Running 'testthat.R' [516s]
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 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
  
  Attaching package: 'Biostrings'
  
  The following object is masked from 'package:base':
  
      strsplit
  
  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 6 | WARN 8 | SKIP 20 | PASS 21 ]
  
  ══ 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_callOpenTiles.R:3:1', 'test_combineSampleTileMatrix.R:32:5',
    '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_testCoAccessibilityChromVar.R:36:3',
    'test_testCoAccessibilityRandom.R:35:3'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_combineSampleTileMatrix.R:12:5'): combineSampleTileMatrix works on a 3-sample dataset ──
  Error in `.local(con, format, text, ...)`: UCSC library operation failed
  Backtrace:
       ▆
    1. └─MOCHA::combineSampleTileMatrix(STObj) at test_combineSampleTileMatrix.R:12:4
    2.   ├─chromVAR::addGCBias(newObj, genome = genome)
    3.   └─chromVAR::addGCBias(newObj, genome = genome)
    4.     └─chromVAR (local) .local(object, ...)
    5.       ├─Biostrings::getSeq(genome, peaks)
    6.       └─BSgenome::getSeq(genome, peaks)
    7.         └─BSgenome (local) .local(x, ...)
    8.           └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
    9.             ├─BiocGenerics::lapply(...)
   10.             └─base::lapply(...)
   11.               └─BSgenome (local) FUN(X[[i]], ...)
   12.                 └─BSgenome:::loadSubseqsFromStrandedSequence(...)
   13.                   ├─BSgenome (local) loadFUN(x, seqname, ranges)
   14.                   └─BSgenome (local) loadFUN(x, seqname, ranges)
   15.                     ├─BiocIO::import(twobitfile, which = which)
   16.                     └─rtracklayer::import(twobitfile, which = which)
   17.                       └─rtracklayer (local) .local(con, format, text, ...)
  ── Error ('test_dimensionalityReduction.R:31:5'): bulkDimReduction works on a 3 sample test dataset ──
  Error in `.local(con, format, text, ...)`: UCSC library operation failed
  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.     ├─chromVAR::addGCBias(newObj, genome = genome)
    6.     └─chromVAR::addGCBias(newObj, genome = genome)
    7.       └─chromVAR (local) .local(object, ...)
    8.         ├─Biostrings::getSeq(genome, peaks)
    9.         └─BSgenome::getSeq(genome, peaks)
   10.           └─BSgenome (local) .local(x, ...)
   11.             └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
   12.               ├─BiocGenerics::lapply(...)
   13.               └─base::lapply(...)
   14.                 └─BSgenome (local) FUN(X[[i]], ...)
   15.                   └─BSgenome:::loadSubseqsFromStrandedSequence(...)
   16.                     ├─BSgenome (local) loadFUN(x, seqname, ranges)
   17.                     └─BSgenome (local) loadFUN(x, seqname, ranges)
   18.                       ├─BiocIO::import(twobitfile, which = which)
   19.                       └─rtracklayer::import(twobitfile, which = which)
   20.                         └─rtracklayer (local) .local(con, format, text, ...)
  ── Error ('test_dimensionalityReduction.R:51:5'): bulkDimReduction errors NA columns ──
  Error in `.local(con, format, text, ...)`: UCSC library operation failed
  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.     ├─chromVAR::addGCBias(newObj, genome = genome)
   10.     └─chromVAR::addGCBias(newObj, genome = genome)
   11.       └─chromVAR (local) .local(object, ...)
   12.         ├─Biostrings::getSeq(genome, peaks)
   13.         └─BSgenome::getSeq(genome, peaks)
   14.           └─BSgenome (local) .local(x, ...)
   15.             └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
   16.               ├─BiocGenerics::lapply(...)
   17.               └─base::lapply(...)
   18.                 └─BSgenome (local) FUN(X[[i]], ...)
   19.                   └─BSgenome:::loadSubseqsFromStrandedSequence(...)
   20.                     ├─BSgenome (local) loadFUN(x, seqname, ranges)
   21.                     └─BSgenome (local) loadFUN(x, seqname, ranges)
   22.                       ├─BiocIO::import(twobitfile, which = which)
   23.                       └─rtracklayer::import(twobitfile, which = which)
   24.                         └─rtracklayer (local) .local(con, format, text, ...)
  ── Error ('test_testCoAccessibilityChromVar.R:65:3'): testCoAccessibleLinks works on a 3 sample test dataset ──
  Error in `.local(con, format, text, ...)`: UCSC library operation failed
  Backtrace:
       ▆
    1. ├─utils::capture.output(...) at test_testCoAccessibilityChromVar.R:65:2
    2. │ └─base::withVisible(...elt(i))
    3. └─MOCHA::testCoAccessibilityChromVar(...)
    4.   └─MOCHA::combineSampleTileMatrix(SampleTileObj)
    5.     ├─chromVAR::addGCBias(newObj, genome = genome)
    6.     └─chromVAR::addGCBias(newObj, genome = genome)
    7.       └─chromVAR (local) .local(object, ...)
    8.         ├─Biostrings::getSeq(genome, peaks)
    9.         └─BSgenome::getSeq(genome, peaks)
   10.           └─BSgenome (local) .local(x, ...)
   11.             └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
   12.               ├─BiocGenerics::lapply(...)
   13.               └─base::lapply(...)
   14.                 └─BSgenome (local) FUN(X[[i]], ...)
   15.                   └─BSgenome:::loadSubseqsFromStrandedSequence(...)
   16.                     ├─BSgenome (local) loadFUN(x, seqname, ranges)
   17.                     └─BSgenome (local) loadFUN(x, seqname, ranges)
   18.                       ├─BiocIO::import(twobitfile, which = which)
   19.                       └─rtracklayer::import(twobitfile, which = which)
   20.                         └─rtracklayer (local) .local(con, format, text, ...)
  ── Error ('test_testCoAccessibilityChromVar.R:107:3'): testCoAccessibleLinks works on a 3 sample test dataset with highMem=TRUE ──
  Error in `.local(con, format, text, ...)`: UCSC library operation failed
  Backtrace:
       ▆
    1. ├─utils::capture.output(...) at test_testCoAccessibilityChromVar.R:107:2
    2. │ └─base::withVisible(...elt(i))
    3. └─MOCHA::testCoAccessibilityChromVar(...)
    4.   └─MOCHA::combineSampleTileMatrix(SampleTileObj)
    5.     ├─chromVAR::addGCBias(newObj, genome = genome)
    6.     └─chromVAR::addGCBias(newObj, genome = genome)
    7.       └─chromVAR (local) .local(object, ...)
    8.         ├─Biostrings::getSeq(genome, peaks)
    9.         └─BSgenome::getSeq(genome, peaks)
   10.           └─BSgenome (local) .local(x, ...)
   11.             └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
   12.               ├─BiocGenerics::lapply(...)
   13.               └─base::lapply(...)
   14.                 └─BSgenome (local) FUN(X[[i]], ...)
   15.                   └─BSgenome:::loadSubseqsFromStrandedSequence(...)
   16.                     ├─BSgenome (local) loadFUN(x, seqname, ranges)
   17.                     └─BSgenome (local) loadFUN(x, seqname, ranges)
   18.                       ├─BiocIO::import(twobitfile, which = which)
   19.                       └─rtracklayer::import(twobitfile, which = which)
   20.                         └─rtracklayer (local) .local(con, format, text, ...)
  ── Error ('test_testCoAccessibilityRandom.R:64:3'): testCoAccessibleLinks works on a 3 sample test dataset ──
  Error in `.local(con, format, text, ...)`: UCSC library operation failed
  Backtrace:
       ▆
    1. ├─utils::capture.output(...) at test_testCoAccessibilityRandom.R:64:2
    2. │ └─base::withVisible(...elt(i))
    3. └─MOCHA::testCoAccessibilityRandom(...)
    4.   └─MOCHA::combineSampleTileMatrix(SampleTileObj)
    5.     ├─chromVAR::addGCBias(newObj, genome = genome)
    6.     └─chromVAR::addGCBias(newObj, genome = genome)
    7.       └─chromVAR (local) .local(object, ...)
    8.         ├─Biostrings::getSeq(genome, peaks)
    9.         └─BSgenome::getSeq(genome, peaks)
   10.           └─BSgenome (local) .local(x, ...)
   11.             └─BSgenome:::.extractFromBSgenomeSingleSequences(...)
   12.               ├─BiocGenerics::lapply(...)
   13.               └─base::lapply(...)
   14.                 └─BSgenome (local) FUN(X[[i]], ...)
   15.                   └─BSgenome:::loadSubseqsFromStrandedSequence(...)
   16.                     ├─BSgenome (local) loadFUN(x, seqname, ranges)
   17.                     └─BSgenome (local) loadFUN(x, seqname, ranges)
   18.                       ├─BiocIO::import(twobitfile, which = which)
   19.                       └─rtracklayer::import(twobitfile, which = which)
   20.                         └─rtracklayer (local) .local(con, format, text, ...)
  
  [ FAIL 6 | WARN 8 | SKIP 20 | PASS 21 ]
  Error: Test failures
  Execution halted