Running ‘AAAtest-all.R’ [133s/236s]
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) (2022-02-14 r81736)
  Platform: x86_64-pc-linux-gnu (64-bit)
  Running under: Debian GNU/Linux bookworm/sid
  
  Matrix products: default
  BLAS:   /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libRblas.so
  LAPACK: /home/hornik/tmp/R.check/r-devel-gcc/Work/build/lib/libRlapack.so
  
  locale:
   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=C              
   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
   [9] LC_ADDRESS=C               LC_TELEPHONE=C            
  [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
  
  attached base packages:
  [1] stats     graphics  grDevices utils     datasets  methods   base     
  
  other attached packages:
  [1] glmmTMB_1.1.2.3 testthat_3.1.2 
  
  loaded via a namespace (and not attached):
   [1] Rcpp_1.0.8          TMB_1.7.22          magrittr_2.0.2     
   [4] splines_4.2.0       MASS_7.3-55         xtable_1.8-4       
   [7] lattice_0.20-45     R6_2.5.1            rlang_1.0.1        
  [10] multcomp_1.4-18     minqa_1.2.4         grid_4.2.0         
  [13] nlme_3.1-155        TH.data_1.1-0       cli_3.2.0          
  [16] coda_0.19-4         emmeans_1.7.2       survival_3.2-13    
  [19] lme4_1.1-28         numDeriv_2016.8-1.1 brio_1.1.3         
  [22] Matrix_1.4-0        nloptr_2.0.0        codetools_0.2-18   
  [25] sandwich_3.0-1      estimability_1.3    compiler_4.2.0     
  [28] boot_1.3-28         mvtnorm_1.1-3       zoo_1.8-9          
  Anova: ..............
  VarCorr: WWWWWWWWWWWWWW1
  altopt: 
  alternative optimizers: S
  basics: W.........2...SS.....S......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: .............34..56789...Wa.S..............b...................
  simulate consistency with glm/lm: ...
  Ranef etc.: .......S...........
  offset: 
  offsets: SSSSSSSS
  predict: c....SSS
  Predict two-column response case: SSWW.................S..SSSS..Sde.S..
  reml: 
  REML: f
  rr: ........g
  saveload: 
  Saving and loading glmmTMB objects: .
  sparseX: 
  sparse X models: Whi.jk..
  start: ..
  utils: .............
  varstruc: 
  variance structures: ........SSS
  weight: 
  weight: WWWWWWWWWWlmWWWWWWWWWWWWWWWWWWWWn
  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:67:3) - Reason: On CRAN
  
  3. Variance structures (test-basics.R:76:3) - Reason: On CRAN
  
  4. Multiple RE, reordering (test-basics.R:106:6) - Reason: On CRAN
  
  5. close to lme4 results (test-basics.R:141:5) - Reason: On CRAN
  
  6. basic zero inflation (test-basics.R:194:8) - Reason: On CRAN
  
  7. alternative binomial model specifications (test-basics.R:212:5) - Reason: On CRAN
  
  8. NA handling (test-basics.R:233:5) - Reason: On CRAN
  
  9. quine NB fit (test-basics.R:251:5) - Reason: On CRAN
  
  10. contrasts arg (test-basics.R:262:5) - Reason: On CRAN
  
  11. zero disp setting (test-basics.R:273:5) - 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:90:3) - Reason: On CRAN
  
  17. nbinom (test-families.R:112:5) - Reason: On CRAN
  
  18. dbetabinom (test-families.R:167:5) - Reason: On CRAN
  
  19. truncated (test-families.R:240:5) - Reason: On CRAN
  
  20. truncated_genpois (test-families.R:317:3) - Reason: On CRAN
  
  21. truncated_compois (test-families.R:334:5) - Reason: On CRAN
  
  22. compois (test-families.R:345:5) - Reason: On CRAN
  
  23. genpois (test-families.R:356:5) - Reason: On CRAN
  
  24. tweedie (test-families.R:365:5) - Reason: On CRAN
  
  25. anova ML/REML checks (test-methods.R:115:5) - Reason: On CRAN
  
  26. various binomial response types work (test-methods.R:398:3) - Reason: On CRAN
  
