Running ‘testthat.R’ [55s/67s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # nolint start
  > library(testthat)
  > library(SCpubr)
  
  
  ── SCpubr 3.0.0 ────────────────────────────────────────────────────────────────
  
  ℹ Have a look at extensive tutorials in SCpubr's book.
  
  ✔ If you use SCpubr in your research, please cite it accordingly.
  
  ★ If the package is useful to you, consider leaving a Star in the GitHub repository.
  
  ! Keep track of the package updates on Twitter (@Enblacar) or in the Official NEWS website.
  
  ♥ Happy plotting!
  
  
  
  ── Tips! ──
  
  ! Check missing dependencies with: SCpubr::do_PackageReport(extended = TRUE)
  
  ℹ To remove the white and black end from continuous palettes, use: options("SCpubr.ColorPaletteEnds" = FALSE)
  
  ℹ Colorblind-safe continuous/divergent color palettes are used by default.
  ℹ For categorical variables, you can use: colorblind = TRUE
  
  ✖ To suppress this startup message, use: suppressPackageStartupMessages(library(SCpubr))
  ✖ Alternatively, you can also set the following option: options("SCpubr.verbose" = FALSE)
    And then load the package normally (and faster) as: library(SCpubr)
  
  ────────────────────────────────────────────────────────────────────────────────
  > # nolint end
  > test_check("SCpubr")
  
  Saving _problems/test-do_ActivityHeatmap-13.R
  Saving _problems/test-do_CNVHeatmap-7.R
  Saving _problems/test-do_CellularStatesPlot-31.R
  Saving _problems/test-do_CorrelationHeatmap-10.R
  Saving _problems/test-do_ExpressionHeatmap-6.R
  Saving _problems/test-do_GroupwiseDEHeatmap-9.R
  Saving _problems/test-do_LoadingsHeatmap-9.R
  Saving _problems/test-do_PathwayActivityHeatmap-6.R
  Saving _problems/test-do_SCExpressionHeatmap-6.R
  Saving _problems/test-do_StripPlot-6.R
  Saving _problems/test-do_TFActivityHeatmap-5.R
  Saving _problems/test-do_ViolinPlot-5.R
  Saving _problems/test-utils-786.R
  [ FAIL 13 | WARN 2 | SKIP 411 | PASS 83 ]
  
