Last updated on 2025-11-25 17:49:56 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.10.0 | 38.63 | 759.46 | 798.09 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.10.0 | 22.05 | 497.09 | 519.14 | OK | |
| r-devel-linux-x86_64-fedora-clang | 0.10.0 | 180.00 | 1176.04 | 1356.04 | OK | |
| r-devel-linux-x86_64-fedora-gcc | 0.10.0 | 170.00 | 1134.68 | 1304.68 | OK | |
| r-devel-windows-x86_64 | 0.10.0 | 44.00 | 529.00 | 573.00 | OK | |
| r-patched-linux-x86_64 | 0.10.0 | 51.71 | 712.35 | 764.06 | OK | |
| r-release-linux-x86_64 | 0.10.0 | 36.90 | 719.55 | 756.45 | ERROR | |
| r-release-macos-arm64 | 0.10.0 | OK | ||||
| r-release-macos-x86_64 | 0.10.0 | 37.00 | 531.00 | 568.00 | OK | |
| r-release-windows-x86_64 | 0.10.0 | 39.00 | 515.00 | 554.00 | OK | |
| r-oldrel-macos-arm64 | 0.10.0 | 9.00 | 114.00 | 123.00 | ERROR | |
| r-oldrel-macos-x86_64 | 0.10.0 | 133.00 | 944.00 | 1077.00 | ERROR | |
| r-oldrel-windows-x86_64 | 0.10.0 | 53.00 | 645.00 | 698.00 | ERROR |
Version: 0.10.0
Check: tests
Result: ERROR
Running ‘testthat.R’ [438s/218s]
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: [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"
> test_pipeop_isomap.R: 2025-11-22 16:12:30.232359: Isomap START
> test_pipeop_isomap.R: 2025-11-22 16:12:30.233057: constructing knn graph
> test_pipeop_isomap.R: 2025-11-22 16:12:30.243508: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-22 16:12:30.263711: Classical Scaling
> test_pipeop_isomap.R: 2025-11-22 16:12:30.314084: Isomap START
> test_pipeop_isomap.R: 2025-11-22 16:12:30.314538: constructing knn graph
> test_pipeop_isomap.R: 2025-11-22 16:12:30.322394: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-22 16:12:30.346589: Classical Scaling
> test_pipeop_isomap.R: 2025-11-22 16:12:30.37029: L-Isomap embed START
> test_pipeop_isomap.R: 2025-11-22 16:12:30.370896: constructing knn graph
> test_pipeop_isomap.R: 2025-11-22 16:12:30.384507: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-22 16:12:30.431091: embedding
> test_pipeop_isomap.R: 2025-11-22 16:12:30.432277: DONE
> test_pipeop_isomap.R: 2025-11-22 16:12:30.457181: L-Isomap embed START
> test_pipeop_isomap.R: 2025-11-22 16:12:30.457661: constructing knn graph
> test_pipeop_isomap.R: 2025-11-22 16:12:30.472389: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-22 16:12:30.518709: embedding
> test_pipeop_isomap.R: 2025-11-22 16:12:30.519943: DONE
> test_pipeop_isomap.R: 2025-11-22 16:12:30.605971: Isomap START
> test_pipeop_isomap.R: 2025-11-22 16:12:30.606414: constructing knn graph
> test_pipeop_isomap.R: 2025-11-22 16:12:30.641751: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-22 16:12:30.744873: Classical Scaling
> test_pipeop_isomap.R: 2025-11-22 16:12:30.777544: L-Isomap embed START
> test_pipeop_isomap.R: 2025-11-22 16:12:30.778197: constructing knn graph
> test_pipeop_isomap.R: 2025-11-22 16:12:30.808877: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-22 16:12:31.011988: embedding
> test_pipeop_isomap.R: 2025-11-22 16:12:31.016407: DONE
> test_pipeop_isomap.R: 2025-11-22 16:12:31.153255: Isomap START
> test_pipeop_isomap.R: 2025-11-22 16:12:31.155127: constructing knn graph
> test_pipeop_isomap.R: 2025-11-22 16:12:31.162551: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-22 16:12:31.181881: Classical Scaling
> test_pipeop_isomap.R: 2025-11-22 16:12:31.21362: L-Isomap embed START
> test_pipeop_isomap.R: 2025-11-22 16:12:31.214286: constructing knn graph
