Running ‘testthat.R’ [72s/96s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(MOCHA)
  > 
  > test_check("MOCHA")
  
  Loading required package: chromVARmotifs
  harmonizing input:
    removing 1 sampleMap rows not in names(experiments)
  harmonizing input:
    removing 3 sampleMap rows not in names(experiments)
  [ FAIL 2 | WARN 13 | SKIP 23 | PASS 21 ]
  
  ══ Skipped tests (23) ══════════════════════════════════════════════════════════
  • BSgenome.Hsapiens.UCSC.hg19 cannot be loaded (1):
    'test_dimensionalityReduction.R:1:1'
  • On CRAN (20): '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_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'
  • chromVAR cannot be loaded (2): 'test_combineSampleTileMatrix.R:1:1',
    'test_testCoAccessibility.R:1:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_exportDifferentials.R:28:3'): exportDifferentials works on a 3 sample test dataset ──
  Error in `.stopOnAvailablePkg(genome)`: BSgenome.Hsapiens.UCSC.hg19 package is not currently installed.
    You first need to install it, which you can do with:
        library(BiocManager)
        install("BSgenome.Hsapiens.UCSC.hg19")
  Backtrace:
      ▆
   1. └─MOCHA::exportDifferentials(...) at test_exportDifferentials.R:28:3
   2.   └─BSgenome::getBSgenome(S4Vectors::metadata(SampleTileObject)$Genome)
   3.     └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked)
   4.       └─BSgenome:::.stopOnAvailablePkg(genome)
  ── Error ('test_exportOpenTiles.R:13:3'): exportDifferentials works on a 3 sample test dataset ──
  Error in `.stopOnAvailablePkg(genome)`: BSgenome.Hsapiens.UCSC.hg19 package is not currently installed.
    You first need to install it, which you can do with:
        library(BiocManager)
        install("BSgenome.Hsapiens.UCSC.hg19")
  Backtrace:
      ▆
   1. └─MOCHA::exportOpenTiles(...) at test_exportOpenTiles.R:13:3
   2.   └─BSgenome::getBSgenome(S4Vectors::metadata(SampleTileObject)$Genome)
   3.     └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked)
   4.       └─BSgenome:::.stopOnAvailablePkg(genome)
  
  [ FAIL 2 | WARN 13 | SKIP 23 | PASS 21 ]
  Error: Test failures
  Execution halted