Last updated on 2026-11-15 07:50:41 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 1.5.1 | 11.73 | 461.40 | 473.13 | OK | |
| r-devel-linux-x86_64-debian-gcc | 1.5.1 | 8.68 | 321.61 | 330.29 | OK | |
| r-devel-linux-x86_64-fedora-clang | 1.5.1 | 326.01 | OK | |||
| r-devel-linux-x86_64-fedora-gcc | 1.5.1 | 343.34 | ERROR | |||
| r-devel-windows-x86_64 | 1.5.1 | 20.00 | 337.00 | 357.00 | OK | |
| r-patched-linux-x86_64 | 1.5.1 | 12.98 | 442.32 | 455.30 | OK | |
| r-release-linux-x86_64 | 1.5.1 | 12.45 | 450.97 | 463.42 | OK | |
| r-release-macos-arm64 | 1.5.1 | 4.00 | 79.00 | 83.00 | OK | |
| r-release-macos-x86_64 | 1.5.1 | 12.00 | 348.00 | 360.00 | OK | |
| r-release-windows-x86_64 | 1.5.1 | 19.00 | 329.00 | 348.00 | OK | |
| r-oldrel-macos-arm64 | 1.5.1 | 5.00 | 98.00 | 103.00 | OK | |
| r-oldrel-macos-x86_64 | 1.5.1 | 11.00 | 333.00 | 344.00 | OK | |
| r-oldrel-windows-x86_64 | 1.5.1 | 25.00 | 452.00 | 477.00 | OK |
Version: 1.5.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [192s/139s]
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: 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: 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-1844.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-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).
> 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-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'
Saving _problems/test-prediction_methods-1071.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-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-resplot.R: Contrasts set to contr.sum for the following variables: treatment, gender
> test-utility_functions.R: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> test-utility_functions.R: | biometryassist version 1.5.1
> test-utility_functions.R: |
> 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 2 | WARN 0 | SKIP 182 | PASS 2242 ]
══ Skipped tests (182) ═════════════════════════════════════════════════════════
• On CRAN (164): '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:1638:1', 'test-mct.R:1664:1', 'test-mct.R:1692:1',
'test-mct.R:1736:1', 'test-mct.R:1780:1', 'test-mct.R:1808:1',
'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:176:1', 'test-resplot.R:187:1',
'test-resplot.R:249:1', 'test-resplot.R:265:1', 'test-resplot.R:301:1',
'test-resplot.R:338:1', 'test-resplot.R:377:1', 'test-resplot.R:396:1'
• On Linux (2): 'test-resplot.R:204:2', 'test-resplot.R:369:2'
• 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: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'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-mct.R:1838:2'): sommer mmes model is supported ─────────────────
Error in `mmes(Yield ~ Env, random = ~Name + Env:Name, rcov = ~units, data = model_mmes$data, verbose = FALSE)`: unused argument (verbose = FALSE)
── Error ('test-prediction_methods.R:1065:2'): get_predictions works for sommer mmes models ──
Error in `mmes(Yield ~ Env, random = ~Name + Env:Name, rcov = ~units, data = model_mmes$data, verbose = FALSE)`: unused argument (verbose = FALSE)
[ FAIL 2 | WARN 0 | SKIP 182 | PASS 2242 ]
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