Running ‘AAAtest-all.R’ [138s/346s]
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) (2021-08-05 r80716)
  Platform: x86_64-pc-linux-gnu (64-bit)
  Running under: Fedora 32 (Workstation Edition)
  
  Matrix products: default
  BLAS:   /data/gannet/ripley/R/R-devel/lib/libRblas.so
  LAPACK: /data/gannet/ripley/R/R-devel/lib/libRlapack.so
  
  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       
  
  attached base packages:
  [1] stats     graphics  grDevices utils     datasets  methods   base     
  
  other attached packages:
  [1] glmmTMB_1.1.2  testthat_3.0.4
  
  loaded via a namespace (and not attached):
   [1] Rcpp_1.0.7          TMB_1.7.20          magrittr_2.0.1     
   [4] splines_4.2.0       MASS_7.3-54         xtable_1.8-4       
   [7] lattice_0.20-44     R6_2.5.0            rlang_0.4.11       
  [10] multcomp_1.4-17     minqa_1.2.4         grid_4.2.0         
  [13] nlme_3.1-152        TH.data_1.0-10      coda_0.19-4        
  [16] emmeans_1.6.2-1     survival_3.2-11     lme4_1.1-27.1      
  [19] numDeriv_2016.8-1.1 Matrix_1.3-4        nloptr_1.2.2.2     
  [22] codetools_0.2-18    sandwich_3.0-1      estimability_1.3   
  [25] compiler_4.2.0      boot_1.3-28         mvtnorm_1.1-2      
  [28] zoo_1.8-9          
  Anova: ..............
  VarCorr: .............
  altopt: 
  alternative optimizers: S
  basics: .............SS.....S....1.S
  trickier examples: SS.SSSS
  bootMer: 
  bootMer: SS
  control: SS
  disp: ...
  downstream: 
  emmeans: .............
  effects: ..
  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: 
  basic methods: ...........................S.S....................................
  simulate consistency with glm/lm: ...
  Ranef etc.: .......S........S.
  offset: 
  offsets: SSSSSSSS
  predict: .....SSS
  Predict two-column response case: SS.................S..SSSS..S...S..
  reml: 
  REML: ......
  rr: .........
  saveload: 
  Saving and loading glmmTMB objects: .
  sparseX: 
  sparse X models: .....S
  start: ..
  utils: .............
  varstruc: 
  variance structures: ........SSS
  weight: 
  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:57:3) - Reason: On CRAN
  
  3. Variance structures (test-basics.R:66:3) - Reason: On CRAN
  
  4. Multiple RE, reordering (test-basics.R:96:6) - Reason: On CRAN
  
  5. close to lme4 results (test-basics.R:131:5) - Reason: On CRAN
  
  6. basic zero inflation (test-basics.R:184:8) - Reason: On CRAN
  
  7. alternative binomial model specifications (test-basics.R:202:5) - Reason: On CRAN
  
  8. NA handling (test-basics.R:223:5) - Reason: On CRAN
  
  9. quine NB fit (test-basics.R:241:5) - Reason: On CRAN
  
  10. contrasts arg (test-basics.R:252:5) - Reason: On CRAN
  
  11. zero disp setting (test-basics.R:263:5) - Reason: On CRAN
  
  12. Bernoulli responses (test-bootMer.R:11:3) - Reason: On CRAN
  
  13. binomial responses (test-bootMer.R:21:5) - 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. beta (test-families.R:88:3) - Reason: On CRAN
  
  17. nbinom (test-families.R:110:5) - Reason: On CRAN
  
  18. dbetabinom (test-families.R:165:5) - Reason: On CRAN
  
  19. truncated (test-families.R:238:5) - Reason: On CRAN
  
  20. truncated_genpois (test-families.R:315:3) - Reason: On CRAN
  
  21. truncated_compois (test-families.R:332:5) - Reason: On CRAN
  
  22. compois (test-families.R:343:5) - Reason: On CRAN
  
  23. genpois (test-families.R:354:5) - Reason: On CRAN
  
  24. tweedie (test-families.R:363:5) - Reason: On CRAN
  
  25. anova ML/REML checks (test-methods.R:114:5) - Reason: On CRAN
  
  26. terms back-compatibility (test-methods.R:157:5) - Reason: skip until TMB fits are back-compatible
  
  27. various binomial response types work (test-methods.R:398:3) - Reason: On CRAN
  
  28. trunc nbinom sim 2 (test-methods.R:524:1) - Reason: empty test
  
  29. LM with offset as argument (test-offset.R:29:3) - Reason: On CRAN
  
  30. LM with offset in formula (test-offset.R:37:5) - Reason: On CRAN
  
  31. LM with offset in formula - variable not in environment (test-offset.R:50:5) - Reason: On CRAN
  
  32. LM with offset in dispersion formula (test-offset.R:59:5) - Reason: On CRAN
  
  33. LM with multiple offsets (cond/dispersion) (test-offset.R:67:5) - Reason: On CRAN
  
  34. LM with random crap in the formula (test-offset.R:76:5) - Reason: On CRAN
  
  35. offset in do.call (test-offset.R:83:5) - Reason: On CRAN
  
  36. LONG offset in do.call (test-offset.R:92:5) - Reason: On CRAN
  
  37. new levels of fixed effect factor (test-predict.R:40:5) - Reason: On CRAN
  
  38. new levels in RE term (test-predict.R:47:5) - Reason: On CRAN
  
  39. new levels in AR1 (OK) (test-predict.R:54:5) - Reason: On CRAN
  
  40. two-column response (test-predict.R:64:5) - Reason: On CRAN
  
  41. Prediction with dispformula=~0 (test-predict.R:72:5) - Reason: On CRAN
  
  42. scale (test-predict.R:186:5) - Reason: On CRAN
  
  43. scale_RE (test-predict.R:208:5) - Reason: On CRAN
  
  44. complex bases in dispformula (test-predict.R:215:5) - Reason: On CRAN
  
  45. fix_predvars works for I(x^2) (test-predict.R:227:5) - Reason: On CRAN
  
  46. contrasts carried over (test-predict.R:247:5) - Reason: On CRAN
  
  47. offset-only model (GH #625) (test-predict.R:286:5) - Reason: On CRAN
  
  48. inverse-link prediction (test-predict.R:305:3) - Reason: On CRAN
  
  49. back-compatibility (test-sparseX.R:20:5) - Reason: skip until TMB fits are back-compatible
  
  50. ar1 requires factor time (test-varstruc.R:52:3) - Reason: On CRAN
  
  51. varcorr_print (test-varstruc.R:72:5) - Reason: On CRAN
  
  52. cov_struct_order (test-varstruc.R:98:5) - Reason: On CRAN
  
  53. zi (test-zi.R:12:3) - Reason: On CRAN
  
  54. zi beta and Gamma (test-zi.R:37:5) - Reason: On CRAN
  
  ══ Failed ══════════════════════════════════════════════════════════════════════
  ── 1. Failure (test-basics.R:121:3): Update Binomial ───────────────────────────
  `gm1` not equal to matchForm(gm1, gm1u).
  Component "sdr": Component "gradient.fixed": Mean relative difference: 2.131994e-08
  
  ══ DONE ════════════════════════════════════════════════════════════════════════
  Error: Test failures
  Execution halted