Running ‘testthat.R’ [107s/108s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(trialr)
  Loading required package: Rcpp
  > 
  > test_check("trialr")
  
  SAMPLING FOR MODEL 'CrmEmpiricNormalPrior' NOW (CHAIN 1).
  Chain 1: 
  Chain 1: Gradient evaluation took 0 seconds
  Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0 seconds.
  Chain 1: Adjust your expectations accordingly!
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  Chain 1: 
  Chain 1:  Elapsed Time: 0.019858 seconds (Warm-up)
  Chain 1:                0.017882 seconds (Sampling)
  Chain 1:                0.03774 seconds (Total)
  Chain 1: 
  
  SAMPLING FOR MODEL 'CrmEmpiricNormalPrior' NOW (CHAIN 2).
  Chain 2: 
  Chain 2: Gradient evaluation took 0 seconds
  Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0 seconds.
  Chain 2: Adjust your expectations accordingly!
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  Chain 2: 
  Chain 2:  Elapsed Time: 0.017854 seconds (Warm-up)
  Chain 2:                0.016875 seconds (Sampling)
  Chain 2:                0.034729 seconds (Total)
  Chain 2: 
  
  SAMPLING FOR MODEL 'CrmEmpiricNormalPrior' NOW (CHAIN 3).
  Chain 3: 
  Chain 3: Gradient evaluation took 0 seconds
  Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0 seconds.
  Chain 3: Adjust your expectations accordingly!
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  Chain 3:  Elapsed Time: 0.014888 seconds (Warm-up)
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  Chain 3:                0.030789 seconds (Total)
  Chain 3: 
  
  SAMPLING FOR MODEL 'CrmEmpiricNormalPrior' NOW (CHAIN 4).
  Chain 4: 
  Chain 4: Gradient evaluation took 0 seconds
  Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0 seconds.
  Chain 4: Adjust your expectations accordingly!
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  Chain 4:  Elapsed Time: 0.015903 seconds (Warm-up)
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  Chain 4:                0.03181 seconds (Total)
  Chain 4: 
  
  SAMPLING FOR MODEL 'CrmEmpiricNormalPrior' NOW (CHAIN 1).
  Chain 1: 
  Chain 1: Gradient evaluation took 0 seconds
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  Chain 1: Adjust your expectations accordingly!
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  Chain 1: 
  Chain 1:  Elapsed Time: 0.016885 seconds (Warm-up)
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  Chain 1:                0.034768 seconds (Total)
  Chain 1: 
  
  SAMPLING FOR MODEL 'CrmEmpiricNormalPrior' NOW (CHAIN 2).
  Chain 2: 
  Chain 2: Gradient evaluation took 0 seconds
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  Chain 2: Adjust your expectations accordingly!
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  Chain 2: 
  Chain 2:  Elapsed Time: 0.018827 seconds (Warm-up)
  Chain 2:                0.016866 seconds (Sampling)
  Chain 2:                0.035693 seconds (Total)
  Chain 2: 
  
  SAMPLING FOR MODEL 'CrmEmpiricNormalPrior' NOW (CHAIN 3).
  Chain 3: 
  Chain 3: Gradient evaluation took 0 seconds
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  Chain 3: Adjust your expectations accordingly!
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  Chain 3: 
  Chain 3:  Elapsed Time: 0.017845 seconds (Warm-up)
  Chain 3:                0.018887 seconds (Sampling)
  Chain 3:                0.036732 seconds (Total)
  Chain 3: 
  
  SAMPLING FOR MODEL 'CrmEmpiricNormalPrior' NOW (CHAIN 4).
  Chain 4: 
  Chain 4: Gradient evaluation took 0 seconds
  Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0 seconds.
  Chain 4: Adjust your expectations accordingly!
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  Chain 4:  Elapsed Time: 0.017881 seconds (Warm-up)
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  Chain 4:                0.034786 seconds (Total)
  Chain 4: 
  
