Running ‘testthat.R’ [325s/414s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > if (requireNamespace("testthat", quietly = TRUE)) {
  +   library("checkmate")
  +   library("testthat")
  +   library("mlr3")
  +   library("paradox")
  +   library("mlr3pipelines")
  +   test_check("mlr3pipelines")
  + }
  Starting 2 test processes.
  > test_Graph.R: Training debug.multi with input list(input_1 = 1, input_2 = 1)
  > test_PipeOp.R: Training test_autotrain
  > test_PipeOp.R: Predicting test_autotrain
  > test_PipeOp.R: Training test_autotrain
  > test_PipeOp.R: Training test_autotrain
  > test_PipeOp.R: Predicting test_autotrain
  > test_PipeOp.R: Predicting test_autotrain
  > test_PipeOp.R: Training test_autotrain
  > test_PipeOp.R: Training test_autotrain
  > test_PipeOp.R: Training test_autotrain
  > test_PipeOp.R: Predicting test_autotrain
  > test_PipeOp.R: Predicting test_autotrain
  > test_PipeOp.R: Predicting test_autotrain
  > test_PipeOp.R: Training test_autotrain
  > test_PipeOp.R: Predicting test_autotrain
  > test_PipeOp.R: Training test_autotrain
  > test_PipeOp.R: Training test_autotrain
  > test_PipeOp.R: Predicting test_autotrain
  > test_PipeOp.R: Predicting test_autotrain
  > test_PipeOp.R: Training test_autotrain
  > test_PipeOp.R: Training test_autotrain
  > test_PipeOp.R: Training test_autotrain
  > test_PipeOp.R: Predicting test_autotrain
  > test_PipeOp.R: 
  > test_PipeOp.R: Predicting test_autotrain
  > test_PipeOp.R: Predicting test_autotrain
  > test_PipeOp.R: Training test_autotrain
  > test_PipeOp.R: Predicting test_autotrain
  > test_filter_ensemble.R: OptimInstanceSingleCrit is deprecated. Use OptimInstanceBatchSingleCrit instead.
  Saving _problems/test_filter_ensemble-294.R
  Saving _problems/test_filter_ensemble-307.R
  > test_mlr_graphs_robustify.R: 'as(<dgCMatrix>, "dgTMatrix")' is deprecated.
  > test_mlr_graphs_robustify.R: Use 'as(., "TsparseMatrix")' instead.
  > test_mlr_graphs_robustify.R: See help("Deprecated") and help("Matrix-deprecated").
  > test_multiplicities.R: 
  > test_multiplicities.R: [[1]]
  > test_multiplicities.R: [1] 0
  > test_multiplicities.R: 
  > test_multiplicities.R: 
  > test_pipeop_blsmote.R: [1] "Borderline-SMOTE done"
  > test_pipeop_blsmote.R: [1] "Borderline-SMOTE done"
  > test_pipeop_blsmote.R: [1] "Borderline-SMOTE done"
  > test_pipeop_blsmote.R: [1] "Borderline-SMOTE done"
  Saving _problems/test_pipeop_datefeatures-7.R
  Saving _problems/test_pipeop_datefeatures-17.R
  > test_pipeop_isomap.R: 2026-01-29 23:10:23.931628: Isomap START
  > test_pipeop_isomap.R: 2026-01-29 23:10:23.932178: constructing knn graph
  > test_pipeop_isomap.R: 2026-01-29 23:10:23.959805: calculating geodesic distances
  > test_pipeop_isomap.R: 2026-01-29 23:10:24.013676: Classical Scaling
  > test_pipeop_isomap.R: 2026-01-29 23:10:24.122822: Isomap START
  > test_pipeop_isomap.R: 2026-01-29 23:10:24.123117: constructing knn graph
  > test_pipeop_isomap.R: 2026-01-29 23:10:24.169656: calculating geodesic distances
  > test_pipeop_isomap.R: 2026-01-29 23:10:24.200254: Classical Scaling
  > test_pipeop_isomap.R: 2026-01-29 23:10:24.265372: L-Isomap embed START
  > test_pipeop_isomap.R: 2026-01-29 23:10:24.265817: constructing knn graph
  > test_pipeop_isomap.R: 2026-01-29 23:10:24.313512: calculating geodesic distances
  > test_pipeop_isomap.R: 2026-01-29 23:10:24.40652: embedding