> test_pipeop_isomap.R: 2025-11-22 16:12:31.240543: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-22 16:12:31.283584: embedding
> test_pipeop_isomap.R: 2025-11-22 16:12:31.286432: DONE
> test_pipeop_isomap.R: 2025-11-22 16:12:31.41966: Isomap START
> test_pipeop_isomap.R: 2025-11-22 16:12:31.422407: constructing knn graph
> test_pipeop_isomap.R: 2025-11-22 16:12:31.429835: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-22 16:12:31.449253: Classical Scaling
> test_pipeop_isomap.R: 2025-11-22 16:12:31.493159: L-Isomap embed START
> test_pipeop_isomap.R: 2025-11-22 16:12:31.493842: constructing knn graph
> test_pipeop_isomap.R: 2025-11-22 16:12:31.508025: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-22 16:12:31.554907: embedding
> test_pipeop_isomap.R: 2025-11-22 16:12:31.556088: DONE
> test_pipeop_isomap.R: 2025-11-22 16:12:31.629682: Isomap START
> test_pipeop_isomap.R: 2025-11-22 16:12:31.630115: constructing knn graph
> test_pipeop_isomap.R: 2025-11-22 16:12:31.637001: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-22 16:12:31.654894: Classical Scaling
> test_pipeop_isomap.R: 2025-11-22 16:12:31.743954: L-Isomap embed START
> test_pipeop_isomap.R: 2025-11-22 16:12:31.744621: constructing knn graph
> test_pipeop_isomap.R: 2025-11-22 16:12:31.774234: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-22 16:12:31.82285: embedding
> test_pipeop_isomap.R: 2025-11-22 16:12:31.824104: DONE
> test_pipeop_isomap.R: 2025-11-22 16:12:31.906486: Isomap START
> test_pipeop_isomap.R: 2025-11-22 16:12:31.90695: constructing knn graph
> test_pipeop_isomap.R: 2025-11-22 16:12:31.915493: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-22 16:12:31.935722: Classical Scaling
> test_pipeop_isomap.R: 2025-11-22 16:12:31.986528: L-Isomap embed START
> test_pipeop_isomap.R: 2025-11-22 16:12:31.987262: constructing knn graph
> test_pipeop_isomap.R: 2025-11-22 16:12:32.001921: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-22 16:12:32.046196: embedding
> test_pipeop_isomap.R: 2025-11-22 16:12:32.047416: DONE
> test_pipeop_isomap.R: 2025-11-22 16:12:32.12589: Isomap START
> test_pipeop_isomap.R: 2025-11-22 16:12:32.126355: constructing knn graph
> test_pipeop_isomap.R: 2025-11-22 16:12:32.13389: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-22 16:12:32.153006: Classical Scaling
> test_pipeop_isomap.R: 2025-11-22 16:12:32.199826: L-Isomap embed START
> test_pipeop_isomap.R: 2025-11-22 16:12:32.200462: constructing knn graph
> test_pipeop_isomap.R: 2025-11-22 16:12:32.226701: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-22 16:12:32.27192: embedding
> test_pipeop_isomap.R: 2025-11-22 16:12:32.273197: DONE
> test_pipeop_isomap.R: 2025-11-22 16:12:32.357986: Isomap START
> test_pipeop_isomap.R: 2025-11-22 16:12:32.358428: constructing knn graph
> test_pipeop_isomap.R: 2025-11-22 16:12:32.365198: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-22 16:12:32.383211: Classical Scaling
> test_pipeop_isomap.R: 2025-11-22 16:12:32.459232: Isomap START
> test_pipeop_isomap.R: 2025-11-22 16:12:32.459711: constructing knn graph
> test_pipeop_isomap.R: 2025-11-22 16:12:32.468831: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-22 16:12:32.488058: Classical Scaling
> test_pipeop_isomap.R: 2025-11-22 16:12:32.511642: Isomap START
> test_pipeop_isomap.R: 2025-11-22 16:12:32.512089: constructing knn graph
