R Under development (unstable) (2024-01-24 r85824 ucrt) -- "Unsuffered Consequences"
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> library(testthat)
> library(MOCHA)
> 
> test_check("MOCHA")


Loading required package: RaggedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

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, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
    union, 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:grDevices':

    windows

Loading required package: GenomeInfoDb

Attaching package: 'Biostrings'

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

    strsplit


Attaching package: 'rtracklayer'

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

    FileForFormat

Exporting: D:\temp\Rtmpgttldo/Differentials.bigBed
Loading required package: chromVARmotifs
harmonizing input:
  removing 1 sampleMap rows not in names(experiments)
  removing 1 sampleMap rows with 'colname' not in colnames of experiments
  removing 1 colData rownames not in sampleMap 'primary'
harmonizing input:
  removing 3 sampleMap rows not in names(experiments)
  removing 3 sampleMap rows with 'colname' not in colnames of experiments
  removing 3 colData rownames not in sampleMap 'primary'
[ FAIL 0 | WARN 13 | SKIP 25 | PASS 24 ]

══ Skipped tests (25) ══════════════════════════════════════════════════════════
• On CRAN (25): 'test_COVID_data_pipeline.R:1:1', 'test_MotifEnrichment.R:1:1',
  'test_MotifSetEnrichmentAnalysis.R:1:1', 'test_addMotifSet.R:1:1',
  'test_callOpenTiles.R:3:1', 'test_combineSampleTileMatrix.R:17:5',
  'test_combineSampleTileMatrix.R:35:5', 'test_dimensionalityReduction.R:37:5',
  'test_exportCoverage.R:1:1', 'test_extractRegion.R:1:1',
  'test_getCoAccessibleLinks.R:22:3', 'test_getCoAccessibleLinks.R:53:3',
  'test_getCoverage.R:1:1', 'test_getDifferentialAccessibleTiles.R:1:1',
  'test_getPopFrags.R:13:1', 'test_getSampleTileMatrix.R:18:3',
  'test_packMOCHA.R:1:1', 'test_plotRegion.R:1:1',
  'test_subsetMOCHAObject.R:13:3', 'test_subsetMOCHAObject.R:25:3',
  'test_subsetMOCHAObject.R:67:3', 'test_subsetMOCHAObject.R:97:3',
  'test_subsetMOCHAObject.R:127:3', 'test_testCoAccessibility.R:39:5',
  'test_testCoAccessibility.R:80:5'

[ FAIL 0 | WARN 13 | SKIP 25 | PASS 24 ]
> 
> proc.time()
   user  system elapsed 
  80.35    4.79  302.00