  ══ Skipped tests (411) ═════════════════════════════════════════════════════════
  • On CRAN (410): 'test-do_ActivityHeatmap.R:29:5',
    'test-do_ActivityHeatmap.R:189:5', 'test-do_ActivityHeatmap.R:236:5',
    'test-do_ActivityHeatmap.R:272:5', 'test-do_ActivityHeatmap.R:336:5',
    'test-do_ActivityHeatmap.R:361:5', 'test-do_ActivityHeatmap.R:378:5',
    'test-do_ActivityHeatmap.R:394:5', 'test-do_ActivityHeatmap.R:410:5',
    'test-do_ActivityHeatmap.R:425:5', 'test-do_AlluvialPlot.R:14:5',
    'test-do_BarPlot.R:100:5', 'test-do_BarPlot.R:109:5',
    'test-do_BarPlot.R:120:5', 'test-do_BarPlot.R:133:5',
    'test-do_BarPlot.R:148:5', 'test-do_BarPlot.R:157:5',
    'test-do_BarPlot.R:166:5', 'test-do_BarPlot.R:174:5',
    'test-do_BarPlot.R:184:5', 'test-do_BarPlot.R:194:5',
    'test-do_BarPlot.R:206:5', 'test-do_BarPlot.R:235:5',
    'test-do_BarPlot.R:257:5', 'test-do_BarPlot.R:268:5',
    'test-do_BarPlot.R:283:5', 'test-do_BarPlot.R:295:5',
    'test-do_BarPlot.R:308:5', 'test-do_BeeSwarmPlot.R:18:5',
    'test-do_BeeSwarmPlot.R:40:5', 'test-do_BeeSwarmPlot.R:49:5',
    'test-do_BeeSwarmPlot.R:145:5', 'test-do_BeeSwarmPlot.R:156:5',
    'test-do_BeeSwarmPlot.R:165:5', 'test-do_BeeSwarmPlot.R:174:5',
    'test-do_BeeSwarmPlot.R:184:5', 'test-do_BeeSwarmPlot.R:196:5',
    'test-do_BeeSwarmPlot.R:205:5', 'test-do_BeeSwarmPlot.R:213:5',
    'test-do_BeeSwarmPlot.R:222:5', 'test-do_BeeSwarmPlot.R:231:5',
    'test-do_BeeSwarmPlot.R:241:5', 'test-do_BeeSwarmPlot.R:251:5',
    'test-do_BeeSwarmPlot.R:260:5', 'test-do_BeeSwarmPlot.R:269:5',
    'test-do_BeeSwarmPlot.R:286:5', 'test-do_BeeSwarmPlot.R:295:5',
    'test-do_BeeSwarmPlot.R:304:5', 'test-do_BeeSwarmPlot.R:313:5',
    'test-do_BeeSwarmPlot.R:322:5', 'test-do_BeeSwarmPlot.R:341:5',
    'test-do_BoxPlot.R:22:5', 'test-do_BoxPlot.R:62:5', 'test-do_BoxPlot.R:83:5',
    'test-do_BoxPlot.R:93:5', 'test-do_BoxPlot.R:101:5',
    'test-do_BoxPlot.R:110:5', 'test-do_BoxPlot.R:124:5',
    'test-do_BoxPlot.R:133:5', 'test-do_CNVHeatmap.R:13:5',
    'test-do_CNVHeatmap.R:115:5', 'test-do_CNVHeatmap.R:124:5',
    'test-do_CNVHeatmap.R:137:5', 'test-do_CNVHeatmap.R:150:5',
    'test-do_CNVHeatmap.R:171:5', 'test-do_CellularStatesPlot.R:50:5',
    'test-do_CellularStatesPlot.R:78:5', 'test-do_CellularStatesPlot.R:152:5',
    'test-do_CellularStatesPlot.R:284:5', 'test-do_CellularStatesPlot.R:305:5',
    'test-do_CellularStatesPlot.R:327:5', 'test-do_CellularStatesPlot.R:349:5',
    'test-do_CellularStatesPlot.R:415:5', 'test-do_CellularStatesPlot.R:436:5',
    'test-do_CellularStatesPlot.R:458:5', 'test-do_CellularStatesPlot.R:478:5',
    'test-do_CellularStatesPlot.R:499:5', 'test-do_CellularStatesPlot.R:519:5',
    'test-do_CellularStatesPlot.R:539:5', 'test-do_CellularStatesPlot.R:559:5',
    'test-do_CellularStatesPlot.R:580:5', 'test-do_CellularStatesPlot.R:598:5',
    'test-do_CellularStatesPlot.R:616:5', 'test-do_CellularStatesPlot.R:634:5',
    'test-do_CellularStatesPlot.R:653:5', 'test-do_CellularStatesPlot.R:683:5',
    'test-do_CellularStatesPlot.R:705:5', 'test-do_CellularStatesPlot.R:727:5',
    'test-do_CellularStatesPlot.R:746:5', 'test-do_CellularStatesPlot.R:765:5',
    'test-do_CellularStatesPlot.R:784:5', 'test-do_CellularStatesPlot.R:803:5',
    'test-do_CellularStatesPlot.R:835:5', 'test-do_CellularStatesPlot.R:858:5',
    'test-do_CellularStatesPlot.R:882:5', 'test-do_CellularStatesPlot.R:902:5',
    'test-do_CellularStatesPlot.R:922:5', 'test-do_CellularStatesPlot.R:942:5',
    'test-do_CellularStatesPlot.R:962:5', 'test-do_CellularStatesPlot.R:982:5',
    'test-do_ChordDiagramPlot.R:19:5', 'test-do_ChordDiagramPlot.R:40:5',
    'test-do_ChordDiagramPlot.R:141:5', 'test-do_ChordDiagramPlot.R:151:5',
    'test-do_ChordDiagramPlot.R:168:5', 'test-do_ChordDiagramPlot.R:179:5',
