CRAN Package Check Results for Package glmmTMB

Last updated on 2025-04-01 18:53:45 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.1.10 227.76 330.00 557.76 ERROR
r-devel-linux-x86_64-debian-gcc 1.1.10 183.21 253.72 436.93 ERROR
r-devel-linux-x86_64-fedora-clang 1.1.10 819.03 ERROR
r-devel-linux-x86_64-fedora-gcc 1.1.10 1007.77 ERROR
r-devel-macos-arm64 1.1.10 256.00 OK
r-devel-macos-x86_64 1.1.10 522.00 NOTE
r-devel-windows-x86_64 1.1.10 233.00 318.00 551.00 ERROR --no-vignettes
r-patched-linux-x86_64 1.1.10 256.17 324.59 580.76 ERROR
r-release-linux-x86_64 1.1.10 250.33 316.56 566.89 ERROR
r-release-macos-arm64 1.1.10 260.00 NOTE
r-release-macos-x86_64 1.1.10 506.00 NOTE
r-release-windows-x86_64 1.1.10 212.00 306.00 518.00 ERROR --no-vignettes
r-oldrel-macos-arm64 1.1.10 NOTE
r-oldrel-macos-x86_64 1.1.10 452.00 NOTE
r-oldrel-windows-x86_64 1.1.10 331.00 348.00 679.00 ERROR --no-vignettes

Check Details

Version: 1.1.10
Check: DESCRIPTION meta-information
Result: NOTE Missing dependency on R >= 4.1.0 because package code uses the pipe |> or function shorthand \(...) syntax added in R 4.1.0. File(s) using such syntax: ‘methods.R’ Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-macos-x86_64, r-patched-linux-x86_64

