CRAN Package Check Results for Package jmv

Last updated on 2020-01-27 00:48:06 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.8 86.18 94.65 180.83 ERROR
r-devel-linux-x86_64-debian-gcc 1.0.8 71.33 74.95 146.28 OK
r-devel-linux-x86_64-fedora-clang 1.0.8 237.79 NOTE
r-devel-linux-x86_64-fedora-gcc 1.0.8 263.80 NOTE
r-devel-windows-ix86+x86_64 1.0.8 160.00 156.00 316.00 OK
r-devel-windows-ix86+x86_64-gcc8 1.0.8 160.00 114.00 274.00 OK
r-patched-linux-x86_64 1.0.8 70.12 90.34 160.46 OK
r-patched-solaris-x86 1.0.8 265.20 NOTE
r-release-linux-x86_64 1.0.8 69.76 85.37 155.13 OK
r-release-windows-ix86+x86_64 1.0.8 97.00 114.00 211.00 OK
r-release-osx-x86_64 1.0.8 NOTE
r-oldrel-windows-ix86+x86_64 1.0.8 88.00 96.00 184.00 OK
r-oldrel-osx-x86_64 1.0.8 NOTE

Check Details

Version: 1.0.8
Check: examples
Result: 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
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.0.8
Check: tests
Result: ERROR
     Running 'testthat.R' [22s/24s]
    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: 0 | FAILED: 1 ]
     1. Error: logregord works (@testlogregord.R#13)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-devel-linux-x86_64-debian-clang

Version: 1.0.8
Check: dependencies in R code
Result: NOTE
    Namespaces in Imports field not imported from:
     ‘BayesFactor’ ‘GGally’ ‘GPArotation’ ‘MASS’ ‘PMCMR’ ‘R6’ ‘ROCR’
     ‘afex’ ‘car’ ‘emmeans’ ‘ggridges’ ‘lavaan’ ‘multcomp’ ‘mvnormtest’
     ‘nnet’ ‘psych’ ‘vcd’ ‘vcdExtra’
     All declared Imports should be used.
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-solaris-x86, r-release-osx-x86_64, r-oldrel-osx-x86_64