Running 'testthat.R' [16s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(MOCHA)
  > 
  > test_check("MOCHA")
  
  Loading required package: MultiAssayExperiment
  Loading required package: SummarizedExperiment
  Loading required package: MatrixGenerics
  Loading required package: matrixStats
  
  Attaching package: 'MatrixGenerics'
  
  The following objects are masked from 'package:matrixStats':
  
      colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
      colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
      colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
      colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
      colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
      colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
      colWeightedMeans, colWeightedMedians, colWeightedSds,
      colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
      rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
      rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
      rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
      rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
      rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
      rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
      rowWeightedSds, rowWeightedVars
  
  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
  Loading required package: Biobase
  Welcome to Bioconductor
  
      Vignettes contain introductory material; view with
      'browseVignettes()'. To cite Bioconductor, see
      'citation("Biobase")', and for packages 'citation("pkgname")'.
  
  
  Attaching package: 'Biobase'
  
  The following object is masked from 'package:MatrixGenerics':
  
      rowMedians
  
  The following objects are masked from 'package:matrixStats':
  
      anyMissing, rowMedians
  
  Error: package or namespace load failed for 'SummarizedExperiment':
   objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
  Failed with error:  'package 'SummarizedExperiment' could not be loaded'
  [ FAIL 21 | WARN 0 | SKIP 10 | PASS 7 ]
  
