Running 'testthat.R' [366s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > 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, sort, 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
  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 9 | WARN 2 | SKIP 17 | PASS 21 ]
  
  ══ Skipped tests (17) ══════════════════════════════════════════════════════════
  • On CRAN (17): '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_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_combineSampleTileMatrix.R:12:5'): combineSampleTileMatrix works on a 3-sample 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::combineSampleTileMatrix(STObj) at test_combineSampleTileMatrix.R:12:4
   2.   └─BSgenome::getBSgenome(genome)
   3.     └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked)
   4.       └─BSgenome:::.stopOnAvailablePkg(genome)
  ── Error ('test_combineSampleTileMatrix.R:30:5'): combineSampleTileMatrix works on a 1-sample 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::combineSampleTileMatrix(STObj) at test_combineSampleTileMatrix.R:30:4
   2.   └─BSgenome::getBSgenome(genome)
   3.     └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked)
   4.       └─BSgenome:::.stopOnAvailablePkg(genome)
  ── Error ('test_dimensionalityReduction.R:31:5'): bulkDimReduction 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. ├─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)
   5.     └─BSgenome::getBSgenome(genome)
   6.       └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked)
   7.         └─BSgenome:::.stopOnAvailablePkg(genome)
  ── Error ('test_dimensionalityReduction.R:51:5'): bulkDimReduction errors NA columns ──
  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. ├─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)
    9.     └─BSgenome::getBSgenome(genome)
   10.       └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked)
   11.         └─BSgenome:::.stopOnAvailablePkg(genome)
  ── Error ('test_testCoAccessibilityChromVar.R:23:3'): testCoAccessibleLinks works on a 1 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. ├─utils::capture.output(...) at test_testCoAccessibilityChromVar.R:23:2
   2. │ └─base::withVisible(...elt(i))
   3. └─MOCHA::testCoAccessibilityChromVar(...)
   4.   └─MOCHA::combineSampleTileMatrix(SampleTileObj)
   5.     └─BSgenome::getBSgenome(genome)
   6.       └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked)
   7.         └─BSgenome:::.stopOnAvailablePkg(genome)
  ── Error ('test_testCoAccessibilityChromVar.R:65:3'): testCoAccessibleLinks 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. ├─utils::capture.output(...) at test_testCoAccessibilityChromVar.R:65:2
   2. │ └─base::withVisible(...elt(i))
   3. └─MOCHA::testCoAccessibilityChromVar(...)
   4.   └─MOCHA::combineSampleTileMatrix(SampleTileObj)
   5.     └─BSgenome::getBSgenome(genome)
   6.       └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked)
   7.         └─BSgenome:::.stopOnAvailablePkg(genome)
  ── Error ('test_testCoAccessibilityChromVar.R:107:3'): testCoAccessibleLinks works on a 3 sample test dataset with highMem=TRUE ──
  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. ├─utils::capture.output(...) at test_testCoAccessibilityChromVar.R:107:2
   2. │ └─base::withVisible(...elt(i))
   3. └─MOCHA::testCoAccessibilityChromVar(...)
   4.   └─MOCHA::combineSampleTileMatrix(SampleTileObj)
   5.     └─BSgenome::getBSgenome(genome)
   6.       └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked)
   7.         └─BSgenome:::.stopOnAvailablePkg(genome)
  ── Error ('test_testCoAccessibilityRandom.R:23:3'): testCoAccessibleLinks works on a 1 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. ├─utils::capture.output(...) at test_testCoAccessibilityRandom.R:23:2
   2. │ └─base::withVisible(...elt(i))
   3. └─MOCHA::testCoAccessibilityRandom(...)
   4.   └─MOCHA::combineSampleTileMatrix(SampleTileObj)
   5.     └─BSgenome::getBSgenome(genome)
   6.       └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked)
   7.         └─BSgenome:::.stopOnAvailablePkg(genome)
  ── Error ('test_testCoAccessibilityRandom.R:64:3'): testCoAccessibleLinks 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. ├─utils::capture.output(...) at test_testCoAccessibilityRandom.R:64:2
   2. │ └─base::withVisible(...elt(i))
   3. └─MOCHA::testCoAccessibilityRandom(...)
   4.   └─MOCHA::combineSampleTileMatrix(SampleTileObj)
   5.     └─BSgenome::getBSgenome(genome)
   6.       └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked)
   7.         └─BSgenome:::.stopOnAvailablePkg(genome)
  
  [ FAIL 9 | WARN 2 | SKIP 17 | PASS 21 ]
  Error: Test failures
  Execution halted