Version: 1.1.10
Check: tests
Result: ERROR Running ‘AAAtest-all.R’ [107s/126s] 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) (2025-03-29 r88074) Platform: x86_64-pc-linux-gnu Running under: Debian GNU/Linux trixie/sid Matrix products: default BLAS: /home/hornik/tmp/R.check/r-devel-clang/Work/build/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_1.1.10 testthat_3.2.3 loaded via a namespace (and not attached): [1] nlme_3.1-167 cli_3.6.4 TH.data_1.1-3 [4] rlang_1.1.5 estimability_1.5.1 reformulas_0.4.0 [7] xtable_1.8-4 minqa_1.2.8 zoo_1.8-13 [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_1.11.0 [22] coda_0.19-4.1 Rcpp_1.0.14 mgcv_1.9-1 [25] lattice_0.22-6 nloptr_2.2.1 R6_2.6.1 [28] Rdpack_2.6.3 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: S1.... edgecases: test edge cases: . env: basic examples: ... families: .....................SSSSSSSSS.................................. formulas: formula parsing: ................ mapequal: ........ mapopt: methods: ...............................S..........................................S..............S....................... misc: . offset: SSSSSSSSS predict: .....SSS Predict two-column response case: SS.................S..SSS....S..S...S.............S....... priors: ...........S propto: ..... reml: ........ rr: ......... saveload: Saving and loading glmmTMB objects: . simulate: ......... simulate_new: ....S......... 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: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: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:225:5') - Reason: On CRAN 48. contrasts carried over ('test-predict.R:293:5') - Reason: On CRAN 49. offset-only model (GH #625) ('test-predict.R:332:5') - Reason: On CRAN 50. inverse-link prediction ('test-predict.R:351:3') - Reason: On CRAN 51. nzprob doesn't segfault ('test-predict.R:442:5') - Reason: On CRAN 52. prior specs ('test-priors.R:125:5') - Reason: On CRAN 53. simulate_new, returning pars ('test-simulate_new.R:49:1') - Reason: empty test 54. ar1 requires factor time ('test-varstruc.R:58:3') - Reason: On CRAN 55. varcorr_print ('test-varstruc.R:78:5') - Reason: On CRAN 56. cov_struct_order ('test-varstruc.R:109:5') - Reason: On CRAN 57. zi ('test-zi.R:12:3') - Reason: On CRAN 58. zi beta and Gamma ('test-zi.R:37:5') - Reason: On CRAN ══ Failed ══════════════════════════════════════════════════════════════════════ ── 1. Failure ('test-downstream.R:71:7'): joint_test with non-estimable terms ── c(suppressMessages(joint_tests(nested0))) not equal to c(suppressMessages(joint_tests(nested))). Component "p.value": Mean relative difference: 1.553134e-05 ══ DONE ════════════════════════════════════════════════════════════════════════ Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.1.10
Check: tests
Result: ERROR Running ‘AAAtest-all.R’ [92s/104s] 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) (2025-03-29 r88074) Platform: x86_64-pc-linux-gnu Running under: Debian GNU/Linux trixie/sid Matrix products: default BLAS: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/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_1.1.10 testthat_3.2.3 loaded via a namespace (and not attached): [1] nlme_3.1-167 cli_3.6.4 TH.data_1.1-3 [4] rlang_1.1.5 estimability_1.5.1 reformulas_0.4.0 [7] xtable_1.8-4 minqa_1.2.8 zoo_1.8-13 [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_1.11.0 [22] coda_0.19-4.1 Rcpp_1.0.14 mgcv_1.9-1 [25] lattice_0.22-6 nloptr_2.2.1 R6_2.6.1 [28] Rdpack_2.6.3 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: S1.... edgecases: test edge cases: . env: basic examples: ... families: .....................SSSSSSSSS.................................. formulas: formula parsing: ................ mapequal: ........ mapopt: methods: ...............................S..........................................S..............S....................... misc: . offset: SSSSSSSSS predict: .....SSS Predict two-column response case: SS.................S..SSS....S..S...S.............S....... priors: ...........S propto: ..... reml: ........ rr: ......... saveload: Saving and loading glmmTMB objects: . simulate: ......... simulate_new: ....S......... 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: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: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:225:5') - Reason: On CRAN 48. contrasts carried over ('test-predict.R:293:5') - Reason: On CRAN 49. offset-only model (GH #625) ('test-predict.R:332:5') - Reason: On CRAN 50. inverse-link prediction ('test-predict.R:351:3') - Reason: On CRAN 51. nzprob doesn't segfault ('test-predict.R:442:5') - Reason: On CRAN 52. prior specs ('test-priors.R:125:5') - Reason: On CRAN 53. simulate_new, returning pars ('test-simulate_new.R:49:1') - Reason: empty test 54. ar1 requires factor time ('test-varstruc.R:58:3') - Reason: On CRAN 55. varcorr_print ('test-varstruc.R:78:5') - Reason: On CRAN 56. cov_struct_order ('test-varstruc.R:109:5') - Reason: On CRAN 57. zi ('test-zi.R:12:3') - Reason: On CRAN 58. zi beta and Gamma ('test-zi.R:37:5') - Reason: On CRAN ══ Failed ══════════════════════════════════════════════════════════════════════ ── 1. Failure ('test-downstream.R:71:7'): joint_test with non-estimable terms ── c(suppressMessages(joint_tests(nested0))) not equal to c(suppressMessages(joint_tests(nested))). Component "p.value": Mean relative difference: 1.553134e-05 ══ DONE ════════════════════════════════════════════════════════════════════════ Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-debian-gcc

