Last updated on 2025-12-14 20:48:56 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.10.0 | 38.89 | 764.75 | 803.64 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.10.0 | 20.57 | 485.03 | 505.60 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.10.0 | 69.00 | 1313.21 | 1382.21 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 0.10.0 | 66.00 | 1250.56 | 1316.56 | OK | |
| r-devel-windows-x86_64 | 0.10.0 | 38.00 | 554.00 | 592.00 | OK | |
| r-patched-linux-x86_64 | 0.10.0 | 54.55 | 699.28 | 753.83 | OK | |
| r-release-linux-x86_64 | 0.10.0 | 36.47 | 698.05 | 734.52 | OK | |
| r-release-macos-arm64 | 0.10.0 | OK | ||||
| r-release-macos-x86_64 | 0.10.0 | 26.00 | 542.00 | 568.00 | OK | |
| r-release-windows-x86_64 | 0.10.0 | 37.00 | 525.00 | 562.00 | OK | |
| r-oldrel-macos-arm64 | 0.10.0 | 8.00 | 115.00 | 123.00 | ERROR | |
| r-oldrel-macos-x86_64 | 0.10.0 | 24.00 | 559.00 | 583.00 | ERROR | |
| r-oldrel-windows-x86_64 | 0.10.0 | 52.00 | 638.00 | 690.00 | ERROR |
Version: 0.10.0
Check: examples
Result: ERROR
Running examples in ‘mlr3pipelines-Ex.R’ failed
The error most likely occurred in:
> ### Name: mlr_pipeops_nmf
> ### Title: Non-negative Matrix Factorization
> ### Aliases: mlr_pipeops_nmf PipeOpNMF
>
> ### ** Examples
>
> ## Don't show:
> if (mlr3misc::require_namespaces(c("NMF", "MASS"), quietly = TRUE)) withAutoprint({ # examplesIf
+ ## End(Don't show)
+ ## Don't show:
+ # NMF attaches these packages to search path on load, #929
+ lapply(c("package:Biobase", "package:BiocGenerics", "package:generics"), detach, character.only = TRUE)
+ ## End(Don't show)
+ library("mlr3")
+
+ task = tsk("iris")
+ pop = po("nmf")
+
+ task$data()
+ pop$train(list(task))[[1]]$data()
+
+ pop$state
+ ## Don't show:
+ # BiocGenerics overwrites printer for our tables mlr-org/mlr3#1112
+ # Necessary as detaching packages does not remove registered S3 methods
+ suppressWarnings(try(rm("format.list", envir = .BaseNamespaceEnv$.__S3MethodsTable__.), silent = TRUE))
+ ## End(Don't show)
+ ## Don't show:
+ }) # examplesIf
> lapply(c("package:Biobase", "package:BiocGenerics", "package:generics"),
+ detach, character.only = TRUE)
Error in FUN(X[[i]], ...) : invalid 'name' argument
Calls: withAutoprint ... withVisible -> eval -> eval -> lapply -> lapply -> FUN
Execution halted
Flavors: r-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64
Version: 0.10.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [101s/49s]
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: 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:
> test_multiplicities.R: [[1]]
> test_multiplicities.R: [1] 0
> 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: 2025-12-15 06:52:23.87952: Isomap START
> test_pipeop_isomap.R: 2025-12-15 06:52:23.879781: constructing knn graph
> test_pipeop_isomap.R: 2025-12-15 06:52:23.88279: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-15 06:52:23.888998: Classical Scaling
> test_pipeop_isomap.R: 2025-12-15 06:52:23.901223: Isomap START
> test_pipeop_isomap.R: 2025-12-15 06:52:23.901366: constructing knn graph
> test_pipeop_isomap.R: 2025-12-15 06:52:23.903778: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-15 06:52:23.909783: Classical Scaling
> test_pipeop_isomap.R: 2025-12-15 06:52:23.916869: L-Isomap embed START
> test_pipeop_isomap.R: 2025-12-15 06:52:23.917052: constructing knn graph
> test_pipeop_isomap.R: 2025-12-15 06:52:23.921551: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-15 06:52:23.93655: embedding
> test_pipeop_isomap.R: 2025-12-15 06:52:23.936968: DONE
> test_pipeop_isomap.R: 2025-12-15 06:52:23.942565: L-Isomap embed START
> test_pipeop_isomap.R: 2025-12-15 06:52:23.942712: constructing knn graph
> test_pipeop_isomap.R: 2025-12-15 06:52:23.947167: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-15 06:52:23.961883: embedding
> test_pipeop_isomap.R: 2025-12-15 06:52:23.962299: DONE
> test_pipeop_isomap.R: 2025-12-15 06:52:23.995715: Isomap START
