* using log directory ‘/srv/hornik/tmp/CRAN_pretest/mlr3pipelines.Rcheck’
* using R Under development (unstable) (2026-02-28 r89499)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 21.1.8 (1+b1)
    Debian flang version 21.1.8 (1+b1)
* running under: Debian GNU/Linux forky/sid
* using session charset: UTF-8
* current time: 2026-02-28 14:33:22 UTC
* checking for file ‘mlr3pipelines/DESCRIPTION’ ... OK
* this is package ‘mlr3pipelines’ version ‘0.11.0’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... [6s/9s] OK
* 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 ... [16s/16s] OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] OK
* checking whether startup messages can be suppressed ... [0s/0s] 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 ... [38s/38s] OK
* checking Rd files ... [2s/2s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 ... [52s/52s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [201s/95s] ERROR
  Running ‘testthat.R’ [201s/95s]
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.
  > 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: 2026-02-28 15:36:27.621728: Isomap START
  > test_pipeop_isomap.R: 2026-02-28 15:36:27.622135: constructing knn graph
  > test_pipeop_isomap.R: 2026-02-28 15:36:27.641475: calculating geodesic distances
  > test_pipeop_isomap.R: 2026-02-28 15:36:27.652689: Classical Scaling
  > test_pipeop_isomap.R: 2026-02-28 15:36:27.680153: Isomap START
  > test_pipeop_isomap.R: 2026-02-28 15:36:27.680369: constructing knn graph
  > test_pipeop_isomap.R: 2026-02-28 15:36:27.684369: calculating geodesic distances
  > test_pipeop_isomap.R: 2026-02-28 15:36:27.69529: Classical Scaling
  > test_pipeop_isomap.R: 2026-02-28 15:36:27.708613: L-Isomap embed START
  > test_pipeop_isomap.R: 2026-02-28 15:36:27.70891: constructing knn graph
  > test_pipeop_isomap.R: 2026-02-28 15:36:27.716835: calculating geodesic distances
  > test_pipeop_isomap.R: 2026-02-28 15:36:27.741857: embedding
  > test_pipeop_isomap.R: 2026-02-28 15:36:27.742418: DONE
  > test_pipeop_isomap.R: 2026-02-28 15:36:27.756024: L-Isomap embed START
  > test_pipeop_isomap.R: 2026-02-28 15:36:27.756227: constructing knn graph
  > test_pipeop_isomap.R: 2026-02-28 15:36:27.764058: calculating geodesic distances
  > test_pipeop_isomap.R: 2026-02-28 15:36:27.789143: embedding
  > test_pipeop_isomap.R: 2026-02-28 15:36:27.789694: DONE
  > test_pipeop_isomap.R: 2026-02-28 15:36:27.882947: Isomap START
  > test_pipeop_isomap.R: 2026-02-28 15:36:27.883179: constructing knn graph
  > test_pipeop_isomap.R: 2026-02-28 15:36:27.890794: calculating geodesic distances
  > test_pipeop_isomap.R: 2026-02-28 15:36:27.950435: Classical Scaling
  > test_pipeop_isomap.R: 2026-02-28 15:36:27.96891: L-Isomap embed START
  > test_pipeop_isomap.R: 2026-02-28 15:36:27.969236: constructing knn graph
  > test_pipeop_isomap.R: 2026-02-28 15:36:27.983834: calculating geodesic distances
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.114066: embedding
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.11616: DONE
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.188158: Isomap START
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.18837: constructing knn graph
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.192341: calculating geodesic distances
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.203182: Classical Scaling
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.21905: L-Isomap embed START
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.219338: constructing knn graph
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.22702: calculating geodesic distances
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.251923: embedding
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.252442: DONE
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.329693: Isomap START
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.329915: constructing knn graph
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.333945: calculating geodesic distances
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.34482: Classical Scaling
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.367747: L-Isomap embed START
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.368038: constructing knn graph
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.375741: calculating geodesic distances
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.400798: embedding
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.401283: DONE
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.439689: Isomap START
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.439889: constructing knn graph
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.450793: calculating geodesic distances
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.461802: Classical Scaling
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.487679: L-Isomap embed START
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.487973: constructing knn graph
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.495831: calculating geodesic distances
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.520924: embedding
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.521461: DONE
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.559577: Isomap START