  SAMPLING FOR MODEL 'CrmEmpiricNormalPrior' NOW (CHAIN 1).
  Chain 1: 
  Chain 1: Gradient evaluation took 0 seconds
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  Chain 1: Adjust your expectations accordingly!
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  Chain 1:                0.039713 seconds (Total)
  Chain 1: 
  
  SAMPLING FOR MODEL 'CrmEmpiricNormalPrior' NOW (CHAIN 2).
  Chain 2: 
  Chain 2: Gradient evaluation took 0 seconds
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  Chain 2: Adjust your expectations accordingly!
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  Chain 2:  Elapsed Time: 0.019837 seconds (Warm-up)
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  Chain 2:                0.038733 seconds (Total)
  Chain 2: 
  
  SAMPLING FOR MODEL 'CrmEmpiricNormalPrior' NOW (CHAIN 3).
  Chain 3: 
  Chain 3: Gradient evaluation took 0 seconds
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  Chain 3:                0.039706 seconds (Total)
  Chain 3: 
  
  SAMPLING FOR MODEL 'CrmEmpiricNormalPrior' NOW (CHAIN 4).
  Chain 4: 
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  SAMPLING FOR MODEL 'CrmEmpiricNormalPrior' NOW (CHAIN 1).
  Chain 1: 
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  Chain 1: 
  
  SAMPLING FOR MODEL 'CrmEmpiricNormalPrior' NOW (CHAIN 2).
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  SAMPLING FOR MODEL 'CrmEmpiricNormalPrior' NOW (CHAIN 3).
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  SAMPLING FOR MODEL 'CrmEmpiricNormalPrior' NOW (CHAIN 4).
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  SAMPLING FOR MODEL 'CrmEmpiricNormalPrior' NOW (CHAIN 1).
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  SAMPLING FOR MODEL 'CrmEmpiricNormalPrior' NOW (CHAIN 2).
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  Chain 2: 
  
  SAMPLING FOR MODEL 'CrmEmpiricNormalPrior' NOW (CHAIN 3).
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  Chain 3: 
  
  SAMPLING FOR MODEL 'CrmEmpiricNormalPrior' NOW (CHAIN 4).
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  Chain 2: 
  
  SAMPLING FOR MODEL 'CrmEmpiricNormalPrior' NOW (CHAIN 3).
  Chain 3: 
  Chain 3: Gradient evaluation took 0 seconds
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  Chain 3: 
  
  SAMPLING FOR MODEL 'CrmEmpiricNormalPrior' NOW (CHAIN 4).
  Chain 4: 
  Chain 4: Gradient evaluation took 0 seconds
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  Chain 4: Adjust your expectations accordingly!
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  Chain 4: 
  ── 1. Error: careful_escalation advocates start_dose when n = 0 (@test_stan_crm.
  Assigned data `draws[, c(".chain", ".iteration", ".draw")]` must be compatible with existing data.
  ✖ Existing data has 16000 rows.
  ✖ Element 1 of assigned data has 4000 rows.
  ℹ Only vectors of size 1 are recycled.
  Backtrace:
    1. trialr::careful_escalation(...)
    3. trialr:::prob_tox_exceeds.dose_finding_fit(...)
   10. tidybayes::gather_draws(., prob_tox[dose])
   12. base::lapply(...)
   13. tidybayes:::FUN(X[[i]], ...)
   16. tidybayes:::spread_draws_(...)
   17. tidybayes:::spread_draws_long_(...)
   19. tibble:::`[<-.tbl_df`(...)
   20. tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   21. tibble:::vectbl_recycle_rhs(...)
   22. base::tryCatch(...)
   23. base:::tryCatchList(expr, classes, parentenv, handlers)
   24. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   25. value[[3L]](cond)
  
  
  SAMPLING FOR MODEL 'CrmEmpiricNormalPrior' NOW (CHAIN 1).
  Chain 1: 
  Chain 1: Gradient evaluation took 0 seconds
  Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0 seconds.
  Chain 1: Adjust your expectations accordingly!
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  Chain 1: 
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  Chain 1:                0.04675 seconds (Total)
  Chain 1: 
  