> test_pipeop_isomap.R: 2025-12-15 06:52:23.995846: constructing knn graph
> test_pipeop_isomap.R: 2025-12-15 06:52:23.999979: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-15 06:52:24.034354: Classical Scaling
> test_pipeop_isomap.R: 2025-12-15 06:52:24.042247: L-Isomap embed START
> test_pipeop_isomap.R: 2025-12-15 06:52:24.042424: constructing knn graph
> test_pipeop_isomap.R: 2025-12-15 06:52:24.051162: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-15 06:52:24.12933: embedding
> test_pipeop_isomap.R: 2025-12-15 06:52:24.135656: DONE
> test_pipeop_isomap.R: 2025-12-15 06:52:24.173004: Isomap START
> test_pipeop_isomap.R: 2025-12-15 06:52:24.17314: constructing knn graph
> test_pipeop_isomap.R: 2025-12-15 06:52:24.175504: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-15 06:52:24.181582: Classical Scaling
> test_pipeop_isomap.R: 2025-12-15 06:52:24.18803: L-Isomap embed START
> test_pipeop_isomap.R: 2025-12-15 06:52:24.18819: constructing knn graph
> test_pipeop_isomap.R: 2025-12-15 06:52:24.192632: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-15 06:52:24.207503: embedding
> test_pipeop_isomap.R: 2025-12-15 06:52:24.207893: DONE
> test_pipeop_isomap.R: 2025-12-15 06:52:24.238124: Isomap START
> test_pipeop_isomap.R: 2025-12-15 06:52:24.238266: constructing knn graph
> test_pipeop_isomap.R: 2025-12-15 06:52:24.240513: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-15 06:52:24.246503: Classical Scaling
> test_pipeop_isomap.R: 2025-12-15 06:52:24.263154: L-Isomap embed START
> test_pipeop_isomap.R: 2025-12-15 06:52:24.263392: constructing knn graph
> test_pipeop_isomap.R: 2025-12-15 06:52:24.268201: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-15 06:52:24.283555: embedding
> test_pipeop_isomap.R: 2025-12-15 06:52:24.284061: DONE
> test_pipeop_isomap.R: 2025-12-15 06:52:24.303136: Isomap START
> test_pipeop_isomap.R: 2025-12-15 06:52:24.303262: constructing knn graph
> test_pipeop_isomap.R: 2025-12-15 06:52:24.305507: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-15 06:52:24.311553: Classical Scaling
> test_pipeop_isomap.R: 2025-12-15 06:52:24.321307: L-Isomap embed START
> test_pipeop_isomap.R: 2025-12-15 06:52:24.321473: constructing knn graph
> test_pipeop_isomap.R: 2025-12-15 06:52:24.359789: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-15 06:52:24.374607: embedding
> test_pipeop_isomap.R: 2025-12-15 06:52:24.375147: DONE
> test_pipeop_isomap.R: 2025-12-15 06:52:24.397406: Isomap START
> test_pipeop_isomap.R: 2025-12-15 06:52:24.397536: constructing knn graph
> test_pipeop_isomap.R: 2025-12-15 06:52:24.399503: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-15 06:52:24.404935: Classical Scaling
> test_pipeop_isomap.R: 2025-12-15 06:52:24.413507: L-Isomap embed START
> test_pipeop_isomap.R: 2025-12-15 06:52:24.413637: constructing knn graph
> test_pipeop_isomap.R: 2025-12-15 06:52:24.417515: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-15 06:52:24.43027: embedding
> test_pipeop_isomap.R: 2025-12-15 06:52:24.430542: DONE
> test_pipeop_isomap.R: 2025-12-15 06:52:24.443502: Isomap START
> test_pipeop_isomap.R: 2025-12-15 06:52:24.443599: constructing knn graph
> test_pipeop_isomap.R: 2025-12-15 06:52:24.445569: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-15 06:52:24.450836: Classical Scaling
> test_pipeop_isomap.R: 2025-12-15 06:52:24.459079: L-Isomap embed START
> test_pipeop_isomap.R: 2025-12-15 06:52:24.459207: constructing knn graph
> test_pipeop_isomap.R: 2025-12-15 06:52:24.463053: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-15 06:52:24.476363: embedding
> test_pipeop_isomap.R: 2025-12-15 06:52:24.476698: DONE
> test_pipeop_isomap.R: 2025-12-15 06:52:24.508917: Isomap START
> test_pipeop_isomap.R: 2025-12-15 06:52:24.509047: constructing knn graph
> test_pipeop_isomap.R: 2025-12-15 06:52:24.511306: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-15 06:52:24.51764: Classical Scaling
