Running ‘testthat.R’ [69s/93s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(psycho)
  > 
  > test_check("psycho")
  Failed with error:  'there is no package called 'GPArotation''
  
  SAMPLING FOR MODEL 'bernoulli' NOW (CHAIN 1).
  Rejecting initial value:
    Log probability evaluates to log(0), i.e. negative infinity.
    Stan can't start sampling from this initial value.
  Rejecting initial value:
    Log probability evaluates to log(0), i.e. negative infinity.
    Stan can't start sampling from this initial value.
  
  Gradient evaluation took 6.2e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.62 seconds.
  Adjust your expectations accordingly!
  
  
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   Elapsed Time: 0.417752 seconds (Warm-up)
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                 0.693029 seconds (Total)
  
  
  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).
  
  Gradient evaluation took 8.9e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.89 seconds.
  Adjust your expectations accordingly!
  
  
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   Elapsed Time: 2.06511 seconds (Warm-up)
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                 3.71547 seconds (Total)
  
  
  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).
  
  Gradient evaluation took 3.9e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.39 seconds.
  Adjust your expectations accordingly!
  
  
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   Elapsed Time: 0.065235 seconds (Warm-up)
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).
  
  Gradient evaluation took 3.4e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.34 seconds.
  Adjust your expectations accordingly!
  
  
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   Elapsed Time: 0.058717 seconds (Warm-up)
                 0.059002 seconds (Sampling)
                 0.117719 seconds (Total)
  
  ------------------------------------------------------------
  EXPERIMENTAL ALGORITHM:
    This procedure has not been thoroughly tested and may be unstable
    or buggy. The interface is subject to change.
  ------------------------------------------------------------
  
  
  
  Gradient evaluation took 6.1e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.61 seconds.
  Adjust your expectations accordingly!
  
  
  Begin eta adaptation.
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  Success! Found best value [eta = 1] earlier than expected.
  
  Begin stochastic gradient ascent.
    iter       ELBO   delta_ELBO_mean   delta_ELBO_med   notes 
     100     -4e+02             1.000            1.000
     200     -2e+02             1.011            1.021
     300     -2e+02             0.682            1.000
     400     -2e+02             0.511            1.000
     500     -2e+02             0.409            0.024
     600     -2e+02             0.341            0.024
     700     -2e+02             0.293            0.002   MEDIAN ELBO CONVERGED
  
  Drawing a sample of size 1000 from the approximate posterior... 
  COMPLETED.
  ------------------------------------------------------------
  EXPERIMENTAL ALGORITHM:
    This procedure has not been thoroughly tested and may be unstable
    or buggy. The interface is subject to change.
  ------------------------------------------------------------
  
  
  
  Gradient evaluation took 5.1e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.51 seconds.
  Adjust your expectations accordingly!
  
  
  Begin eta adaptation.
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  Success! Found best value [eta = 1] earlier than expected.
  
  Begin stochastic gradient ascent.
    iter       ELBO   delta_ELBO_mean   delta_ELBO_med   notes 
     100     -9e+04             1.000            1.000
     200     -6e+02            79.074          157.147
     300     -5e+02            52.759            1.000
     400     -2e+02            39.982            1.651
     500     -2e+02            31.989            1.000
     600     -2e+02            26.660            1.000
     700     -2e+02            22.854            0.130
     800     -2e+02            19.999            0.130
     900     -2e+02            17.778            0.018
    1000     -2e+02            16.000            0.018
    1100     -2e+02            15.902            0.016   MAY BE DIVERGING... INSPECT ELBO
    1200     -2e+02             0.188            0.014
    1300     -2e+02             0.176            0.014
    1400     -2e+02             0.011            0.014
    1500     -2e+02             0.010            0.013   MEAN ELBO CONVERGED
  
  Drawing a sample of size 1000 from the approximate posterior... 
  COMPLETED.
  Initial log joint probability = -100816
  Optimization terminated normally: 
    Convergence detected: relative gradient magnitude is below tolerance
  The Crawford-Howell (1998) t-test suggests no dissociation between test X and test Y (t(5) = 2.10, p = 0.09<b0>). The patient's score on test X is not significantly altered compared to its score on test Y.
  
  Error in x$.self$finalize() : attempt to apply non-function
  Error in x$.self$finalize() : attempt to apply non-function
  Error in (function (x)  : attempt to apply non-function
  Error in (function (x)  : attempt to apply non-function
  
  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).
  
  Gradient evaluation took 0.000155 seconds
  1000 transitions using 10 leapfrog steps per transition would take 1.55 seconds.
  Adjust your expectations accordingly!
  
  
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   Elapsed Time: 0.723559 seconds (Warm-up)
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                 1.48633 seconds (Total)
  
  
  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 2).
  
  Gradient evaluation took 9.3e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.93 seconds.
  Adjust your expectations accordingly!
  
  
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   Elapsed Time: 0.705837 seconds (Warm-up)
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                 1.42247 seconds (Total)
  
  
  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 3).
  
  Gradient evaluation took 0.000128 seconds
  1000 transitions using 10 leapfrog steps per transition would take 1.28 seconds.
  Adjust your expectations accordingly!
  
  
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   Elapsed Time: 0.705536 seconds (Warm-up)
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                 1.46649 seconds (Total)
  
  
  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 4).
  
  Gradient evaluation took 0.00024 seconds
  1000 transitions using 10 leapfrog steps per transition would take 2.4 seconds.
  Adjust your expectations accordingly!
  
  
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   Elapsed Time: 0.748527 seconds (Warm-up)
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  ── 1. Error: If it works. (@test-get_contrasts.stanreg.R#10)  ──────────────────
  number of items to replace is not a multiple of replacement length
  1: psycho::get_contrasts(fit, "Salary") at testthat/test-get_contrasts.stanreg.R:10
  2: get_contrasts.stanreg(fit, "Salary")
  3: fit %>% emmeans::emmeans(formula) %>% coda::as.mcmc() %>% as.matrix() %>% coda::as.mcmc() %>% 
         as.data.frame()
  4: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  5: eval(quote(`_fseq`(`_lhs`)), env, env)
  6: eval(quote(`_fseq`(`_lhs`)), env, env)
  7: `_fseq`(`_lhs`)
  8: freduce(value, `_function_list`)
  9: function_list[[i]](value)
  10: as.matrix(.)
  11: as.matrix.mcmc(.)
  
  
  SAMPLING FOR MODEL 'bernoulli' NOW (CHAIN 1).
  
  Gradient evaluation took 5.9e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.59 seconds.
  Adjust your expectations accordingly!
  
  
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   Elapsed Time: 0.144678 seconds (Warm-up)
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                 0.291464 seconds (Total)
  
  
  SAMPLING FOR MODEL 'bernoulli' NOW (CHAIN 2).
  
  Gradient evaluation took 3.5e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.35 seconds.
  Adjust your expectations accordingly!
  
  
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   Elapsed Time: 0.140728 seconds (Warm-up)
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                 0.306855 seconds (Total)
  
  
  SAMPLING FOR MODEL 'bernoulli' NOW (CHAIN 3).
  
  Gradient evaluation took 4e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.4 seconds.
  Adjust your expectations accordingly!
  
  
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   Elapsed Time: 0.133705 seconds (Warm-up)
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                 0.261923 seconds (Total)
  
  
  SAMPLING FOR MODEL 'bernoulli' NOW (CHAIN 4).
  
  Gradient evaluation took 3.8e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.38 seconds.
  Adjust your expectations accordingly!
  
  
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   Elapsed Time: 0.123198 seconds (Warm-up)
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                 0.234115 seconds (Total)
  
  
  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).
  
  Gradient evaluation took 5.7e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.57 seconds.
  Adjust your expectations accordingly!
  
  
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   Elapsed Time: 0.111536 seconds (Warm-up)
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                 0.222273 seconds (Total)
  
  
  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 2).
  
  Gradient evaluation took 5e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.5 seconds.
  Adjust your expectations accordingly!
  
  
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   Elapsed Time: 0.114152 seconds (Warm-up)
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                 0.215233 seconds (Total)
  
  
  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 3).
  
  Gradient evaluation took 3.2e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.32 seconds.
  Adjust your expectations accordingly!
  
  
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   Elapsed Time: 0.108818 seconds (Warm-up)
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 4).
  
  Gradient evaluation took 3.8e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.38 seconds.
  Adjust your expectations accordingly!
  
  
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   Elapsed Time: 0.128714 seconds (Warm-up)
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).
  
  Gradient evaluation took 7.2e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.72 seconds.
  Adjust your expectations accordingly!
  
  
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   Elapsed Time: 0.296902 seconds (Warm-up)
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 2).
  
  Gradient evaluation took 4.4e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.44 seconds.
  Adjust your expectations accordingly!
  
  
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   Elapsed Time: 0.302737 seconds (Warm-up)
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 3).
  
  Gradient evaluation took 4.2e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.42 seconds.
  Adjust your expectations accordingly!
  
  
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   Elapsed Time: 0.295916 seconds (Warm-up)
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 4).
  
  Gradient evaluation took 3.6e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.36 seconds.
  Adjust your expectations accordingly!
  
  
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).
  
  Gradient evaluation took 0.000323 seconds
  1000 transitions using 10 leapfrog steps per transition would take 3.23 seconds.
  Adjust your expectations accordingly!
  
  
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 2).
  
