R Under development (unstable) (2026-08-03 r90347 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # 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/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(bifrost)
> 
> test_check("bifrost")
NULL


[?7hv ============================== 100% [1/1] [0.0s] [1/3] Candidate scoring done
v ============================== 100% [1/1] [0.0s] [2/3] Greedy shift search...
[?7li ============================== 100% [1/1] [0.0s] [1/1] complete

[?7hi ============================== 100% [1/1] [0.0s] [1/1] complete
[?7l- ------------------------------   0% [0/1] (ETA: ?) 

- ============================== 100% [1/1] (ETA: 0.0s) [1/3] Candidate scoring complete

- ============================== 100% [1/1] (ETA: 0.0s) [1/3] Candidate scoring done

v ============================== 100% [1/1] [0.0s] [1/3] Candidate scoring done

v ============================== 100% [1/1] [0.0s] [1/3] Candidate scoring done
- ------------------------------   0% [0/1] (ETA: ?) 


v ============================== 100% [1/1] [0.0s] [1/3] Candidate scoring done
- ============================== 100% [1/1] (ETA: 0.0s) [2/3] Greedy shift search complete


v ============================== 100% [1/1] [0.0s] [1/3] Candidate scoring done
- ============================== 100% [1/1] (ETA: 0.0s) [2/3] Greedy shift search done


v ============================== 100% [1/1] [0.0s] [1/3] Candidate scoring done
v ============================== 100% [1/1] [0.0s] [2/3] Greedy shift search done


[?7hv ============================== 100% [1/1] [0.0s] [1/3] Candidate scoring done
v ============================== 100% [1/1] [0.0s] [2/3] Greedy shift search...
Loading required namespace: intervals
[ FAIL 0 | WARN 0 | SKIP 131 | PASS 2275 ]