Version: 1.1.10
Check: tests
Result: ERROR Running ‘AAAtest-all.R’ [92s/92s] 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) (2025-03-27 r88062) Platform: x86_64-pc-linux-gnu Running under: Fedora Linux 40 (Workstation Edition) Matrix products: default BLAS: /data/gannet/ripley/R/R-clang/lib/libRblas.so LAPACK: /data/gannet/ripley/R/R-clang/lib/libRlapack.so; LAPACK version 3.12.1 locale: [1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=C [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C time zone: Europe/London tzcode source: system (glibc) attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] glmmTMB_1.1.10 testthat_3.2.3 loaded via a namespace (and not attached): [1] nlme_3.1-167 cli_3.6.4 TH.data_1.1-3 [4] rlang_1.1.5 estimability_1.5.1 reformulas_0.4.0 [7] xtable_1.8-4 minqa_1.2.8 zoo_1.8-13 [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_1.11.0 [22] coda_0.19-4.1 Rcpp_1.0.14 mgcv_1.9-1 [25] lattice_0.22-6 nloptr_2.2.1 R6_2.6.1 [28] Rdpack_2.6.3 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: S1.... edgecases: test edge cases: . env: basic examples: ... families: .....................SSSSSSSSS.................................. formulas: formula parsing: ................ mapequal: ........ mapopt: methods: ...............................S..........................................S..............S....................... misc: . offset: SSSSSSSSS predict: .....SSS Predict two-column response case: SS.................S..SSS....S..S...S.............S....... priors: ...........S propto: ..... reml: ........ rr: ......... saveload: Saving and loading glmmTMB objects: . simulate: ......... simulate_new: ....S......... 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: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: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:225:5') - Reason: On CRAN 48. contrasts carried over ('test-predict.R:293:5') - Reason: On CRAN 49. offset-only model (GH #625) ('test-predict.R:332:5') - Reason: On CRAN 50. inverse-link prediction ('test-predict.R:351:3') - Reason: On CRAN 51. nzprob doesn't segfault ('test-predict.R:442:5') - Reason: On CRAN 52. prior specs ('test-priors.R:125:5') - Reason: On CRAN 53. simulate_new, returning pars ('test-simulate_new.R:49:1') - Reason: empty test 54. ar1 requires factor time ('test-varstruc.R:58:3') - Reason: On CRAN 55. varcorr_print ('test-varstruc.R:78:5') - Reason: On CRAN 56. cov_struct_order ('test-varstruc.R:109:5') - Reason: On CRAN 57. zi ('test-zi.R:12:3') - Reason: On CRAN 58. zi beta and Gamma ('test-zi.R:37:5') - Reason: On CRAN ══ Failed ══════════════════════════════════════════════════════════════════════ ── 1. Failure ('test-downstream.R:71:7'): joint_test with non-estimable terms ── c(suppressMessages(joint_tests(nested0))) not equal to c(suppressMessages(joint_tests(nested))). Component "p.value": Mean relative difference: 1.553134e-05 ══ DONE ════════════════════════════════════════════════════════════════════════ Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-fedora-clang

Version: 1.1.10
Check: tests
Result: ERROR Running ‘AAAtest-all.R’ [153s/233s] 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) (2025-03-26 r88060) Platform: x86_64-pc-linux-gnu Running under: Fedora Linux 40 (Workstation Edition) Matrix products: default BLAS: /data/gannet/ripley/R/R-devel/lib/libRblas.so LAPACK: /usr/lib64/liblapack.so.3.12.0 LAPACK version 3.12.0 locale: [1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=C [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C time zone: Europe/London tzcode source: system (glibc) attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] glmmTMB_1.1.10 testthat_3.2.3 loaded via a namespace (and not attached): [1] nlme_3.1-167 cli_3.6.4 TH.data_1.1-3 [4] rlang_1.1.5 estimability_1.5.1 reformulas_0.4.0 [7] xtable_1.8-4 minqa_1.2.8 zoo_1.8-13 [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_1.11.0 [22] coda_0.19-4.1 Rcpp_1.0.14 mgcv_1.9-1 [25] lattice_0.22-6 nloptr_2.2.1 R6_2.6.1 [28] Rdpack_2.6.3 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: S1.... edgecases: test edge cases: . env: basic examples: ... families: .....................SSSSSSSSS.................................. formulas: formula parsing: ................ mapequal: ........ mapopt: methods: ...............................S..........................................S..............S....................... misc: . offset: SSSSSSSSS predict: .....SSS Predict two-column response case: SS.................S..SSS....S..S...S.............S....... priors: ...........S propto: ..... reml: ........ rr: ......... saveload: Saving and loading glmmTMB objects: . simulate: ......... simulate_new: ....S......... 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: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: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:225:5') - Reason: On CRAN 48. contrasts carried over ('test-predict.R:293:5') - Reason: On CRAN 49. offset-only model (GH #625) ('test-predict.R:332:5') - Reason: On CRAN 50. inverse-link prediction ('test-predict.R:351:3') - Reason: On CRAN 51. nzprob doesn't segfault ('test-predict.R:442:5') - Reason: On CRAN 52. prior specs ('test-priors.R:125:5') - Reason: On CRAN 53. simulate_new, returning pars ('test-simulate_new.R:49:1') - Reason: empty test 54. ar1 requires factor time ('test-varstruc.R:58:3') - Reason: On CRAN 55. varcorr_print ('test-varstruc.R:78:5') - Reason: On CRAN 56. cov_struct_order ('test-varstruc.R:109:5') - Reason: On CRAN 57. zi ('test-zi.R:12:3') - Reason: On CRAN 58. zi beta and Gamma ('test-zi.R:37:5') - Reason: On CRAN ══ Failed ══════════════════════════════════════════════════════════════════════ ── 1. Failure ('test-downstream.R:71:7'): joint_test with non-estimable terms ── c(suppressMessages(joint_tests(nested0))) not equal to c(suppressMessages(joint_tests(nested))). Component "p.value": Mean relative difference: 1.553134e-05 ══ DONE ════════════════════════════════════════════════════════════════════════ Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-fedora-gcc

