Running ‘testthat.R’ [169s/211s]
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 your testing?
  > # - If you are developing a package, run your tests using covr::report(),
  > #   devtools::test(), or by pressing Ctrl/Cmd + Shift + T.
  > # - If you are testing a script, run your tests using testthat::test_file()
  > 
  > library(testthat)
  > library(MAIHDA)
  > 
  > test_check("MAIHDA")
  ── Intersectional interactions ─────────────────────────────────────────────────
  4 of 9 strata flagged (95% interval).
  Interaction reported on the link (latent) scale.
  
   stratum label  n interaction     se  lower  upper   p_value p_adjusted flagged
         1 1 × 1 60       2.613 0.1245  2.369  2.857 8.752e-98  7.877e-97    TRUE
         2 2 × 1 60      -2.608 0.1245 -2.852 -2.364 1.866e-97  8.398e-97    TRUE
         5 2 × 2 60       2.568 0.1245  2.324  2.812 1.442e-94  4.326e-94    TRUE
         4 1 × 2 60      -2.518 0.1245 -2.762 -2.274 5.585e-91  1.257e-90    TRUE
   direction
       above
       below
       above
       below
  
  Interaction BLUPs are shrunken (partially pooled) estimates; treat flags as
    exploratory. See ?maihda_interactions.
  ── Intersectional interactions ─────────────────────────────────────────────────
  3 of 3 strata flagged (95% interval).
  Interaction reported on the link (latent) scale.
  
   stratum label  n interaction     se  lower  upper   p_value p_adjusted flagged
         1 1 × 1 60       2.613 0.1245  2.369  2.857 8.752e-98  7.877e-97    TRUE
         2 2 × 1 60      -2.608 0.1245 -2.852 -2.364 1.866e-97  8.398e-97    TRUE
         5 2 × 2 60       2.568 0.1245  2.324  2.812 1.442e-94  4.326e-94    TRUE
   direction
       above
       below
       above
  
  Interaction BLUPs are shrunken (partially pooled) estimates; treat flags as
    exploratory. See ?maihda_interactions.
  ── Intersectional interactions ─────────────────────────────────────────────────
  ? of 9 strata flagged (95% interval).
  Interaction reported on the link (latent) scale.
  
   stratum label interaction
         1 1 × 1    2.612662
         2 2 × 1   -2.608177
         5 2 × 2    2.568450
         4 1 × 2   -2.518223
         7 1 × 3   -0.094440
         9 3 × 3    0.054712
         6 3 × 2   -0.050227
         8 2 × 3    0.039727
         3 3 × 1   -0.004485
  
  Interaction BLUPs are shrunken (partially pooled) estimates; treat flags as
    exploratory. See ?maihda_interactions.
  Intersectional interactions: 4 of 9 strata flagged (95% interval, no multiplicity correction)
    strongest: 1 × 1 (+2.613, above)
    uncorrected across 9 strata; maihda_interactions(x, adjust = "BH") for an FDR screen
  ── Intersectional interactions ─────────────────────────────────────────────────
  4 of 9 strata flagged (95% interval; BH-adjusted p-values).
  Model: adjusted (two-model); interaction on the link (latent) scale.
  
   stratum label  n interaction     se  lower  upper   p_value p_adjusted flagged
         1 1 × 1 60       2.613 0.1245  2.369  2.857 8.752e-98  7.877e-97    TRUE
         2 2 × 1 60      -2.608 0.1245 -2.852 -2.364 1.866e-97  8.398e-97    TRUE
         5 2 × 2 60       2.568 0.1245  2.324  2.812 1.442e-94  4.326e-94    TRUE
   direction
       above
       below
       above
  
  Interaction BLUPs are shrunken (partially pooled) estimates; treat flags as
    exploratory. See ?maihda_interactions.
  ── Intersectional interactions ─────────────────────────────────────────────────
  4 of 9 strata flagged (95% interval; BH-adjusted p-values).
  Model: adjusted (two-model); interaction on the link (latent) scale.
  
   stratum label  n interaction     se  lower  upper   p_value p_adjusted flagged
         1 1 × 1 60       2.613 0.1245  2.369  2.857 8.752e-98  7.877e-97    TRUE
         2 2 × 1 60      -2.608 0.1245 -2.852 -2.364 1.866e-97  8.398e-97    TRUE
         5 2 × 2 60       2.568 0.1245  2.324  2.812 1.442e-94  4.326e-94    TRUE
   direction
       above
       below
       above
  
  Interaction BLUPs are shrunken (partially pooled) estimates; treat flags as
    exploratory. See ?maihda_interactions.
  ── Intersectional interactions ─────────────────────────────────────────────────
  4 of 9 strata flagged (95% interval; BH-adjusted p-values).
  Model: adjusted (two-model); interaction on the link (latent) scale.
  
   stratum label  n interaction     se  lower  upper   p_value p_adjusted flagged
         1 1 × 1 60       2.613 0.1245  2.369  2.857 8.752e-98  7.877e-97    TRUE
         2 2 × 1 60      -2.608 0.1245 -2.852 -2.364 1.866e-97  8.398e-97    TRUE
         5 2 × 2 60       2.568 0.1245  2.324  2.812 1.442e-94  4.326e-94    TRUE
         4 1 × 2 60      -2.518 0.1245 -2.762 -2.274 5.585e-91  1.257e-90    TRUE
   direction
       above
       below
       above
       below
  
