Last updated on 2023-10-01 08:52:10 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.0.1 | 15.34 | 303.35 | 318.69 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 2.0.1 | 13.34 | 224.65 | 237.99 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 2.0.1 | 399.21 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 2.0.1 | 407.34 | ERROR | |||
| r-devel-windows-x86_64 | 2.0.1 | 14.00 | 239.00 | 253.00 | ERROR | |
| r-patched-linux-x86_64 | 2.0.1 | 18.25 | 303.01 | 321.26 | OK | |
| r-release-linux-x86_64 | 2.0.1 | 16.63 | 282.07 | 298.70 | ERROR | |
| r-release-macos-arm64 | 2.0.1 | 123.00 | NOTE | |||
| r-release-macos-x86_64 | 2.0.1 | 270.00 | NOTE | |||
| r-release-windows-x86_64 | 2.0.1 | 14.00 | 298.00 | 312.00 | ERROR | |
| r-oldrel-macos-arm64 | 2.0.1 | 120.00 | NOTE | |||
| r-oldrel-macos-x86_64 | 2.0.1 | 162.00 | NOTE | |||
| r-oldrel-windows-x86_64 | 2.0.1 | 21.00 | 285.00 | 306.00 | ERROR |
Version: 2.0.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [185s/249s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # nolint start
> library(testthat)
> library(SCpubr)
── SCpubr 2.0.1 ────────────────────────────────────────────────────────────────
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! ──
ℹ To remove the white and black end from continuous palettes, use: options("SCpubr.ColorPaletteEnds" = FALSE)
✖ 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")
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
The sp package is now running under evolution status 2
(status 2 uses the sf package in place of rgdal)
[ FAIL 10 | WARN 0 | SKIP 391 | PASS 75 ]
══ Skipped tests (391) ═════════════════════════════════════════════════════════
• On CRAN (391): 'test-do_AlluvialPlot.R:14:5', 'test-do_BarPlot.R:26:5',
'test-do_BarPlot.R:35:5', 'test-do_BarPlot.R:46:5', 'test-do_BarPlot.R:59:5',
'test-do_BarPlot.R:74:5', 'test-do_BarPlot.R:83:5', 'test-do_BarPlot.R:92:5',
'test-do_BarPlot.R:100:5', 'test-do_BarPlot.R:110:5',
'test-do_BarPlot.R:120:5', 'test-do_BarPlot.R:132:5',
'test-do_BarPlot.R:155:5', 'test-do_BarPlot.R:177:5',
'test-do_BarPlot.R:188:5', 'test-do_BarPlot.R:203:5',
'test-do_BarPlot.R:215:5', 'test-do_BarPlot.R:228:5',
'test-do_BeeSwarmPlot.R:18:5', 'test-do_BeeSwarmPlot.R:40:5',
'test-do_BeeSwarmPlot.R:49:5', 'test-do_BeeSwarmPlot.R:81:5',
'test-do_BeeSwarmPlot.R:92:5', 'test-do_BeeSwarmPlot.R:101:5',
'test-do_BeeSwarmPlot.R:110:5', 'test-do_BeeSwarmPlot.R:120:5',
'test-do_BeeSwarmPlot.R:132:5', 'test-do_BeeSwarmPlot.R:141:5',
'test-do_BeeSwarmPlot.R:149:5', 'test-do_BeeSwarmPlot.R:158:5',
'test-do_BeeSwarmPlot.R:167:5', 'test-do_BeeSwarmPlot.R:177:5',
'test-do_BeeSwarmPlot.R:187:5', 'test-do_BeeSwarmPlot.R:196:5',
'test-do_BeeSwarmPlot.R:205:5', 'test-do_BeeSwarmPlot.R:222:5',
'test-do_BeeSwarmPlot.R:231:5', 'test-do_BeeSwarmPlot.R:240:5',
'test-do_BeeSwarmPlot.R:249:5', 'test-do_BeeSwarmPlot.R:258:5',
'test-do_BeeSwarmPlot.R:277:5', 'test-do_BoxPlot.R:22:5',
'test-do_BoxPlot.R:41:5', 'test-do_BoxPlot.R:62:5', 'test-do_BoxPlot.R:72:5',
'test-do_BoxPlot.R:80:5', 'test-do_BoxPlot.R:89:5',
'test-do_BoxPlot.R:103:5', 'test-do_BoxPlot.R:112:5',
'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:49:5', 'test-do_ChordDiagramPlot.R:150:5',
'test-do_ChordDiagramPlot.R:160:5', 'test-do_ChordDiagramPlot.R:177:5',
'test-do_ChordDiagramPlot.R:188:5', 'test-do_CopyNumberVariantPlot.R:13:5',
'test-do_CopyNumberVariantPlot.R:74:5',
'test-do_CopyNumberVariantPlot.R:83:5',
'test-do_CopyNumberVariantPlot.R:96:5',
'test-do_CopyNumberVariantPlot.R:109:5',
'test-do_CopyNumberVariantPlot.R:130:5', 'test-do_CorrelationPlot.R:16:5',
'test-do_CorrelationPlot.R:34:5', 'test-do_CorrelationPlot.R:58:5',
'test-do_CorrelationPlot.R:70:5', '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:16:5',
'test-do_DotPlot.R:77:5', 'test-do_DotPlot.R:92:5',
'test-do_DotPlot.R:109:5', 'test-do_DotPlot.R:119:5',
'test-do_DotPlot.R:133:5', 'test-do_DotPlot.R:144:5',
'test-do_DotPlot.R:155:5', 'test-do_DotPlot.R:166:5',
'test-do_DotPlot.R:176:5', 'test-do_DotPlot.R:195:5',
'test-do_DotPlot.R:215:5', 'test-do_DotPlot.R:236:5',
'test-do_DotPlot.R:254:5', 'test-do_DotPlot.R:273:5',
'test-do_DotPlot.R:295:5', 'test-do_EnrichmentHeatmap.R:19:5',
'test-do_EnrichmentHeatmap.R:193:5', 'test-do_EnrichmentHeatmap.R:224:5',
'test-do_EnrichmentHeatmap.R:241:5', 'test-do_EnrichmentHeatmap.R:275:5',
'test-do_EnrichmentHeatmap.R:314:5', 'test-do_EnrichmentHeatmap.R:337:5',
'test-do_EnrichmentHeatmap.R:356:5', 'test-do_ExpressionHeatmap.R:12:5',
'test-do_ExpressionHeatmap.R:150:5', 'test-do_ExpressionHeatmap.R:168:5',
'test-do_ExpressionHeatmap.R:186:5', 'test-do_ExpressionHeatmap.R:215:5',
'test-do_FeaturePlot.R:15:5', 'test-do_FeaturePlot.R:24:5',
'test-do_FeaturePlot.R:429:5', 'test-do_FeaturePlot.R:470:5',
'test-do_FeaturePlot.R:577:5', 'test-do_FeaturePlot.R:598:5',
'test-do_FeaturePlot.R:616:5', 'test-do_FeaturePlot.R:633:5',
'test-do_FeaturePlot.R:642:5', 'test-do_FeaturePlot.R:652:5',
'test-do_FeaturePlot.R:662:5', 'test-do_FeaturePlot.R:672:5',
'test-do_FeaturePlot.R:682:5', 'test-do_FeaturePlot.R:692:5',
'test-do_FeaturePlot.R:702:5', 'test-do_FeaturePlot.R:712:5',
'test-do_FeaturePlot.R:723:5', 'test-do_FeaturePlot.R:733:5',
'test-do_FeaturePlot.R:745:5', 'test-do_FeaturePlot.R:755:5',
'test-do_FeaturePlot.R:766:5', 'test-do_FeaturePlot.R:777:5',
'test-do_FeaturePlot.R:787:5', 'test-do_FeaturePlot.R:795:5',
'test-do_FeaturePlot.R:810:5', 'test-do_FeaturePlot.R:821:5',
'test-do_FeaturePlot.R:835:5', 'test-do_FeaturePlot.R:846:5',
'test-do_FeaturePlot.R:855:5', 'test-do_FeaturePlot.R:866:5',
'test-do_FeaturePlot.R:879:5', 'test-do_FeaturePlot.R:890:5',
'test-do_FeaturePlot.R:905:5', 'test-do_FeaturePlot.R:915:5',
'test-do_FeaturePlot.R:925:5', 'test-do_FeaturePlot.R:937:5',
'test-do_FeaturePlot.R:948:5', 'test-do_FeaturePlot.R:961:5',
'test-do_FeaturePlot.R:970:5', 'test-do_FeaturePlot.R:978:5',
'test-do_FeaturePlot.R:987:5', 'test-do_FunctionalAnnotationPlot.R:15:5',
'test-do_GeyserPlot.R:18:5', 'test-do_GeyserPlot.R:64:5',
'test-do_GeyserPlot.R:93:5', 'test-do_GeyserPlot.R:154:5',
'test-do_GeyserPlot.R:170:5', 'test-do_GeyserPlot.R:189:5',
'test-do_GeyserPlot.R:208:5', 'test-do_GeyserPlot.R:225:5',
'test-do_GeyserPlot.R:242:5', 'test-do_GeyserPlot.R:262:5',
'test-do_GeyserPlot.R:280:5', 'test-do_GeyserPlot.R:293:5',
'test-do_GroupedGOTermPlot.R:16:5', 'test-do_GroupwiseDEPlot.R:24:5',
'test-do_GroupwiseDEPlot.R:107:5', 'test-do_GroupwiseDEPlot.R:133:5',
'test-do_GroupwiseDEPlot.R:157:5', 'test-do_GroupwiseDEPlot.R:179:5',
'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_PathwayActivityPlot.R:12:5', 'test-do_PathwayActivityPlot.R:66:5',
'test-do_PathwayActivityPlot.R:78:5', 'test-do_PathwayActivityPlot.R:117:5',
'test-do_RidgePlot.R:41:5', 'test-do_RidgePlot.R:137:5',
'test-do_RidgePlot.R:153:5', 'test-do_RidgePlot.R:163:5',
'test-do_RidgePlot.R:180:5', 'test-do_RidgePlot.R:190:5',
'test-do_RidgePlot.R:210:5', 'test-do_RidgePlot.R:230:5',
'test-do_RidgePlot.R:242:5', 'test-do_TFActivityPlot.R:11:5',
'test-do_TFActivityPlot.R:72:5', 'test-do_TFActivityPlot.R:85:5',
'test-do_TFActivityPlot.R:99:5', 'test-do_TermEnrichmentPlot.R:11:5',
'test-do_TermEnrichmentPlot.R:24:5', 'test-do_TermEnrichmentPlot.R:31:5',
'test-do_TermEnrichmentPlot.R:39:5', 'test-do_TermEnrichmentPlot.R:47:5',
'test-do_TermEnrichmentPlot.R:56:5', 'test-do_ViolinPlot.R:10:5',
'test-do_ViolinPlot.R:25:5', 'test-do_ViolinPlot.R:37:5',
'test-do_ViolinPlot.R:49:5', 'test-do_ViolinPlot.R:65:5',
'test-do_ViolinPlot.R:94:5', 'test-do_ViolinPlot.R:113:5',
'test-do_ViolinPlot.R:123:5', 'test-do_ViolinPlot.R:133:5',
'test-do_ViolinPlot.R:146:5', 'test-do_ViolinPlot.R:158:5',
'test-do_ViolinPlot.R:170:5', 'test-do_ViolinPlot.R:182:5',
'test-do_ViolinPlot.R:205:5', 'test-do_ViolinPlot.R:217:5',
'test-do_ViolinPlot.R:240:5', 'test-do_ViolinPlot.R:264:5',
'test-do_ViolinPlot.R:277:5', 'test-do_ViolinPlot.R:295:5',
'test-do_ViolinPlot.R:304:5', '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:40:5', 'test-utils.R:45:5', 'test-utils.R:54:5',
'test-utils.R:60:5', 'test-utils.R:65:5', 'test-utils.R:70:5',
'test-utils.R:80:5', 'test-utils.R:89:5', 'test-utils.R:98:5',
'test-utils.R:107:5', 'test-utils.R:123:5', 'test-utils.R:134:5',
'test-utils.R:144:5', 'test-utils.R:152:5', 'test-utils.R:161:5',
'test-utils.R:172:5', 'test-utils.R:180:5', 'test-utils.R:188:5',
'test-utils.R:196:5', 'test-utils.R:205:5', 'test-utils.R:214:5',
'test-utils.R:223:5', 'test-utils.R:232:5', 'test-utils.R:246:5',
'test-utils.R:258:5', 'test-utils.R:269:5', 'test-utils.R:279:5',
'test-utils.R:291:5', 'test-utils.R:300:5', 'test-utils.R:309:5',
'test-utils.R:318:5', 'test-utils.R:329:5', 'test-utils.R:340:5',
'test-utils.R:354:5', 'test-utils.R:362:5', 'test-utils.R:371:5',
'test-utils.R:380:5', 'test-utils.R:393:5', 'test-utils.R:400:5',
'test-utils.R:410:5', 'test-utils.R:421:5', 'test-utils.R:427:5',
'test-utils.R:437:5', 'test-utils.R:446:5', 'test-utils.R:461:5',
'test-utils.R:468:5', 'test-utils.R:475:5', 'test-utils.R:482:5',
'test-utils.R:492:5', 'test-utils.R:500:5', 'test-utils.R:508:5',
'test-utils.R:518:5', 'test-utils.R:525:5', 'test-utils.R:535:5',
'test-utils.R:542:5', 'test-utils.R:550:5', 'test-utils.R:558:5',
'test-utils.R:570:5', 'test-utils.R:578:5', 'test-utils.R:585:5',
'test-utils.R:593:5', 'test-utils.R:600:5', 'test-utils.R:608:5',
'test-utils.R:615:5', 'test-utils.R:623:5', 'test-utils.R:630:5',
'test-utils.R:641:5', 'test-utils.R:646:5', 'test-utils.R:658:5',
'test-utils.R:666:5', 'test-utils.R:673:5', 'test-utils.R:683:5',
'test-utils.R:690:5', 'test-utils.R:745:5', 'test-utils.R:757:5',
'test-utils.R:789:5', 'test-utils.R:798:5', 'test-utils.R:825:5',
'test-utils.R:843:5', 'test-utils.R:850:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-do_CellularStatesPlot.R:21:5'): do_CellularStatesPlot: CRAN essentials ──
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. └─SCpubr::do_CellularStatesPlot(...) at test-do_CellularStatesPlot.R:21:4
2. └─SCpubr::do_FeaturePlot(...)
3. └─SCpubr:::compute_scales(...)
4. └─SCpubr:::compute_scale_limits(...)
5. └─SCpubr:::.GetAssayData(sample, assay = assay, slot = slot)
── Error ('test-do_CopyNumberVariantPlot.R:4:5'): do_BarPlot: CRAN essentials ──
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_CopyNumberVariantPlot(...) at test-do_CopyNumberVariantPlot.R:4:4
2. │ ├─... %>% ...
3. │ └─SCpubr:::.GetAssayData(...)
4. ├─dplyr::summarise(., mean = mean(.data$CNV_score, na.rm = TRUE))
5. ├─dplyr::group_by(., .data[[group]], .data$Event)
6. ├─tidyr::pivot_longer(...)
7. ├─dplyr::left_join(...)
8. ├─tibble::rownames_to_column(., var = "Cell")
9. ├─base::as.data.frame(.)
10. ├─base::t(.)
11. └─base::as.matrix(.)
── Error ('test-do_CorrelationPlot.R:10:5'): do_CorrelationPlot: CRAN essentials ──
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. └─SCpubr::do_CorrelationPlot(sample = sample, legend.position = "top") at test-do_CorrelationPlot.R:10:4
2. ├─base::rownames(...)
3. └─SCpubr:::.GetAssayData(sample = sample, assay = assay, slot = "data")
── Error ('test-do_ExpressionHeatmap.R:5:5'): do_ExpressionHeatmap: CRAN essential tests ──
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_ExpressionHeatmap(sample, features = rownames(sample)[1:5]) at test-do_ExpressionHeatmap.R:5:4
2. │ ├─base::suppressMessages(...)
3. │ │ └─base::withCallingHandlers(...)
4. │ ├─... %>% ...
5. │ └─SCpubr:::.GetAssayData(sample, assay = assay, slot = slot)
6. ├─dplyr::summarise(., mean = mean(.data$expression, na.rm = TRUE))
7. ├─dplyr::group_by(., .data$group.by, .data$gene)
8. ├─tidyr::pivot_longer(...)
9. ├─dplyr::select(., -"cell")
10. ├─dplyr::left_join(...)
11. ├─tibble::rownames_to_column(., var = "cell")
12. ├─base::as.data.frame(.)
13. ├─base::t(.)
14. └─base::as.matrix(.)
── Error ('test-do_GeyserPlot.R:5:5'): do_GeyserPlot: CRAN essentials ──────────
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_GeyserPlot(sample = sample, features = "EPC1") at test-do_GeyserPlot.R:5:4
2. │ ├─... %>% ...
3. │ └─SCpubr:::.GetAssayData(sample = sample, assay = assay, slot = slot)
4. ├─dplyr::left_join(...)
5. ├─tibble::tibble(.)
6. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)
7. │ └─rlang::eval_tidy(xs[[j]], mask)
8. ├─tibble::rownames_to_column(., var = "cell")
9. ├─base::as.data.frame(.)
10. ├─base::t(.)
11. └─base::as.matrix(.)
── Error ('test-do_GroupwiseDEPlot.R:3:5'): do_GroupwiseDEPlot: CRAN essentials ──
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr:::.SetAssayData(...) at test-do_GroupwiseDEPlot.R:3:4
2. ├─base::as.matrix(...)
3. └─SCpubr:::.GetAssayData(sample = sample, assay = "SCT", slot = "data")
── Error ('test-do_PathwayActivityPlot.R:5:5'): do_PathwayActivityPlot: CRAN essentials ──
Error in `sample@assays[[assay]]$scale.data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_PathwayActivityPlot(sample = sample, activities = progeny_activities) at test-do_PathwayActivityPlot.R:5:4
2. │ ├─base::suppressMessages(...)
3. │ │ └─base::withCallingHandlers(...)
4. │ ├─... %>% ...
5. │ ├─base::t(...)
6. │ ├─base::as.matrix(...)
7. │ └─SCpubr:::.GetAssayData(sample = sample, assay = "progeny", slot = slot)
8. ├─dplyr::summarise(., mean = mean(.data$score, na.rm = TRUE))
9. ├─dplyr::group_by(., .data$group.by, .data$source)
10. ├─tidyr::pivot_longer(...)
11. ├─dplyr::select(., -"cell")
12. ├─dplyr::left_join(...)
13. ├─tibble::rownames_to_column(., var = "cell")
14. └─base::as.data.frame(.)
── Error ('test-do_TFActivityPlot.R:4:5'): do_TFActivityPlot: PASS - minimal input ──
Error in `sample@assays[[assay]]$scale.data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_TFActivityPlot(sample = sample, activities = dorothea_activities) at test-do_TFActivityPlot.R:4:4
2. │ ├─base::suppressMessages(...)
3. │ │ └─base::withCallingHandlers(...)
4. │ ├─... %>% ...
5. │ ├─base::t(...)
6. │ ├─base::as.matrix(...)
7. │ └─SCpubr:::.GetAssayData(sample = sample, assay = "dorothea", slot = slot)
8. ├─dplyr::summarise(., mean = mean(.data$score, na.rm = TRUE))
9. ├─dplyr::group_by(., .data$group.by, .data$source)
10. ├─tidyr::pivot_longer(...)
