Package: rliger Check: examples New result: ERROR Running examples in ‘rliger-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: plotPairwiseDEGHeatmap > ### Title: Create heatmap for pairwise DEG analysis result > ### Aliases: plotPairwiseDEGHeatmap > > ### ** Examples > > defaultCluster(pbmc) <- pbmcPlot$leiden_cluster ℹ Storing given cluster labels to `cellMeta(x)` field: "defaultCluster". > pbmc$condition_cluster <- interaction(pbmc$dataset, pbmc$defaultCluster) > deg <- runPairwiseDEG(pbmc, 'stim.0', 'stim.1', 'condition_cluster') ℹ Calling pairwise DESeq2 Wald test ✖ Error when computing on "stim.0": invalid class “DESeqDataSet” object: superclass "ExpData" not defined in the environment of the object's class ℹ Calling pairwise DESeq2 Wald test ! Empty result returned for this test. ℹ Calling pairwise DESeq2 Wald test ✖ Calling pairwise DESeq2 Wald test ... failed > pbmc <- normalize(pbmc) ℹ Normalizing datasets "ctrl" ✔ Normalizing datasets "ctrl" ... done ℹ Normalizing datasets "stim" ✔ Normalizing datasets "stim" ... done > plotPairwiseDEGHeatmap(pbmc, deg, 'stim.0') Error in `subsetLiger()`: ! No feature can be retrieved Backtrace: ▆ 1. └─rliger::plotPairwiseDEGHeatmap(pbmc, deg, "stim.0") 2. └─rliger::plotGeneHeatmap(...) 3. └─rliger::retrieveCellFeature(...) 4. └─rliger::subsetLiger(...) 5. └─cli::cli_abort("No feature can be retrieved") 6. └─rlang::abort(...) Execution halted Package: rliger Check: tests New result: ERROR Running ‘testthat.R’ [60s/59s] Running the tests in ‘tests/testthat.R’ failed. Complete output: > library(testthat) > library(rliger) Package `rliger` has been updated massively since version 1.99.0, including the object structure which is not compatible with old versions. We recommand you backup your old analysis before overwriting any existing result. `readLiger()` is provided for reading an RDS file storing an old object and it converts the object to the up-to-date structure. > > test_check("rliger") Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Reading input file... Number of nodes: 600 Number of edges: 18017 Running Louvain algorithm... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Modularity: 0.7390 Number of communities: 8 Elapsed time: 0 seconds Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck Reading input file... Number of nodes: 600 Number of edges: 17528 Running Louvain algorithm... 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Modularity: 0.7567 Number of communities: 8 Elapsed time: 0 seconds Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Wilcoxon rank-sum test over 266 features across 300 cells 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Wilcoxon rank-sum test over 249 features across 600 cells 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| INMF started, niter=2 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Total time: 0 sec Objective error: 49910.7 UINMF started, niter=2 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Total time: 0 sec Objective error: 4377.62 UINMF started, niter=2 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Total time: 0 sec Objective error: 4629.63 UINMF started, niter=2 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Total time: 0 sec Objective error: 11026.4 Starting online iNMF scenario 1, factorize all datasets 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| ************************************************Total iterations: 30 Total time: 0 sec Objective error: 45414.7 **| INMF started, niter=2 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Total time: 0 sec Objective error: 41528.3 INMF started, niter=2 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Total time: 0 sec Objective error: 47418.4 INMF started, niter=2 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Total time: 0 sec Objective error: 45693.4 INMF started, niter=2 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Total time: 0 sec Objective error: 45973.6 INMF started, niter=2 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Total time: 0 sec Objective error: 22149.3 INMF started, niter=2 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Total time: 0 sec Objective error: 66227.2 INMF started, niter=2 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Total time: 0 sec Objective error: 66117.9 Starting online iNMF scenario 1, factorize all datasets 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| ************************************************Total iterations: 30 Total time: 0 sec