R Under development (unstable) (2025-08-18 r88641 ucrt) -- "Unsuffered Consequences"
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Platform: x86_64-w64-mingw32/x64

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> # 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")

[ FAIL 4 | WARN 8 | SKIP 411 | PASS 100 ]

══ Skipped tests (411) ═════════════════════════════════════════════════════════
• On CRAN (411): '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:19:5',
  'test-do_NebulosaPlot.R:102:5', 'test-do_NebulosaPlot.R:112:5',
  'test-do_NebulosaPlot.R:122:5', 'test-do_NebulosaPlot.R:134:5',
  'test-do_NebulosaPlot.R:143:5', 'test-do_NebulosaPlot.R:152:5',
  'test-do_NebulosaPlot.R:161:5', 'test-do_NebulosaPlot.R:171:5',
  'test-do_NebulosaPlot.R:185:5', 'test-do_NebulosaPlot.R:194:5',
  'test-do_NebulosaPlot.R:204:5', 'test-do_NebulosaPlot.R:215:5',
  'test-do_NebulosaPlot.R:227:5', 'test-do_NebulosaPlot.R:239:5',
  'test-do_NebulosaPlot.R:252:5', 'test-do_NebulosaPlot.R:262:5',
  'test-do_NebulosaPlot.R:272:5', 'test-do_NebulosaPlot.R:282:5',
  'test-do_NebulosaPlot.R:292:5', 'test-do_NebulosaPlot.R:302:5',
  'test-do_NebulosaPlot.R:314:5', '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-do_WafflePlot.R:11:5',
  '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',
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  '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'

══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-do_CNVHeatmap.R:8:5'): do_BarPlot: CRAN essentials ───────────
`out` has type 'object', not 'list'.
── Error ('test-do_NebulosaPlot.R:3:5'): do_NebulosaPlot: CRAN essentials ──────
<subscriptOutOfBoundsError/error/condition>
Error in `S7::prop(x, "meta")[[i]]`: subscript out of bounds
Backtrace:
    ▆
 1. └─SCpubr::do_NebulosaPlot(sample = sample, features = "EPC1") at test-do_NebulosaPlot.R:3:5
 2.   ├─`*tmp*`[[counter]]
 3.   └─ggplot2 (local) `[[.ggplot2::gg`(`*tmp*`, counter)
── Failure ('test-do_PathwayActivityHeatmap.R:7:5'): do_PathwayActivityHeatmap: CRAN essentials ──
`out` has type 'object', not 'list'.
── Failure ('test-do_TFActivityHeatmap.R:6:5'): do_TFActivityHeatmap: PASS - minimal input ──
`out` has type 'object', not 'list'.

[ FAIL 4 | WARN 8 | SKIP 411 | PASS 100 ]
Error: Test failures
In addition: Warning message:
`aes_string()` was deprecated in ggplot2 3.0.0.
ℹ Please use tidy evaluation idioms with `aes()`.
ℹ See also `vignette("ggplot2-in-packages")` for more information.
ℹ The deprecated feature was likely used in the Seurat package.
  Please report the issue at <https://github.com/satijalab/seurat/issues>. 
Execution halted