R Under development (unstable) (2023-10-06 r85276 ucrt) -- "Unsuffered Consequences" Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > 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) (2023-10-06 r85276 ucrt) Platform: x86_64-w64-mingw32/x64 Running under: Windows Server 2022 x64 (build 20348) Matrix products: default locale: [1] LC_COLLATE=C LC_CTYPE=German_Germany.utf8 [3] LC_MONETARY=C LC_NUMERIC=C [5] LC_TIME=C time zone: Europe/Berlin tzcode source: internal attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] glmmTMB_1.1.8 testthat_3.2.0 loaded via a namespace (and not attached): [1] nlme_3.1-163 cli_3.6.1 TH.data_1.1-2 [4] rlang_1.1.1 estimability_1.4.1 xtable_1.8-4 [7] minqa_1.2.6 zoo_1.8-12 TMB_1.9.6 [10] lme4_1.1-34 brio_1.1.3 grid_4.4.0 [13] MASS_7.3-60.1 mvtnorm_1.2-3 numDeriv_2016.8-1.1 [16] compiler_4.4.0 multcomp_1.4-25 codetools_0.2-19 [19] sandwich_3.0-2 emmeans_1.8.8 coda_0.19-4 [22] Rcpp_1.0.11 mgcv_1.9-0 lattice_0.21-9 [25] nloptr_2.0.3 R6_2.5.1 splines_4.4.0 [28] magrittr_2.0.3 Matrix_1.6-1.1 boot_1.3-28.1 [31] survival_3.5-7 Anova: ............... VarCorr: ............. altopt: alternative optimizers: S basics: .............SS.....S......S trickier examples: SS.SSSS........ bootMer: bootMer: SS checkRank: ....................................W..W....W..W.... control: SS diagnose: .S disp: ... downstream: S..... edgecases: test edge cases: . env: basic examples: ... families: alternative binomial specifications: .......... non-integer count warnings: ....... fitting exotic families: SSSSS trunc compois: S compois: S genpois: S tweedie: S......................... formulas: formula parsing: ................ mapopt: methods: ............................S.................................................... simulate consistency with glm/lm: ... Ranef etc.: .......S.................S misc: . offset: SSSSSSSSS predict: .....SSS Predict two-column response case: SS.................S..SSS...S..S...S.............S...... reml: REML: ....... rr: ......... saveload: Saving and loading glmmTMB objects: . smooths: ... sparseX: sparse X models: ....... start: .. utils: .............. varstruc: variance structures: ........SSS. 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:68:3') - Reason: On CRAN 3. Variance structures ('test-basics.R:77:3') - Reason: On CRAN 4. Multiple RE, reordering ('test-basics.R:107:6') - Reason: On CRAN 5. close to lme4 results ('test-basics.R:142:5') - Reason: On CRAN 6. basic zero inflation ('test-basics.R:195:8') - Reason: On CRAN 7. alternative binomial model specifications ('test-basics.R:214:5') - Reason: On CRAN 8. NA handling ('test-basics.R:235:5') - Reason: On CRAN 9. quine NB fit ('test-basics.R:253:5') - Reason: On CRAN 10. contrasts arg ('test-basics.R:264:5') - Reason: On CRAN 11. zero disp setting ('test-basics.R:275:5') - 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:89:3') - Reason: On CRAN 19. nbinom ('test-families.R:111:5') - Reason: On CRAN 20. dbetabinom ('test-families.R:172:5') - Reason: On CRAN 21. truncated ('test-families.R:245:5') - Reason: On CRAN 22. truncated_genpois ('test-families.R:322:3') - Reason: On CRAN 23. truncated_compois ('test-families.R:339:5') - Reason: On CRAN 24. compois ('test-families.R:350:5') - Reason: On CRAN 25. genpois ('test-families.R:361:5') - Reason: On CRAN 26. tweedie ('test-families.R:370:5') - Reason: On CRAN 27. anova ML/REML checks ('test-methods.R:117:5') - Reason: On CRAN 28. various binomial response types work ('test-methods.R:478:3') - Reason: On CRAN 29. bad inversion in vcov ('test-methods.R:646:5') - Reason: On Windows 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:61:5') - Reason: On CRAN 43. Prediction with dispformula=~0 ('test-predict.R:69:5') - Reason: On CRAN 44. scale ('test-predict.R:183:5') - Reason: On CRAN 45. scale_RE ('test-predict.R:205:5') - Reason: On CRAN 46. complex bases in dispformula ('test-predict.R:212:5') - Reason: On CRAN 47. fix_predvars works for I(x^2) ('test-predict.R:224:5') - Reason: On CRAN 48. contrasts carried over ('test-predict.R:285:5') - Reason: On CRAN 49. offset-only model (GH #625) ('test-predict.R:324:5') - Reason: On CRAN 50. inverse-link prediction ('test-predict.R:343:3') - Reason: On CRAN 51. nzprob doesn't segfault ('test-predict.R:434:5') - Reason: On CRAN 52. ar1 requires factor time ('test-varstruc.R:52:3') - Reason: On CRAN 53. varcorr_print ('test-varstruc.R:72:5') - Reason: On CRAN 54. cov_struct_order ('test-varstruc.R:103:5') - Reason: On CRAN 55. zi ('test-zi.R:12:3') - Reason: On CRAN 56. zi beta and Gamma ('test-zi.R:37:5') - Reason: On CRAN ══ Warnings ════════════════════════════════════════════════════════════════════ 1. equivalence between 'skip' and 'warn' when confronted with identifiable and non-identifiable fixed effects ('test-checkRank.R:152:5') - Model convergence problem; extreme or very small eigenvalues detected. See vignette('troubleshooting') 2. equivalence between 'skip' and 'warn' when confronted with identifiable and non-identifiable fixed effects ('test-checkRank.R:158:5') - Model convergence problem; extreme or very small eigenvalues detected. See vignette('troubleshooting') 3. equivalence between 'skip' and 'warn' when confronted with identifiable and non-identifiable fixed effects ('test-checkRank.R:172:5') - Model convergence problem; extreme or very small eigenvalues detected. See vignette('troubleshooting') 4. equivalence between 'skip' and 'warn' when confronted with identifiable and non-identifiable fixed effects ('test-checkRank.R:178:5') - Model convergence problem; extreme or very small eigenvalues detected. See vignette('troubleshooting') ══ DONE ════════════════════════════════════════════════════════════════════════ NULL > > proc.time() user system elapsed 84.40 3.23 87.67