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.55977: constructing knn graph
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.563671: calculating geodesic distances
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.574493: Classical Scaling
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.605002: L-Isomap embed START
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.605379: constructing knn graph
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.61386: calculating geodesic distances
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.63921: embedding
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.639838: DONE
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.67938: Isomap START
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.679584: constructing knn graph
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.683485: calculating geodesic distances
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.694287: Classical Scaling
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.717417: L-Isomap embed START
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.717722: constructing knn graph
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.76446: calculating geodesic distances
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.789839: embedding
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.790494: DONE
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.83667: Isomap START
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.836872: constructing knn graph
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.840813: calculating geodesic distances
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.851583: Classical Scaling
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.890485: Isomap START
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.89068: constructing knn graph
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.894507: calculating geodesic distances
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.905291: Classical Scaling
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.917188: Isomap START
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.91736: constructing knn graph
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.92103: calculating geodesic distances
  > test_pipeop_isomap.R: 2026-02-28 15:36:28.931847: Classical Scaling
  Saving _problems/test_pipeop_learnercv-741.R
  > 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 1 | WARN 1 | SKIP 102 | PASS 11632 ]
  
  ══ Skipped tests (102) ═════════════════════════════════════════════════════════
  • On CRAN (99): '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_classweightsex.R:9:3', '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_datefeatures.R:10:3',
    '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_imputelearner.R:43:3',
    'test_pipeop_impute.R:4:3', 'test_pipeop_info.R:3:1',
    'test_pipeop_kernelpca.R:9:3', 'test_pipeop_isomap.R:10:3',
    '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_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_spatialsign.R:3:1',
    'test_pipeop_splines.R:3:1', 'test_pipeop_nmf.R:6:3',
    'test_pipeop_targetinvert.R:4:3', 'test_pipeop_targetmutate.R:5:3',
    'test_pipeop_subsample.R:6:3', '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_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_ppl.R:63:3', 'test_typecheck.R:188:3',
    'test_pipeop_tunethreshold.R:111:3', 'test_pipeop_tunethreshold.R:191:3'
  • Skipping (1): 'test_GraphLearner.R:1278:3'
  • empty test (2): 'test_pipeop_isomap.R:111:1', 'test_pipeop_missind.R:101:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_pipeop_learnercv.R:741:3'): PipeOpLearnerCV cv ensemble handles unsorted, subsetted row_ids (classif) ──
  <subscriptOutOfBoundsError/error/condition>
  Error in `frame$yval2[where, 1L + nclass + 1L:nclass, drop = FALSE]`: subscript out of bounds
  This happened in PipeOp classif.rpart's $train()
  Backtrace:
       ▆
    1. ├─op$train(list(task)) at test_pipeop_learnercv.R:741:3
    2. │ └─mlr3pipelines:::.__PipeOp__train(...)
    3. │   ├─base::withCallingHandlers(...)
    4. │   └─private$.train(input)
    5. │     └─mlr3pipelines:::.__PipeOpTaskPreproc__.train(...)
    6. │       └─private$.train_task(intask)
    7. │         └─mlr3pipelines:::.__PipeOpLearnerCV__.train_task(...)
    8. │           └─mlr3::resample(...)
    9. │             └─mlr3:::future_map(...)
   10. │               └─future.apply::future_mapply(...)
   11. │                 └─future.apply:::future_xapply(...)
   12. │                   └─base::tryCatch(...)
   13. │                     └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   14. │                       └─base (local) tryCatchOne(...)
   15. │                         └─value[[3L]](cond)
   16. │                           └─future.apply:::onError(e, futures = fs, debug = debug)
   17. │                             └─base::stop(ex)
   18. └─mlr3pipelines (local) `<fn>`(`<sbscOOBE>`)
  
  [ FAIL 1 | WARN 1 | SKIP 102 | PASS 11632 ]
  Error:
  ! Test failures.
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [2s/2s] OK
* checking PDF version of manual ... [13s/13s] OK
* checking HTML version of manual ... [23s/23s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR