• using R Under development (unstable) (2019-12-11 r77556)
• using platform: x86_64-pc-linux-gnu (64-bit)
• using session charset: ISO8859-15
• checking for file 'jmv/DESCRIPTION' ... OK
• checking extension type ... Package
• this is package 'jmv' version '1.0.8'
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking serialization versions ... OK
• checking whether package 'jmv' can be installed ... OK
• checking package directory ... OK
• checking for future file timestamps ... OK
• checking 'build' directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking R files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... OK
• checking whether the package can be loaded with stated dependencies ... OK
• checking whether the package can be unloaded cleanly ... OK
• checking whether the namespace can be loaded with stated dependencies ... OK
• checking whether the namespace can be unloaded cleanly ... OK
• checking loading without being on the library search path ... OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [19s/22s] OK
• checking Rd files ... OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... OK
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking contents of 'data' directory ... OK
• checking data for non-ASCII characters ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking installed files from 'inst/doc' ... OK
• checking files in 'vignettes' ... OK
• checking examples ... ERROR
  Running examples in 'jmv-Ex.R' failed
  The error most likely occurred in:
  
  > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
  > ### Name: logRegOrd
  > ### Title: Ordinal Logistic Regression
  > ### Aliases: logRegOrd
  >
  > ### ** Examples
  >
  > set.seed(1337)
  >
  > y <- factor(sample(1:3, 100, replace = TRUE))
  > x1 <- rnorm(100)
  > x2 <- rnorm(100)
  >
  > df <- data.frame(y=y, x1=x1, x2=x2)
  >
  > logRegOrd(data = df, dep = y,
  + covs = vars(x1, x2),
  + blocks = list(list("x1", "x2")))
   ----------- FAILURE REPORT --------------
   --- failure: the condition has length > 1 ---
   --- srcref ---
  :
   --- package (from environment) ---
  jmv
   --- call from context ---
  NULL
   --- call from argument ---
  if (class(CI[[i]]) == "try-error") CI[[i]] <- confint.default(models[[i]],
      level = self$options$ciWidth/100)
   --- R stacktrace ---
  where 1: withCallingHandlers(expr, message = function(c) invokeRestart("muffleMessage"))
  where 2: suppressMessages({
      models <- list()
      modelTest <- list()
      lrTestTerms <- list()
      dev <- list()
      AIC <- list()
      BIC <- list()
      pseudoR <- list()
      CI <- list()
      CIOR <- list()
      nullFormula <- as.formula(paste0(jmvcore::toB64(self$options$dep),
          "~ 1"))
      nullModel <- MASS::polr(nullFormula, data = data, model = TRUE,
          Hess = TRUE)
      null <- list(dev = nullModel$deviance, df = nullModel$edf)
      for (i in seq_along(formulas)) {
          models[[i]] <- MASS::polr(formulas[[i]], data = data,
              model = TRUE, Hess = TRUE)
          models[[i]]$call$formula <- formulas[[i]]
          lrTestTerms[[i]] <- car::Anova(models[[i]], test = "LR",
              type = 3, singular.ok = TRUE)
          modelTest[[i]] <- private$.modelTest(models[[i]], null)
          dev[[i]] <- models[[i]]$deviance
          AIC[[i]] <- stats::AIC(models[[i]])
          BIC[[i]] <- stats::BIC(models[[i]])
          pseudoR[[i]] <- private$.pseudoR2(models[[i]], null)
          CI[[i]] <- try(confint(models[[i]], level = self$options$ciWidth/100),
              silent = TRUE)
          if (class(CI[[i]]) == "try-error")
              CI[[i]] <- confint.default(models[[i]], level = self$options$ciWidth/100)
          CILO <- try(confint(models[[i]], level = self$options$ciWidthOR/100),
              silent = TRUE)
          if (class(CILO[[i]]) == "try-error")
              CILO <- confint.default(models[[i]], level = self$options$ciWidthOR/100)
          CIOR[[i]] <- exp(CILO)
      }
      if (length(formulas) > 1)
          lrTest <- do.call(stats::anova, c(models, test = "Chisq"))
      else lrTest <- NULL
  })
  where 3: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  where 4: suppressWarnings({
      suppressMessages({
          models <- list()
          modelTest <- list()
          lrTestTerms <- list()
          dev <- list()
          AIC <- list()
          BIC <- list()
          pseudoR <- list()
          CI <- list()
          CIOR <- list()
          nullFormula <- as.formula(paste0(jmvcore::toB64(self$options$dep),
              "~ 1"))
          nullModel <- MASS::polr(nullFormula, data = data, model = TRUE,
              Hess = TRUE)
          null <- list(dev = nullModel$deviance, df = nullModel$edf)
          for (i in seq_along(formulas)) {
              models[[i]] <- MASS::polr(formulas[[i]], data = data,
                  model = TRUE, Hess = TRUE)
              models[[i]]$call$formula <- formulas[[i]]
              lrTestTerms[[i]] <- car::Anova(models[[i]], test = "LR",
                  type = 3, singular.ok = TRUE)
              modelTest[[i]] <- private$.modelTest(models[[i]],
                  null)
              dev[[i]] <- models[[i]]$deviance
              AIC[[i]] <- stats::AIC(models[[i]])
              BIC[[i]] <- stats::BIC(models[[i]])
              pseudoR[[i]] <- private$.pseudoR2(models[[i]], null)
              CI[[i]] <- try(confint(models[[i]], level = self$options$ciWidth/100),
                  silent = TRUE)
              if (class(CI[[i]]) == "try-error")
                  CI[[i]] <- confint.default(models[[i]], level = self$options$ciWidth/100)
              CILO <- try(confint(models[[i]], level = self$options$ciWidthOR/100),
                  silent = TRUE)
              if (class(CILO[[i]]) == "try-error")
                  CILO <- confint.default(models[[i]], level = self$options$ciWidthOR/100)
              CIOR[[i]] <- exp(CILO)
          }
          if (length(formulas) > 1)
              lrTest <- do.call(stats::anova, c(models, test = "Chisq"))
          else lrTest <- NULL
      })
  })
  where 5: private$.compute(data)
  where 6: private$.run()
  where 7: eval(expr)
  where 8: try({
      result <- private$.run()
      for (addon in private$.addons) {
          private$.checkpoint()
          addon$.__enclos_env__$private$.run()
      }
  }, silent = TRUE)
  where 9: analysis$run()
  where 10: logRegOrd(data = df, dep = y, covs = vars(x1, x2), blocks = list(list("x1",
      "x2")))
  
   --- value of length: 2 type: logical ---
  [1] FALSE FALSE
   --- function from context ---
   --- function search by body ---
   ----------- END OF FAILURE REPORT --------------
  Error in if (class(CI[[i]]) == "try-error") CI[[i]] <- confint.default(models[[i]], :
    the condition has length > 1
  Calls: logRegOrd ... <Anonymous> -> try -> eval -> <Anonymous> -> <Anonymous>
  Execution halted
• checking for unstated dependencies in 'tests' ... OK
• checking tests ... [23s/24s] ERROR
    Running 'testthat.R' [22s/23s]
  Running the tests in 'tests/testthat.R' failed.
  Complete output:
    > library(testthat)
    > library(jmv)
    >
    > test_check("jmv")
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    jmv
     --- call from context ---
    NULL
     --- call from argument ---
    if (class(CI[[i]]) == "try-error") CI[[i]] <- confint.default(models[[i]],
        level = self$options$ciWidth/100)
     --- R stacktrace ---
    where 1: withCallingHandlers(expr, message = function(c) invokeRestart("muffleMessage"))
    where 2: suppressMessages({
        models <- list()
        modelTest <- list()
        lrTestTerms <- list()
        dev <- list()
        AIC <- list()
        BIC <- list()
        pseudoR <- list()
        CI <- list()
        CIOR <- list()
        nullFormula <- as.formula(paste0(jmvcore::toB64(self$options$dep),
            "~ 1"))
        nullModel <- MASS::polr(nullFormula, data = data, model = TRUE,
            Hess = TRUE)
        null <- list(dev = nullModel$deviance, df = nullModel$edf)
        for (i in seq_along(formulas)) {
            models[[i]] <- MASS::polr(formulas[[i]], data = data,
                model = TRUE, Hess = TRUE)
            models[[i]]$call$formula <- formulas[[i]]
            lrTestTerms[[i]] <- car::Anova(models[[i]], test = "LR",
                type = 3, singular.ok = TRUE)
            modelTest[[i]] <- private$.modelTest(models[[i]], null)
            dev[[i]] <- models[[i]]$deviance
            AIC[[i]] <- stats::AIC(models[[i]])
            BIC[[i]] <- stats::BIC(models[[i]])
            pseudoR[[i]] <- private$.pseudoR2(models[[i]], null)
            CI[[i]] <- try(confint(models[[i]], level = self$options$ciWidth/100),
                silent = TRUE)
            if (class(CI[[i]]) == "try-error")
                CI[[i]] <- confint.default(models[[i]], level = self$options$ciWidth/100)
