Running ‘testthat.R’ [11s/15s]
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(clmstan)
  
  Attaching package: 'clmstan'
  
  The following object is masked from 'package:base':
  
      gamma
  
  > 
  > test_check("clmstan")
  MCMC Diagnostics: Issues detected
  ======================================== 
  
  HMC Diagnostics:
    Divergences: 0 (OK)
    Treedepth: OK
    E-BFMI: OK
  
  Convergence Diagnostics:
    Max Rhat: 1.014 (WARNING!)
    Min ESS bulk: 318 (WARNING!)
    Min ESS tail: 320 (WARNING!)
  
    Problematic parameters:
  # A tibble: 4 x 4
    variable          rhat ess_bulk ess_tail
    <chr>            <dbl>    <dbl>    <dbl>
  1 beta[2]          0.998      363      320
  2 c_transformed[1] 1.01       387      369
  3 c_transformed[3] 1.01       318      368
  4 beta0            0.997      386      364
  MCMC Diagnostics: Issues detected
  ======================================== 
  
  HMC Diagnostics:
    Divergences: 0 (OK)
    Treedepth: OK
    E-BFMI: OK
  
  Convergence Diagnostics:
    Max Rhat: 1.014 (WARNING!)
    Min ESS bulk: 318 (WARNING!)
    Min ESS tail: 320 (WARNING!)
  
    Problematic parameters:
  # A tibble: 4 x 4
    variable          rhat ess_bulk ess_tail
    <chr>            <dbl>    <dbl>    <dbl>
  1 beta[2]          0.998      363      320
  2 c_transformed[1] 1.01       387      369
  3 c_transformed[3] 1.01       318      368
  4 beta0            0.997      386      364
  MCMC Diagnostics: All OK
  ======================================== 
  
  HMC Diagnostics:
    Divergences: 0 (OK)
    Treedepth: OK
    E-BFMI: OK
  
  Convergence Diagnostics:
    All Rhat < 1.01 (max: 1.001)
    All ESS > 100 (min bulk: 1900, min tail: 1729)
  MCMC Diagnostics: Issues detected
  ======================================== 
  
  HMC Diagnostics:
    Divergences: 10 (WARNING!)
    Treedepth: OK
    E-BFMI: OK
  
  Convergence Diagnostics:
    Max Rhat: 1.014 (WARNING!)
    Min ESS bulk: 318 (WARNING!)
    Min ESS tail: 320 (WARNING!)
  
    Problematic parameters:
  # A tibble: 4 x 4
    variable          rhat ess_bulk ess_tail
    <chr>            <dbl>    <dbl>    <dbl>
  1 beta[2]          0.998      363      320
  2 c_transformed[1] 1.01       387      369
  3 c_transformed[3] 1.01       318      368
  4 beta0            0.997      386      364
  MCMC Diagnostics: Issues detected
  ======================================== 
  
  HMC Diagnostics:
    Divergences: 0 (OK)
    Max treedepth: 5 transitions hit limit
    E-BFMI: OK
  
  Convergence Diagnostics:
    Max Rhat: 1.014 (WARNING!)
    Min ESS bulk: 318 (WARNING!)
    Min ESS tail: 320 (WARNING!)
  
    Problematic parameters:
  # A tibble: 4 x 4
    variable          rhat ess_bulk ess_tail
    <chr>            <dbl>    <dbl>    <dbl>
  1 beta[2]          0.998      363      320
  2 c_transformed[1] 1.01       387      369
  3 c_transformed[3] 1.01       318      368
  4 beta0            0.997      386      364
  MCMC Diagnostics: Issues detected
  ======================================== 
  
  HMC Diagnostics:
    Divergences: 0 (OK)
    Treedepth: OK
    E-BFMI: Low in chain(s) 1, 2 (WARNING!)
  
  Convergence Diagnostics:
    Max Rhat: 1.014 (WARNING!)
    Min ESS bulk: 318 (WARNING!)
    Min ESS tail: 320 (WARNING!)
  
    Problematic parameters:
  # A tibble: 4 x 4
    variable          rhat ess_bulk ess_tail
    <chr>            <dbl>    <dbl>    <dbl>
  1 beta[2]          0.998      363      320
  2 c_transformed[1] 1.01       387      369
  3 c_transformed[3] 1.01       318      368
  4 beta0            0.997      386      364
  MCMC Diagnostics: Issues detected
  ======================================== 
  
  HMC Diagnostics:
    Divergences: 0 (OK)
    Treedepth: OK
    E-BFMI: OK
  
  Convergence Diagnostics:
    Max Rhat: 1.014 (WARNING!)
    Min ESS bulk: 318 (WARNING!)
    Min ESS tail: 320 (WARNING!)
  
    Problematic parameters:
  # A tibble: 4 x 4
    variable          rhat ess_bulk ess_tail
    <chr>            <dbl>    <dbl>    <dbl>
  1 beta[2]          0.998      363      320
  2 c_transformed[1] 1.01       387      369
  3 c_transformed[3] 1.01       318      368
  4 beta0            0.997      386      364
  Saving _problems/test-loo-waic-263.R
  Saving _problems/test-loo-waic-279.R
  [ FAIL 2 | WARN 0 | SKIP 23 | PASS 841 ]
  
  ══ Skipped tests (23) ══════════════════════════════════════════════════════════
  • On CRAN (18): 'test-clm_stan.R:24:3', 'test-clm_stan.R:47:3',
    'test-clm_stan.R:74:3', 'test-link-sampling.R:50:3',
    'test-link-sampling.R:70:3', 'test-link-sampling.R:90:3',
    'test-link-sampling.R:110:3', 'test-link-sampling.R:130:3',
    'test-link-sampling.R:154:3', 'test-link-sampling.R:180:3',
    'test-link-sampling.R:206:3', 'test-link-sampling.R:233:3',
    'test-link-sampling.R:259:3', 'test-link-sampling.R:285:3',
    'test-link-sampling.R:315:3', 'test-link-sampling.R:342:3',
    'test-link-sampling.R:372:3', 'test-link-sampling.R:393:3'
  • empty test (5): 'test-model-consistency.R:60:1',
    'test-model-consistency.R:83:1', 'test-model-consistency.R:106:1',
    'test-model-consistency.R:130:1', 'test-model-consistency.R:161:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-loo-waic.R:263:3'): loo results can be used with loo_compare ──
  Expected `is.matrix(comparison)` to be TRUE.
  Differences:
  `actual`:   FALSE
  `expected`: TRUE 
  
  ── Failure ('test-loo-waic.R:279:3'): waic results can be used with loo_compare ──
  Expected `is.matrix(comparison)` to be TRUE.
  Differences:
  `actual`:   FALSE
  `expected`: TRUE 
  
  
  [ FAIL 2 | WARN 0 | SKIP 23 | PASS 841 ]
  Error:
  ! Test failures.
  Execution halted