  Gradient evaluation took 0.000234 seconds
  1000 transitions using 10 leapfrog steps per transition would take 2.34 seconds.
  Adjust your expectations accordingly!
  
  
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 3).
  
  Gradient evaluation took 0.000149 seconds
  1000 transitions using 10 leapfrog steps per transition would take 1.49 seconds.
  Adjust your expectations accordingly!
  
  
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 4).
  
  Gradient evaluation took 0.000128 seconds
  1000 transitions using 10 leapfrog steps per transition would take 1.28 seconds.
  Adjust your expectations accordingly!
  
  
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   Elapsed Time: 0.825735 seconds (Warm-up)
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).
  
  Gradient evaluation took 6.8e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.68 seconds.
  Adjust your expectations accordingly!
  
  
  WARNING: There aren't enough warmup iterations to fit the
           three stages of adaptation as currently configured.
           Reducing each adaptation stage to 15%/75%/10% of
           the given number of warmup iterations:
             init_buffer = 7
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   Elapsed Time: 0.014529 seconds (Warm-up)
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 2).
  
  Gradient evaluation took 4.1e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.41 seconds.
  Adjust your expectations accordingly!
  
  
  WARNING: There aren't enough warmup iterations to fit the
           three stages of adaptation as currently configured.
           Reducing each adaptation stage to 15%/75%/10% of
           the given number of warmup iterations:
             init_buffer = 7
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             term_buffer = 5
  
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 3).
  
  Gradient evaluation took 4.3e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.43 seconds.
  Adjust your expectations accordingly!
  
  
  WARNING: There aren't enough warmup iterations to fit the
           three stages of adaptation as currently configured.
           Reducing each adaptation stage to 15%/75%/10% of
           the given number of warmup iterations:
             init_buffer = 7
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             term_buffer = 5
  
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 4).
  
  Gradient evaluation took 3.8e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.38 seconds.
  Adjust your expectations accordingly!
  
  
  WARNING: There aren't enough warmup iterations to fit the
           three stages of adaptation as currently configured.
           Reducing each adaptation stage to 15%/75%/10% of
           the given number of warmup iterations:
             init_buffer = 7
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             term_buffer = 5
  
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).
  
  Gradient evaluation took 7.8e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.78 seconds.
  Adjust your expectations accordingly!
  
  
  WARNING: There aren't enough warmup iterations to fit the
           three stages of adaptation as currently configured.
           Reducing each adaptation stage to 15%/75%/10% of
           the given number of warmup iterations:
             init_buffer = 7
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 2).
  
  Gradient evaluation took 5.3e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.53 seconds.
  Adjust your expectations accordingly!
  
  
  WARNING: There aren't enough warmup iterations to fit the
           three stages of adaptation as currently configured.
           Reducing each adaptation stage to 15%/75%/10% of
           the given number of warmup iterations:
             init_buffer = 7
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             term_buffer = 5
  
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 3).
  
  Gradient evaluation took 4.6e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.46 seconds.
  Adjust your expectations accordingly!
  
  
  WARNING: There aren't enough warmup iterations to fit the
           three stages of adaptation as currently configured.
           Reducing each adaptation stage to 15%/75%/10% of
           the given number of warmup iterations:
             init_buffer = 7
             adapt_window = 38
             term_buffer = 5
  
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 4).
  
  Gradient evaluation took 4.9e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.49 seconds.
  Adjust your expectations accordingly!
  
  
  WARNING: There aren't enough warmup iterations to fit the
           three stages of adaptation as currently configured.
           Reducing each adaptation stage to 15%/75%/10% of
           the given number of warmup iterations:
             init_buffer = 7
             adapt_window = 38
             term_buffer = 5
  
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   Elapsed Time: 0.347025 seconds (Warm-up)
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).
  
  Gradient evaluation took 5.9e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.59 seconds.
  Adjust your expectations accordingly!
  
  
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 2).
  
  Gradient evaluation took 4.3e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.43 seconds.
  Adjust your expectations accordingly!
  
  
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   Elapsed Time: 0.195899 seconds (Warm-up)
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 3).
  
  Gradient evaluation took 5.1e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.51 seconds.
  Adjust your expectations accordingly!
  
  
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   Elapsed Time: 0.214416 seconds (Warm-up)
                 0.22071 seconds (Sampling)
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 4).
  
  Gradient evaluation took 4.7e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.47 seconds.
  Adjust your expectations accordingly!
  
  
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   Elapsed Time: 0.211705 seconds (Warm-up)
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  .0%
  .33%
  .67%
  .100%
  1
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 136 SKIPPED: 0 FAILED: 1
  1. Error: If it works. (@test-get_contrasts.stanreg.R#10) 
  
  Error: testthat unit tests failed
  Execution halted