  > test_pipeop_isomap.R: 2026-01-29 23:10:24.407685: DONE
  > test_pipeop_isomap.R: 2026-01-29 23:10:24.450692: L-Isomap embed START
  > test_pipeop_isomap.R: 2026-01-29 23:10:24.451027: constructing knn graph
  > test_pipeop_isomap.R: 2026-01-29 23:10:24.509381: calculating geodesic distances
  > test_pipeop_isomap.R: 2026-01-29 23:10:24.618225: embedding
  > test_pipeop_isomap.R: 2026-01-29 23:10:24.619355: DONE
  > test_pipeop_isomap.R: 2026-01-29 23:10:24.961454: Isomap START
  > test_pipeop_isomap.R: 2026-01-29 23:10:24.961813: constructing knn graph
  > test_pipeop_isomap.R: 2026-01-29 23:10:25.0046: calculating geodesic distances
  > test_pipeop_isomap.R: 2026-01-29 23:10:25.246261: Classical Scaling
  > test_pipeop_isomap.R: 2026-01-29 23:10:25.318875: L-Isomap embed START
  > test_pipeop_isomap.R: 2026-01-29 23:10:25.319308: constructing knn graph
  > test_pipeop_isomap.R: 2026-01-29 23:10:25.391796: calculating geodesic distances
  > test_pipeop_isomap.R: 2026-01-29 23:10:25.884968: embedding
  > test_pipeop_isomap.R: 2026-01-29 23:10:25.929442: DONE
  > test_pipeop_isomap.R: 2026-01-29 23:10:26.235142: Isomap START
  > test_pipeop_isomap.R: 2026-01-29 23:10:26.235442: constructing knn graph
  > test_pipeop_isomap.R: 2026-01-29 23:10:26.25669: calculating geodesic distances
  > test_pipeop_isomap.R: 2026-01-29 23:10:26.306104: Classical Scaling
  > test_pipeop_isomap.R: 2026-01-29 23:10:26.364133: L-Isomap embed START
  > test_pipeop_isomap.R: 2026-01-29 23:10:26.364562: constructing knn graph
  > test_pipeop_isomap.R: 2026-01-29 23:10:26.397886: calculating geodesic distances
  > test_pipeop_isomap.R: 2026-01-29 23:10:26.502084: embedding
  > test_pipeop_isomap.R: 2026-01-29 23:10:26.503279: DONE
  > test_pipeop_isomap.R: 2026-01-29 23:10:26.831695: Isomap START
  > test_pipeop_isomap.R: 2026-01-29 23:10:26.832051: constructing knn graph
  > test_pipeop_isomap.R: 2026-01-29 23:10:26.855376: calculating geodesic distances
  > test_pipeop_isomap.R: 2026-01-29 23:10:26.905818: Classical Scaling
  > test_pipeop_isomap.R: 2026-01-29 23:10:26.988674: L-Isomap embed START
  > test_pipeop_isomap.R: 2026-01-29 23:10:27.005858: constructing knn graph
  > test_pipeop_isomap.R: 2026-01-29 23:10:27.034599: calculating geodesic distances
  > test_pipeop_isomap.R: 2026-01-29 23:10:27.134626: embedding
  > test_pipeop_isomap.R: 2026-01-29 23:10:27.136003: DONE
  > test_pipeop_isomap.R: 2026-01-29 23:10:27.320678: Isomap START
  > test_pipeop_isomap.R: 2026-01-29 23:10:27.320977: constructing knn graph
  > test_pipeop_isomap.R: 2026-01-29 23:10:27.343458: calculating geodesic distances
  > test_pipeop_isomap.R: 2026-01-29 23:10:27.389036: Classical Scaling
  > test_pipeop_isomap.R: 2026-01-29 23:10:27.474965: L-Isomap embed START
  > test_pipeop_isomap.R: 2026-01-29 23:10:27.47541: constructing knn graph
  > test_pipeop_isomap.R: 2026-01-29 23:10:27.532535: calculating geodesic distances
  > test_pipeop_isomap.R: 2026-01-29 23:10:27.640181: embedding
  > test_pipeop_isomap.R: 2026-01-29 23:10:27.641444: DONE
  > test_pipeop_isomap.R: 2026-01-29 23:10:27.801009: Isomap START
  > test_pipeop_isomap.R: 2026-01-29 23:10:27.80134: constructing knn graph
  > test_pipeop_isomap.R: 2026-01-29 23:10:27.808312: calculating geodesic distances
  > test_pipeop_isomap.R: 2026-01-29 23:10:27.854888: Classical Scaling
  > test_pipeop_isomap.R: 2026-01-29 23:10:27.957884: L-Isomap embed START