Version: 1.1.10
Flags: --no-vignettes
Check: DESCRIPTION meta-information
Result: NOTE Missing dependency on R >= 4.1.0 because package code uses the pipe |> or function shorthand \(...) syntax added in R 4.1.0. File(s) using such syntax: 'methods.R' Flavor: r-devel-windows-x86_64

Version: 1.1.10
Flags: --no-vignettes
Check: tests
Result: ERROR Running 'AAAtest-all.R' [103s] 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 version 4.5.0 beta (2025-03-27 r88067 ucrt) Platform: x86_64-w64-mingw32/x64 Running under: Windows Server 2022 x64 (build 20348) Matrix products: default LAPACK version 3.12.1 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_1.1.10 testthat_3.2.3 loaded via a namespace (and not attached): [1] nlme_3.1-167 cli_3.6.4 TH.data_1.1-3 [4] rlang_1.1.5 estimability_1.5.1 reformulas_0.4.0 [7] xtable_1.8-4 minqa_1.2.8 zoo_1.8-13 [10] TMB_1.9.17 lme4_1.1-37 brio_1.1.5 [13] grid_4.5.0 MASS_7.3-65 mvtnorm_1.3-3 [16] numDeriv_2016.8-1.1 multcomp_1.4-28 compiler_4.5.0 [19] codetools_0.2-20 sandwich_3.1-1 emmeans_1.11.0 [22] coda_0.19-4.1 Rcpp_1.0.14 mgcv_1.9-1 [25] lattice_0.22-6 nloptr_2.2.1 R6_2.6.1 [28] Rdpack_2.6.3 splines_4.5.0 rbibutils_2.3 [31] magrittr_2.0.3 Matrix_1.7-3 tools_4.5.0 [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: S1.... edgecases: test edge cases: . env: basic examples: ... families: .....................SSSSSSSSS.................................. formulas: formula parsing: ................ mapequal: ........ mapopt: methods: ...............................S..........................................S..............S....................... misc: . offset: SSSSSSSSS predict: .....SSS Predict two-column response case: SS.................S..SSS....S..S...S.............S....... priors: ...........S propto: ..... reml: ........ rr: ......... saveload: Saving and loading glmmTMB objects: . simulate: ......... simulate_new: ....S......... 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: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: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:225:5') - Reason: On CRAN 48. contrasts carried over ('test-predict.R:293:5') - Reason: On CRAN 49. offset-only model (GH #625) ('test-predict.R:332:5') - Reason: On CRAN 50. inverse-link prediction ('test-predict.R:351:3') - Reason: On CRAN 51. nzprob doesn't segfault ('test-predict.R:442:5') - Reason: On CRAN 52. prior specs ('test-priors.R:125:5') - Reason: On CRAN 53. simulate_new, returning pars ('test-simulate_new.R:49:1') - Reason: empty test 54. ar1 requires factor time ('test-varstruc.R:58:3') - Reason: On CRAN 55. varcorr_print ('test-varstruc.R:78:5') - Reason: On CRAN 56. cov_struct_order ('test-varstruc.R:109:5') - Reason: On CRAN 57. zi ('test-zi.R:12:3') - Reason: On CRAN 58. zi beta and Gamma ('test-zi.R:37:5') - Reason: On CRAN ══ Failed ══════════════════════════════════════════════════════════════════════ ── 1. Failure ('test-downstream.R:71:7'): joint_test with non-estimable terms ── c(suppressMessages(joint_tests(nested0))) not equal to c(suppressMessages(joint_tests(nested))). Component "p.value": Mean relative difference: 1.553134e-05 ══ DONE ════════════════════════════════════════════════════════════════════════ Error: Test failures Execution halted Flavor: r-devel-windows-x86_64

