R Under development (unstable) (2026-06-16 r90166 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.

> library(testthat)
> library(biometryassist)
> 
> test_check("biometryassist")
Starting 2 test processes.
> test-mct.R: Note: re-fitting model with sum-to-zero contrasts
> test-mct.R: NOTE: Results may be misleading due to involvement in interactions
> test-prediction_methods.R: Note: re-fitting model with sum-to-zero contrasts
> test-prediction_methods.R: Note: re-fitting model with sum-to-zero contrasts
> test-prediction_methods.R: Note: re-fitting model with sum-to-zero contrasts
> test-reference_comparisons.R: Note: confidence intervals are per-comparison (not adjusted for multiplicity), while the p-values are adjusted. A comparison's interval can therefore exclude zero when its adjusted p-value is not significant at `sig` (or, less often, the reverse).
> test-reference_comparisons.R: Note: confidence intervals are per-comparison (not adjusted for multiplicity), while the p-values are adjusted. A comparison's interval can therefore exclude zero when its adjusted p-value is not significant at `sig` (or, less often, the reverse).
> test-reference_comparisons.R: Note: re-fitting model with sum-to-zero contrasts
> test-satab.R: Source of Variation                     df
> test-satab.R: =============================================

> test-satab.R: trt                                     3

> test-satab.R: Residual                                16

> test-satab.R: =============================================

> test-satab.R: Total                                   19

> test-utility_functions.R:     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> test-utility_functions.R:     |  biometryassist version 1.5.0                                     |
> test-utility_functions.R:     |  Authors: Sharon Nielsen, Sam Rogers, Annie Conway                |
> test-utility_functions.R:     |  Developed at the University of Adelaide with funding provided    |
> test-utility_functions.R:     |  by the Australian Grains Research and Development Corporation.   |
> test-utility_functions.R:     |  Package website: https://biometryhub.github.io/biometryassist    |
> test-utility_functions.R:     |                                                                   |
> test-utility_functions.R:     |  If you have used this package in your work, please cite it.      |
> test-utility_functions.R:     |  Type 'citation('biometryassist')' for the citation details.      |
> test-utility_functions.R:     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> test-utility_functions.R: 
> test-utility_functions.R: NULL
> test-resplot.R: [[1]]
> test-resplot.R: 
> test-resplot.R: [[1]]
> test-resplot.R: 
> test-resplot.R: [[1]]
> test-resplot.R: 
[ FAIL 0 | WARN 1 | SKIP 194 | PASS 2122 ]