  SAMPLING FOR MODEL 'CrmEmpiricNormalPrior' NOW (CHAIN 2).
  Chain 2: 
  Chain 2: Gradient evaluation took 0 seconds
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  Chain 2: Adjust your expectations accordingly!
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  Chain 2:                0.045751 seconds (Total)
  Chain 2: 
  
  SAMPLING FOR MODEL 'CrmEmpiricNormalPrior' NOW (CHAIN 3).
  Chain 3: 
  Chain 3: Gradient evaluation took 0 seconds
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  Chain 3: Adjust your expectations accordingly!
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  Chain 3: 
  
  SAMPLING FOR MODEL 'CrmEmpiricNormalPrior' NOW (CHAIN 4).
  Chain 4: 
  Chain 4: Gradient evaluation took 0 seconds
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  Chain 4: Adjust your expectations accordingly!
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  Chain 4:                0.046759 seconds (Total)
  Chain 4: 
  ── 2. Error: careful_escalation does not skip doses (@test_stan_crm.R#386)  ────
  Assigned data `draws[, c(".chain", ".iteration", ".draw")]` must be compatible with existing data.
  ✖ Existing data has 16000 rows.
  ✖ Element 1 of assigned data has 4000 rows.
  ℹ Only vectors of size 1 are recycled.
  Backtrace:
    1. trialr::careful_escalation(fit1, tox_threshold = 0.33, certainty_threshold = 0.8)
    3. trialr:::prob_tox_exceeds.dose_finding_fit(...)
   10. tidybayes::gather_draws(., prob_tox[dose])
   12. base::lapply(...)
   13. tidybayes:::FUN(X[[i]], ...)
   16. tidybayes:::spread_draws_(...)
   17. tidybayes:::spread_draws_long_(...)
   19. tibble:::`[<-.tbl_df`(...)
   20. tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   21. tibble:::vectbl_recycle_rhs(...)
   22. base::tryCatch(...)
   23. base:::tryCatchList(expr, classes, parentenv, handlers)
   24. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   25. value[[3L]](cond)
  
  
  SAMPLING FOR MODEL 'CrmEmpiricNormalPrior' NOW (CHAIN 1).
  Chain 1: 
  Chain 1: Gradient evaluation took 0 seconds
  Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0 seconds.
  Chain 1: Adjust your expectations accordingly!
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  Chain 1: 
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  Chain 1:                0.030847 seconds (Sampling)
  Chain 1:                0.060635 seconds (Total)
  Chain 1: 
  
  SAMPLING FOR MODEL 'CrmEmpiricNormalPrior' NOW (CHAIN 2).
  Chain 2: 
  Chain 2: Gradient evaluation took 0 seconds
  Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0 seconds.
  Chain 2: Adjust your expectations accordingly!
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  Chain 2: 
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  Chain 2:                0.060663 seconds (Total)
  Chain 2: 
  
  SAMPLING FOR MODEL 'CrmEmpiricNormalPrior' NOW (CHAIN 3).
  Chain 3: 
  Chain 3: Gradient evaluation took 0 seconds
  Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0 seconds.
  Chain 3: Adjust your expectations accordingly!
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  Chain 3:                0.061629 seconds (Total)
  Chain 3: 
  