11. ├─dplyr::select(., -"cell")
12. ├─dplyr::left_join(...)
13. ├─tibble::rownames_to_column(., var = "cell")
14. └─base::as.data.frame(.)
── Error ('test-do_ViolinPlot.R:4:5'): do_ViolinPlot: CRAN essentials ──────────
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_ViolinPlot(sample = sample, features = "EPC1") at test-do_ViolinPlot.R:4:4
2. │ ├─base::append(...)
3. │ └─SCpubr:::get_data_column(...)
4. │ ├─... %>% dplyr::rename(feature = dplyr::all_of(c(feature)))
5. │ └─SCpubr:::.GetAssayData(sample = sample, assay = assay, slot = slot)
6. ├─dplyr::rename(., feature = dplyr::all_of(c(feature)))
7. ├─tibble::rownames_to_column(., var = "cell")
8. ├─base::as.data.frame(.)
9. ├─base::t(.)
10. └─base::as.matrix(.)
── Error ('test-utils.R:775:5'): utils: add_scale - PASS - checks ──────────────
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. └─SCpubr::do_FeaturePlot(sample, features = "EPC1") at test-utils.R:775:4
2. └─SCpubr:::compute_scales(...)
3. └─SCpubr:::compute_scale_limits(...)
4. └─SCpubr:::.GetAssayData(sample, assay = assay, slot = slot)
[ FAIL 10 | WARN 0 | SKIP 391 | PASS 75 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 2.0.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [139s/238s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # nolint start
> library(testthat)
> library(SCpubr)
── SCpubr 2.0.1 ────────────────────────────────────────────────────────────────
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! ──
ℹ To remove the white and black end from continuous palettes, use: options("SCpubr.ColorPaletteEnds" = FALSE)
✖ 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")
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
The sp package is now running under evolution status 2
(status 2 uses the sf package in place of rgdal)
[ FAIL 10 | WARN 0 | SKIP 391 | PASS 75 ]
══ Skipped tests (391) ═════════════════════════════════════════════════════════
• On CRAN (391): 'test-do_AlluvialPlot.R:14:5', 'test-do_BarPlot.R:26:5',
'test-do_BarPlot.R:35:5', 'test-do_BarPlot.R:46:5', 'test-do_BarPlot.R:59:5',
'test-do_BarPlot.R:74:5', 'test-do_BarPlot.R:83:5', 'test-do_BarPlot.R:92:5',
'test-do_BarPlot.R:100:5', 'test-do_BarPlot.R:110:5',
'test-do_BarPlot.R:120:5', 'test-do_BarPlot.R:132:5',
'test-do_BarPlot.R:155:5', 'test-do_BarPlot.R:177:5',
'test-do_BarPlot.R:188:5', 'test-do_BarPlot.R:203:5',
'test-do_BarPlot.R:215:5', 'test-do_BarPlot.R:228:5',
'test-do_BeeSwarmPlot.R:18:5', 'test-do_BeeSwarmPlot.R:40:5',
'test-do_BeeSwarmPlot.R:49:5', 'test-do_BeeSwarmPlot.R:81:5',
'test-do_BeeSwarmPlot.R:92:5', 'test-do_BeeSwarmPlot.R:101:5',
'test-do_BeeSwarmPlot.R:110:5', 'test-do_BeeSwarmPlot.R:120:5',
'test-do_BeeSwarmPlot.R:132:5', 'test-do_BeeSwarmPlot.R:141:5',
'test-do_BeeSwarmPlot.R:149:5', 'test-do_BeeSwarmPlot.R:158:5',
'test-do_BeeSwarmPlot.R:167:5', 'test-do_BeeSwarmPlot.R:177:5',
'test-do_BeeSwarmPlot.R:187:5', 'test-do_BeeSwarmPlot.R:196:5',
'test-do_BeeSwarmPlot.R:205:5', 'test-do_BeeSwarmPlot.R:222:5',
'test-do_BeeSwarmPlot.R:231:5', 'test-do_BeeSwarmPlot.R:240:5',
'test-do_BeeSwarmPlot.R:249:5', 'test-do_BeeSwarmPlot.R:258:5',
'test-do_BeeSwarmPlot.R:277:5', 'test-do_BoxPlot.R:22:5',
'test-do_BoxPlot.R:41:5', 'test-do_BoxPlot.R:62:5', 'test-do_BoxPlot.R:72:5',
'test-do_BoxPlot.R:80:5', 'test-do_BoxPlot.R:89:5',
'test-do_BoxPlot.R:103:5', 'test-do_BoxPlot.R:112:5',
'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:49:5', 'test-do_ChordDiagramPlot.R:150:5',
'test-do_ChordDiagramPlot.R:160:5', 'test-do_ChordDiagramPlot.R:177:5',
'test-do_ChordDiagramPlot.R:188:5', 'test-do_CopyNumberVariantPlot.R:13:5',
'test-do_CopyNumberVariantPlot.R:74:5',
'test-do_CopyNumberVariantPlot.R:83:5',
'test-do_CopyNumberVariantPlot.R:96:5',
'test-do_CopyNumberVariantPlot.R:109:5',
'test-do_CopyNumberVariantPlot.R:130:5', 'test-do_CorrelationPlot.R:16:5',
'test-do_CorrelationPlot.R:34:5', 'test-do_CorrelationPlot.R:58:5',
'test-do_CorrelationPlot.R:70:5', '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:16:5',
'test-do_DotPlot.R:77:5', 'test-do_DotPlot.R:92:5',
'test-do_DotPlot.R:109:5', 'test-do_DotPlot.R:119:5',
'test-do_DotPlot.R:133:5', 'test-do_DotPlot.R:144:5',
'test-do_DotPlot.R:155:5', 'test-do_DotPlot.R:166:5',
'test-do_DotPlot.R:176:5', 'test-do_DotPlot.R:195:5',
'test-do_DotPlot.R:215:5', 'test-do_DotPlot.R:236:5',
'test-do_DotPlot.R:254:5', 'test-do_DotPlot.R:273:5',
'test-do_DotPlot.R:295:5', 'test-do_EnrichmentHeatmap.R:19:5',
'test-do_EnrichmentHeatmap.R:193:5', 'test-do_EnrichmentHeatmap.R:224:5',
'test-do_EnrichmentHeatmap.R:241:5', 'test-do_EnrichmentHeatmap.R:275:5',
'test-do_EnrichmentHeatmap.R:314:5', 'test-do_EnrichmentHeatmap.R:337:5',
'test-do_EnrichmentHeatmap.R:356:5', 'test-do_ExpressionHeatmap.R:12:5',
'test-do_ExpressionHeatmap.R:150:5', 'test-do_ExpressionHeatmap.R:168:5',
'test-do_ExpressionHeatmap.R:186:5', 'test-do_ExpressionHeatmap.R:215:5',
'test-do_FeaturePlot.R:15:5', 'test-do_FeaturePlot.R:24:5',
'test-do_FeaturePlot.R:429:5', 'test-do_FeaturePlot.R:470:5',
'test-do_FeaturePlot.R:577:5', 'test-do_FeaturePlot.R:598:5',
'test-do_FeaturePlot.R:616:5', 'test-do_FeaturePlot.R:633:5',
'test-do_FeaturePlot.R:642:5', 'test-do_FeaturePlot.R:652:5',
'test-do_FeaturePlot.R:662:5', 'test-do_FeaturePlot.R:672:5',
'test-do_FeaturePlot.R:682:5', 'test-do_FeaturePlot.R:692:5',
'test-do_FeaturePlot.R:702:5', 'test-do_FeaturePlot.R:712:5',
'test-do_FeaturePlot.R:723:5', 'test-do_FeaturePlot.R:733:5',
'test-do_FeaturePlot.R:745:5', 'test-do_FeaturePlot.R:755:5',
'test-do_FeaturePlot.R:766:5', 'test-do_FeaturePlot.R:777:5',
'test-do_FeaturePlot.R:787:5', 'test-do_FeaturePlot.R:795:5',
'test-do_FeaturePlot.R:810:5', 'test-do_FeaturePlot.R:821:5',
'test-do_FeaturePlot.R:835:5', 'test-do_FeaturePlot.R:846:5',
'test-do_FeaturePlot.R:855:5', 'test-do_FeaturePlot.R:866:5',
'test-do_FeaturePlot.R:879:5', 'test-do_FeaturePlot.R:890:5',
'test-do_FeaturePlot.R:905:5', 'test-do_FeaturePlot.R:915:5',
'test-do_FeaturePlot.R:925:5', 'test-do_FeaturePlot.R:937:5',
'test-do_FeaturePlot.R:948:5', 'test-do_FeaturePlot.R:961:5',
'test-do_FeaturePlot.R:970:5', 'test-do_FeaturePlot.R:978:5',
'test-do_FeaturePlot.R:987:5', 'test-do_FunctionalAnnotationPlot.R:15:5',
'test-do_GeyserPlot.R:18:5', 'test-do_GeyserPlot.R:64:5',
'test-do_GeyserPlot.R:93:5', 'test-do_GeyserPlot.R:154:5',
'test-do_GeyserPlot.R:170:5', 'test-do_GeyserPlot.R:189:5',
'test-do_GeyserPlot.R:208:5', 'test-do_GeyserPlot.R:225:5',
'test-do_GeyserPlot.R:242:5', 'test-do_GeyserPlot.R:262:5',
'test-do_GeyserPlot.R:280:5', 'test-do_GeyserPlot.R:293:5',
'test-do_GroupedGOTermPlot.R:16:5', 'test-do_GroupwiseDEPlot.R:24:5',
'test-do_GroupwiseDEPlot.R:107:5', 'test-do_GroupwiseDEPlot.R:133:5',
'test-do_GroupwiseDEPlot.R:157:5', 'test-do_GroupwiseDEPlot.R:179:5',
'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_PathwayActivityPlot.R:12:5', 'test-do_PathwayActivityPlot.R:66:5',
'test-do_PathwayActivityPlot.R:78:5', 'test-do_PathwayActivityPlot.R:117:5',
'test-do_RidgePlot.R:41:5', 'test-do_RidgePlot.R:137:5',
'test-do_RidgePlot.R:153:5', 'test-do_RidgePlot.R:163:5',
'test-do_RidgePlot.R:180:5', 'test-do_RidgePlot.R:190:5',
'test-do_RidgePlot.R:210:5', 'test-do_RidgePlot.R:230:5',
'test-do_RidgePlot.R:242:5', 'test-do_TFActivityPlot.R:11:5',
'test-do_TFActivityPlot.R:72:5', 'test-do_TFActivityPlot.R:85:5',
'test-do_TFActivityPlot.R:99:5', 'test-do_TermEnrichmentPlot.R:11:5',
'test-do_TermEnrichmentPlot.R:24:5', 'test-do_TermEnrichmentPlot.R:31:5',
'test-do_TermEnrichmentPlot.R:39:5', 'test-do_TermEnrichmentPlot.R:47:5',
'test-do_TermEnrichmentPlot.R:56:5', 'test-do_ViolinPlot.R:10:5',
'test-do_ViolinPlot.R:25:5', 'test-do_ViolinPlot.R:37:5',
'test-do_ViolinPlot.R:49:5', 'test-do_ViolinPlot.R:65:5',
'test-do_ViolinPlot.R:94:5', 'test-do_ViolinPlot.R:113:5',
'test-do_ViolinPlot.R:123:5', 'test-do_ViolinPlot.R:133:5',
'test-do_ViolinPlot.R:146:5', 'test-do_ViolinPlot.R:158:5',
'test-do_ViolinPlot.R:170:5', 'test-do_ViolinPlot.R:182:5',
'test-do_ViolinPlot.R:205:5', 'test-do_ViolinPlot.R:217:5',
'test-do_ViolinPlot.R:240:5', 'test-do_ViolinPlot.R:264:5',
'test-do_ViolinPlot.R:277:5', 'test-do_ViolinPlot.R:295:5',
'test-do_ViolinPlot.R:304:5', '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:40:5', 'test-utils.R:45:5', 'test-utils.R:54:5',
'test-utils.R:60:5', 'test-utils.R:65:5', 'test-utils.R:70:5',
'test-utils.R:80:5', 'test-utils.R:89:5', 'test-utils.R:98:5',
'test-utils.R:107:5', 'test-utils.R:123:5', 'test-utils.R:134:5',
'test-utils.R:144:5', 'test-utils.R:152:5', 'test-utils.R:161:5',
'test-utils.R:172:5', 'test-utils.R:180:5', 'test-utils.R:188:5',
'test-utils.R:196:5', 'test-utils.R:205:5', 'test-utils.R:214:5',
'test-utils.R:223:5', 'test-utils.R:232:5', 'test-utils.R:246:5',
'test-utils.R:258:5', 'test-utils.R:269:5', 'test-utils.R:279:5',
'test-utils.R:291:5', 'test-utils.R:300:5', 'test-utils.R:309:5',
'test-utils.R:318:5', 'test-utils.R:329:5', 'test-utils.R:340:5',
'test-utils.R:354:5', 'test-utils.R:362:5', 'test-utils.R:371:5',
'test-utils.R:380:5', 'test-utils.R:393:5', 'test-utils.R:400:5',
'test-utils.R:410:5', 'test-utils.R:421:5', 'test-utils.R:427:5',
'test-utils.R:437:5', 'test-utils.R:446:5', 'test-utils.R:461:5',
'test-utils.R:468:5', 'test-utils.R:475:5', 'test-utils.R:482:5',
'test-utils.R:492:5', 'test-utils.R:500:5', 'test-utils.R:508:5',
'test-utils.R:518:5', 'test-utils.R:525:5', 'test-utils.R:535:5',
'test-utils.R:542:5', 'test-utils.R:550:5', 'test-utils.R:558:5',
'test-utils.R:570:5', 'test-utils.R:578:5', 'test-utils.R:585:5',
'test-utils.R:593:5', 'test-utils.R:600:5', 'test-utils.R:608:5',
'test-utils.R:615:5', 'test-utils.R:623:5', 'test-utils.R:630:5',
'test-utils.R:641:5', 'test-utils.R:646:5', 'test-utils.R:658:5',
'test-utils.R:666:5', 'test-utils.R:673:5', 'test-utils.R:683:5',
'test-utils.R:690:5', 'test-utils.R:745:5', 'test-utils.R:757:5',
'test-utils.R:789:5', 'test-utils.R:798:5', 'test-utils.R:825:5',
'test-utils.R:843:5', 'test-utils.R:850:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-do_CellularStatesPlot.R:21:5'): do_CellularStatesPlot: CRAN essentials ──
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. └─SCpubr::do_CellularStatesPlot(...) at test-do_CellularStatesPlot.R:21:4
2. └─SCpubr::do_FeaturePlot(...)
3. └─SCpubr:::compute_scales(...)
4. └─SCpubr:::compute_scale_limits(...)
5. └─SCpubr:::.GetAssayData(sample, assay = assay, slot = slot)
── Error ('test-do_CopyNumberVariantPlot.R:4:5'): do_BarPlot: CRAN essentials ──
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_CopyNumberVariantPlot(...) at test-do_CopyNumberVariantPlot.R:4:4
2. │ ├─... %>% ...
3. │ └─SCpubr:::.GetAssayData(...)
4. ├─dplyr::summarise(., mean = mean(.data$CNV_score, na.rm = TRUE))
5. ├─dplyr::group_by(., .data[[group]], .data$Event)
6. ├─tidyr::pivot_longer(...)
7. ├─dplyr::left_join(...)
8. ├─tibble::rownames_to_column(., var = "Cell")
9. ├─base::as.data.frame(.)
10. ├─base::t(.)
11. └─base::as.matrix(.)
── Error ('test-do_CorrelationPlot.R:10:5'): do_CorrelationPlot: CRAN essentials ──
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. └─SCpubr::do_CorrelationPlot(sample = sample, legend.position = "top") at test-do_CorrelationPlot.R:10:4
2. ├─base::rownames(...)
3. └─SCpubr:::.GetAssayData(sample = sample, assay = assay, slot = "data")
── Error ('test-do_ExpressionHeatmap.R:5:5'): do_ExpressionHeatmap: CRAN essential tests ──
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_ExpressionHeatmap(sample, features = rownames(sample)[1:5]) at test-do_ExpressionHeatmap.R:5:4
2. │ ├─base::suppressMessages(...)
3. │ │ └─base::withCallingHandlers(...)
4. │ ├─... %>% ...
5. │ └─SCpubr:::.GetAssayData(sample, assay = assay, slot = slot)
6. ├─dplyr::summarise(., mean = mean(.data$expression, na.rm = TRUE))
7. ├─dplyr::group_by(., .data$group.by, .data$gene)
8. ├─tidyr::pivot_longer(...)
9. ├─dplyr::select(., -"cell")
10. ├─dplyr::left_join(...)
11. ├─tibble::rownames_to_column(., var = "cell")
12. ├─base::as.data.frame(.)
13. ├─base::t(.)
14. └─base::as.matrix(.)
── Error ('test-do_GeyserPlot.R:5:5'): do_GeyserPlot: CRAN essentials ──────────
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_GeyserPlot(sample = sample, features = "EPC1") at test-do_GeyserPlot.R:5:4
2. │ ├─... %>% ...
3. │ └─SCpubr:::.GetAssayData(sample = sample, assay = assay, slot = slot)
4. ├─dplyr::left_join(...)
5. ├─tibble::tibble(.)
6. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)
7. │ └─rlang::eval_tidy(xs[[j]], mask)
8. ├─tibble::rownames_to_column(., var = "cell")
9. ├─base::as.data.frame(.)
10. ├─base::t(.)
11. └─base::as.matrix(.)
── Error ('test-do_GroupwiseDEPlot.R:3:5'): do_GroupwiseDEPlot: CRAN essentials ──
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr:::.SetAssayData(...) at test-do_GroupwiseDEPlot.R:3:4
2. ├─base::as.matrix(...)
3. └─SCpubr:::.GetAssayData(sample = sample, assay = "SCT", slot = "data")
── Error ('test-do_PathwayActivityPlot.R:5:5'): do_PathwayActivityPlot: CRAN essentials ──
Error in `sample@assays[[assay]]$scale.data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_PathwayActivityPlot(sample = sample, activities = progeny_activities) at test-do_PathwayActivityPlot.R:5:4
2. │ ├─base::suppressMessages(...)
3. │ │ └─base::withCallingHandlers(...)
4. │ ├─... %>% ...
5. │ ├─base::t(...)
6. │ ├─base::as.matrix(...)
7. │ └─SCpubr:::.GetAssayData(sample = sample, assay = "progeny", slot = slot)
8. ├─dplyr::summarise(., mean = mean(.data$score, na.rm = TRUE))
9. ├─dplyr::group_by(., .data$group.by, .data$source)
10. ├─tidyr::pivot_longer(...)
11. ├─dplyr::select(., -"cell")
12. ├─dplyr::left_join(...)
13. ├─tibble::rownames_to_column(., var = "cell")
14. └─base::as.data.frame(.)
── Error ('test-do_TFActivityPlot.R:4:5'): do_TFActivityPlot: PASS - minimal input ──
Error in `sample@assays[[assay]]$scale.data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_TFActivityPlot(sample = sample, activities = dorothea_activities) at test-do_TFActivityPlot.R:4:4
2. │ ├─base::suppressMessages(...)
3. │ │ └─base::withCallingHandlers(...)
4. │ ├─... %>% ...
5. │ ├─base::t(...)
6. │ ├─base::as.matrix(...)