    'test-do_CorrelationHeatmap.R:16:5', 'test-do_CorrelationHeatmap.R:34:5',
    'test-do_CorrelationHeatmap.R:58:5', 'test-do_CorrelationHeatmap.R:99:5',
    'test-do_DimPlot.R:19:5', 'test-do_DimPlot.R:27:5',
    'test-do_DimPlot.R:134:5', 'test-do_DimPlot.R:170:5',
    'test-do_DimPlot.R:191:5', 'test-do_DimPlot.R:211:5',
    'test-do_DimPlot.R:246:5', 'test-do_DimPlot.R:258:5',
    'test-do_DimPlot.R:268:5', 'test-do_DimPlot.R:278:5',
    'test-do_DimPlot.R:298:5', 'test-do_DimPlot.R:307:5',
    'test-do_DimPlot.R:316:5', 'test-do_DimPlot.R:325:5',
    'test-do_DimPlot.R:334:5', 'test-do_DimPlot.R:341:5',
    'test-do_DimPlot.R:352:5', 'test-do_DimPlot.R:360:5',
    'test-do_DimPlot.R:368:5', 'test-do_DimPlot.R:376:5',
    'test-do_DimPlot.R:384:5', 'test-do_DimPlot.R:392:5',
    'test-do_DimPlot.R:400:5', 'test-do_DimPlot.R:424:5',
    'test-do_DimPlot.R:432:5', 'test-do_DimPlot.R:440:5',
    'test-do_DimPlot.R:448:5', 'test-do_DimPlot.R:456:5',
    'test-do_DimPlot.R:463:5', 'test-do_DimPlot.R:470:5',
    'test-do_DimPlot.R:477:5', 'test-do_DimPlot.R:484:5',
    'test-do_DimPlot.R:501:5', 'test-do_DimPlot.R:509:5',
    'test-do_DimPlot.R:517:5', 'test-do_DimPlot.R:524:5',
    'test-do_DimPlot.R:531:5', 'test-do_DimPlot.R:538:5',
    'test-do_DimPlot.R:546:5', 'test-do_DimPlot.R:557:5',
    'test-do_DimPlot.R:566:5', 'test-do_DimPlot.R:575:5',
    'test-do_DimPlot.R:585:5', 'test-do_DimPlot.R:596:5',
    'test-do_DimPlot.R:605:5', 'test-do_DimPlot.R:614:5',
    'test-do_DotPlot.R:12:5', 'test-do_DotPlot.R:97:5',
    'test-do_DotPlot.R:112:5', 'test-do_DotPlot.R:122:5',
    'test-do_DotPlot.R:132:5', 'test-do_DotPlot.R:146:5',
    'test-do_DotPlot.R:157:5', 'test-do_DotPlot.R:168:5',
    'test-do_DotPlot.R:179:5', 'test-do_DotPlot.R:189:5',
    'test-do_DotPlot.R:199:5', 'test-do_DotPlot.R:211:5',
    'test-do_DotPlot.R:227:5', 'test-do_EnrichmentHeatmap.R:19:5',
    'test-do_EnrichmentHeatmap.R:194:5', 'test-do_EnrichmentHeatmap.R:225:5',
    'test-do_EnrichmentHeatmap.R:242:5', 'test-do_EnrichmentHeatmap.R:276:5',
    'test-do_EnrichmentHeatmap.R:315:5', 'test-do_EnrichmentHeatmap.R:338:5',
    'test-do_EnrichmentHeatmap.R:357:5', 'test-do_ExpressionHeatmap.R:12:5',
    'test-do_ExpressionHeatmap.R:157:5', 'test-do_ExpressionHeatmap.R:175:5',
    'test-do_ExpressionHeatmap.R:193:5', 'test-do_ExpressionHeatmap.R:222:5',
    'test-do_FeaturePlot.R:15:5', 'test-do_FeaturePlot.R:29:5',
    'test-do_FeaturePlot.R:434:5', 'test-do_FeaturePlot.R:475:5',
    'test-do_FeaturePlot.R:582:5', 'test-do_FeaturePlot.R:603:5',
    'test-do_FeaturePlot.R:621:5', 'test-do_FeaturePlot.R:638:5',
    'test-do_FeaturePlot.R:647:5', 'test-do_FeaturePlot.R:657:5',
    'test-do_FeaturePlot.R:667:5', 'test-do_FeaturePlot.R:677:5',
    'test-do_FeaturePlot.R:687:5', 'test-do_FeaturePlot.R:697:5',
    'test-do_FeaturePlot.R:707:5', 'test-do_FeaturePlot.R:717:5',
    'test-do_FeaturePlot.R:728:5', 'test-do_FeaturePlot.R:738:5',
    'test-do_FeaturePlot.R:750:5', 'test-do_FeaturePlot.R:760:5',
    'test-do_FeaturePlot.R:771:5', 'test-do_FeaturePlot.R:782:5',
    'test-do_FeaturePlot.R:792:5', 'test-do_FeaturePlot.R:800:5',
    'test-do_FeaturePlot.R:815:5', 'test-do_FeaturePlot.R:826:5',
    'test-do_FeaturePlot.R:840:5', 'test-do_FeaturePlot.R:851:5',
    'test-do_FeaturePlot.R:860:5', 'test-do_FeaturePlot.R:871:5',
    'test-do_FeaturePlot.R:884:5', 'test-do_FeaturePlot.R:895:5',
    'test-do_FeaturePlot.R:910:5', 'test-do_FeaturePlot.R:920:5',
    'test-do_FeaturePlot.R:930:5', 'test-do_FeaturePlot.R:942:5',
    'test-do_FeaturePlot.R:953:5', 'test-do_FeaturePlot.R:966:5',
    'test-do_FeaturePlot.R:975:5', 'test-do_FeaturePlot.R:983:5',
    'test-do_FeaturePlot.R:992:5', 'test-do_FeaturePlot.R:1013:5',
    'test-do_GroupwiseDEHeatmap.R:26:5', 'test-do_GroupwiseDEHeatmap.R:157:5',