            CILO <- try(confint(models[[i]], level = self$options$ciWidthOR/100),
                silent = TRUE)
            if (class(CILO[[i]]) == "try-error")
                CILO <- confint.default(models[[i]], level = self$options$ciWidthOR/100)
            CIOR[[i]] <- exp(CILO)
        }
        if (length(formulas) > 1)
            lrTest <- do.call(stats::anova, c(models, test = "Chisq"))
        else lrTest <- NULL
    })
    where 3: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
    where 4: suppressWarnings({
        suppressMessages({
            models <- list()
            modelTest <- list()
            lrTestTerms <- list()
            dev <- list()
            AIC <- list()
            BIC <- list()
            pseudoR <- list()
            CI <- list()
            CIOR <- list()
            nullFormula <- as.formula(paste0(jmvcore::toB64(self$options$dep),
                "~ 1"))
            nullModel <- MASS::polr(nullFormula, data = data, model = TRUE,
                Hess = TRUE)
            null <- list(dev = nullModel$deviance, df = nullModel$edf)
            for (i in seq_along(formulas)) {
                models[[i]] <- MASS::polr(formulas[[i]], data = data,
                    model = TRUE, Hess = TRUE)
                models[[i]]$call$formula <- formulas[[i]]
                lrTestTerms[[i]] <- car::Anova(models[[i]], test = "LR",
                    type = 3, singular.ok = TRUE)
                modelTest[[i]] <- private$.modelTest(models[[i]],
                    null)
                dev[[i]] <- models[[i]]$deviance
                AIC[[i]] <- stats::AIC(models[[i]])
                BIC[[i]] <- stats::BIC(models[[i]])
                pseudoR[[i]] <- private$.pseudoR2(models[[i]], null)
                CI[[i]] <- try(confint(models[[i]], level = self$options$ciWidth/100),
                    silent = TRUE)
                if (class(CI[[i]]) == "try-error")
                    CI[[i]] <- confint.default(models[[i]], level = self$options$ciWidth/100)
                CILO <- try(confint(models[[i]], level = self$options$ciWidthOR/100),
                    silent = TRUE)
                if (class(CILO[[i]]) == "try-error")
                    CILO <- confint.default(models[[i]], level = self$options$ciWidthOR/100)
                CIOR[[i]] <- exp(CILO)
            }
            if (length(formulas) > 1)
                lrTest <- do.call(stats::anova, c(models, test = "Chisq"))
            else lrTest <- NULL
        })
    })
    where 5: private$.compute(data)
    where 6: private$.run()
    where 7: eval(expr)
    where 8: try({
        result <- private$.run()
        for (addon in private$.addons) {
            private$.checkpoint()
            addon$.__enclos_env__$private$.run()
        }
    }, silent = TRUE)
    where 9: analysis$run()
    where 10 at testthat/testlogregord.R#13: jmv::logRegOrd(data = df, dep = "y", covs = c("x1", "x2"), blocks = list(list("x1",
        "x2")))
    where 11: eval(code, test_env)
    where 12: eval(code, test_env)
    where 13: withCallingHandlers({
        eval(code, test_env)
        if (!handled && !is.null(test)) {
            skip_empty()
        }
    }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
        message = handle_message, error = handle_error)
    where 14: doTryCatch(return(expr), name, parentenv, handler)
    where 15: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    where 16: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
    where 17: doTryCatch(return(expr), name, parentenv, handler)
    where 18: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
        names[nh], parentenv, handlers[[nh]])
    where 19: tryCatchList(expr, classes, parentenv, handlers)
    where 20: tryCatch(withCallingHandlers({
        eval(code, test_env)
        if (!handled && !is.null(test)) {
            skip_empty()
        }
    }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
        message = handle_message, error = handle_error), error = handle_fatal,
        skip = function(e) {
        })
    where 21: test_code(desc, code, env = parent.frame())
    where 22 at testthat/testlogregord.R#3: test_that("logregord works", {
        set.seed(1337)
        y <- factor(sample(1:3, 100, replace = TRUE))
        x1 <- rnorm(100)
        x2 <- rnorm(100)
        df <- data.frame(y = y, x1 = x1, x2 = x2)