══ Skipped tests (131) ═════════════════════════════════════════════════════════
• Development-only comparison script is excluded from source tarballs (6):
  'test-compare-simulation-generators.R:16:3',
  'test-compare-simulation-generators.R:33:3',
  'test-compare-simulation-generators.R:50:3',
  'test-compare-simulation-generators.R:63:3',
  'test-compare-simulation-generators.R:79:3',
  'test-compare-simulation-generators.R:85:3'
• Development-only simulation regeneration scripts are excluded from source
  tarballs (7): 'test-simulation-vignette-cache.R:158:3',
  'test-simulation-vignette-cache.R:264:3',
  'test-simulation-vignette-cache.R:314:3',
  'test-simulation-vignette-cache.R:370:3',
  'test-simulation-vignette-cache.R:477:3',
  'test-simulation-vignette-cache.R:538:3',
  'test-simulation-vignette-cache.R:612:3'
• Lineage-rate vignette source is unavailable in installed tests (1):
  'test-vignette-html-widgets.R:5:3'
• On CRAN (91): 'test-createSimulationTemplate.R:8:3',
  'test-createSimulationTemplate.R:34:3',
  'test-createSimulationTemplate.R:65:3',
  'test-createSimulationTemplate.R:89:3',
  'test-createSimulationTemplate.R:291:3',
  'test-createSimulationTemplate.R:310:3',
  'test-createSimulationTemplate.R:361:3',
  'test-createSimulationTemplate.R:401:3',
  'test-createSimulationTemplate.R:458:3',
  'test-createSimulationTemplate.R:490:3',
  'test-createSimulationTemplate.R:520:3', 'test-print-bifrost_search.R:3:1',
  'test-print-bifrost_simulation_template.R:8:3',
  'test-print-bifrost_simulation_template.R:27:3',
  'test-print-bifrost_simulation_template.R:51:3',
  'test-print-bifrost_simulation_template.R:69:3',
  'test-runFalsePositiveSimulationStudy.R:74:3',
  'test-runFalsePositiveSimulationStudy.R:119:3',
  'test-runFalsePositiveSimulationStudy.R:147:3',
  'test-runFalsePositiveSimulationStudy.R:207:3',
  'test-runFalsePositiveSimulationStudy.R:233:3',
  'test-runFalsePositiveSimulationStudy.R:263:3',
  'test-runFalsePositiveSimulationStudy.R:288:3',
  'test-runFalsePositiveSimulationStudy.R:314:3',
  'test-runFalsePositiveSimulationStudy.R:375:3',
  'test-runFalsePositiveSimulationStudy.R:423:3',
  'test-runFalsePositiveSimulationStudy.R:461:3',
  'test-runFalsePositiveSimulationStudy.R:491:3',
  'test-runFalsePositiveSimulationStudy.R:519:3',
  'test-runFalsePositiveSimulationStudy.R:556:3',
  'test-runFalsePositiveSimulationStudy.R:622:3',
  'test-runFalsePositiveSimulationStudy.R:657:3',
  'test-runFalsePositiveSimulationStudy.R:707:3',
  'test-runFalsePositiveSimulationStudy.R:772:3',
  'test-runFalsePositiveSimulationStudy.R:800:3',
  'test-runFalsePositiveSimulationStudy.R:838:3',
  'test-runSearchTuningGrid.R:88:3', 'test-runSearchTuningGrid.R:150:3',
  'test-runSearchTuningGrid.R:190:3', 'test-runSearchTuningGrid.R:393:3',
  'test-runSearchTuningGrid.R:462:3', 'test-runSearchTuningGrid.R:602:3',
  'test-runSearchTuningGrid.R:669:3', 'test-runSearchTuningGrid.R:713:3',
  'test-runSearchTuningGrid.R:788:3', 'test-runSearchTuningGrid.R:963:3',
  'test-runShiftRecoverySimulationStudy.R:75:3',
  'test-runShiftRecoverySimulationStudy.R:133:3',
  'test-runShiftRecoverySimulationStudy.R:174:3',
  'test-runShiftRecoverySimulationStudy.R:246:3',
  'test-runShiftRecoverySimulationStudy.R:280:3',
  'test-runShiftRecoverySimulationStudy.R:321:3',
  'test-runShiftRecoverySimulationStudy.R:358:3',
  'test-runShiftRecoverySimulationStudy.R:391:3',
  'test-runShiftRecoverySimulationStudy.R:475:3',
  'test-runShiftRecoverySimulationStudy.R:533:3',
  'test-runShiftRecoverySimulationStudy.R:578:3',
  'test-runShiftRecoverySimulationStudy.R:614:3',
  'test-runShiftRecoverySimulationStudy.R:649:3',
  'test-runShiftRecoverySimulationStudy.R:700:3',
  'test-runShiftRecoverySimulationStudy.R:775:3',
  'test-runShiftRecoverySimulationStudy.R:836:3',
  'test-runShiftRecoverySimulationStudy.R:894:3',
  'test-runShiftRecoverySimulationStudy.R:992:3',
  'test-runShiftRecoverySimulationStudy.R:1027:3',
  'test-runShiftRecoverySimulationStudy.R:1081:3',
  'test-runShiftRecoverySimulationStudy.R:1118:3',
  'test-runShiftRecoverySimulationStudy.R:1213:3',
  'test-search-characterization.R:3:1',
  'test-searchOptimalConfiguration.R:3:1', 'test-simulateNullDataset.R:132:3',
  'test-simulateNullDataset.R:147:3', 'test-simulateNullDataset.R:199:3',
  'test-simulateNullDataset.R:222:3', 'test-simulateNullDataset.R:237:3',
  'test-simulateNullDataset.R:249:3', 'test-simulateNullDataset.R:264:3',
  'test-simulateNullDataset.R:296:3', 'test-simulateShiftedDataset.R:133:3',
  'test-simulateShiftedDataset.R:179:3', 'test-simulateShiftedDataset.R:200:3',
  'test-simulateShiftedDataset.R:293:3', 'test-simulateShiftedDataset.R:343:3',
  'test-simulateShiftedDataset.R:368:3', 'test-simulateShiftedDataset.R:395:3',
  'test-simulateShiftedDataset.R:430:3', 'test-simulateShiftedDataset.R:494:3',
  'test-simulateShiftedDataset.R:513:3', 'test-simulateShiftedDataset.R:536:3',
  'test-simulateShiftedDataset.R:559:3', 'test-simulateShiftedDataset.R:622:3'
• On Windows (5): 'test-example-data.R:214:3', 'test-example-data.R:415:3',
  'test-example-data.R:511:3', 'test-example-data.R:535:3',
  'test-example-data.R:590:3'
• Part 1 vignette source is unavailable in installed tests (1):
  'test-simulation-terminology.R:40:3'
• Simulation documentation sources are unavailable in installed tests (1):
  'test-simulation-terminology.R:14:3'
• Simulation vignette not present (3):
  'test-simulation-vignette-cache.R:791:3',
  'test-simulation-vignette-cache.R:918:3',
  'test-simulation-vignette-cache.R:946:3'
• Simulation vignette sources are unavailable in installed tests (2):
  'test-simulation-terminology.R:101:3', 'test-simulation-terminology.R:127:3'
• Simulation vignettes not present (1):
  'test-simulation-vignette-cache.R:825:3'
• Vignette not present: avian-skeleton-part-1 (1):
  'test-vignette-figure-captions.R:17:5'
• Vignette sources are unavailable in installed tests (2):
  'test-vignette-ai-assistance.R:9:3', 'test-vignette-code-comments.R:33:3'
• repository empirical artifact directory unavailable for focal search (2):
  'test-lineage_rates.R:684:3', 'test-shift-distributions.R:1865:3'
• repository empirical artifact directory unavailable for post-hoc object (5):
  'test-regime-integration.R:1934:3', 'test-regime-integration.R:1976:3',
  'test-regime-integration.R:2010:3', 'test-regime-integration.R:2308:3',
  'test-regime-integration.R:2368:3'
• repository empirical artifact directory unavailable for sensitivity bundle
  (1): 'test-shift-distributions.R:1335:3'
• repository empirical artifact directory unavailable for serialized artifacts
  (1): 'test-serialized-artifacts.R:28:3'
• repository empirical artifact directory unavailable for simulation vignette
  cache (1): 'test-simulation-vignette-cache.R:3:3'

[ FAIL 0 | WARN 0 | SKIP 131 | PASS 2275 ]
Warning message:
In .Internal(gc(verbose, reset, full)) :
  closing unused connection 4 (<-CRANwin3.fb05.statistik.uni-dortmund.de:35558)
> 
> proc.time()
   user  system elapsed 
  42.03    4.17  124.15