Running ‘testthat.R’ [52s/78s]
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 4.6e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.46 seconds.
  Adjust your expectations accordingly!
  
  
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   Elapsed Time: 0.260651 seconds (Warm-up)
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                 0.428849 seconds (Total)
  
  
  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!
  
  
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   Elapsed Time: 1.41841 seconds (Warm-up)
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                 2.6029 seconds (Total)
  
  
  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: 0.034585 seconds (Warm-up)
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).
  
  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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   Elapsed Time: 0.033817 seconds (Warm-up)
                 0.033275 seconds (Sampling)
                 0.067092 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 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     -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 4.9e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.49 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.
  
  
  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).
  
  Gradient evaluation took 0.000157 seconds
  1000 transitions using 10 leapfrog steps per transition would take 1.57 seconds.
  Adjust your expectations accordingly!
  
  
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   Elapsed Time: 0.556364 seconds (Warm-up)
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                 1.13935 seconds (Total)
  
  
  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 2).
  
  Gradient evaluation took 7.3e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.73 seconds.
  Adjust your expectations accordingly!
  
  
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   Elapsed Time: 0.533814 seconds (Warm-up)
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 3).
  
  Gradient evaluation took 7e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.7 seconds.
  Adjust your expectations accordingly!
  
  
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   Elapsed Time: 0.559541 seconds (Warm-up)
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                 1.10899 seconds (Total)
  
  
  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 4).
  
  Gradient evaluation took 6.8e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.68 seconds.
  Adjust your expectations accordingly!
  
  
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   Elapsed Time: 0.520307 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 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: 0.093872 seconds (Warm-up)
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                 0.187178 seconds (Total)
  
  
  SAMPLING FOR MODEL 'bernoulli' NOW (CHAIN 2).
  
  Gradient evaluation took 2.2e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.22 seconds.
  Adjust your expectations accordingly!
  
  
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   Elapsed Time: 0.086294 seconds (Warm-up)
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                 0.19002 seconds (Total)
  
  
  SAMPLING FOR MODEL 'bernoulli' NOW (CHAIN 3).
  
  Gradient evaluation took 2.3e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.23 seconds.
  Adjust your expectations accordingly!
  
  
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   Elapsed Time: 0.08671 seconds (Warm-up)
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                 0.171079 seconds (Total)
  
  
  SAMPLING FOR MODEL 'bernoulli' NOW (CHAIN 4).
  
  Gradient evaluation took 2e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.2 seconds.
  Adjust your expectations accordingly!
  
  
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   Elapsed Time: 0.079221 seconds (Warm-up)
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).
  
  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: 0.075743 seconds (Warm-up)
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                 0.148492 seconds (Total)
  
  
  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 2).
  
  Gradient evaluation took 1.9e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.19 seconds.
  Adjust your expectations accordingly!
  
  
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   Elapsed Time: 0.07603 seconds (Warm-up)
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 3).
  
  Gradient evaluation took 2.5e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.25 seconds.
  Adjust your expectations accordingly!
  
  
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   Elapsed Time: 0.070035 seconds (Warm-up)
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 4).
  
  Gradient evaluation took 1.9e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.19 seconds.
  Adjust your expectations accordingly!
  
  
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   Elapsed Time: 0.085724 seconds (Warm-up)
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).
  
  Gradient evaluation took 5.5e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.55 seconds.
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   Elapsed Time: 0.209424 seconds (Warm-up)
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 2).
  
  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: 0.222861 seconds (Warm-up)
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                 0.434473 seconds (Total)
  
  
  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 3).
  
  Gradient evaluation took 3.1e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.31 seconds.
  Adjust your expectations accordingly!
  
  
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   Elapsed Time: 0.211654 seconds (Warm-up)
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 4).
  
  Gradient evaluation took 3.3e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.33 seconds.
  Adjust your expectations accordingly!
  
  
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 3).
  
  Gradient evaluation took 9.6e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.96 seconds.
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 4).
  
  Gradient evaluation took 9.6e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.96 seconds.
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).
  
  Gradient evaluation took 5e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.5 seconds.
  Adjust your expectations accordingly!
  
  
  WARNING: There aren't enough warmup iterations to fit the
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           Reducing each adaptation stage to 15%/75%/10% of
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 2).
  
  Gradient evaluation took 2.6e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.26 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:
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 3).
  
  Gradient evaluation took 2.5e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.25 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
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 4).
  
  Gradient evaluation took 2.7e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.27 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:
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).
  
  Gradient evaluation took 9.7e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.97 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
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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
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 3).
  
  Gradient evaluation took 3.6e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.36 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:
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             term_buffer = 5
  
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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!
  
  
  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 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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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 2).
  
  Gradient evaluation took 2.9e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.29 seconds.
  Adjust your expectations accordingly!
  
  
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 3).
  
  Gradient evaluation took 2.8e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.28 seconds.
  Adjust your expectations accordingly!
  
  
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 4).
  
  Gradient evaluation took 2.9e-05 seconds
  1000 transitions using 10 leapfrog steps per transition would take 0.29 seconds.
  Adjust your expectations accordingly!
  
  
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  .0%
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  .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