Last updated on 2026-10-05 09:49:27 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.5.0 | 10.57 | 478.59 | 489.16 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.5.0 | 8.69 | 309.22 | 317.91 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.5.0 | 300.82 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.5.0 | 8.00 | 319.71 | 327.71 | ERROR | |
| r-devel-windows-x86_64 | 1.5.0 | 19.00 | 327.00 | 346.00 | OK | |
| r-patched-linux-x86_64 | 1.5.0 | 13.42 | 443.04 | 456.46 | OK | |
| r-release-linux-x86_64 | 1.5.0 | OK | ||||
| r-release-macos-arm64 | 1.5.0 | 4.00 | 81.00 | 85.00 | OK | |
| r-release-macos-x86_64 | 1.5.0 | 11.00 | 310.00 | 321.00 | OK | |
| r-release-windows-x86_64 | 1.5.0 | 18.00 | 311.00 | 329.00 | OK | |
| r-oldrel-macos-arm64 | 1.5.0 | 4.00 | 79.00 | 83.00 | OK | |
| r-oldrel-macos-x86_64 | 1.5.0 | 11.00 | 317.00 | 328.00 | OK | |
| r-oldrel-windows-x86_64 | 1.5.0 | 26.00 | 439.00 | 465.00 | OK |
Version: 1.5.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [186s/123s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(biometryassist)
>
> test_check("biometryassist")
Starting 2 test processes.
> test-mct.R: Loading required package: Matrix
> test-mct.R: Contrasts set to contr.sum for the following variables: treatment, gender
> test-mct.R: Found more than one class "lmerMod" in cache; using the first, from namespace 'lme4'
> test-mct.R: Also defined by 'lme4breeding'
> test-mct.R: Found more than one class "lmerMod" in cache; using the first, from namespace 'lme4'
> test-mct.R: Also defined by 'lme4breeding'
> test-mct.R: Found more than one class "lmerMod" in cache; using the first, from namespace 'lme4'
> test-mct.R: Also defined by 'lme4breeding'
> test-mct.R: Found more than one class "lmerMod" in cache; using the first, from namespace 'lme4'
> test-mct.R: Also defined by 'lme4breeding'
> test-mct.R: Note: re-fitting model with sum-to-zero contrasts
> test-mct.R: Found more than one class "lmerMod" in cache; using the first, from namespace 'lme4'
> test-mct.R: Also defined by 'lme4breeding'
> test-mct.R: Found more than one class "lmerMod" in cache; using the first, from namespace 'lme4'
> test-mct.R: Also defined by 'lme4breeding'
> test-mct.R: Found more than one class "lmerMod" in cache; using the first, from namespace 'lme4'
> test-mct.R: Also defined by 'lme4breeding'
> test-mct.R: Found more than one class "lmerMod" in cache; using the first, from namespace 'lme4'
> test-mct.R: Also defined by 'lme4breeding'
> test-mct.R:
> test-mct.R: Attaching package: 'lmerTest'
> test-mct.R:
> test-mct.R: The following object is masked from 'package:lme4':
> test-mct.R:
> test-mct.R: lmer
> test-mct.R:
> test-mct.R: The following object is masked from 'package:stats':
> test-mct.R:
> test-mct.R: step
> test-mct.R:
> test-mct.R: NOTE: Results may be misleading due to involvement in interactions
Saving _problems/test-mct-1836.R
> 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-prediction_methods.R: Contrasts set to contr.sum for the following variables: treatment, gender
> test-prediction_methods.R: Contrasts set to contr.sum for the following variables: treatment, gender
> test-prediction_methods.R: Found more than one class "lmerMod" in cache; using the first, from namespace 'lme4'
> test-prediction_methods.R: Also defined by 'lme4breeding'
> test-prediction_methods.R: Found more than one class "lmerMod" in cache; using the first, from namespace 'lme4'
> test-prediction_methods.R: Also defined by 'lme4breeding'
> test-prediction_methods.R: Found more than one class "lmerMod" in cache; using the first, from namespace 'lme4'
> test-prediction_methods.R: Also defined by 'lme4breeding'
> test-prediction_methods.R: Found more than one class "lmerMod" in cache; using the first, from namespace 'lme4'
> test-prediction_methods.R: Also defined by 'lme4breeding'
> test-prediction_methods.R: Found more than one class "lmerMod" in cache; using the first, from namespace 'lme4'
> test-prediction_methods.R: Also defined by 'lme4breeding'
> test-prediction_methods.R: Found more than one class "lmerMod" in cache; using the first, from namespace 'lme4'
> test-prediction_methods.R: Also defined by 'lme4breeding'
> test-prediction_methods.R: Found more than one class "lmerMod" in cache; using the first, from namespace 'lme4'
> test-prediction_methods.R: Also defined by 'lme4breeding'
> test-prediction_methods.R: Found more than one class "lmerMod" in cache; using the first, from namespace 'lme4'
> test-prediction_methods.R: Also defined by 'lme4breeding'
> test-prediction_methods.R: Found more than one class "lmerMod" in cache; using the first, from namespace 'lme4'
> test-prediction_methods.R: Also defined by 'lme4breeding'
> test-pairwise_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).
