CRAN Package Check Results for Package umx

Last updated on 2018-05-14 01:47:07 CEST.

Check Details

Version: 2.6.5
Check: examples
Result: ERROR
    Running examples in ‘umx-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: umx
    > ### Title: Helper Functions for Structural Equation Modelling in OpenMx
    > ### Aliases: umx umx-package
    >
    > ### ** Examples
    >
    > require("umx")
    > data(demoOneFactor)
    > myData = mxData(cov(demoOneFactor), type = "cov", numObs = nrow(demoOneFactor))
    > latents = c("G")
    > manifests = names(demoOneFactor)
    > m1 <- umxRAM("One Factor", data = myData,
    + umxPath(latents, to = manifests),
    + umxPath(var = manifests),
    + umxPath(var = latents , fixedAt=1)
    + )
    A latent variable 'G' was created.
    Running One Factor with 10 parameters
    ?umxSummary showEstimates='raw|std', digits, report= 'html', filter= 'NS' & more
    [1] "χ²(5) = 7.39, p = 0.193; CFI = 0.999; TLI = 0.999; RMSEA = 0.031"
    >
    > # umx added informative labels, created starting values,
    > # Ran you model (if autoRun is on), and displayed a brief summary
    > # including a comparison if you modified a model...!
    >
    > # Let's get some journal-ready fit information
    >
    > umxSummary(m1)
    ?umxSummary showEstimates='raw|std', digits, report= 'html', filter= 'NS' & more
    
    
    |name | Estimate| SE|
    |:----------|--------:|----:|
    |G_to_x1 | 0.40| 0.02|
    |G_to_x2 | 0.50| 0.02|
    |G_to_x3 | 0.58| 0.02|
    |G_to_x4 | 0.70| 0.02|
    |G_to_x5 | 0.80| 0.03|
    |x1_with_x1 | 0.04| 0.00|
    |x2_with_x2 | 0.04| 0.00|
    |x3_with_x3 | 0.04| 0.00|
    |x4_with_x4 | 0.04| 0.00|
    |x5_with_x5 | 0.04| 0.00|
    |G_with_G | 1.00| 0.00|
    [1] "χ²(5) = 7.39, p = 0.193; CFI = 0.999; TLI = 0.999; RMSEA = 0.031"
    > umxSummary(m1, show = "std") #also display parameter estimates
    ?umxSummary showEstimates='raw|std', digits, report= 'html', filter= 'NS' & more
    
    
    |name | Std.Estimate| Std.SE|CI |
    |:----------|------------:|------:|:-----------------|
    |G_to_x1 | 0.89| 0.01|0.89 [0.87, 0.91] |
    |G_to_x2 | 0.93| 0.01|0.93 [0.92, 0.95] |
    |G_to_x3 | 0.94| 0.01|0.94 [0.93, 0.95] |
    |G_to_x4 | 0.96| 0.00|0.96 [0.95, 0.97] |
    |G_to_x5 | 0.97| 0.00|0.97 [0.97, 0.98] |
    |x1_with_x1 | 0.21| 0.02|0.21 [0.17, 0.24] |
    |x2_with_x2 | 0.13| 0.01|0.13 [0.11, 0.15] |
    |x3_with_x3 | 0.11| 0.01|0.11 [0.09, 0.13] |
    |x4_with_x4 | 0.07| 0.01|0.07 [0.06, 0.09] |
    |x5_with_x5 | 0.05| 0.01|0.05 [0.04, 0.07] |
    |G_with_G | 1.00| 0.00|1 [1, 1] |
    [1] "χ²(5) = 7.39, p = 0.193; CFI = 0.999; TLI = 0.999; RMSEA = 0.031"
    > # You can get the coefficients of an MxModel with coef(), just like for lm etc.
    > coef(m1)
     G_to_x1 G_to_x2 G_to_x3 G_to_x4 G_to_x5 x1_with_x1 x2_with_x2
    0.39675479 0.50315708 0.57666362 0.70207039 0.79545313 0.04073255 0.03794395
    x3_with_x3 x4_with_x4 x5_with_x5
    0.04074551 0.03930826 0.03621450
    >
    > # ==================
    > # = Model updating =
    > # ==================
    > # Can we set the loading of X5 on G to zero?
    > m2 = omxSetParameters(m1, labels = "G_to_x1", values = 0, free = FALSE, name = "no_g_on_X5")
    > m2 = mxRun(m2)
    Running no_g_on_X5 with 9 parameters
    > # Compare the two models
    > umxCompare(m1, m2)
    