> test_pipeop_isomap.R: 2025-12-15 06:52:24.534063: Isomap START
> test_pipeop_isomap.R: 2025-12-15 06:52:24.534188: constructing knn graph
> test_pipeop_isomap.R: 2025-12-15 06:52:24.536463: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-15 06:52:24.542438: Classical Scaling
> test_pipeop_isomap.R: 2025-12-15 06:52:24.547259: Isomap START
> test_pipeop_isomap.R: 2025-12-15 06:52:24.547385: constructing knn graph
> test_pipeop_isomap.R: 2025-12-15 06:52:24.549577: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-15 06:52:24.5555: 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_classweights.R:10:3', 'test_pipeop_boxcox.R:7:3',
'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_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_nmf.R:6:3',
'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_rowapply.R:6:3',
'test_pipeop_smote.R:10:3', '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: 0.6186105')
`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
Flavor: r-oldrel-macos-arm64
Version: 0.10.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [307s/284s]
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:
> test_PipeOp.R: Predicting test_autotrain
> test_PipeOp.R:
> 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: 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.
> 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:
> 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: 2025-12-14 10:27:06.751303: Isomap START
> test_pipeop_isomap.R: 2025-12-14 10:27:06.751893: constructing knn graph
> test_pipeop_isomap.R: 2025-12-14 10:27:06.769042: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-14 10:27:06.787199: Classical Scaling
> test_pipeop_isomap.R: 2025-12-14 10:27:06.886101: Isomap START
> test_pipeop_isomap.R: 2025-12-14 10:27:06.886507: constructing knn graph
> test_pipeop_isomap.R: 2025-12-14 10:27:06.899709: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-14 10:27:06.924926: Classical Scaling
> test_pipeop_isomap.R: 2025-12-14 10:27:06.969396: L-Isomap embed START
> test_pipeop_isomap.R: 2025-12-14 10:27:06.96995: constructing knn graph
> test_pipeop_isomap.R: 2025-12-14 10:27:07.006847: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-14 10:27:07.067958: embedding
> test_pipeop_isomap.R: 2025-12-14 10:27:07.069381: DONE
> test_pipeop_isomap.R: 2025-12-14 10:27:07.134217: L-Isomap embed START
> test_pipeop_isomap.R: 2025-12-14 10:27:07.134547: constructing knn graph
> test_pipeop_isomap.R: 2025-12-14 10:27:07.148214: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-14 10:27:07.204031: embedding
> test_pipeop_isomap.R: 2025-12-14 10:27:07.205274: DONE
> test_pipeop_isomap.R: 2025-12-14 10:27:07.356352: Isomap START
> test_pipeop_isomap.R: 2025-12-14 10:27:07.356666: constructing knn graph
> test_pipeop_isomap.R: 2025-12-14 10:27:07.381508: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-14 10:27:07.558631: Classical Scaling
> test_pipeop_isomap.R: 2025-12-14 10:27:07.602052: L-Isomap embed START
> test_pipeop_isomap.R: 2025-12-14 10:27:07.602599: constructing knn graph
> test_pipeop_isomap.R: 2025-12-14 10:27:07.65509: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-14 10:27:08.025442: embedding
> test_pipeop_isomap.R: 2025-12-14 10:27:08.042624: DONE
> test_pipeop_isomap.R: 2025-12-14 10:27:08.240841: Isomap START
> test_pipeop_isomap.R: 2025-12-14 10:27:08.241156: constructing knn graph
> test_pipeop_isomap.R: 2025-12-14 10:27:08.28252: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-14 10:27:08.312192: Classical Scaling
> test_pipeop_isomap.R: 2025-12-14 10:27:08.348479: L-Isomap embed START
> test_pipeop_isomap.R: 2025-12-14 10:27:08.351339: constructing knn graph
> test_pipeop_isomap.R: 2025-12-14 10:27:08.369839: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-14 10:27:08.44578: embedding
> test_pipeop_isomap.R: 2025-12-14 10:27:08.446953: DONE
> test_pipeop_isomap.R: 2025-12-14 10:27:08.662401: Isomap START