> test_pipeop_isomap.R: 2025-11-22 16:12:32.519428: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-22 16:12:32.538722: Classical Scaling
> test_pipeop_nmf.R: [PipeOpNMFstate]
> test_pipeop_nmf.R: [PipeOpNMFstate]
> 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_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 2 | WARN 0 | SKIP 100 | PASS 13055 ]
══ Skipped tests (100) ═════════════════════════════════════════════════════════
• On CRAN (96): '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_datefeatures.R:10:3',
'test_pipeop_encodelmer.R:15:3', 'test_pipeop_encodelmer.R:37:3',
'test_pipeop_encodelmer.R:80:3', 'test_pipeop_encodepl.R:5:3',
'test_pipeop_encodepl.R:72:3', '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_learnercv.R:31:3',
'test_pipeop_missind.R:6:3', 'test_pipeop_modelmatrix.R:7:3',
'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_scalerange.R:7:3',
'test_pipeop_select.R:9:3', 'test_pipeop_smote.R:10:3',
'test_pipeop_smotenc.R:8:3', 'test_pipeop_nmf.R:6:3',
'test_pipeop_spatialsign.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_subsample.R:6:3',
'test_pipeop_task_preproc.R:4:3', 'test_pipeop_task_preproc.R:14:3',
'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: 0.2977876')
`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(...)
[ FAIL 2 | WARN 0 | SKIP 100 | PASS 13055 ]
Error:
! Test failures.
Execution halted
Flavor: r-release-linux-x86_64
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’ [102s/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: [[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: 2025-11-26 05:08:58.646122: Isomap START
> test_pipeop_isomap.R: 2025-11-26 05:08:58.646381: constructing knn graph
> test_pipeop_isomap.R: 2025-11-26 05:08:58.649442: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-26 05:08:58.655814: Classical Scaling
> test_pipeop_isomap.R: 2025-11-26 05:08:58.666222: Isomap START
> test_pipeop_isomap.R: 2025-11-26 05:08:58.666363: constructing knn graph
> test_pipeop_isomap.R: 2025-11-26 05:08:58.66874: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-26 05:08:58.675007: Classical Scaling
> test_pipeop_isomap.R: 2025-11-26 05:08:58.682595: L-Isomap embed START
> test_pipeop_isomap.R: 2025-11-26 05:08:58.682792: constructing knn graph
> test_pipeop_isomap.R: 2025-11-26 05:08:58.687615: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-26 05:08:58.703525: embedding
> test_pipeop_isomap.R: 2025-11-26 05:08:58.703916: DONE
> test_pipeop_isomap.R: 2025-11-26 05:08:58.708563: L-Isomap embed START
> test_pipeop_isomap.R: 2025-11-26 05:08:58.708656: constructing knn graph
> test_pipeop_isomap.R: 2025-11-26 05:08:58.713087: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-26 05:08:58.728851: embedding
> test_pipeop_isomap.R: 2025-11-26 05:08:58.729296: DONE
> test_pipeop_isomap.R: 2025-11-26 05:08:58.751667: Isomap START
> test_pipeop_isomap.R: 2025-11-26 05:08:58.751802: constructing knn graph
> test_pipeop_isomap.R: 2025-11-26 05:08:58.756367: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-26 05:08:58.790751: Classical Scaling
> test_pipeop_isomap.R: 2025-11-26 05:08:58.799234: L-Isomap embed START
> test_pipeop_isomap.R: 2025-11-26 05:08:58.79947: constructing knn graph
> test_pipeop_isomap.R: 2025-11-26 05:08:58.808205: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-26 05:08:58.897043: embedding
> test_pipeop_isomap.R: 2025-11-26 05:08:58.899292: DONE
> test_pipeop_isomap.R: 2025-11-26 05:08:58.933575: Isomap START
