CRAN Package Check Results for Package umx

Last updated on 2019-10-31 00:51:10 CET.

Check Details

Version: 3.0.0
Check: dependencies in R code
Result: NOTE
    Namespaces in Imports field not imported from:
     ‘numDeriv’ ‘sfsmisc’
     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

Version: 3.0.0
Check: installed package size
Result: NOTE
     installed size is 5.6Mb
     sub-directories of 1Mb or more:
     R 1.0Mb
     help 4.1Mb
Flavor: r-patched-solaris-x86

Version: 3.0.0
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)
    > manifests = names(demoOneFactor)
    >
    > m1 = umxRAM("One Factor", data = demoOneFactor, type = "cov",
    + umxPath("G", to = manifests),
    + umxPath(var = manifests),
    + umxPath(var = "G", fixedAt = 1.0)
    + )
    A latent variable 'G' was created.
    Running One Factor with 10 parameters
    Error: C stack usage 251958420 is too close to the limit
    Error incurred trying to run model: model = mxTryHard(model) might help?
    The job for model 'One Factor' exited abnormally with the error message: User interrupt>
    > # ===================================
    > # = Show the residuals of the model =
    > # ===================================
    > residuals(m1)
    Error in dimnames(expCov) <- list(manifestNames, manifestNames) :
     attempt to set an attribute on NULL
    Calls: residuals -> residuals.MxModel -> umxExpCov
    Execution halted
Flavor: r-patched-solaris-x86

Version: 3.0.0
Check: tests
Result: ERROR
     Running ‘testthat.R’ [30s/70s]
    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(key='Number of Threads', value=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")
     Error: C stack usage 252089492 is too close to the limit
     ── 1. Error: (unknown) (@test_residuals.MxModel.r#15) ─────────────────────────
     The job for model 'test' exited abnormally with the error message: User interrupt
     1: umxRAM("test", data = mxData(cov(demoOneFactor), type = "cov", numObs = 500), umxPath("g",
     to = manifests), umxPath(var = manifests), umxPath(var = "g", fixedAt = 1)) at testthat/test_residuals.MxModel.r:15
     2: xmu_safe_run_summary(newModel, autoRun = autoRun, tryHard = tryHard, std = std, show = show)
     3: tryCatch({
     if (tryHard == "no") {
     model1 = mxRun(model1, beginMessage = !umx_set_silent(silent = TRUE), silent = umx_set_silent(silent = TRUE))
     }
     else if (tryHard == "mxTryHard") {
     model1 = mxTryHard(model1)
     }
     else if (tryHard == "mxTryHardOrdinal") {
     model1 = mxTryHardOrdinal(model1)
     }
     else if (tryHard == "mxTryHardWideSearch") {
     model1 = mxTryHardWideSearch(model1)
     }
     }, error = function(e) {
     if (tryHard == "no") {
     message("Error incurred trying to run model: model = mxTryHard(model) might help?")
     }
     else {
     message("Error incurred trying to run model")
     }
     message(e)
     })
     4: tryCatchList(expr, classes, parentenv, handlers)
     5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     6: value[[3L]](cond)
     7: message(e)
     8: withRestarts({
     signalCondition(cond)
     defaultHandler(cond)
     }, muffleMessage = function() NULL)
     9: withOneRestart(expr, restarts[[1L]])
     10: doWithOneRestart(return(expr), restart)
    
    
    
     | | ai1| ci1| ei1|
     |:---|-----:|-----:|-----:|
     |gff | 0.408| 0.408| 0.408|
     |fc | 0.408| 0.408| 0.408|
     |qol | 0.408| 0.408| 0.408|
     |hap | 0.408| 0.408| 0.408|
     |sat | 0.408| 0.408| 0.408|
     |AD | 0.408| 0.408| 0.408|
    
    
     | | gff| fc| qol| hap| sat| AD|
     |:----------|-----:|-----:|-----:|-----:|-----:|-----:|
     |Specific a | 0.408| 0.408| 0.408| 0.408| 0.408| 0.408|
     |Specific c | 0.408| 0.408| 0.408| 0.408| 0.408| 0.408|
     |Specific e | 0.408| 0.408| 0.408| 0.408| 0.408| 0.408|
     Error: C stack usage 252089460 is too close to the limit
     Error: C stack usage 252089460 is too close to the limit
     ── 2. Error: testing umx twin models (@test_umx_ACE_etc.r#21) ─────────────────
     The job for model 'IPa1c1e1' exited abnormally with the error message: 1:User interrupt
     2:User interrupt
     1: umxIP(selDVs = selDVs, sep = "_T", dzData = dzData, mzData = mzData, type = "DWLS",
     allContinuousMethod = "marginals") at testthat/test_umx_ACE_etc.r:21
     2: xmu_safe_run_summary(model, autoRun = autoRun, tryHard = tryHard)
     3: tryCatch({
     if (tryHard == "no") {
     model1 = mxRun(model1, beginMessage = !umx_set_silent(silent = TRUE), silent = umx_set_silent(silent = TRUE))
     }
     else if (tryHard == "mxTryHard") {
     model1 = mxTryHard(model1)
     }
     else if (tryHard == "mxTryHardOrdinal") {
     model1 = mxTryHardOrdinal(model1)
     }
     else if (tryHard == "mxTryHardWideSearch") {
     model1 = mxTryHardWideSearch(model1)
     }
     }, error = function(e) {
     if (tryHard == "no") {
     message("Error incurred trying to run model: model = mxTryHard(model) might help?")
     }
     else {
     message("Error incurred trying to run model")
     }
     message(e)
     })
     4: tryCatchList(expr, classes, parentenv, handlers)
     5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     6: value[[3L]](cond)
     7: message(e)
     8: withRestarts({
     signalCondition(cond)
     defaultHandler(cond)
     }, muffleMessage = function() NULL)
     9: withOneRestart(expr, restarts[[1L]])
     10: doWithOneRestart(return(expr), restart)
    
    
     *** caught segfault ***
     address fbfbadc0, cause 'memory not mapped'
    
     Traceback:
     1: runHelper(model, frontendStart, intervals, silent, suppressWarnings, unsafe, checkpoint, useSocket, onlyFrontend, useOptimizer, beginMessage)
     2: mxRun(m2, intervals = TRUE)
     3: eval(code, test_env)
     4: eval(code, test_env)
     5: 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)
     6: doTryCatch(return(expr), name, parentenv, handler)
     7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     8: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     9: doTryCatch(return(expr), name, parentenv, handler)
     10: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
     11: tryCatchList(expr, classes, parentenv, handlers)
     12: 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) { })
     13: test_code(NULL, exprs, env)
     14: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
     15: force(code)
     16: 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() })
     17: FUN(X[[i]], ...)
     18: lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
     19: force(code)
     20: with_reporter(reporter = current_reporter, results <- lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap))
     21: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
     22: 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)
     23: 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)
     24: test_check("umx")
     An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86