7. │ └─SCpubr:::.GetAssayData(sample = sample, assay = "dorothea", slot = slot)
8. ├─dplyr::summarise(., mean = mean(.data$score, na.rm = TRUE))
9. ├─dplyr::group_by(., .data$group.by, .data$source)
10. ├─tidyr::pivot_longer(...)
11. ├─dplyr::select(., -"cell")
12. ├─dplyr::left_join(...)
13. ├─tibble::rownames_to_column(., var = "cell")
14. └─base::as.data.frame(.)
── Error ('test-do_ViolinPlot.R:4:5'): do_ViolinPlot: CRAN essentials ──────────
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_ViolinPlot(sample = sample, features = "EPC1") at test-do_ViolinPlot.R:4:4
2. │ ├─base::append(...)
3. │ └─SCpubr:::get_data_column(...)
4. │ ├─... %>% dplyr::rename(feature = dplyr::all_of(c(feature)))
5. │ └─SCpubr:::.GetAssayData(sample = sample, assay = assay, slot = slot)
6. ├─dplyr::rename(., feature = dplyr::all_of(c(feature)))
7. ├─tibble::rownames_to_column(., var = "cell")
8. ├─base::as.data.frame(.)
9. ├─base::t(.)
10. └─base::as.matrix(.)
── Error ('test-utils.R:775:5'): utils: add_scale - PASS - checks ──────────────
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. └─SCpubr::do_FeaturePlot(sample, features = "EPC1") at test-utils.R:775:4
2. └─SCpubr:::compute_scales(...)
3. └─SCpubr:::compute_scale_limits(...)
4. └─SCpubr:::.GetAssayData(sample, assay = assay, slot = slot)
[ FAIL 10 | WARN 0 | SKIP 391 | PASS 75 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 2.0.1
Check: package dependencies
Result: NOTE
Packages suggested but not available for checking:
'AUCell', 'decoupleR', 'infercnv', 'Nebulosa'
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-release-macos-arm64, r-release-macos-x86_64, r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 2.0.1
Check: Rd cross-references
Result: NOTE
Package unavailable to check Rd xrefs: ‘infercnv’
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-release-macos-arm64, r-release-macos-x86_64
Version: 2.0.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [4m/10m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # nolint start
> library(testthat)
> library(SCpubr)
── SCpubr 2.0.1 ────────────────────────────────────────────────────────────────
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! ──
ℹ To remove the white and black end from continuous palettes, use: options("SCpubr.ColorPaletteEnds" = FALSE)
✖ 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")
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
The sp package is now running under evolution status 2
(status 2 uses the sf package in place of rgdal)
[ FAIL 10 | WARN 0 | SKIP 361 | PASS 71 ]
══ Skipped tests (361) ═════════════════════════════════════════════════════════
• On CRAN (361): 'test-do_AlluvialPlot.R:14:5', 'test-do_BarPlot.R:26:5',
'test-do_BarPlot.R:35:5', 'test-do_BarPlot.R:46:5', 'test-do_BarPlot.R:59:5',
'test-do_BarPlot.R:74:5', 'test-do_BarPlot.R:83:5', 'test-do_BarPlot.R:92:5',
'test-do_BarPlot.R:100:5', 'test-do_BarPlot.R:110:5',
'test-do_BarPlot.R:120:5', 'test-do_BarPlot.R:132:5',
'test-do_BarPlot.R:155:5', 'test-do_BarPlot.R:177:5',
'test-do_BarPlot.R:188:5', 'test-do_BarPlot.R:203:5',
'test-do_BarPlot.R:215:5', 'test-do_BarPlot.R:228:5',
'test-do_BeeSwarmPlot.R:18:5', 'test-do_BeeSwarmPlot.R:40:5',
'test-do_BeeSwarmPlot.R:49:5', 'test-do_BeeSwarmPlot.R:81:5',
'test-do_BeeSwarmPlot.R:92:5', 'test-do_BeeSwarmPlot.R:101:5',
'test-do_BeeSwarmPlot.R:110:5', 'test-do_BeeSwarmPlot.R:120:5',
'test-do_BeeSwarmPlot.R:132:5', 'test-do_BeeSwarmPlot.R:141:5',
'test-do_BeeSwarmPlot.R:149:5', 'test-do_BeeSwarmPlot.R:158:5',
'test-do_BeeSwarmPlot.R:167:5', 'test-do_BeeSwarmPlot.R:177:5',
'test-do_BeeSwarmPlot.R:187:5', 'test-do_BeeSwarmPlot.R:196:5',
'test-do_BeeSwarmPlot.R:205:5', 'test-do_BeeSwarmPlot.R:222:5',
'test-do_BeeSwarmPlot.R:231:5', 'test-do_BeeSwarmPlot.R:240:5',
'test-do_BeeSwarmPlot.R:249:5', 'test-do_BeeSwarmPlot.R:258:5',
'test-do_BeeSwarmPlot.R:277:5', 'test-do_BoxPlot.R:22:5',
'test-do_BoxPlot.R:41:5', 'test-do_BoxPlot.R:62:5', 'test-do_BoxPlot.R:72:5',
'test-do_BoxPlot.R:80:5', 'test-do_BoxPlot.R:89:5',
'test-do_BoxPlot.R:103:5', 'test-do_BoxPlot.R:112:5',
'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',
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'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',
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'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:49:5', 'test-do_ChordDiagramPlot.R:150:5',
'test-do_ChordDiagramPlot.R:160:5', 'test-do_ChordDiagramPlot.R:177:5',
'test-do_ChordDiagramPlot.R:188:5', 'test-do_CopyNumberVariantPlot.R:13:5',
'test-do_CopyNumberVariantPlot.R:74:5',
'test-do_CopyNumberVariantPlot.R:83:5',
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'test-do_CopyNumberVariantPlot.R:109:5',
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'test-do_CorrelationPlot.R:70:5', 'test-do_DimPlot.R:19:5',
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'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',
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'test-do_DimPlot.R:575:5', 'test-do_DimPlot.R:585:5',
'test-do_DimPlot.R:596:5', 'test-do_DimPlot.R:605:5',
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'test-do_DotPlot.R:77:5', 'test-do_DotPlot.R:92:5',
'test-do_DotPlot.R:109:5', 'test-do_DotPlot.R:119:5',
'test-do_DotPlot.R:133:5', 'test-do_DotPlot.R:144:5',
'test-do_DotPlot.R:155:5', 'test-do_DotPlot.R:166:5',
'test-do_DotPlot.R:176:5', 'test-do_DotPlot.R:195:5',
'test-do_DotPlot.R:215:5', 'test-do_DotPlot.R:236:5',
'test-do_DotPlot.R:254:5', 'test-do_DotPlot.R:273:5',
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'test-do_FeaturePlot.R:723:5', 'test-do_FeaturePlot.R:733:5',
'test-do_FeaturePlot.R:745:5', 'test-do_FeaturePlot.R:755:5',
'test-do_FeaturePlot.R:766:5', 'test-do_FeaturePlot.R:777:5',
'test-do_FeaturePlot.R:787:5', 'test-do_FeaturePlot.R:795:5',
'test-do_FeaturePlot.R:810:5', 'test-do_FeaturePlot.R:821:5',
'test-do_FeaturePlot.R:835:5', 'test-do_FeaturePlot.R:846:5',
'test-do_FeaturePlot.R:855:5', 'test-do_FeaturePlot.R:866:5',
'test-do_FeaturePlot.R:879:5', 'test-do_FeaturePlot.R:890:5',
'test-do_FeaturePlot.R:905:5', 'test-do_FeaturePlot.R:915:5',
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'test-do_FeaturePlot.R:948:5', 'test-do_FeaturePlot.R:961:5',
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'test-do_GroupwiseDEPlot.R:157:5', 'test-do_GroupwiseDEPlot.R:179:5',
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'test-do_RidgePlot.R:153:5', 'test-do_RidgePlot.R:163:5',
'test-do_RidgePlot.R:180:5', 'test-do_RidgePlot.R:190:5',
'test-do_RidgePlot.R:210:5', 'test-do_RidgePlot.R:230:5',
'test-do_RidgePlot.R:242:5', 'test-do_TFActivityPlot.R:11:5',
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'test-do_TermEnrichmentPlot.R:39:5', 'test-do_TermEnrichmentPlot.R:47:5',
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'test-do_ViolinPlot.R:94:5', 'test-do_ViolinPlot.R:113:5',
'test-do_ViolinPlot.R:123:5', 'test-do_ViolinPlot.R:133:5',
'test-do_ViolinPlot.R:146:5', 'test-do_ViolinPlot.R:158:5',
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'test-do_ViolinPlot.R:205:5', 'test-do_ViolinPlot.R:217:5',
'test-do_ViolinPlot.R:240:5', 'test-do_ViolinPlot.R:264:5',
'test-do_ViolinPlot.R:277:5', 'test-do_ViolinPlot.R:295:5',
'test-do_ViolinPlot.R:304:5', '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:40:5', 'test-utils.R:45:5', 'test-utils.R:54:5',
'test-utils.R:60:5', 'test-utils.R:65:5', 'test-utils.R:70:5',
'test-utils.R:80:5', 'test-utils.R:89:5', 'test-utils.R:98:5',
'test-utils.R:107:5', 'test-utils.R:123:5', 'test-utils.R:134:5',
'test-utils.R:144:5', 'test-utils.R:152:5', 'test-utils.R:161:5',
'test-utils.R:172:5', 'test-utils.R:180:5', 'test-utils.R:188:5',
'test-utils.R:196:5', 'test-utils.R:205:5', 'test-utils.R:214:5',
'test-utils.R:223:5', 'test-utils.R:232:5', 'test-utils.R:246:5',
'test-utils.R:258:5', 'test-utils.R:269:5', 'test-utils.R:279:5',
'test-utils.R:291:5', 'test-utils.R:300:5', 'test-utils.R:309:5',
'test-utils.R:318:5', 'test-utils.R:329:5', 'test-utils.R:340:5',
'test-utils.R:354:5', 'test-utils.R:362:5', 'test-utils.R:371:5',
'test-utils.R:380:5', 'test-utils.R:393:5', 'test-utils.R:400:5',
'test-utils.R:410:5', 'test-utils.R:421:5', 'test-utils.R:427:5',
'test-utils.R:437:5', 'test-utils.R:446:5', 'test-utils.R:461:5',
'test-utils.R:468:5', 'test-utils.R:475:5', 'test-utils.R:482:5',
'test-utils.R:492:5', 'test-utils.R:500:5', 'test-utils.R:508:5',
'test-utils.R:518:5', 'test-utils.R:525:5', 'test-utils.R:535:5',
'test-utils.R:542:5', 'test-utils.R:550:5', 'test-utils.R:558:5',
'test-utils.R:570:5', 'test-utils.R:578:5', 'test-utils.R:585:5',
'test-utils.R:593:5', 'test-utils.R:600:5', 'test-utils.R:608:5',
'test-utils.R:615:5', 'test-utils.R:623:5', 'test-utils.R:630:5',
'test-utils.R:641:5', 'test-utils.R:646:5', 'test-utils.R:658:5',
'test-utils.R:666:5', 'test-utils.R:673:5', 'test-utils.R:683:5',
'test-utils.R:690:5', 'test-utils.R:745:5', 'test-utils.R:757:5',
'test-utils.R:789:5', 'test-utils.R:798:5', 'test-utils.R:825:5',
'test-utils.R:843:5', 'test-utils.R:850:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-do_CellularStatesPlot.R:21:5'): do_CellularStatesPlot: CRAN essentials ──
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. └─SCpubr::do_CellularStatesPlot(...) at test-do_CellularStatesPlot.R:21:4
2. └─SCpubr::do_FeaturePlot(...)
3. └─SCpubr:::compute_scales(...)
4. └─SCpubr:::compute_scale_limits(...)
5. └─SCpubr:::.GetAssayData(sample, assay = assay, slot = slot)
── Error ('test-do_CopyNumberVariantPlot.R:4:5'): do_BarPlot: CRAN essentials ──
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_CopyNumberVariantPlot(...) at test-do_CopyNumberVariantPlot.R:4:4
2. │ ├─... %>% ...
3. │ └─SCpubr:::.GetAssayData(...)
4. ├─dplyr::summarise(., mean = mean(.data$CNV_score, na.rm = TRUE))
5. ├─dplyr::group_by(., .data[[group]], .data$Event)
6. ├─tidyr::pivot_longer(...)
7. ├─dplyr::left_join(...)
8. ├─tibble::rownames_to_column(., var = "Cell")
9. ├─base::as.data.frame(.)
10. ├─base::t(.)
11. └─base::as.matrix(.)
── Error ('test-do_CorrelationPlot.R:10:5'): do_CorrelationPlot: CRAN essentials ──
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. └─SCpubr::do_CorrelationPlot(sample = sample, legend.position = "top") at test-do_CorrelationPlot.R:10:4
2. ├─base::rownames(...)
3. └─SCpubr:::.GetAssayData(sample = sample, assay = assay, slot = "data")
── Error ('test-do_ExpressionHeatmap.R:5:5'): do_ExpressionHeatmap: CRAN essential tests ──
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_ExpressionHeatmap(sample, features = rownames(sample)[1:5]) at test-do_ExpressionHeatmap.R:5:4
2. │ ├─base::suppressMessages(...)
3. │ │ └─base::withCallingHandlers(...)
4. │ ├─... %>% ...
5. │ └─SCpubr:::.GetAssayData(sample, assay = assay, slot = slot)
6. ├─dplyr::summarise(., mean = mean(.data$expression, na.rm = TRUE))
7. ├─dplyr::group_by(., .data$group.by, .data$gene)
8. ├─tidyr::pivot_longer(...)
9. ├─dplyr::select(., -"cell")
10. ├─dplyr::left_join(...)
11. ├─tibble::rownames_to_column(., var = "cell")
12. ├─base::as.data.frame(.)
13. ├─base::t(.)
14. └─base::as.matrix(.)
── Error ('test-do_GeyserPlot.R:5:5'): do_GeyserPlot: CRAN essentials ──────────
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_GeyserPlot(sample = sample, features = "EPC1") at test-do_GeyserPlot.R:5:4
2. │ ├─... %>% ...
3. │ └─SCpubr:::.GetAssayData(sample = sample, assay = assay, slot = slot)
4. ├─dplyr::left_join(...)
5. ├─tibble::tibble(.)
6. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)
7. │ └─rlang::eval_tidy(xs[[j]], mask)
8. ├─tibble::rownames_to_column(., var = "cell")
9. ├─base::as.data.frame(.)
10. ├─base::t(.)
11. └─base::as.matrix(.)
── Error ('test-do_GroupwiseDEPlot.R:3:5'): do_GroupwiseDEPlot: CRAN essentials ──
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr:::.SetAssayData(...) at test-do_GroupwiseDEPlot.R:3:4
2. ├─base::as.matrix(...)
3. └─SCpubr:::.GetAssayData(sample = sample, assay = "SCT", slot = "data")
── Error ('test-do_PathwayActivityPlot.R:5:5'): do_PathwayActivityPlot: CRAN essentials ──
Error in `sample@assays[[assay]]$scale.data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_PathwayActivityPlot(sample = sample, activities = progeny_activities) at test-do_PathwayActivityPlot.R:5:4
2. │ ├─base::suppressMessages(...)
3. │ │ └─base::withCallingHandlers(...)
4. │ ├─... %>% ...
5. │ ├─base::t(...)
6. │ ├─base::as.matrix(...)
7. │ └─SCpubr:::.GetAssayData(sample = sample, assay = "progeny", slot = slot)
8. ├─dplyr::summarise(., mean = mean(.data$score, na.rm = TRUE))
9. ├─dplyr::group_by(., .data$group.by, .data$source)
10. ├─tidyr::pivot_longer(...)
11. ├─dplyr::select(., -"cell")
12. ├─dplyr::left_join(...)
13. ├─tibble::rownames_to_column(., var = "cell")
14. └─base::as.data.frame(.)
── Error ('test-do_TFActivityPlot.R:4:5'): do_TFActivityPlot: PASS - minimal input ──
Error in `sample@assays[[assay]]$scale.data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_TFActivityPlot(sample = sample, activities = dorothea_activities) at test-do_TFActivityPlot.R:4:4
2. │ ├─base::suppressMessages(...)
3. │ │ └─base::withCallingHandlers(...)
4. │ ├─... %>% ...
5. │ ├─base::t(...)
6. │ ├─base::as.matrix(...)
7. │ └─SCpubr:::.GetAssayData(sample = sample, assay = "dorothea", slot = slot)
8. ├─dplyr::summarise(., mean = mean(.data$score, na.rm = TRUE))
9. ├─dplyr::group_by(., .data$group.by, .data$source)
10. ├─tidyr::pivot_longer(...)
11. ├─dplyr::select(., -"cell")
12. ├─dplyr::left_join(...)
13. ├─tibble::rownames_to_column(., var = "cell")
14. └─base::as.data.frame(.)
── Error ('test-do_ViolinPlot.R:4:5'): do_ViolinPlot: CRAN essentials ──────────
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_ViolinPlot(sample = sample, features = "EPC1") at test-do_ViolinPlot.R:4:4
2. │ ├─base::append(...)
3. │ └─SCpubr:::get_data_column(...)
4. │ ├─... %>% dplyr::rename(feature = dplyr::all_of(c(feature)))
5. │ └─SCpubr:::.GetAssayData(sample = sample, assay = assay, slot = slot)
6. ├─dplyr::rename(., feature = dplyr::all_of(c(feature)))
7. ├─tibble::rownames_to_column(., var = "cell")
8. ├─base::as.data.frame(.)
9. ├─base::t(.)
10. └─base::as.matrix(.)
── Error ('test-utils.R:775:5'): utils: add_scale - PASS - checks ──────────────
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. └─SCpubr::do_FeaturePlot(sample, features = "EPC1") at test-utils.R:775:4
2. └─SCpubr:::compute_scales(...)
3. └─SCpubr:::compute_scale_limits(...)
