Running 'testthat.R' [249s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This file is part of the standard setup for testthat.
  > # It is recommended that you do not modify it.
  > #
  > # Where should you do additional test configuration?
  > # Learn more about the roles of various files in:
  > # * https://r-pkgs.org/tests.html
  > # * https://testthat.r-lib.org/reference/test_package.html#special-files
  > 
  > library(testthat)
  > library(cloneRate)
  > 
  > test_check("cloneRate")
  
  CHECKING DATA AND PREPROCESSING FOR MODEL 'bdSampler' NOW.
  
  COMPILING MODEL 'bdSampler' NOW.
  
  STARTING SAMPLER FOR MODEL 'bdSampler' NOW.
  
  SAMPLING FOR MODEL 'bdSampler' NOW (CHAIN 1).
  Chain 1: 
  Chain 1: Gradient evaluation took 0.000106 seconds
  Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.06 seconds.
  Chain 1: Adjust your expectations accordingly!
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  Chain 1: 
  Chain 1:  Elapsed Time: 1.377 seconds (Warm-up)
  Chain 1:                1.544 seconds (Sampling)
  Chain 1:                2.921 seconds (Total)
  Chain 1: 
  
  SAMPLING FOR MODEL 'bdSampler' NOW (CHAIN 2).
  Chain 2: 
  Chain 2: Gradient evaluation took 2.6e-05 seconds
  Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.26 seconds.
  Chain 2: Adjust your expectations accordingly!
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  Chain 2: 
  Chain 2:  Elapsed Time: 1.353 seconds (Warm-up)
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  Chain 2:                2.83 seconds (Total)
  Chain 2: 
  
  SAMPLING FOR MODEL 'bdSampler' NOW (CHAIN 3).
  Chain 3: 
  Chain 3: Gradient evaluation took 2.5e-05 seconds
  Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.25 seconds.
  Chain 3: Adjust your expectations accordingly!
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  Chain 3: 
  Chain 3:  Elapsed Time: 1.344 seconds (Warm-up)
  Chain 3:                1.473 seconds (Sampling)
  Chain 3:                2.817 seconds (Total)
  Chain 3: 
  
  SAMPLING FOR MODEL 'bdSampler' NOW (CHAIN 4).
  Chain 4: 
  Chain 4: Gradient evaluation took 2.7e-05 seconds
  Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.27 seconds.
  Chain 4: Adjust your expectations accordingly!
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  Chain 4: 
  Chain 4:  Elapsed Time: 1.258 seconds (Warm-up)
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  Chain 4:                2.511 seconds (Total)
  Chain 4: 
  
  CHECKING DATA AND PREPROCESSING FOR MODEL 'bdSampler' NOW.
  
  COMPILING MODEL 'bdSampler' NOW.
  
  STARTING SAMPLER FOR MODEL 'bdSampler' NOW.
  
  SAMPLING FOR MODEL 'bdSampler' NOW (CHAIN 1).
  Chain 1: 
  Chain 1: Gradient evaluation took 2.9e-05 seconds
  Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.29 seconds.
  Chain 1: Adjust your expectations accordingly!
  Chain 1: 
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  Chain 1: 
  Chain 1:  Elapsed Time: 0.351 seconds (Warm-up)
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  Chain 1:                0.597 seconds (Total)
  Chain 1: 
  
  SAMPLING FOR MODEL 'bdSampler' NOW (CHAIN 2).
  Chain 2: 
  Chain 2: Gradient evaluation took 2.6e-05 seconds
  Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.26 seconds.
  Chain 2: Adjust your expectations accordingly!
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  Chain 2: 
  Chain 2:  Elapsed Time: 0.299 seconds (Warm-up)
  Chain 2:                0.22 seconds (Sampling)
  Chain 2:                0.519 seconds (Total)
  Chain 2: 
  
