Package: GLMMadaptive Check: dependencies in R code New result: WARNING Missing or unexported object: ‘effects::Effect.default’ Package: glmmTMB Check: dependencies in R code New result: WARNING Missing or unexported object: ‘effects::Effect.default’ Package: glmmTMB Check: examples New result: ERROR Running examples in ‘glmmTMB-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: Anova.glmmTMB > ### Title: Downstream methods > ### Aliases: Anova.glmmTMB Effect.glmmTMB downstream_methods > ### emmeans.glmmTMB > > ### ** Examples > > warp.lm <- glmmTMB(breaks ~ wool * tension, data = warpbreaks) > salamander1 <- up2date(readRDS(system.file("example_files","salamander1.rds",package="glmmTMB"))) > if (require(emmeans)) withAutoprint({ + emmeans(warp.lm, poly ~ tension | wool) + emmeans(salamander1, ~ mined, type="response") # conditional means + emmeans(salamander1, ~ mined, component="cmean") # same as above, but re-gridded + emmeans(salamander1, ~ mined, component="zi", type="response") # zero probabilities + emmeans(salamander1, ~ mined, component="response") # response means including both components + }) Loading required package: emmeans Welcome to emmeans. Caution: You lose important information if you filter this package's results. See '? untidy' > emmeans(warp.lm, poly ~ tension | wool) $emmeans wool = A: tension emmean SE df lower.CL upper.CL L 44.6 3.44 47 37.6 51.5 M 24.0 3.44 47 17.1 30.9 H 24.6 3.44 47 17.6 31.5 wool = B: tension emmean SE df lower.CL upper.CL L 28.2 3.44 47 21.3 35.1 M 28.8 3.44 47 21.9 35.7 H 18.8 3.44 47 11.9 25.7 Confidence level used: 0.95 $contrasts wool = A: contrast estimate SE df t.ratio p.value linear -20.00 4.86 47 -4.113 0.0002 quadratic 21.11 8.42 47 2.507 0.0157 wool = B: contrast estimate SE df t.ratio p.value linear -9.44 4.86 47 -1.942 0.0581 quadratic -10.56 8.42 47 -1.253 0.2163 > emmeans(salamander1, ~mined, type = "response") mined rate SE df asymp.LCL asymp.UCL yes 1.09 0.254 Inf 0.692 1.72 no 3.42 0.311 Inf 2.862 4.09 Confidence level used: 0.95 Intervals are back-transformed from the log scale > emmeans(salamander1, ~mined, component = "cmean") mined emmean SE df asymp.LCL asymp.UCL yes 1.09 0.254 Inf 0.594 1.59 no 3.42 0.311 Inf 2.811 4.03 Confidence level used: 0.95 > emmeans(salamander1, ~mined, component = "zi", type = "response") mined response SE df asymp.LCL asymp.UCL yes 0.758 0.0432 Inf 0.663 0.832 no 0.355 0.0279 Inf 0.303 0.411 Confidence level used: 0.95 Intervals are back-transformed from the logit scale > emmeans(salamander1, ~mined, component = "response") mined emmean SE df asymp.LCL asymp.UCL yes 0.265 0.0484 Inf 0.17 0.36 no 2.206 0.2170 Inf 1.78 2.63 Confidence level used: 0.95 > if (getRversion() >= "3.6.0") { + if (require(car)) withAutoprint({ + Anova(warp.lm,type="III") + Anova(salamander1) + Anova(salamander1, component="zi") + }) + if (require(effects)) withAutoprint({ + plot(allEffects(warp.lm)) + plot(allEffects(salamander1)) + }) + } Loading required package: car Loading required package: carData > Anova(warp.lm, type = "III") Analysis of Deviance Table (Type III Wald chisquare tests) Response: breaks Chisq Df Pr(>Chisq) (Intercept) 167.9350 1 < 2.2e-16 *** wool 11.2839 1 0.0007818 *** tension 23.2022 2 9.156e-06 *** wool:tension 9.4254 2 0.0089806 ** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 > Anova(salamander1) Analysis of Deviance Table (Type II Wald chisquare tests) Response: count Chisq Df Pr(>Chisq) mined 21.522 1 3.499e-06 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 > Anova(salamander1, component = "zi") Analysis of Deviance Table (Type II Wald chisquare tests) Response: count Chisq Df Pr(>Chisq) mined 43.907 1 3.444e-11 *** --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Loading