    'test-do_GroupwiseDEHeatmap.R:185:5', 'test-do_GroupwiseDEHeatmap.R:195:5',
    'test-do_LigandReceptorPlot.R:8:5', 'test-do_LigandReceptorPlot.R:348:5',
    'test-do_LigandReceptorPlot.R:356:5', 'test-do_LigandReceptorPlot.R:367:5',
    'test-do_LigandReceptorPlot.R:383:5', 'test-do_LigandReceptorPlot.R:399:5',
    'test-do_LigandReceptorPlot.R:412:5', 'test-do_LoadingsHeatmap.R:16:5',
    'test-do_MetadataHeatmap.R:16:5', 'test-do_NebulosaPlot.R:4:5',
    'test-do_NebulosaPlot.R:99:5', 'test-do_NebulosaPlot.R:109:5',
    'test-do_NebulosaPlot.R:119:5', 'test-do_NebulosaPlot.R:131:5',
    'test-do_NebulosaPlot.R:140:5', 'test-do_NebulosaPlot.R:149:5',
    'test-do_NebulosaPlot.R:158:5', 'test-do_NebulosaPlot.R:168:5',
    'test-do_NebulosaPlot.R:182:5', 'test-do_NebulosaPlot.R:191:5',
    'test-do_NebulosaPlot.R:201:5', 'test-do_NebulosaPlot.R:212:5',
    'test-do_NebulosaPlot.R:224:5', 'test-do_NebulosaPlot.R:236:5',
    'test-do_NebulosaPlot.R:249:5', 'test-do_NebulosaPlot.R:259:5',
    'test-do_NebulosaPlot.R:269:5', 'test-do_NebulosaPlot.R:279:5',
    'test-do_NebulosaPlot.R:289:5', 'test-do_NebulosaPlot.R:299:5',
    'test-do_NebulosaPlot.R:311:5', 'test-do_PathwayActivityHeatmap.R:12:5',
    'test-do_PathwayActivityHeatmap.R:84:5',
    'test-do_PathwayActivityHeatmap.R:96:5',
    'test-do_PathwayActivityHeatmap.R:135:5',
    'test-do_RankedEnrichmentHeatmap.R:22:5',
    'test-do_RankedExpressionHeatmap.R:18:5', 'test-do_RidgePlot.R:22:5',
    'test-do_RidgePlot.R:104:5', 'test-do_RidgePlot.R:132:5',
    'test-do_RidgePlot.R:142:5', 'test-do_RidgePlot.R:159:5',
    'test-do_RidgePlot.R:172:5', 'test-do_SCEnrichmentHeatmap.R:20:5',
    'test-do_SCExpressionHeatmap.R:13:5', 'test-do_StripPlot.R:18:5',
    'test-do_StripPlot.R:64:5', 'test-do_StripPlot.R:93:5',
    'test-do_StripPlot.R:154:5', 'test-do_StripPlot.R:170:5',
    'test-do_StripPlot.R:189:5', 'test-do_StripPlot.R:208:5',
    'test-do_StripPlot.R:225:5', 'test-do_StripPlot.R:242:5',
    'test-do_StripPlot.R:262:5', 'test-do_StripPlot.R:280:5',
    'test-do_StripPlot.R:293:5', 'test-do_TFActivityHeatmap.R:11:5',
    'test-do_TFActivityHeatmap.R:84:5', 'test-do_TFActivityHeatmap.R:97:5',
    'test-do_TFActivityHeatmap.R:111:5', 'test-do_TermEnrichmentPlot.R:12:5',
    'test-do_TermEnrichmentPlot.R:19:5', 'test-do_TermEnrichmentPlot.R:27:5',
    'test-do_TermEnrichmentPlot.R:35:5', 'test-do_TermEnrichmentPlot.R:44:5',
    'test-do_TermEnrichmentPlot.R:58:5', 'test-do_TermEnrichmentPlot.R:65:5',
    'test-do_TermEnrichmentPlot.R:72:5', 'test-do_ViolinPlot.R:15:5',
    'test-do_ViolinPlot.R:30:5', 'test-do_ViolinPlot.R:43:5',
    'test-do_ViolinPlot.R:55:5', 'test-do_ViolinPlot.R:71:5',
    'test-do_ViolinPlot.R:100:5', 'test-do_ViolinPlot.R:119:5',
    'test-do_ViolinPlot.R:129:5', 'test-do_ViolinPlot.R:139:5',
    'test-do_ViolinPlot.R:152:5', 'test-do_ViolinPlot.R:164:5',
    'test-do_ViolinPlot.R:176:5', 'test-do_ViolinPlot.R:188:5',
    'test-do_ViolinPlot.R:211:5', 'test-do_ViolinPlot.R:224:5',
    'test-do_ViolinPlot.R:249:5', 'test-do_ViolinPlot.R:273:5',
    'test-do_ViolinPlot.R:286:5', 'test-do_ViolinPlot.R:304:5',
    'test-do_ViolinPlot.R:313:5', 'test-do_VolcanoPlot.R:12:5',
    'test-do_VolcanoPlot.R:39:5', 'test-do_VolcanoPlot.R:49:5',
    'test-do_VolcanoPlot.R:64:5', 'test-do_VolcanoPlot.R:79:5',
    'test-do_VolcanoPlot.R:102:5', 'test-utils.R:4:5', 'test-utils.R:9:5',
    'test-utils.R:14:5', 'test-utils.R:19:5', 'test-utils.R:30:5',
    'test-utils.R:42:5', 'test-utils.R:47:5', 'test-utils.R:56:5',
    'test-utils.R:62:5', 'test-utils.R:67:5', 'test-utils.R:72:5',
    'test-utils.R:82:5', 'test-utils.R:91:5', 'test-utils.R:100:5',
    'test-utils.R:109:5', 'test-utils.R:125:5', 'test-utils.R:136:5',
