Check results for 'MOCHA'

using R version 4.4.1 (2024-06-14)
using platform: aarch64-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 13.4
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 ... [12s/13s] 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 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 ... [6s/7s] OK
checking Rd files ... [0s/0s] 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 ... [2s/2s] 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 ... [0s/0s] OK
checking for unstated dependencies in ‘tests’ ... OK
checking tests ... [50s/57s] ERROR Running ‘testthat.R’ [50s/57s] 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) ══════════════════════════════════════════════════════════ • BSgenome.Hsapiens.UCSC.hg19 cannot be loaded (3): 'test_combineSampleTileMatrix.R:2:1', 'test_dimensionalityReduction.R:1:1', 'test_testCoAccessibility.R:2:1' • 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' ══ 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/10s] OK
checking PDF version of manual ... [5s/5s] OK
DONE Status: 1 ERROR, 1 NOTE
using check arguments '--no-clean-on-error '