4. └─SCpubr:::.GetAssayData(sample, assay = assay, slot = slot)
[ FAIL 10 | WARN 0 | SKIP 361 | PASS 71 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 2.0.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [4m/14m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # nolint start
> library(testthat)
> library(SCpubr)
── SCpubr 2.0.1 ────────────────────────────────────────────────────────────────
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! ──
ℹ To remove the white and black end from continuous palettes, use: options("SCpubr.ColorPaletteEnds" = FALSE)
✖ 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")
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
The sp package is now running under evolution status 2
(status 2 uses the sf package in place of rgdal)
[ FAIL 10 | WARN 0 | SKIP 361 | PASS 71 ]
══ Skipped tests (361) ═════════════════════════════════════════════════════════
• On CRAN (361): 'test-do_AlluvialPlot.R:14:5', 'test-do_BarPlot.R:26:5',
'test-do_BarPlot.R:35:5', 'test-do_BarPlot.R:46:5', 'test-do_BarPlot.R:59:5',
'test-do_BarPlot.R:74:5', 'test-do_BarPlot.R:83:5', 'test-do_BarPlot.R:92:5',
'test-do_BarPlot.R:100:5', 'test-do_BarPlot.R:110:5',
'test-do_BarPlot.R:120:5', 'test-do_BarPlot.R:132:5',
'test-do_BarPlot.R:155:5', 'test-do_BarPlot.R:177:5',
'test-do_BarPlot.R:188:5', 'test-do_BarPlot.R:203:5',
'test-do_BarPlot.R:215:5', 'test-do_BarPlot.R:228:5',
'test-do_BeeSwarmPlot.R:18:5', 'test-do_BeeSwarmPlot.R:40:5',
'test-do_BeeSwarmPlot.R:49:5', 'test-do_BeeSwarmPlot.R:81:5',
'test-do_BeeSwarmPlot.R:92:5', 'test-do_BeeSwarmPlot.R:101:5',
'test-do_BeeSwarmPlot.R:110:5', 'test-do_BeeSwarmPlot.R:120:5',
'test-do_BeeSwarmPlot.R:132:5', 'test-do_BeeSwarmPlot.R:141:5',
'test-do_BeeSwarmPlot.R:149:5', 'test-do_BeeSwarmPlot.R:158:5',
'test-do_BeeSwarmPlot.R:167:5', 'test-do_BeeSwarmPlot.R:177:5',
'test-do_BeeSwarmPlot.R:187:5', 'test-do_BeeSwarmPlot.R:196:5',
'test-do_BeeSwarmPlot.R:205:5', 'test-do_BeeSwarmPlot.R:222:5',
'test-do_BeeSwarmPlot.R:231:5', 'test-do_BeeSwarmPlot.R:240:5',
'test-do_BeeSwarmPlot.R:249:5', 'test-do_BeeSwarmPlot.R:258:5',
'test-do_BeeSwarmPlot.R:277:5', 'test-do_BoxPlot.R:22:5',
'test-do_BoxPlot.R:41:5', 'test-do_BoxPlot.R:62:5', 'test-do_BoxPlot.R:72:5',
'test-do_BoxPlot.R:80:5', 'test-do_BoxPlot.R:89:5',
'test-do_BoxPlot.R:103:5', 'test-do_BoxPlot.R:112:5',
'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:49:5', 'test-do_ChordDiagramPlot.R:150:5',
'test-do_ChordDiagramPlot.R:160:5', 'test-do_ChordDiagramPlot.R:177:5',
'test-do_ChordDiagramPlot.R:188:5', 'test-do_CopyNumberVariantPlot.R:13:5',
'test-do_CopyNumberVariantPlot.R:74:5',
'test-do_CopyNumberVariantPlot.R:83:5',
'test-do_CopyNumberVariantPlot.R:96:5',
'test-do_CopyNumberVariantPlot.R:109:5',
'test-do_CopyNumberVariantPlot.R:130:5', 'test-do_CorrelationPlot.R:16:5',
'test-do_CorrelationPlot.R:34:5', 'test-do_CorrelationPlot.R:58:5',
'test-do_CorrelationPlot.R:70:5', '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:16:5',
'test-do_DotPlot.R:77:5', 'test-do_DotPlot.R:92:5',
'test-do_DotPlot.R:109:5', 'test-do_DotPlot.R:119:5',
'test-do_DotPlot.R:133:5', 'test-do_DotPlot.R:144:5',
'test-do_DotPlot.R:155:5', 'test-do_DotPlot.R:166:5',
'test-do_DotPlot.R:176:5', 'test-do_DotPlot.R:195:5',
'test-do_DotPlot.R:215:5', 'test-do_DotPlot.R:236:5',
'test-do_DotPlot.R:254:5', 'test-do_DotPlot.R:273:5',
'test-do_DotPlot.R:295:5', 'test-do_ExpressionHeatmap.R:12:5',
'test-do_ExpressionHeatmap.R:150:5', 'test-do_ExpressionHeatmap.R:168:5',
'test-do_ExpressionHeatmap.R:186:5', 'test-do_ExpressionHeatmap.R:215:5',
'test-do_FeaturePlot.R:15:5', 'test-do_FeaturePlot.R:24:5',
'test-do_FeaturePlot.R:429:5', 'test-do_FeaturePlot.R:470:5',
'test-do_FeaturePlot.R:577:5', 'test-do_FeaturePlot.R:598:5',
'test-do_FeaturePlot.R:616:5', 'test-do_FeaturePlot.R:633:5',
'test-do_FeaturePlot.R:642:5', 'test-do_FeaturePlot.R:652:5',
'test-do_FeaturePlot.R:662:5', 'test-do_FeaturePlot.R:672:5',
'test-do_FeaturePlot.R:682:5', 'test-do_FeaturePlot.R:692:5',
'test-do_FeaturePlot.R:702:5', 'test-do_FeaturePlot.R:712:5',
'test-do_FeaturePlot.R:723:5', 'test-do_FeaturePlot.R:733:5',
'test-do_FeaturePlot.R:745:5', 'test-do_FeaturePlot.R:755:5',
'test-do_FeaturePlot.R:766:5', 'test-do_FeaturePlot.R:777:5',
'test-do_FeaturePlot.R:787:5', 'test-do_FeaturePlot.R:795:5',
'test-do_FeaturePlot.R:810:5', 'test-do_FeaturePlot.R:821:5',
'test-do_FeaturePlot.R:835:5', 'test-do_FeaturePlot.R:846:5',
'test-do_FeaturePlot.R:855:5', 'test-do_FeaturePlot.R:866:5',
'test-do_FeaturePlot.R:879:5', 'test-do_FeaturePlot.R:890:5',
'test-do_FeaturePlot.R:905:5', 'test-do_FeaturePlot.R:915:5',
'test-do_FeaturePlot.R:925:5', 'test-do_FeaturePlot.R:937:5',
'test-do_FeaturePlot.R:948:5', 'test-do_FeaturePlot.R:961:5',
'test-do_FeaturePlot.R:970:5', 'test-do_FeaturePlot.R:978:5',
'test-do_FeaturePlot.R:987:5', 'test-do_FunctionalAnnotationPlot.R:15:5',
'test-do_GeyserPlot.R:18:5', 'test-do_GeyserPlot.R:64:5',
'test-do_GeyserPlot.R:93:5', 'test-do_GeyserPlot.R:154:5',
'test-do_GeyserPlot.R:170:5', 'test-do_GeyserPlot.R:189:5',
'test-do_GeyserPlot.R:208:5', 'test-do_GeyserPlot.R:225:5',
'test-do_GeyserPlot.R:242:5', 'test-do_GeyserPlot.R:262:5',
'test-do_GeyserPlot.R:280:5', 'test-do_GeyserPlot.R:293:5',
'test-do_GroupedGOTermPlot.R:16:5', 'test-do_GroupwiseDEPlot.R:24:5',
'test-do_GroupwiseDEPlot.R:107:5', 'test-do_GroupwiseDEPlot.R:133:5',
'test-do_GroupwiseDEPlot.R:157:5', 'test-do_GroupwiseDEPlot.R:179:5',
'test-do_PathwayActivityPlot.R:12:5', 'test-do_PathwayActivityPlot.R:66:5',
'test-do_PathwayActivityPlot.R:78:5', 'test-do_PathwayActivityPlot.R:117:5',
'test-do_RidgePlot.R:41:5', 'test-do_RidgePlot.R:137:5',
'test-do_RidgePlot.R:153:5', 'test-do_RidgePlot.R:163:5',
'test-do_RidgePlot.R:180:5', 'test-do_RidgePlot.R:190:5',
'test-do_RidgePlot.R:210:5', 'test-do_RidgePlot.R:230:5',
'test-do_RidgePlot.R:242:5', 'test-do_TFActivityPlot.R:11:5',
'test-do_TFActivityPlot.R:72:5', 'test-do_TFActivityPlot.R:85:5',
'test-do_TFActivityPlot.R:99:5', 'test-do_TermEnrichmentPlot.R:11:5',
'test-do_TermEnrichmentPlot.R:24:5', 'test-do_TermEnrichmentPlot.R:31:5',
'test-do_TermEnrichmentPlot.R:39:5', 'test-do_TermEnrichmentPlot.R:47:5',
'test-do_TermEnrichmentPlot.R:56:5', 'test-do_ViolinPlot.R:10:5',
'test-do_ViolinPlot.R:25:5', 'test-do_ViolinPlot.R:37:5',
'test-do_ViolinPlot.R:49:5', 'test-do_ViolinPlot.R:65:5',
'test-do_ViolinPlot.R:94:5', 'test-do_ViolinPlot.R:113:5',
'test-do_ViolinPlot.R:123:5', 'test-do_ViolinPlot.R:133:5',
'test-do_ViolinPlot.R:146:5', 'test-do_ViolinPlot.R:158:5',
'test-do_ViolinPlot.R:170:5', 'test-do_ViolinPlot.R:182:5',
'test-do_ViolinPlot.R:205:5', 'test-do_ViolinPlot.R:217:5',
'test-do_ViolinPlot.R:240:5', 'test-do_ViolinPlot.R:264:5',
'test-do_ViolinPlot.R:277:5', 'test-do_ViolinPlot.R:295:5',
'test-do_ViolinPlot.R:304:5', '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:40:5', 'test-utils.R:45:5', 'test-utils.R:54:5',
'test-utils.R:60:5', 'test-utils.R:65:5', 'test-utils.R:70:5',
'test-utils.R:80:5', 'test-utils.R:89:5', 'test-utils.R:98:5',
'test-utils.R:107:5', 'test-utils.R:123:5', 'test-utils.R:134:5',
'test-utils.R:144:5', 'test-utils.R:152:5', 'test-utils.R:161:5',
'test-utils.R:172:5', 'test-utils.R:180:5', 'test-utils.R:188:5',
'test-utils.R:196:5', 'test-utils.R:205:5', 'test-utils.R:214:5',
'test-utils.R:223:5', 'test-utils.R:232:5', 'test-utils.R:246:5',
'test-utils.R:258:5', 'test-utils.R:269:5', 'test-utils.R:279:5',
'test-utils.R:291:5', 'test-utils.R:300:5', 'test-utils.R:309:5',
'test-utils.R:318:5', 'test-utils.R:329:5', 'test-utils.R:340:5',
'test-utils.R:354:5', 'test-utils.R:362:5', 'test-utils.R:371:5',
'test-utils.R:380:5', 'test-utils.R:393:5', 'test-utils.R:400:5',
'test-utils.R:410:5', 'test-utils.R:421:5', 'test-utils.R:427:5',
'test-utils.R:437:5', 'test-utils.R:446:5', 'test-utils.R:461:5',
'test-utils.R:468:5', 'test-utils.R:475:5', 'test-utils.R:482:5',
'test-utils.R:492:5', 'test-utils.R:500:5', 'test-utils.R:508:5',
'test-utils.R:518:5', 'test-utils.R:525:5', 'test-utils.R:535:5',
'test-utils.R:542:5', 'test-utils.R:550:5', 'test-utils.R:558:5',
'test-utils.R:570:5', 'test-utils.R:578:5', 'test-utils.R:585:5',
'test-utils.R:593:5', 'test-utils.R:600:5', 'test-utils.R:608:5',
'test-utils.R:615:5', 'test-utils.R:623:5', 'test-utils.R:630:5',
'test-utils.R:641:5', 'test-utils.R:646:5', 'test-utils.R:658:5',
'test-utils.R:666:5', 'test-utils.R:673:5', 'test-utils.R:683:5',
'test-utils.R:690:5', 'test-utils.R:745:5', 'test-utils.R:757:5',
'test-utils.R:789:5', 'test-utils.R:798:5', 'test-utils.R:825:5',
'test-utils.R:843:5', 'test-utils.R:850:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-do_CellularStatesPlot.R:21:5'): do_CellularStatesPlot: CRAN essentials ──
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. └─SCpubr::do_CellularStatesPlot(...) at test-do_CellularStatesPlot.R:21:4
2. └─SCpubr::do_FeaturePlot(...)
3. └─SCpubr:::compute_scales(...)
4. └─SCpubr:::compute_scale_limits(...)
5. └─SCpubr:::.GetAssayData(sample, assay = assay, slot = slot)
── Error ('test-do_CopyNumberVariantPlot.R:4:5'): do_BarPlot: CRAN essentials ──
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_CopyNumberVariantPlot(...) at test-do_CopyNumberVariantPlot.R:4:4
2. │ ├─... %>% ...
3. │ └─SCpubr:::.GetAssayData(...)
4. ├─dplyr::summarise(., mean = mean(.data$CNV_score, na.rm = TRUE))
5. ├─dplyr::group_by(., .data[[group]], .data$Event)
6. ├─tidyr::pivot_longer(...)
7. ├─dplyr::left_join(...)
8. ├─tibble::rownames_to_column(., var = "Cell")
9. ├─base::as.data.frame(.)
10. ├─base::t(.)
11. └─base::as.matrix(.)
── Error ('test-do_CorrelationPlot.R:10:5'): do_CorrelationPlot: CRAN essentials ──
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. └─SCpubr::do_CorrelationPlot(sample = sample, legend.position = "top") at test-do_CorrelationPlot.R:10:4
2. ├─base::rownames(...)
3. └─SCpubr:::.GetAssayData(sample = sample, assay = assay, slot = "data")
── Error ('test-do_ExpressionHeatmap.R:5:5'): do_ExpressionHeatmap: CRAN essential tests ──
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_ExpressionHeatmap(sample, features = rownames(sample)[1:5]) at test-do_ExpressionHeatmap.R:5:4
2. │ ├─base::suppressMessages(...)
3. │ │ └─base::withCallingHandlers(...)
4. │ ├─... %>% ...
5. │ └─SCpubr:::.GetAssayData(sample, assay = assay, slot = slot)
6. ├─dplyr::summarise(., mean = mean(.data$expression, na.rm = TRUE))
7. ├─dplyr::group_by(., .data$group.by, .data$gene)
8. ├─tidyr::pivot_longer(...)
9. ├─dplyr::select(., -"cell")
10. ├─dplyr::left_join(...)
11. ├─tibble::rownames_to_column(., var = "cell")
12. ├─base::as.data.frame(.)
13. ├─base::t(.)
14. └─base::as.matrix(.)
── Error ('test-do_GeyserPlot.R:5:5'): do_GeyserPlot: CRAN essentials ──────────
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_GeyserPlot(sample = sample, features = "EPC1") at test-do_GeyserPlot.R:5:4
2. │ ├─... %>% ...
3. │ └─SCpubr:::.GetAssayData(sample = sample, assay = assay, slot = slot)
4. ├─dplyr::left_join(...)
5. ├─tibble::tibble(.)
6. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)
7. │ └─rlang::eval_tidy(xs[[j]], mask)
8. ├─tibble::rownames_to_column(., var = "cell")
9. ├─base::as.data.frame(.)
10. ├─base::t(.)
11. └─base::as.matrix(.)
── Error ('test-do_GroupwiseDEPlot.R:3:5'): do_GroupwiseDEPlot: CRAN essentials ──
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr:::.SetAssayData(...) at test-do_GroupwiseDEPlot.R:3:4
2. ├─base::as.matrix(...)
3. └─SCpubr:::.GetAssayData(sample = sample, assay = "SCT", slot = "data")
── Error ('test-do_PathwayActivityPlot.R:5:5'): do_PathwayActivityPlot: CRAN essentials ──
Error in `sample@assays[[assay]]$scale.data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_PathwayActivityPlot(sample = sample, activities = progeny_activities) at test-do_PathwayActivityPlot.R:5:4
2. │ ├─base::suppressMessages(...)
3. │ │ └─base::withCallingHandlers(...)
4. │ ├─... %>% ...
5. │ ├─base::t(...)
6. │ ├─base::as.matrix(...)
7. │ └─SCpubr:::.GetAssayData(sample = sample, assay = "progeny", slot = slot)
8. ├─dplyr::summarise(., mean = mean(.data$score, na.rm = TRUE))
9. ├─dplyr::group_by(., .data$group.by, .data$source)
10. ├─tidyr::pivot_longer(...)
11. ├─dplyr::select(., -"cell")
12. ├─dplyr::left_join(...)
13. ├─tibble::rownames_to_column(., var = "cell")
14. └─base::as.data.frame(.)
── Error ('test-do_TFActivityPlot.R:4:5'): do_TFActivityPlot: PASS - minimal input ──
Error in `sample@assays[[assay]]$scale.data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_TFActivityPlot(sample = sample, activities = dorothea_activities) at test-do_TFActivityPlot.R:4:4
2. │ ├─base::suppressMessages(...)
3. │ │ └─base::withCallingHandlers(...)
4. │ ├─... %>% ...
5. │ ├─base::t(...)
6. │ ├─base::as.matrix(...)
7. │ └─SCpubr:::.GetAssayData(sample = sample, assay = "dorothea", slot = slot)
8. ├─dplyr::summarise(., mean = mean(.data$score, na.rm = TRUE))
9. ├─dplyr::group_by(., .data$group.by, .data$source)
10. ├─tidyr::pivot_longer(...)
11. ├─dplyr::select(., -"cell")
12. ├─dplyr::left_join(...)
13. ├─tibble::rownames_to_column(., var = "cell")
14. └─base::as.data.frame(.)
── Error ('test-do_ViolinPlot.R:4:5'): do_ViolinPlot: CRAN essentials ──────────
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_ViolinPlot(sample = sample, features = "EPC1") at test-do_ViolinPlot.R:4:4
2. │ ├─base::append(...)
3. │ └─SCpubr:::get_data_column(...)
4. │ ├─... %>% dplyr::rename(feature = dplyr::all_of(c(feature)))
5. │ └─SCpubr:::.GetAssayData(sample = sample, assay = assay, slot = slot)
6. ├─dplyr::rename(., feature = dplyr::all_of(c(feature)))
7. ├─tibble::rownames_to_column(., var = "cell")
8. ├─base::as.data.frame(.)
9. ├─base::t(.)
10. └─base::as.matrix(.)
── Error ('test-utils.R:775:5'): utils: add_scale - PASS - checks ──────────────
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. └─SCpubr::do_FeaturePlot(sample, features = "EPC1") at test-utils.R:775:4
2. └─SCpubr:::compute_scales(...)
3. └─SCpubr:::compute_scale_limits(...)
