Running ‘testthat.R’ [95s/123s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(MOCHA)
  > 
  > test_check("MOCHA")
  
  'select()' returned 1:1 mapping between keys and columns
  
  Attaching package: 'Biostrings'
  
  The following object is masked from 'package:base':
  
      strsplit
  
  harmonizing input:
    removing 1 sampleMap rows not in names(experiments)
  harmonizing input:
    removing 3 sampleMap rows not in names(experiments)
  [ FAIL 7 | WARN 11 | SKIP 20 | PASS 26 ]
  
  ══ Skipped tests (20) ══════════════════════════════════════════════════════════
  • 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_annotateTiles.R:21:5', 'test_annotateTiles.R:44:5',
    'test_annotateTiles.R:70:5', 'test_callOpenTiles.R:3:1',
    '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_subsetMOCHAObject.R:13:3',
    'test_subsetMOCHAObject.R:25:3', 'test_subsetMOCHAObject.R:67:3',
    'test_subsetMOCHAObject.R:97:3', 'test_subsetMOCHAObject.R:127:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_dimensionalityReduction.R:31:5'): bulkDimReduction works on a 3 sample test dataset ──
  Error in `combineSampleTileMatrix(SampleTileObj)`: Package 'chromVAR' is required for combineSampleTileMatrix. Please install 'chromVAR' to proceed.
  Backtrace:
      ▆
   1. ├─utils::capture.output(...) at test_dimensionalityReduction.R:31:4
   2. │ └─base::withVisible(...elt(i))
   3. └─MOCHA::bulkDimReduction(SampleTileMatrix, cellType = "all", componentNumber = 2)
   4.   └─MOCHA::combineSampleTileMatrix(SampleTileObj)
  ── Error ('test_dimensionalityReduction.R:51:5'): bulkDimReduction errors NA columns ──
  Error in `combineSampleTileMatrix(SampleTileObj)`: Package 'chromVAR' is required for combineSampleTileMatrix. Please install 'chromVAR' to proceed.
  Backtrace:
      ▆
   1. ├─testthat::expect_error(...) at test_dimensionalityReduction.R:51:4
   2. │ └─testthat:::expect_condition_matching(...)
   3. │   └─testthat:::quasi_capture(...)
   4. │     ├─testthat (local) .capture(...)
   5. │     │ └─base::withCallingHandlers(...)
   6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
   7. └─MOCHA::bulkDimReduction(SampleTileMatrix, cellType = "all", componentNumber = 2)
   8.   └─MOCHA::combineSampleTileMatrix(SampleTileObj)
  ── Error ('test_testCoAccessibilityChromVar.R:23:3'): testCoAccessibleLinks works on a 1 sample test dataset ──
  Error in `MOCHA::testCoAccessibilityChromVar(SampleTileMatrix, tile1 = links$Tile1, 
      tile2 = links$Tile2, numCores = 1, ZI = TRUE, backNumber = 1000, 
      highMem = FALSE, verbose = FALSE)`: Package 'chromVAR' is required for combineSampleTileMatrix. Please install 'chromVAR' to proceed.
  Backtrace:
      ▆
   1. ├─utils::capture.output(...) at test_testCoAccessibilityChromVar.R:23:2
   2. │ └─base::withVisible(...elt(i))
   3. └─MOCHA::testCoAccessibilityChromVar(...)
  ── Error ('test_testCoAccessibilityChromVar.R:65:3'): testCoAccessibleLinks works on a 3 sample test dataset ──
  Error in `MOCHA::testCoAccessibilityChromVar(SampleTileMatrix, tile1 = links$Tile1, 
      tile2 = links$Tile2, numCores = 1, ZI = TRUE, backNumber = 1000, 
      highMem = FALSE, verbose = FALSE)`: Package 'chromVAR' is required for combineSampleTileMatrix. Please install 'chromVAR' to proceed.
  Backtrace:
      ▆
   1. ├─utils::capture.output(...) at test_testCoAccessibilityChromVar.R:65:2
   2. │ └─base::withVisible(...elt(i))
   3. └─MOCHA::testCoAccessibilityChromVar(...)
  ── Error ('test_testCoAccessibilityChromVar.R:107:3'): testCoAccessibleLinks works on a 3 sample test dataset with highMem=TRUE ──
  Error in `MOCHA::testCoAccessibilityChromVar(SampleTileMatrix, tile1 = links$Tile1, 
      tile2 = links$Tile2, numCores = 1, ZI = TRUE, backNumber = 1000, 
      highMem = TRUE, verbose = FALSE)`: Package 'chromVAR' is required for combineSampleTileMatrix. Please install 'chromVAR' to proceed.
  Backtrace:
      ▆
   1. ├─utils::capture.output(...) at test_testCoAccessibilityChromVar.R:107:2
   2. │ └─base::withVisible(...elt(i))
   3. └─MOCHA::testCoAccessibilityChromVar(...)
  ── Error ('test_testCoAccessibilityRandom.R:23:3'): testCoAccessibleLinks works on a 1 sample test dataset ──
  Error in `combineSampleTileMatrix(SampleTileObj)`: Package 'chromVAR' is required for combineSampleTileMatrix. Please install 'chromVAR' to proceed.
  Backtrace:
      ▆
   1. ├─utils::capture.output(...) at test_testCoAccessibilityRandom.R:23:2
   2. │ └─base::withVisible(...elt(i))
   3. └─MOCHA::testCoAccessibilityRandom(...)
   4.   └─MOCHA::combineSampleTileMatrix(SampleTileObj)
  ── Error ('test_testCoAccessibilityRandom.R:64:3'): testCoAccessibleLinks works on a 3 sample test dataset ──
  Error in `combineSampleTileMatrix(SampleTileObj)`: Package 'chromVAR' is required for combineSampleTileMatrix. Please install 'chromVAR' to proceed.
  Backtrace:
      ▆
   1. ├─utils::capture.output(...) at test_testCoAccessibilityRandom.R:64:2
   2. │ └─base::withVisible(...elt(i))
   3. └─MOCHA::testCoAccessibilityRandom(...)
   4.   └─MOCHA::combineSampleTileMatrix(SampleTileObj)
  
  [ FAIL 7 | WARN 11 | SKIP 20 | PASS 26 ]
  Error: Test failures
  Execution halted