Running ‘AAAtest-all.R’ [118s/479s]
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) (2023-03-28 r84105)
  Platform: x86_64-pc-linux-gnu (64-bit)
  Running under: Fedora Linux 36 (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 3.11.0
  
  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_1.1.6  testthat_3.1.7
  
  loaded via a namespace (and not attached):
   [1] nlme_3.1-162        cli_3.6.1           rlang_1.1.0        
   [4] TH.data_1.1-1       estimability_1.4.1  xtable_1.8-4       
   [7] minqa_1.2.5         zoo_1.8-11          TMB_1.9.3          
  [10] lme4_1.1-32         brio_1.1.3          grid_4.4.0         
  [13] MASS_7.3-58.3       mvtnorm_1.1-3       numDeriv_2016.8-1.1
  [16] compiler_4.4.0      multcomp_1.4-23     codetools_0.2-19   
  [19] sandwich_3.0-2      emmeans_1.8.5       coda_0.19-4        
  [22] Rcpp_1.0.10         lattice_0.20-45     nloptr_2.0.3       
  [25] R6_2.5.1            splines_4.4.0       magrittr_2.0.3     
  [28] Matrix_1.5-3        boot_1.3-28.1       survival_3.5-5     
  Anova: ..............
  VarCorr: .............
  altopt: 
  alternative optimizers: S
  basics: .............SS.....S12..3.S
  trickier examples: SS.SSSS......
  bootMer: 
  bootMer: SS
  checkRank: ..................................W......W..
  control: SS
  diagnose: .S
  disp: ...
  downstream: S..
  edgecases: 
  test edge cases: .
  env: 
  basic examples: ...
  families: 
  alternative binomial specifications: ..........
  non-integer count warnings: .......
  fitting exotic families: SSSSS
  trunc compois: S
  compois: S
  genpois: S
  tweedie: S.
  link function info available: ............
  link info added to family: ......
  formulas: 
  formula parsing: ................
  mapopt: 
  methods: ............................S....................................................
  simulate consistency with glm/lm: ...
  Ranef etc.: .......S.............
  misc: .
  offset: SSSSSSSSS
  predict: .....SSS
  Predict two-column response case: SS.................S..SSS...S..S...S.............S.W.W..
  reml: 
  REML: .......
  rr: .........
  saveload: 
  Saving and loading glmmTMB objects: .
  sparseX: 
  sparse X models: .......
  start: ..
  utils: ..............
  varstruc: 
  variance structures: ........SSS.
  weight: .........
  zi: 
  ZI models: SS
  
  ══ Skipped ═════════════════════════════════════════════════════════════════════
  1. downstream methods work with optim() ('test-altopt.R:11:3') - Reason: On CRAN
  
  2. Update Gaussian ('test-basics.R:68:3') - Reason: On CRAN
  
  3. Variance structures ('test-basics.R:77:3') - Reason: On CRAN
  
  4. Multiple RE, reordering ('test-basics.R:107:6') - Reason: On CRAN
  
  5. close to lme4 results ('test-basics.R:142:5') - Reason: On CRAN
  
  6. basic zero inflation ('test-basics.R:195:8') - Reason: On CRAN
  
  7. alternative binomial model specifications ('test-basics.R:213:5') - Reason: On CRAN
  
  8. NA handling ('test-basics.R:234:5') - Reason: On CRAN
  
  9. quine NB fit ('test-basics.R:252:5') - Reason: On CRAN
  
  10. contrasts arg ('test-basics.R:263:5') - Reason: On CRAN
  
  11. zero disp setting ('test-basics.R:274:5') - 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:8:5') - Reason: On CRAN
  
  18. beta ('test-families.R:90:3') - Reason: On CRAN
  
  19. nbinom ('test-families.R:112:5') - Reason: On CRAN
  
  20. dbetabinom ('test-families.R:167:5') - Reason: On CRAN
  
  21. truncated ('test-families.R:240:5') - Reason: On CRAN
  
  22. truncated_genpois ('test-families.R:317:3') - Reason: On CRAN
  
  23. truncated_compois ('test-families.R:334:5') - Reason: On CRAN
  
  24. compois ('test-families.R:345:5') - Reason: On CRAN
  
  25. genpois ('test-families.R:356:5') - Reason: On CRAN
  
  26. tweedie ('test-families.R:365:5') - Reason: On CRAN
  
  27. anova ML/REML checks ('test-methods.R:117:5') - Reason: On CRAN
  
  28. various binomial response types work ('test-methods.R:478:3') - Reason: On CRAN
  
