CRAN Package Check Results for Package glmmTMB

Last updated on 2025-02-16 10:50:47 CET.

Flavor	Version	Tinstall	Tcheck	Ttotal	Status	Flags
r-devel-linux-x86_64-debian-clang	1.1.10	218.95	332.59	551.54	NOTE
r-devel-linux-x86_64-debian-gcc	1.1.10	183.98	256.08	440.06	NOTE
r-devel-linux-x86_64-fedora-clang	1.1.10			935.84	ERROR
r-devel-linux-x86_64-fedora-gcc	1.1.10			1017.16	NOTE
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	211.00	308.00	519.00	NOTE	--no-vignettes
r-patched-linux-x86_64	1.1.10	266.98	0.02	267.00	FAIL
r-release-linux-x86_64	1.1.10	238.57	316.36	554.93	OK
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	221.00	313.00	534.00	NOTE	--no-vignettes
r-oldrel-macos-arm64	1.1.10			256.00	NOTE
r-oldrel-macos-x86_64	1.1.10			452.00	NOTE
r-oldrel-windows-x86_64	1.1.10	326.00	348.00	674.00	NOTE	--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

Version: 1.1.10
Check: tests
Result: ERROR Running ‘AAAtest-all.R’ [156s/160s] 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) (2025-02-14 r87717) 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 3.12.0 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_1.8-12 [10] TMB_1.9.16 lme4_1.1-36 brio_1.1.5 [13] grid_4.5.0 MASS_7.3-64 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_1.10.7 [22] coda_0.19-4.1 Rcpp_1.0.14 mgcv_1.9-1 [25] lattice_0.22-6 nloptr_2.1.1 R6_2.6.0 [28] Rdpack_2.6.2 splines_4.5.0 rbibutils_2.3 [31] magrittr_2.0.3 Matrix_1.7-2 tools_4.5.0 [34] boot_1.3-31 survival_3.8-3 Anova: WW12............. VarCorr: WWW3.4.WWW........... altopt: alternative optimizers: S basics: .............SS.....S......S trickier examples: SS.SSSS........ bootMer: bootMer: SS checkRank: ................................................ control: SS. diagnose: .S disp: ... downstream: S..... 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..WWW.5S..S...S.............S....... priors: ...........S propto: ..... reml: WWW678WWW9ab.. 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 ══ Warnings ════════════════════════════════════════════════════════════════════ 1. basic car::Anova ('test-Anova.R:27:5') - convergence code -2 from nloptwrap: NLOPT_INVALID_ARGS: Invalid arguments (e.g. lower bounds are bigger than upper bounds, an unknown algorithm was specified, etcetera). 2. basic car::Anova ('test-Anova.R:27:5') - Model failed to converge with max|grad| = 1.84934 (tol = 0.002, component 1) 3. (code run outside of `test_that()`) ('test-VarCorr.R:9:1') - convergence code -2 from nloptwrap: NLOPT_INVALID_ARGS: Invalid arguments (e.g. lower bounds are bigger than upper bounds, an unknown algorithm was specified, etcetera). 4. (code run outside of `test_that()`) ('test-VarCorr.R:9:1') - unable to evaluate scaled gradient 5. (code run outside of `test_that()`) ('test-VarCorr.R:9:1') - Model failed to converge: degenerate Hessian with 2 negative eigenvalues 6. (code run outside of `test_that()`) ('test-VarCorr.R:53:1') - convergence code -2 from nloptwrap: NLOPT_INVALID_ARGS: Invalid arguments (e.g. lower bounds are bigger than upper bounds, an unknown algorithm was specified, etcetera). 7. (code run outside of `test_that()`) ('test-VarCorr.R:53:1') - unable to evaluate scaled gradient 8. (code run outside of `test_that()`) ('test-VarCorr.R:53:1') - Model failed to converge: degenerate Hessian with 2 negative eigenvalues 9. predvars with differing splines in fixed and RE (GH#632) ('test-predict.R:279:5') - convergence code -2 from nloptwrap: NLOPT_INVALID_ARGS: Invalid arguments (e.g. lower bounds are bigger than upper bounds, an unknown algorithm was specified, etcetera). 10. predvars with differing splines in fixed and RE (GH#632) ('test-predict.R:279:5') - unable to evaluate scaled gradient 11. predvars with differing splines in fixed and RE (GH#632) ('test-predict.R:279:5') - Model failed to converge: degenerate Hessian with 1 negative eigenvalues 12. REML check against lmer ('test-reml.R:11:5') - convergence code -2 from nloptwrap: NLOPT_INVALID_ARGS: Invalid arguments (e.g. lower bounds are bigger than upper bounds, an unknown algorithm was specified, etcetera). 