4. └─SCpubr:::.GetAssayData(sample, assay = assay, slot = slot)
[ FAIL 10 | WARN 0 | SKIP 361 | PASS 71 ]
Error: Test failures
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 2.0.1
Check: tests
Result: ERROR
Running 'testthat.R' [132s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> # nolint start
> library(testthat)
> library(SCpubr)
── SCpubr 2.0.1 ────────────────────────────────────────────────────────────────
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! ──
ℹ To remove the white and black end from continuous palettes, use: options("SCpubr.ColorPaletteEnds" = FALSE)
✖ 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")
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
The sp package is now running under evolution status 2
(status 2 uses the sf package in place of rgdal)
[ FAIL 10 | WARN 0 | SKIP 391 | PASS 75 ]
══ Skipped tests (391) ═════════════════════════════════════════════════════════
• On CRAN (391): 'test-do_AlluvialPlot.R:14:5', 'test-do_BarPlot.R:26:5',
'test-do_BarPlot.R:35:5', 'test-do_BarPlot.R:46:5', 'test-do_BarPlot.R:59:5',
'test-do_BarPlot.R:74:5', 'test-do_BarPlot.R:83:5', 'test-do_BarPlot.R:92:5',
'test-do_BarPlot.R:100:5', 'test-do_BarPlot.R:110:5',
'test-do_BarPlot.R:120:5', 'test-do_BarPlot.R:132:5',
'test-do_BarPlot.R:155:5', 'test-do_BarPlot.R:177:5',
'test-do_BarPlot.R:188:5', 'test-do_BarPlot.R:203:5',
'test-do_BarPlot.R:215:5', 'test-do_BarPlot.R:228:5',
'test-do_BeeSwarmPlot.R:18:5', 'test-do_BeeSwarmPlot.R:40:5',
'test-do_BeeSwarmPlot.R:49:5', 'test-do_BeeSwarmPlot.R:81:5',
'test-do_BeeSwarmPlot.R:92:5', 'test-do_BeeSwarmPlot.R:101:5',
'test-do_BeeSwarmPlot.R:110:5', 'test-do_BeeSwarmPlot.R:120:5',
'test-do_BeeSwarmPlot.R:132:5', 'test-do_BeeSwarmPlot.R:141:5',
'test-do_BeeSwarmPlot.R:149:5', 'test-do_BeeSwarmPlot.R:158:5',
'test-do_BeeSwarmPlot.R:167:5', 'test-do_BeeSwarmPlot.R:177:5',
'test-do_BeeSwarmPlot.R:187:5', 'test-do_BeeSwarmPlot.R:196:5',
'test-do_BeeSwarmPlot.R:205:5', 'test-do_BeeSwarmPlot.R:222:5',
'test-do_BeeSwarmPlot.R:231:5', 'test-do_BeeSwarmPlot.R:240:5',
'test-do_BeeSwarmPlot.R:249:5', 'test-do_BeeSwarmPlot.R:258:5',
'test-do_BeeSwarmPlot.R:277:5', 'test-do_BoxPlot.R:22:5',
'test-do_BoxPlot.R:41:5', 'test-do_BoxPlot.R:62:5', 'test-do_BoxPlot.R:72:5',
'test-do_BoxPlot.R:80:5', 'test-do_BoxPlot.R:89:5',
'test-do_BoxPlot.R:103:5', 'test-do_BoxPlot.R:112:5',
'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:49:5', 'test-do_ChordDiagramPlot.R:150:5',
'test-do_ChordDiagramPlot.R:160:5', 'test-do_ChordDiagramPlot.R:177:5',
'test-do_ChordDiagramPlot.R:188:5', 'test-do_CopyNumberVariantPlot.R:13:5',
'test-do_CopyNumberVariantPlot.R:74:5',
'test-do_CopyNumberVariantPlot.R:83:5',
'test-do_CopyNumberVariantPlot.R:96:5',
'test-do_CopyNumberVariantPlot.R:109:5',
'test-do_CopyNumberVariantPlot.R:130:5', 'test-do_CorrelationPlot.R:16:5',
'test-do_CorrelationPlot.R:34:5', 'test-do_CorrelationPlot.R:58:5',
'test-do_CorrelationPlot.R:70:5', '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:16:5',
'test-do_DotPlot.R:77:5', 'test-do_DotPlot.R:92:5',
'test-do_DotPlot.R:109:5', 'test-do_DotPlot.R:119:5',
'test-do_DotPlot.R:133:5', 'test-do_DotPlot.R:144:5',
'test-do_DotPlot.R:155:5', 'test-do_DotPlot.R:166:5',
'test-do_DotPlot.R:176:5', 'test-do_DotPlot.R:195:5',
'test-do_DotPlot.R:215:5', 'test-do_DotPlot.R:236:5',
'test-do_DotPlot.R:254:5', 'test-do_DotPlot.R:273:5',
'test-do_DotPlot.R:295:5', 'test-do_EnrichmentHeatmap.R:19:5',
'test-do_EnrichmentHeatmap.R:193:5', 'test-do_EnrichmentHeatmap.R:224:5',
'test-do_EnrichmentHeatmap.R:241:5', 'test-do_EnrichmentHeatmap.R:275:5',
'test-do_EnrichmentHeatmap.R:314:5', 'test-do_EnrichmentHeatmap.R:337:5',
'test-do_EnrichmentHeatmap.R:356:5', 'test-do_ExpressionHeatmap.R:12:5',
'test-do_ExpressionHeatmap.R:150:5', 'test-do_ExpressionHeatmap.R:168:5',
'test-do_ExpressionHeatmap.R:186:5', 'test-do_ExpressionHeatmap.R:215:5',
'test-do_FeaturePlot.R:15:5', 'test-do_FeaturePlot.R:24:5',
'test-do_FeaturePlot.R:429:5', 'test-do_FeaturePlot.R:470:5',
'test-do_FeaturePlot.R:577:5', 'test-do_FeaturePlot.R:598:5',
'test-do_FeaturePlot.R:616:5', 'test-do_FeaturePlot.R:633:5',
'test-do_FeaturePlot.R:642:5', 'test-do_FeaturePlot.R:652:5',
'test-do_FeaturePlot.R:662:5', 'test-do_FeaturePlot.R:672:5',
'test-do_FeaturePlot.R:682:5', 'test-do_FeaturePlot.R:692:5',
'test-do_FeaturePlot.R:702:5', 'test-do_FeaturePlot.R:712:5',
'test-do_FeaturePlot.R:723:5', 'test-do_FeaturePlot.R:733:5',
'test-do_FeaturePlot.R:745:5', 'test-do_FeaturePlot.R:755:5',
'test-do_FeaturePlot.R:766:5', 'test-do_FeaturePlot.R:777:5',
'test-do_FeaturePlot.R:787:5', 'test-do_FeaturePlot.R:795:5',
'test-do_FeaturePlot.R:810:5', 'test-do_FeaturePlot.R:821:5',
'test-do_FeaturePlot.R:835:5', 'test-do_FeaturePlot.R:846:5',
'test-do_FeaturePlot.R:855:5', 'test-do_FeaturePlot.R:866:5',
'test-do_FeaturePlot.R:879:5', 'test-do_FeaturePlot.R:890:5',
'test-do_FeaturePlot.R:905:5', 'test-do_FeaturePlot.R:915:5',
'test-do_FeaturePlot.R:925:5', 'test-do_FeaturePlot.R:937:5',
'test-do_FeaturePlot.R:948:5', 'test-do_FeaturePlot.R:961:5',
'test-do_FeaturePlot.R:970:5', 'test-do_FeaturePlot.R:978:5',
'test-do_FeaturePlot.R:987:5', 'test-do_FunctionalAnnotationPlot.R:15:5',
'test-do_GeyserPlot.R:18:5', 'test-do_GeyserPlot.R:64:5',
'test-do_GeyserPlot.R:93:5', 'test-do_GeyserPlot.R:154:5',
'test-do_GeyserPlot.R:170:5', 'test-do_GeyserPlot.R:189:5',
'test-do_GeyserPlot.R:208:5', 'test-do_GeyserPlot.R:225:5',
'test-do_GeyserPlot.R:242:5', 'test-do_GeyserPlot.R:262:5',
'test-do_GeyserPlot.R:280:5', 'test-do_GeyserPlot.R:293:5',
'test-do_GroupedGOTermPlot.R:16:5', 'test-do_GroupwiseDEPlot.R:24:5',
'test-do_GroupwiseDEPlot.R:107:5', 'test-do_GroupwiseDEPlot.R:133:5',
'test-do_GroupwiseDEPlot.R:157:5', 'test-do_GroupwiseDEPlot.R:179:5',
'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_PathwayActivityPlot.R:12:5', 'test-do_PathwayActivityPlot.R:66:5',
'test-do_PathwayActivityPlot.R:78:5', 'test-do_PathwayActivityPlot.R:117:5',
'test-do_RidgePlot.R:41:5', 'test-do_RidgePlot.R:137:5',
'test-do_RidgePlot.R:153:5', 'test-do_RidgePlot.R:163:5',
'test-do_RidgePlot.R:180:5', 'test-do_RidgePlot.R:190:5',
'test-do_RidgePlot.R:210:5', 'test-do_RidgePlot.R:230:5',
'test-do_RidgePlot.R:242:5', 'test-do_TFActivityPlot.R:11:5',
'test-do_TFActivityPlot.R:72:5', 'test-do_TFActivityPlot.R:85:5',
'test-do_TFActivityPlot.R:99:5', 'test-do_TermEnrichmentPlot.R:11:5',
'test-do_TermEnrichmentPlot.R:24:5', 'test-do_TermEnrichmentPlot.R:31:5',
'test-do_TermEnrichmentPlot.R:39:5', 'test-do_TermEnrichmentPlot.R:47:5',
'test-do_TermEnrichmentPlot.R:56:5', 'test-do_ViolinPlot.R:10:5',
'test-do_ViolinPlot.R:25:5', 'test-do_ViolinPlot.R:37:5',
'test-do_ViolinPlot.R:49:5', 'test-do_ViolinPlot.R:65:5',
'test-do_ViolinPlot.R:94:5', 'test-do_ViolinPlot.R:113:5',
'test-do_ViolinPlot.R:123:5', 'test-do_ViolinPlot.R:133:5',
'test-do_ViolinPlot.R:146:5', 'test-do_ViolinPlot.R:158:5',
'test-do_ViolinPlot.R:170:5', 'test-do_ViolinPlot.R:182:5',
'test-do_ViolinPlot.R:205:5', 'test-do_ViolinPlot.R:217:5',
'test-do_ViolinPlot.R:240:5', 'test-do_ViolinPlot.R:264:5',
'test-do_ViolinPlot.R:277:5', 'test-do_ViolinPlot.R:295:5',
'test-do_ViolinPlot.R:304:5', '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:40:5', 'test-utils.R:45:5', 'test-utils.R:54:5',
'test-utils.R:60:5', 'test-utils.R:65:5', 'test-utils.R:70:5',
'test-utils.R:80:5', 'test-utils.R:89:5', 'test-utils.R:98:5',
'test-utils.R:107:5', 'test-utils.R:123:5', 'test-utils.R:134:5',
'test-utils.R:144:5', 'test-utils.R:152:5', 'test-utils.R:161:5',
'test-utils.R:172:5', 'test-utils.R:180:5', 'test-utils.R:188:5',
'test-utils.R:196:5', 'test-utils.R:205:5', 'test-utils.R:214:5',
'test-utils.R:223:5', 'test-utils.R:232:5', 'test-utils.R:246:5',
'test-utils.R:258:5', 'test-utils.R:269:5', 'test-utils.R:279:5',
'test-utils.R:291:5', 'test-utils.R:300:5', 'test-utils.R:309:5',
'test-utils.R:318:5', 'test-utils.R:329:5', 'test-utils.R:340:5',
'test-utils.R:354:5', 'test-utils.R:362:5', 'test-utils.R:371:5',
'test-utils.R:380:5', 'test-utils.R:393:5', 'test-utils.R:400:5',
'test-utils.R:410:5', 'test-utils.R:421:5', 'test-utils.R:427:5',
'test-utils.R:437:5', 'test-utils.R:446:5', 'test-utils.R:461:5',
'test-utils.R:468:5', 'test-utils.R:475:5', 'test-utils.R:482:5',
'test-utils.R:492:5', 'test-utils.R:500:5', 'test-utils.R:508:5',
'test-utils.R:518:5', 'test-utils.R:525:5', 'test-utils.R:535:5',
'test-utils.R:542:5', 'test-utils.R:550:5', 'test-utils.R:558:5',
'test-utils.R:570:5', 'test-utils.R:578:5', 'test-utils.R:585:5',
'test-utils.R:593:5', 'test-utils.R:600:5', 'test-utils.R:608:5',
'test-utils.R:615:5', 'test-utils.R:623:5', 'test-utils.R:630:5',
'test-utils.R:641:5', 'test-utils.R:646:5', 'test-utils.R:658:5',
'test-utils.R:666:5', 'test-utils.R:673:5', 'test-utils.R:683:5',
'test-utils.R:690:5', 'test-utils.R:745:5', 'test-utils.R:757:5',
'test-utils.R:789:5', 'test-utils.R:798:5', 'test-utils.R:825:5',
'test-utils.R:843:5', 'test-utils.R:850:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-do_CellularStatesPlot.R:21:5'): do_CellularStatesPlot: CRAN essentials ──
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. └─SCpubr::do_CellularStatesPlot(...) at test-do_CellularStatesPlot.R:21:4
2. └─SCpubr::do_FeaturePlot(...)
3. └─SCpubr:::compute_scales(...)
4. └─SCpubr:::compute_scale_limits(...)
5. └─SCpubr:::.GetAssayData(sample, assay = assay, slot = slot)
── Error ('test-do_CopyNumberVariantPlot.R:4:5'): do_BarPlot: CRAN essentials ──
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_CopyNumberVariantPlot(...) at test-do_CopyNumberVariantPlot.R:4:4
2. │ ├─... %>% ...
3. │ └─SCpubr:::.GetAssayData(...)
4. ├─dplyr::summarise(., mean = mean(.data$CNV_score, na.rm = TRUE))
5. ├─dplyr::group_by(., .data[[group]], .data$Event)
6. ├─tidyr::pivot_longer(...)
7. ├─dplyr::left_join(...)
8. ├─tibble::rownames_to_column(., var = "Cell")
9. ├─base::as.data.frame(.)
10. ├─base::t(.)
11. └─base::as.matrix(.)
── Error ('test-do_CorrelationPlot.R:10:5'): do_CorrelationPlot: CRAN essentials ──
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. └─SCpubr::do_CorrelationPlot(sample = sample, legend.position = "top") at test-do_CorrelationPlot.R:10:4
2. ├─base::rownames(...)
3. └─SCpubr:::.GetAssayData(sample = sample, assay = assay, slot = "data")
── Error ('test-do_ExpressionHeatmap.R:5:5'): do_ExpressionHeatmap: CRAN essential tests ──
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_ExpressionHeatmap(sample, features = rownames(sample)[1:5]) at test-do_ExpressionHeatmap.R:5:4
2. │ ├─base::suppressMessages(...)
3. │ │ └─base::withCallingHandlers(...)
4. │ ├─... %>% ...
5. │ └─SCpubr:::.GetAssayData(sample, assay = assay, slot = slot)
6. ├─dplyr::summarise(., mean = mean(.data$expression, na.rm = TRUE))
7. ├─dplyr::group_by(., .data$group.by, .data$gene)
8. ├─tidyr::pivot_longer(...)
9. ├─dplyr::select(., -"cell")
10. ├─dplyr::left_join(...)
11. ├─tibble::rownames_to_column(., var = "cell")
12. ├─base::as.data.frame(.)
13. ├─base::t(.)
14. └─base::as.matrix(.)
── Error ('test-do_GeyserPlot.R:5:5'): do_GeyserPlot: CRAN essentials ──────────
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_GeyserPlot(sample = sample, features = "EPC1") at test-do_GeyserPlot.R:5:4
2. │ ├─... %>% ...
3. │ └─SCpubr:::.GetAssayData(sample = sample, assay = assay, slot = slot)
4. ├─dplyr::left_join(...)
5. ├─tibble::tibble(.)
6. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)
7. │ └─rlang::eval_tidy(xs[[j]], mask)
8. ├─tibble::rownames_to_column(., var = "cell")
9. ├─base::as.data.frame(.)
10. ├─base::t(.)
11. └─base::as.matrix(.)
── Error ('test-do_GroupwiseDEPlot.R:3:5'): do_GroupwiseDEPlot: CRAN essentials ──
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr:::.SetAssayData(...) at test-do_GroupwiseDEPlot.R:3:4
2. ├─base::as.matrix(...)
3. └─SCpubr:::.GetAssayData(sample = sample, assay = "SCT", slot = "data")
── Error ('test-do_PathwayActivityPlot.R:5:5'): do_PathwayActivityPlot: CRAN essentials ──
Error in `sample@assays[[assay]]$scale.data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_PathwayActivityPlot(sample = sample, activities = progeny_activities) at test-do_PathwayActivityPlot.R:5:4
2. │ ├─base::suppressMessages(...)
3. │ │ └─base::withCallingHandlers(...)
4. │ ├─... %>% ...
5. │ ├─base::t(...)
6. │ ├─base::as.matrix(...)
7. │ └─SCpubr:::.GetAssayData(sample = sample, assay = "progeny", slot = slot)
8. ├─dplyr::summarise(., mean = mean(.data$score, na.rm = TRUE))
9. ├─dplyr::group_by(., .data$group.by, .data$source)
10. ├─tidyr::pivot_longer(...)
11. ├─dplyr::select(., -"cell")
12. ├─dplyr::left_join(...)
13. ├─tibble::rownames_to_column(., var = "cell")
14. └─base::as.data.frame(.)
── Error ('test-do_TFActivityPlot.R:4:5'): do_TFActivityPlot: PASS - minimal input ──
Error in `sample@assays[[assay]]$scale.data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_TFActivityPlot(sample = sample, activities = dorothea_activities) at test-do_TFActivityPlot.R:4:4
2. │ ├─base::suppressMessages(...)
3. │ │ └─base::withCallingHandlers(...)
4. │ ├─... %>% ...
5. │ ├─base::t(...)
6. │ ├─base::as.matrix(...)
7. │ └─SCpubr:::.GetAssayData(sample = sample, assay = "dorothea", slot = slot)
8. ├─dplyr::summarise(., mean = mean(.data$score, na.rm = TRUE))
9. ├─dplyr::group_by(., .data$group.by, .data$source)
10. ├─tidyr::pivot_longer(...)
11. ├─dplyr::select(., -"cell")
12. ├─dplyr::left_join(...)
13. ├─tibble::rownames_to_column(., var = "cell")
14. └─base::as.data.frame(.)
── Error ('test-do_ViolinPlot.R:4:5'): do_ViolinPlot: CRAN essentials ──────────
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_ViolinPlot(sample = sample, features = "EPC1") at test-do_ViolinPlot.R:4:4
2. │ ├─base::append(...)
3. │ └─SCpubr:::get_data_column(...)
4. │ ├─... %>% dplyr::rename(feature = dplyr::all_of(c(feature)))
5. │ └─SCpubr:::.GetAssayData(sample = sample, assay = assay, slot = slot)
6. ├─dplyr::rename(., feature = dplyr::all_of(c(feature)))
7. ├─tibble::rownames_to_column(., var = "cell")
8. ├─base::as.data.frame(.)
9. ├─base::t(.)
10. └─base::as.matrix(.)
── Error ('test-utils.R:775:5'): utils: add_scale - PASS - checks ──────────────
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. └─SCpubr::do_FeaturePlot(sample, features = "EPC1") at test-utils.R:775:4
2. └─SCpubr:::compute_scales(...)
3. └─SCpubr:::compute_scale_limits(...)