> test_pipeop_isomap.R: 2025-11-26 05:08:58.933713: constructing knn graph
> test_pipeop_isomap.R: 2025-11-26 05:08:58.935889: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-26 05:08:58.942116: Classical Scaling
> test_pipeop_isomap.R: 2025-11-26 05:08:58.948386: L-Isomap embed START
> test_pipeop_isomap.R: 2025-11-26 05:08:58.948571: constructing knn graph
> test_pipeop_isomap.R: 2025-11-26 05:08:58.953302: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-26 05:08:58.968802: embedding
> test_pipeop_isomap.R: 2025-11-26 05:08:58.969243: DONE
> test_pipeop_isomap.R: 2025-11-26 05:08:58.999265: Isomap START
> test_pipeop_isomap.R: 2025-11-26 05:08:58.999404: constructing knn graph
> test_pipeop_isomap.R: 2025-11-26 05:08:59.001825: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-26 05:08:59.008342: Classical Scaling
> test_pipeop_isomap.R: 2025-11-26 05:08:59.019555: L-Isomap embed START
> test_pipeop_isomap.R: 2025-11-26 05:08:59.019729: constructing knn graph
> test_pipeop_isomap.R: 2025-11-26 05:08:59.024277: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-26 05:08:59.039087: embedding
> test_pipeop_isomap.R: 2025-11-26 05:08:59.039515: DONE
> test_pipeop_isomap.R: 2025-11-26 05:08:59.056666: Isomap START
> test_pipeop_isomap.R: 2025-11-26 05:08:59.056776: constructing knn graph
> test_pipeop_isomap.R: 2025-11-26 05:08:59.05915: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-26 05:08:59.065441: Classical Scaling
> test_pipeop_isomap.R: 2025-11-26 05:08:59.083728: L-Isomap embed START
> test_pipeop_isomap.R: 2025-11-26 05:08:59.083959: constructing knn graph
> test_pipeop_isomap.R: 2025-11-26 05:08:59.088606: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-26 05:08:59.103833: embedding
> test_pipeop_isomap.R: 2025-11-26 05:08:59.10432: DONE
> test_pipeop_isomap.R: 2025-11-26 05:08:59.121346: Isomap START
> test_pipeop_isomap.R: 2025-11-26 05:08:59.121484: constructing knn graph
> test_pipeop_isomap.R: 2025-11-26 05:08:59.123847: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-26 05:08:59.130432: Classical Scaling
> test_pipeop_isomap.R: 2025-11-26 05:08:59.140673: L-Isomap embed START
> test_pipeop_isomap.R: 2025-11-26 05:08:59.140857: constructing knn graph
> test_pipeop_isomap.R: 2025-11-26 05:08:59.145484: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-26 05:08:59.160801: embedding
> test_pipeop_isomap.R: 2025-11-26 05:08:59.161283: DONE
> test_pipeop_isomap.R: 2025-11-26 05:08:59.178597: Isomap START
> test_pipeop_isomap.R: 2025-11-26 05:08:59.178732: constructing knn graph
> test_pipeop_isomap.R: 2025-11-26 05:08:59.180998: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-26 05:08:59.186919: Classical Scaling
> test_pipeop_isomap.R: 2025-11-26 05:08:59.19775: L-Isomap embed START
> test_pipeop_isomap.R: 2025-11-26 05:08:59.197919: constructing knn graph
> test_pipeop_isomap.R: 2025-11-26 05:08:59.20235: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-26 05:08:59.216982: embedding
> test_pipeop_isomap.R: 2025-11-26 05:08:59.217359: DONE
> test_pipeop_isomap.R: 2025-11-26 05:08:59.236244: Isomap START
> test_pipeop_isomap.R: 2025-11-26 05:08:59.236363: constructing knn graph
> test_pipeop_isomap.R: 2025-11-26 05:08:59.244382: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-26 05:08:59.250167: Classical Scaling
> test_pipeop_isomap.R: 2025-11-26 05:08:59.270668: Isomap START
> test_pipeop_isomap.R: 2025-11-26 05:08:59.270806: constructing knn graph
