Running ‘testthat.R’ [134s/161s]
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, 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
  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
  
  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 3 | WARN 2 | SKIP 22 | PASS 22 ]
  
  ══ Skipped tests (22) ══════════════════════════════════════════════════════════
  • On CRAN (22): '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:14:5',
    'test_combineSampleTileMatrix.R:32:5', 'test_dimensionalityReduction.R:35:5',
    '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',
    'test_testCoAccessibilityRandom.R:35:3',
    'test_testCoAccessibilityRandom.R:76:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_testCoAccessibilityChromVar.R:23:3'): testCoAccessibleLinks works on a 1 sample test dataset ──
  Error in `Matrix::rowSums(counts(object))`: object 'R_dense_rowSums' not found
  Backtrace:
       ▆
    1. ├─utils::capture.output(...) at test_testCoAccessibilityChromVar.R:23:3
    2. │ └─base::withVisible(...elt(i))
    3. └─MOCHA::testCoAccessibilityChromVar(...)
    4.   ├─chromVAR::getBackgroundPeaks(fullObj)
    5.   └─chromVAR::getBackgroundPeaks(fullObj)
    6.     └─chromVAR (local) .local(object, ...)
    7.       └─chromVAR:::get_background_peaks_core(...)
    8.         ├─chromVAR::getFragmentsPerPeak(object)
    9.         └─chromVAR::getFragmentsPerPeak(object)
   10.           ├─Matrix::rowSums(counts(object))
   11.           └─Matrix::rowSums(counts(object))
  ── Error ('test_testCoAccessibilityChromVar.R:65:3'): testCoAccessibleLinks works on a 3 sample test dataset ──
  Error in `.local(x, na.rm, dims, ...)`: object 'CRsparse_rowSums' not found
  Backtrace:
       ▆
    1. ├─utils::capture.output(...) at test_testCoAccessibilityChromVar.R:65:3
    2. │ └─base::withVisible(...elt(i))
    3. └─MOCHA::testCoAccessibilityChromVar(...)
    4.   ├─chromVAR::getBackgroundPeaks(fullObj)
    5.   └─chromVAR::getBackgroundPeaks(fullObj)
    6.     └─chromVAR (local) .local(object, ...)
    7.       └─chromVAR:::get_background_peaks_core(...)
    8.         ├─chromVAR::getFragmentsPerPeak(object)
    9.         └─chromVAR::getFragmentsPerPeak(object)
   10.           ├─Matrix::rowSums(counts(object))
   11.           └─Matrix::rowSums(counts(object))
   12.             └─Matrix (local) .local(x, na.rm, dims, ...)
  ── Error ('test_testCoAccessibilityChromVar.R:107:3'): testCoAccessibleLinks works on a 3 sample test dataset with highMem=TRUE ──
  Error in `.local(x, na.rm, dims, ...)`: object 'CRsparse_rowSums' not found
  Backtrace:
       ▆
    1. ├─utils::capture.output(...) at test_testCoAccessibilityChromVar.R:107:3
    2. │ └─base::withVisible(...elt(i))
    3. └─MOCHA::testCoAccessibilityChromVar(...)
    4.   ├─chromVAR::getBackgroundPeaks(fullObj)
    5.   └─chromVAR::getBackgroundPeaks(fullObj)
    6.     └─chromVAR (local) .local(object, ...)
    7.       └─chromVAR:::get_background_peaks_core(...)
    8.         ├─chromVAR::getFragmentsPerPeak(object)
    9.         └─chromVAR::getFragmentsPerPeak(object)
   10.           ├─Matrix::rowSums(counts(object))
   11.           └─Matrix::rowSums(counts(object))
   12.             └─Matrix (local) .local(x, na.rm, dims, ...)
  
  [ FAIL 3 | WARN 2 | SKIP 22 | PASS 22 ]
  Error: Test failures
  Execution halted