required package: effects lattice theme set by effectsTheme() See ?effectsTheme for details. > plot(allEffects(warp.lm)) Error: 'Effect.default' is not an exported object from 'namespace:effects' Execution halted Package: glmmTMB Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘covstruct.rmd’ using rmarkdown --- finished re-building ‘covstruct.rmd’ --- re-building ‘hacking.rmd’ using rmarkdown --- finished re-building ‘hacking.rmd’ --- re-building ‘mcmc.rmd’ using rmarkdown --- finished re-building ‘mcmc.rmd’ --- re-building ‘miscEx.rmd’ using rmarkdown --- finished re-building ‘miscEx.rmd’ --- re-building ‘parallel.rmd’ using rmarkdown --- finished re-building ‘parallel.rmd’ --- re-building ‘priors.rmd’ using rmarkdown --- finished re-building ‘priors.rmd’ --- re-building ‘sim.rmd’ using rmarkdown --- finished re-building ‘sim.rmd’ --- re-building ‘troubleshooting.rmd’ using rmarkdown --- finished re-building ‘troubleshooting.rmd’ --- re-building ‘glmmTMB.Rnw’ using knitr --- finished re-building ‘glmmTMB.Rnw’ --- re-building ‘model_evaluation.Rnw’ using knitr Quitting from model_evaluation.Rnw:206-212 [effects1] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: ! 'Effect.default' is not an exported object from 'namespace:effects' --- Backtrace: x 1. +-effects::allEffects(owls_nb1) 2. \-effects:::allEffects.default(owls_nb1) 3. \-base::lapply(terms, effect, mod = mod, ...) 4. +-effects (local) FUN(X[[i]], ...) 5. \-effects:::effect.default(X[[i]], ...) 6. +-effects::Effect(predictors, mod, vcov. = vcov., ...) 7. \-glmmTMB:::Effect.glmmTMB(predictors, mod, vcov. = vcov., ...) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'model_evaluation.Rnw' failed with diagnostics: 'Effect.default' is not an exported object from 'namespace:effects' --- failed re-building ‘model_evaluation.Rnw’ SUMMARY: processing the following file failed: ‘model_evaluation.Rnw’ Error: Vignette re-building failed. Execution halted Package: glmmTMB Check: tests New result: ERROR Running ‘AAAtest-all.R’ [71s/71s] Running the tests in ‘tests/AAAtest-all.R’ failed. Complete output: > if (require("testthat")) { + pkg <- "glmmTMB" + require(pkg, character.only=TRUE) + print(sessionInfo()) + test_check(pkg, reporter="summary") + print(warnings()) # TODO? catch most of these by expect_warning(..) + } else { + warnings("Package 'testthat' not available, cannot run unit tests for package", + sQuote(pkg)) + } Loading required package: testthat Loading required package: glmmTMB R Under development (unstable) (2025-07-27 r88459) Platform: x86_64-pc-linux-gnu Running under: Debian GNU/Linux 13 (trixie) Matrix products: default BLAS: /home/hornik/tmp/R-d-gcc-14/lib/libRblas.so LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.1; LAPACK version 3.12.0 locale: [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 [4] LC_COLLATE=C LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C time zone: Europe/Vienna tzcode source: system (glibc) attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] glmmTMB_1.1.11 testthat_3.2.3 loaded via a namespace (and not attached): [1] nlme_3.1-168 cli_3.6.5 TH.data_1.1-3 [4] rlang_1.1.6 estimability_1.5.1 reformulas_0.4.1 [7] xtable_1.8-4 minqa_1.2.8 zoo_1.8-14 [10] TMB_1.9.17 lme4_1.1-37 brio_1.1.5 [13] grid_4.6.0 MASS_7.3-65 mvtnorm_1.3-3 [16] numDeriv_2016.8-1.1 multcomp_1.4-28 compiler_4.6.0 [19] codetools_0.2-20 sandwich_3.1-1 emmeans_1.11.2 [22] coda_0.19-4.1 Rcpp_1.1.0 mgcv_1.9-3 [25] lattice_0.22-7 nloptr_2.2.1 R6_2.6.1 [28] Rdpack_2.6.4 splines_4.6.0 rbibutils_2.3 [31] magrittr_2.0.3 Matrix_1.7-3 tools_4.6.0 [34] boot_1.3-31 survival_3.8-3 Anova: ............... VarCorr: ............... altopt: alternative optimizers: S basics: .............SS.....S......S trickier examples: SS.SSSS........... bootMer: bootMer: SS checkRank: ................................................ control: SS..... diagnose: .S.. disp: ... downstream: S...1 edgecases: test edge cases: . env: basic examples: ... families: .....................SSSSSSSSS..................................2.... formulas: formula parsing: ................ mapequal: ........ mapopt: methods: ...............................S..........................................S..............S.............................. misc: . offset: SSSSSSSSS predict: .....SSSSS.................S..SSS....S..S...S.............S........ priors: ...........SS propto: ...... reml: ........ rr: .......... saveload: Saving and loading glmmTMB objects: . simulate: ......... simulate_new: ....S......... smooths: ...... sparseX: sparse X models: ....... start: .. utils: ......................................................................................................... varstruc: .........SSS.S weight: ......... zi: ZI models: SS ══ Skipped ═════════════════════════════════════════════════════════════════════ 1. downstream methods work with optim() ('test-altopt.R:11:3') - Reason: On CRAN 2. Update Gaussian ('test-basics.R:85:3') - Reason: On CRAN 3. Variance structures ('test-basics.R:94:3') - Reason: On CRAN 4. Multiple RE, reordering ('test-basics.R:124:6') - Reason: On CRAN 5. close to lme4 results ('test-basics.R:164:5') - Reason: On CRAN 6. basic zero inflation ('test-basics.R:217:8') - Reason: On CRAN 7. alternative binomial model specifications ('test-basics.R:236:5') - Reason: On CRAN 8. NA handling ('test-basics.R:257:5') - Reason: On CRAN 9. quine NB fit ('test-basics.R:275:5') - Reason: On CRAN 10. contrasts arg ('test-basics.R:286:5') - Reason: On CRAN 11. zero disp setting ('test-basics.R:297:5') - Reason: On CRAN 12. Bernoulli responses ('test-bootMer.R:12:3') - Reason: On CRAN 13. binomial responses ('test-bootMer.R:22:5') - Reason: On CRAN 14. profile method ('test-control.R:16:3') - Reason: On CRAN 15. parallel regions ('test-control.R:50:3') - Reason: On CRAN 16. diagnose works with Tweedie fits ('test-diagnose.R:16:5') - Reason: On CRAN 17. emmeans ('test-downstream.R:22:5') - Reason: On CRAN 18. beta ('test-families.R:103:3') - Reason: On CRAN 19. nbinom ('test-families.R:125:5') - Reason: On CRAN 20. dbetabinom ('test-families.R:186:5') - Reason: On CRAN 21. truncated ('test-families.R:259:5') - Reason: On CRAN 22. truncated_genpois ('test-families.R:336:3') - Reason: On CRAN 23. truncated_compois ('test-families.R:352:5') - Reason: On CRAN 24. compois ('test-families.R:362:5') - Reason: On CRAN 25. genpois ('test-families.R:372:5') - Reason: On CRAN 26. tweedie ('test-families.R:380:5') - Reason: On CRAN 27. anova ML/REML checks ('test-methods.R:135:5') - Reason: On CRAN 28. simulate with re.form = NA ('test-methods.R:410:1') - Reason: empty test 29. various binomial response types work ('test-methods.R:490:3') - Reason: On CRAN 30. LM with offset as argument ('test-offset.R:27:3') - Reason: On CRAN 31. LM with offset in formula ('test-offset.R:35:5') - Reason: On CRAN 32. LM with offset in formula - variable not in environment ('test-offset.R:48:5') - Reason: On CRAN 33. LM with offset in dispersion formula ('test-offset.R:57:5') - Reason: On CRAN 34. LM with multiple offsets (cond/dispersion) ('test-offset.R:65:5') - Reason: On CRAN 35. LM with random crap in the formula ('test-offset.R:74:5') - Reason: On CRAN 36. offset in do.call ('test-offset.R:81:5') - Reason: On CRAN 37. LONG offset in do.call ('test-offset.R:90:5') - Reason: On CRAN 38. offset works with attributes ('test-offset.R:101:3') - Reason: On CRAN 39. new levels of fixed effect factor ('test-predict.R:37:5') - Reason: On CRAN 