13. REML check against lmer ('test-reml.R:11:5') - unable to evaluate scaled gradient 14. REML check against lmer ('test-reml.R:11:5') - Model failed to converge: degenerate Hessian with 1 negative eigenvalues 15. REML check against lmer ('test-reml.R:22:5') - convergence code -2 from nloptwrap: NLOPT_INVALID_ARGS: Invalid arguments (e.g. lower bounds are bigger than upper bounds, an unknown algorithm was specified, etcetera). 16. REML check against lmer ('test-reml.R:22:5') - unable to evaluate scaled gradient 17. REML check against lmer ('test-reml.R:22:5') - Model failed to converge: degenerate Hessian with 2 negative eigenvalues ══ Failed ══════════════════════════════════════════════════════════════════════ ── 1. Failure ('test-Anova.R:28:5'): basic car::Anova ────────────────────────── Anova(fm1) not equal to Anova(fm0). Component "Chisq": Mean relative difference: 0.06009598 ── 2. Failure ('test-Anova.R:29:5'): basic car::Anova ────────────────────────── Anova(fm1, type = "III") not equal to Anova(fm0, type = "III"). Component "Chisq": Mean relative difference: 0.342178 ── 3. Failure ('test-VarCorr.R:29:5'): basic glmer vs glmmTMB ────────────────── stripTMBVC(fm1) not equal to unclass(VarCorr(fm1C)). Attributes: < Component "sc": Mean relative difference: 0.0960177 > Component "Subject": Attributes: < Component "correlation": Mean relative difference: 1 > Component "Subject": Attributes: < Component "stddev": Mean relative difference: 0.8215676 > Component "Subject": Mean relative difference: 0.9829192 ── 4. Failure ('test-VarCorr.R:38:1'): (code run outside of `test_that()`) ───── tail(pfun(fm1), 4) not equal to pfun(fm1C). 3/4 mismatches x[2]: "Subject (Intercept) 2.19" y[2]: "Subject (Intercept) 1.2" x[3]: "age 0.21 -0.58" y[3]: "age 1.2 0.00" x[4]: "Residual 1.31" y[4]: "Residual 1.2" ── 5. Failure ('test-predict.R:289:5'): predvars with differing splines in fixed unname(ppB) not equal to `pp`. 3/3 mismatches (average diff: 1.18) [1] 309 - 309 == -0.512 [2] 320 - 321 == -1.234 [3] 332 - 334 == -1.806 ── 6. Failure ('test-reml.R:13:5'): REML check against lmer ──────────────────── logLik(fm1.lmer) not equal to logLik(fm1.glmmTMB). Mean absolute difference: Inf ── 7. Failure ('test-reml.R:14:5'): REML check against lmer ──────────────────── as.vector(predict(fm1.lmer)) not equal to predict(fm1.glmmTMB). 179/180 mismatches (average diff: 1.93) [1] 246 - 254 == -7.177 [2] 268 - 273 == -5.479 [3] 289 - 293 == -3.781 [4] 311 - 313 == -2.083 [5] 332 - 332 == -0.385 [6] 353 - 352 == 1.313 [7] 375 - 372 == 3.011 [8] 396 - 391 == 4.709 [9] 417 - 411 == 6.407 ... ── 8. Failure ('test-reml.R:16:5'): REML check against lmer ──────────────────── vcov(fm1.glmmTMB)$cond not equal to as.matrix(vcov(fm1.lmer)). 4/4 mismatches (average diff: 8.47) [1] 46.57 - 44.4 == 2.223 [2] -1.45 - -1.8 == 0.347 [3] -1.45 - -1.8 == 0.347 [4] 2.39 - 33.4 == -30.974 ── 9. Failure ('test-reml.R:27:5'): REML check against lmer ──────────────────── logLik(fm2.lmer) not equal to logLik(fm2.glmmTMB). Mean absolute difference: Inf ── 10. Failure ('test-reml.R:28:5'): REML check against lmer ─────────────────── as.vector(predict(fm2.lmer)) not equal to predict(fm2.glmmTMB). 108/108 mismatches (average diff: 0.161) [1] 24.8 - 24.8 == -0.03191 [2] 26.8 - 26.6 == 0.17897 [3] 28.7 - 28.3 == 0.38985 [4] 30.7 - 30.1 == 0.60073 [5] 21.5 - 21.4 == 0.06339 [6] 22.8 - 22.8 == 0.00647 [7] 24.1 - 24.1 == -0.05045 [8] 25.4 - 25.5 == -0.10737 [9] 22.2 - 22.2 == 0.02640 ... ... and 1 more Maximum number of 10 failures reached, some test results may be missing. ══ DONE ════════════════════════════════════════════════════════════════════════ Error: Test failures Execution halted Flavor: r-devel-linux-x86_64-fedora-clang

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
Check: tests
Result: FAIL
Flavor: r-patched-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