RUNIT TEST PROTOCOL--Fri Jul 13 19:24:18 2007

Number of test functions: 49

Number of errors: 12

Number of failures: 1

1 Test suite

Errors

Failures

Details

Test Suite: MSToolkit unit testing

• Test file: runit.analyzeRep.R
  • test.analyseRep: ERROR !! Error in checkCsvFile(infile, doseCol) : The file `../MSToolkit/Runit/data/analyseRep/ReplicateData/replicate0001.csv` does not exist ---------------------------------------------------------------------- source > eval.with.vis > eval.with.vis > runTestSuite > .sourceTestFile > .executeTestCase > try > system.time > eval > eval > func > analyzeRep > checkCsvFile > ectdStop ----------------------------------------------------------------------
    Call Stack:
    
    1. eval(expr, envir = loc.frame)
    2. eval(expr, envir, enclos)
    3. func()
    4. analyzeRep(replicate = 1, analysisCode = anaCode, interimCode = interimCode, infile = "../MSToolkit/Runit/data/analyseRep/ReplicateData/replicate0001.csv")
    5. checkCsvFile(infile, doseCol)
    6. ectdStop("The file `$file` does not exist")
• Test file: runit.data.allocate.R
  • test.data.allocate.inputs: ... OK (0.41 seconds)
    
  • test.data.allocate.names: ... OK (0.07 seconds)
    
  • test.data.allocate.ordered: ... OK (0.02 seconds)
    
• Test file: runit.data.covariates.R
  • test.data.covariates.cont: ... OK (0.65 seconds)
    
  • test.data.covariates.disc: ... OK (0.42 seconds)
    
  • test.data.covariates.ext: ERROR !! Error in checkCsvFile(file, c(dataId, names)) : The file `../MSToolkit/Runit/data/createCovariates/testCovariates.csv` does not exist ---------------------------------------------------------------------- source > eval.with.vis > eval.with.vis > runTestSuite > .sourceTestFile > .executeTestCase > try > system.time > eval > eval > func > checkTrue > eval > all > createExternalCovariates > checkCsvFile > ectdStop ----------------------------------------------------------------------
    Call Stack:
    
    1. eval(expr, envir = loc.frame)
    2. eval(expr, envir, enclos)
    3. func()
    4. checkTrue(all(createExternalCovariates(20, names = "X1", subset = "X1 > 0", file = "../MSToolkit/Runit/data/createCovariates/testCovariates.csv")$X1 > 0), msg = "subset correctly applied")
    5. eval(expr)
    6. all(createExternalCovariates(20, names = "X1", subset = "X1 > 0", file = "../MSToolkit/Runit/data/createCovariates/testCovariates.csv")$X1 > 0)
    7. createExternalCovariates(20, names = "X1", subset = "X1 > 0", file = "../MSToolkit/Runit/data/createCovariates/testCovariates.csv")
    8. checkCsvFile(file, c(dataId, names))
    9. ectdStop("The file `$file` does not exist")
  • test.data.covariates.wrapper: ERROR !! Error in checkCsvFile(file, c(dataId, names)) : The file `../MSToolkit/Runit/data/createCovariates/testCovariates.csv` does not exist ---------------------------------------------------------------------- source > eval.with.vis > eval.with.vis > runTestSuite > .sourceTestFile > .executeTestCase > try > system.time > eval > eval > func > createExternalCovariates > checkCsvFile > ectdStop ----------------------------------------------------------------------
    Call Stack:
    
    1. eval(expr, envir = loc.frame)
    2. eval(expr, envir, enclos)
    3. func()
    4. createExternalCovariates(80, names = "X1", subset = c(".7 < X1 < .8", "-1 <= X2 <= 1"), file = "../MSToolkit/Runit/data/createCovariates/testCovariates.csv")
    5. checkCsvFile(file, c(dataId, names))
    6. ectdStop("The file `$file` does not exist")
• Test file: runit.data.interim.R
  • test.data.interim.1: ... OK (0.25 seconds)
    
  • test.data.interim.2: ... OK (0.21 seconds)
    
  • test.data.interim.3: ... OK (0.01 seconds)
    
  • test.data.interim.4: ... OK (0.02 seconds)
    
  • test.data.interim.5: ... OK (0.01 seconds)
    
• Test file: runit.data.missing.R
  • test.data.checkDropuOutFun: ... OK (0.52 seconds)
    
  • test.data.missing.drop: ... OK (0.94 seconds)
    
  • test.data.missing.mcar: ... OK (0.38 seconds)
    
• Test file: runit.data.parameter.R
  • test.data.param.ext: ERROR !! Error in checkCsvFile(file, allnames) : The file `../MSToolkit/Runit/data/createParameters/testParam.csv` does not exist ---------------------------------------------------------------------- source > eval.with.vis > eval.with.vis > runTestSuite > .sourceTestFile > .executeTestCase > try > system.time > eval > eval > func > createExternalParameters > checkCsvFile > ectdStop ----------------------------------------------------------------------
    Call Stack:
    
    1. eval(expr, envir = loc.frame)
    2. eval(expr, envir, enclos)
    3. func()
    4. createExternalParameters(20, names = "E0,ED50", file = "../MSToolkit/Runit/data/createParameters/testParam.csv", errStruc = "n", betNames = "B1,B2", seed = 2)
    5. checkCsvFile(file, allnames)
    6. ectdStop("The file `$file` does not exist")
  • test.data.param.norm: ... OK (1.47 seconds)
    
  • test.data.param.wrap: ERROR !! Error in checkCsvFile(file, allnames) : The file `../MSToolkit/Runit/data/createParameters/testParam.csv` does not exist ---------------------------------------------------------------------- source > eval.with.vis > eval.with.vis > runTestSuite > .sourceTestFile > .executeTestCase > try > system.time > eval > eval > func > createExternalParameters > checkCsvFile > ectdStop ----------------------------------------------------------------------
    Call Stack:
    