40. new levels in RE term ('test-predict.R:44:5') - Reason: On CRAN 41. new levels in AR1 (OK) ('test-predict.R:51:5') - Reason: On CRAN 42. two-column response ('test-predict.R:59:5') - Reason: On CRAN 43. Prediction with dispformula=~0 ('test-predict.R:67:5') - Reason: On CRAN 44. scale ('test-predict.R:181:5') - Reason: On CRAN 45. scale_RE ('test-predict.R:203:5') - Reason: On CRAN 46. complex bases in dispformula ('test-predict.R:210:5') - Reason: On CRAN 47. fix_predvars works for I(x^2) ('test-predict.R:223:5') - Reason: On CRAN 48. contrasts carried over ('test-predict.R:291:5') - Reason: On CRAN 49. offset-only model (GH #625) ('test-predict.R:330:5') - Reason: On CRAN 50. inverse-link prediction ('test-predict.R:349:3') - Reason: On CRAN 51. nzprob doesn't segfault ('test-predict.R:440:5') - Reason: On CRAN 52. prior specs ('test-priors.R:125:5') - Reason: On CRAN 53. dropping priors for rank-def X matrix ('test-priors.R:166:1') - Reason: empty test 54. simulate_new, returning pars ('test-simulate_new.R:49:1') - Reason: empty test 55. ar1 requires factor time ('test-varstruc.R:66:3') - Reason: On CRAN 56. varcorr_print ('test-varstruc.R:86:5') - Reason: On CRAN 57. cov_struct_order ('test-varstruc.R:139:5') - Reason: On CRAN 58. het ar1 ('test-varstruc.R:156:5') - Reason: On CRAN 59. zi ('test-zi.R:12:3') - Reason: On CRAN 60. zi beta and Gamma ('test-zi.R:37:5') - Reason: On CRAN ══ Failed ══════════════════════════════════════════════════════════════════════ ── 1. Error ('test-downstream.R:97:9'): (code run outside of `test_that()`) ──── Error: 'Effect.default' is not an exported object from 'namespace:effects' Backtrace: ▆ 1. ├─testthat::expect_equal(f(fm2_tmb), f(fm2_lmer), tolerance = 2e-05) at test-downstream.R:108:9 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─glmmTMB (local) f(fm2_tmb) 5. ├─base::sapply(...) at test-downstream.R:97:9 6. │ └─base::lapply(X = X, FUN = FUN, ...) 7. ├─effects::allEffects(x) 8. └─effects:::allEffects.default(x) 9. └─base::lapply(terms, effect, mod = mod, ...) 10. ├─effects (local) FUN(X[[i]], ...) 11. └─effects:::effect.default(X[[i]], ...) 12. ├─effects::Effect(predictors, mod, vcov. = vcov., ...) 13. └─glmmTMB:::Effect.glmmTMB(predictors, mod, vcov. = vcov., ...) ── 2. Error ('test-families.R:552:9'): make_family initialize works ──────────── Error: 'Effect.default' is not an exported object from 'namespace:effects' Backtrace: ▆ 1. ├─base::suppressWarnings(effects::Effect("Days", m2)) at test-families.R:552:9 2. │ └─base::withCallingHandlers(...) 3. ├─effects::Effect("Days", m2) 4. └─glmmTMB:::Effect.glmmTMB("Days", m2) ══ DONE ════════════════════════════════════════════════════════════════════════ Error: Test failures Execution halted Package: sdmTMB Check: dependencies in R code New result: WARNING Missing or unexported object: ‘effects::Effect.default’ Package: sdmTMB Check: examples New result: ERROR Running examples in ‘sdmTMB-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: Effect.sdmTMB > ### Title: Calculate effects > ### Aliases: Effect.sdmTMB > > ### ** Examples > > ## Don't show: > if (require("effects", quietly = TRUE)) (if (getRversion() >= "3.4") withAutoprint else force)({ # examplesIf + ## End(Don't show) + fit <- sdmTMB(present ~ depth_scaled, data = pcod_2011, family = binomial(), + spatial = "off") + effects::effect("depth_scaled", fit) + plot(effects::effect("depth_scaled", fit)) + ## Don't show: + }) # examplesIf lattice theme set by effectsTheme() See ?effectsTheme for details. > fit <- sdmTMB(present ~ depth_scaled, data = pcod_2011, family = binomial(), + spatial = "off") > effects::effect("depth_scaled", fit) Error: 'Effect.default' is not an exported object from 'namespace:effects' Execution halted