  > test_pipeop_isomap.R: 2026-01-29 23:10:27.958377: constructing knn graph
  > test_pipeop_isomap.R: 2026-01-29 23:10:27.990246: calculating geodesic distances
  > test_pipeop_isomap.R: 2026-01-29 23:10:28.082236: embedding
  > test_pipeop_isomap.R: 2026-01-29 23:10:28.083454: DONE
  > test_pipeop_isomap.R: 2026-01-29 23:10:28.281981: Isomap START
  > test_pipeop_isomap.R: 2026-01-29 23:10:28.282284: constructing knn graph
  > test_pipeop_isomap.R: 2026-01-29 23:10:28.289198: calculating geodesic distances
  > test_pipeop_isomap.R: 2026-01-29 23:10:28.356191: Classical Scaling
  > test_pipeop_isomap.R: 2026-01-29 23:10:28.437432: L-Isomap embed START
  > test_pipeop_isomap.R: 2026-01-29 23:10:28.437876: constructing knn graph
  > test_pipeop_isomap.R: 2026-01-29 23:10:28.474952: calculating geodesic distances
  > test_pipeop_isomap.R: 2026-01-29 23:10:28.565707: embedding
  > test_pipeop_isomap.R: 2026-01-29 23:10:28.5669: DONE
  > test_pipeop_isomap.R: 2026-01-29 23:10:28.739224: Isomap START
  > test_pipeop_isomap.R: 2026-01-29 23:10:28.73953: constructing knn graph
  > test_pipeop_isomap.R: 2026-01-29 23:10:28.770715: calculating geodesic distances
  > test_pipeop_isomap.R: 2026-01-29 23:10:28.800856: Classical Scaling
  > test_pipeop_isomap.R: 2026-01-29 23:10:28.975373: Isomap START
  > test_pipeop_isomap.R: 2026-01-29 23:10:28.990205: constructing knn graph
  > test_pipeop_isomap.R: 2026-01-29 23:10:28.998217: calculating geodesic distances
  > test_pipeop_isomap.R: 2026-01-29 23:10:29.041105: Classical Scaling
  > test_pipeop_isomap.R: 2026-01-29 23:10:29.074599: Isomap START
  > test_pipeop_isomap.R: 2026-01-29 23:10:29.074892: constructing knn graph
  > test_pipeop_isomap.R: 2026-01-29 23:10:29.112803: calculating geodesic distances
  > test_pipeop_isomap.R: 2026-01-29 23:10:29.155812: Classical Scaling
  Saving _problems/test_pipeop_nmf-45.R
  Saving _problems/test_pipeop_nmf-73.R
  Saving _problems/test_pipeop_nmf-93.R
  Saving _problems/test_pipeop_nmf-98.R
  > test_pipeop_task_preproc.R: Training debug_affectcols
  > test_pipeop_task_preproc.R: Training debug_affectcols
  > test_pipeop_task_preproc.R: Training debug_affectcols
  > test_pipeop_task_preproc.R: Training debug_affectcols
  > test_pipeop_task_preproc.R: Training debug_affectcols
  > test_pipeop_task_preproc.R: Training debug_affectcols
  > test_pipeop_task_preproc.R: Training debug_affectcols
  > test_pipeop_task_preproc.R: Training debug_affectcols
  > test_pipeop_task_preproc.R: Training debug_affectcols
  > test_pipeop_task_preproc.R: Training debug_affectcols
  > test_pipeop_task_preproc.R: Training debug_affectcols
  > test_pipeop_task_preproc.R: Training debug_affectcols
  > test_pipeop_task_preproc.R: Training debug_affectcols
  > test_pipeop_task_preproc.R: Training debug_affectcols
  > test_pipeop_task_preproc.R: Training debug_affectcols
  > test_pipeop_task_preproc.R: Training debug_affectcols
  > test_pipeop_task_preproc.R: Training debug_affectcols
  > test_pipeop_task_preproc.R: Training debug_affectcols
  > test_pipeop_task_preproc.R: Training debug_affectcols
  > test_pipeop_task_preproc.R: Training debug_affectcols
  > test_pipeop_task_preproc.R: Training debug_affectcols
  > test_pipeop_task_preproc.R: Training debug_affectcols
  > test_pipeop_textvectorizer.R: 'as(<dgCMatrix>, "dgTMatrix")' is deprecated.