> test_pipeop_isomap.R: 2025-11-26 05:08:59.273164: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-26 05:08:59.279501: Classical Scaling
> test_pipeop_isomap.R: 2025-11-26 05:08:59.285327: Isomap START
> test_pipeop_isomap.R: 2025-11-26 05:08:59.285469: constructing knn graph
> test_pipeop_isomap.R: 2025-11-26 05:08:59.287962: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-26 05:08:59.294356: 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_colapply.R:9:3', 'test_pipeop_collapsefactors.R:6:3',
'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_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_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 absolute difference: Inf')
`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’ [385s/510s]
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_Graph.R:
> 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_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: 2025-11-25 07:59:34.174635: Isomap START
> test_pipeop_isomap.R: 2025-11-25 07:59:34.176374: constructing knn graph
> test_pipeop_isomap.R: 2025-11-25 07:59:34.193349: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-25 07:59:34.241773: Classical Scaling
> test_pipeop_isomap.R: 2025-11-25 07:59:34.434436: Isomap START
> test_pipeop_isomap.R: 2025-11-25 07:59:34.436592: constructing knn graph
> test_pipeop_isomap.R: 2025-11-25 07:59:34.472773: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-25 07:59:34.531754: Classical Scaling
> test_pipeop_isomap.R: 2025-11-25 07:59:34.568803: L-Isomap embed START
> test_pipeop_isomap.R: 2025-11-25 07:59:34.569385: constructing knn graph
> test_pipeop_isomap.R: 2025-11-25 07:59:34.649846: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-25 07:59:34.714732: embedding
> test_pipeop_isomap.R: 2025-11-25 07:59:34.725776: DONE
> test_pipeop_isomap.R: 2025-11-25 07:59:34.759: L-Isomap embed START
> test_pipeop_isomap.R: 2025-11-25 07:59:34.759505: constructing knn graph
> test_pipeop_isomap.R: 2025-11-25 07:59:34.796164: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-25 07:59:34.875152: embedding
> test_pipeop_isomap.R: 2025-11-25 07:59:34.876817: DONE
> test_pipeop_isomap.R: 2025-11-25 07:59:35.013765: Isomap START
> test_pipeop_isomap.R: 2025-11-25 07:59:35.014161: constructing knn graph
> test_pipeop_isomap.R: 2025-11-25 07:59:35.038187: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-25 07:59:35.198852: Classical Scaling
> test_pipeop_isomap.R: 2025-11-25 07:59:35.234432: L-Isomap embed START
> test_pipeop_isomap.R: 2025-11-25 07:59:35.235675: constructing knn graph
> test_pipeop_isomap.R: 2025-11-25 07:59:35.337377: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-25 07:59:35.674108: embedding
> test_pipeop_isomap.R: 2025-11-25 07:59:35.68372: DONE
> test_pipeop_isomap.R: 2025-11-25 07:59:36.030537: Isomap START
> test_pipeop_isomap.R: 2025-11-25 07:59:36.030902: constructing knn graph
> test_pipeop_isomap.R: 2025-11-25 07:59:36.04445: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-25 07:59:36.087762: Classical Scaling
> test_pipeop_isomap.R: 2025-11-25 07:59:36.122062: L-Isomap embed START
> test_pipeop_isomap.R: 2025-11-25 07:59:36.122861: constructing knn graph
> test_pipeop_isomap.R: 2025-11-25 07:59:36.16831: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-25 07:59:36.247321: embedding
> test_pipeop_isomap.R: 2025-11-25 07:59:36.251221: DONE
> test_pipeop_isomap.R: 2025-11-25 07:59:36.456581: Isomap START
> test_pipeop_isomap.R: 2025-11-25 07:59:36.456917: constructing knn graph
> test_pipeop_isomap.R: 2025-11-25 07:59:36.4868: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-25 07:59:36.504141: Classical Scaling
> test_pipeop_isomap.R: 2025-11-25 07:59:36.588718: L-Isomap embed START
> test_pipeop_isomap.R: 2025-11-25 07:59:36.589354: constructing knn graph
> test_pipeop_isomap.R: 2025-11-25 07:59:36.612328: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-25 07:59:36.679352: embedding
> test_pipeop_isomap.R: 2025-11-25 07:59:36.683614: DONE
> test_pipeop_isomap.R: 2025-11-25 07:59:36.780127: Isomap START
> test_pipeop_isomap.R: 2025-11-25 07:59:36.780429: constructing knn graph
> test_pipeop_isomap.R: 2025-11-25 07:59:36.794821: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-25 07:59:36.827898: Classical Scaling
> test_pipeop_isomap.R: 2025-11-25 07:59:36.883708: L-Isomap embed START
> test_pipeop_isomap.R: 2025-11-25 07:59:36.885525: constructing knn graph
> test_pipeop_isomap.R: 2025-11-25 07:59:36.907588: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-25 07:59:37.077565: embedding
> test_pipeop_isomap.R: 2025-11-25 07:59:37.079816: DONE
> test_pipeop_isomap.R: 2025-11-25 07:59:37.340595: Isomap START
> test_pipeop_isomap.R: 2025-11-25 07:59:37.341729: constructing knn graph
> test_pipeop_isomap.R: 2025-11-25 07:59:37.375789: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-25 07:59:37.432013: Classical Scaling
> test_pipeop_isomap.R: 2025-11-25 07:59:37.66087: L-Isomap embed START
> test_pipeop_isomap.R: 2025-11-25 07:59:37.661389: constructing knn graph
> test_pipeop_isomap.R: 2025-11-25 07:59:37.72812: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-25 07:59:37.823314: embedding
> test_pipeop_isomap.R: 2025-11-25 07:59:37.82543: DONE
> test_pipeop_isomap.R: 2025-11-25 07:59:37.984411: Isomap START
> test_pipeop_isomap.R: 2025-11-25 07:59:37.984719: constructing knn graph
> test_pipeop_isomap.R: 2025-11-25 07:59:37.998292: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-25 07:59:38.024105: Classical Scaling
> test_pipeop_isomap.R: 2025-11-25 07:59:38.089582: L-Isomap embed START
> test_pipeop_isomap.R: 2025-11-25 07:59:38.090159: constructing knn graph
> test_pipeop_isomap.R: 2025-11-25 07:59:38.126074: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-25 07:59:38.243107: embedding
> test_pipeop_isomap.R: 2025-11-25 07:59:38.244305: DONE
> test_pipeop_isomap.R: 2025-11-25 07:59:38.339703: Isomap START
> test_pipeop_isomap.R: 2025-11-25 07:59:38.340023: constructing knn graph
> test_pipeop_isomap.R: 2025-11-25 07:59:38.358217: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-25 07:59:38.380216: Classical Scaling
> test_pipeop_isomap.R: 2025-11-25 07:59:38.515011: Isomap START
> test_pipeop_isomap.R: 2025-11-25 07:59:38.515315: constructing knn graph
> test_pipeop_isomap.R: 2025-11-25 07:59:38.522665: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-25 07:59:38.564064: Classical Scaling
> test_pipeop_isomap.R: 2025-11-25 07:59:38.631747: Isomap START
> test_pipeop_isomap.R: 2025-11-25 07:59:38.632069: constructing knn graph
> test_pipeop_isomap.R: 2025-11-25 07:59:38.65845: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-25 07:59:38.748713: 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:
> test_pipeop_task_preproc.R: Training debug_affectcols
> test_pipeop_task_preproc.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_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_imputelearner.R:43:3',
'test_pipeop_impute.R:4:3', '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_nmf.R:6:3',
'test_pipeop_randomresponse.R:5:3', 'test_pipeop_renamecolumns.R:6:3',
'test_pipeop_removeconstants.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 ════════════════════════════════════════════════════════════════
── 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: 0.4544238')
`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-x86_64
Version: 0.10.0
Check: tests
Result: ERROR
Running 'testthat.R' [272s]
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:
> 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:
> 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: 2025-11-24 10:56:27.688069: Isomap START
> test_pipeop_isomap.R: 2025-11-24 10:56:27.689056: constructing knn graph
> test_pipeop_isomap.R: 2025-11-24 10:56:27.70484: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-24 10:56:27.726329: Classical Scaling
> test_pipeop_isomap.R: 2025-11-24 10:56:27.803813: Isomap START
> test_pipeop_isomap.R: 2025-11-24 10:56:27.804431: constructing knn graph
> test_pipeop_isomap.R: 2025-11-24 10:56:27.817121: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-24 10:56:27.839414: Classical Scaling
> test_pipeop_isomap.R: 2025-11-24 10:56:27.900034: L-Isomap embed START
> test_pipeop_isomap.R: 2025-11-24 10:56:27.900926: constructing knn graph
> test_pipeop_isomap.R: 2025-11-24 10:56:27.920126: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-24 10:56:27.97052: embedding
> test_pipeop_isomap.R: 2025-11-24 10:56:27.97209: DONE
> test_pipeop_isomap.R: 2025-11-24 10:56:28.008689: L-Isomap embed START
> test_pipeop_isomap.R: 2025-11-24 10:56:28.009324: constructing knn graph
> test_pipeop_isomap.R: 2025-11-24 10:56:28.031016: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-24 10:56:28.079877: embedding
> test_pipeop_isomap.R: 2025-11-24 10:56:28.081495: DONE
> test_pipeop_isomap.R: 2025-11-24 10:56:28.19345: Isomap START
> test_pipeop_isomap.R: 2025-11-24 10:56:28.194089: constructing knn graph
> test_pipeop_isomap.R: 2025-11-24 10:56:28.217797: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-24 10:56:28.334509: Classical Scaling
> test_pipeop_isomap.R: 2025-11-24 10:56:28.383638: L-Isomap embed START
> test_pipeop_isomap.R: 2025-11-24 10:56:28.384559: constructing knn graph
> test_pipeop_isomap.R: 2025-11-24 10:56:28.43295: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-24 10:56:28.669693: embedding
> test_pipeop_isomap.R: 2025-11-24 10:56:28.675276: DONE
> test_pipeop_isomap.R: 2025-11-24 10:56:28.883591: Isomap START
> test_pipeop_isomap.R: 2025-11-24 10:56:28.884237: constructing knn graph
> test_pipeop_isomap.R: 2025-11-24 10:56:28.895921: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-24 10:56:28.916922: Classical Scaling
> test_pipeop_isomap.R: 2025-11-24 10:56:28.960041: L-Isomap embed START
> test_pipeop_isomap.R: 2025-11-24 10:56:28.960663: constructing knn graph
> test_pipeop_isomap.R: 2025-11-24 10:56:28.987946: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-24 10:56:29.025404: embedding
> test_pipeop_isomap.R: 2025-11-24 10:56:29.026744: DONE
> test_pipeop_isomap.R: 2025-11-24 10:56:29.193243: Isomap START
> test_pipeop_isomap.R: 2025-11-24 10:56:29.193924: constructing knn graph
> test_pipeop_isomap.R: 2025-11-24 10:56:29.205184: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-24 10:56:29.227791: Classical Scaling