4. └─SCpubr:::.GetAssayData(sample, assay = assay, slot = slot)
[ FAIL 10 | WARN 0 | SKIP 391 | PASS 75 ]
Error: Test failures
Execution halted
Flavor: r-devel-windows-x86_64
Version: 2.0.1
Check: tests
Result: ERROR
Running ‘testthat.R’ [170s/199s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # nolint start
> library(testthat)
> library(SCpubr)
── SCpubr 2.0.1 ────────────────────────────────────────────────────────────────
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! ──
ℹ To remove the white and black end from continuous palettes, use: options("SCpubr.ColorPaletteEnds" = FALSE)
✖ 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")
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
The sp package is now running under evolution status 2
(status 2 uses the sf package in place of rgdal)
[ FAIL 10 | WARN 0 | SKIP 391 | PASS 75 ]
══ Skipped tests (391) ═════════════════════════════════════════════════════════
• On CRAN (391): 'test-do_AlluvialPlot.R:14:5', 'test-do_BarPlot.R:26:5',
'test-do_BarPlot.R:35:5', 'test-do_BarPlot.R:46:5', 'test-do_BarPlot.R:59:5',
'test-do_BarPlot.R:74:5', 'test-do_BarPlot.R:83:5', 'test-do_BarPlot.R:92:5',
'test-do_BarPlot.R:100:5', 'test-do_BarPlot.R:110:5',
'test-do_BarPlot.R:120:5', 'test-do_BarPlot.R:132:5',
'test-do_BarPlot.R:155:5', 'test-do_BarPlot.R:177:5',
'test-do_BarPlot.R:188:5', 'test-do_BarPlot.R:203:5',
'test-do_BarPlot.R:215:5', 'test-do_BarPlot.R:228:5',
'test-do_BeeSwarmPlot.R:18:5', 'test-do_BeeSwarmPlot.R:40:5',
'test-do_BeeSwarmPlot.R:49:5', 'test-do_BeeSwarmPlot.R:81:5',
'test-do_BeeSwarmPlot.R:92:5', 'test-do_BeeSwarmPlot.R:101:5',
'test-do_BeeSwarmPlot.R:110:5', 'test-do_BeeSwarmPlot.R:120:5',
'test-do_BeeSwarmPlot.R:132:5', 'test-do_BeeSwarmPlot.R:141:5',
'test-do_BeeSwarmPlot.R:149:5', 'test-do_BeeSwarmPlot.R:158:5',
'test-do_BeeSwarmPlot.R:167:5', 'test-do_BeeSwarmPlot.R:177:5',
'test-do_BeeSwarmPlot.R:187:5', 'test-do_BeeSwarmPlot.R:196:5',
'test-do_BeeSwarmPlot.R:205:5', 'test-do_BeeSwarmPlot.R:222:5',
'test-do_BeeSwarmPlot.R:231:5', 'test-do_BeeSwarmPlot.R:240:5',
'test-do_BeeSwarmPlot.R:249:5', 'test-do_BeeSwarmPlot.R:258:5',
'test-do_BeeSwarmPlot.R:277:5', 'test-do_BoxPlot.R:22:5',
'test-do_BoxPlot.R:41:5', 'test-do_BoxPlot.R:62:5', 'test-do_BoxPlot.R:72:5',
'test-do_BoxPlot.R:80:5', 'test-do_BoxPlot.R:89:5',
'test-do_BoxPlot.R:103:5', 'test-do_BoxPlot.R:112:5',
'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:49:5', 'test-do_ChordDiagramPlot.R:150:5',
'test-do_ChordDiagramPlot.R:160:5', 'test-do_ChordDiagramPlot.R:177:5',
'test-do_ChordDiagramPlot.R:188:5', 'test-do_CopyNumberVariantPlot.R:13:5',
'test-do_CopyNumberVariantPlot.R:74:5',
'test-do_CopyNumberVariantPlot.R:83:5',
'test-do_CopyNumberVariantPlot.R:96:5',
'test-do_CopyNumberVariantPlot.R:109:5',
'test-do_CopyNumberVariantPlot.R:130:5', 'test-do_CorrelationPlot.R:16:5',
'test-do_CorrelationPlot.R:34:5', 'test-do_CorrelationPlot.R:58:5',
'test-do_CorrelationPlot.R:70:5', '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:16:5',
'test-do_DotPlot.R:77:5', 'test-do_DotPlot.R:92:5',
'test-do_DotPlot.R:109:5', 'test-do_DotPlot.R:119:5',
'test-do_DotPlot.R:133:5', 'test-do_DotPlot.R:144:5',
'test-do_DotPlot.R:155:5', 'test-do_DotPlot.R:166:5',
'test-do_DotPlot.R:176:5', 'test-do_DotPlot.R:195:5',
'test-do_DotPlot.R:215:5', 'test-do_DotPlot.R:236:5',
'test-do_DotPlot.R:254:5', 'test-do_DotPlot.R:273:5',
'test-do_DotPlot.R:295:5', 'test-do_EnrichmentHeatmap.R:19:5',
'test-do_EnrichmentHeatmap.R:193:5', 'test-do_EnrichmentHeatmap.R:224:5',
'test-do_EnrichmentHeatmap.R:241:5', 'test-do_EnrichmentHeatmap.R:275:5',
'test-do_EnrichmentHeatmap.R:314:5', 'test-do_EnrichmentHeatmap.R:337:5',
'test-do_EnrichmentHeatmap.R:356:5', 'test-do_ExpressionHeatmap.R:12:5',
'test-do_ExpressionHeatmap.R:150:5', 'test-do_ExpressionHeatmap.R:168:5',
'test-do_ExpressionHeatmap.R:186:5', 'test-do_ExpressionHeatmap.R:215:5',
'test-do_FeaturePlot.R:15:5', 'test-do_FeaturePlot.R:24:5',
'test-do_FeaturePlot.R:429:5', 'test-do_FeaturePlot.R:470:5',
'test-do_FeaturePlot.R:577:5', 'test-do_FeaturePlot.R:598:5',
'test-do_FeaturePlot.R:616:5', 'test-do_FeaturePlot.R:633:5',
'test-do_FeaturePlot.R:642:5', 'test-do_FeaturePlot.R:652:5',
'test-do_FeaturePlot.R:662:5', 'test-do_FeaturePlot.R:672:5',
'test-do_FeaturePlot.R:682:5', 'test-do_FeaturePlot.R:692:5',
'test-do_FeaturePlot.R:702:5', 'test-do_FeaturePlot.R:712:5',
'test-do_FeaturePlot.R:723:5', 'test-do_FeaturePlot.R:733:5',
'test-do_FeaturePlot.R:745:5', 'test-do_FeaturePlot.R:755:5',
'test-do_FeaturePlot.R:766:5', 'test-do_FeaturePlot.R:777:5',
'test-do_FeaturePlot.R:787:5', 'test-do_FeaturePlot.R:795:5',
'test-do_FeaturePlot.R:810:5', 'test-do_FeaturePlot.R:821:5',
'test-do_FeaturePlot.R:835:5', 'test-do_FeaturePlot.R:846:5',
'test-do_FeaturePlot.R:855:5', 'test-do_FeaturePlot.R:866:5',
'test-do_FeaturePlot.R:879:5', 'test-do_FeaturePlot.R:890:5',
'test-do_FeaturePlot.R:905:5', 'test-do_FeaturePlot.R:915:5',
'test-do_FeaturePlot.R:925:5', 'test-do_FeaturePlot.R:937:5',
'test-do_FeaturePlot.R:948:5', 'test-do_FeaturePlot.R:961:5',
'test-do_FeaturePlot.R:970:5', 'test-do_FeaturePlot.R:978:5',
'test-do_FeaturePlot.R:987:5', 'test-do_FunctionalAnnotationPlot.R:15:5',
'test-do_GeyserPlot.R:18:5', 'test-do_GeyserPlot.R:64:5',
'test-do_GeyserPlot.R:93:5', 'test-do_GeyserPlot.R:154:5',
'test-do_GeyserPlot.R:170:5', 'test-do_GeyserPlot.R:189:5',
'test-do_GeyserPlot.R:208:5', 'test-do_GeyserPlot.R:225:5',
'test-do_GeyserPlot.R:242:5', 'test-do_GeyserPlot.R:262:5',
'test-do_GeyserPlot.R:280:5', 'test-do_GeyserPlot.R:293:5',
'test-do_GroupedGOTermPlot.R:16:5', 'test-do_GroupwiseDEPlot.R:24:5',
'test-do_GroupwiseDEPlot.R:107:5', 'test-do_GroupwiseDEPlot.R:133:5',
'test-do_GroupwiseDEPlot.R:157:5', 'test-do_GroupwiseDEPlot.R:179:5',
'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_PathwayActivityPlot.R:12:5', 'test-do_PathwayActivityPlot.R:66:5',
'test-do_PathwayActivityPlot.R:78:5', 'test-do_PathwayActivityPlot.R:117:5',
'test-do_RidgePlot.R:41:5', 'test-do_RidgePlot.R:137:5',
'test-do_RidgePlot.R:153:5', 'test-do_RidgePlot.R:163:5',
'test-do_RidgePlot.R:180:5', 'test-do_RidgePlot.R:190:5',
'test-do_RidgePlot.R:210:5', 'test-do_RidgePlot.R:230:5',
'test-do_RidgePlot.R:242:5', 'test-do_TFActivityPlot.R:11:5',
'test-do_TFActivityPlot.R:72:5', 'test-do_TFActivityPlot.R:85:5',
'test-do_TFActivityPlot.R:99:5', 'test-do_TermEnrichmentPlot.R:11:5',
'test-do_TermEnrichmentPlot.R:24:5', 'test-do_TermEnrichmentPlot.R:31:5',
'test-do_TermEnrichmentPlot.R:39:5', 'test-do_TermEnrichmentPlot.R:47:5',
'test-do_TermEnrichmentPlot.R:56:5', 'test-do_ViolinPlot.R:10:5',
'test-do_ViolinPlot.R:25:5', 'test-do_ViolinPlot.R:37:5',
'test-do_ViolinPlot.R:49:5', 'test-do_ViolinPlot.R:65:5',
'test-do_ViolinPlot.R:94:5', 'test-do_ViolinPlot.R:113:5',
'test-do_ViolinPlot.R:123:5', 'test-do_ViolinPlot.R:133:5',
'test-do_ViolinPlot.R:146:5', 'test-do_ViolinPlot.R:158:5',
'test-do_ViolinPlot.R:170:5', 'test-do_ViolinPlot.R:182:5',
'test-do_ViolinPlot.R:205:5', 'test-do_ViolinPlot.R:217:5',
'test-do_ViolinPlot.R:240:5', 'test-do_ViolinPlot.R:264:5',
'test-do_ViolinPlot.R:277:5', 'test-do_ViolinPlot.R:295:5',
'test-do_ViolinPlot.R:304:5', '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:40:5', 'test-utils.R:45:5', 'test-utils.R:54:5',
'test-utils.R:60:5', 'test-utils.R:65:5', 'test-utils.R:70:5',
'test-utils.R:80:5', 'test-utils.R:89:5', 'test-utils.R:98:5',
'test-utils.R:107:5', 'test-utils.R:123:5', 'test-utils.R:134:5',
'test-utils.R:144:5', 'test-utils.R:152:5', 'test-utils.R:161:5',
'test-utils.R:172:5', 'test-utils.R:180:5', 'test-utils.R:188:5',
'test-utils.R:196:5', 'test-utils.R:205:5', 'test-utils.R:214:5',
'test-utils.R:223:5', 'test-utils.R:232:5', 'test-utils.R:246:5',
'test-utils.R:258:5', 'test-utils.R:269:5', 'test-utils.R:279:5',
'test-utils.R:291:5', 'test-utils.R:300:5', 'test-utils.R:309:5',
'test-utils.R:318:5', 'test-utils.R:329:5', 'test-utils.R:340:5',
'test-utils.R:354:5', 'test-utils.R:362:5', 'test-utils.R:371:5',
'test-utils.R:380:5', 'test-utils.R:393:5', 'test-utils.R:400:5',
'test-utils.R:410:5', 'test-utils.R:421:5', 'test-utils.R:427:5',
'test-utils.R:437:5', 'test-utils.R:446:5', 'test-utils.R:461:5',
'test-utils.R:468:5', 'test-utils.R:475:5', 'test-utils.R:482:5',
'test-utils.R:492:5', 'test-utils.R:500:5', 'test-utils.R:508:5',
'test-utils.R:518:5', 'test-utils.R:525:5', 'test-utils.R:535:5',
'test-utils.R:542:5', 'test-utils.R:550:5', 'test-utils.R:558:5',
'test-utils.R:570:5', 'test-utils.R:578:5', 'test-utils.R:585:5',
'test-utils.R:593:5', 'test-utils.R:600:5', 'test-utils.R:608:5',
'test-utils.R:615:5', 'test-utils.R:623:5', 'test-utils.R:630:5',
'test-utils.R:641:5', 'test-utils.R:646:5', 'test-utils.R:658:5',
'test-utils.R:666:5', 'test-utils.R:673:5', 'test-utils.R:683:5',
'test-utils.R:690:5', 'test-utils.R:745:5', 'test-utils.R:757:5',
'test-utils.R:789:5', 'test-utils.R:798:5', 'test-utils.R:825:5',
'test-utils.R:843:5', 'test-utils.R:850:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-do_CellularStatesPlot.R:21:5'): do_CellularStatesPlot: CRAN essentials ──
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. └─SCpubr::do_CellularStatesPlot(...) at test-do_CellularStatesPlot.R:21:4
2. └─SCpubr::do_FeaturePlot(...)
3. └─SCpubr:::compute_scales(...)
4. └─SCpubr:::compute_scale_limits(...)
5. └─SCpubr:::.GetAssayData(sample, assay = assay, slot = slot)
── Error ('test-do_CopyNumberVariantPlot.R:4:5'): do_BarPlot: CRAN essentials ──
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_CopyNumberVariantPlot(...) at test-do_CopyNumberVariantPlot.R:4:4
2. │ ├─... %>% ...
3. │ └─SCpubr:::.GetAssayData(...)
4. ├─dplyr::summarise(., mean = mean(.data$CNV_score, na.rm = TRUE))
5. ├─dplyr::group_by(., .data[[group]], .data$Event)
6. ├─tidyr::pivot_longer(...)
7. ├─dplyr::left_join(...)
8. ├─tibble::rownames_to_column(., var = "Cell")
9. ├─base::as.data.frame(.)
10. ├─base::t(.)
11. └─base::as.matrix(.)
── Error ('test-do_CorrelationPlot.R:10:5'): do_CorrelationPlot: CRAN essentials ──
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. └─SCpubr::do_CorrelationPlot(sample = sample, legend.position = "top") at test-do_CorrelationPlot.R:10:4
2. ├─base::rownames(...)
3. └─SCpubr:::.GetAssayData(sample = sample, assay = assay, slot = "data")
── Error ('test-do_ExpressionHeatmap.R:5:5'): do_ExpressionHeatmap: CRAN essential tests ──
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_ExpressionHeatmap(sample, features = rownames(sample)[1:5]) at test-do_ExpressionHeatmap.R:5:4
2. │ ├─base::suppressMessages(...)
3. │ │ └─base::withCallingHandlers(...)
4. │ ├─... %>% ...
5. │ └─SCpubr:::.GetAssayData(sample, assay = assay, slot = slot)
6. ├─dplyr::summarise(., mean = mean(.data$expression, na.rm = TRUE))
7. ├─dplyr::group_by(., .data$group.by, .data$gene)
8. ├─tidyr::pivot_longer(...)
9. ├─dplyr::select(., -"cell")
10. ├─dplyr::left_join(...)
11. ├─tibble::rownames_to_column(., var = "cell")
12. ├─base::as.data.frame(.)
13. ├─base::t(.)
14. └─base::as.matrix(.)
── Error ('test-do_GeyserPlot.R:5:5'): do_GeyserPlot: CRAN essentials ──────────
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_GeyserPlot(sample = sample, features = "EPC1") at test-do_GeyserPlot.R:5:4
2. │ ├─... %>% ...
3. │ └─SCpubr:::.GetAssayData(sample = sample, assay = assay, slot = slot)
4. ├─dplyr::left_join(...)
5. ├─tibble::tibble(.)
6. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)
7. │ └─rlang::eval_tidy(xs[[j]], mask)
8. ├─tibble::rownames_to_column(., var = "cell")
9. ├─base::as.data.frame(.)
10. ├─base::t(.)
11. └─base::as.matrix(.)
── Error ('test-do_GroupwiseDEPlot.R:3:5'): do_GroupwiseDEPlot: CRAN essentials ──
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr:::.SetAssayData(...) at test-do_GroupwiseDEPlot.R:3:4
2. ├─base::as.matrix(...)
3. └─SCpubr:::.GetAssayData(sample = sample, assay = "SCT", slot = "data")
── Error ('test-do_PathwayActivityPlot.R:5:5'): do_PathwayActivityPlot: CRAN essentials ──
Error in `sample@assays[[assay]]$scale.data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_PathwayActivityPlot(sample = sample, activities = progeny_activities) at test-do_PathwayActivityPlot.R:5:4
2. │ ├─base::suppressMessages(...)
3. │ │ └─base::withCallingHandlers(...)
4. │ ├─... %>% ...
5. │ ├─base::t(...)
6. │ ├─base::as.matrix(...)
7. │ └─SCpubr:::.GetAssayData(sample = sample, assay = "progeny", slot = slot)
8. ├─dplyr::summarise(., mean = mean(.data$score, na.rm = TRUE))
9. ├─dplyr::group_by(., .data$group.by, .data$source)
10. ├─tidyr::pivot_longer(...)
11. ├─dplyr::select(., -"cell")
12. ├─dplyr::left_join(...)
13. ├─tibble::rownames_to_column(., var = "cell")
14. └─base::as.data.frame(.)
── Error ('test-do_TFActivityPlot.R:4:5'): do_TFActivityPlot: PASS - minimal input ──
Error in `sample@assays[[assay]]$scale.data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_TFActivityPlot(sample = sample, activities = dorothea_activities) at test-do_TFActivityPlot.R:4:4
2. │ ├─base::suppressMessages(...)
3. │ │ └─base::withCallingHandlers(...)
4. │ ├─... %>% ...
5. │ ├─base::t(...)
6. │ ├─base::as.matrix(...)
7. │ └─SCpubr:::.GetAssayData(sample = sample, assay = "dorothea", slot = slot)
8. ├─dplyr::summarise(., mean = mean(.data$score, na.rm = TRUE))
9. ├─dplyr::group_by(., .data$group.by, .data$source)
10. ├─tidyr::pivot_longer(...)
11. ├─dplyr::select(., -"cell")
12. ├─dplyr::left_join(...)
13. ├─tibble::rownames_to_column(., var = "cell")
14. └─base::as.data.frame(.)
── Error ('test-do_ViolinPlot.R:4:5'): do_ViolinPlot: CRAN essentials ──────────
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_ViolinPlot(sample = sample, features = "EPC1") at test-do_ViolinPlot.R:4:4
2. │ ├─base::append(...)
3. │ └─SCpubr:::get_data_column(...)
4. │ ├─... %>% dplyr::rename(feature = dplyr::all_of(c(feature)))
5. │ └─SCpubr:::.GetAssayData(sample = sample, assay = assay, slot = slot)
6. ├─dplyr::rename(., feature = dplyr::all_of(c(feature)))
7. ├─tibble::rownames_to_column(., var = "cell")
8. ├─base::as.data.frame(.)
9. ├─base::t(.)
10. └─base::as.matrix(.)
── Error ('test-utils.R:775:5'): utils: add_scale - PASS - checks ──────────────
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. └─SCpubr::do_FeaturePlot(sample, features = "EPC1") at test-utils.R:775:4
2. └─SCpubr:::compute_scales(...)
3. └─SCpubr:::compute_scale_limits(...)