    'test-utils.R:155:5', 'test-utils.R:163:5', 'test-utils.R:172:5',
    'test-utils.R:183:5', 'test-utils.R:191:5', 'test-utils.R:199:5',
    'test-utils.R:207:5', 'test-utils.R:216:5', 'test-utils.R:225:5',
    'test-utils.R:234:5', 'test-utils.R:243:5', 'test-utils.R:257:5',
    'test-utils.R:269:5', 'test-utils.R:280:5', 'test-utils.R:290:5',
    'test-utils.R:302:5', 'test-utils.R:311:5', 'test-utils.R:320:5',
    'test-utils.R:329:5', 'test-utils.R:340:5', 'test-utils.R:351:5',
    'test-utils.R:365:5', 'test-utils.R:373:5', 'test-utils.R:382:5',
    'test-utils.R:391:5', 'test-utils.R:404:5', 'test-utils.R:411:5',
    'test-utils.R:421:5', 'test-utils.R:432:5', 'test-utils.R:438:5',
    'test-utils.R:448:5', 'test-utils.R:457:5', 'test-utils.R:472:5',
    'test-utils.R:479:5', 'test-utils.R:486:5', 'test-utils.R:493:5',
    'test-utils.R:503:5', 'test-utils.R:511:5', 'test-utils.R:519:5',
    'test-utils.R:529:5', 'test-utils.R:536:5', 'test-utils.R:546:5',
    'test-utils.R:553:5', 'test-utils.R:561:5', 'test-utils.R:569:5',
    'test-utils.R:581:5', 'test-utils.R:589:5', 'test-utils.R:596:5',
    'test-utils.R:604:5', 'test-utils.R:611:5', 'test-utils.R:619:5',
    'test-utils.R:626:5', 'test-utils.R:634:5', 'test-utils.R:641:5',
    'test-utils.R:652:5', 'test-utils.R:657:5', 'test-utils.R:669:5',
    'test-utils.R:677:5', 'test-utils.R:684:5', 'test-utils.R:694:5',
    'test-utils.R:701:5', 'test-utils.R:756:5', 'test-utils.R:768:5',
    'test-utils.R:800:5', 'test-utils.R:809:5', 'test-utils.R:832:5',
    'test-utils.R:850:5', 'test-utils.R:860:5', 'test-utils.R:882:5',
    'test-utils.R:889:5'
  • empty test (1):
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test-do_ActivityHeatmap.R:8:5'): do_ActivityHeatmap: CRAN essentials ──
  <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
  Error: The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct.
  i Please use the `layer` argument instead.
  Backtrace:
      ▆
   1. └─SCpubr::do_ActivityHeatmap(...) at test-do_ActivityHeatmap.R:8:5
   2.   ├─base::suppressWarnings(...)
   3.   │ └─base::withCallingHandlers(...)
   4.   ├─SeuratObject::GetAssayData(sample, assay = assay, slot = slot)
   5.   └─SeuratObject:::GetAssayData.Seurat(sample, assay = assay, slot = slot)
   6.     └─SeuratObject::.Deprecate(...)
   7.       └─lifecycle::deprecate_stop(...)
   8.         └─lifecycle:::deprecate_stop0(msg)
   9.           └─rlang::cnd_signal(...)
  ── Error ('test-do_CNVHeatmap.R:4:5'): do_BarPlot: CRAN essentials ─────────────
  <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
  Error: The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct.
  i Please use the `layer` argument instead.
  Backtrace:
       ▆
    1. ├─SCpubr::do_CNVHeatmap(...) at test-do_CNVHeatmap.R:4:5
    2. │ ├─base::suppressWarnings(...)
    3. │ │ └─base::withCallingHandlers(...)
    4. │ ├─... %>% ...
    5. │ ├─SeuratObject::GetAssayData(...)
    6. │ └─SeuratObject:::GetAssayData.Seurat(...)
    7. │   └─SeuratObject::.Deprecate(...)
    8. │     └─lifecycle::deprecate_stop(...)
    9. │       └─lifecycle:::deprecate_stop0(msg)
   10. │         └─rlang::cnd_signal(...)
   11. ├─dplyr::summarise(., mean = mean(.data$CNV_score, na.rm = TRUE))
   12. ├─dplyr::group_by(., .data[[group]], .data$Event)
   13. ├─tidyr::pivot_longer(...)
   14. ├─dplyr::left_join(...)
   15. ├─tibble::rownames_to_column(., var = "Cell")
   16. ├─base::as.data.frame(.)
   17. ├─base::t(.)
   18. └─base::as.matrix(.)
  ── Error ('test-do_CellularStatesPlot.R:21:5'): do_CellularStatesPlot: CRAN essentials ──
  <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
  Error: The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct.
  i Please use the `layer` argument instead.
  Backtrace:
       ▆
    1. └─SCpubr::do_CellularStatesPlot(...) at test-do_CellularStatesPlot.R:21:5