══ Skipped tests (194) ═════════════════════════════════════════════════════════
• On CRAN (156): 'test-all-w2.r:19:2', 'test-all-w2.r:44:2',
  'test-all-w2.r:68:2', 'test-all-w2.r:92:2', 'test-all-w2.r:116:2',
  'test-all-w2.r:143:2', 'test-all-w2.r:171:2', 'test-all-w2.r:247:2',
  'test-all-w2.r:298:2', 'test-all-w2.r:355:2', 'test-all-w2.r:402:2',
  'test-all-w2.r:431:2', 'test-all-w2.r:456:2', 'test-all-w2.r:470:2',
  'test-all-w2.r:494:2', 'test-all-w2.r:518:2', 'test-all-w2.r:545:2',
  'test-all-w2.r:563:2', 'test-all-w2.r:590:2', 'test-all-w2.r:617:2',
  'test-all-w2.r:657:2', 'test-all-w2.r:687:2', 'test-all-w2.r:753:2',
  'test-all-w2.r:860:2', 'test-heatmap.R:24:1', 'test-heatmap.R:38:1',
  'test-heatmap.R:45:1', 'test-heatmap.R:53:1', 'test-heatmap.R:64:1',
  'test-heatmap.R:75:1', 'test-design.R:1:1', 'test-design.R:26:1',
  'test-design.R:53:1', 'test-design.R:79:1', 'test-design.R:103:1',
  'test-design.R:126:1', 'test-design.R:218:1', 'test-design.R:262:1',
  'test-design.R:300:1', 'test-design.R:338:1', 'test-design.R:377:1',
  'test-design.R:435:1', 'test-design.R:464:1', 'test-design.R:492:1',
  'test-design.R:519:1', 'test-design.R:545:1', 'test-design.R:572:1',
  'test-design.R:596:1', 'test-design.R:621:1', 'test-design.R:643:1',
  'test-design.R:696:1', 'test-design.R:973:1', 'test-design.R:1308:1',
  'test-design.R:1397:1', 'test-design.R:1418:1', 'test-design.R:1435:1',
  'test-design.R:1452:1', 'test-design.R:1469:1', 'test-design.R:1486:1',
  'test-design.R:1525:1', 'test-design.R:1562:1', 'test-design.R:1599:1',
  'test-design.R:1636:1', 'test-design.R:1673:1', 'test-design.R:1710:1',
  'test-design.R:1799:1', 'test-design.R:1856:1', 'test-design.R:1916:1',
  'test-design.R:2011:1', 'test-design.R:2158:1', 'test-design.R:2176:1',
  'test-mct.R:685:1', 'test-mct.R:704:1', 'test-mct.R:837:1',
  'test-mct.R:881:1', 'test-mct.R:925:1', 'test-mct.R:969:1',
  'test-mct.R:1013:1', 'test-mct.R:1322:1', 'test-mct.R:1361:1',
  'test-mct.R:1405:1', 'test-mct.R:1482:1', 'test-mct.R:1521:1',
  'test-mct.R:1667:1', 'test-mct.R:1695:1', 'test-mct.R:1749:1',
  'test-mct.R:1906:1', 'test-mct.R:1962:1', 'test-mct.R:1992:1',
  'test-pairwise_comparisons.R:460:1', 'test-reference_comparisons.R:291:1',
  'test-reference_comparisons.R:313:2', 'test-reference_comparisons.R:505:2',
  'test-summary_graph.R:7:1', 'test-summary_graph.R:14:1',
  'test-summary_graph.R:21:1', 'test-use_template.R:9:2',
  'test-use_template.R:18:2', 'test-use_template.R:27:2',
  'test-use_template.R:38:2', 'test-use_template.R:52:2',
  'test-use_template.R:62:2', 'test-use_template.R:78:2',
  'test-use_template.R:120:2', 'test-use_template.R:147:2',
  'test-utility_functions.R:50:1', 'test-variogram.r:125:1',
  'test-variogram.r:204:1', 'test-zzz_install_asreml.R:286:2',
  'test-zzz_install_asreml.R:312:2', 'test-zzz_install_asreml.R:331:2',
  'test-zzz_install_asreml.R:497:2', 'test-zzz_install_asreml.R:506:2',
  'test-zzz_install_asreml.R:518:2', 'test-zzz_install_asreml.R:555:2',
  'test-zzz_install_asreml.R:571:2', 'test-zzz_install_asreml.R:606:2',
  'test-zzz_install_asreml.R:634:2', 'test-zzz_install_asreml.R:648:2',
  'test-zzz_install_asreml.R:714:2', 'test-zzz_install_asreml.R:730:2',
  'test-zzz_install_asreml.R:761:2', 'test-zzz_install_asreml.R:784:2',
