Running ‘testthat.R’ [77s/108s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(psycho)
  message: psycho's `analyze()` is deprecated in favour of the report package. Check it out at https://github.com/easystats/report
  > 
  > test_check("psycho")
  ── 1. Failure: analyze.stanreg (@test-deprecated.R#231)  ───────────────────────
  round(values$effects$Sepal.Width$median, 2) not equal to -0.46.
  1/1 mismatches
  [1] 0.98 - -0.46 == 1.44
  
  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).
  Chain 1: 
  Chain 1: Gradient evaluation took 0.000147 seconds
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  Chain 1: 
  
  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 2).
  Chain 2: 
  Chain 2: Gradient evaluation took 8.6e-05 seconds
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 4).
  Chain 4: 
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  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).
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 3).
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).
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  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 2).
  Chain 2: 
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  Chain 3: 
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  SAMPLING FOR MODEL 'bernoulli' NOW (CHAIN 1).
  Chain 1: 
  Chain 1: Gradient evaluation took 4e-05 seconds
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  SAMPLING FOR MODEL 'bernoulli' NOW (CHAIN 2).
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  SAMPLING FOR MODEL 'bernoulli' NOW (CHAIN 3).
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  SAMPLING FOR MODEL 'bernoulli' NOW (CHAIN 4).
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  Chain 3: 
  
  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 4).
  Chain 4: 
  Chain 4: Gradient evaluation took 1.7e-05 seconds
  Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.17 seconds.
  Chain 4: Adjust your expectations accordingly!
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  Chain 4: 
  
  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).
  Chain 1: 
  Chain 1: Gradient evaluation took 5e-05 seconds
  Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.5 seconds.
  Chain 1: Adjust your expectations accordingly!
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  Chain 1: 
  
  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 2).
  Chain 2: 
  Chain 2: Gradient evaluation took 2.4e-05 seconds
  Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.24 seconds.
  Chain 2: Adjust your expectations accordingly!
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  Chain 2: 
  
  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 3).
  Chain 3: 
  Chain 3: Gradient evaluation took 2.6e-05 seconds
  Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.26 seconds.
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  Chain 3: 
  
  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 4).
  Chain 4: 
  Chain 4: Gradient evaluation took 2.5e-05 seconds
  Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.25 seconds.
  Chain 4: Adjust your expectations accordingly!
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  Chain 4: 
  
  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).
  Chain 1: 
  Chain 1: Gradient evaluation took 0.000141 seconds
  Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 1.41 seconds.
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  Chain 1: 
  
  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 2).
  Chain 2: 
  Chain 2: Gradient evaluation took 9.4e-05 seconds
  Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.94 seconds.
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  Chain 2: 
  
  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 3).
  Chain 3: 
  Chain 3: Gradient evaluation took 9.2e-05 seconds
  Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.92 seconds.
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  Chain 3: 
  
  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 4).
  Chain 4: 
  Chain 4: Gradient evaluation took 9.4e-05 seconds
  Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.94 seconds.
  Chain 4: Adjust your expectations accordingly!
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  Chain 4: 
  
  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).
  Chain 1: 
  Chain 1: Gradient evaluation took 5.1e-05 seconds
  Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.51 seconds.
  Chain 1: Adjust your expectations accordingly!
  Chain 1: 
  Chain 1: 
  Chain 1: WARNING: There aren't enough warmup iterations to fit the
  Chain 1:          three stages of adaptation as currently configured.
  Chain 1:          Reducing each adaptation stage to 15%/75%/10% of
  Chain 1:          the given number of warmup iterations:
  Chain 1:            init_buffer = 7
  Chain 1:            adapt_window = 38
  Chain 1:            term_buffer = 5
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  Chain 1: 
  
  SAMPLING FOR MODEL 'continuous' 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!
  Chain 2: 
  Chain 2: 
  Chain 2: WARNING: There aren't enough warmup iterations to fit the
  Chain 2:          three stages of adaptation as currently configured.
  Chain 2:          Reducing each adaptation stage to 15%/75%/10% of
  Chain 2:          the given number of warmup iterations:
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  Chain 2: 
  
  SAMPLING FOR MODEL 'continuous' 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!
  Chain 3: 
  Chain 3: 
  Chain 3: WARNING: There aren't enough warmup iterations to fit the
  Chain 3:          three stages of adaptation as currently configured.
  Chain 3:          Reducing each adaptation stage to 15%/75%/10% of
  Chain 3:          the given number of warmup iterations:
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  Chain 3: 
  
  SAMPLING FOR MODEL 'continuous' 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!
  Chain 4: 
  Chain 4: 
  Chain 4: WARNING: There aren't enough warmup iterations to fit the
  Chain 4:          three stages of adaptation as currently configured.
  Chain 4:          Reducing each adaptation stage to 15%/75%/10% of
  Chain 4:          the given number of warmup iterations:
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  Chain 4: 
  