> test_pipeop_isomap.R: 2025-12-14 10:27:08.662753: constructing knn graph
> test_pipeop_isomap.R: 2025-12-14 10:27:08.685037: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-14 10:27:08.712963: Classical Scaling
> test_pipeop_isomap.R: 2025-12-14 10:27:08.775491: L-Isomap embed START
> test_pipeop_isomap.R: 2025-12-14 10:27:08.775915: constructing knn graph
> test_pipeop_isomap.R: 2025-12-14 10:27:08.798708: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-14 10:27:08.864652: embedding
> test_pipeop_isomap.R: 2025-12-14 10:27:08.866074: DONE
> test_pipeop_isomap.R: 2025-12-14 10:27:08.958734: Isomap START
> test_pipeop_isomap.R: 2025-12-14 10:27:08.95911: constructing knn graph
> test_pipeop_isomap.R: 2025-12-14 10:27:08.967042: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-14 10:27:09.009659: Classical Scaling
> test_pipeop_isomap.R: 2025-12-14 10:27:09.074934: L-Isomap embed START
> test_pipeop_isomap.R: 2025-12-14 10:27:09.075623: constructing knn graph
> test_pipeop_isomap.R: 2025-12-14 10:27:09.098675: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-14 10:27:09.186171: embedding
> test_pipeop_isomap.R: 2025-12-14 10:27:09.188624: DONE
> test_pipeop_isomap.R: 2025-12-14 10:27:09.293523: Isomap START
> test_pipeop_isomap.R: 2025-12-14 10:27:09.293946: constructing knn graph
> test_pipeop_isomap.R: 2025-12-14 10:27:09.304721: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-14 10:27:09.356654: Classical Scaling
> test_pipeop_isomap.R: 2025-12-14 10:27:09.406027: L-Isomap embed START
> test_pipeop_isomap.R: 2025-12-14 10:27:09.406495: constructing knn graph
> test_pipeop_isomap.R: 2025-12-14 10:27:09.428639: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-14 10:27:09.49129: embedding
> test_pipeop_isomap.R: 2025-12-14 10:27:09.492543: DONE
> test_pipeop_isomap.R: 2025-12-14 10:27:09.621269: Isomap START
> test_pipeop_isomap.R: 2025-12-14 10:27:09.622102: constructing knn graph
> test_pipeop_isomap.R: 2025-12-14 10:27:09.630867: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-14 10:27:09.66264: Classical Scaling
> test_pipeop_isomap.R: 2025-12-14 10:27:09.718202: L-Isomap embed START
> test_pipeop_isomap.R: 2025-12-14 10:27:09.718699: constructing knn graph
> test_pipeop_isomap.R: 2025-12-14 10:27:09.802519: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-14 10:27:09.87133: embedding
> test_pipeop_isomap.R: 2025-12-14 10:27:09.872589: DONE
> test_pipeop_isomap.R: 2025-12-14 10:27:09.96043: Isomap START
> test_pipeop_isomap.R: 2025-12-14 10:27:09.960732: constructing knn graph
> test_pipeop_isomap.R: 2025-12-14 10:27:09.969551: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-14 10:27:09.986914: Classical Scaling
> test_pipeop_isomap.R: 2025-12-14 10:27:10.105604: Isomap START
> test_pipeop_isomap.R: 2025-12-14 10:27:10.106155: constructing knn graph
> test_pipeop_isomap.R: 2025-12-14 10:27:10.11759: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-14 10:27:10.144833: Classical Scaling
> test_pipeop_isomap.R: 2025-12-14 10:27:10.164605: Isomap START
> test_pipeop_isomap.R: 2025-12-14 10:27:10.1649: constructing knn graph
> test_pipeop_isomap.R: 2025-12-14 10:27:10.175489: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-14 10:27:10.199202: 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 6 | WARN 0 | SKIP 99 | PASS 13006 ]
══ 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_ica.R:7:3',
'test_pipeop_ensemble.R:6:3', '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_quantilebin.R:5:3',
'test_pipeop_randomprojection.R:6:3', 'test_pipeop_randomresponse.R:5:3',
'test_pipeop_nmf.R:6:3', '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_smotenc.R:8:3', 'test_pipeop_rowapply.R:6:3',
'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 ════════════════════════════════════════════════════════════════
── 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 6 | WARN 0 | SKIP 99 | PASS 13006 ]
Error:
! Test failures.
