CRAN Package Check Results for Package hopit

Last updated on 2019-12-05 00:51:56 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 0.10.2 53.03 97.78 150.81 ERROR
r-devel-linux-x86_64-debian-gcc 0.10.2 34.96 76.48 111.44 ERROR
r-devel-linux-x86_64-fedora-clang 0.10.2 205.67 NOTE
r-devel-linux-x86_64-fedora-gcc 0.10.2 195.63 NOTE
r-devel-windows-ix86+x86_64 0.10.2 74.00 283.00 357.00 OK
r-devel-windows-ix86+x86_64-gcc8 0.10.2 80.00 231.00 311.00 OK
r-patched-linux-x86_64 0.10.2 36.98 105.71 142.69 OK
r-patched-solaris-x86 0.10.2 286.00 NOTE
r-release-linux-x86_64 0.10.2 36.75 110.64 147.39 OK
r-release-windows-ix86+x86_64 0.10.2 76.00 217.00 293.00 OK
r-release-osx-x86_64 0.10.2 NOTE
r-oldrel-windows-ix86+x86_64 0.10.2 63.00 262.00 325.00 OK
r-oldrel-osx-x86_64 0.10.2 NOTE

Check Details

Version: 0.10.2
Check: examples
Result: ERROR
    Running examples in 'hopit-Ex.R' failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: getCutPoints
    > ### Title: Calculate the threshold cut-points and individual adjusted
    > ### responses using Jurges' method
    > ### Aliases: getCutPoints
    >
    > ### ** Examples
    >
    > # DATA
    > data(healthsurvey)
    >
    > # the order of response levels decreases from the best health to
    > # the worst health; hence the hopit() parameter decreasing.levels
    > # is set to TRUE
    > levels(healthsurvey$health)
    [1] "Excellent" "Very good" "Good" "Fair" "Poor"
    >
    > # Example 1 ---------------------
    >
    > # fit a model
    > model1 <- hopit(latent.formula = health ~ hypertension + high_cholesterol +
    + heart_attack_or_stroke + poor_mobility + very_poor_grip +
    + depression + respiratory_problems +
    + IADL_problems + obese + diabetes + other_diseases,
    + thresh.formula = ~ sex + ageclass + country,
    + decreasing.levels = TRUE,
    + control = list(trace = FALSE),
    + data = healthsurvey)
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    hopit
     --- call from context ---
    check_vcov(model$vcov.basic)
     --- call from argument ---
    if (class(vcov) == "try-error") {
     warning(call. = FALSE, hopit_msg(32))
     vcov <- NA
    }
     --- R stacktrace ---
    where 1: check_vcov(model$vcov.basic)
    where 2: hopit(latent.formula = health ~ hypertension + high_cholesterol +
     heart_attack_or_stroke + poor_mobility + very_poor_grip +
     depression + respiratory_problems + IADL_problems + obese +
     diabetes + other_diseases, thresh.formula = ~sex + ageclass +
     country, decreasing.levels = TRUE, control = list(trace = FALSE),
     data = healthsurvey)
    
     --- value of length: 2 type: logical ---
    [1] FALSE FALSE
     --- function from context ---
    function (vcov)
    {
     if (class(vcov) == "try-error") {
     warning(call. = FALSE, hopit_msg(32))
     vcov <- NA
     }
     vcov
    }
    <bytecode: 0x6f1b1c8>
    <environment: namespace:hopit>
     --- function search by body ---
    Function check_vcov in namespace hopit has this body.
     ----------- END OF FAILURE REPORT --------------
    Fatal error: the condition has length > 1
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.10.2
Check: tests
Result: ERROR
     Running 'testthat.R' [9s/10s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(hopit)
     Loading required package: survey
     Loading required package: grid
     Loading required package: Matrix
     Loading required package: survival
    
     Attaching package: 'survey'
    
     The following object is masked from 'package:graphics':
    
     dotchart
    
     >
     > test_check("hopit")
     Calculating the starting parameters... done
     Fitting the model... done
     Calculating the maximum latent range... done
     Calculating the Hessian matrix... ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
     :
     --- package (from environment) ---
     hopit
     --- call from context ---
     check_vcov(model$vcov.basic)
     --- call from argument ---
     if (class(vcov) == "try-error") {
     warning(call. = FALSE, hopit_msg(32))
     vcov <- NA
     }
     --- R stacktrace ---
     where 1: check_vcov(model$vcov.basic)
     where 2: hopit(latent.formula = latent.formula.I, thresh.formula = thresh.formula.O,
     data = newhealthsurvey, decreasing.levels = TRUE)
     where 3: eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
     where 4: withCallingHandlers(code, message = function(condition) {
     out$push(condition)
     maybe_restart("muffleMessage")
     })
     where 5: .capture(act$val <- eval_bare(quo_get_expr(.quo), quo_get_env(.quo)),
     ...)
     where 6: quasi_capture(enquo(object), label, capture_messages)
     where 7 at testthat/test-hopit.R#163: expect_message(hopit(latent.formula = latent.formula.I, thresh.formula = thresh.formula.O,
     data = newhealthsurvey, decreasing.levels = TRUE))
     where 8: eval(code, test_env)
     where 9: eval(code, test_env)
     where 10: 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 11: doTryCatch(return(expr), name, parentenv, handler)
     where 12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     where 13: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     where 14: doTryCatch(return(expr), name, parentenv, handler)
     where 15: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
     names[nh], parentenv, handlers[[nh]])
     where 16: tryCatchList(expr, classes, parentenv, handlers)
     where 17: 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 18: test_code(NULL, exprs, env)
     where 19: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
     where 20: force(code)
     where 21: doWithOneRestart(return(expr), restart)
     where 22: withOneRestart(expr, restarts[[1L]])
     where 23: withRestarts(testthat_abort_reporter = function() NULL, force(code))
     where 24: 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 25: FUN(X[[i]], ...)
     where 26: lapply(paths, test_file, env = env, reporter = current_reporter,
     start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
     where 27: force(code)
     where 28: doWithOneRestart(return(expr), restart)
     where 29: withOneRestart(expr, restarts[[1L]])
     where 30: withRestarts(testthat_abort_reporter = function() NULL, force(code))
     where 31: 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 32: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
     stop_on_warning = stop_on_warning, wrap = wrap)
     where 33: 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 34: 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 35: test_check("hopit")
    
     --- value of length: 2 type: logical ---
     [1] FALSE FALSE
     --- function from context ---
     function (vcov)
     {
     if (class(vcov) == "try-error") {
     warning(call. = FALSE, hopit_msg(32))
     vcov <- NA
     }
     vcov
     }
     <bytecode: 0x9a08150>
     <environment: namespace:hopit>
     --- function search by body ---
     Function check_vcov in namespace hopit has this body.
     ----------- END OF FAILURE REPORT --------------
     Fatal error: the condition has length > 1
Flavor: r-devel-linux-x86_64-debian-clang

Version: 0.10.2
Check: examples
Result: ERROR
    Running examples in ‘hopit-Ex.R’ failed
    The error most likely occurred in:
    
    > base::assign(".ptime", proc.time(), pos = "CheckExEnv")
    > ### Name: getCutPoints
    > ### Title: Calculate the threshold cut-points and individual adjusted
    > ### responses using Jurges' method
    > ### Aliases: getCutPoints
    >
    > ### ** Examples
    >
    > # DATA
    > data(healthsurvey)
    >
    > # the order of response levels decreases from the best health to
    > # the worst health; hence the hopit() parameter decreasing.levels
    > # is set to TRUE
    > levels(healthsurvey$health)
    [1] "Excellent" "Very good" "Good" "Fair" "Poor"
    >
    > # Example 1 ---------------------
    >
    > # fit a model
    > model1 <- hopit(latent.formula = health ~ hypertension + high_cholesterol +
    + heart_attack_or_stroke + poor_mobility + very_poor_grip +
    + depression + respiratory_problems +
    + IADL_problems + obese + diabetes + other_diseases,
    + thresh.formula = ~ sex + ageclass + country,
    + decreasing.levels = TRUE,
    + control = list(trace = FALSE),
    + data = healthsurvey)
     ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
    :
     --- package (from environment) ---
    hopit
     --- call from context ---
    check_vcov(model$vcov.basic)
     --- call from argument ---
    if (class(vcov) == "try-error") {
     warning(call. = FALSE, hopit_msg(32))
     vcov <- NA
    }
     --- R stacktrace ---
    where 1: check_vcov(model$vcov.basic)
    where 2: hopit(latent.formula = health ~ hypertension + high_cholesterol +
     heart_attack_or_stroke + poor_mobility + very_poor_grip +
     depression + respiratory_problems + IADL_problems + obese +
     diabetes + other_diseases, thresh.formula = ~sex + ageclass +
     country, decreasing.levels = TRUE, control = list(trace = FALSE),
     data = healthsurvey)
    