  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).
  Chain 1: 
  Chain 1: Gradient evaluation took 5.7e-05 seconds
  Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.57 seconds.
  Chain 1: Adjust your expectations accordingly!
  Chain 1: 
  Chain 1: 
  Chain 1: WARNING: There aren't enough warmup iterations to fit the
  Chain 1:          three stages of adaptation as currently configured.
  Chain 1:          Reducing each adaptation stage to 15%/75%/10% of
  Chain 1:          the given number of warmup iterations:
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  Chain 1: 
  
  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 2).
  Chain 2: 
  Chain 2: Gradient evaluation took 3.9e-05 seconds
  Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.39 seconds.
  Chain 2: Adjust your expectations accordingly!
  Chain 2: 
  Chain 2: 
  Chain 2: WARNING: There aren't enough warmup iterations to fit the
  Chain 2:          three stages of adaptation as currently configured.
  Chain 2:          Reducing each adaptation stage to 15%/75%/10% of
  Chain 2:          the given number of warmup iterations:
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  Chain 2:            term_buffer = 5
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  Chain 2: 
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  Chain 2: 
  
  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 3).
  Chain 3: 
  Chain 3: Gradient evaluation took 3.1e-05 seconds
  Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 0.31 seconds.
  Chain 3: Adjust your expectations accordingly!
  Chain 3: 
  Chain 3: 
  Chain 3: WARNING: There aren't enough warmup iterations to fit the
  Chain 3:          three stages of adaptation as currently configured.
  Chain 3:          Reducing each adaptation stage to 15%/75%/10% of
  Chain 3:          the given number of warmup iterations:
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  Chain 3: 
  
  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 4).
  Chain 4: 
  Chain 4: Gradient evaluation took 3.5e-05 seconds
  Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 0.35 seconds.
  Chain 4: Adjust your expectations accordingly!
  Chain 4: 
  Chain 4: 
  Chain 4: WARNING: There aren't enough warmup iterations to fit the
  Chain 4:          three stages of adaptation as currently configured.
  Chain 4:          Reducing each adaptation stage to 15%/75%/10% of
  Chain 4:          the given number of warmup iterations:
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  Chain 4:            term_buffer = 5
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  Chain 4: 
  
  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 1).
  Chain 1: 
  Chain 1: Gradient evaluation took 4.8e-05 seconds
  Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.48 seconds.
  Chain 1: Adjust your expectations accordingly!
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  Chain 1:  Elapsed Time: 0.134479 seconds (Warm-up)
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  Chain 1:                0.282816 seconds (Total)
  Chain 1: 
  
  SAMPLING FOR MODEL 'continuous' NOW (CHAIN 2).
  Chain 2: 
  Chain 2: Gradient evaluation took 2.5e-05 seconds
  Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.25 seconds.
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  Chain 2:                0.285519 seconds (Total)
  Chain 2: 
  
  SAMPLING FOR MODEL 'continuous' 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.
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  Chain 3: 
  
  SAMPLING FOR MODEL 'continuous' 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.
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  Chain 4: 
  .0.00%
  .33.00%
  .67.00%
  .100.00%
  1
  Chain 1: ------------------------------------------------------------
  Chain 1: EXPERIMENTAL ALGORITHM:
  Chain 1:   This procedure has not been thoroughly tested and may be unstable
  Chain 1:   or buggy. The interface is subject to change.
  Chain 1: ------------------------------------------------------------
  Chain 1: 
  Chain 1: 
  Chain 1: 
  Chain 1: Gradient evaluation took 5.1e-05 seconds
  Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.51 seconds.
  Chain 1: Adjust your expectations accordingly!
  Chain 1: 
  Chain 1: 
  Chain 1: Begin eta adaptation.
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  Chain 1: Iteration: 200 / 250 [ 80%]  (Adaptation)
  Chain 1: Success! Found best value [eta = 1] earlier than expected.
  Chain 1: 
  Chain 1: Begin stochastic gradient ascent.
  Chain 1:   iter             ELBO   delta_ELBO_mean   delta_ELBO_med   notes 
  Chain 1:    100         -403.800             1.000            1.000
  Chain 1:    200         -199.756             1.011            1.021
  Chain 1:    300         -195.131             0.682            1.000
  Chain 1:    400         -195.234             0.511            1.000
  Chain 1:    500         -194.906             0.409            0.024
  Chain 1:    600         -195.149             0.341            0.024
  Chain 1:    700         -195.587             0.293            0.002   MEDIAN ELBO CONVERGED
  Chain 1: 
  Chain 1: Drawing a sample of size 1000 from the approximate posterior... 
  Chain 1: COMPLETED.
  ── 2. Failure: standardize (@test-deprecated.R#1189)  ──────────────────────────
  mean(std) not equal to -0.24.
  1/1 mismatches
  [1] NA - -0.24 == NA
  
  ── 3. Failure: standardize (@test-deprecated.R#1192)  ──────────────────────────
  mean(std) not equal to 1.34.
  1/1 mismatches
  [1] 0.0759 - 1.34 == -1.26
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 155 SKIPPED: 0 WARNINGS: 1002 FAILED: 3
  1. Failure: analyze.stanreg (@test-deprecated.R#231) 
  2. Failure: standardize (@test-deprecated.R#1189) 
  3. Failure: standardize (@test-deprecated.R#1192) 
  
  Error: testthat unit tests failed
  Execution halted