    2.   └─SCpubr::do_FeaturePlot(...)
    3.     └─SCpubr:::compute_scales(...)
    4.       └─SCpubr:::compute_scale_limits(...)
    5.         ├─base::suppressWarnings(...)
    6.         │ └─base::withCallingHandlers(...)
    7.         ├─SeuratObject::GetAssayData(sample, assay = assay, slot = slot)
    8.         └─SeuratObject:::GetAssayData.Seurat(sample, assay = assay, slot = slot)
    9.           └─SeuratObject::.Deprecate(...)
   10.             └─lifecycle::deprecate_stop(...)
   11.               └─lifecycle:::deprecate_stop0(msg)
   12.                 └─rlang::cnd_signal(...)
  ── Error ('test-do_CorrelationHeatmap.R:10:5'): do_CorrelationHeatmap: CRAN essentials ──
  <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
  Error: The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct.
  i Please use the `layer` argument instead.
  Backtrace:
       ▆
    1. └─SCpubr::do_CorrelationHeatmap(sample = sample, legend.position = "top") at test-do_CorrelationHeatmap.R:10:5
    2.   ├─base::suppressWarnings(...)
    3.   │ └─base::withCallingHandlers(...)
    4.   ├─base::rownames(...)
    5.   │ └─dimnames(x)[[1L]] %||% ...
    6.   ├─SeuratObject::GetAssayData(object = sample, assay = assay, slot = "data")
    7.   └─SeuratObject:::GetAssayData.Seurat(...)
    8.     └─SeuratObject::.Deprecate(...)
    9.       └─lifecycle::deprecate_stop(...)
   10.         └─lifecycle:::deprecate_stop0(msg)
   11.           └─rlang::cnd_signal(...)
  ── Error ('test-do_ExpressionHeatmap.R:5:5'): do_ExpressionHeatmap: CRAN essential tests ──
  <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
  Error: The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct.
  i Please use the `layer` argument instead.
  Backtrace:
       ▆
    1. ├─SCpubr::do_ExpressionHeatmap(sample, features = rownames(sample)[1:5]) at test-do_ExpressionHeatmap.R:5:5
    2. │ ├─base::suppressMessages(...)
    3. │ │ └─base::withCallingHandlers(...)
    4. │ ├─base::suppressWarnings(...)
    5. │ │ └─base::withCallingHandlers(...)
    6. │ ├─... %>% ...
    7. │ ├─SeuratObject::GetAssayData(sample, assay = assay, slot = slot)
    8. │ └─SeuratObject:::GetAssayData.Seurat(sample, assay = assay, slot = slot)
    9. │   └─SeuratObject::.Deprecate(...)
   10. │     └─lifecycle::deprecate_stop(...)
   11. │       └─lifecycle:::deprecate_stop0(msg)
   12. │         └─rlang::cnd_signal(...)
   13. ├─dplyr::summarise(., mean = mean(.data$expression, na.rm = TRUE))
   14. ├─dplyr::group_by(., .data$group.by, .data$gene)
   15. ├─tidyr::pivot_longer(...)
   16. ├─dplyr::select(., -"cell")
   17. ├─dplyr::left_join(...)
   18. ├─tibble::rownames_to_column(., var = "cell")
   19. ├─base::as.data.frame(.)
   20. ├─base::t(.)
   21. └─base::as.matrix(.)
  ── Error ('test-do_GroupwiseDEHeatmap.R:4:5'): do_GroupwiseDEHeatmap: CRAN essentials ──
  <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
  Error: The `slot` argument of `SetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct.
  i Please use the `layer` argument instead.
  Backtrace:
      ▆
   1. ├─base::suppressWarnings(...) at test-do_GroupwiseDEHeatmap.R:3:5
   2. │ └─base::withCallingHandlers(...)
   3. ├─SeuratObject::SetAssayData(...) at test-do_GroupwiseDEHeatmap.R:4:5
   4. └─SeuratObject:::SetAssayData.Seurat(...)
   5.   └─SeuratObject::.Deprecate(...)
   6.     └─lifecycle::deprecate_stop(...)
   7.       └─lifecycle:::deprecate_stop0(msg)
   8.         └─rlang::cnd_signal(...)
  ── Error ('test-do_LoadingsHeatmap.R:8:5'): do_LoadingsHeatmap: CRAN essentials ──
  <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
  Error: The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct.
  i Please use the `layer` argument instead.
  Backtrace:
       ▆