  27. LM with offset as argument (test-offset.R:29:3) - Reason: On CRAN
  
  28. LM with offset in formula (test-offset.R:37:5) - Reason: On CRAN
  
  29. LM with offset in formula - variable not in environment (test-offset.R:50:5) - Reason: On CRAN
  
  30. LM with offset in dispersion formula (test-offset.R:59:5) - Reason: On CRAN
  
  31. LM with multiple offsets (cond/dispersion) (test-offset.R:67:5) - Reason: On CRAN
  
  32. LM with random crap in the formula (test-offset.R:76:5) - Reason: On CRAN
  
  33. offset in do.call (test-offset.R:83:5) - Reason: On CRAN
  
  34. LONG offset in do.call (test-offset.R:92:5) - Reason: On CRAN
  
  35. new levels of fixed effect factor (test-predict.R:40:5) - Reason: On CRAN
  
  36. new levels in RE term (test-predict.R:47:5) - Reason: On CRAN
  
  37. new levels in AR1 (OK) (test-predict.R:54:5) - Reason: On CRAN
  
  38. two-column response (test-predict.R:64:5) - Reason: On CRAN
  
  39. Prediction with dispformula=~0 (test-predict.R:72:5) - Reason: On CRAN
  
  40. scale (test-predict.R:186:5) - Reason: On CRAN
  
  41. scale_RE (test-predict.R:208:5) - Reason: On CRAN
  
  42. complex bases in dispformula (test-predict.R:215:5) - Reason: On CRAN
  
  43. fix_predvars works for I(x^2) (test-predict.R:227:5) - Reason: On CRAN
  
  44. contrasts carried over (test-predict.R:247:5) - Reason: On CRAN
  
  45. offset-only model (GH #625) (test-predict.R:286:5) - Reason: On CRAN
  
  46. inverse-link prediction (test-predict.R:305:3) - Reason: On CRAN
  
  47. ar1 requires factor time (test-varstruc.R:52:3) - Reason: On CRAN
  
  48. varcorr_print (test-varstruc.R:72:5) - Reason: On CRAN
  
  49. cov_struct_order (test-varstruc.R:98:5) - Reason: On CRAN
  
  50. zi (test-zi.R:12:3) - Reason: On CRAN
  
  51. zi beta and Gamma (test-zi.R:37:5) - Reason: On CRAN
  
  ══ Warnings ════════════════════════════════════════════════════════════════════
  1. (code run outside of `test_that()`) (test-VarCorr.R:8:1) - NA/NaN function evaluation
  
  2. (code run outside of `test_that()`) (test-VarCorr.R:8:1) - NA/NaN function evaluation
  
  3. (code run outside of `test_that()`) (test-VarCorr.R:8:1) - NA/NaN function evaluation
  
  4. (code run outside of `test_that()`) (test-VarCorr.R:8:1) - NA/NaN function evaluation
  
  5. (code run outside of `test_that()`) (test-VarCorr.R:8:1) - NA/NaN function evaluation
  
  6. (code run outside of `test_that()`) (test-VarCorr.R:8:1) - NA/NaN function evaluation
  
  7. (code run outside of `test_that()`) (test-VarCorr.R:8:1) - NA/NaN function evaluation
  
  8. (code run outside of `test_that()`) (test-VarCorr.R:8:1) - NA/NaN function evaluation
  
  9. (code run outside of `test_that()`) (test-VarCorr.R:8:1) - NA/NaN function evaluation
  
  10. (code run outside of `test_that()`) (test-VarCorr.R:8:1) - NA/NaN function evaluation
  
  11. (code run outside of `test_that()`) (test-VarCorr.R:8:1) - NA/NaN function evaluation
  
  12. (code run outside of `test_that()`) (test-VarCorr.R:8:1) - NA/NaN function evaluation
  
  13. (code run outside of `test_that()`) (test-VarCorr.R:8:1) - NA/NaN function evaluation
  