Version: 1.1.10
Check: tests
Result: ERROR Running ‘AAAtest-all.R’ [104s/135s] 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 version 4.5.0 beta (2025-03-27 r88065) Platform: x86_64-pc-linux-gnu Running under: Debian GNU/Linux trixie/sid Matrix products: default BLAS: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/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_1.1.10 testthat_3.2.3 loaded via a namespace (and not attached): [1] nlme_3.1-167 cli_3.6.4 TH.data_1.1-3 [4] rlang_1.1.5 estimability_1.5.1 reformulas_0.4.0 [7] xtable_1.8-4 minqa_1.2.8 zoo_1.8-13 [10] TMB_1.9.17 lme4_1.1-37 brio_1.1.5 [13] grid_4.5.0 MASS_7.3-65 mvtnorm_1.3-3 [16] numDeriv_2016.8-1.1 multcomp_1.4-28 compiler_4.5.0 [19] codetools_0.2-20 sandwich_3.1-1 emmeans_1.11.0 [22] coda_0.19-4.1 Rcpp_1.0.14 mgcv_1.9-1 [25] lattice_0.22-6 nloptr_2.2.1 R6_2.6.1 [28] Rdpack_2.6.3 splines_4.5.0 rbibutils_2.3 [31] magrittr_2.0.3 Matrix_1.7-3 tools_4.5.0 [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: S1.... edgecases: test edge cases: . env: basic examples: ... families: .....................SSSSSSSSS.................................. formulas: formula parsing: ................ mapequal: ........ mapopt: methods: ...............................S..........................................S..............S....................... misc: . offset: SSSSSSSSS predict: .....SSS Predict two-column response case: SS.................S..SSS....S..S...S.............S....... priors: ...........S propto: ..... reml: ........ rr: ......... saveload: Saving and loading glmmTMB objects: . simulate: ......... simulate_new: ....S......... 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: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: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:225:5') - Reason: On CRAN 48. contrasts carried over ('test-predict.R:293:5') - Reason: On CRAN 49. offset-only model (GH #625) ('test-predict.R:332:5') - Reason: On CRAN 50. inverse-link prediction ('test-predict.R:351:3') - Reason: On CRAN 51. nzprob doesn't segfault ('test-predict.R:442:5') - Reason: On CRAN 52. prior specs ('test-priors.R:125:5') - Reason: On CRAN 53. simulate_new, returning pars ('test-simulate_new.R:49:1') - Reason: empty test 54. ar1 requires factor time ('test-varstruc.R:58:3') - Reason: On CRAN 55. varcorr_print ('test-varstruc.R:78:5') - Reason: On CRAN 56. cov_struct_order ('test-varstruc.R:109:5') - Reason: On CRAN 57. zi ('test-zi.R:12:3') - Reason: On CRAN 58. zi beta and Gamma ('test-zi.R:37:5') - Reason: On CRAN ══ Failed ══════════════════════════════════════════════════════════════════════ ── 1. Failure ('test-downstream.R:71:7'): joint_test with non-estimable terms ── c(suppressMessages(joint_tests(nested0))) not equal to c(suppressMessages(joint_tests(nested))). Component "p.value": Mean relative difference: 1.553134e-05 ══ DONE ════════════════════════════════════════════════════════════════════════ Error: Test failures Execution halted Flavor: r-patched-linux-x86_64

