Package check result: OK Changes to worse in reverse depends: Package: Platypus Check: examples New result: ERROR Running examples in ‘Platypus-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: GEX_coexpression_coefficient > ### Title: Coexpression of selected genes > ### Aliases: GEX_coexpression_coefficient > > ### ** Examples > > GEX_coexpression_coefficient(GEX = Platypus::small_vgm[[2]] + , genes = c("CD19", "CD83"), subsample.n = "none", plot.dotmap = FALSE) Error: ! The `slot` argument of `FetchData()` was deprecated in SeuratObject 5.0.0 and is now defunct. ℹ Please use the `layer` argument instead. Backtrace: ▆ 1. └─Platypus::GEX_coexpression_coefficient(...) 2. ├─SeuratObject::FetchData(GEX, vars = genes, slot = "counts") 3. └─SeuratObject:::FetchData.Seurat(GEX, vars = genes, slot = "counts") 4. └─SeuratObject::.Deprecate(...) 5. └─lifecycle::deprecate_stop(...) 6. └─lifecycle:::deprecate_stop0(msg) 7. └─rlang::cnd_signal(...) Execution halted Package: scpoisson Check: examples New result: ERROR Running examples in ‘scpoisson-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: LouvainDepart > ### Title: Louvain clustering using departure as data representation > ### Aliases: LouvainDepart > > ### ** Examples > > > set.seed(1234) > test_set <- matrix(rpois(500, 2), nrow = 20) > rownames(test_set) <- paste0("gene", 1:nrow(test_set)) > colnames(test_set) <- paste0("cell", 1:ncol(test_set)) > LouvainDepart(test_set) 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. ├─scpoisson::LouvainDepart(test_set) 2. └─scpoisson:::LouvainDepart.matrix(test_set) 3. ├─SeuratObject::SetAssayData(...) 4. └─SeuratObject:::SetAssayData.Assay(...) 5. └─SeuratObject::.Deprecate(...) 6. └─lifecycle::deprecate_stop(...) 7. └─lifecycle:::deprecate_stop0(msg) 8. └─rlang::cnd_signal(...) Execution halted Package: scpoisson Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘scpoissonmodel.Rmd’ using rmarkdown Quitting from scpoissonmodel.Rmd:78-85 [example3] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NULL ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'scpoissonmodel.Rmd' failed with diagnostics: The `slot` argument of `SetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct. ℹ Please use the `layer` argument instead. --- failed re-building ‘scpoissonmodel.Rmd’ SUMMARY: processing the following file failed: ‘scpoissonmodel.Rmd’ Error: Vignette re-building failed. Execution halted Package: SCpubr Check: tests New result: ERROR Running ‘testthat.R’ [63s/63s] 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 ── 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 ───────────── 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 ── 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 ── 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 ── 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$gene) 15. ├─tidyr::pivot_longer(...) 16. ├─dplyr::select(., -"cell") 17. ├─dplyr::left_join(...) 18. ├─tibble::rownames_to_column(., var = "cell") 19. ├─base::as.data.frame(.) 20. ├─base::t(.) 21. └─base::as.matrix(.) ── Error ('test-do_GroupwiseDEHeatmap.R:4:5'): do_GroupwiseDEHeatmap: CRAN essentials ── Error: The `slot` argument of `SetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct. i Please use the `layer` argument instead. Backtrace: ▆ 1. ├─base::suppressWarnings(...) at test-do_GroupwiseDEHeatmap.R:3:5 2. │ └─base::withCallingHandlers(...) 3. ├─SeuratObject::SetAssayData(...) at test-do_GroupwiseDEHeatmap.R:4:5 4. └─SeuratObject:::SetAssayData.Seurat(...) 5. └─SeuratObject::.Deprecate(...) 6. └─lifecycle::deprecate_stop(...) 7. └─lifecycle:::deprecate_stop0(msg) 8. └─rlang::cnd_signal(...) ── Error ('test-do_LoadingsHeatmap.R:8:5'): do_LoadingsHeatmap: CRAN essentials ── Error: The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct. i Please use the `layer` argument instead. Backtrace: ▆ 1. ├─SCpubr::do_LoadingsHeatmap(sample = sample, dims = 1:5) at test-do_LoadingsHeatmap.R:8:5 2. │ ├─base::suppressWarnings(...) 3. │ │ └─base::withCallingHandlers(...) 4. │ └─... %>% ... 5. ├─dplyr::mutate(., Gene = factor(.data$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 ── 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 ── 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 ──────────── 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 ── 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 ────────── 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 ────────────── 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 Package: Seurat Check: examples New result: ERROR Running examples in ‘Seurat-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: CustomDistance > ### Title: Run a custom distance function on an input data matrix > ### Aliases: CustomDistance > > ### ** Examples > > data("pbmc_small") > # Define custom distance matrix > manhattan.distance <- function(x, y) return(sum(abs(x-y))) > > input.data <- GetAssayData(pbmc_small, assay.type = "RNA", slot = "scale.data") Warning: The following arguments are not used: assay.type 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. ├─SeuratObject::GetAssayData(pbmc_small, assay.type = "RNA", slot = "scale.data") 2. └─SeuratObject:::GetAssayData.Seurat(...) 3. └─SeuratObject::.Deprecate(...) 4. └─lifecycle::deprecate_stop(...) 5. └─lifecycle:::deprecate_stop0(msg) 6. └─rlang::cnd_signal(...) Execution halted Package: Seurat Check: tests New result: ERROR Running ‘testthat.R’ [160s/160s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(Seurat) Loading required package: SeuratObject Loading required package: sp Attaching package: 'SeuratObject' The following objects are masked from 'package:base': intersect, t > # > # # Run tests for 'v3' > # message('Run tests for v3 assay') > # options(Seurat.object.assay.version = 'v3') > # test_check("Seurat") > > # Run tests for 'v5' > message('Run tests for v5 assay') Run tests for v5 assay > options(Seurat.object.assay.version = 'v5') > test_check("Seurat") | | | 0% | |======================================================================| 100% Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 80 Number of edges: 525 Running Louvain algorithm... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.8255 Number of communities: 6 Elapsed time: 0 seconds Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 80 Number of edges: 525 Running Louvain algorithm... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.8255 Number of communities: 6 Elapsed time: 0 seconds Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 80 Number of edges: 525 Running Louvain algorithm with multilevel refinement... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.8255 Number of communities: 6 Elapsed time: 0 seconds Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 80 Number of edges: 525 Running smart local moving algorithm... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: 0.8255 Number of communities: 6 Elapsed time: 0 seconds 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Saving _problems/test_preprocessing-197.R Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| | | | 0% | |======================================================================| 100% Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Number of nodes: 80 Number of edges: 2045 Running Louvain algorithm... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Maximum modularity in 10 random starts: -0.0613 Number of communities: 64 Elapsed time: 0 seconds Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% | | | 0% | |======================================================================| 100% Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% | | | 0% | |======================================================================| 100% Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% | | | 0% | |======================= | 33% | |=============================================== | 67% | |======================================================================| 100% | | | 0% | |======================================================================| 100% Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| | | | 0% | |======== | 11% | |================ | 22% | |======================= | 33% | |=============================== | 44% | |======================================= | 56% | |=============================================== | 67% | |====================================================== | 78% | |============================================================== | 89% | |======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======== | 11% | |================ | 22% | |======================= | 33% | |=============================== | 44% 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|======================================================================| 100% | | | 0% | |======================================================================| 100% | | | 0% | |======================================================================| 100% [ FAIL 1 | WARN 0 | SKIP 24 | PASS 700 ] ══ Skipped tests (24) ══════════════════════════════════════════════════════════ • On CRAN (24): 'test_differential_expression.R:307:3', 'test_differential_expression.R:349:3', 'test_differential_expression.R:455:3', 'test_integratedata.R:111:3', 'test_integration.R:74:3', 'test_integration.R:105:3', 'test_integration.R:136:3', 'test_integration.R:170:3', 'test_integration.R:202:3', 'test_integration.R:234:3', 'test_integration.R:264:3', 'test_integration.R:306:3', 'test_integration.R:335:3', 'test_integration.R:365:3', 'test_integration5.R:38:3', 'test_integration5.R:331:3', 'test_objects.R:6:3', 'test_preprocessing.R:140:3', 'test_preprocessing.R:158:3', 'test_transferdata.R:65:3', 'test_transferdata.R:88:3', 'test_transferdata.R:100:3', 'test_transferdata.R:112:3', 'test_transferdata.R:128:3' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Error ('test_preprocessing.R:192:1'): (code run outside of `test_that()`) ─── 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. ├─SeuratObject::SetAssayData(...) at test_preprocessing.R:192:1 2. └─SeuratObject:::SetAssayData.Seurat(...) 3. └─SeuratObject::.Deprecate(...) 4. └─lifecycle::deprecate_stop(...) 5. └─lifecycle:::deprecate_stop0(msg) 6. └─rlang::cnd_signal(...) [ FAIL 1 | WARN 0 | SKIP 24 | PASS 700 ] Error: ! Test failures. Execution halted Package: SpaTopic Check: whether package can be installed New result: ERROR Installation failed. Package: XYomics Check: re-building of vignette outputs New result: ERROR Error(s) in re-building vignettes: ... --- re-building ‘XYomics_bulk_example.Rmd’ using rmarkdown [WARNING] Deprecated: --highlight-style. Use --syntax-highlighting instead. --- finished re-building ‘XYomics_bulk_example.Rmd’ --- re-building ‘XYomics_sc_example.Rmd’ using rmarkdown Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Performing log-normalization 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating gene variances 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Calculating feature variances of standardized and clipped values 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| | | | 0% | |======================================================================| 100% 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Quitting from XYomics_sc_example.Rmd:146-154 [sex-interaction-analysis] ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NULL ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Error: processing vignette 'XYomics_sc_example.Rmd' failed with diagnostics: The `slot` argument of `GetAssayData()` was deprecated in SeuratObject 5.0.0 and is now defunct. ℹ Please use the `layer` argument instead. --- failed re-building ‘XYomics_sc_example.Rmd’ SUMMARY: processing the following file failed: ‘XYomics_sc_example.Rmd’ Error: Vignette re-building failed. Execution halted