    1. ├─SCpubr::do_LoadingsHeatmap(sample = sample, dims = 1:5) at test-do_LoadingsHeatmap.R:8:5
    2. │ ├─base::suppressWarnings(...)
    3. │ │ └─base::withCallingHandlers(...)
    4. │ └─... %>% ...
    5. ├─dplyr::mutate(., Gene = factor(.data$Gene, levels = genes.use))
    6. ├─dplyr::left_join(...)
    7. ├─dplyr:::left_join.data.frame(...)
    8. │ └─dplyr::auto_copy(x, y, copy = copy)
    9. │   ├─dplyr::same_src(x, y)
   10. │   └─dplyr:::same_src.data.frame(x, y)
   11. │     └─base::is.data.frame(y)
   12. ├─... %>% ...
   13. ├─tidyr::pivot_longer(...)
   14. ├─tibble::rownames_to_column(., var = "Cell")
   15. ├─base::as.data.frame(.)
   16. ├─base::t(.)
   17. ├─base::as.matrix(.)
   18. ├─SeuratObject::GetAssayData(sample, assay = assay, slot = slot)
   19. └─SeuratObject:::GetAssayData.Seurat(sample, assay = assay, slot = slot)
   20.   └─SeuratObject::.Deprecate(...)
   21.     └─lifecycle::deprecate_stop(...)
   22.       └─lifecycle:::deprecate_stop0(msg)
   23.         └─rlang::cnd_signal(...)
  ── Error ('test-do_PathwayActivityHeatmap.R:5:5'): do_PathwayActivityHeatmap: CRAN essentials ──
  <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
  Error: The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct.
  i Please use the `layer` argument instead.
  Backtrace:
       ▆
    1. ├─SCpubr::do_PathwayActivityHeatmap(sample = sample, activities = progeny_activities) at test-do_PathwayActivityHeatmap.R:5:5
    2. │ ├─base::suppressMessages(...)
    3. │ │ └─base::withCallingHandlers(...)
    4. │ ├─base::suppressWarnings(...)
    5. │ │ └─base::withCallingHandlers(...)
    6. │ ├─... %>% ...
    7. │ ├─base::t(...)
    8. │ ├─base::as.matrix(...)
    9. │ ├─SeuratObject::GetAssayData(...)
   10. │ └─SeuratObject:::GetAssayData.Seurat(...)
   11. │   └─SeuratObject::.Deprecate(...)
   12. │     └─lifecycle::deprecate_stop(...)
   13. │       └─lifecycle:::deprecate_stop0(msg)
   14. │         └─rlang::cnd_signal(...)
   15. ├─dplyr::summarise(., mean = mean(.data$score, na.rm = TRUE))
   16. ├─dplyr::group_by(., .data$group.by, .data$source)
   17. ├─tidyr::pivot_longer(...)
   18. ├─dplyr::select(., -"cell")
   19. ├─dplyr::left_join(...)
   20. ├─tibble::rownames_to_column(., var = "cell")
   21. └─base::as.data.frame(.)
  ── Error ('test-do_SCExpressionHeatmap.R:5:5'): do_SCExpressionHeatmap: CRAN essentials ──
  <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
  Error: The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct.
  i Please use the `layer` argument instead.
  Backtrace:
       ▆
    1. └─SCpubr::do_SCExpressionHeatmap(sample = sample, features = rownames(sample)[1:5]) at test-do_SCExpressionHeatmap.R:5:5
    2.   ├─base::suppressWarnings(...)
    3.   │ └─base::withCallingHandlers(...)
    4.   ├─base::rownames(...)
    5.   │ └─dimnames(x)[[1L]] %||% ...
    6.   ├─SeuratObject::GetAssayData(sample, slot = slot, assay = assay)
    7.   └─SeuratObject:::GetAssayData.Seurat(sample, slot = slot, assay = assay)
    8.     └─SeuratObject::.Deprecate(...)
    9.       └─lifecycle::deprecate_stop(...)
   10.         └─lifecycle:::deprecate_stop0(msg)
   11.           └─rlang::cnd_signal(...)
  ── Error ('test-do_StripPlot.R:5:5'): do_StripPlot: CRAN essentials ────────────
  <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
  Error: The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct.
  i Please use the `layer` argument instead.
  Backtrace:
       ▆
    1. ├─SCpubr::do_StripPlot(sample = sample, features = "EPC1") at test-do_StripPlot.R:5:5
    2. │ ├─base::suppressWarnings(...)
    3. │ │ └─base::withCallingHandlers(...)
    4. │ ├─... %>% ...
    5. │ ├─SeuratObject::GetAssayData(object = sample, assay = assay, slot = slot)
    6. │ └─SeuratObject:::GetAssayData.Seurat(...)
    7. │   └─SeuratObject::.Deprecate(...)