  'test-zzz_install_asreml.R:815:2', 'test-zzz_install_asreml.R:828:2',
  'test-zzz_install_asreml.R:843:2', 'test-zzz_install_asreml.R:853:2',
  'test-zzz_install_asreml.R:872:2', 'test-zzz_install_asreml.R:888:2',
  'test-zzz_install_asreml.R:921:2', 'test-zzz_install_asreml.R:942:2',
  'test-zzz_install_asreml.R:990:2', 'test-zzz_install_asreml.R:1043:2',
  'test-zzz_install_asreml.R:1142:2', 'test-zzz_install_asreml.R:1172:2',
  'test-zzz_install_asreml.R:1204:2', 'test-zzz_install_asreml.R:1234:2',
  'test-zzz_install_asreml.R:1269:2', 'test-zzz_install_asreml.R:1305:2',
  'test-zzz_install_asreml.R:1342:2', 'test-zzz_install_asreml.R:1391:2',
  'test-zzz_install_asreml.R:1440:2', 'test-zzz_install_asreml.R:1489:2',
  'test-zzz_install_asreml.R:1995:2', 'test-resplot.R:19:1',
  'test-resplot.R:29:1', 'test-resplot.R:48:1', 'test-resplot.R:86:2',
  'test-resplot.R:125:1', 'test-resplot.R:186:1', 'test-resplot.R:196:1',
  'test-resplot.R:248:1', 'test-resplot.R:337:1', 'test-resplot.R:353:1',
  'test-resplot.R:376:1', 'test-resplot.R:395:1'
• rlang::is_installed("asreml") is not TRUE (8): 'test-logltest.R:4:2',
  'test-logltest.R:51:2', 'test-logltest.R:61:2', 'test-logltest.R:77:2',
  'test-logltest.R:92:2', 'test-logltest.R:110:2', 'test-logltest.R:131:2',
  'test-logltest.R:142:2'
• {ARTool} is not installed (1): 'test-prediction_methods.R:812:2'
• {afex} is not installed (4): 'test-mct.R:1781:2',
  'test-prediction_methods.R:828:2', 'test-prediction_methods.R:871:2',
  'test-resplot.R:265:2'
• {asreml} is not installed (8): 'test-mct.R:1386:2', 'test-mct.R:1444:2',
  'test-mct.R:1538:2', 'test-mct.R:1633:2', 'test-mct.R:2229:2',
  'test-prediction_methods.R:729:2', 'test-prediction_methods.R:1004:2',
  'test-pairwise_comparisons.R:830:2'
• {glmmTMB} is not installed (3): 'test-mct.R:1809:2',
  'test-prediction_methods.R:889:2', 'test-resplot.R:301:2'
• {lme4breeding} is not installed (3): 'test-mct.R:1851:2',
  'test-prediction_methods.R:962:2', 'test-resplot.R:217:2'
• {lme4} is not installed (7): 'test-mct.R:1642:2', 'test-mct.R:2250:2',
  'test-prediction_methods.R:1036:2', 'test-prediction_methods.R:1061:2',
  'test-pairwise_comparisons.R:618:2', 'test-reference_comparisons.R:242:2',
  'test-resplot.R:176:2'
• {lmerTest} is not installed (1): 'test-mct.R:2270:2'
• {sommer} is not installed (3): 'test-mct.R:1833:2',
  'test-prediction_methods.R:926:2', 'test-prediction_methods.R:947:2'

[ FAIL 0 | WARN 1 | SKIP 194 | PASS 2122 ]
Deleting unused snapshots: 'all-w2/example1autoplot.svg',
'all-w2/example2autoplot.svg', 'all-w2/example3autoplot.svg',
'all-w2/example3lmmautoplot.svg', 'all-w2/example4autoplot.svg',
'all-w2/example4lmmautoplot.svg', 'all-w2/example5lmmautoplot1.svg',
'all-w2/example5lmmautoplot2.svg', 'all-w2/example6lmmautoplot2.svg',
'all-w2/example7lmmautoplot.svg', 'all-w2/exercise10autoplot.svg',
'all-w2/exercise11autoplot1.svg', 'all-w2/exercise11autoplot2.svg',
'all-w2/exercise12autoplot.svg', 'all-w2/exercise13autoplot1.svg',
'all-w2/exercise13autoplot2.svg', 'all-w2/exercise14autoplot.svg',
'all-w2/exercise15autoplot1.svg', …, 'mct/sommer-mmes-output.svg', and
'prediction_methods/asreml-predictions.svg'
> 
> proc.time()
   user  system elapsed 
  39.10    2.06  133.79