* using log directory ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.4/MOCHA.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.3.1
* using session charset: UTF-8
* checking for file ‘MOCHA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MOCHA’ version ‘1.1.0’
* 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',
  'TxDb.Hsapiens.UCSC.hg19.knownGene', 'BSgenome.Hsapiens.UCSC.hg19'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘MOCHA’ can be installed ... [15s/20s] OK
See 'https://www.r-project.org/nosvn/R.check/r-release-macos-x86_64/MOCHA-00install.html' 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] 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 ... [9s/10s] OK
* checking Rd files ... [0s/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 ... [3s/6s] 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 ... [1s/1s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [76s/97s] ERROR
  Running ‘testthat.R’ [76s/97s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(MOCHA)
  > 
  > test_check("MOCHA")
  
  
  Loading required package: chromVARmotifs
  harmonizing input:
    removing 1 sampleMap rows not in names(experiments)
  harmonizing input:
    removing 3 sampleMap rows not in names(experiments)
  [ FAIL 2 | WARN 13 | SKIP 23 | PASS 21 ]
  
  ══ Skipped tests (23) ══════════════════════════════════════════════════════════
  • 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_exportCoverage.R:1:1',
    '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_packMOCHA.R:1:1',
    'test_plotRegion.R:1:1', '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'
  • {BSgenome.Hsapiens.UCSC.hg19} is not installed (3):
    'test_combineSampleTileMatrix.R:2:1', 'test_dimensionalityReduction.R:1:1',
    'test_testCoAccessibility.R:2:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_exportDifferentials.R:28:3'): exportDifferentials 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. └─MOCHA::exportDifferentials(...) at test_exportDifferentials.R:28:3
   2.   └─BSgenome::getBSgenome(S4Vectors::metadata(SampleTileObject)$Genome)
   3.     └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked)
   4.       └─BSgenome:::.stopOnAvailablePkg(genome)
  ── Error ('test_exportOpenTiles.R:13:3'): exportDifferentials works on a 3 sample test dataset ──
  Error in `.stopOnAvailablePkg(genome)`: BSgenome.Hsapiens.UCSC.hg19 package is not currently installed.
    You first need to install it, which you can do with:
        library(BiocManager)
        install("BSgenome.Hsapiens.UCSC.hg19")
  Backtrace:
      ▆
   1. └─MOCHA::exportOpenTiles(...) at test_exportOpenTiles.R:13:3
   2.   └─BSgenome::getBSgenome(S4Vectors::metadata(SampleTileObject)$Genome)
   3.     └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked)
   4.       └─BSgenome:::.stopOnAvailablePkg(genome)
  
  [ FAIL 2 | WARN 13 | SKIP 23 | PASS 21 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [10s/11s] OK
* checking PDF version of manual ... [5s/6s] OK
* DONE
Status: 1 ERROR, 1 NOTE
* using check arguments '--no-clean-on-error '

* elapsed time (check, wall clock): 3:32