Version: 1.1.10
Check: tests
Result: ERROR Running ‘AAAtest-all.R’ [101s/112s] 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 version 4.4.3 (2025-02-28) Platform: x86_64-pc-linux-gnu Running under: Debian GNU/Linux trixie/sid Matrix products: default BLAS: /home/hornik/tmp/R.check/r-release-gcc/Work/build/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_1.1.10 testthat_3.2.3 loaded via a namespace (and not attached): [1] nlme_3.1-167 cli_3.6.4 TH.data_1.1-3 [4] rlang_1.1.5 estimability_1.5.1 reformulas_0.4.0 [7] xtable_1.8-4 minqa_1.2.8 zoo_1.8-13 [10] TMB_1.9.17 lme4_1.1-37 brio_1.1.5 [13] grid_4.4.3 MASS_7.3-65 mvtnorm_1.3-3 [16] numDeriv_2016.8-1.1 multcomp_1.4-28 compiler_4.4.3 [19] codetools_0.2-20 sandwich_3.1-1 emmeans_1.11.0 [22] coda_0.19-4.1 Rcpp_1.0.14 mgcv_1.9-1 [25] lattice_0.22-6 nloptr_2.2.1 R6_2.6.1 [28] Rdpack_2.6.3 splines_4.4.3 rbibutils_2.3 [31] magrittr_2.0.3 Matrix_1.7-3 tools_4.4.3 [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: S1.... edgecases: test edge cases: . env: basic examples: ... families: .....................SSSSSSSSS.................................. formulas: formula parsing: ................ mapequal: ........ mapopt: methods: ...............................S..........................................S..............S....................... misc: . offset: SSSSSSSSS predict: .....SSS Predict two-column response case: SS.................S..SSS....S..S...S.............S....... priors: ...........S propto: ..... reml: ........ rr: ......... saveload: Saving and loading glmmTMB objects: . simulate: ......... simulate_new: ....S......... 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: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: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:225:5') - Reason: On CRAN 48. contrasts carried over ('test-predict.R:293:5') - Reason: On CRAN 49. offset-only model (GH #625) ('test-predict.R:332:5') - Reason: On CRAN 50. inverse-link prediction ('test-predict.R:351:3') - Reason: On CRAN 51. nzprob doesn't segfault ('test-predict.R:442:5') - Reason: On CRAN 52. prior specs ('test-priors.R:125:5') - Reason: On CRAN 53. simulate_new, returning pars ('test-simulate_new.R:49:1') - Reason: empty test 54. ar1 requires factor time ('test-varstruc.R:58:3') - Reason: On CRAN 55. varcorr_print ('test-varstruc.R:78:5') - Reason: On CRAN 56. cov_struct_order ('test-varstruc.R:109:5') - Reason: On CRAN 57. zi ('test-zi.R:12:3') - Reason: On CRAN 58. zi beta and Gamma ('test-zi.R:37:5') - Reason: On CRAN ══ Failed ══════════════════════════════════════════════════════════════════════ ── 1. Failure ('test-downstream.R:71:7'): joint_test with non-estimable terms ── c(suppressMessages(joint_tests(nested0))) not equal to c(suppressMessages(joint_tests(nested))). Component "p.value": Mean relative difference: 1.553134e-05 ══ DONE ════════════════════════════════════════════════════════════════════════ Error: Test failures Execution halted Flavor: r-release-linux-x86_64

Version: 1.1.10
Check: installed package size
Result: NOTE installed size is 98.1Mb sub-directories of 1Mb or more: doc 1.3Mb libs 91.6Mb test_data 2.3Mb vignette_data 2.1Mb Flavors: r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64

Version: 1.1.10
Flags: --no-vignettes
Check: installed package size
Result: NOTE installed size is 10.8Mb sub-directories of 1Mb or more: doc 1.3Mb libs 4.4Mb test_data 2.3Mb vignette_data 2.1Mb Flavors: r-release-windows-x86_64, r-oldrel-windows-x86_64

Version: 1.1.10
Flags: --no-vignettes
Check: tests
Result: ERROR Running 'AAAtest-all.R' [95s] 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 version 4.4.3 (2025-02-28 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_1.1.10 testthat_3.2.3 loaded via a namespace (and not attached): [1] nlme_3.1-167 cli_3.6.4 TH.data_1.1-3 [4] rlang_1.1.5 estimability_1.5.1 reformulas_0.4.0 [7] xtable_1.8-4 minqa_1.2.8 zoo_1.8-13 [10] TMB_1.9.17 lme4_1.1-37 brio_1.1.5 [13] grid_4.4.3 MASS_7.3-65 mvtnorm_1.3-3 [16] numDeriv_2016.8-1.1 multcomp_1.4-28 compiler_4.4.3 [19] codetools_0.2-20 sandwich_3.1-1 emmeans_1.11.0 [22] coda_0.19-4.1 Rcpp_1.0.14 mgcv_1.9-1 [25] lattice_0.22-6 nloptr_2.2.1 R6_2.6.1 [28] Rdpack_2.6.3 splines_4.4.3 rbibutils_2.3 [31] magrittr_2.0.3 Matrix_1.7-3 tools_4.4.3 [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: S1.... edgecases: test edge cases: . env: basic examples: ... families: .....................SSSSSSSSS.................................. formulas: formula parsing: ................ mapequal: ........ mapopt: methods: ...............................S..........................................S..............S....................... misc: . offset: SSSSSSSSS predict: .....SSS Predict two-column response case: SS.................S..SSS....S..S...S.............S....... priors: ...........S propto: ..... reml: ........ rr: ......... saveload: Saving and loading glmmTMB objects: . simulate: ......... simulate_new: ....S......... 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: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: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:225:5') - Reason: On CRAN 48. contrasts carried over ('test-predict.R:293:5') - Reason: On CRAN 49. offset-only model (GH #625) ('test-predict.R:332:5') - Reason: On CRAN 50. inverse-link prediction ('test-predict.R:351:3') - Reason: On CRAN 51. nzprob doesn't segfault ('test-predict.R:442:5') - Reason: On CRAN 52. prior specs ('test-priors.R:125:5') - Reason: On CRAN 53. simulate_new, returning pars ('test-simulate_new.R:49:1') - Reason: empty test 54. ar1 requires factor time ('test-varstruc.R:58:3') - Reason: On CRAN 55. varcorr_print ('test-varstruc.R:78:5') - Reason: On CRAN 56. cov_struct_order ('test-varstruc.R:109:5') - Reason: On CRAN 57. zi ('test-zi.R:12:3') - Reason: On CRAN 58. zi beta and Gamma ('test-zi.R:37:5') - Reason: On CRAN ══ Failed ══════════════════════════════════════════════════════════════════════ ── 1. Failure ('test-downstream.R:71:7'): joint_test with non-estimable terms ── c(suppressMessages(joint_tests(nested0))) not equal to c(suppressMessages(joint_tests(nested))). Component "p.value": Mean relative difference: 1.553134e-05 ══ DONE ════════════════════════════════════════════════════════════════════════ Error: Test failures Execution halted Flavor: r-release-windows-x86_64

