CRAN Package Check Results for Package mxmmod

Last updated on 2020-08-07 01:49:53 CEST.

Check Details

Version: 1.0.1
Check: examples
Result: ERROR
    Running examples in ‘mxmmod-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: mxMmodModel
    > ### Title: Create an MMOD
    > ### Aliases: mxMmodModel
    >
    > ### ** Examples
    >
    > data(nlsy97depression)
    > # Fit one factor MMOD
    > structure <- list(
    + F1 = c('nervous', 'down', 'depressed', 'calm', 'happy')
    + )
    > mmod_model <- mxMmodModel(data=nlsy97depression,
    + modelName='1 Factor MMOD',
    + idvar='pid', timevar='occasion', structure=structure)
    Warning in mxMmodModel(data = nlsy97depression, modelName = "1 Factor MMOD", :
     Missing values detected; omitting them.
    > mmod_fit <- OpenMx::mxRun(mmod_model)
    Running 1 Factor MMOD with 33 parameters
    
     *** caught segfault ***
    address 961de2e8, cause 'memory not mapped'
    
    Traceback:
     1: runHelper(model, frontendStart, intervals, silent, suppressWarnings, unsafe, checkpoint, useSocket, onlyFrontend, useOptimizer, beginMessage)
     2: OpenMx::mxRun(mmod_model)
    An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86

Version: 1.0.1
Check: tests
Result: ERROR
     Running ‘testthat.R’ [12s/39s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(mxmmod)
     >
     > test_check("mxmmod")
     Error: C stack usage 271357076 is too close to the limit
     ── 1. Error: Same results as Estabrook 2015 (@test-refimpl.R#104) ─────────────
     The job for model '1 Factor MMOD' exited abnormally with the error message: User interrupt
     Backtrace:
     1. mxmmod:::mxmmod_ref(df)
     3. OpenMx::mxRun(mmod_model)
     4. OpenMx:::runHelper(...)
     5. OpenMx:::processErrorConditions(model, unsafe, suppressWarnings)
    
    
     *** caught segfault ***
     address 585aa898, cause 'memory not mapped'
    
     Traceback:
     1: runHelper(model, frontendStart, intervals, silent, suppressWarnings, unsafe, checkpoint, useSocket, onlyFrontend, useOptimizer, beginMessage)
     2: mxRun(mmod_model)
     3: summary(mxRun(mmod_model))
     4: mxmmod_ref(scaled_nlsy)
     5: eval(code, test_env)
     6: eval(code, test_env)
     7: 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)
     8: doTryCatch(return(expr), name, parentenv, handler)
     9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     10: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     11: doTryCatch(return(expr), name, parentenv, handler)
     12: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
     13: tryCatchList(expr, classes, parentenv, handlers)
     14: 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) { })
     15: test_code(desc, code, env = parent.frame())
     16: test_that("Floating point occasions", { df <- nlsy97_1983_cohort() scale_val <- 2 scaled_nlsy <- df scaled_nlsy$occasion <- scaled_nlsy$occasion/scale_val trans <- rep(1, 33) trans[6:10] <- scale_val trans[11:15] <- scale_val^2 trans[24:33] <- scale_val^2 trans[29:33] <- scale_val^4 a <- mxmmod_ref(scaled_nlsy) b <- estabrook_ref(df) a$parameters$Estimate <- a$parameters$Estimate/trans a$parameters$Std.Error <- a$parameters$Std.Error/trans expect_equal(a$parameters$Estimate, b$parameters$Estimate, tolerance = 0.001) expect_equal(a$parameters$Std.Error, b$parameters$Std.Error, tolerance = 0.001)})
     17: eval(code, test_env)
     18: eval(code, test_env)
     19: 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)
     20: doTryCatch(return(expr), name, parentenv, handler)
     21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     22: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     23: doTryCatch(return(expr), name, parentenv, handler)
     24: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
     25: tryCatchList(expr, classes, parentenv, handlers)
     26: 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) { })
     27: test_code(NULL, exprs, env)
     28: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
     29: force(code)
     30: doWithOneRestart(return(expr), restart)
     31: withOneRestart(expr, restarts[[1L]])
     32: withRestarts(testthat_abort_reporter = function() NULL, force(code))
     33: 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() })
     34: FUN(X[[i]], ...)
     35: lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
     36: force(code)
     37: doWithOneRestart(return(expr), restart)
     38: withOneRestart(expr, restarts[[1L]])
     39: withRestarts(testthat_abort_reporter = function() NULL, force(code))
     40: with_reporter(reporter = current_reporter, results <- lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap))
     41: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
     42: 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)
     43: 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)
     44: test_check("mxmmod")
     An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86

Version: 1.0.1
Check: re-building of vignette outputs
Result: WARN
    Error(s) in re-building vignettes:
     ...
    --- re-building ‘mmod_tutorial.Rmd’ using rmarkdown
    Warning in engine$weave(file, quiet = quiet, encoding = enc) :
     Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
    ── Attaching packages ─────────────────────────────────────── tidyverse 1.3.0 ──
    ✔ ggplot2 3.3.2 ✔ purrr 0.3.4
    ✔ tibble 3.0.3 ✔ dplyr 1.0.0
    ✔ tidyr 1.1.0 ✔ stringr 1.4.0
    ✔ readr 1.3.1 ✔ forcats 0.5.0
    ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
    ✖ dplyr::filter() masks stats::filter()
    ✖ dplyr::lag() masks stats::lag()
    To take full advantage of multiple cores, use:
     mxOption(key='Number of Threads', value=parallel::detectCores()) #now
     Sys.setenv(OMP_NUM_THREADS=parallel::detectCores()) #before library(OpenMx)
    Error: C stack usage 327718036 is too close to the limit
    Quitting from lines 96-104 (mmod_tutorial.Rmd)
    Error: processing vignette 'mmod_tutorial.Rmd' failed with diagnostics:
    The job for model '1 Factor MMOD' exited abnormally with the error message: User interrupt
    --- failed re-building ‘mmod_tutorial.Rmd’
    
    SUMMARY: processing the following file failed:
     ‘mmod_tutorial.Rmd’
    
    Error: Vignette re-building failed.
    Execution halted
Flavor: r-patched-solaris-x86