  ══ Skipped tests (10) ══════════════════════════════════════════════════════════
  • On CRAN (10): '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_getCoverage.R:1:1', 'test_getDifferentialAccessibleTiles.R:1:1',
    'test_getPopFrags.R:13:1', 'test_subsetMOCHAObject.R:25:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_dimensionalityReduction.R:6:5'): bulkDimReduction works on a 3 sample test dataset ──
  Error: objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
  Backtrace:
       ▆
    1. ├─utils::capture.output(...) at test_dimensionalityReduction.R:6:4
    2. │ └─base::withVisible(...elt(i))
    3. ├─MOCHA::getSampleTileMatrix(...)
    4. └─base::loadNamespace(x)
    5.   ├─base::namespaceImport(...)
    6.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    7.     ├─base::namespaceImport(...)
    8.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    9.       └─base::namespaceImportFrom(...)
   10.         └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test_dimensionalityReduction.R:42:5'): bulkDimReduction errors NA columns ──
  Error: objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
  Backtrace:
       ▆
    1. ├─utils::capture.output(...) at test_dimensionalityReduction.R:42:4
    2. │ └─base::withVisible(...elt(i))
    3. ├─MOCHA::getSampleTileMatrix(...)
    4. └─base::loadNamespace(x)
    5.   ├─base::namespaceImport(...)
    6.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    7.     ├─base::namespaceImport(...)
    8.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    9.       └─base::namespaceImportFrom(...)
   10.         └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test_getCoAccessibleLinks.R:3:3'): FindCoAccessibleLinks works on a 1 sample test dataset ──
  Error: objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
  Backtrace:
       ▆
    1. ├─utils::capture.output(...) at test_getCoAccessibleLinks.R:3:2
    2. │ └─base::withVisible(...elt(i))
    3. ├─MOCHA::getSampleTileMatrix(...)
    4. └─base::loadNamespace(x)
    5.   ├─base::namespaceImport(...)
    6.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    7.     ├─base::namespaceImport(...)
    8.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    9.       └─base::namespaceImportFrom(...)
   10.         └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test_getCoAccessibleLinks.R:34:3'): FindCoAccessibleLinks works on a 3 sample test dataset ──
  Error: objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
  Backtrace:
       ▆
    1. ├─utils::capture.output(...) at test_getCoAccessibleLinks.R:34:2
    2. │ └─base::withVisible(...elt(i))
    3. ├─MOCHA::getSampleTileMatrix(...)
    4. └─base::loadNamespace(x)
    5.   ├─base::namespaceImport(...)
    6.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    7.     ├─base::namespaceImport(...)
    8.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    9.       └─base::namespaceImportFrom(...)
   10.         └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test_getCoAccessibleLinks.R:65:3'): FindCoAccessibleLinks errors with regions that are not valid tiles ──
  Error: objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
  Backtrace:
       ▆
    1. ├─utils::capture.output(...) at test_getCoAccessibleLinks.R:65:2
    2. │ └─base::withVisible(...elt(i))
    3. ├─MOCHA::getSampleTileMatrix(...)
    4. └─base::loadNamespace(x)
    5.   ├─base::namespaceImport(...)
    6.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    7.     ├─base::namespaceImport(...)
    8.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    9.       └─base::namespaceImportFrom(...)
   10.         └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test_getSampleTileMatrix.R:4:3'): getSampleTileMatrices works on a 1 sample test dataset ──
  Error: objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
  Backtrace:
       ▆
    1. ├─utils::capture.output(...) at test_getSampleTileMatrix.R:4:2
    2. │ └─base::withVisible(...elt(i))
    3. ├─MOCHA::getSampleTileMatrix(...)
    4. └─base::loadNamespace(x)
    5.   ├─base::namespaceImport(...)
    6.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    7.     ├─base::namespaceImport(...)
    8.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    9.       └─base::namespaceImportFrom(...)
   10.         └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test_runLMEM.R:5:5'): runLMEM errors when failing to converge on a 1 sample test dataset ──
  Error: objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
  Backtrace:
       ▆
    1. ├─utils::capture.output(...) at test_runLMEM.R:5:4
    2. │ └─base::withVisible(...elt(i))
    3. ├─MOCHA::getSampleTileMatrix(...)
    4. └─base::loadNamespace(x)
    5.   ├─base::namespaceImport(...)
    6.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    7.     ├─base::namespaceImport(...)
    8.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    9.       └─base::namespaceImportFrom(...)
   10.         └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test_runLMEM.R:30:5'): runLMEM errors when failing to converge on a 3-sample dataset ──
  Error: objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
  Backtrace:
       ▆
    1. ├─utils::capture.output(...) at test_runLMEM.R:30:4
    2. │ └─base::withVisible(...elt(i))
    3. ├─MOCHA::getSampleTileMatrix(...)
    4. └─base::loadNamespace(x)
    5.   ├─base::namespaceImport(...)
    6.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    7.     ├─base::namespaceImport(...)
    8.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    9.       └─base::namespaceImportFrom(...)
   10.         └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test_runLMEM.R:55:5'): pilotLMEM errors with formula on a 1-sample dataset ──
  Error: objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
  Backtrace:
       ▆
    1. ├─utils::capture.output(...) at test_runLMEM.R:55:4
    2. │ └─base::withVisible(...elt(i))
    3. ├─MOCHA::getSampleTileMatrix(...)
    4. └─base::loadNamespace(x)
    5.   ├─base::namespaceImport(...)
    6.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    7.     ├─base::namespaceImport(...)
    8.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    9.       └─base::namespaceImportFrom(...)
   10.         └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test_runLMEM.R:76:5'): pilotLMEM errors with formula on a 3-sample dataset ──
  Error: objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
  Backtrace:
       ▆
    1. ├─utils::capture.output(...) at test_runLMEM.R:76:4
    2. │ └─base::withVisible(...elt(i))
    3. ├─MOCHA::getSampleTileMatrix(...)
    4. └─base::loadNamespace(x)
    5.   ├─base::namespaceImport(...)
    6.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    7.     ├─base::namespaceImport(...)
    8.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    9.       └─base::namespaceImportFrom(...)
   10.         └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test_runLMEM.R:94:5'): runLMEM errors with invalid formula ──────────
  Error: objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
  Backtrace:
       ▆
    1. ├─utils::capture.output(...) at test_runLMEM.R:94:4
    2. │ └─base::withVisible(...elt(i))
    3. ├─MOCHA::getSampleTileMatrix(...)
