tests/doRUnit.R

In MinimumDistance: A Package for De Novo CNV Detection in Case-Parent Trios

## from xmapcore package
if( require( "RUnit", quietly=TRUE ) ) {
  pkg <- "MinimumDistance"

  if( Sys.getenv( "RCMDCHECK" ) == "FALSE" ) {
    path <- file.path( getwd(), "..", "inst", "unitTests" )
  } else {
    path <- system.file( package=pkg, "unitTests" )
  }

  cat( "\nRunning unit tests\n" )
  print( list( pkg=pkg, getwd=getwd(), pathToUnitTests=path ) )
  library( package=pkg, character.only=TRUE )

  ##xmap.clear.cache()

  ##Fail on warnings
  options( warn=1 )

  ## Get the pattern (if there is one?)
  patt <- Sys.getenv( "RUNITFILEPATTERN" )
  if( is.null( patt ) || nchar( patt ) == 0 ) {
    testSuite <- defineTestSuite(name=paste( pkg, "unit testing" ),
                                 dirs=path,
                                 testFileRegexp=paste( "^test.+", patt, "\\.[rR]$", sep="" ))
  } else {
    ##testSuite <- defineTestSuite( name=paste( pkg, "unit testing" ), testFileRegexp=paste( "^runit\\.", patt, "\\.[rR]$", sep="" ), dirs=path )
    testSuite <- defineTestSuite(name=paste( pkg, "unit testing" ),
                                 testFileRegexp=paste( "^test.+", patt, "\\.[rR]$", sep="" ),
                                 dirs=path )
  }
  tests <- runTestSuite( testSuite )

  pathReport <- file.path( path, "report" )

  cat( "------------------- UNIT TEST SUMMARY ---------------------\n\n" )
  printTextProtocol( tests, showDetails=FALSE )
  printTextProtocol( tests, showDetails=FALSE, fileName=paste( pathReport, "Summary.txt", sep="" ) )
  printTextProtocol( tests, showDetails=TRUE,  fileName=paste( pathReport, ".txt", sep="" ) )

  printHTMLProtocol( tests, fileName=paste( pathReport, ".html", sep="" ) )

  tmp <- getErrors( tests )
  if( tmp$nFail > 0 | tmp$nErr > 0 ){
    stop( paste( "\n\nunit testing failed (#test failures: ",
                tmp$nFail, ", #R errors: ",
                tmp$nErr, ")\n\n", sep=""))
  }
} else {
  warning( "cannot run unit tests -- package RUnit is not available" )
}