     --- value of length: 2 type: logical ---
    [1] FALSE FALSE
     --- function from context ---
    function (vcov)
    {
     if (class(vcov) == "try-error") {
     warning(call. = FALSE, hopit_msg(32))
     vcov <- NA
     }
     vcov
    }
    <bytecode: 0x55ec24c98d80>
    <environment: namespace:hopit>
     --- function search by body ---
    Function check_vcov in namespace hopit has this body.
     ----------- END OF FAILURE REPORT --------------
    Fatal error: the condition has length > 1
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.10.2
Check: tests
Result: ERROR
     Running ‘testthat.R’ [7s/10s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(hopit)
     Loading required package: survey
     Loading required package: grid
     Loading required package: Matrix
     Loading required package: survival
    
     Attaching package: 'survey'
    
     The following object is masked from 'package:graphics':
    
     dotchart
    
     >
     > test_check("hopit")
     Calculating the starting parameters... done
     Fitting the model... done
     Calculating the maximum latent range... done
     Calculating the Hessian matrix... ----------- FAILURE REPORT --------------
     --- failure: the condition has length > 1 ---
     --- srcref ---
     :
     --- package (from environment) ---
     hopit
     --- call from context ---
     check_vcov(model$vcov.basic)
     --- call from argument ---
     if (class(vcov) == "try-error") {
     warning(call. = FALSE, hopit_msg(32))
     vcov <- NA
     }
     --- R stacktrace ---
     where 1: check_vcov(model$vcov.basic)
     where 2: hopit(latent.formula = latent.formula.I, thresh.formula = thresh.formula.O,
     data = newhealthsurvey, decreasing.levels = TRUE)
     where 3: eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
     where 4: withCallingHandlers(code, message = function(condition) {
     out$push(condition)
     maybe_restart("muffleMessage")
     })
     where 5: .capture(act$val <- eval_bare(quo_get_expr(.quo), quo_get_env(.quo)),
     ...)
     where 6: quasi_capture(enquo(object), label, capture_messages)
     where 7 at testthat/test-hopit.R#163: expect_message(hopit(latent.formula = latent.formula.I, thresh.formula = thresh.formula.O,
     data = newhealthsurvey, decreasing.levels = TRUE))
     where 8: eval(code, test_env)
     where 9: eval(code, test_env)
     where 10: 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 11: doTryCatch(return(expr), name, parentenv, handler)
     where 12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     where 13: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     where 14: doTryCatch(return(expr), name, parentenv, handler)
     where 15: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]),
     names[nh], parentenv, handlers[[nh]])
     where 16: tryCatchList(expr, classes, parentenv, handlers)
     where 17: 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 18: test_code(NULL, exprs, env)
     where 19: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
     where 20: force(code)
     where 21: doWithOneRestart(return(expr), restart)
     where 22: withOneRestart(expr, restarts[[1L]])
     where 23: withRestarts(testthat_abort_reporter = function() NULL, force(code))
     where 24: 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 25: FUN(X[[i]], ...)
     where 26: lapply(paths, test_file, env = env, reporter = current_reporter,
     start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
     where 27: force(code)
     where 28: doWithOneRestart(return(expr), restart)
     where 29: withOneRestart(expr, restarts[[1L]])
     where 30: withRestarts(testthat_abort_reporter = function() NULL, force(code))
     where 31: 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 32: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,
     stop_on_warning = stop_on_warning, wrap = wrap)
     where 33: 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 34: 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 35: test_check("hopit")
    
     --- value of length: 2 type: logical ---
     [1] FALSE FALSE
     --- function from context ---
     function (vcov)
     {
     if (class(vcov) == "try-error") {
     warning(call. = FALSE, hopit_msg(32))
     vcov <- NA
     }
     vcov
     }
     <bytecode: 0x55e2f42ba6d0>
     <environment: namespace:hopit>
     --- function search by body ---
     Function check_vcov in namespace hopit has this body.
     ----------- END OF FAILURE REPORT --------------
     Fatal error: the condition has length > 1
Flavor: r-devel-linux-x86_64-debian-gcc

Version: 0.10.2
Check: installed package size
Result: NOTE
     installed size is 9.7Mb
     sub-directories of 1Mb or more:
     libs 9.0Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-release-osx-x86_64, r-oldrel-osx-x86_64

Version: 0.10.2
Check: dependencies in R code
Result: NOTE
    Namespace in Imports field not imported from: ‘Matrix’
     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