4. └─SCpubr:::.GetAssayData(sample, assay = assay, slot = slot)
[ FAIL 10 | WARN 0 | SKIP 391 | PASS 75 ]
Error: Test failures
Execution halted
Flavor: r-release-linux-x86_64
Version: 2.0.1
Check: tests
Result: ERROR
Running 'testthat.R' [179s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> # nolint start
> library(testthat)
> library(SCpubr)
── SCpubr 2.0.1 ────────────────────────────────────────────────────────────────
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! ──
ℹ To remove the white and black end from continuous palettes, use: options("SCpubr.ColorPaletteEnds" = FALSE)
✖ 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")
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
The sp package is now running under evolution status 2
(status 2 uses the sf package in place of rgdal)
[ FAIL 10 | WARN 0 | SKIP 391 | PASS 75 ]
══ Skipped tests (391) ═════════════════════════════════════════════════════════
• On CRAN (391): 'test-do_AlluvialPlot.R:14:5', 'test-do_BarPlot.R:26:5',
'test-do_BarPlot.R:35:5', 'test-do_BarPlot.R:46:5', 'test-do_BarPlot.R:59:5',
'test-do_BarPlot.R:74:5', 'test-do_BarPlot.R:83:5', 'test-do_BarPlot.R:92:5',
'test-do_BarPlot.R:100:5', 'test-do_BarPlot.R:110:5',
'test-do_BarPlot.R:120:5', 'test-do_BarPlot.R:132:5',
'test-do_BarPlot.R:155:5', 'test-do_BarPlot.R:177:5',
'test-do_BarPlot.R:188:5', 'test-do_BarPlot.R:203:5',
'test-do_BarPlot.R:215:5', 'test-do_BarPlot.R:228:5',
'test-do_BeeSwarmPlot.R:18:5', 'test-do_BeeSwarmPlot.R:40:5',
'test-do_BeeSwarmPlot.R:49:5', 'test-do_BeeSwarmPlot.R:81:5',
'test-do_BeeSwarmPlot.R:92:5', 'test-do_BeeSwarmPlot.R:101:5',
'test-do_BeeSwarmPlot.R:110:5', 'test-do_BeeSwarmPlot.R:120:5',
'test-do_BeeSwarmPlot.R:132:5', 'test-do_BeeSwarmPlot.R:141:5',
'test-do_BeeSwarmPlot.R:149:5', 'test-do_BeeSwarmPlot.R:158:5',
'test-do_BeeSwarmPlot.R:167:5', 'test-do_BeeSwarmPlot.R:177:5',
'test-do_BeeSwarmPlot.R:187:5', 'test-do_BeeSwarmPlot.R:196:5',
'test-do_BeeSwarmPlot.R:205:5', 'test-do_BeeSwarmPlot.R:222:5',
'test-do_BeeSwarmPlot.R:231:5', 'test-do_BeeSwarmPlot.R:240:5',
'test-do_BeeSwarmPlot.R:249:5', 'test-do_BeeSwarmPlot.R:258:5',
'test-do_BeeSwarmPlot.R:277:5', 'test-do_BoxPlot.R:22:5',
'test-do_BoxPlot.R:41:5', 'test-do_BoxPlot.R:62:5', 'test-do_BoxPlot.R:72:5',
'test-do_BoxPlot.R:80:5', 'test-do_BoxPlot.R:89:5',
'test-do_BoxPlot.R:103:5', 'test-do_BoxPlot.R:112:5',
'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:49:5', 'test-do_ChordDiagramPlot.R:150:5',
'test-do_ChordDiagramPlot.R:160:5', 'test-do_ChordDiagramPlot.R:177:5',
'test-do_ChordDiagramPlot.R:188:5', 'test-do_CopyNumberVariantPlot.R:13:5',
'test-do_CopyNumberVariantPlot.R:74:5',
'test-do_CopyNumberVariantPlot.R:83:5',
'test-do_CopyNumberVariantPlot.R:96:5',
'test-do_CopyNumberVariantPlot.R:109:5',
'test-do_CopyNumberVariantPlot.R:130:5', 'test-do_CorrelationPlot.R:16:5',
'test-do_CorrelationPlot.R:34:5', 'test-do_CorrelationPlot.R:58:5',
'test-do_CorrelationPlot.R:70:5', '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:16:5',
'test-do_DotPlot.R:77:5', 'test-do_DotPlot.R:92:5',
'test-do_DotPlot.R:109:5', 'test-do_DotPlot.R:119:5',
'test-do_DotPlot.R:133:5', 'test-do_DotPlot.R:144:5',
'test-do_DotPlot.R:155:5', 'test-do_DotPlot.R:166:5',
'test-do_DotPlot.R:176:5', 'test-do_DotPlot.R:195:5',
'test-do_DotPlot.R:215:5', 'test-do_DotPlot.R:236:5',
'test-do_DotPlot.R:254:5', 'test-do_DotPlot.R:273:5',
'test-do_DotPlot.R:295:5', 'test-do_EnrichmentHeatmap.R:19:5',
'test-do_EnrichmentHeatmap.R:193:5', 'test-do_EnrichmentHeatmap.R:224:5',
'test-do_EnrichmentHeatmap.R:241:5', 'test-do_EnrichmentHeatmap.R:275:5',
'test-do_EnrichmentHeatmap.R:314:5', 'test-do_EnrichmentHeatmap.R:337:5',
'test-do_EnrichmentHeatmap.R:356:5', 'test-do_ExpressionHeatmap.R:12:5',
'test-do_ExpressionHeatmap.R:150:5', 'test-do_ExpressionHeatmap.R:168:5',
'test-do_ExpressionHeatmap.R:186:5', 'test-do_ExpressionHeatmap.R:215:5',
'test-do_FeaturePlot.R:15:5', 'test-do_FeaturePlot.R:24:5',
'test-do_FeaturePlot.R:429:5', 'test-do_FeaturePlot.R:470:5',
'test-do_FeaturePlot.R:577:5', 'test-do_FeaturePlot.R:598:5',
'test-do_FeaturePlot.R:616:5', 'test-do_FeaturePlot.R:633:5',
'test-do_FeaturePlot.R:642:5', 'test-do_FeaturePlot.R:652:5',
'test-do_FeaturePlot.R:662:5', 'test-do_FeaturePlot.R:672:5',
'test-do_FeaturePlot.R:682:5', 'test-do_FeaturePlot.R:692:5',
'test-do_FeaturePlot.R:702:5', 'test-do_FeaturePlot.R:712:5',
'test-do_FeaturePlot.R:723:5', 'test-do_FeaturePlot.R:733:5',
'test-do_FeaturePlot.R:745:5', 'test-do_FeaturePlot.R:755:5',
'test-do_FeaturePlot.R:766:5', 'test-do_FeaturePlot.R:777:5',
'test-do_FeaturePlot.R:787:5', 'test-do_FeaturePlot.R:795:5',
'test-do_FeaturePlot.R:810:5', 'test-do_FeaturePlot.R:821:5',
'test-do_FeaturePlot.R:835:5', 'test-do_FeaturePlot.R:846:5',
'test-do_FeaturePlot.R:855:5', 'test-do_FeaturePlot.R:866:5',
'test-do_FeaturePlot.R:879:5', 'test-do_FeaturePlot.R:890:5',
'test-do_FeaturePlot.R:905:5', 'test-do_FeaturePlot.R:915:5',
'test-do_FeaturePlot.R:925:5', 'test-do_FeaturePlot.R:937:5',
'test-do_FeaturePlot.R:948:5', 'test-do_FeaturePlot.R:961:5',
'test-do_FeaturePlot.R:970:5', 'test-do_FeaturePlot.R:978:5',
'test-do_FeaturePlot.R:987:5', 'test-do_FunctionalAnnotationPlot.R:15:5',
'test-do_GeyserPlot.R:18:5', 'test-do_GeyserPlot.R:64:5',
'test-do_GeyserPlot.R:93:5', 'test-do_GeyserPlot.R:154:5',
'test-do_GeyserPlot.R:170:5', 'test-do_GeyserPlot.R:189:5',
'test-do_GeyserPlot.R:208:5', 'test-do_GeyserPlot.R:225:5',
'test-do_GeyserPlot.R:242:5', 'test-do_GeyserPlot.R:262:5',
'test-do_GeyserPlot.R:280:5', 'test-do_GeyserPlot.R:293:5',
'test-do_GroupedGOTermPlot.R:16:5', 'test-do_GroupwiseDEPlot.R:24:5',
'test-do_GroupwiseDEPlot.R:107:5', 'test-do_GroupwiseDEPlot.R:133:5',
'test-do_GroupwiseDEPlot.R:157:5', 'test-do_GroupwiseDEPlot.R:179:5',
'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_PathwayActivityPlot.R:12:5', 'test-do_PathwayActivityPlot.R:66:5',
'test-do_PathwayActivityPlot.R:78:5', 'test-do_PathwayActivityPlot.R:117:5',
'test-do_RidgePlot.R:41:5', 'test-do_RidgePlot.R:137:5',
'test-do_RidgePlot.R:153:5', 'test-do_RidgePlot.R:163:5',
'test-do_RidgePlot.R:180:5', 'test-do_RidgePlot.R:190:5',
'test-do_RidgePlot.R:210:5', 'test-do_RidgePlot.R:230:5',
'test-do_RidgePlot.R:242:5', 'test-do_TFActivityPlot.R:11:5',
'test-do_TFActivityPlot.R:72:5', 'test-do_TFActivityPlot.R:85:5',
'test-do_TFActivityPlot.R:99:5', 'test-do_TermEnrichmentPlot.R:11:5',
'test-do_TermEnrichmentPlot.R:24:5', 'test-do_TermEnrichmentPlot.R:31:5',
'test-do_TermEnrichmentPlot.R:39:5', 'test-do_TermEnrichmentPlot.R:47:5',
'test-do_TermEnrichmentPlot.R:56:5', 'test-do_ViolinPlot.R:10:5',
'test-do_ViolinPlot.R:25:5', 'test-do_ViolinPlot.R:37:5',
'test-do_ViolinPlot.R:49:5', 'test-do_ViolinPlot.R:65:5',
'test-do_ViolinPlot.R:94:5', 'test-do_ViolinPlot.R:113:5',
'test-do_ViolinPlot.R:123:5', 'test-do_ViolinPlot.R:133:5',
'test-do_ViolinPlot.R:146:5', 'test-do_ViolinPlot.R:158:5',
'test-do_ViolinPlot.R:170:5', 'test-do_ViolinPlot.R:182:5',
'test-do_ViolinPlot.R:205:5', 'test-do_ViolinPlot.R:217:5',
'test-do_ViolinPlot.R:240:5', 'test-do_ViolinPlot.R:264:5',
'test-do_ViolinPlot.R:277:5', 'test-do_ViolinPlot.R:295:5',
'test-do_ViolinPlot.R:304:5', '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:40:5', 'test-utils.R:45:5', 'test-utils.R:54:5',
'test-utils.R:60:5', 'test-utils.R:65:5', 'test-utils.R:70:5',
'test-utils.R:80:5', 'test-utils.R:89:5', 'test-utils.R:98:5',
'test-utils.R:107:5', 'test-utils.R:123:5', 'test-utils.R:134:5',
'test-utils.R:144:5', 'test-utils.R:152:5', 'test-utils.R:161:5',
'test-utils.R:172:5', 'test-utils.R:180:5', 'test-utils.R:188:5',
'test-utils.R:196:5', 'test-utils.R:205:5', 'test-utils.R:214:5',
'test-utils.R:223:5', 'test-utils.R:232:5', 'test-utils.R:246:5',
'test-utils.R:258:5', 'test-utils.R:269:5', 'test-utils.R:279:5',
'test-utils.R:291:5', 'test-utils.R:300:5', 'test-utils.R:309:5',
'test-utils.R:318:5', 'test-utils.R:329:5', 'test-utils.R:340:5',
'test-utils.R:354:5', 'test-utils.R:362:5', 'test-utils.R:371:5',
'test-utils.R:380:5', 'test-utils.R:393:5', 'test-utils.R:400:5',
'test-utils.R:410:5', 'test-utils.R:421:5', 'test-utils.R:427:5',
'test-utils.R:437:5', 'test-utils.R:446:5', 'test-utils.R:461:5',
'test-utils.R:468:5', 'test-utils.R:475:5', 'test-utils.R:482:5',
'test-utils.R:492:5', 'test-utils.R:500:5', 'test-utils.R:508:5',
'test-utils.R:518:5', 'test-utils.R:525:5', 'test-utils.R:535:5',
'test-utils.R:542:5', 'test-utils.R:550:5', 'test-utils.R:558:5',
'test-utils.R:570:5', 'test-utils.R:578:5', 'test-utils.R:585:5',
'test-utils.R:593:5', 'test-utils.R:600:5', 'test-utils.R:608:5',
'test-utils.R:615:5', 'test-utils.R:623:5', 'test-utils.R:630:5',
'test-utils.R:641:5', 'test-utils.R:646:5', 'test-utils.R:658:5',
'test-utils.R:666:5', 'test-utils.R:673:5', 'test-utils.R:683:5',
'test-utils.R:690:5', 'test-utils.R:745:5', 'test-utils.R:757:5',
'test-utils.R:789:5', 'test-utils.R:798:5', 'test-utils.R:825:5',
'test-utils.R:843:5', 'test-utils.R:850:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-do_CellularStatesPlot.R:21:5'): do_CellularStatesPlot: CRAN essentials ──
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. └─SCpubr::do_CellularStatesPlot(...) at test-do_CellularStatesPlot.R:21:4
2. └─SCpubr::do_FeaturePlot(...)
3. └─SCpubr:::compute_scales(...)
4. └─SCpubr:::compute_scale_limits(...)
5. └─SCpubr:::.GetAssayData(sample, assay = assay, slot = slot)
── Error ('test-do_CopyNumberVariantPlot.R:4:5'): do_BarPlot: CRAN essentials ──
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_CopyNumberVariantPlot(...) at test-do_CopyNumberVariantPlot.R:4:4
2. │ ├─... %>% ...
3. │ └─SCpubr:::.GetAssayData(...)
4. ├─dplyr::summarise(., mean = mean(.data$CNV_score, na.rm = TRUE))
5. ├─dplyr::group_by(., .data[[group]], .data$Event)
6. ├─tidyr::pivot_longer(...)
7. ├─dplyr::left_join(...)
8. ├─tibble::rownames_to_column(., var = "Cell")
9. ├─base::as.data.frame(.)
10. ├─base::t(.)
11. └─base::as.matrix(.)
── Error ('test-do_CorrelationPlot.R:10:5'): do_CorrelationPlot: CRAN essentials ──
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. └─SCpubr::do_CorrelationPlot(sample = sample, legend.position = "top") at test-do_CorrelationPlot.R:10:4
2. ├─base::rownames(...)
3. └─SCpubr:::.GetAssayData(sample = sample, assay = assay, slot = "data")
── Error ('test-do_ExpressionHeatmap.R:5:5'): do_ExpressionHeatmap: CRAN essential tests ──
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_ExpressionHeatmap(sample, features = rownames(sample)[1:5]) at test-do_ExpressionHeatmap.R:5:4
2. │ ├─base::suppressMessages(...)
3. │ │ └─base::withCallingHandlers(...)
4. │ ├─... %>% ...
5. │ └─SCpubr:::.GetAssayData(sample, assay = assay, slot = slot)
6. ├─dplyr::summarise(., mean = mean(.data$expression, na.rm = TRUE))
7. ├─dplyr::group_by(., .data$group.by, .data$gene)
8. ├─tidyr::pivot_longer(...)
9. ├─dplyr::select(., -"cell")
10. ├─dplyr::left_join(...)
11. ├─tibble::rownames_to_column(., var = "cell")
12. ├─base::as.data.frame(.)
13. ├─base::t(.)
14. └─base::as.matrix(.)
── Error ('test-do_GeyserPlot.R:5:5'): do_GeyserPlot: CRAN essentials ──────────
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_GeyserPlot(sample = sample, features = "EPC1") at test-do_GeyserPlot.R:5:4
2. │ ├─... %>% ...
3. │ └─SCpubr:::.GetAssayData(sample = sample, assay = assay, slot = slot)
4. ├─dplyr::left_join(...)
5. ├─tibble::tibble(.)
6. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)
7. │ └─rlang::eval_tidy(xs[[j]], mask)
8. ├─tibble::rownames_to_column(., var = "cell")
9. ├─base::as.data.frame(.)
10. ├─base::t(.)
11. └─base::as.matrix(.)
── Error ('test-do_GroupwiseDEPlot.R:3:5'): do_GroupwiseDEPlot: CRAN essentials ──
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr:::.SetAssayData(...) at test-do_GroupwiseDEPlot.R:3:4
2. ├─base::as.matrix(...)
3. └─SCpubr:::.GetAssayData(sample = sample, assay = "SCT", slot = "data")
── Error ('test-do_PathwayActivityPlot.R:5:5'): do_PathwayActivityPlot: CRAN essentials ──
Error in `sample@assays[[assay]]$scale.data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_PathwayActivityPlot(sample = sample, activities = progeny_activities) at test-do_PathwayActivityPlot.R:5:4
2. │ ├─base::suppressMessages(...)
3. │ │ └─base::withCallingHandlers(...)
4. │ ├─... %>% ...
5. │ ├─base::t(...)
6. │ ├─base::as.matrix(...)
7. │ └─SCpubr:::.GetAssayData(sample = sample, assay = "progeny", slot = slot)
8. ├─dplyr::summarise(., mean = mean(.data$score, na.rm = TRUE))
9. ├─dplyr::group_by(., .data$group.by, .data$source)
10. ├─tidyr::pivot_longer(...)
11. ├─dplyr::select(., -"cell")
12. ├─dplyr::left_join(...)
13. ├─tibble::rownames_to_column(., var = "cell")
14. └─base::as.data.frame(.)
── Error ('test-do_TFActivityPlot.R:4:5'): do_TFActivityPlot: PASS - minimal input ──
Error in `sample@assays[[assay]]$scale.data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_TFActivityPlot(sample = sample, activities = dorothea_activities) at test-do_TFActivityPlot.R:4:4
2. │ ├─base::suppressMessages(...)
3. │ │ └─base::withCallingHandlers(...)
4. │ ├─... %>% ...
5. │ ├─base::t(...)
6. │ ├─base::as.matrix(...)
7. │ └─SCpubr:::.GetAssayData(sample = sample, assay = "dorothea", slot = slot)
8. ├─dplyr::summarise(., mean = mean(.data$score, na.rm = TRUE))
9. ├─dplyr::group_by(., .data$group.by, .data$source)
10. ├─tidyr::pivot_longer(...)
11. ├─dplyr::select(., -"cell")
12. ├─dplyr::left_join(...)
13. ├─tibble::rownames_to_column(., var = "cell")
14. └─base::as.data.frame(.)
── Error ('test-do_ViolinPlot.R:4:5'): do_ViolinPlot: CRAN essentials ──────────
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_ViolinPlot(sample = sample, features = "EPC1") at test-do_ViolinPlot.R:4:4
2. │ ├─base::append(...)
3. │ └─SCpubr:::get_data_column(...)
4. │ ├─... %>% dplyr::rename(feature = dplyr::all_of(c(feature)))
5. │ └─SCpubr:::.GetAssayData(sample = sample, assay = assay, slot = slot)
6. ├─dplyr::rename(., feature = dplyr::all_of(c(feature)))
7. ├─tibble::rownames_to_column(., var = "cell")
8. ├─base::as.data.frame(.)
9. ├─base::t(.)
10. └─base::as.matrix(.)
── Error ('test-utils.R:775:5'): utils: add_scale - PASS - checks ──────────────
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. └─SCpubr::do_FeaturePlot(sample, features = "EPC1") at test-utils.R:775:4
2. └─SCpubr:::compute_scales(...)
3. └─SCpubr:::compute_scale_limits(...)
4. └─SCpubr:::.GetAssayData(sample, assay = assay, slot = slot)
[ FAIL 10 | WARN 0 | SKIP 391 | PASS 75 ]
Error: Test failures
Execution halted
Flavor: r-release-windows-x86_64
Version: 2.0.1
Check: Rd cross-references
Result: NOTE
Unknown package ‘infercnv’ in Rd xrefs
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64
Version: 2.0.1
Check: tests
Result: ERROR
Running 'testthat.R' [150s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
> # nolint start
> library(testthat)
> library(SCpubr)
── SCpubr 2.0.1 ────────────────────────────────────────────────────────────────
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! ──
ℹ To remove the white and black end from continuous palettes, use: options("SCpubr.ColorPaletteEnds" = FALSE)
✖ 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")
The legacy packages maptools, rgdal, and rgeos, underpinning the sp package,
which was just loaded, will retire in October 2023.
