CRAN Package Check Results for Package umx

Last updated on 2018-07-17 01:47:28 CEST.

Check Details

Version: 2.8.0
Check: examples
Result: ERROR
    Running examples in ‘umx-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: GFF
    > ### Title: Twin data: General Family Functioning, divorce, and wellbeing.
    > ### Aliases: GFF
    > ### Keywords: datasets
    >
    > ### ** Examples
    >
    > # Twin 1 variables (end in '_T1')
    > data(GFF)
    > umx_names(GFF, "1$") # Just variables ending in 1 (twin 1)
     [1] "sex_T1" "age_T1" "gff_T1" "fc_T1" "qol_T1" "hap_T1" "sat_T1"
     [8] "AD_T1" "SOMA_T1" "SOC_T1" "THOU_T1"
    > str(GFF) # first few rows
    'data.frame': 3185 obs. of 47 variables:
     $ zyg_6grp: Factor w/ 6 levels "MZMM","DZMM",..: 3 5 6 3 4 4 5 5 3 3 ...
     $ zyg_2grp: Factor w/ 2 levels "MZ","DZ": 1 2 2 1 2 2 2 2 1 1 ...
     $ divorce : int 0 0 0 0 0 0 0 0 1 0 ...
     $ sex_T1 : Factor w/ 2 levels "male","female": 2 1 NA 2 2 2 NA 1 2 2 ...
     $ age_T1 : num 18.1 18.3 NA 18.1 18.5 ...
     $ gff_T1 : int 46 48 NA 39 46 36 NA 32 45 48 ...
     $ fc_T1 : int -12 -12 NA -18 -11 -12 NA -15 -11 -11 ...
     $ qol_T1 : int 9 8 NA 9 8 8 NA 7 7 10 ...
     $ hap_T1 : int 20 28 NA 27 26 25 NA 25 27 28 ...
     $ sat_T1 : num 31 29 NA 35 35 27 NA 25 29 29 ...
     $ AD_T1 : num 1 1 NA 8 3 2 NA 0 11 2 ...
     $ SOMA_T1 : num 2 0 NA 2 2 4 NA 0 0 0 ...
     $ SOC_T1 : num 1 3 NA 0 0 0 NA 0 1 1 ...
     $ THOU_T1 : num 1 0 NA 0 2 0 NA 2 2 0 ...
     $ sex_T2 : Factor w/ 2 levels "male","female": 2 2 1 2 2 2 2 2 2 2 ...
     $ age_T2 : num 18.1 18.3 18.3 18.1 18.5 ...
     $ gff_T2 : int 47 48 32 45 48 36 36 29 45 41 ...
     $ fc_T2 : int -12 -10 -12 -15 -13 -15 -15 -13 -11 -11 ...
     $ qol_T2 : int 7 9 7 8 10 7 7 7 10 8 ...
     $ hap_T2 : int 15 27 15 24 28 24 24 23 28 25 ...
     $ sat_T2 : num 25 33 20 26 35 26 27 24 32 32 ...
     $ AD_T2 : num 23 3 7 7 2 6 3 5 0 2 ...
     $ SOMA_T2 : num 9 3 0 4 1 5 5 1 0 1 ...
     $ SOC_T2 : num 3 0 3 0 1 4 1 0 0 1 ...
     $ THOU_T2 : num 5 0 1 1 0 1 0 0 2 0 ...
     $ sex_Tb : Factor w/ 2 levels "male","female": NA NA NA NA NA NA NA NA NA NA ...
     $ age_Tb : num NA NA NA NA NA NA NA NA NA NA ...
     $ gff_Tb : int NA NA NA NA NA NA NA NA NA NA ...
     $ fc_Tb : int NA NA NA NA NA NA NA NA NA NA ...
     $ qol_Tb : int NA NA NA NA NA NA NA NA NA NA ...
     $ hap_Tb : int NA NA NA NA NA NA NA NA NA NA ...
     $ sat_Tb : num NA NA NA NA NA NA NA NA NA NA ...
     $ AD_Tb : num NA NA NA NA NA NA NA NA NA NA ...
     $ SOMA_Tb : num NA NA NA NA NA NA NA NA NA NA ...
     $ SOC_Tb : num NA NA NA NA NA NA NA NA NA NA ...
     $ THOU_Tb : num NA NA NA NA NA NA NA NA NA NA ...
     $ sex_Ts : Factor w/ 2 levels "male","female": NA NA NA NA NA NA NA NA NA NA ...
     $ age_Ts : num NA NA NA NA NA NA NA NA NA NA ...
     $ gff_Ts : int NA NA NA NA NA NA NA NA NA NA ...
     $ fc_Ts : int NA NA NA NA NA NA NA NA NA NA ...
     $ qol_Ts : int NA NA NA NA NA NA NA NA NA NA ...
     $ hap_Ts : int NA NA NA NA NA NA NA NA NA NA ...
     $ sat_Ts : num NA NA NA NA NA NA NA NA NA NA ...
     $ AD_Ts : num NA NA NA NA NA NA NA NA NA NA ...
     $ SOMA_Ts : num NA NA NA NA NA NA NA NA NA NA ...
     $ SOC_Ts : num NA NA NA NA NA NA NA NA NA NA ...
     $ THOU_Ts : num NA NA NA NA NA NA NA NA NA NA ...
    >
    > m1 = umxACE(selDVs= "gff", sep = "_T",
    + mzData = subset(GFF, zyg_2grp == "MZ"),
    + dzData = subset(GFF, zyg_2grp == "DZ")
    + )
    All variables continuous
    treating data as raw
    Running ACE with 4 parameters
    
     *** caught segfault ***
    address 9e238e28, cause 'memory not mapped'
Flavor: r-patched-solaris-x86

Version: 2.8.0
Check: tests
Result: ERROR
     Running ‘testthat.R’ [10s/35s]
    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 6. The model does not satisfy the first-order optimality conditions to the required accuracy, and no improved point for the merit function could be found during the final linesearch (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 fc120350, cause 'memory not mapped'
    
     Traceback:
     1: runHelper(model, frontendStart, intervals, silent, suppressWarnings, unsafe, checkpoint, useSocket, onlyFrontend, useOptimizer)
     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, { lister$start_file(basename(path)) source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap) end_context() })
     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

Version: 2.8.0
Check: R code for possible problems
Result: NOTE
    umxConfint: no visible global function definition for ‘omxRunCI’
    Undefined global functions or variables:
     omxRunCI
Flavor: r-oldrel-osx-x86_64

Version: 2.8.0
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: 2.8.0
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