    4. └─base::loadNamespace(x)
    5.   ├─base::namespaceImport(...)
    6.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    7.     ├─base::namespaceImport(...)
    8.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    9.       └─base::namespaceImportFrom(...)
   10.         └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test_runLMEM.R:126:5'): pilotLMEM errors with invalid formula ───────
  Error: objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
  Backtrace:
       ▆
    1. ├─utils::capture.output(...) at test_runLMEM.R:126:4
    2. │ └─base::withVisible(...elt(i))
    3. ├─MOCHA::getSampleTileMatrix(...)
    4. └─base::loadNamespace(x)
    5.   ├─base::namespaceImport(...)
    6.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    7.     ├─base::namespaceImport(...)
    8.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    9.       └─base::namespaceImportFrom(...)
   10.         └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test_subsetMOCHAObject.R:2:3'): We can subset a tileResults object by celltypes ──
  Error in `.requirePackage(package)`: unable to find required package 'MultiAssayExperiment'
  Backtrace:
      ▆
   1. ├─utils::capture.output(...) at test_subsetMOCHAObject.R:2:2
   2. │ └─base::withVisible(...elt(i))
   3. └─MOCHA::subsetMOCHAObject(...)
   4.   └─S4Vectors::metadata(Object)
   5.     └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
   6.       └─methods:::.findInheritedMethods(classes, fdef, mtable)
   7.         └─methods::getClass(cl1, where = where, .Force = TRUE)
   8.           └─methods::getClassDef(Class, where)
   9.             └─methods:::.requirePackage(package)
  ── Error ('test_subsetMOCHAObject.R:48:3'): We can subset a sampleTileMatrix object by celltypes ──
  Error: objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
  Backtrace:
       ▆
    1. ├─utils::capture.output(...) at test_subsetMOCHAObject.R:48:2
    2. │ └─base::withVisible(...elt(i))
    3. ├─MOCHA::getSampleTileMatrix(...)
    4. └─base::loadNamespace(x)
    5.   ├─base::namespaceImport(...)
    6.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    7.     ├─base::namespaceImport(...)
    8.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    9.       └─base::namespaceImportFrom(...)
   10.         └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test_subsetMOCHAObject.R:78:3'): We can subset a sampleTileMatrix object by Sample ──
  Error: objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
  Backtrace:
       ▆
    1. ├─utils::capture.output(...) at test_subsetMOCHAObject.R:78:2
    2. │ └─base::withVisible(...elt(i))
    3. ├─MOCHA::getSampleTileMatrix(...)
    4. └─base::loadNamespace(x)
    5.   ├─base::namespaceImport(...)
    6.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    7.     ├─base::namespaceImport(...)
    8.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    9.       └─base::namespaceImportFrom(...)
   10.         └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test_subsetMOCHAObject.R:108:3'): We can subset a sampleTileMatrix object - and peaks - by celltypes ──
  Error: objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
  Backtrace:
       ▆
    1. ├─utils::capture.output(...) at test_subsetMOCHAObject.R:108:2
    2. │ └─base::withVisible(...elt(i))
    3. ├─MOCHA::getSampleTileMatrix(...)
    4. └─base::loadNamespace(x)
    5.   ├─base::namespaceImport(...)
    6.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    7.     ├─base::namespaceImport(...)
    8.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    9.       └─base::namespaceImportFrom(...)
   10.         └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test_testCoAccessibilityChromVar.R:3:3'): testCoAccessibleLinks works on a 1 sample test dataset ──
  Error: objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
  Backtrace:
       ▆
    1. ├─utils::capture.output(...) at test_testCoAccessibilityChromVar.R:3:2
    2. │ └─base::withVisible(...elt(i))
    3. ├─MOCHA::getSampleTileMatrix(...)
    4. └─base::loadNamespace(x)
    5.   ├─base::namespaceImport(...)
    6.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    7.     ├─base::namespaceImport(...)
    8.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    9.       └─base::namespaceImportFrom(...)
   10.         └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test_testCoAccessibilityChromVar.R:44:3'): testCoAccessibleLinks works on a 3 sample test dataset ──
  Error: objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
  Backtrace:
       ▆
    1. ├─utils::capture.output(...) at test_testCoAccessibilityChromVar.R:44:2
    2. │ └─base::withVisible(...elt(i))
    3. ├─MOCHA::getSampleTileMatrix(...)
    4. └─base::loadNamespace(x)
    5.   ├─base::namespaceImport(...)
    6.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    7.     ├─base::namespaceImport(...)
    8.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    9.       └─base::namespaceImportFrom(...)
   10.         └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test_testCoAccessibilityChromVar.R:87:3'): testCoAccessibleLinks works on a 3 sample test dataset with highMem=TRUE ──
  Error: objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
  Backtrace:
       ▆
    1. ├─utils::capture.output(...) at test_testCoAccessibilityChromVar.R:87:2
    2. │ └─base::withVisible(...elt(i))
    3. ├─MOCHA::getSampleTileMatrix(...)
    4. └─base::loadNamespace(x)
    5.   ├─base::namespaceImport(...)
    6.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    7.     ├─base::namespaceImport(...)
    8.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    9.       └─base::namespaceImportFrom(...)
   10.         └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test_testCoAccessibilityRandom.R:3:3'): testCoAccessibleLinks works on a 1 sample test dataset ──
  Error: objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
  Backtrace:
       ▆
    1. ├─utils::capture.output(...) at test_testCoAccessibilityRandom.R:3:2
    2. │ └─base::withVisible(...elt(i))
    3. ├─MOCHA::getSampleTileMatrix(...)
    4. └─base::loadNamespace(x)
    5.   ├─base::namespaceImport(...)
    6.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    7.     ├─base::namespaceImport(...)
    8.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    9.       └─base::namespaceImportFrom(...)
   10.         └─base::importIntoEnv(impenv, impnames, ns, impvars)
  ── Error ('test_testCoAccessibilityRandom.R:43:3'): testCoAccessibleLinks works on a 3 sample test dataset ──
  Error: objects 'crossprod', 'tcrossprod' are not exported by 'namespace:Matrix'
  Backtrace:
       ▆
    1. ├─utils::capture.output(...) at test_testCoAccessibilityRandom.R:43:2
    2. │ └─base::withVisible(...elt(i))
    3. ├─MOCHA::getSampleTileMatrix(...)
    4. └─base::loadNamespace(x)
    5.   ├─base::namespaceImport(...)
    6.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    7.     ├─base::namespaceImport(...)
    8.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    9.       └─base::namespaceImportFrom(...)
   10.         └─base::importIntoEnv(impenv, impnames, ns, impvars)
  
  [ FAIL 21 | WARN 0 | SKIP 10 | PASS 7 ]
  Error: Test failures
  Execution halted