  14. (code run outside of `test_that()`) (test-VarCorr.R:8:1) - NA/NaN function evaluation
  
  15. (code run outside of `test_that()`) (test-basics.R:39:1) - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
  
  16. drop1 (test-methods.R:104:7) - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
  
  17. (code run outside of `test_that()`) (???) - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
  
  18. (code run outside of `test_that()`) (???) - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
  
  19. basic fits (???) - Model convergence problem; non-positive-definite Hessian matrix. See vignette('troubleshooting')
  
  20. Weights can be an argument (test-weight.R:35:5) - NA/NaN function evaluation
  
  21. Weights can be an argument (test-weight.R:35:5) - NA/NaN function evaluation
  
  22. Weights can be an argument (test-weight.R:35:5) - NA/NaN function evaluation
  
  23. Weights can be an argument (test-weight.R:35:5) - NA/NaN function evaluation
  
  24. Weights can be an argument (test-weight.R:35:5) - NA/NaN function evaluation
  
  25. Weights can be an argument (test-weight.R:35:5) - NA/NaN function evaluation
  
  26. Weights can be an argument (test-weight.R:35:5) - NA/NaN function evaluation
  
  27. Weights can be an argument (test-weight.R:35:5) - NA/NaN function evaluation
  
  28. Weights can be an argument (test-weight.R:35:5) - NA/NaN function evaluation
  
  29. Weights can be an argument (test-weight.R:35:5) - NA/NaN function evaluation
  
  30. (code run outside of `test_that()`) (test-weight.R:55:1) - NA/NaN function evaluation
  
  31. (code run outside of `test_that()`) (test-weight.R:55:1) - NA/NaN function evaluation
  
  32. (code run outside of `test_that()`) (test-weight.R:55:1) - NA/NaN function evaluation
  
  33. (code run outside of `test_that()`) (test-weight.R:55:1) - NA/NaN function evaluation
  
  34. (code run outside of `test_that()`) (test-weight.R:55:1) - NA/NaN function evaluation
  
  35. (code run outside of `test_that()`) (test-weight.R:55:1) - NA/NaN function evaluation
  
  36. (code run outside of `test_that()`) (test-weight.R:55:1) - NA/NaN function evaluation
  
  37. (code run outside of `test_that()`) (test-weight.R:55:1) - NA/NaN function evaluation
  
  38. (code run outside of `test_that()`) (test-weight.R:55:1) - NA/NaN function evaluation
  
  39. (code run outside of `test_that()`) (test-weight.R:55:1) - NA/NaN function evaluation
  
  40. (code run outside of `test_that()`) (test-weight.R:55:1) - NA/NaN function evaluation
  
  41. (code run outside of `test_that()`) (test-weight.R:55:1) - NA/NaN function evaluation
  
  42. (code run outside of `test_that()`) (test-weight.R:55:1) - NA/NaN function evaluation
  
  43. (code run outside of `test_that()`) (test-weight.R:55:1) - NA/NaN function evaluation
  
  44. (code run outside of `test_that()`) (test-weight.R:55:1) - NA/NaN function evaluation
  
  45. (code run outside of `test_that()`) (test-weight.R:55:1) - NA/NaN function evaluation
  
  46. (code run outside of `test_that()`) (test-weight.R:55:1) - NA/NaN function evaluation
  
  47. (code run outside of `test_that()`) (test-weight.R:55:1) - NA/NaN function evaluation
  
  48. (code run outside of `test_that()`) (test-weight.R:55:1) - NA/NaN function evaluation
  
  49. (code run outside of `test_that()`) (test-weight.R:55:1) - NA/NaN function evaluation
  
  ══ Failed ══════════════════════════════════════════════════════════════════════
  ── 1. Error (test-VarCorr.R:8:1): (code run outside of `test_that()`) ──────────
  Error in `optimHess(par.fixed, obj$fn, obj$gr)`: gradient in optim evaluated to length 1 not 6
  Backtrace:
   1. glmmTMB::glmmTMB(distance ~ age + (age | Subject), data = Orthodont)
        at test-VarCorr.R:8:0
   2. glmmTMB::fitTMB(TMBStruc)
   3. TMB::sdreport(obj, getJointPrecision = TMBStruc$REML)
   4. stats::optimHess(par.fixed, obj$fn, obj$gr)
  