  SAMPLING FOR MODEL 'CrmEmpiricNormalPrior' NOW (CHAIN 4).
  Chain 4: 
  Chain 4: Gradient evaluation took 0.000992 seconds
  Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 9.92 seconds.
  Chain 4: Adjust your expectations accordingly!
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  Chain 4:                0.056655 seconds (Total)
  Chain 4: 
  ── 3. Error: careful_escalation stops appropriately (@test_stan_crm.R#405)  ────
  Assigned data `draws[, c(".chain", ".iteration", ".draw")]` must be compatible with existing data.
  ✖ Existing data has 16000 rows.
  ✖ Element 1 of assigned data has 4000 rows.
  ℹ Only vectors of size 1 are recycled.
  Backtrace:
    1. trialr::careful_escalation(...)
    3. trialr:::prob_tox_exceeds.dose_finding_fit(...)
   10. tidybayes::gather_draws(., prob_tox[dose])
   12. base::lapply(...)
   13. tidybayes:::FUN(X[[i]], ...)
   16. tidybayes:::spread_draws_(...)
   17. tidybayes:::spread_draws_long_(...)
   19. tibble:::`[<-.tbl_df`(...)
   20. tibble:::tbl_subassign(x, i, j, value, i_arg, j_arg, substitute(value))
   21. tibble:::vectbl_recycle_rhs(...)
   22. base::tryCatch(...)
   23. base:::tryCatchList(expr, classes, parentenv, handlers)
   24. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   25. value[[3L]](cond)
  
  
  SAMPLING FOR MODEL 'EffTox' NOW (CHAIN 1).
  Chain 1: 
  Chain 1: Gradient evaluation took 0 seconds
  Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0 seconds.
  Chain 1: Adjust your expectations accordingly!
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  Chain 1: 
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  Chain 1:                0.05466 seconds (Sampling)
  Chain 1:                0.15612 seconds (Total)
  Chain 1: 
  
  SAMPLING FOR MODEL 'EffTox' NOW (CHAIN 2).
  Chain 2: 
  Chain 2: Gradient evaluation took 0 seconds
  Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0 seconds.
  Chain 2: Adjust your expectations accordingly!
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  Chain 2:                0.156104 seconds (Total)
  Chain 2: 
  
  SAMPLING FOR MODEL 'EffTox' NOW (CHAIN 1).
  Chain 1: 
  Chain 1: Gradient evaluation took 0 seconds
  Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0 seconds.
  Chain 1: Adjust your expectations accordingly!
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  Chain 1:                0.291289 seconds (Total)
  Chain 1: 
  
  SAMPLING FOR MODEL 'EffTox' NOW (CHAIN 2).
  Chain 2: 
  Chain 2: Gradient evaluation took 0 seconds
  Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0 seconds.
  Chain 2: Adjust your expectations accordingly!
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  Chain 2:                0.320158 seconds (Total)
  Chain 2: 
  
  SAMPLING FOR MODEL 'EffTox' NOW (CHAIN 3).
  Chain 3: 
  Chain 3: Gradient evaluation took 0 seconds
  Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0 seconds.
  Chain 3: Adjust your expectations accordingly!
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  Chain 3:                0.202725 seconds (Total)
  Chain 3: 
  
  SAMPLING FOR MODEL 'EffTox' NOW (CHAIN 4).
  Chain 4: 
  Chain 4: Gradient evaluation took 0 seconds
  Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0 seconds.
  Chain 4: Adjust your expectations accordingly!
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  Chain 4: Iteration: 1200 / 2000 [ 60%]  (Sampling)
  Chain 4: Iteration: 1400 / 2000 [ 70%]  (Sampling)
  Chain 4: Iteration: 1600 / 2000 [ 80%]  (Sampling)
  Chain 4: Iteration: 1800 / 2000 [ 90%]  (Sampling)
  Chain 4: Iteration: 2000 / 2000 [100%]  (Sampling)
  Chain 4: 
  Chain 4:  Elapsed Time: 0.235405 seconds (Warm-up)
  Chain 4:                0.194698 seconds (Sampling)
  Chain 4:                0.430103 seconds (Total)
  Chain 4: 
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 732 | SKIPPED: 0 | WARNINGS: 37 | FAILED: 3 ]
  1. Error: careful_escalation advocates start_dose when n = 0 (@test_stan_crm.R#361) 
  2. Error: careful_escalation does not skip doses (@test_stan_crm.R#386) 
  3. Error: careful_escalation stops appropriately (@test_stan_crm.R#405) 
  
  Error: testthat unit tests failed
  Execution halted