Running ‘AAAtest-all.R’
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) (2019-11-28 r77466)
  Platform: x86_64-pc-linux-gnu (64-bit)
  Running under: Fedora 30 (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_0.2.3  testthat_2.3.0
  
  loaded via a namespace (and not attached):
   [1] Rcpp_1.0.3      lattice_0.20-38 MASS_7.3-51.4   grid_4.0.0     
   [5] R6_2.4.1        nlme_3.1-142    magrittr_1.5    rlang_0.4.2    
   [9] minqa_1.2.4     nloptr_1.2.1    Matrix_1.2-18   boot_1.3-23    
  [13] splines_4.0.0   lme4_1.1-21     TMB_1.7.15      compiler_4.0.0 
  VarCorr: 1
  Very basic glmmTMB fitting: 2
  glmmTMBControl: 3
  Testing dispersion: 4
  emmeans: 5
  test edge cases: 6
  basic examples: 78.
  alternative binomial specifications: 9
  fitting exotic families: abc..................
  trunc compois: ...
  compois: ...
  genpois: ..
  tweedie: .....
  link function info available: ............
  link info added to family: ...
  
  ══ Failed ══════════════════════════════════════════════════════════════════════
  ── 1. Error: (unknown) (@test-VarCorr.R#11)  ───────────────────────────────────
  object 'age' not found
  Backtrace:
    1. glmmTMB::glmmTMB(distance ~ age + (age | Subject), data = Orthodont) test-VarCorr.R:11:0
    2. glmmTMB:::mkTMBStruc(...)
    3. glmmTMB:::getXReTrms(formula, mf, fr, contrasts = contrasts)
    4. glmmTMB::splitForm(formula)
    5. glmmTMB:::fbx(formula, debug, specials)
    6. glmmTMB:::fbx(term[[3]], debug, specials)
    7. glmmTMB:::fbx(term[[3]], debug, specials)
    9. utils:::head.default(term)
   10. base::do.call(`[`, c(list(x), indvecs, if (!is.null(dim(x))) list(drop = FALSE)))
  
  ── 2. Error: (unknown) (@test-basics.R#29)  ────────────────────────────────────
  object 'Subject' not found
  Backtrace:
    1. glmmTMB::glmmTMB(Reaction ~ 1 + (1 | Subject), sleepstudy) test-basics.R:29:0
    2. glmmTMB:::mkTMBStruc(...)
    3. glmmTMB:::getXReTrms(formula, mf, fr, contrasts = contrasts)
    4. glmmTMB::splitForm(formula)
    5. glmmTMB:::fbx(formula, debug, specials)
    6. glmmTMB:::fbx(term[[3]], debug, specials)
    7. glmmTMB:::fbx(term[[3]], debug, specials)
    9. utils:::head.default(term)
   10. base::do.call(`[`, c(list(x), indvecs, if (!is.null(dim(x))) list(drop = FALSE)))
  
  ── 3. Error: profile method (@test-control.R#26)  ──────────────────────────────
  object 'site' not found
  Backtrace:
    1. glmmTMB:::myfit(profile = FALSE) test-control.R:26:4
    2. glmmTMB::glmmTMB(...) test-control.R:20:8
    3. glmmTMB:::mkTMBStruc(...)
    4. glmmTMB:::getXReTrms(formula, mf, fr, contrasts = contrasts)
    5. glmmTMB::splitForm(formula)
    6. glmmTMB:::fbx(formula, debug, specials)
    7. glmmTMB:::fbx(term[[3]], debug, specials)
    8. glmmTMB:::fbx(term[[3]], debug, specials)
   10. utils:::head.default(term)
   11. base::do.call(`[`, c(list(x), indvecs, if (!is.null(dim(x))) list(drop = FALSE)))
  
  ── 4. Error: (unknown) (@test-disp.R#32)  ──────────────────────────────────────
  object 'fac' not found
  Backtrace:
    1. glmmTMB::glmmTMB(x ~ disp + (1 | fac), dispformula = ~disp, dat) test-disp.R:32:0
    2. glmmTMB:::mkTMBStruc(...)
    3. glmmTMB:::getXReTrms(formula, mf, fr, contrasts = contrasts)
    4. glmmTMB::splitForm(formula)
    5. glmmTMB:::fbx(formula, debug, specials)
    6. glmmTMB:::fbx(term[[3]], debug, specials)
    7. glmmTMB:::fbx(term[[3]], debug, specials)
    9. utils:::head.default(term)
   10. base::do.call(`[`, c(list(x), indvecs, if (!is.null(dim(x))) list(drop = FALSE)))
  
