* using log directory ‘/data/gannet/ripley/R/packages/tests-Suggests/MOCHA.Rcheck’
* using R Under development (unstable) (2024-04-19 r86451)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc-13 (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Fedora Linux 36 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* 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', 'org.Hs.eg.db',
  '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 ... [36s/63s] 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 ... 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 ... [37s/51s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Failed with error:  ‘package ‘GenomeInfoDb’ could not be loaded’
Error in .requirePackage(package) : 
  unable to find required package ‘GenomicRanges’
Calls: <Anonymous> ... withCallingHandlers -> is -> getClassDef -> .requirePackage
Execution halted
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... WARNING
  Failed with error:  'package 'GenomeInfoDb' could not be loaded'
  Error loading dataset 'exampleBlackList':
   Error in .requirePackage(package) : 
    unable to find required package 'GenomicRanges'
  
  Failed with error:  'package 'GenomeInfoDb' could not be loaded'
  Error loading dataset 'exampleFragments':
   Error in .requirePackage(package) : 
    unable to find required package 'GenomicRanges'
  
  The dataset(s) may use package(s) not declared in Depends/Imports.
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’ [12s/16s]
 [12s/17s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(MOCHA)
  > 
  > test_check("MOCHA")
  Loading required package: chromVARmotifs
  Loading required package: MultiAssayExperiment
  Loading required package: SummarizedExperiment
  Loading required package: MatrixGenerics
  Loading required package: matrixStats
  
  Attaching package: 'MatrixGenerics'
  
  The following objects are masked from 'package:matrixStats':
  
      colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
      colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
      colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
      colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
      colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
      colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
      colWeightedMeans, colWeightedMedians, colWeightedSds,
      colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
      rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
      rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
      rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
      rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
      rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
      rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
      rowWeightedSds, rowWeightedVars
  
  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, table, tapply,
      union, unique, unsplit, which.max, which.min
  
  Loading required package: S4Vectors
  
  Attaching package: 'S4Vectors'
  
  The following object is masked from 'package:utils':
  
      findMatches
  
  The following objects are masked from 'package:base':
  
      I, expand.grid, unname
  
  Loading required package: IRanges
  Loading required package: GenomeInfoDb
  Error: package or namespace load failed for 'GenomeInfoDb' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
   there is no package called 'GenomeInfoDbData'
  Failed with error:  'package 'GenomeInfoDb' could not be loaded'
  [ FAIL 10 | WARN 1 | SKIP 16 | PASS 7 ]
  
  ══ Skipped tests (16) ══════════════════════════════════════════════════════════
  • BSgenome.Hsapiens.UCSC.hg19 cannot be loaded (1):
    'test_dimensionalityReduction.R:1:1'
  • On CRAN (13): '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_getCoverage.R:1:1',
    'test_getDifferentialAccessibleTiles.R:1:1', 'test_getPopFrags.R:13:1',
    'test_packMOCHA.R:1:1', 'test_plotRegion.R:1:1',
    'test_subsetMOCHAObject.R:25:3'
  • chromVAR cannot be loaded (2): 'test_combineSampleTileMatrix.R:1:1',
    'test_testCoAccessibility.R:1:1'
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Error ('test_exportDifferentials.R:3:3'): exportDifferentials works on a 3 sample test dataset ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])`: there is no package called 'GenomeInfoDbData'
  Backtrace:
       ▆
    1. ├─utils::capture.output(...) at test_exportDifferentials.R:3:3
    2. │ └─base::withVisible(...elt(i))
    3. ├─MOCHA::getSampleTileMatrix(...)
    4. └─base::loadNamespace(x)
    5.   ├─base::namespaceImport(...)
    6.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    7.     ├─base::namespaceImport(...)
    8.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    9.       ├─base::namespaceImport(...)
   10.       └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   11.         └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   12.           └─base (local) withOneRestart(expr, restarts[[1L]])
   13.             └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test_exportOpenTiles.R:3:3'): exportDifferentials works on a 3 sample test dataset ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])`: there is no package called 'GenomeInfoDbData'
  Backtrace:
       ▆
    1. ├─utils::capture.output(...) at test_exportOpenTiles.R:3:3
    2. │ └─base::withVisible(...elt(i))
    3. ├─MOCHA::getSampleTileMatrix(...)
    4. └─base::loadNamespace(x)
    5.   ├─base::namespaceImport(...)
    6.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    7.     ├─base::namespaceImport(...)
    8.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    9.       ├─base::namespaceImport(...)
   10.       └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   11.         └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   12.           └─base (local) withOneRestart(expr, restarts[[1L]])
   13.             └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test_getCoAccessibleLinks.R:3:3'): FindCoAccessibleLinks works on a 1 sample test dataset ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])`: there is no package called 'GenomeInfoDbData'
  Backtrace:
       ▆
    1. ├─utils::capture.output(...) at test_getCoAccessibleLinks.R:3:3
    2. │ └─base::withVisible(...elt(i))
    3. ├─MOCHA::getSampleTileMatrix(...)
    4. └─base::loadNamespace(x)
    5.   ├─base::namespaceImport(...)
    6.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    7.     ├─base::namespaceImport(...)
    8.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    9.       ├─base::namespaceImport(...)
   10.       └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   11.         └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   12.           └─base (local) withOneRestart(expr, restarts[[1L]])
   13.             └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test_getCoAccessibleLinks.R:34:3'): FindCoAccessibleLinks works on a 3 sample test dataset ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])`: there is no package called 'GenomeInfoDbData'
  Backtrace:
       ▆
    1. ├─utils::capture.output(...) at test_getCoAccessibleLinks.R:34:3
    2. │ └─base::withVisible(...elt(i))
    3. ├─MOCHA::getSampleTileMatrix(...)
    4. └─base::loadNamespace(x)
    5.   ├─base::namespaceImport(...)
    6.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    7.     ├─base::namespaceImport(...)
    8.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    9.       ├─base::namespaceImport(...)
   10.       └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   11.         └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   12.           └─base (local) withOneRestart(expr, restarts[[1L]])
   13.             └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test_getCoAccessibleLinks.R:65:3'): FindCoAccessibleLinks errors with regions that are not valid tiles ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])`: there is no package called 'GenomeInfoDbData'
  Backtrace:
       ▆
    1. ├─utils::capture.output(...) at test_getCoAccessibleLinks.R:65:3
    2. │ └─base::withVisible(...elt(i))
    3. ├─MOCHA::getSampleTileMatrix(...)
    4. └─base::loadNamespace(x)
    5.   ├─base::namespaceImport(...)
    6.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    7.     ├─base::namespaceImport(...)
    8.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    9.       ├─base::namespaceImport(...)
   10.       └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   11.         └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   12.           └─base (local) withOneRestart(expr, restarts[[1L]])
   13.             └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test_getSampleTileMatrix.R:4:3'): getSampleTileMatrices works on a 1 sample test dataset ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])`: there is no package called 'GenomeInfoDbData'
  Backtrace:
       ▆
    1. ├─utils::capture.output(...) at test_getSampleTileMatrix.R:4:3
    2. │ └─base::withVisible(...elt(i))
    3. ├─MOCHA::getSampleTileMatrix(...)
    4. └─base::loadNamespace(x)
    5.   ├─base::namespaceImport(...)
    6.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    7.     ├─base::namespaceImport(...)
    8.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    9.       ├─base::namespaceImport(...)
   10.       └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   11.         └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   12.           └─base (local) withOneRestart(expr, restarts[[1L]])
   13.             └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test_subsetMOCHAObject.R:2:3'): We can subset a tileResults object by celltypes ──
  Error in `.requirePackage(package)`: unable to find required package 'MultiAssayExperiment'
  Backtrace:
      ▆
   1. ├─utils::capture.output(...) at test_subsetMOCHAObject.R:2:3
   2. │ └─base::withVisible(...elt(i))
   3. └─MOCHA::subsetMOCHAObject(...)
   4.   └─S4Vectors::metadata(Object)
   5.     └─methods (local) `<fn>`(`<list>`, `<stndrdGn>`, `<env>`)
   6.       └─methods:::.findInheritedMethods(classes, fdef, mtable)
   7.         └─methods::getClass(cl1, where = where, .Force = TRUE)
   8.           └─methods::getClassDef(Class, where)
   9.             └─methods:::.requirePackage(package)
  ── Error ('test_subsetMOCHAObject.R:48:3'): We can subset a sampleTileMatrix object by celltypes ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])`: there is no package called 'GenomeInfoDbData'
  Backtrace:
       ▆
    1. ├─utils::capture.output(...) at test_subsetMOCHAObject.R:48:3
    2. │ └─base::withVisible(...elt(i))
    3. ├─MOCHA::getSampleTileMatrix(...)
    4. └─base::loadNamespace(x)
    5.   ├─base::namespaceImport(...)
    6.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    7.     ├─base::namespaceImport(...)
    8.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    9.       ├─base::namespaceImport(...)
   10.       └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   11.         └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   12.           └─base (local) withOneRestart(expr, restarts[[1L]])
   13.             └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test_subsetMOCHAObject.R:78:3'): We can subset a sampleTileMatrix object by Sample ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])`: there is no package called 'GenomeInfoDbData'
  Backtrace:
       ▆
    1. ├─utils::capture.output(...) at test_subsetMOCHAObject.R:78:3
    2. │ └─base::withVisible(...elt(i))
    3. ├─MOCHA::getSampleTileMatrix(...)
    4. └─base::loadNamespace(x)
    5.   ├─base::namespaceImport(...)
    6.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    7.     ├─base::namespaceImport(...)
    8.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    9.       ├─base::namespaceImport(...)
   10.       └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   11.         └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   12.           └─base (local) withOneRestart(expr, restarts[[1L]])
   13.             └─base (local) doWithOneRestart(return(expr), restart)
  ── Error ('test_subsetMOCHAObject.R:108:3'): We can subset a sampleTileMatrix object - and peaks - by celltypes ──
  <packageNotFoundError/error/condition>
  Error in `loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])`: there is no package called 'GenomeInfoDbData'
  Backtrace:
       ▆
    1. ├─utils::capture.output(...) at test_subsetMOCHAObject.R:108:3
    2. │ └─base::withVisible(...elt(i))
    3. ├─MOCHA::getSampleTileMatrix(...)
    4. └─base::loadNamespace(x)
    5.   ├─base::namespaceImport(...)
    6.   └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    7.     ├─base::namespaceImport(...)
    8.     └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
    9.       ├─base::namespaceImport(...)
   10.       └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   11.         └─base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   12.           └─base (local) withOneRestart(expr, restarts[[1L]])
   13.             └─base (local) doWithOneRestart(return(expr), restart)
  
  [ FAIL 10 | WARN 1 | SKIP 16 | PASS 7 ]
  Error: Test failures
  Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [8s/14s] OK
* checking PDF version of manual ... [11s/15s] OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE

Status: 1 ERROR, 2 WARNINGs, 1 NOTE
See
  ‘/data/gannet/ripley/R/packages/tests-Suggests/MOCHA.Rcheck/00check.log’
for details.

Command exited with non-zero status 1
Time 4:44.08, 168.78 + 17.33