Running ‘AAAtest-all.R’ [154s/208s]
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) (2025-03-04 r87879)
  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_1.9.16          lme4_1.1-36         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_1.10.7     
  [22] coda_0.19-4.1       Rcpp_1.0.14         mgcv_1.9-1         
  [25] lattice_0.22-6      nloptr_2.1.1        R6_2.6.1           
  [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