Package check result: NOTE Check: CRAN incoming feasibility, Result: NOTE Maintainer: ‘Brad Price ’ New maintainer: Brad Price Old maintainer(s): John Fox Changes to worse in reverse depends: 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 Loading the 'metafor' package (version 4.8-0). For an introduction to the package please type: help(metafor) [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘covstruct.rmd’ --- re-building ‘hacking.rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘hacking.rmd’ --- re-building ‘mcmc.rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘mcmc.rmd’ --- re-building ‘miscEx.rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘miscEx.rmd’ --- re-building ‘parallel.rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘parallel.rmd’ --- re-building ‘priors.rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘priors.rmd’ --- re-building ‘sim.rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘sim.rmd’ --- re-building ‘troubleshooting.rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- 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’ [39s/39s] 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) (2026-02-03 r89375) Platform: x86_64-pc-linux-gnu Running under: Debian GNU/Linux forky/sid Matrix products: default BLAS: /home/hornik/tmp/R-d-gcc-15/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_1.1.14 testthat_3.3.2 loaded via a namespace (and not attached): [1] nlme_3.1-168 cli_3.6.5 TH.data_1.1-5 [4] rlang_1.1.7 estimability_1.5.1 otel_0.2.0 [7] reformulas_0.4.4 xtable_1.8-4 minqa_1.2.8 [10] zoo_1.8-15 TMB_1.9.19 lme4_1.1-38 [13] brio_1.1.5 grid_4.6.0 MASS_7.3-65 [16] mvtnorm_1.3-3 lifecycle_1.0.5 numDeriv_2016.8-1.1 [19] multcomp_1.4-29 compiler_4.6.0 codetools_0.2-20 [22] coda_0.19-4.1 emmeans_2.0.1 sandwich_3.1-1 [25] Rcpp_1.1.1 mgcv_1.9-4 lattice_0.22-7 [28] nloptr_2.2.1 R6_2.6.1 Rdpack_2.6.5 [31] splines_4.6.0 rbibutils_2.4.1 magrittr_2.0.4 [34] Matrix_1.7-4 tools_4.6.0 boot_1.3-32 [37] survival_3.8-6 Anova: ............... VarCorr: ............... altopt: alternative optimizers: S basics: .............SS.....S......S trickier examples: SS.SSSS............. bootMer: bootMer: SS checkRank: ................................................ control: SS..... ddf: .... diagnose: .S.. disp: ... downstream: S...1 edgecases: test edge cases: . env: basic examples: ... equalto: ......... families: .....................SSSSSSSSS..................................2...... formulas: formula parsing: ................ mapequal: ........ mapopt: S 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:218:8') - Reason: On CRAN 7. alternative binomial model specifications ('test-basics.R:237:5') - Reason: On CRAN 8. NA handling ('test-basics.R:258:5') - Reason: On CRAN 9. quine NB fit ('test-basics.R:276:5') - Reason: On CRAN 10. contrasts arg ('test-basics.R:287:5') - Reason: On CRAN 11. zero disp setting ('test-basics.R:298:5') - 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. (code run outside of `test_that()`) - Reason: empty test 28. anova ML/REML checks ('test-methods.R:135:5') - Reason: On CRAN 29. simulate with re.form = NA ('test-methods.R:410:1') - Reason: empty test 30. various binomial response types work ('test-methods.R:490:3') - Reason: On CRAN 31. LM with offset as argument ('test-offset.R:27:3') - Reason: On CRAN 32. LM with offset in formula ('test-offset.R:35:5') - Reason: On CRAN 33. LM with offset in formula - variable not in environment ('test-offset.R:48:5') - Reason: On CRAN 34. LM with offset in dispersion formula ('test-offset.R:57:5') - Reason: On CRAN 35. LM with multiple offsets (cond/dispersion) ('test-offset.R:65:5') - Reason: On CRAN 36. LM with random crap in the formula ('test-offset.R:74:5') - Reason: On CRAN 37. offset in do.call ('test-offset.R:81:5') - Reason: On CRAN 38. LONG offset in do.call ('test-offset.R:90:5') - Reason: On CRAN 39. offset works with attributes ('test-offset.R:101:3') - Reason: On CRAN 40. new levels of fixed effect factor ('test-predict.R:37:5') - Reason: On CRAN 41. new levels in RE term ('test-predict.R:44:5') - Reason: On CRAN 42. new levels in AR1 (OK) ('test-predict.R:51:5') - Reason: On CRAN 43. two-column response ('test-predict.R:59:5') - Reason: On CRAN 44. Prediction with dispformula=~0 ('test-predict.R:67:5') - Reason: On CRAN 45. scale ('test-predict.R:181:5') - Reason: On CRAN 46. scale_RE ('test-predict.R:203:5') - Reason: On CRAN 47. complex bases in dispformula ('test-predict.R:210:5') - Reason: On CRAN 48. fix_predvars works for I(x^2) ('test-predict.R:223:5') - Reason: On CRAN 49. contrasts carried over ('test-predict.R:292:5') - Reason: On CRAN 50. offset-only model (GH #625) ('test-predict.R:345:5') - Reason: On CRAN 51. inverse-link prediction ('test-predict.R:364:3') - Reason: On CRAN 52. nzprob doesn't segfault ('test-predict.R:455:5') - Reason: On CRAN 53. prior specs ('test-priors.R:125:5') - Reason: On CRAN 54. dropping priors for rank-def X matrix ('test-priors.R:166:1') - Reason: empty test 55. simulate_new, returning pars ('test-simulate_new.R:49:1') - Reason: empty test 56. ar1 and hetar1 require factor time ('test-varstruc.R:97:3') - Reason: On CRAN 57. varcorr_print ('test-varstruc.R:124:5') - Reason: On CRAN 58. cov_struct_order ('test-varstruc.R:177:5') - Reason: On CRAN 59. basic hetar1 ('test-varstruc.R:194:5') - Reason: On CRAN 60. zi ('test-zi.R:12:3') - Reason: On CRAN 61. zi beta and Gamma ('test-zi.R:37:5') - Reason: On CRAN ══ Failed ══════════════════════════════════════════════════════════════════════ ── 1. Error ('test-downstream.R:106:9'): (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:117:9 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─glmmTMB (local) f(fm2_tmb) 5. ├─base::sapply(...) at test-downstream.R:106:9 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: ivreg Check: tests New result: ERROR Running ‘testthat.R’ [1s/2s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library("testthat") > library("ivreg") > > test_check("ivreg") Saving _problems/test-case-deletion-31.R Saving _problems/test-case-deletion-43.R [ FAIL 2 | WARN 0 | SKIP 0 | PASS 50 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test-case-deletion.R:31:3'): deletion statistics computed correctly with na.exclude ── Error in `match.arg(type, c("variance", "robustness"))`: 'arg' should be one of "variance", "robustness" Backtrace: ▆ 1. ├─testthat::expect_true(all(is.na(dffits(m.miss)[c(1, 4, 10)]))) at test-case-deletion.R:31:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─stats::dffits(m.miss) 5. └─stats::weighted.residuals(model) 6. ├─stats::weights(obj, type = "working") 7. └─ivreg:::weights.ivreg(obj, type = "working") 8. └─base::match.arg(type, c("variance", "robustness")) ── Error ('test-case-deletion.R:43:3'): rownames of deletion statistics preserved with na.omit ── Error in `match.arg(type, c("variance", "robustness"))`: 'arg' should be one of "variance", "robustness" Backtrace: ▆ 1. ├─testthat::expect_equal(names(dffits(m.miss.2)), nms) at test-case-deletion.R:43:3 2. │ └─testthat::quasi_label(enquo(object), label) 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─stats::dffits(m.miss.2) 5. └─stats::weighted.residuals(model) 6. ├─stats::weights(obj, type = "working") 7. └─ivreg:::weights.ivreg(obj, type = "working") 8. └─base::match.arg(type, c("variance", "robustness")) [ FAIL 2 | WARN 0 | SKIP 0 | PASS 50 ] Error: ! Test failures. Execution halted