R Under development (unstable) (2026-10-05 r90641 ucrt) -- "Unsuffered Consequences"
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Platform: x86_64-w64-mingw32/x64

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> 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: re-fitting model with sum-to-zero contrasts
> test-mct.R: NOTE: Results may be misleading due to involvement in interactions
> test-mct.R: Note: re-fitting model with sum-to-zero contrasts
> test-mct.R: Note: re-fitting model with sum-to-zero contrasts
> test-mct.R: Note: re-fitting model with sum-to-zero contrasts
> test-mct.R: Note: re-fitting model with sum-to-zero contrasts
> test-mct.R: Note: re-fitting model with sum-to-zero contrasts
> 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 1.5.1                                     |
> test-utility_functions.R:     |  Authors: Sharon Nielsen, Sam Rogers, Annie Conway                |
> test-utility_functions.R:     |  Developed at Adelaide University 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 200 | PASS 2156 ]

══ Skipped tests (200) ═════════════════════════════════════════════════════════
• On CRAN (160): 'test-all-w2.r:22:2', 'test-all-w2.r:47:2',
  'test-all-w2.r:71:2', 'test-all-w2.r:95:2', 'test-all-w2.r:119:2',
  'test-all-w2.r:146:2', 'test-all-w2.r:174:2', 'test-all-w2.r:250:2',
  'test-all-w2.r:301:2', 'test-all-w2.r:358:2', 'test-all-w2.r:405:2',
  'test-all-w2.r:434:2', 'test-all-w2.r:459:2', 'test-all-w2.r:473:2',
  'test-all-w2.r:497:2', 'test-all-w2.r:521:2', 'test-all-w2.r:548:2',
  'test-all-w2.r:566:2', 'test-all-w2.r:593:2', 'test-all-w2.r:620:2',
  'test-all-w2.r:660:2', 'test-all-w2.r:690:2', 'test-all-w2.r:756:2',
  'test-all-w2.r:863:2', '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:1478:1', 'test-mct.R:1517:1',
  'test-mct.R:1664:1', 'test-mct.R:1692:1', 'test-mct.R:1736:1',
  'test-mct.R:1916:1', 'test-mct.R:1972:1', 'test-mct.R:2002:1',
  'test-pairwise_comparisons.R:460:1', 'test-prediction_methods.R:742:2',
  'test-prediction_methods.R:790:2', 'test-prediction_methods.R:818:2',
  'test-reference_comparisons.R:292:1', 'test-reference_comparisons.R:314:2',
  'test-reference_comparisons.R:506:2', '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-use_template.R:196:2',
  'test-utility_functions.R:50:1', 'test-variogram.r:128:1',
  'test-variogram.r:207:1', 'test-zzz_install_asreml.R:286:2',
  'test-zzz_install_asreml.R:313:2', 'test-zzz_install_asreml.R:332:2',
  'test-zzz_install_asreml.R:498:2', 'test-zzz_install_asreml.R:507:2',
  'test-zzz_install_asreml.R:519:2', 'test-zzz_install_asreml.R:556:2',
  'test-zzz_install_asreml.R:572:2', 'test-zzz_install_asreml.R:607:2',
  'test-zzz_install_asreml.R:635:2', 'test-zzz_install_asreml.R:649:2',
  'test-zzz_install_asreml.R:715:2', 'test-zzz_install_asreml.R:731:2',
  'test-zzz_install_asreml.R:762:2', 'test-zzz_install_asreml.R:785:2',
  'test-zzz_install_asreml.R:816:2', 'test-zzz_install_asreml.R:829:2',
  'test-zzz_install_asreml.R:844:2', 'test-zzz_install_asreml.R:854:2',
  'test-zzz_install_asreml.R:873:2', 'test-zzz_install_asreml.R:889:2',
  'test-zzz_install_asreml.R:922:2', 'test-zzz_install_asreml.R:943:2',
  'test-zzz_install_asreml.R:991:2', 'test-zzz_install_asreml.R:1044:2',
  'test-zzz_install_asreml.R:1143:2', 'test-zzz_install_asreml.R:1173:2',
  'test-zzz_install_asreml.R:1205:2', 'test-zzz_install_asreml.R:1235:2',
  'test-zzz_install_asreml.R:1270:2', 'test-zzz_install_asreml.R:1306:2',
  'test-zzz_install_asreml.R:1343:2', 'test-zzz_install_asreml.R:1392:2',
  'test-zzz_install_asreml.R:1441:2', 'test-zzz_install_asreml.R:1490:2',
  'test-zzz_install_asreml.R:1996:2', 'test-resplot.R:19:1',
  'test-resplot.R:29:1', 'test-resplot.R:48:1', 'test-resplot.R:87:2',
  'test-resplot.R:126:1', 'test-resplot.R:187:1', 'test-resplot.R:197:1',
  'test-resplot.R:249:1', 'test-resplot.R:338:1', 'test-resplot.R:354:1',
  'test-resplot.R:377:1', 'test-resplot.R:396:1'
• 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:945:2'
• {afex} is not installed (4): 'test-mct.R:1781:2',
  'test-prediction_methods.R:961:2', 'test-prediction_methods.R:1003:2',
  'test-resplot.R:266:2'
• {asreml} is not installed (8): 'test-mct.R:1386:2', 'test-mct.R:1440:2',
  'test-mct.R:1534:2', 'test-mct.R:1630:2', 'test-mct.R:2308:2',
  'test-pairwise_comparisons.R:830:2', 'test-prediction_methods.R:863:2',
  'test-prediction_methods.R:1148:2'
• {glmmTMB} is not installed (3): 'test-mct.R:1809:2',
  'test-prediction_methods.R:1021:2', 'test-resplot.R:302:2'
• {lme4breeding} is not installed (3): 'test-mct.R:1861:2',
  'test-prediction_methods.R:1106:2', 'test-resplot.R:218:2'
• {lme4} is not installed (9): 'test-mct.R:1639:2', 'test-mct.R:2329:2',
  'test-pairwise_comparisons.R:618:2', 'test-prediction_methods.R:1180:2',
  'test-prediction_methods.R:1202:2', 'test-prediction_methods.R:1221:2',
  'test-prediction_methods.R:1243:2', 'test-reference_comparisons.R:243:2',
  'test-resplot.R:177:2'
• {lmerTest} is not installed (1): 'test-mct.R:2349:2'
• {sommer} is not installed (3): 'test-mct.R:1833:2',
  'test-prediction_methods.R:1057:2', 'test-prediction_methods.R:1091:2'

[ FAIL 0 | WARN 1 | SKIP 200 | PASS 2156 ]
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 
  42.93    3.18  137.96