Objective error: 37129 **| Starting online iNMF scenario 2, update factorization with new datasets 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **********************************************Total iterations: 15 Total time: 0 sec Objective error: 54366.5 ****| Starting online iNMF scenario 2, update factorization with new datasets 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **********************************************Total iterations: 15 Total time: 0 sec Objective error: 54366.5 ****| Starting online iNMF scenario 1, factorize all datasets 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| ************************************************Total iterations: 30 Total time: 0 sec Objective error: 37129 **| Starting online iNMF scenario 1, factorize all datasets 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| ************************************************Total iterations: 30 Total time: 0 sec Objective error: 37129 **| INMF started, niter=30 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Total time: 0 sec Objective error: 35967.3 Starting online iNMF scenario 1, factorize all datasets 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| ************************************************Total iterations: 30 Total time: 0 sec Objective error: 45414.7 **| Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| A liger command record, performed at 05-07-2025 12:51:14 EDT Call: normalize.liger(object) Parameters: useDatasets : "ctrl", "stim" verbose : TRUE Starting online iNMF scenario 1, factorize all datasets 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| ************************************************Total iterations: 30 Total time: 0 sec Objective error: 45414.7 **| Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Working ctrl H5 file path: /home/hornik/tmp/scratch/RtmpzkMNlv/ctrltest_454413d7062dc.h5 Working stim H5 file path: /home/hornik/tmp/scratch/RtmpzkMNlv/stimtest_454418cd25a3.h5 Working ctrl H5 file path: /home/hornik/tmp/scratch/RtmpzkMNlv/ctrltest_454415435baf.h5 Working stim H5 file path: /home/hornik/tmp/scratch/RtmpzkMNlv/stimtest_45441ac93ced.h5 Working ctrl H5 file path: /home/hornik/tmp/scratch/RtmpzkMNlv/ctrltest_4544144b2d782.h5 Working stim H5 file path: /home/hornik/tmp/scratch/RtmpzkMNlv/stimtest_454415e4d2bff.h5 Working ctrl H5 file path: /home/hornik/tmp/scratch/RtmpzkMNlv/ctrltest_454412238a62a.h5 Working stim H5 file path: /home/hornik/tmp/scratch/RtmpzkMNlv/stimtest_454414bab9082.h5 Starting online iNMF scenario 1, factorize all datasets 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| ************************************************Total iterations: 30 Total time: 0 sec Objective error: 37129 **| Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Working ctrl H5 file path: /home/hornik/tmp/scratch/RtmpzkMNlv/ctrltest_454417395d0db.h5 Working stim H5 file path: /home/hornik/tmp/scratch/RtmpzkMNlv/stimtest_454416326f42.h5 Starting online iNMF scenario 1, factorize all datasets 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| ************************************************Total iterations: 30 Total time: 0 sec Objective error: 37129 **| Using method 'umap' 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| [ FAIL 2 | WARN 0 | SKIP 18 | PASS 1233 ] ══ Skipped tests (18) ══════════════════════════════════════════════════════════ • On CRAN (11): 'test_downstream.R:83:5', 'test_downstream.R:152:5', 'test_downstream.R:190:5', 'test_downstream.R:283:5', 'test_downstream.R:308:5', 'test_factorization.R:232:5', 'test_factorization.R:264:5', 'test_factorization.R:299:5', 'test_object.R:390:5', 'test_object.R:443:5', 'test_object.R:530:5' • Skipping (6): 'test_object.R:68:5', 'test_object.R:321:5', 'test_preprocessing.R:41:13', 'test_preprocessing.R:153:13', 'test_preprocessing.R:218:13', 'test_preprocessing.R:285:13' • {fields} is not installed (1): 'test_preprocessing.R:94:5' ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test_downstream.R:247:5'): pseudo bulk ──────────────────────────── all.equal(dim(res1), c(nIsecGenes, 7)) is not TRUE `actual` is a character vector ('Mean relative difference: 50.2') `expected` is a logical vector (TRUE) ── Failure ('test_downstream.R:253:5'): pseudo bulk ──────────────────────────── all.equal(dim(res2), c(nIsecGenes, 7)) is not TRUE `actual` is a character vector ('Mean relative difference: 50.2') `expected` is a logical vector (TRUE) [ FAIL 2 | WARN 0 | SKIP 18 | PASS 1233 ] Error: Test failures Execution halted