Version: 1.1.10
Flags: --no-vignettes
Check: tests
Result: ERROR Running 'AAAtest-all.R' [113s] 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 version 4.3.3 (2024-02-29 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) 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_1.1.10 testthat_3.2.3 loaded via a namespace (and not attached): [1] nlme_3.1-167 cli_3.6.4 TH.data_1.1-3 [4] rlang_1.1.5 estimability_1.5.1 reformulas_0.4.0 [7] xtable_1.8-4 minqa_1.2.8 zoo_1.8-13 [10] TMB_1.9.17 lme4_1.1-37 brio_1.1.5 [13] grid_4.3.3 MASS_7.3-60.0.1 mvtnorm_1.3-3 [16] numDeriv_2016.8-1.1 multcomp_1.4-28 compiler_4.3.3 [19] codetools_0.2-20 sandwich_3.1-1 emmeans_1.11.0 [22] coda_0.19-4.1 Rcpp_1.0.14 mgcv_1.9-1 [25] lattice_0.22-6 nloptr_2.2.1 R6_2.6.1 [28] Rdpack_2.6.3 splines_4.3.3 rbibutils_2.3 [31] magrittr_2.0.3 Matrix_1.6-5 tools_4.3.3 [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: S1.... edgecases: test edge cases: . env: basic examples: ... families: .....................SSSSSSSSS.................................. formulas: formula parsing: ................ mapequal: ........ mapopt: methods: ...............................S..........................................S..............S....................... misc: . offset: SSSSSSSSS predict: .....SSS Predict two-column response case: SS.................S..SSS....S..S...S.............S....... priors: ...........S propto: ..... reml: ........ rr: ......... saveload: Saving and loading glmmTMB objects: . simulate: ......... simulate_new: ....S......... 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: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: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:225:5') - Reason: On CRAN 48. contrasts carried over ('test-predict.R:293:5') - Reason: On CRAN 49. offset-only model (GH #625) ('test-predict.R:332:5') - Reason: On CRAN 50. inverse-link prediction ('test-predict.R:351:3') - Reason: On CRAN 51. nzprob doesn't segfault ('test-predict.R:442:5') - Reason: On CRAN 52. prior specs ('test-priors.R:125:5') - Reason: On CRAN 53. simulate_new, returning pars ('test-simulate_new.R:49:1') - Reason: empty test 54. ar1 requires factor time ('test-varstruc.R:58:3') - Reason: On CRAN 55. varcorr_print ('test-varstruc.R:78:5') - Reason: On CRAN 56. cov_struct_order ('test-varstruc.R:109:5') - Reason: On CRAN 57. zi ('test-zi.R:12:3') - Reason: On CRAN 58. zi beta and Gamma ('test-zi.R:37:5') - Reason: On CRAN ══ Failed ══════════════════════════════════════════════════════════════════════ ── 1. Failure ('test-downstream.R:71:7'): joint_test with non-estimable terms ── c(suppressMessages(joint_tests(nested0))) not equal to c(suppressMessages(joint_tests(nested))). Component "p.value": Mean relative difference: 1.553134e-05 ══ DONE ════════════════════════════════════════════════════════════════════════ Error: Test failures Execution halted Flavor: r-oldrel-windows-x86_64

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