  > test_pipeop_textvectorizer.R: Use 'as(., "TsparseMatrix")' instead.
  > test_pipeop_textvectorizer.R: See help("Deprecated") and help("Matrix-deprecated").
  > test_pipeop_tunethreshold.R: OptimInstanceSingleCrit is deprecated. Use OptimInstanceBatchSingleCrit instead.
  > test_pipeop_tunethreshold.R: OptimInstanceSingleCrit is deprecated. Use OptimInstanceBatchSingleCrit instead.
  > test_pipeop_tunethreshold.R: OptimInstanceSingleCrit is deprecated. Use OptimInstanceBatchSingleCrit instead.
  > test_pipeop_tunethreshold.R: OptimInstanceSingleCrit is deprecated. Use OptimInstanceBatchSingleCrit instead.
  > test_pipeop_tunethreshold.R: OptimInstanceSingleCrit is deprecated. Use OptimInstanceBatchSingleCrit instead.
  > test_pipeop_tunethreshold.R: OptimInstanceSingleCrit is deprecated. Use OptimInstanceBatchSingleCrit instead.
  > test_pipeop_tunethreshold.R: OptimInstanceSingleCrit is deprecated. Use OptimInstanceBatchSingleCrit instead.
  [ FAIL 8 | WARN 0 | SKIP 99 | PASS 13004 ]
  
  ══ Skipped tests (99) ══════════════════════════════════════════════════════════
  • On CRAN (95): 'test_CnfFormula_simplify.R:6:3', 'test_CnfFormula.R:591:3',
    'test_Graph.R:283:3', 'test_PipeOp.R:32:1', 'test_GraphLearner.R:5:3',
    'test_GraphLearner.R:221:3', 'test_GraphLearner.R:343:3',
    'test_GraphLearner.R:408:3', 'test_GraphLearner.R:571:3',
    'test_dictionary.R:7:3', 'test_learner_weightedaverage.R:5:3',
    'test_learner_weightedaverage.R:57:3',
    'test_learner_weightedaverage.R:105:3',
    'test_learner_weightedaverage.R:152:3', 'test_meta.R:39:3',
    'test_mlr_graphs_branching.R:26:3', 'test_mlr_graphs_bagging.R:6:3',
    'test_mlr_graphs_robustify.R:5:3', 'test_pipeop_adas.R:8:3',
    'test_pipeop_blsmote.R:8:3', 'test_pipeop_branch.R:4:3',
    'test_pipeop_chunk.R:4:3', 'test_pipeop_classbalancing.R:7:3',
    'test_pipeop_boxcox.R:7:3', 'test_pipeop_classweights.R:10:3',
    'test_pipeop_collapsefactors.R:6:3', 'test_pipeop_colapply.R:9:3',
    'test_pipeop_copy.R:5:3', 'test_pipeop_colroles.R:6:3',
    'test_pipeop_decode.R:14:3', 'test_pipeop_encode.R:21:3',
    'test_pipeop_encodeimpact.R:11:3', 'test_pipeop_encodepl.R:5:3',
    'test_pipeop_encodepl.R:72:3', 'test_pipeop_encodelmer.R:15:3',
    'test_pipeop_encodelmer.R:37:3', 'test_pipeop_encodelmer.R:80:3',
    'test_pipeop_featureunion.R:9:3', 'test_pipeop_featureunion.R:134:3',
    'test_pipeop_filter.R:7:3', 'test_pipeop_fixfactors.R:9:3',