  SAMPLING FOR MODEL 'bdSampler' NOW (CHAIN 3).
  Chain 3: 
  Chain 3: Gradient evaluation took 2e-05 seconds
  Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.2 seconds.
  Chain 3: Adjust your expectations accordingly!
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  Chain 3: 
  Chain 3:  Elapsed Time: 0.342 seconds (Warm-up)
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  Chain 3:                0.607 seconds (Total)
  Chain 3: 
  
  SAMPLING FOR MODEL 'bdSampler' NOW (CHAIN 4).
  Chain 4: 
  Chain 4: Gradient evaluation took 2.6e-05 seconds
  Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.26 seconds.
  Chain 4: Adjust your expectations accordingly!
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  Chain 4: 
  Chain 4:  Elapsed Time: 0.423 seconds (Warm-up)
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  Chain 4:                0.64 seconds (Total)
  Chain 4: 
  
  CHECKING DATA AND PREPROCESSING FOR MODEL 'bdSampler' NOW.
  
  COMPILING MODEL 'bdSampler' NOW.
  
  STARTING SAMPLER FOR MODEL 'bdSampler' NOW.
  
  SAMPLING FOR MODEL 'bdSampler' NOW (CHAIN 1).
  Chain 1: 
  Chain 1: Gradient evaluation took 2.4e-05 seconds
  Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.24 seconds.
  Chain 1: Adjust your expectations accordingly!
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  Chain 1:  Elapsed Time: 3.217 seconds (Warm-up)
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  Chain 1:                6.053 seconds (Total)
  Chain 1: 
  
  SAMPLING FOR MODEL 'bdSampler' NOW (CHAIN 2).
  Chain 2: 
  Chain 2: Gradient evaluation took 2.2e-05 seconds
  Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.22 seconds.
  Chain 2: Adjust your expectations accordingly!
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  Chain 2: 
  Chain 2:  Elapsed Time: 3.417 seconds (Warm-up)
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  Chain 2:                5.794 seconds (Total)
  Chain 2: 
  
  SAMPLING FOR MODEL 'bdSampler' NOW (CHAIN 3).
  Chain 3: 
  Chain 3: Gradient evaluation took 2.5e-05 seconds
  Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.25 seconds.
  Chain 3: Adjust your expectations accordingly!
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  Chain 3:  Elapsed Time: 3.527 seconds (Warm-up)
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  Chain 3:                4.971 seconds (Total)
  Chain 3: 
  
  SAMPLING FOR MODEL 'bdSampler' NOW (CHAIN 4).
  Chain 4: 
  Chain 4: Gradient evaluation took 2.3e-05 seconds
  Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.23 seconds.
  Chain 4: Adjust your expectations accordingly!
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  Chain 4:  Elapsed Time: 3.418 seconds (Warm-up)
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  Chain 4:                5.561 seconds (Total)
  Chain 4: 
  
  CHECKING DATA AND PREPROCESSING FOR MODEL 'bdSampler' NOW.
  
  COMPILING MODEL 'bdSampler' NOW.
  
  STARTING SAMPLER FOR MODEL 'bdSampler' NOW.
  
  SAMPLING FOR MODEL 'bdSampler' NOW (CHAIN 1).
  Chain 1: 
  Chain 1: Gradient evaluation took 2.5e-05 seconds
  Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.25 seconds.
  Chain 1: Adjust your expectations accordingly!
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  Chain 1:  Elapsed Time: 1.593 seconds (Warm-up)
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  Chain 1:                3.24 seconds (Total)
  Chain 1: 
  
  SAMPLING FOR MODEL 'bdSampler' NOW (CHAIN 2).
  Chain 2: 
  Chain 2: Gradient evaluation took 2.6e-05 seconds
  Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.26 seconds.
  Chain 2: Adjust your expectations accordingly!
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  Chain 2: 
  Chain 2:  Elapsed Time: 1.6 seconds (Warm-up)
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  Chain 2:                3.103 seconds (Total)
  Chain 2: 
  
