Running 'doRUnit.R' [223s]
Running the tests in 'tests/doRUnit.R' failed.
Complete output:
  > ## unit tests will not be done if RUnit is not available
  > if(require("RUnit", quietly=TRUE)) {    
  +  
  +   ## --- Setup ---
  +  
  +   pkg <- "chngpt" # <-- 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(), "unitTests")
  +   } else {
  +     ## Path to unit tests for R CMD check
  +     ## PKG.Rcheck/tests/../PKG/unitTests
  +     path <- system.file("unitTests", package=pkg)
  +   }
  +   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, "unit testing"),
  +                                           dirs=path)
  +   ## Run
  +   tests <- runTestSuite(testSuite)
  +  
  +   ## Default report name
  +   pathReport <- tempdir() #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")
  + }
  
  Running unit tests
  $pkg
  [1] "chngpt"
  
  $getwd
  [1] "d:/Rcompile/CRANpkg/local/4.4/chngpt.Rcheck/tests"
  
  $pathToUnitTests
  [1] "D:/temp/RtmpamRzNU/RLIBS_17b3c3874ecf/chngpt/unitTests"
  
  
  The package 'chngpt' has been loaded. If used for a publication, please cite:
  
      Fong, Huang, Gilbert, Permar (2017), BMC Bioinformatics, DOI:10.1186/s12859-017-1863-x
      chngpt: threshold regression model estimation and inference
  
  
  
  Executing test function test.chngpt.test  ... Loading required namespace: mvtnorm
   done successfully.
  
  
  
  Executing test function test.chngptm.linear  ... [1] tol: 0.1
  [1] "########  segmented"
       est       lb       ub 
  4.235847 3.345270 3.651209 
  [1] "########  random intercept"
  [1] "########  M12c"
  [1] "########  M21c"
  [1] "########  offset "
  [1] "########  step model m out of n bootstrap"
  [1] "########  step model subsampling bootstrap"
  [1] "########  step"
  [1] "########  segmented hinge upperhinge"
  [1] "########  M02 and M20"
  [1] "########  M12"
  [1] "########  M21 and M12"
  [1] "########  M22"
  [1] "########  M22c"
  [1] "########  M30 and M03"
  [1] "########  M33c"
  [1] "########  M31 and M13"
  [1] "########  M04, M40"
  [1] "########  thinned thresholds, only for grid"
  [1] "hinge"
  [1] "upperhinge"
   done successfully.
  
  
  
  Executing test function test.chngptm.logistic  ... [1] 0.1
  y ~ X2 + X3 + x.mod.e + X2:x.mod.e + X3:x.mod.e
  <environment: 0x000001b00de1a630>
  stratified = FALSE 
  family = binomial 
  threshold.type = step ; imodel = NA ; hinge.to.upperhinge = FALSE 
  est.method = grid ; fastgrid.ok = FALSE ; var.type = none 
  has.quad = FALSE ; has.cubic = FALSE ; has.itxn = TRUE 
  p.z = 3 ; p.2.itxn = 2 ; p = 6 
  chngpts = -1.73 -0.621 -0.0359 0.612 1.74 
  find e.final
  logliks = -648.7544908 -637.7213383 -589.8536385 -618.656863 -642.0551031 
  (Intercept) X2 X3 X1>chngpt X2:I(X1>chngpt) X3:I(X1>chngpt) chngpt 
  
  Point estimate over search bound. Not computing variance estimate. 
  Point estimate over search bound. Not computing variance estimate. 
  Point estimate over search bound. Not computing variance estimate. 
  scale.chisq is negative
   done successfully.
  
  
  
  Executing test function test.double.hinge  ... [1] "tol: 0.1"
   done successfully.
  
  
  
  Executing test function test.hinge.test  ...  done successfully.
  
  ------------------- UNIT TEST SUMMARY ---------------------
  
  RUNIT TEST PROTOCOL -- Sat Mar 23 12:02:25 2024 
  *********************************************** 
  Number of test functions: 5 
  Number of errors: 0 
  Number of failures: 0 
  
   
  1 Test Suite : 
  chngpt unit testing - 5 test functions, 0 errors, 0 failures
  Warning messages:
  1: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
    RNGkind: Marsaglia-Multicarry has poor statistical properties
  2: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
    RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
  3: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
    RNGkind: Marsaglia-Multicarry has poor statistical properties
  4: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
    RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
  5: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
    RNGkind: Marsaglia-Multicarry has poor statistical properties
  6: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
    RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
  7: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
    RNGkind: Marsaglia-Multicarry has poor statistical properties
  8: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
    RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
  9: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
    RNGkind: Marsaglia-Multicarry has poor statistical properties
  10: In RNGkind(kind = testSuite$rngKind, normal.kind = testSuite$rngNormalKind) :
    RNGkind: severe deviations from normality for Kinderman-Ramage + Marsaglia-Multicarry
  > 
  > proc.time()
     user  system elapsed 
    57.23    3.71   60.92