    'test_pipeop_histbin.R:7:3', 'test_pipeop_ensemble.R:6:3',
    'test_pipeop_ica.R:7:3', 'test_pipeop_impute.R:4:3',
    'test_pipeop_imputelearner.R:43:3', 'test_pipeop_isomap.R:10:3',
    'test_pipeop_kernelpca.R:9:3', 'test_pipeop_learner.R:17:3',
    'test_pipeop_info.R:6:3', 'test_pipeop_learnerpicvplus.R:163:3',
    'test_pipeop_missind.R:6:3', 'test_pipeop_modelmatrix.R:7:3',
    'test_pipeop_multiplicityexply.R:9:3', 'test_pipeop_multiplicityimply.R:9:3',
    'test_pipeop_mutate.R:9:3', 'test_pipeop_nearmiss.R:7:3',
    'test_pipeop_learnercv.R:31:3', 'test_pipeop_ovr.R:9:3',
    'test_pipeop_ovr.R:48:3', 'test_pipeop_pca.R:8:3',
    'test_pipeop_proxy.R:14:3', 'test_pipeop_nmf.R:6:3',
    'test_pipeop_quantilebin.R:5:3', 'test_pipeop_randomprojection.R:6:3',
    'test_pipeop_randomresponse.R:5:3', 'test_pipeop_removeconstants.R:6:3',
    'test_pipeop_renamecolumns.R:6:3', 'test_pipeop_replicate.R:9:3',
    'test_pipeop_scale.R:6:3', 'test_pipeop_scale.R:10:3',
    'test_pipeop_scalemaxabs.R:6:3', 'test_pipeop_scalerange.R:7:3',
    'test_pipeop_select.R:9:3', 'test_pipeop_smote.R:10:3',
    'test_pipeop_rowapply.R:6:3', 'test_pipeop_smotenc.R:8:3',
    'test_pipeop_subsample.R:6:3', 'test_pipeop_targetinvert.R:4:3',
    'test_pipeop_targetmutate.R:5:3', 'test_pipeop_targettrafo.R:4:3',
    'test_pipeop_targettrafoscalerange.R:5:3', 'test_pipeop_task_preproc.R:4:3',
    'test_pipeop_task_preproc.R:14:3', 'test_pipeop_spatialsign.R:6:3',
    'test_pipeop_tomek.R:7:3', 'test_pipeop_textvectorizer.R:37:3',
    'test_pipeop_textvectorizer.R:186:3', 'test_pipeop_unbranch.R:10:3',
    'test_pipeop_updatetarget.R:89:3', 'test_pipeop_vtreat.R:9:3',
    'test_pipeop_yeojohnson.R:7:3', 'test_pipeop_tunethreshold.R:111:3',
    'test_pipeop_tunethreshold.R:191:3', 'test_typecheck.R:188:3'
  • Skipping (1): 'test_GraphLearner.R:1278:3'
  • empty test (3): 'test_pipeop_isomap.R:111:1', 'test_pipeop_missind.R:101:1',
    'test_ppl.R:61:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test_filter_ensemble.R:294:3'): FilterEnsemble ignores NA scores from wrapped filters ──
  Expected `all(is.nan(permutation_filter$scores[task$feature_names]))` to be TRUE.
  Differences:
  `actual`:   FALSE
  `expected`: TRUE 
  
  ── Failure ('test_filter_ensemble.R:307:3'): FilterEnsemble ignores NA scores from wrapped filters ──
  Expected `all.equal(object, expected, check.environment = FALSE, ...)` to be TRUE.
