tests/doRUnit.R

In benjiec/xcms: LC/MS and GC/MS Data Analysis

## unit tests will not be done if RUnit is not available
if(require("RUnit", quietly=TRUE)) {

    ## --- Setup ---

    pkg <- "xcms" # <-- 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)
    library(package="faahKO", character.only=TRUE)

    attr(faahko, "filepaths") <- sapply(as.list(basename(attr(faahko, "filepaths"))),
                                        function(x) system.file("cdf", if (length(grep("ko",x)) > 0) "KO" else  "WT" ,x, package = "faahKO"))

    ## 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, "unit testing"),
                                 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")
}