Execution halted
Flavor: r-oldrel-macos-x86_64
Version: 0.10.0
Check: tests
Result: ERROR
Running 'testthat.R' [270s]
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: 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:
> test_multiplicities.R: [1] 0
> 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: 2025-12-12 19:20:25.870782: Isomap START
> test_pipeop_isomap.R: 2025-12-12 19:20:25.87195: constructing knn graph
> test_pipeop_isomap.R: 2025-12-12 19:20:25.887949: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-12 19:20:25.912321: Classical Scaling
> test_pipeop_isomap.R: 2025-12-12 19:20:25.974434: Isomap START
> test_pipeop_isomap.R: 2025-12-12 19:20:25.975244: constructing knn graph
> test_pipeop_isomap.R: 2025-12-12 19:20:25.986304: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-12 19:20:26.007274: Classical Scaling
> test_pipeop_isomap.R: 2025-12-12 19:20:26.049057: L-Isomap embed START
> test_pipeop_isomap.R: 2025-12-12 19:20:26.050026: constructing knn graph
> test_pipeop_isomap.R: 2025-12-12 19:20:26.071395: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-12 19:20:26.113423: embedding
> test_pipeop_isomap.R: 2025-12-12 19:20:26.11517: DONE
> test_pipeop_isomap.R: 2025-12-12 19:20:26.148747: L-Isomap embed START
> test_pipeop_isomap.R: 2025-12-12 19:20:26.149405: constructing knn graph
> test_pipeop_isomap.R: 2025-12-12 19:20:26.188813: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-12 19:20:26.240473: embedding
> test_pipeop_isomap.R: 2025-12-12 19:20:26.242336: DONE
> test_pipeop_isomap.R: 2025-12-12 19:20:26.340739: Isomap START
> test_pipeop_isomap.R: 2025-12-12 19:20:26.341192: constructing knn graph
> test_pipeop_isomap.R: 2025-12-12 19:20:26.357552: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-12 19:20:26.442076: Classical Scaling
> test_pipeop_isomap.R: 2025-12-12 19:20:26.47549: L-Isomap embed START
> test_pipeop_isomap.R: 2025-12-12 19:20:26.476157: constructing knn graph
> test_pipeop_isomap.R: 2025-12-12 19:20:26.523032: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-12 19:20:26.757585: embedding
> test_pipeop_isomap.R: 2025-12-12 19:20:26.762056: DONE
> test_pipeop_isomap.R: 2025-12-12 19:20:26.940653: Isomap START
> test_pipeop_isomap.R: 2025-12-12 19:20:26.941359: constructing knn graph
> test_pipeop_isomap.R: 2025-12-12 19:20:26.952443: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-12 19:20:26.976071: Classical Scaling
> test_pipeop_isomap.R: 2025-12-12 19:20:27.032392: L-Isomap embed START
> test_pipeop_isomap.R: 2025-12-12 19:20:27.033331: constructing knn graph
> test_pipeop_isomap.R: 2025-12-12 19:20:27.052443: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-12 19:20:27.099888: embedding
> test_pipeop_isomap.R: 2025-12-12 19:20:27.101545: DONE
> test_pipeop_isomap.R: 2025-12-12 19:20:27.298994: Isomap START
> test_pipeop_isomap.R: 2025-12-12 19:20:27.299604: constructing knn graph
> test_pipeop_isomap.R: 2025-12-12 19:20:27.308668: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-12 19:20:27.325218: Classical Scaling
> test_pipeop_isomap.R: 2025-12-12 19:20:27.372726: L-Isomap embed START
> test_pipeop_isomap.R: 2025-12-12 19:20:27.373643: constructing knn graph
> test_pipeop_isomap.R: 2025-12-12 19:20:27.468466: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-12 19:20:27.518838: embedding
> test_pipeop_isomap.R: 2025-12-12 19:20:27.520794: DONE
> test_pipeop_isomap.R: 2025-12-12 19:20:27.63686: Isomap START