    8. │     └─lifecycle::deprecate_stop(...)
    9. │       └─lifecycle:::deprecate_stop0(msg)
   10. │         └─rlang::cnd_signal(...)
   11. ├─dplyr::left_join(...)
   12. ├─tibble::tibble(.)
   13. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)
   14. │   └─rlang::eval_tidy(xs[[j]], mask)
   15. ├─tibble::rownames_to_column(., var = "cell")
   16. ├─base::as.data.frame(.)
   17. ├─base::t(.)
   18. └─base::as.matrix(.)
  ── Error ('test-do_TFActivityHeatmap.R:4:5'): do_TFActivityHeatmap: PASS - minimal input ──
  <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
  Error: The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct.
  i Please use the `layer` argument instead.
  Backtrace:
       ▆
    1. ├─SCpubr::do_TFActivityHeatmap(sample = sample, activities = dorothea_activities) at test-do_TFActivityHeatmap.R:4:5
    2. │ ├─base::suppressMessages(...)
    3. │ │ └─base::withCallingHandlers(...)
    4. │ ├─base::suppressWarnings(...)
    5. │ │ └─base::withCallingHandlers(...)
    6. │ ├─... %>% ...
    7. │ ├─base::t(...)
    8. │ ├─base::as.matrix(...)
    9. │ ├─SeuratObject::GetAssayData(...)
   10. │ └─SeuratObject:::GetAssayData.Seurat(...)
   11. │   └─SeuratObject::.Deprecate(...)
   12. │     └─lifecycle::deprecate_stop(...)
   13. │       └─lifecycle:::deprecate_stop0(msg)
   14. │         └─rlang::cnd_signal(...)
   15. ├─dplyr::summarise(., mean = mean(.data$score, na.rm = TRUE))
   16. ├─dplyr::group_by(., .data$group.by, .data$source)
   17. ├─tidyr::pivot_longer(...)
   18. ├─dplyr::select(., -"cell")
   19. ├─dplyr::left_join(...)
   20. ├─tibble::rownames_to_column(., var = "cell")
   21. └─base::as.data.frame(.)
  ── Error ('test-do_ViolinPlot.R:4:5'): do_ViolinPlot: CRAN essentials ──────────
  <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
  Error: The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct.
  i Please use the `layer` argument instead.
  Backtrace:
       ▆
    1. ├─SCpubr::do_ViolinPlot(sample = sample, features = "EPC1") at test-do_ViolinPlot.R:4:5
    2. │ ├─base::append(...)
    3. │ └─SCpubr:::get_data_column(...)
    4. │   ├─base::suppressWarnings(...)
    5. │   │ └─base::withCallingHandlers(...)
    6. │   ├─... %>% dplyr::rename(feature = dplyr::all_of(c(feature)))
    7. │   ├─SeuratObject::GetAssayData(object = sample, assay = assay, slot = slot)
    8. │   └─SeuratObject:::GetAssayData.Seurat(...)
    9. │     └─SeuratObject::.Deprecate(...)
   10. │       └─lifecycle::deprecate_stop(...)
   11. │         └─lifecycle:::deprecate_stop0(msg)
   12. │           └─rlang::cnd_signal(...)
   13. ├─dplyr::rename(., feature = dplyr::all_of(c(feature)))
   14. ├─tibble::rownames_to_column(., var = "cell")
   15. ├─base::as.data.frame(.)
   16. ├─base::t(.)
   17. └─base::as.matrix(.)
  ── Error ('test-utils.R:786:5'): utils: add_scale - PASS - checks ──────────────
  <lifecycle_error_deprecated/defunctError/rlang_error/error/condition>
  Error: The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct.
  i Please use the `layer` argument instead.
  Backtrace:
       ▆
    1. └─SCpubr::do_FeaturePlot(sample, features = "EPC1") at test-utils.R:786:5
    2.   └─SCpubr:::compute_scales(...)
    3.     └─SCpubr:::compute_scale_limits(...)
    4.       ├─base::suppressWarnings(...)
    5.       │ └─base::withCallingHandlers(...)
    6.       ├─SeuratObject::GetAssayData(sample, assay = assay, slot = slot)
    7.       └─SeuratObject:::GetAssayData.Seurat(sample, assay = assay, slot = slot)
    8.         └─SeuratObject::.Deprecate(...)
    9.           └─lifecycle::deprecate_stop(...)
   10.             └─lifecycle:::deprecate_stop0(msg)
   11.               └─rlang::cnd_signal(...)
  
  [ FAIL 13 | WARN 2 | SKIP 411 | PASS 83 ]
  Error:
  ! Test failures.
  Execution halted