Please refer to R-spatial evolution reports for details, especially
https://r-spatial.org/r/2023/05/15/evolution4.html.
It may be desirable to make the sf package available;
package maintainers should consider adding sf to Suggests:.
The sp package is now running under evolution status 2
(status 2 uses the sf package in place of rgdal)
[ FAIL 10 | WARN 0 | SKIP 391 | PASS 75 ]
══ Skipped tests (391) ═════════════════════════════════════════════════════════
• On CRAN (391): 'test-do_AlluvialPlot.R:14:5', 'test-do_BarPlot.R:26:5',
'test-do_BarPlot.R:35:5', 'test-do_BarPlot.R:46:5', 'test-do_BarPlot.R:59:5',
'test-do_BarPlot.R:74:5', 'test-do_BarPlot.R:83:5', 'test-do_BarPlot.R:92:5',
'test-do_BarPlot.R:100:5', 'test-do_BarPlot.R:110:5',
'test-do_BarPlot.R:120:5', 'test-do_BarPlot.R:132:5',
'test-do_BarPlot.R:155:5', 'test-do_BarPlot.R:177:5',
'test-do_BarPlot.R:188:5', 'test-do_BarPlot.R:203:5',
'test-do_BarPlot.R:215:5', 'test-do_BarPlot.R:228:5',
'test-do_BeeSwarmPlot.R:18:5', 'test-do_BeeSwarmPlot.R:40:5',
'test-do_BeeSwarmPlot.R:49:5', 'test-do_BeeSwarmPlot.R:81:5',
'test-do_BeeSwarmPlot.R:92:5', 'test-do_BeeSwarmPlot.R:101:5',
'test-do_BeeSwarmPlot.R:110:5', 'test-do_BeeSwarmPlot.R:120:5',
'test-do_BeeSwarmPlot.R:132:5', 'test-do_BeeSwarmPlot.R:141:5',
'test-do_BeeSwarmPlot.R:149:5', 'test-do_BeeSwarmPlot.R:158:5',
'test-do_BeeSwarmPlot.R:167:5', 'test-do_BeeSwarmPlot.R:177:5',
'test-do_BeeSwarmPlot.R:187:5', 'test-do_BeeSwarmPlot.R:196:5',
'test-do_BeeSwarmPlot.R:205:5', 'test-do_BeeSwarmPlot.R:222:5',
'test-do_BeeSwarmPlot.R:231:5', 'test-do_BeeSwarmPlot.R:240:5',
'test-do_BeeSwarmPlot.R:249:5', 'test-do_BeeSwarmPlot.R:258:5',
'test-do_BeeSwarmPlot.R:277:5', 'test-do_BoxPlot.R:22:5',
'test-do_BoxPlot.R:41:5', 'test-do_BoxPlot.R:62:5', 'test-do_BoxPlot.R:72:5',
'test-do_BoxPlot.R:80:5', 'test-do_BoxPlot.R:89:5',
'test-do_BoxPlot.R:103:5', 'test-do_BoxPlot.R:112:5',
'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:49:5', 'test-do_ChordDiagramPlot.R:150:5',
'test-do_ChordDiagramPlot.R:160:5', 'test-do_ChordDiagramPlot.R:177:5',
'test-do_ChordDiagramPlot.R:188:5', 'test-do_CopyNumberVariantPlot.R:13:5',
'test-do_CopyNumberVariantPlot.R:74:5',
'test-do_CopyNumberVariantPlot.R:83:5',
'test-do_CopyNumberVariantPlot.R:96:5',
'test-do_CopyNumberVariantPlot.R:109:5',
'test-do_CopyNumberVariantPlot.R:130:5', 'test-do_CorrelationPlot.R:16:5',
'test-do_CorrelationPlot.R:34:5', 'test-do_CorrelationPlot.R:58:5',
'test-do_CorrelationPlot.R:70:5', '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:16:5',
'test-do_DotPlot.R:77:5', 'test-do_DotPlot.R:92:5',
'test-do_DotPlot.R:109:5', 'test-do_DotPlot.R:119:5',
'test-do_DotPlot.R:133:5', 'test-do_DotPlot.R:144:5',
'test-do_DotPlot.R:155:5', 'test-do_DotPlot.R:166:5',
'test-do_DotPlot.R:176:5', 'test-do_DotPlot.R:195:5',
'test-do_DotPlot.R:215:5', 'test-do_DotPlot.R:236:5',
'test-do_DotPlot.R:254:5', 'test-do_DotPlot.R:273:5',
'test-do_DotPlot.R:295:5', 'test-do_EnrichmentHeatmap.R:19:5',
'test-do_EnrichmentHeatmap.R:193:5', 'test-do_EnrichmentHeatmap.R:224:5',
'test-do_EnrichmentHeatmap.R:241:5', 'test-do_EnrichmentHeatmap.R:275:5',
'test-do_EnrichmentHeatmap.R:314:5', 'test-do_EnrichmentHeatmap.R:337:5',
'test-do_EnrichmentHeatmap.R:356:5', 'test-do_ExpressionHeatmap.R:12:5',
'test-do_ExpressionHeatmap.R:150:5', 'test-do_ExpressionHeatmap.R:168:5',
'test-do_ExpressionHeatmap.R:186:5', 'test-do_ExpressionHeatmap.R:215:5',
'test-do_FeaturePlot.R:15:5', 'test-do_FeaturePlot.R:24:5',
'test-do_FeaturePlot.R:429:5', 'test-do_FeaturePlot.R:470:5',
'test-do_FeaturePlot.R:577:5', 'test-do_FeaturePlot.R:598:5',
'test-do_FeaturePlot.R:616:5', 'test-do_FeaturePlot.R:633:5',
'test-do_FeaturePlot.R:642:5', 'test-do_FeaturePlot.R:652:5',
'test-do_FeaturePlot.R:662:5', 'test-do_FeaturePlot.R:672:5',
'test-do_FeaturePlot.R:682:5', 'test-do_FeaturePlot.R:692:5',
'test-do_FeaturePlot.R:702:5', 'test-do_FeaturePlot.R:712:5',
'test-do_FeaturePlot.R:723:5', 'test-do_FeaturePlot.R:733:5',
'test-do_FeaturePlot.R:745:5', 'test-do_FeaturePlot.R:755:5',
'test-do_FeaturePlot.R:766:5', 'test-do_FeaturePlot.R:777:5',
'test-do_FeaturePlot.R:787:5', 'test-do_FeaturePlot.R:795:5',
'test-do_FeaturePlot.R:810:5', 'test-do_FeaturePlot.R:821:5',
'test-do_FeaturePlot.R:835:5', 'test-do_FeaturePlot.R:846:5',
'test-do_FeaturePlot.R:855:5', 'test-do_FeaturePlot.R:866:5',
'test-do_FeaturePlot.R:879:5', 'test-do_FeaturePlot.R:890:5',
'test-do_FeaturePlot.R:905:5', 'test-do_FeaturePlot.R:915:5',
'test-do_FeaturePlot.R:925:5', 'test-do_FeaturePlot.R:937:5',
'test-do_FeaturePlot.R:948:5', 'test-do_FeaturePlot.R:961:5',
'test-do_FeaturePlot.R:970:5', 'test-do_FeaturePlot.R:978:5',
'test-do_FeaturePlot.R:987:5', 'test-do_FunctionalAnnotationPlot.R:15:5',
'test-do_GeyserPlot.R:18:5', 'test-do_GeyserPlot.R:64:5',
'test-do_GeyserPlot.R:93:5', 'test-do_GeyserPlot.R:154:5',
'test-do_GeyserPlot.R:170:5', 'test-do_GeyserPlot.R:189:5',
'test-do_GeyserPlot.R:208:5', 'test-do_GeyserPlot.R:225:5',
'test-do_GeyserPlot.R:242:5', 'test-do_GeyserPlot.R:262:5',
'test-do_GeyserPlot.R:280:5', 'test-do_GeyserPlot.R:293:5',
'test-do_GroupedGOTermPlot.R:16:5', 'test-do_GroupwiseDEPlot.R:24:5',
'test-do_GroupwiseDEPlot.R:107:5', 'test-do_GroupwiseDEPlot.R:133:5',
'test-do_GroupwiseDEPlot.R:157:5', 'test-do_GroupwiseDEPlot.R:179:5',
'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_PathwayActivityPlot.R:12:5', 'test-do_PathwayActivityPlot.R:66:5',
'test-do_PathwayActivityPlot.R:78:5', 'test-do_PathwayActivityPlot.R:117:5',
'test-do_RidgePlot.R:41:5', 'test-do_RidgePlot.R:137:5',
'test-do_RidgePlot.R:153:5', 'test-do_RidgePlot.R:163:5',
'test-do_RidgePlot.R:180:5', 'test-do_RidgePlot.R:190:5',
'test-do_RidgePlot.R:210:5', 'test-do_RidgePlot.R:230:5',
'test-do_RidgePlot.R:242:5', 'test-do_TFActivityPlot.R:11:5',
'test-do_TFActivityPlot.R:72:5', 'test-do_TFActivityPlot.R:85:5',
'test-do_TFActivityPlot.R:99:5', 'test-do_TermEnrichmentPlot.R:11:5',
'test-do_TermEnrichmentPlot.R:24:5', 'test-do_TermEnrichmentPlot.R:31:5',
'test-do_TermEnrichmentPlot.R:39:5', 'test-do_TermEnrichmentPlot.R:47:5',
'test-do_TermEnrichmentPlot.R:56:5', 'test-do_ViolinPlot.R:10:5',
'test-do_ViolinPlot.R:25:5', 'test-do_ViolinPlot.R:37:5',
'test-do_ViolinPlot.R:49:5', 'test-do_ViolinPlot.R:65:5',
'test-do_ViolinPlot.R:94:5', 'test-do_ViolinPlot.R:113:5',
'test-do_ViolinPlot.R:123:5', 'test-do_ViolinPlot.R:133:5',
'test-do_ViolinPlot.R:146:5', 'test-do_ViolinPlot.R:158:5',
'test-do_ViolinPlot.R:170:5', 'test-do_ViolinPlot.R:182:5',
'test-do_ViolinPlot.R:205:5', 'test-do_ViolinPlot.R:217:5',
'test-do_ViolinPlot.R:240:5', 'test-do_ViolinPlot.R:264:5',
'test-do_ViolinPlot.R:277:5', 'test-do_ViolinPlot.R:295:5',
'test-do_ViolinPlot.R:304:5', '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:40:5', 'test-utils.R:45:5', 'test-utils.R:54:5',
'test-utils.R:60:5', 'test-utils.R:65:5', 'test-utils.R:70:5',
'test-utils.R:80:5', 'test-utils.R:89:5', 'test-utils.R:98:5',
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'test-utils.R:144:5', 'test-utils.R:152:5', 'test-utils.R:161:5',
'test-utils.R:172:5', 'test-utils.R:180:5', 'test-utils.R:188:5',
'test-utils.R:196:5', 'test-utils.R:205:5', 'test-utils.R:214:5',
'test-utils.R:223:5', 'test-utils.R:232:5', 'test-utils.R:246:5',
'test-utils.R:258:5', 'test-utils.R:269:5', 'test-utils.R:279:5',
'test-utils.R:291:5', 'test-utils.R:300:5', 'test-utils.R:309:5',
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'test-utils.R:354:5', 'test-utils.R:362:5', 'test-utils.R:371:5',
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'test-utils.R:492:5', 'test-utils.R:500:5', 'test-utils.R:508:5',
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'test-utils.R:542:5', 'test-utils.R:550:5', 'test-utils.R:558:5',
'test-utils.R:570:5', 'test-utils.R:578:5', 'test-utils.R:585:5',
'test-utils.R:593:5', 'test-utils.R:600:5', 'test-utils.R:608:5',
'test-utils.R:615:5', 'test-utils.R:623:5', 'test-utils.R:630:5',
'test-utils.R:641:5', 'test-utils.R:646:5', 'test-utils.R:658:5',
'test-utils.R:666:5', 'test-utils.R:673:5', 'test-utils.R:683:5',
'test-utils.R:690:5', 'test-utils.R:745:5', 'test-utils.R:757:5',
'test-utils.R:789:5', 'test-utils.R:798:5', 'test-utils.R:825:5',
'test-utils.R:843:5', 'test-utils.R:850:5'
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-do_CellularStatesPlot.R:21:5'): do_CellularStatesPlot: CRAN essentials ──
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. └─SCpubr::do_CellularStatesPlot(...) at test-do_CellularStatesPlot.R:21:4
2. └─SCpubr::do_FeaturePlot(...)
3. └─SCpubr:::compute_scales(...)
4. └─SCpubr:::compute_scale_limits(...)
5. └─SCpubr:::.GetAssayData(sample, assay = assay, slot = slot)
── Error ('test-do_CopyNumberVariantPlot.R:4:5'): do_BarPlot: CRAN essentials ──
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_CopyNumberVariantPlot(...) at test-do_CopyNumberVariantPlot.R:4:4
2. │ ├─... %>% ...
3. │ └─SCpubr:::.GetAssayData(...)
4. ├─dplyr::summarise(., mean = mean(.data$CNV_score, na.rm = TRUE))
5. ├─dplyr::group_by(., .data[[group]], .data$Event)
6. ├─tidyr::pivot_longer(...)
7. ├─dplyr::left_join(...)
8. ├─tibble::rownames_to_column(., var = "Cell")
9. ├─base::as.data.frame(.)
10. ├─base::t(.)
11. └─base::as.matrix(.)
── Error ('test-do_CorrelationPlot.R:10:5'): do_CorrelationPlot: CRAN essentials ──
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. └─SCpubr::do_CorrelationPlot(sample = sample, legend.position = "top") at test-do_CorrelationPlot.R:10:4
2. ├─base::rownames(...)
3. └─SCpubr:::.GetAssayData(sample = sample, assay = assay, slot = "data")
── Error ('test-do_ExpressionHeatmap.R:5:5'): do_ExpressionHeatmap: CRAN essential tests ──
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_ExpressionHeatmap(sample, features = rownames(sample)[1:5]) at test-do_ExpressionHeatmap.R:5:4
2. │ ├─base::suppressMessages(...)
3. │ │ └─base::withCallingHandlers(...)
4. │ ├─... %>% ...
5. │ └─SCpubr:::.GetAssayData(sample, assay = assay, slot = slot)
6. ├─dplyr::summarise(., mean = mean(.data$expression, na.rm = TRUE))
7. ├─dplyr::group_by(., .data$group.by, .data$gene)
8. ├─tidyr::pivot_longer(...)
9. ├─dplyr::select(., -"cell")
10. ├─dplyr::left_join(...)
11. ├─tibble::rownames_to_column(., var = "cell")
12. ├─base::as.data.frame(.)
13. ├─base::t(.)
14. └─base::as.matrix(.)
── Error ('test-do_GeyserPlot.R:5:5'): do_GeyserPlot: CRAN essentials ──────────
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_GeyserPlot(sample = sample, features = "EPC1") at test-do_GeyserPlot.R:5:4
2. │ ├─... %>% ...
3. │ └─SCpubr:::.GetAssayData(sample = sample, assay = assay, slot = slot)
4. ├─dplyr::left_join(...)
5. ├─tibble::tibble(.)
6. │ └─tibble:::tibble_quos(xs, .rows, .name_repair)
7. │ └─rlang::eval_tidy(xs[[j]], mask)
8. ├─tibble::rownames_to_column(., var = "cell")
9. ├─base::as.data.frame(.)
10. ├─base::t(.)
11. └─base::as.matrix(.)
── Error ('test-do_GroupwiseDEPlot.R:3:5'): do_GroupwiseDEPlot: CRAN essentials ──
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr:::.SetAssayData(...) at test-do_GroupwiseDEPlot.R:3:4
2. ├─base::as.matrix(...)
3. └─SCpubr:::.GetAssayData(sample = sample, assay = "SCT", slot = "data")
── Error ('test-do_PathwayActivityPlot.R:5:5'): do_PathwayActivityPlot: CRAN essentials ──
Error in `sample@assays[[assay]]$scale.data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_PathwayActivityPlot(sample = sample, activities = progeny_activities) at test-do_PathwayActivityPlot.R:5:4
2. │ ├─base::suppressMessages(...)
3. │ │ └─base::withCallingHandlers(...)
4. │ ├─... %>% ...
5. │ ├─base::t(...)
6. │ ├─base::as.matrix(...)
7. │ └─SCpubr:::.GetAssayData(sample = sample, assay = "progeny", slot = slot)
8. ├─dplyr::summarise(., mean = mean(.data$score, na.rm = TRUE))
9. ├─dplyr::group_by(., .data$group.by, .data$source)
10. ├─tidyr::pivot_longer(...)
11. ├─dplyr::select(., -"cell")
12. ├─dplyr::left_join(...)
13. ├─tibble::rownames_to_column(., var = "cell")
14. └─base::as.data.frame(.)
── Error ('test-do_TFActivityPlot.R:4:5'): do_TFActivityPlot: PASS - minimal input ──
Error in `sample@assays[[assay]]$scale.data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_TFActivityPlot(sample = sample, activities = dorothea_activities) at test-do_TFActivityPlot.R:4:4
2. │ ├─base::suppressMessages(...)
3. │ │ └─base::withCallingHandlers(...)
4. │ ├─... %>% ...
5. │ ├─base::t(...)
6. │ ├─base::as.matrix(...)
7. │ └─SCpubr:::.GetAssayData(sample = sample, assay = "dorothea", slot = slot)
8. ├─dplyr::summarise(., mean = mean(.data$score, na.rm = TRUE))
9. ├─dplyr::group_by(., .data$group.by, .data$source)
10. ├─tidyr::pivot_longer(...)
11. ├─dplyr::select(., -"cell")
12. ├─dplyr::left_join(...)
13. ├─tibble::rownames_to_column(., var = "cell")
14. └─base::as.data.frame(.)
── Error ('test-do_ViolinPlot.R:4:5'): do_ViolinPlot: CRAN essentials ──────────
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. ├─SCpubr::do_ViolinPlot(sample = sample, features = "EPC1") at test-do_ViolinPlot.R:4:4
2. │ ├─base::append(...)
3. │ └─SCpubr:::get_data_column(...)
4. │ ├─... %>% dplyr::rename(feature = dplyr::all_of(c(feature)))
5. │ └─SCpubr:::.GetAssayData(sample = sample, assay = assay, slot = slot)
6. ├─dplyr::rename(., feature = dplyr::all_of(c(feature)))
7. ├─tibble::rownames_to_column(., var = "cell")
8. ├─base::as.data.frame(.)
9. ├─base::t(.)
10. └─base::as.matrix(.)
── Error ('test-utils.R:775:5'): utils: add_scale - PASS - checks ──────────────
Error in `sample@assays[[assay]]$data`: $ operator not defined for this S4 class
Backtrace:
▆
1. └─SCpubr::do_FeaturePlot(sample, features = "EPC1") at test-utils.R:775:4
2. └─SCpubr:::compute_scales(...)
3. └─SCpubr:::compute_scale_limits(...)
4. └─SCpubr:::.GetAssayData(sample, assay = assay, slot = slot)
[ FAIL 10 | WARN 0 | SKIP 391 | PASS 75 ]
Error: Test failures
Execution halted
Flavor: r-oldrel-windows-x86_64