> test_pipeop_isomap.R: 2025-12-12 19:20:27.637492: constructing knn graph
> test_pipeop_isomap.R: 2025-12-12 19:20:27.648632: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-12 19:20:27.665086: Classical Scaling
> test_pipeop_isomap.R: 2025-12-12 19:20:27.725201: L-Isomap embed START
> test_pipeop_isomap.R: 2025-12-12 19:20:27.726059: constructing knn graph
> test_pipeop_isomap.R: 2025-12-12 19:20:27.747256: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-12 19:20:27.79538: embedding
> test_pipeop_isomap.R: 2025-12-12 19:20:27.79725: DONE
> test_pipeop_isomap.R: 2025-12-12 19:20:27.898375: Isomap START
> test_pipeop_isomap.R: 2025-12-12 19:20:27.898864: constructing knn graph
> test_pipeop_isomap.R: 2025-12-12 19:20:27.91084: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-12 19:20:27.948593: Classical Scaling
> test_pipeop_isomap.R: 2025-12-12 19:20:28.027047: L-Isomap embed START
> test_pipeop_isomap.R: 2025-12-12 19:20:28.028026: constructing knn graph
> test_pipeop_isomap.R: 2025-12-12 19:20:28.046903: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-12 19:20:28.09513: embedding
> test_pipeop_isomap.R: 2025-12-12 19:20:28.096837: DONE
> test_pipeop_isomap.R: 2025-12-12 19:20:28.205505: Isomap START
> test_pipeop_isomap.R: 2025-12-12 19:20:28.206151: constructing knn graph
> test_pipeop_isomap.R: 2025-12-12 19:20:28.216088: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-12 19:20:28.237871: Classical Scaling
> test_pipeop_isomap.R: 2025-12-12 19:20:28.301304: L-Isomap embed START
> test_pipeop_isomap.R: 2025-12-12 19:20:28.301932: constructing knn graph
> test_pipeop_isomap.R: 2025-12-12 19:20:28.315374: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-12 19:20:28.35887: embedding
> test_pipeop_isomap.R: 2025-12-12 19:20:28.360566: DONE
> test_pipeop_isomap.R: 2025-12-12 19:20:28.50801: Isomap START
> test_pipeop_isomap.R: 2025-12-12 19:20:28.50853: constructing knn graph
> test_pipeop_isomap.R: 2025-12-12 19:20:28.518106: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-12 19:20:28.540897: Classical Scaling
> test_pipeop_isomap.R: 2025-12-12 19:20:28.651146: Isomap START
> test_pipeop_isomap.R: 2025-12-12 19:20:28.651824: constructing knn graph
> test_pipeop_isomap.R: 2025-12-12 19:20:28.661601: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-12 19:20:28.683349: Classical Scaling
> test_pipeop_isomap.R: 2025-12-12 19:20:28.715768: Isomap START
> test_pipeop_isomap.R: 2025-12-12 19:20:28.716413: constructing knn graph
> test_pipeop_isomap.R: 2025-12-12 19:20:28.72631: calculating geodesic distances
> test_pipeop_isomap.R: 2025-12-12 19:20:28.748001: 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_ensemble.R:6:3', 'test_pipeop_histbin.R:7:3',
'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_learnercv.R:31:3', 'test_pipeop_multiplicityexply.R:9:3',
'test_pipeop_mutate.R:9:3', 'test_pipeop_nearmiss.R:7:3',
'test_pipeop_multiplicityimply.R:9:3', '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_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_rowapply.R:6:3',
'test_pipeop_scale.R:6:3', 'test_pipeop_scale.R:10:3',
'test_pipeop_scalemaxabs.R:6:3', 'test_pipeop_nmf.R:6:3',
'test_pipeop_scalerange.R:7:3', 'test_pipeop_select.R:9:3',
'test_pipeop_smote.R:10:3', '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: 0.3961464')
`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
Flavor: r-oldrel-windows-x86_64