* 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/19s] 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/11s] 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/3s] 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 ... [79s/105s] ERROR Running ‘testthat.R’ [79s/105s] 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 ] â•â• Skipped tests (23) â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â• • 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' â•â• Failed tests â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â•â• ── 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: â–† 1. └─MOCHA::exportDifferentials(...) at test_exportDifferentials.R:28:3 2. └─BSgenome::getBSgenome(S4Vectors::metadata(SampleTileObject)$Genome) 3. └─BSgenome:::.getInstalledPkgnameFromGenome(genome, masked = masked) 4. └─BSgenome:::.stopOnAvailablePkg(genome) ── Error ('test_exportOpenTiles.R:13:3'): exportDifferentials works on a 3 sample test dataset ── Error in `.stopOnAvailablePkg(genome)`: BSgenome.Hsapiens.UCSC.hg19 package is not currently installed. You first need to install it, which you can do with: library(BiocManager) install("BSgenome.Hsapiens.UCSC.hg19") Backtrace: â–† 1. └─MOCHA::exportOpenTiles(...) at test_exportOpenTiles.R:13:3 2. └─BSgenome::getBSgenome(S4Vectors::metadata(SampleTileObject)$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 ... [13s/21s] OK * checking PDF version of manual ... [7s/13s] OK * DONE Status: 1 ERROR, 1 NOTE * using check arguments '--no-clean-on-error ' * elapsed time (check, wall clock): 3:48