• using R version 4.2.3 (2023-03-15 ucrt)
• using platform: x86_64-w64-mingw32 (64-bit)
• using session charset: UTF-8
• checking for file 'MOCHA/DESCRIPTION' ... OK
• checking extension type ... Package
• this is package 'MOCHA' version '1.0.0'
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... NOTE
  Packages suggested but not available for checking:
    'ArchR', 'TxDb.Hsapiens.UCSC.hg38.refGene',
    'BSgenome.Hsapiens.UCSC.hg19'
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking whether package 'MOCHA' can be installed ... OK
  See the install log for details.
• checking installed package size ... OK
• checking package directory ... OK
• checking 'build' directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking R files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [15s] OK
• checking Rd files ... [1s] OK
• checking Rd metadata ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking contents of 'data' directory ... OK
• checking data for non-ASCII characters ... OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking R/sysdata.rda ... OK
• checking installed files from 'inst/doc' ... OK
• checking files in 'vignettes' ... OK
• checking examples ... [2s] OK
• checking for unstated dependencies in 'tests' ... OK
• checking tests ... [340s] ERROR
    Running 'testthat.R' [339s]
  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
    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
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in 'inst/doc' ... OK
• checking re-building of vignette outputs ... [6s] OK
• checking PDF version of manual ... OK
• DONE

Status: 1 ERROR, 1 NOTE