  29. LM with offset as argument ('test-offset.R:27:3') - Reason: On CRAN
  
  30. LM with offset in formula ('test-offset.R:35:5') - Reason: On CRAN
  
  31. LM with offset in formula - variable not in environment ('test-offset.R:48:5') - Reason: On CRAN
  
  32. LM with offset in dispersion formula ('test-offset.R:57:5') - Reason: On CRAN
  
  33. LM with multiple offsets (cond/dispersion) ('test-offset.R:65:5') - Reason: On CRAN
  
  34. LM with random crap in the formula ('test-offset.R:74:5') - Reason: On CRAN
  
  35. offset in do.call ('test-offset.R:81:5') - Reason: On CRAN
  
  36. LONG offset in do.call ('test-offset.R:90:5') - Reason: On CRAN
  
  37. offset works with attributes ('test-offset.R:101:3') - Reason: On CRAN
  
  38. new levels of fixed effect factor ('test-predict.R:37:5') - Reason: On CRAN
  
  39. new levels in RE term ('test-predict.R:44:5') - Reason: On CRAN
  
  40. new levels in AR1 (OK) ('test-predict.R:51:5') - Reason: On CRAN
  
  41. two-column response ('test-predict.R:61:5') - Reason: On CRAN
  
  42. Prediction with dispformula=~0 ('test-predict.R:69:5') - Reason: On CRAN
  
  43. scale ('test-predict.R:183:5') - Reason: On CRAN
  
  44. scale_RE ('test-predict.R:205:5') - Reason: On CRAN
  
  45. complex bases in dispformula ('test-predict.R:212:5') - Reason: On CRAN
  
  46. fix_predvars works for I(x^2) ('test-predict.R:224:5') - Reason: On CRAN
  
  47. contrasts carried over ('test-predict.R:285:5') - Reason: On CRAN
  
  48. offset-only model (GH #625) ('test-predict.R:324:5') - Reason: On CRAN
  
  49. inverse-link prediction ('test-predict.R:343:3') - Reason: On CRAN
  
  50. nzprob doesn't segfault ('test-predict.R:434:5') - Reason: On CRAN
  
  51. ar1 requires factor time ('test-varstruc.R:52:3') - Reason: On CRAN
  
  52. varcorr_print ('test-varstruc.R:72:5') - Reason: On CRAN
  
  53. cov_struct_order ('test-varstruc.R:103:5') - Reason: On CRAN
  
  54. zi ('test-zi.R:12:3') - Reason: On CRAN
  
  55. zi beta and Gamma ('test-zi.R:37:5') - Reason: On CRAN
  
  ══ Warnings ════════════════════════════════════════════════════════════════════
  1. equivalence between 'skip' and 'warn' when confronted with identifiable and non-identifiable fixed effects ('test-checkRank.R:138:5') - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
  
  2. equivalence between 'skip' and 'warn' when confronted with identifiable and non-identifiable fixed effects ('test-checkRank.R:157:5') - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
  
  3. nzprob computed for non-fast pred (???) - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
  
  4. nzprob computed for non-fast pred (???) - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
  
  ══ Failed ══════════════════════════════════════════════════════════════════════
  ── 1. Failure ('test-basics.R:120:5'): Alternative family specifications [via up
  `gm0` not equal to `res_chr`.
  Component "modelInfo": Component "family": Length mismatch: comparison on first 12 components
  
  ── 2. Failure ('test-basics.R:121:5'): Alternative family specifications [via up
  `gm0` not equal to matchForm(gm0, update(gm0, family = binomial()), fn = TRUE).
  Component "modelInfo": Component "family": Length mismatch: comparison on first 12 components
  
  ── 3. Failure ('test-basics.R:132:3'): Update Binomial ─────────────────────────
  `gm1` not equal to matchForm(gm1, gm1u, fn = TRUE).
  Component "modelInfo": Component "family": Length mismatch: comparison on first 12 components
  
  ══ DONE ════════════════════════════════════════════════════════════════════════
  Error: Test failures
  Execution halted