  Differences:
  `actual` is a character vector ('Mean relative difference: 1.914248')
  `expected` is a logical vector (TRUE)
  
  Backtrace:
      ▆
   1. └─global expect_equal(combined_scores, variance_scores * weights[["variance"]]) at test_filter_ensemble.R:307:3
   2.   └─testthat::expect_true(...)
  ── Error ('test_pipeop_datefeatures.R:7:3'): PipeOpDateFeatures - basic properties ──
  Error in `seq.Date(as.Date("2020-01-31"), length.out = 150L)`: exactly two of 'to', 'by' and 'length.out' / 'along.with' must be specified
  Backtrace:
      ▆
   1. ├─base::seq(as.Date("2020-01-31"), length.out = 150L) at test_pipeop_datefeatures.R:7:3
   2. └─base::seq.Date(as.Date("2020-01-31"), length.out = 150L)
  ── Error ('test_pipeop_datefeatures.R:17:3'): PipeOpDateFeatures - finds POSIXct column ──
  Error in `seq.Date(as.Date("2020-01-31"), length.out = 150L)`: exactly two of 'to', 'by' and 'length.out' / 'along.with' must be specified
  Backtrace:
      ▆
   1. ├─base::seq(as.Date("2020-01-31"), length.out = 150L) at test_pipeop_datefeatures.R:17:3
   2. └─base::seq.Date(as.Date("2020-01-31"), length.out = 150L)
  ── Error ('test_pipeop_nmf.R:45:3'): PipeOpNMF - does not modify search path when NMF is not loaded, fix for #929 ──
  Error in `detach(package:generics)`: invalid 'name' argument
  Backtrace:
      ▆
   1. └─base::detach(package:generics) at test_pipeop_nmf.R:45:3
  ── Failure ('test_pipeop_nmf.R:73:3'): PipeOpNMF - does not modify search path when NMF is loaded, fix for #929 ──
  Expected `all(...)` to be TRUE.
  Differences:
  `actual`:   FALSE
  `expected`: TRUE 
  
  ── Failure ('test_pipeop_nmf.R:93:3'): PipeOpNMF - does not modify search path when some of NMF's dependencies are loaded, fix for #929 ──
  Expected `all(paste0("package:", c("BiocGenerics", "generics")) %in% search())` to be TRUE.
  Differences:
  `actual`:   FALSE
  `expected`: TRUE 
  
  ── Error ('test_pipeop_nmf.R:98:3'): PipeOpNMF - does not modify search path when some of NMF's dependencies are loaded, fix for #929 ──
  Error in `FUN(X[[i]], ...)`: invalid 'name' argument
  This happened in PipeOp nmf's $train()
  Backtrace:
       ▆
    1. ├─op$train(list(tsk("iris"))) at test_pipeop_nmf.R:98:3
    2. │ └─mlr3pipelines:::.__PipeOp__train(...)
    3. │   ├─base::withCallingHandlers(...)
    4. │   └─private$.train(input)
    5. │     └─mlr3pipelines:::.__PipeOpTaskPreproc__.train(...)
    6. │       └─private$.train_task(intask)
    7. │         └─mlr3pipelines:::.__PipeOpTaskPreproc__.train_task(...)
    8. │           ├─data.table::as.data.table(...)
    9. │           └─private$.train_dt(dt, task$levels(cols), task$truth())
   10. │             └─mlr3pipelines:::.__PipeOpNMF__.train_dt(...)
   11. │               └─mlr3misc::map(to_be_detached, detach, character.only = TRUE)
   12. │                 └─base::lapply(.x, .f, ...)
   13. │                   └─base (local) FUN(X[[i]], ...)
   14. │                     └─base::stop("invalid 'name' argument")
   15. └─base::.handleSimpleError(...)
   16.   └─mlr3pipelines (local) h(simpleError(msg, call))
  
  [ FAIL 8 | WARN 0 | SKIP 99 | PASS 13004 ]
  Error:
  ! Test failures.
  Execution halted