  Interaction BLUPs are shrunken (partially pooled) estimates; treat flags as
    exploratory. See ?maihda_interactions.
  ── Intersectional interactions ─────────────────────────────────────────────────
  ? of 9 strata flagged (95% interval).
  Interaction reported on the link (latent) scale.
  
   stratum label interaction
         1 1 × 1    2.612662
         2 2 × 1   -2.608177
         5 2 × 2    2.568450
         4 1 × 2   -2.518223
         7 1 × 3   -0.094440
         9 3 × 3    0.054712
         6 3 × 2   -0.050227
         8 2 × 3    0.039727
         3 3 × 1   -0.004485
  
  Interaction BLUPs are shrunken (partially pooled) estimates; treat flags as
    exploratory. See ?maihda_interactions.
  Saving _problems/test-plot_upset-94.R
  [ FAIL 1 | WARN 0 | SKIP 58 | PASS 1704 ]
  
  ══ Skipped tests (58) ══════════════════════════════════════════════════════════
  • On CRAN (57): 'test-contextual.R:633:3', 'test-contextual.R:776:3',
    'test-cross-classified.R:268:3', 'test-design-weights.R:266:3',
    'test-design-weights.R:306:3', 'test-design-weights.R:326:3',
    'test-design-weights.R:343:3', 'test-design-weights.R:364:3',
    'test-design-weights.R:397:3', 'test-design-weights.R:423:3',
    'test-design-weights.R:451:3', 'test-design-weights.R:472:3',
    'test-design-weights.R:488:3', 'test-design-weights.R:517:3',
    'test-design-weights.R:541:3', 'test-design-weights.R:557:3',
    'test-design-weights.R:572:3', 'test-design-weights.R:591:3',
    'test-design-weights.R:924:3', 'test-design-weights.R:983:3',
    'test-discriminatory-accuracy.R:144:3',
    'test-discriminatory-accuracy.R:226:3',
    'test-discriminatory-accuracy.R:287:3',
    'test-discriminatory-accuracy.R:394:3',
    'test-discriminatory-accuracy.R:417:3',
    'test-discriminatory-accuracy.R:438:3', 'test-fit_maihda.R:161:3',
    'test-information_criteria.R:102:3', 'test-information_criteria.R:125:3',
    'test-longitudinal.R:175:1', 'test-negbinomial.R:72:3',
    'test-negbinomial.R:112:3', 'test-negbinomial.R:150:3',
    'test-negbinomial.R:185:3', 'test-negbinomial.R:199:3',
    'test-negbinomial.R:209:3', 'test-negbinomial.R:224:3',
    'test-negbinomial.R:237:3', 'test-negbinomial.R:291:3',
    'test-negbinomial.R:309:3', 'test-ordinal-engine.R:157:3',
    'test-ordinal-engine.R:199:3', 'test-ordinal-engine.R:222:3',
    'test-ordinal-engine.R:263:3', 'test-ordinal-engine.R:315:3',
    'test-ordinal-engine.R:361:3', 'test-ordinal-engine.R:381:3',
    'test-ordinal-engine.R:423:3', 'test-ordinal-engine.R:453:3',
    'test-ordinal-engine.R:607:3', 'test-run_app.R:119:3',
    'test-run_app.R:308:3', 'test-run_app.R:424:3',
    'test-summary_variance.R:270:3', 'test-tidiers.R:148:3',
    'test-weighted-count-vpc.R:32:3', 'test-weighted-count-vpc.R:80:3'
  • brms Stan tests are opt-in; set MAIHDA_TEST_BRMS=true to run them (1):
    'test-interactions.R:460:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-plot_upset.R:93:3'): plot.maihda_analysis dispatches type = 'upset' and forwards rope ──
  <Rcpp::exception/C++Error/error/condition>
  Error: Downdated VtV is not positive definite
  Backtrace:
       ▆
    1. └─MAIHDA::maihda(...) at test-plot_upset.R:93:3
    2.   └─MAIHDA (local) fit_maihda_fwd(...)
    3.     ├─base::do.call(fit_maihda, c(list(...), dots_eval))
    4.     └─MAIHDA (local) `<fn>`(...)
    5.       └─base::eval(fit_call, fit_env)
    6.         └─base::eval(fit_call, fit_env)
    7.           └─lme4::glmer(...)
    8.             └─lme4::optimizeGlmer(...)
    9.               └─lme4:::optwrap(...)
   10.                 ├─base::withCallingHandlers(...)
   11.                 ├─base::do.call(optfun, arglist)
   12.                 └─lme4 (local) `<fn>`(...)
   13.                   ├─nM$newf(fn(nM$xeval()))
   14.                   │ └─base::stopifnot(length(value <- as.numeric(value)) == 1L)
   15.                   └─lme4 (local) fn(nM$xeval())
   16.                     └─lme4 (local) pwrssUpdate(...)
  
  [ FAIL 1 | WARN 0 | SKIP 58 | PASS 1704 ]
  Error:
  ! Test failures.
  Execution halted