CRAN Package Check Results for Package mxmmod

Last updated on 2020-07-04 14:48:27 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.1 2.37 52.03 54.40 OK
r-devel-linux-x86_64-debian-gcc 1.0.1 1.90 38.36 40.26 OK
r-devel-linux-x86_64-fedora-clang 1.0.1 71.10 OK
r-devel-linux-x86_64-fedora-gcc 1.0.1 61.39 OK
r-devel-windows-ix86+x86_64 1.0.1 9.00 61.00 70.00 OK
r-patched-linux-x86_64 1.0.1 2.27 48.89 51.16 OK
r-patched-solaris-x86 1.0.1 87.10 ERROR
r-release-linux-x86_64 1.0.1 2.39 48.37 50.76 OK
r-release-osx-x86_64 1.0.1 OK
r-release-windows-ix86+x86_64 1.0.1 6.00 56.00 62.00 OK
r-oldrel-osx-x86_64 1.0.1 OK
r-oldrel-windows-ix86+x86_64 1.0.1 12.00 81.00 93.00 OK

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 726ba460, 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’ [11s/36s]
    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: 1:User interrupt
     2:std::bad_alloc
     Backtrace:
     1. mxmmod:::mxmmod_ref(df)
     3. OpenMx::mxRun(mmod_model)
     4. OpenMx:::runHelper(...)
     5. OpenMx:::processErrorConditions(model, unsafe, suppressWarnings)
    
    
     *** caught segfault ***
     address 4c, 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 3.0.1 ✔ 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 328373396 is too close to the limit
    
     *** caught segfault ***
    address b19b3a7e, cause 'memory not mapped'
    
    Traceback:
     1: runHelper(model, frontendStart, intervals, silent, suppressWarnings, unsafe, checkpoint, useSocket, onlyFrontend, useOptimizer, beginMessage)
     2: mxRun(mmod_model)
     3: eval(expr, envir, enclos)
     4: eval(expr, envir, enclos)
     5: withVisible(eval(expr, envir, enclos))
     6: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)
     7: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler))
     8: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
     9: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos, debug = debug, last = i == length(out), use_try = stop_on_error != 2L, keep_warning = keep_warning, keep_message = keep_message, output_handler = output_handler, include_timing = include_timing)
    10: evaluate::evaluate(...)
    11: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options))
    12: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message), stop_on_error = if (options$error && options$include) 0L else 2L, output_handler = knit_handlers(options$render, options)))
    13: block_exec(params)
    14: call_block(x)
    15: process_group.block(group)
    16: process_group(group)
    17: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group), error = function(e) { setwd(wd) cat(res, sep = "\n", file = output %n% "") message("Quitting from lines ", paste(current_lines(i), collapse = "-"), " (", knit_concord$get("infile"), ") ") })
    18: process_file(text, output)
    19: knit(input, text = text, envir = envir, quiet = quiet)
    20: knit2html(..., force_v1 = TRUE)
    21: (if (grepl("\\.[Rr]md$", file)) knit2html_v1 else if (grepl("\\.[Rr]rst$", file)) knit2pandoc else knit)(file, encoding = encoding, quiet = quiet, envir = globalenv(), ...)
    22: vweave(...)
    23: engine$weave(file, quiet = quiet, encoding = enc)
    24: doTryCatch(return(expr), name, parentenv, handler)
    25: tryCatchOne(expr, names, parentenv, handlers[[1L]])
    26: tryCatchList(expr, classes, parentenv, handlers)
    27: tryCatch({ engine$weave(file, quiet = quiet, encoding = enc) setwd(startdir) output <- find_vignette_product(name, by = "weave", engine = engine) if (!have.makefile && vignette_is_tex(output)) { texi2pdf(file = output, clean = FALSE, quiet = quiet) output <- find_vignette_product(name, by = "texi2pdf", engine = engine) } outputs <- c(outputs, output)}, error = function(e) { thisOK <<- FALSE fails <<- c(fails, file) message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s", file, conditionMessage(e)))})
    28: tools:::buildVignettes(dir = "/home/ripley/R/packages/tests32/mxmmod.Rcheck/vign_test/mxmmod", ser_elibs = "/tmp/RtmpbZaiSl/file176134b04b14.rds")
    An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86