    
    |Model | EP|∆ -2LL |∆ df |p | AIC|Compare with Model |
    |:----------|--:|:----------|:----|:-------|----------:|:------------------|
    |One Factor | 10| | | | -2.606207| |
    |no_g_on_X5 | 9|750.416577 |1 |< 0.001 | 745.810370|One Factor |
    >
    > # Use umxModify to do the same thing in 1-line
    > m2 = umxModify(m1, "G_to_x1", name = "no_effect_of_g_on_X5", comparison = TRUE)
    Running no_effect_of_g_on_X5 with 9 parameters
    ?umxSummary showEstimates='raw|std', digits, report= 'html', filter= 'NS' & more
    
    
    |name | Estimate| SE|
    |:----------|--------:|----:|
    |G_to_x2 | 0.50| 0.02|
    |G_to_x3 | 0.58| 0.02|
    |G_to_x4 | 0.70| 0.02|
    |G_to_x5 | 0.80| 0.03|
    |x1_with_x1 | 0.20| 0.01|
    |x2_with_x2 | 0.04| 0.00|
    |x3_with_x3 | 0.04| 0.00|
    |x4_with_x4 | 0.04| 0.00|
    |x5_with_x5 | 0.04| 0.00|
    |G_with_G | 1.00| 0.00|
    [1] "χ²(6) = 757.81, p < 0.001; CFI = 0.798; TLI = 0.663; RMSEA = 0.501"
    TLI is worse than desired
    RMSEA is worse than desired
    
    
    |Model | EP|∆ -2LL |∆ df |p | AIC|Compare with Model |
    |:--------------------|--:|:----------|:----|:-------|----------:|:------------------|
    |One Factor | 10| | | | -2.606207| |
    |no_effect_of_g_on_X5 | 9|750.416577 |1 |< 0.001 | 745.810370|One Factor |
    >
    > # ========================
    > # = Confidence intervals =
    > # ========================
    >
    > # umxSummary() will show these, but you can also use the confint() function
    > confint(m1) # OpenMx's SE-based confidence intervals
    Wald type confidence intervals (see ?mxCI for likelihood-based CIs)
     2.5% 97.5%
    G_to_x1 0.36633882 0.42717077
    G_to_x2 0.46749358 0.53882058
    G_to_x3 0.53666576 0.61666147
    G_to_x4 0.65510313 0.74903765
    G_to_x5 0.74328665 0.84761961
    x1_with_x1 0.03523626 0.04622885
    x2_with_x2 0.03246119 0.04342671
    x3_with_x3 0.03458563 0.04690539
    x4_with_x4 0.03264703 0.04596949
    x5_with_x5 0.02902628 0.04340272
    > umxConfint(m1, parm = 'all', run = TRUE) # likelihood-based CIs
    Running One Factor with 10 parameters
    
     *** caught segfault ***
    address fc120350, cause 'memory not mapped'
    
    Traceback:
     1: runHelper(model, frontendStart, intervals, silent, suppressWarnings, unsafe, checkpoint, useSocket, onlyFrontend, useOptimizer)
     2: mxRun(model, suppressWarnings = TRUE)
     3: omxParallelCI(model = model, run = TRUE, verbose = verbose, independentSubmodels = FALSE, optimizer = optimizer)
     4: omxRunCI(object, optimizer = optimizer)
     5: umxConfint(m1, parm = "all", run = TRUE)
    An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86

Version: 2.6.5
Check: tests
Result: ERROR
     Running ‘testthat.R’ [17s/50s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(umx)
     Loading required package: OpenMx
     To take full advantage of multiple cores, use:
     mxOption(NULL, 'Number of Threads', parallel::detectCores()) #now
     Sys.setenv(OMP_NUM_THREADS=parallel::detectCores()) #before library(OpenMx)
     For an overview type '?umx'
    
     Attaching package: 'umx'
    
     The following object is masked from 'package:stats':
    