        logReg <- jmv::logRegOrd(data = df, dep = "y", covs = c("x1",
            "x2"), blocks = list(list("x1", "x2")))
        modelFit <- logReg$modelFit$asDF
        coef <- logReg$models[[1]]$coef$asDF
        expect_equal(0.000568, modelFit$r2mf[1], tolerance = 1e-06)
        expect_equal(217.779, modelFit$dev[1], tolerance = 0.001)
        expect_equal(0.058, coef$est[1], tolerance = 0.001)
        expect_equal(0.172, coef$se[2], tolerance = 0.001)
        expect_equal(0.848, coef$p[2], tolerance = 0.001)
    })
    where 23: eval(code, test_env)
    where 24: eval(code, test_env)
    where 25: withCallingHandlers({
        eval(code, test_env)
        if (!handled && !is.null(test)) {
            skip_empty()
        }
    }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
        message = handle_message, error = handle_error)
    where 26: doTryCatch(return(expr), name, parentenv, handler)
    where 27: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    where 28: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
    where 29: doTryCatch(return(expr), name, parentenv, handler)
    where 30: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
        names[nh], parentenv, handlers[[nh]])
    where 31: tryCatchList(expr, classes, parentenv, handlers)
    where 32: tryCatch(withCallingHandlers({
        eval(code, test_env)
        if (!handled && !is.null(test)) {
            skip_empty()
        }
    }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,
        message = handle_message, error = handle_error), error = handle_fatal,
        skip = function(e) {
        })
    where 33: test_code(NULL, exprs, env)
    where 34: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
    where 35: force(code)
    where 36: doWithOneRestart(return(expr), restart)
    where 37: withOneRestart(expr, restarts[[1L]])
    where 38: withRestarts(testthat_abort_reporter = function() NULL, force(code))
    where 39: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,
        {
            reporter$start_file(basename(path))
            lister$start_file(basename(path))
            source_file(path, new.env(parent = env), chdir = TRUE,
                wrap = wrap)
            reporter$.end_context()
            reporter$end_file()
        })
    where 40: FUN(X[[i]], ...)
    where 41: lapply(paths, test_file, env = env, reporter = current_reporter,
        start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
    where 42: force(code)
    where 43: doWithOneRestart(return(expr), restart)
    where 44: withOneRestart(expr, restarts[[1L]])
    where 45: withRestarts(testthat_abort_reporter = function() NULL, force(code))
    where 46: with_reporter(reporter = current_reporter, results <- lapply(paths,
        test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,
        load_helpers = FALSE, wrap = wrap))
    where 47: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
        stop_on_warning = stop_on_warning, wrap = wrap)
    where 48: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,
        ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,
        wrap = wrap)
    where 49: test_package_dir(package = package, test_path = test_path, filter = filter,
        reporter = reporter, ..., stop_on_failure = stop_on_failure,
        stop_on_warning = stop_on_warning, wrap = wrap)
    where 50: test_check("jmv")
    
     --- value of length: 2 type: logical ---
    [1] FALSE FALSE
     --- function from context ---
     --- function search by body ---
     ----------- END OF FAILURE REPORT --------------
    -- 1. Error: logregord works (@testlogregord.R#13) ----------------------------
    the condition has length > 1
    Backtrace:
      1. jmv::logRegOrd(...)
      2. analysis$run()
      5. private$.run()
      6. private$.compute(data)
      9. base::suppressMessages(...)
     10. base::withCallingHandlers(expr, message = function(c) invokeRestart("muffleMessage"))
    
    == testthat results ===========================================================
    [ OK: 145 | SKIPPED: 0 | WARNINGS: 14 | FAILED: 1 ]
    1. Error: logregord works (@testlogregord.R#13)
    
    Error: testthat unit tests failed
    Execution halted
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes in 'inst/doc' ... OK
• checking re-building of vignette outputs ... [1s/2s] OK
• checking PDF version of manual ... OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 2 ERRORs