ...) 4. └─modelbased:::.p_adjust_esarey(params) 5. ├─insight::get_df(model, type = "wald") 6. └─insight:::get_df.default(model, type = "wald") 7. ├─insight::find_statistic(x) 8. └─insight:::find_statistic.default(x) 9. └─insight::format_error("The entered object is not a model object.") 10. └─insight::format_alert(..., type = "error") [ FAIL 2 | WARN 0 | SKIP 46 | PASS 224 ] Error: Test failures Execution halted Package: mvgam Check: S3 generic/method consistency New result: WARNING get_predict: function(model, newdata, type, mfx, newparams, ndraws, se.fit, ...) get_predict.mvgam: function(model, newdata, type, process_error, ...) See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. Package: parameters Check: tests New result: ERROR Running ‘testthat.R’ [84s/43s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(parameters) > library(testthat) > > test_check("parameters") Starting 2 test processes [ FAIL 1 | WARN 4 | SKIP 124 | PASS 692 ] ══ Skipped tests (124) ═════════════════════════════════════════════════════════ • On CRAN (115): 'test-GLMMadaptive.R:1:1', 'test-averaging.R:1:1', 'test-backticks.R:1:1', 'test-bootstrap_emmeans.R:1:1', 'test-bootstrap_parameters.R:1:1', 'test-brms.R:1:1', 'test-compare_parameters.R:91:7', 'test-compare_parameters.R:95:5', 'test-complete_separation.R:14:5', 'test-complete_separation.R:24:5', 'test-complete_separation.R:35:5', 'test-coxph.R:79:5', 'test-efa.R:1:1', 'test-emmGrid-df_colname.R:1:1', 'test-equivalence_test.R:10:3', 'test-equivalence_test.R:18:3', 'test-equivalence_test.R:82:3', 'test-factor_analysis.R:2:3', 'test-factor_analysis.R:124:3', 'test-format_model_parameters2.R:2:3', 'test-gam.R:30:1', 'test-get_scores.R:1:1', 'test-glmer.R:1:1', 'test-glmmTMB-2.R:1:1', 'test-glmmTMB-profile_CI.R:2:3', 'test-glmmTMB.R:8:1', 'test-group_level_total.R:2:1', 'test-helper.R:1:1', 'test-ivreg.R:54:3', 'test-include_reference.R:16:3', 'test-include_reference.R:69:3', 'test-include_reference.R:121:3', 'test-lmerTest.R:1:1', 'test-mipo.R:19:3', 'test-mipo.R:33:3', 'test-mmrm.R:1:1', 'test-model_parameters.anova.R:1:1', 'test-model_parameters.aov.R:1:1', 'test-model_parameters.aov_es_ci.R:158:3', 'test-model_parameters.aov_es_ci.R:269:3', 'test-model_parameters.aov_es_ci.R:319:3', 'test-model_parameters.aov_es_ci.R:372:3', 'test-marginaleffects.R:131:3', 'test-marginaleffects.R:154:3', 'test-marginaleffects.R:173:3', 'test-model_parameters.bracl.R:5:1', 'test-model_parameters.cgam.R:1:1', 'test-model_parameters.coxme.R:1:1', 'test-model_parameters.epi2x2.R:1:1', 'test-model_parameters.fixest_multi.R:3:1', 'test-model_parameters.fixest.R:2:3', 'test-model_parameters.fixest.R:77:3', 'test-model_parameters.fixest.R:147:5', 'test-model_parameters.glmgee.R:1:1', 'test-model_parameters.logistf.R:1:1', 'test-model_parameters.logitr.R:1:1', 'test-model_parameters.glm.R:40:3', 'test-model_parameters.glm.R:76:3', 'test-model_parameters.mclogit.R:5:1', 'test-model_parameters.mediate.R:32:3', 'test-model_parameters.mixed.R:2:1', 'test-model_parameters.nnet.R:5:1', 'test-model_parameters_df.R:1:1', 'test-model_parameters.vgam.R:3:1', 'test-model_parameters_ordinal.R:1:1', 'test-model_parameters_random_pars.R:1:1', 'test-model_parameters_std.R:1:1', 'test-model_parameters_std_mixed.R:3:1', 'test-n_factors.R:10:3', 'test-n_factors.R:26:3', 'test-n_factors.R:76:3', 'test-p_adjust.R:1:1', 'test-p_direction.R:1:1', 'test-p_significance.R:1:1', 'test-p_value.R:14:1', 'test-panelr.R:1:1', 'test-pipe.R:1:1', 'test-pca.R:66:3', 'test-polr.R:2:1', 'test-plm.R:111:3', 'test-posterior.R:2:1', 'test-pool_parameters.R:11:3', 'test-pool_parameters.R:32:1', 'test-print_AER_labels.R:11:5', 'test-printing-stan.R:2:1', 'test-printing.R:1:1', 'test-pretty_names.R:65:5', 'test-pretty_names.R:82:7', 'test-quantreg.R:1:1', 'test-random_effects_ci.R:4:1', 'test-robust.R:2:1', 'test-rstanarm.R:2:1', 'test-sampleSelection.R:2:1', 'test-serp.R:16:5', 'test-printing2.R:15:7', 'test-printing2.R:22:7', 'test-printing2.R:27:7', 'test-printing2.R:32:7', 'test-printing2.R:37:7', 'test-printing2.R:49:7', 'test-printing2.R:91:7', 'test-printing2.R:127:7', 'test-svylme.R:1:1', 'test-visualisation_recipe.R:7:3', 'test-weightit.R:23:3', 'test-weightit.R:43:3', 'test-wrs2.R:58:3', 'test-standardize_parameters.R:31:3', 'test-standardize_parameters.R:36:3', 'test-standardize_parameters.R:61:3', 'test-standardize_parameters.R:173:3', 'test-standardize_parameters.R:298:3', 'test-standardize_parameters.R:333:3', 'test-standardize_parameters.R:426:3', 'test-standardize_parameters.R:516:3' • On Linux (5): 'test-model_parameters.BFBayesFactor.R:1:1', 'test-nestedLogit.R:78:3', 'test-random_effects_ci-glmmTMB.R:3:1', 'test-simulate_model.R:1:1', 'test-simulate_parameters.R:1:1' • TODO: fix this test (1): 'test-model_parameters.lqmm.R:40:3' • TODO: this one actually is not correct. (1): 'test-model_parameters_robust.R:127:3' • empty test (2): 'test-wrs2.R:69:1', 'test-wrs2.R:81:1' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-marginaleffects.R:52:3'): predictions() ────────────────────── Names of `out` ('Predicted', 'SE', 'CI', 'CI_low', 'CI_high', 'S', 'Statistic', 'df', 'p', 'Species') don't match 'Predicted', 'Species', 'SE', 'CI', 'CI_low', 'CI_high', 'S', 'Statistic', 'df', 'p' [ FAIL 1 | WARN 4 | SKIP 124 | PASS 692 ] Error: Test failures Execution halted Package: VizTest Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘viztest_intro.Rmd’ using rmarkdown Quitting from viztest_intro.Rmd:352-358 [unnamed-chunk-3] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error in `t.default()`: ! argument is not a matrix --- Backtrace: ▆ 1. ├─base::t(attr(ap_sim, "posterior")) 2. ├─base::t(attr(ap_sim, "posterior")) 3. └─base::t.default(attr(ap_sim, "posterior")) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'viztest_intro.Rmd' failed with diagnostics: argument is not a matrix --- failed re-building ‘viztest_intro.Rmd’ SUMMARY: processing the following file failed: ‘viztest_intro.Rmd’ Error: Vignette re-building failed. Execution halted