* using log directory ‘/srv/hornik/tmp/CRAN/MOCHA.Rcheck’
* using R Under development (unstable) (2024-01-24 r85824)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    Debian clang version 17.0.6 (3)
    Debian flang-new version 17.0.6 (3)
* running under: Debian GNU/Linux trixie/sid
* 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 CRAN incoming feasibility ... [4s/6s] NOTE
Maintainer: ‘Imran McGrath <aifi.compbio.support@alleninstitute.org>’

Suggests or Enhances not in mainstream repositories:
  ArchR
Availability using Additional_repositories specification:
  ArchR   yes   https://imran-aifi.github.io/drat
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package suggested but not available for checking: ‘ArchR’
* 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 ... [10s/10s] OK
* checking package directory ... OK
* checking for future file timestamps ... 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 ... [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 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 ... [10s/10s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 ... [1s/1s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [65s/70s] ERROR
  Running ‘testthat.R’ [65s/70s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(MOCHA)
  > 
  > test_check("MOCHA")
  
  Loading required package: TxDb.Hsapiens.UCSC.hg38.refGene
  Loading required package: GenomicFeatures
  Loading required package: AnnotationDbi
  Loading required package: Biobase
  Welcome to Bioconductor
  
      Vignettes contain introductory material; view with
      'browseVignettes()'. To cite Bioconductor, see
      'citation("Biobase")', and for packages 'citation("pkgname")'.
  
  Loading required package: org.Hs.eg.db
  
  
  Attaching package: 'Biostrings'
  
  The following object is masked from 'package:base':
  
      strsplit
  
  
  Attaching package: 'rtracklayer'
  
  The following object is masked from 'package:BiocIO':
  
      FileForFormat
  
  Exporting: /tmp/Rtmpueopkb/working_dir/Rtmpd8nqaD/Differentials.bigBed
  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 16 | SKIP 26 | PASS 29 ]
  
  ══ Skipped tests (26) ══════════════════════════════════════════════════════════
  • On CRAN (26): 'test_COVID_data_pipeline.R:1:1', 'test_MotifEnrichment.R:1:1',
    'test_MotifSetEnrichmentAnalysis.R:1:1', 'test_addMotifSet.R:1:1',
    'test_annotateTiles.R:72:5', 'test_callOpenTiles.R:3:1',
    'test_combineSampleTileMatrix.R:17:5', 'test_combineSampleTileMatrix.R:35:5',
    'test_dimensionalityReduction.R:37:5', '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',
    'test_testCoAccessibility.R:39:5', 'test_testCoAccessibility.R:80:5'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_annotateTiles.R:14:5'): annotateTiles works on a 1 sample test dataset ──
  Error in `getAnnotationDbFromInstalledPkgname(objMeta$TxDb$pkgname, "TxDb")`: Package TxDb.Hsapiens.UCSC.hg19.knownGene is not available. Please install and provide the name of a Bioconductor AnnotationData Package for your organism.
  Backtrace:
      ▆
   1. ├─utils::capture.output(...) at test_annotateTiles.R:14:5
   2. │ └─base::withVisible(...elt(i))
   3. └─MOCHA::annotateTiles(...)
   4.   └─MOCHA:::getAnnotationDbFromInstalledPkgname(...)
  ── Error ('test_annotateTiles.R:38:5'): annotateTiles works on a 3 sample test dataset ──
  Error in `getAnnotationDbFromInstalledPkgname(objMeta$TxDb$pkgname, "TxDb")`: Package TxDb.Hsapiens.UCSC.hg19.knownGene is not available. Please install and provide the name of a Bioconductor AnnotationData Package for your organism.
  Backtrace:
      ▆
   1. ├─utils::capture.output(...) at test_annotateTiles.R:38:5
   2. │ └─base::withVisible(...elt(i))
   3. └─MOCHA::annotateTiles(...)
   4.   └─MOCHA:::getAnnotationDbFromInstalledPkgname(...)
  
  [ FAIL 2 | WARN 16 | SKIP 26 | PASS 29 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [2s/2s] OK
* checking PDF version of manual ... [3s/3s] OK
* checking HTML version of manual ... [1s/1s] OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 ERROR, 2 NOTEs