R Under development (unstable) (2025-10-28 r88973 ucrt) -- "Unsuffered Consequences"
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> library(testthat)
> library(mikropml)
> test_check("mikropml")
Fraction of data in the training set: 0.778 
	Groups in the training set: A C D 
	Groups in the testing set: B
Fraction of data in the training set: 0.778 
	Groups in the training set: A C D 
	Groups in the testing set: B
Fraction of data in the training set: 0.333 
	Groups in the training set: A D 
	Groups in the testing set: A B C D
Fraction of data in the training set: 0.785 
	Groups in the training set: A B E F G H 
	Groups in the testing set: C D
Fraction of data in the training set: 0.2 
	Groups in the training set: A B 
	Groups in the testing set: A B C D E F G H
Using 'dx' as the outcome column.
Using 'dx' as the outcome column.
Using 'dx' as the outcome column.
Using 'y' as the outcome column.
Using 'y' as the outcome column.
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: generics

Attaching package: 'generics'

The following objects are masked from 'package:base':

    as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
    setequal, union


Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, is.unsorted, lapply,
    mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
    rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:purrr':

    reduce

The following object is masked from 'package:grDevices':

    windows

Loading required package: Seqinfo
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'XVector'

The following object is masked from 'package:purrr':

    compact


Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit


Attaching package: 'dplyr'

The following objects are masked from 'package:Biostrings':

    collapse, intersect, setdiff, setequal, union

The following object is masked from 'package:XVector':

    slice

The following object is masked from 'package:Biobase':

    combine

The following objects are masked from 'package:GenomicRanges':

    intersect, setdiff, union

The following object is masked from 'package:Seqinfo':

    intersect

The following objects are masked from 'package:IRanges':

    collapse, desc, intersect, setdiff, slice, union

The following objects are masked from 'package:S4Vectors':

    first, intersect, rename, setdiff, setequal, union

The following objects are masked from 'package:BiocGenerics':

    combine, intersect, setdiff, setequal, union

The following object is masked from 'package:generics':

    explain

The following object is masked from 'package:matrixStats':

    count

The following object is masked from 'package:testthat':

    matches

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Using 'dx' as the outcome column.
Groups will not be kept together in CV partitions because the number of groups in the training set is not larger than `kfold`
Training the model...
Training complete.
Fraction of data in the training set: 0.785 
	Groups in the training set: A B E F G H 
	Groups in the testing set: C D
Using 'dx' as the outcome column.
Using 'dx' as the outcome column.
[ FAIL 0 | WARN 0 | SKIP 13 | PASS 327 ]

══ Skipped tests (13) ══════════════════════════════════════════════════════════
• On CRAN (13): 'test-feature_importance.R:14:3',
  'test-feature_importance.R:142:3', 'test-feature_importance.R:162:3',
  'test-run_ml.R:64:3', 'test-run_ml.R:82:3', 'test-run_ml.R:97:3',
  'test-run_ml.R:114:3', 'test-run_ml.R:134:3', 'test-run_ml.R:150:3',
  'test-run_ml.R:188:3', 'test-run_ml.R:279:3', 'test-run_ml.R:315:3',
  'test-train.R:44:3'

[ FAIL 0 | WARN 0 | SKIP 13 | PASS 327 ]
> 
> proc.time()
   user  system elapsed 
  63.98    3.18   70.18