> test_pipeop_isomap.R: 2025-11-24 10:56:29.29715: L-Isomap embed START
> test_pipeop_isomap.R: 2025-11-24 10:56:29.29817: constructing knn graph
> test_pipeop_isomap.R: 2025-11-24 10:56:29.318752: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-24 10:56:29.369182: embedding
> test_pipeop_isomap.R: 2025-11-24 10:56:29.370843: DONE
> test_pipeop_isomap.R: 2025-11-24 10:56:29.479893: Isomap START
> test_pipeop_isomap.R: 2025-11-24 10:56:29.480579: constructing knn graph
> test_pipeop_isomap.R: 2025-11-24 10:56:29.491266: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-24 10:56:29.514993: Classical Scaling
> test_pipeop_isomap.R: 2025-11-24 10:56:29.591268: L-Isomap embed START
> test_pipeop_isomap.R: 2025-11-24 10:56:29.592218: constructing knn graph
> test_pipeop_isomap.R: 2025-11-24 10:56:29.612254: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-24 10:56:29.663322: embedding
> test_pipeop_isomap.R: 2025-11-24 10:56:29.664978: DONE
> test_pipeop_isomap.R: 2025-11-24 10:56:29.765927: Isomap START
> test_pipeop_isomap.R: 2025-11-24 10:56:29.766555: constructing knn graph
> test_pipeop_isomap.R: 2025-11-24 10:56:29.777571: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-24 10:56:29.799118: Classical Scaling
> test_pipeop_isomap.R: 2025-11-24 10:56:29.901431: L-Isomap embed START
> test_pipeop_isomap.R: 2025-11-24 10:56:29.902512: constructing knn graph
> test_pipeop_isomap.R: 2025-11-24 10:56:29.924147: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-24 10:56:29.980419: embedding
> test_pipeop_isomap.R: 2025-11-24 10:56:29.982364: DONE
> test_pipeop_isomap.R: 2025-11-24 10:56:30.077604: Isomap START
> test_pipeop_isomap.R: 2025-11-24 10:56:30.078214: constructing knn graph
> test_pipeop_isomap.R: 2025-11-24 10:56:30.089732: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-24 10:56:30.111332: Classical Scaling
> test_pipeop_isomap.R: 2025-11-24 10:56:30.167366: L-Isomap embed START
> test_pipeop_isomap.R: 2025-11-24 10:56:30.168254: constructing knn graph
> test_pipeop_isomap.R: 2025-11-24 10:56:30.191787: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-24 10:56:30.231392: embedding
> test_pipeop_isomap.R: 2025-11-24 10:56:30.232764: DONE
> test_pipeop_isomap.R: 2025-11-24 10:56:30.342122: Isomap START
> test_pipeop_isomap.R: 2025-11-24 10:56:30.342668: constructing knn graph
> test_pipeop_isomap.R: 2025-11-24 10:56:30.351792: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-24 10:56:30.368357: Classical Scaling
> test_pipeop_isomap.R: 2025-11-24 10:56:30.458361: Isomap START
> test_pipeop_isomap.R: 2025-11-24 10:56:30.458905: constructing knn graph
> test_pipeop_isomap.R: 2025-11-24 10:56:30.468153: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-24 10:56:30.485519: Classical Scaling
> test_pipeop_isomap.R: 2025-11-24 10:56:30.520799: Isomap START
> test_pipeop_isomap.R: 2025-11-24 10:56:30.521374: constructing knn graph
> test_pipeop_isomap.R: 2025-11-24 10:56:30.532066: calculating geodesic distances
> test_pipeop_isomap.R: 2025-11-24 10:56:30.54784: 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_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_learnercv.R:31:3',
'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_scalerange.R:7:3',
'test_pipeop_select.R:9:3', 'test_pipeop_nmf.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: 0.9014729')
`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