     loadings
    
     >
     > test_check("umx")
     ── 1. Error: (unknown) (@test_residuals.MxModel.r#16) ─────────────────────────
     no 'restart' 'muffleWarning' found
     1: umxRAM("test", data = mxData(cov(demoOneFactor), type = "cov", numObs = 500), umxPath(latents,
     to = manifests), umxPath(var = manifests), umxPath(var = latents, fixedAt = 1)) at testthat/test_residuals.MxModel.r:16
     2: tryCatch({
     m1 = mxRun(m1)
     umxSummary(m1, refModels = refModels, showEstimates = showEstimates)
     }, warning = function(w) {
     message("Warning incurred trying to run model")
     message(w)
     }, error = function(e) {
     message("Error incurred trying to run model")
     message(e)
     })
     3: tryCatchList(expr, classes, parentenv, handlers)
     4: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh],
     parentenv, handlers[[nh]])
     5: doTryCatch(return(expr), name, parentenv, handler)
     6: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     8: value[[3L]](cond)
     9: message(w)
     10: withRestarts({
     signalCondition(cond)
     defaultHandler(cond)
     }, muffleMessage = function() NULL)
     11: withOneRestart(expr, restarts[[1L]])
     12: doWithOneRestart(return(expr), restart)
     13: signalCondition(cond)
     14: (function (e)
     {
     handled <<- TRUE
     e$expectation_calls <- frame_calls(11, 5)
     register_expectation(e)
     invokeRestart("muffleWarning")
     })(structure(list(message = "In model 'test' Optimizer returned a non-zero status code 5. The Hessian at the solution does not appear to be convex. See ?mxCheckIdentification for possible diagnosis (Mx status RED).",
     call = NULL), class = c("simpleWarning", "warning", "condition")))
     15: invokeRestart("muffleWarning")
     16: stop(gettextf("no 'restart' '%s' found", as.character(r)), domain = NA)
    
    
     *** caught segfault ***
     address 0, cause 'memory not mapped'
    
     Traceback:
     1: runHelper(model, frontendStart, intervals, silent, suppressWarnings, unsafe, checkpoint, useSocket, onlyFrontend, useOptimizer)
     2: mxRun(model, silent = FALSE)
     3: FUN(X[[i]], ...)
     4: lapply(ReferenceModelHelper(x, distribution), function(model) { if (!isS4(model)) return(model) model <- omxAssignFirstParameters(model) model <- mxOption(model, "Standard Errors", "No") model <- mxOption(model, "Calculate Hessian", "No") if (run) { model <- mxRun(model, silent = FALSE) } model})
     5: mxRefModels(model, run = TRUE)
     6: umxRun(m2, setLabels = TRUE, setValues = TRUE)
     7: eval(code, test_env)
     8: eval(code, test_env)
     9: 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)
     10: doTryCatch(return(expr), name, parentenv, handler)
     11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     12: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     13: doTryCatch(return(expr), name, parentenv, handler)
     14: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
     15: tryCatchList(expr, classes, parentenv, handlers)
     16: 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) { })
     17: test_code(NULL, exprs, env)
     18: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
     19: force(code)
     20: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter, { lister$start_file(basename(path)) source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap) end_context() })
     21: FUN(X[[i]], ...)
     22: lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
     23: force(code)
     24: with_reporter(reporter = current_reporter, results <- lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap))
     25: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
     26: 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)
     27: 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)
     28: test_check("umx")
     An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86

Version: 2.4.0
Check: examples
Result: ERROR
    Running examples in ‘umx-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: residuals.MxModel
    > ### Title: Get residuals from an MxModel
    > ### Aliases: residuals.MxModel
    >
    > ### ** Examples
    >
    > require(umx)
    > data(demoOneFactor)
    > latents = c("g")
    > manifests = names(demoOneFactor)
    > m1 <- mxModel("One Factor", type = "RAM",
    + manifestVars = manifests, latentVars = latents,
    + mxPath(from = latents, to = manifests),
    + mxPath(from = manifests, arrows = 2),
    + mxPath(from = latents, arrows = 2, free = FALSE, values = 1.0),
    + mxData(cov(demoOneFactor), type = "cov", numObs = 500)
    + )
    > m1 = umxRun(m1, setLabels = TRUE, setValues = TRUE)
    Running One Factor with 10 parameters
    Error in runHelper(model, frontendStart, intervals, silent, suppressWarnings, :
     c++ exception (unknown reason)
    Calls: umxRun -> mxRun -> runHelper
    Execution halted
Flavor: r-oldrel-osx-x86_64

Version: 2.4.0
Check: tests
Result: ERROR
     Running ‘testthat.R’ [11s/11s]
    Running the tests in ‘tests/testthat.R’ failed.
    Last 13 lines of output:
     6: message(e)
     7: withRestarts({
     signalCondition(cond)
     defaultHandler(cond)
     }, muffleMessage = function() NULL)
     8: withOneRestart(expr, restarts[[1L]])
     9: doWithOneRestart(return(expr), restart)
    
     ══ testthat results ═══════════════════════════════════════════════════════════
     OK: 54 SKIPPED: 0 FAILED: 2
     1. Error: (unknown) (@test_umx_has_CI.r#41)
     2. Error: (unknown) (@test_umx_is_RAM.r#10)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-oldrel-osx-x86_64