* using log directory ‘/Users/ripley/R/packages/tests-devel/mlr3pipelines.Rcheck’
* using R Under development (unstable) (2025-11-25 r89060)
* using platform: aarch64-apple-darwin25.1.0
* R was compiled by
    Apple clang version 17.0.0 (clang-1700.6.3.2)
    GNU Fortran (GCC) 14.2.0
* running under: macOS Tahoe 26.1
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘mlr3pipelines/DESCRIPTION’ ... OK
* this is package ‘mlr3pipelines’ version ‘0.10.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘mlr3pipelines’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [19s/19s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [17s/17s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [146s/72s]
 [146s/72s] ERROR
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: 2025-11-25 07:28:09.127499: Isomap START
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.127993: constructing knn graph
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.132305: calculating geodesic distances
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.14178: Classical Scaling
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.160406: Isomap START
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.160606: constructing knn graph
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.163584: calculating geodesic distances
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.173458: Classical Scaling
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.187061: L-Isomap embed START
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.187357: constructing knn graph
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.193384: calculating geodesic distances
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.213255: embedding
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.21368: DONE
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.219893: L-Isomap embed START
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.220056: constructing knn graph
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.225035: calculating geodesic distances
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.244353: embedding
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.244781: DONE
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.268799: Isomap START
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.268958: constructing knn graph
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.279458: calculating geodesic distances
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.333532: Classical Scaling
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.343045: L-Isomap embed START
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.343265: constructing knn graph
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.356405: calculating geodesic distances
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.468808: embedding
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.469883: DONE
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.516015: Isomap START
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.51616: constructing knn graph
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.518837: calculating geodesic distances
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.526449: Classical Scaling
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.534722: L-Isomap embed START
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.534954: constructing knn graph
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.539854: calculating geodesic distances
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.559231: embedding
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.559685: DONE
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.596473: Isomap START
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.596627: constructing knn graph
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.599204: calculating geodesic distances
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.606774: Classical Scaling
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.619703: L-Isomap embed START
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.61993: constructing knn graph
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.62988: calculating geodesic distances
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.649401: embedding
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.649786: DONE
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.671455: Isomap START
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.671622: constructing knn graph
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.674275: calculating geodesic distances
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.681888: Classical Scaling
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.694558: L-Isomap embed START
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.694752: constructing knn graph
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.699619: calculating geodesic distances
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.718975: embedding
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.719427: DONE
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.747878: Isomap START
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.748067: constructing knn graph
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.750885: calculating geodesic distances
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.758565: Classical Scaling
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.773757: L-Isomap embed START
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.774045: constructing knn graph
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.779351: calculating geodesic distances
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.79899: embedding
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.799403: DONE
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.819403: Isomap START
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.819578: constructing knn graph
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.822224: calculating geodesic distances
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.829825: Classical Scaling
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.843205: L-Isomap embed START
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.843427: constructing knn graph
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.853588: calculating geodesic distances
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.873061: embedding
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.873491: DONE
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.910981: Isomap START
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.911142: constructing knn graph
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.913804: calculating geodesic distances
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.921637: Classical Scaling
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.944184: Isomap START
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.944336: constructing knn graph
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.946951: calculating geodesic distances
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.954478: Classical Scaling
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.960882: Isomap START
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.961029: constructing knn graph
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.968178: calculating geodesic distances
  > test_pipeop_isomap.R: 2025-11-25 07:28:09.975753: 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_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 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_boxcox.R:7:3',
    'test_pipeop_classbalancing.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_datefeatures.R:10:3',
    '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_info.R:6:3', 'test_pipeop_learner.R:17:3',
    '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_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_spatialsign.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: 0.7932806')
  `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
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... [13s/13s] OK
* checking HTML version of manual ... [12s/12s] OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR
See
  ‘/Users/ripley/R/packages/tests-devel/mlr3pipelines.Rcheck/00check.log’
for details.

      171.93 real       226.37 user        17.32 sys