  ── 2. Failure (test-basics.R:56:5): Basic Gaussian Sleepdata examples ──────────
  fixef(fm2)$cond not equal to fixef(fm1)$cond.
  2/2 mismatches (average diff: 151)
  [1]  8.72 - 251.4 == -243
  [2] 69.51 -  10.5 ==   59
  
  ── 3. Failure (test-methods.R:72:5): Predict ───────────────────────────────────
  predict(fm2) not equal to predict(fm2, newdata = sleepstudy).
  180/180 mismatches (average diff: 3.85)
  [1] 254 - 239 == 14.731
  [2] 274 - 261 == 12.345
  [3] 293 - 283 ==  9.960
  [4] 313 - 305 ==  7.574
  [5] 332 - 327 ==  5.189
  [6] 352 - 349 ==  2.803
  [7] 371 - 371 ==  0.418
  [8] 391 - 393 == -1.968
  [9] 411 - 415 == -4.353
  ...
  
  ── 4. Failure (test-methods.R:77:5): Predict ───────────────────────────────────
  pr2se$fit not equivalent to predict(fm2).
  180/180 mismatches (average diff: 3.85)
  [1] 239 - 254 == -14.731
  [2] 261 - 274 == -12.345
  [3] 283 - 293 ==  -9.960
  [4] 305 - 313 ==  -7.574
  [5] 327 - 332 ==  -5.189
  [6] 349 - 352 ==  -2.803
  [7] 371 - 371 ==  -0.418
  [8] 393 - 391 ==   1.968
  [9] 415 - 411 ==   4.353
  ...
  
  ── 5. Failure (test-methods.R:80:5): Predict ───────────────────────────────────
  unname(pr2se$fit[1]) not equal to 254.2208.
  1/1 mismatches
  [1] 239 - 254 == -14.7
  
  ── 6. Failure (test-methods.R:81:5): Predict ───────────────────────────────────
  unname(pr2se$se.fit[1]) not equal to 12.94514.
  1/1 mismatches
  [1] NaN - 12.9 == NaN
  
  ── 7. Failure (test-methods.R:82:5): Predict ───────────────────────────────────
  unname(pr2se$fit[100]) not equal to 457.9684.
  1/1 mismatches
  [1] 455 - 458 == -2.66
  
  ── 8. Failure (test-methods.R:83:5): Predict ───────────────────────────────────
  unname(pr2se$se.fit[100]) not equal to 14.13943.
  1/1 mismatches
  [1] NaN - 14.1 == NaN
  
  ── 9. Failure (test-methods.R:86:5): Predict ───────────────────────────────────
  predict(fm2) not equal to predict(fm2, newdata = sleepstudy[, c("Days", "Subject")]).
  180/180 mismatches (average diff: 3.85)
  [1] 254 - 239 == 14.731
  [2] 274 - 261 == 12.345
  [3] 293 - 283 ==  9.960
  [4] 313 - 305 ==  7.574
  [5] 332 - 327 ==  5.189
  [6] 352 - 349 ==  2.803
  [7] 371 - 371 ==  0.418
  [8] 391 - 393 == -1.968
  [9] 411 - 415 == -4.353
  ...
  
  ── 10. Failure (test-methods.R:105:7): drop1 ───────────────────────────────────
  dd$AIC not equal to c(1763.94, 1785.48).
  2/2 mismatches (average diff: 0.000656)
  [1] 1764 - 1764 == -0.000656
  [2]   NA - 1785 ==        NA
    ... and 13 more
  
  
  Maximum number of 10 failures reached, some test results may be missing.
  
  ══ DONE ════════════════════════════════════════════════════════════════════════
  Error: Test failures
  Execution halted