  SAMPLING FOR MODEL 'bdSampler' NOW (CHAIN 3).
  Chain 3: 
  Chain 3: Gradient evaluation took 2.2e-05 seconds
  Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.22 seconds.
  Chain 3: Adjust your expectations accordingly!
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  Chain 3: 
  Chain 3:  Elapsed Time: 1.742 seconds (Warm-up)
  Chain 3:                2.112 seconds (Sampling)
  Chain 3:                3.854 seconds (Total)
  Chain 3: 
  
  SAMPLING FOR MODEL 'bdSampler' NOW (CHAIN 4).
  Chain 4: 
  Chain 4: Gradient evaluation took 2.4e-05 seconds
  Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.24 seconds.
  Chain 4: Adjust your expectations accordingly!
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  Chain 4:                3.573 seconds (Total)
  Chain 4: 
  
  CHECKING DATA AND PREPROCESSING FOR MODEL 'bdSampler' NOW.
  
  COMPILING MODEL 'bdSampler' NOW.
  
  STARTING SAMPLER FOR MODEL 'bdSampler' NOW.
  
  SAMPLING FOR MODEL 'bdSampler' NOW (CHAIN 1).
  Chain 1: 
  Chain 1: Gradient evaluation took 3.4e-05 seconds
  Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.34 seconds.
  Chain 1: Adjust your expectations accordingly!
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  Chain 1: 
  Chain 1:  Elapsed Time: 1.8 seconds (Warm-up)
  Chain 1:                1.856 seconds (Sampling)
  Chain 1:                3.656 seconds (Total)
  Chain 1: 
  
  SAMPLING FOR MODEL 'bdSampler' NOW (CHAIN 2).
  Chain 2: 
  Chain 2: Gradient evaluation took 2.6e-05 seconds
  Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.26 seconds.
  Chain 2: Adjust your expectations accordingly!
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  Chain 2: 
  Chain 2:  Elapsed Time: 1.76 seconds (Warm-up)
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  Chain 2:                3.487 seconds (Total)
  Chain 2: 
  
  SAMPLING FOR MODEL 'bdSampler' NOW (CHAIN 3).
  Chain 3: 
  Chain 3: Gradient evaluation took 2.1e-05 seconds
  Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.21 seconds.
  Chain 3: Adjust your expectations accordingly!
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  Chain 3: 
  Chain 3:  Elapsed Time: 2.026 seconds (Warm-up)
  Chain 3:                2.008 seconds (Sampling)
  Chain 3:                4.034 seconds (Total)
  Chain 3: 
  
  SAMPLING FOR MODEL 'bdSampler' NOW (CHAIN 4).
  Chain 4: 
  Chain 4: Gradient evaluation took 1.9e-05 seconds
  Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.19 seconds.
  Chain 4: Adjust your expectations accordingly!
  Chain 4: 
  Chain 4: 
  Chain 4: Iteration:    1 / 2000 [  0%]  (Warmup)
  Chain 4: Iteration:  200 / 2000 [ 10%]  (Warmup)
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  Chain 4: Iteration: 1001 / 2000 [ 50%]  (Sampling)
  Chain 4: Iteration: 1200 / 2000 [ 60%]  (Sampling)
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  Chain 4: Iteration: 1800 / 2000 [ 90%]  (Sampling)
  Chain 4: Iteration: 2000 / 2000 [100%]  (Sampling)
  Chain 4: 
  Chain 4:  Elapsed Time: 1.366 seconds (Warm-up)
  Chain 4:                2.033 seconds (Sampling)
  Chain 4:                3.399 seconds (Total)
  Chain 4: 
  You have set includeStem = TRUE. Note that we do not include the stem
              as part of the site frequency calculation in our work (Johnson et
              al. 2022), due to the fact that we don't know when clone initiation
              actually occurs.
  [ FAIL 0 | WARN 6 | SKIP 0 | PASS 82 ]
  
  [ FAIL 0 | WARN 6 | SKIP 0 | PASS 82 ]
  > 
  > proc.time()
     user  system elapsed 
    92.60    0.89   93.54