CRAN Package Check Results for Package mxmmod

Last updated on 2021-01-25 00:48:04 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.0.1 2.38 57.81 60.19 OK
r-devel-linux-x86_64-debian-gcc 1.0.1 1.81 41.11 42.92 OK
r-devel-linux-x86_64-fedora-clang 1.0.1 76.07 OK
r-devel-linux-x86_64-fedora-gcc 1.0.1 66.11 OK
r-devel-windows-ix86+x86_64 1.0.1 5.00 55.00 60.00 OK
r-patched-linux-x86_64 1.0.1 2.29 50.84 53.13 OK
r-patched-solaris-x86 1.0.1 92.60 ERROR
r-release-linux-x86_64 1.0.1 2.26 52.81 55.07 OK
r-release-macos-x86_64 1.0.1 OK
r-release-windows-ix86+x86_64 1.0.1 11.00 73.00 84.00 OK
r-oldrel-macos-x86_64 1.0.1 OK
r-oldrel-windows-ix86+x86_64 1.0.1 3.00 77.00 80.00 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 4ebf8a20, 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’ [9s/32s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(mxmmod)
     >
     > test_check("mxmmod")
    
     *** caught segfault ***
     address 51ac94f8, 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(df)
     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(), reporter = reporter)
     16: test_that("Same results as Estabrook 2015", { df <- nlsy97_1983_cohort() a <- mxmmod_ref(df) b <- estabrook_ref(df) 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, child_env(env), wrap = wrap)
     29: FUN(X[[i]], ...)
     30: lapply(test_paths, test_one_file, env = env, wrap = wrap)
     31: force(code)
     32: doWithOneRestart(return(expr), restart)
     33: withOneRestart(expr, restarts[[1L]])
     34: withRestarts(testthat_abort_reporter = function() NULL, force(code))
     35: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, wrap = wrap))
     36: test_files(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap, load_package = load_package)
     37: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap, load_package = load_package, parallel = parallel)
     38: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
     39: 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 3.0.4 ✔ dplyr 1.0.2
    ✔ tidyr 1.1.2 ✔ stringr 1.4.0
    ✔ readr 1.4.0 ✔ 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)
    
     *** caught segfault ***
    address 64d822c4, 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/RtmpIcaakW/file60507cfb3d44.rds")
    An irrecoverable exception occurred. R is aborting now ...
    
     *** caught segfault ***
    address 64218764, 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/RtmpIcaakW/file60507cfb3d44.rds")
    An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86