tests/doRUnit.R

In rcdk: Interface to the 'CDK' Libraries

# Set JAVA_TOOL_OPTIONS BEFORE any library loads (including RUnit)
# This will force JVM to use single-threaded execution during tests
# to avoid CRAN NOTE: "CPU time > elapsed time"
java_opts <- paste(
  "-XX:ActiveProcessorCount=1",
  "-XX:ParallelGCThreads=1",
  "-XX:ConcGCThreads=1",
  "-XX:+UseSerialGC",
  "-XX:CICompilerCount=1",
  "-XX:-TieredCompilation",
  "-XX:-BackgroundCompilation",
  "-Djava.util.concurrent.ForkJoinPool.common.parallelism=1",
  sep=" "
)
Sys.setenv("JAVA_TOOL_OPTIONS" = java_opts)
Sys.setenv("_JAVA_OPTIONS" = java_opts)

# Also set thread-limiting environment variables for native libraries
Sys.setenv("OMP_NUM_THREADS" = "1")
Sys.setenv("OPENBLAS_NUM_THREADS" = "1")
Sys.setenv("MKL_NUM_THREADS" = "1")
Sys.setenv("VECLIB_MAXIMUM_THREADS" = "1")

if(require("RUnit", quietly=TRUE)) {

   library(rJava)
   library(fingerprint)

  ## --- Setup ---

  pkg <- "rcdk" # <-- Change to package name!
  if(Sys.getenv("RCMDCHECK") == "FALSE") {
    ## Path to unit tests for standalone running under Makefile (not R CMD check)
    ## PKG/tests/../inst/unitTests
    path <- file.path(getwd(), "..", "inst", "unitTests")
  } else {
    ## Path to unit tests for R CMD check
    ## PKG.Rcheck/tests/../PKG/unitTests
    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)

  ## If desired, load the name space to allow testing of private functions
  ## if (is.element(pkg, loadedNamespaces()))
  ##     attach(loadNamespace(pkg), name=paste("namespace", pkg, sep=":"), pos=3)
  ##
  ## or simply call PKG:::myPrivateFunction() in tests

  ## --- Testing ---

  ## Define tests
  testSuite <- defineTestSuite(name=paste(pkg, "rcdk Unit Tests"),
                                          dirs=path)
  ## Run
  tests <- runTestSuite(testSuite)

  ## Default report name
  #pathReport <- file.path(path, "report")

  ## Report to stdout and text files
  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=""))

  ## Report to HTML file
  #printHTMLProtocol(tests, fileName=paste(pathReport, ".html", sep=""))

  ## Return stop() to cause R CMD check stop in case of
  ##  - failures i.e. FALSE to unit tests or
  ##  - errors i.e. R errors
  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")
}