  ── 5. Error: (unknown) (@test-downstream.R#8)  ─────────────────────────────────
  object 'Nest' not found
  Backtrace:
    1. glmmTMB::glmmTMB(...) test-downstream.R:8:4
    2. glmmTMB:::mkTMBStruc(...)
    3. glmmTMB:::getXReTrms(formula, mf, fr, contrasts = contrasts)
    4. glmmTMB::splitForm(formula)
    5. glmmTMB:::fbx(formula, debug, specials)
    6. glmmTMB:::fbx(term[[3]], debug, specials)
    7. glmmTMB:::fbx(term[[2]], debug, specials)
    8. glmmTMB:::fbx(term[[3]], debug, specials)
   10. utils:::head.default(term)
   11. base::do.call(`[`, c(list(x), indvecs, if (!is.null(dim(x))) list(drop = FALSE)))
  
  ── 6. Error: profiling failure (@test-edgecases.R#9)  ──────────────────────────
  object 'Year' not found
  Backtrace:
    1. testthat::expect_warning(...) test-edgecases.R:9:4
    6. glmmTMB::glmmTMB(...)
    7. glmmTMB:::mkTMBStruc(...)
    8. glmmTMB:::getXReTrms(formula, mf, fr, contrasts = contrasts)
    9. glmmTMB::splitForm(formula)
   10. glmmTMB:::fbx(formula, debug, specials)
   11. glmmTMB:::fbx(term[[3]], debug, specials)
   12. glmmTMB:::fbx(term[[2]], debug, specials)
   13. glmmTMB:::fbx(term[[2]], debug, specials)
   14. glmmTMB:::fbx(term[[3]], debug, specials)
   16. utils:::head.default(term)
   17. base::do.call(`[`, c(list(x), indvecs, if (!is.null(dim(x))) list(drop = FALSE)))
  
  ── 7. Error: basic example #1 (@test-env.R#18)  ────────────────────────────────
  object 'Subject' not found
  Backtrace:
    1. glmmTMB::glmmTMB(Reaction ~ Days + (1 | Subject), data = sleepstudy) test-env.R:18:4
    2. glmmTMB:::mkTMBStruc(...)
    3. glmmTMB:::getXReTrms(formula, mf, fr, contrasts = contrasts)
    4. glmmTMB::splitForm(formula)
    5. glmmTMB:::fbx(formula, debug, specials)
    6. glmmTMB:::fbx(term[[3]], debug, specials)
    7. glmmTMB:::fbx(term[[3]], debug, specials)
    9. utils:::head.default(term)
   10. base::do.call(`[`, c(list(x), indvecs, if (!is.null(dim(x))) list(drop = FALSE)))
  
  ── 8. Error: paranoia (@test-env.R#34)  ────────────────────────────────────────
  object 'Subject' not found
  Backtrace:
    1. glmmTMB::glmmTMB(Reaction ~ Days + (1 | Subject), data = sleepstudy) test-env.R:34:4
    2. glmmTMB:::mkTMBStruc(...)
    3. glmmTMB:::getXReTrms(formula, mf, fr, contrasts = contrasts)
    4. glmmTMB::splitForm(formula)
    5. glmmTMB:::fbx(formula, debug, specials)
    6. glmmTMB:::fbx(term[[3]], debug, specials)
    7. glmmTMB:::fbx(term[[3]], debug, specials)
    9. utils:::head.default(term)
   10. base::do.call(`[`, c(list(x), indvecs, if (!is.null(dim(x))) list(drop = FALSE)))
  
  ── 9. Error: binomial (@test-families.R#23)  ───────────────────────────────────
  object 'species' not found
  Backtrace:
    1. glmmTMB::glmmTMB(...) test-families.R:23:4
    2. glmmTMB:::mkTMBStruc(...)
    3. glmmTMB:::getXReTrms(formula, mf, fr, contrasts = contrasts)
    4. glmmTMB::splitForm(formula)
    5. glmmTMB:::fbx(formula, debug, specials)
    6. glmmTMB:::fbx(term[[3]], debug, specials)
    7. glmmTMB:::fbx(term[[3]], debug, specials)
    9. utils:::head.default(term)
   10. base::do.call(`[`, c(list(x), indvecs, if (!is.null(dim(x))) list(drop = FALSE)))
  
  ── 10. Error: beta (@test-families.R#73)  ──────────────────────────────────────
  object 'f' not found
  Backtrace:
    1. glmmTMB::glmmTMB(y ~ x + (1 | f), family = beta_family(), data = dd) test-families.R:73:4
    2. glmmTMB:::mkTMBStruc(...)
    3. glmmTMB:::getXReTrms(formula, mf, fr, contrasts = contrasts)
    4. glmmTMB::splitForm(formula)
    5. glmmTMB:::fbx(formula, debug, specials)
    6. glmmTMB:::fbx(term[[3]], debug, specials)
    7. glmmTMB:::fbx(term[[3]], debug, specials)
    9. utils:::head.default(term)
   10. base::do.call(`[`, c(list(x), indvecs, if (!is.null(dim(x))) list(drop = FALSE)))
    ... and 2 more
  
  
  Maximum number of 10 failures reached, some test results may be missing.
  
  ══ DONE ════════════════════════════════════════════════════════════════════════
  Frustration is a natural part of programming :)
  Error: Test failures
  Execution halted