    1. eval(expr, envir = loc.frame)
    2. eval(expr, envir, enclos)
    3. func()
    4. createExternalParameters(20, names = "E0,ED50,EMAX", file = "../MSToolkit/Runit/data/createParameters/testParam.csv", errStruc = "a", betNames = "B1,B2", betNums = "1,3", seed = 81)
    5. checkCsvFile(file, allnames)
    6. ectdStop("The file `$file` does not exist")
• Test file: runit.data.response.R
  • test.data.response.addResidualError: ... OK (0.39 seconds)
    
  • test.data.response.createResponse: ... OK (0.54 seconds)
    
  • test.data.response.createResponseVariable: ... OK (0.5 seconds)
    
• Test file: runit.data.treatment.R
  • test.data.treatments.1: ... OK (0.39 seconds)
    
  • test.data.treatments.crossover: ... OK (0.2 seconds)
    
  • test.data.treatments.parallel: ... OK (0.01 seconds)
    
• Test file: runit.datastorage2.R
  • test.createDirectories: ... OK (0 seconds)
    
  • test.readAllMacroData: ... OK (0 seconds)
    
  • test.readAllMicroData: ERROR !! Error in file(file, "r") : unable to open connection
    Call Stack:
    
    1. eval(expr, envir = loc.frame)
    2. eval(expr, envir, enclos)
    3. func()
    4. read.csv(file.path(testDir, "microSummary.csv"), row.names = 1)
    5. read.table(file = file, header = header, sep = sep, quote = quote, dec = dec, fill = fill, ...)
    6. file(file, "r")
  • test.readData: ERROR !! Error in file(file, "r") : unable to open connection
    Call Stack:
    
    1. eval(expr, envir = loc.frame)
    2. eval(expr, envir, enclos)
    3. func()
    4. read.csv(paste(testDir, "microSummary.csv", sep = ""))
    5. read.table(file = file, header = header, sep = sep, quote = quote, dec = dec, fill = fill, ...)
    6. file(file, "r")
  • test.removeMacroDirectory: ... OK (0 seconds)
    
  • test.removeMicroDirectory: ... OK (0 seconds)
    
  • test.removeRepData: ERROR !! Error in file(file, "r") : unable to open connection
    Call Stack:
    
    1. eval(expr, envir = loc.frame)
    2. eval(expr, envir, enclos)
    3. func()
    4. read.csv(paste(testDir, "ReplicateSample.csv", sep = ""))
    5. read.table(file = file, header = header, sep = sep, quote = quote, dec = dec, fill = fill, ...)
    6. file(file, "r")
  • test.removeSingleRepData: ERROR !! Error in file(file, "r") : unable to open connection
    Call Stack:
    
    1. eval(expr, envir = loc.frame)
    2. eval(expr, envir, enclos)
    3. func()
    4. read.csv(paste(testDir, "ReplicateSample.csv", sep = ""))
    5. read.table(file = file, header = header, sep = sep, quote = quote, dec = dec, fill = fill, ...)
    6. file(file, "r")
  • test.writeData: ERROR !! Error in file(file, "r") : unable to open connection
    Call Stack:
    
    1. eval(expr, envir = loc.frame)
    2. eval(expr, envir, enclos)
    3. func()
    4. read.csv(paste(testDir, "/ReplicateSample.csv", sep = ""))
    5. read.table(file = file, header = header, sep = sep, quote = quote, dec = dec, fill = fill, ...)
    6. file(file, "r")
• Test file: runit.interimAnalysis.R
  • test.interimAnalysis: ... OK (0.74 seconds)
    
• Test file: runit.macroEvaluation.R
  • test.analysis.macro: ERROR !! Error in file(file, "r") : unable to open connection
    Call Stack:
    
    1. eval(expr, envir = loc.frame)
    2. eval(expr, envir, enclos)
    3. func()
    4. read.csv("../MSToolkit/Runit/data/macroEvaluation/micro0001.csv", header = TRUE)
    5. read.table(file = file, header = header, sep = sep, quote = quote, dec = dec, fill = fill, ...)
    6. file(file, "r")
• Test file: runit.performAnalysis.R
  • test.performAnalysis: ... OK (0 seconds)
    
• Test file: runit.supportfunctions.R
  • test.checkCsvFile: ... OK (0 seconds)
    
  • test.checkMicroFormat: ERROR !! Error in file(file, "r") : unable to open connection
    Call Stack:
    
    1. eval(expr, envir = loc.frame)
    2. eval(expr, envir, enclos)
    3. func()
    4. read.csv(paste(testdata.supportfunctions.dir, "micro0001.csv", sep = "/"))
    5. read.table(file = file, header = header, sep = sep, quote = quote, dec = dec, fill = fill, ...)
    6. file(file, "r")
  • test.checkSymmetricPDMatrix: ... OK (0.32 seconds)
    
  • test.createEmptyMicro: ... OK (0.32 seconds)
    
  • test.ectdStop: ... OK (0.06 seconds)
    
  • test.ectdWarning: ... OK (0 seconds)
    
  • test.initialChar: FAILURE !! (check number 1) Error in checkEquals(initialChar("2352435�$!A"), "a") : 1 string mismatches
    
  • test.parseCharInput: ... OK (0.24 seconds)
    
  • test.parseCovMatrix: ... OK (0.13 seconds)
    
  • test.parseHashString: ... OK (0.18 seconds)
    
  • test.parseRangeCode: ... OK (0.19 seconds)
    
  • test.validNames: ... OK (0.2 seconds)