Saving _problems/test-prediction_methods-929.R
> 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-reference_comparisons.R: Found more than one class "lmerMod" in cache; using the first, from namespace 'lme4'
> test-reference_comparisons.R: Also defined by 'lme4breeding'
> test-reference_comparisons.R: Found more than one class "lmerMod" in cache; using the first, from namespace 'lme4'
> test-reference_comparisons.R: Also defined by 'lme4breeding'
> test-reference_comparisons.R: Found more than one class "lmerMod" in cache; using the first, from namespace 'lme4'
> test-reference_comparisons.R: Also defined by 'lme4breeding'
> test-reference_comparisons.R: Found more than one class "lmerMod" in cache; using the first, from namespace 'lme4'
> test-reference_comparisons.R: Also defined by 'lme4breeding'
> 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: Contrasts set to contr.sum for the following variables: treatment, gender
> test-resplot.R: [[1]]
> test-resplot.R:
> test-resplot.R: [[1]]
> test-resplot.R:
> test-resplot.R: [[1]]
> test-resplot.R:
[ FAIL 2 | WARN 0 | SKIP 178 | PASS 2206 ]
══ Skipped tests (178) ═════════════════════════════════════════════════════════
• On CRAN (160): '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:1641:1', 'test-mct.R:1667:1', 'test-mct.R:1695:1',
'test-mct.R:1749:1', 'test-mct.R:1780:1', 'test-mct.R:1808:1',
'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:175:1', 'test-resplot.R:186:1',
'test-resplot.R:248:1', 'test-resplot.R:264:1', 'test-resplot.R:300:1',
'test-resplot.R:337:1', 'test-resplot.R:376:1', 'test-resplot.R:395:1'
• On Linux (2): 'test-resplot.R:203:2', 'test-resplot.R:368:2'
• 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'
• {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'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-mct.R:1836:2'): sommer mmes model is supported ─────────────────
<Rcpp::exception/C++Error/error/condition>
Error: The fitted model does not contain C. Refit with ai_mme_sp2() returning C.
Backtrace:
▆
1. └─biometryassist::multiple_comparisons(model_mmes, classify = "Env") at test-mct.R:1836:9
2. ├─biometryassist:::get_predictions(model.obj, classify, ...)
3. └─biometryassist:::get_predictions.mmes(model.obj, classify, ...)
4. ├─stats::predict(model.obj, D = classify)
5. └─sommer::predict.mmes(model.obj, D = classify)
6. └─sommer:::predict_mmes_vcov_cpp(...)
── Error ('test-prediction_methods.R:929:2'): get_predictions works for sommer mmes models ──
<Rcpp::exception/C++Error/error/condition>
Error: The fitted model does not contain C. Refit with ai_mme_sp2() returning C.
Backtrace:
▆
1. └─biometryassist:::get_predictions.mmes(model_mmes, classify = "Env") at test-prediction_methods.R:929:9
2. ├─stats::predict(model.obj, D = classify)
3. └─sommer::predict.mmes(model.obj, D = classify)
4. └─sommer:::predict_mmes_vcov_cpp(...)
[ FAIL 2 | WARN 0 | SKIP 178 | PASS 2206 ]
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'
Error:
! Test failures.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc