CRAN Package Check Results for Package umx

Last updated on 2019-03-18 22:54:36 CET.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.9.9 28.25 375.77 404.02 WARN
r-devel-linux-x86_64-debian-gcc 2.9.9 26.00 266.07 292.07 OK
r-devel-linux-x86_64-fedora-clang 2.9.9 414.23 OK
r-devel-linux-x86_64-fedora-gcc 2.9.9 381.42 OK
r-devel-windows-ix86+x86_64 2.9.9 72.00 378.00 450.00 OK
r-patched-linux-x86_64 2.9.9 22.29 337.63 359.92 OK
r-patched-solaris-x86 2.9.9 353.70 ERROR
r-release-linux-x86_64 2.9.9 24.79 332.51 357.30 OK
r-release-windows-ix86+x86_64 2.9.9 40.00 393.00 433.00 OK
r-release-osx-x86_64 2.9.9 NOTE
r-oldrel-windows-ix86+x86_64 2.9.9 42.00 405.00 447.00 OK
r-oldrel-osx-x86_64 2.9.9 NOTE

Check Details

Version: 2.9.9
Check: whether package can be installed
Result: WARN
    Found the following significant warnings:
     Warning: unable to re-encode 'misc_and_utility.R' lines 277, 278
     Warning: unable to re-encode 'tmx.R' lines 17, 20
     Warning: unable to re-encode 'umx_build_umxACEv.R' line 496
     Warning: unable to re-encode 'umx_build_umxGxEbiv.R' line 131
     Warning: unable to re-encode 'xmu.r' line 109
Flavor: r-devel-linux-x86_64-debian-clang

Version: 2.9.9
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘devtools’
Flavor: r-patched-solaris-x86

Version: 2.9.9
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 well-being.
    > ### 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 0, cause 'memory not mapped'
    
    Traceback:
     1: runHelper(model, frontendStart, intervals, silent, suppressWarnings, unsafe, checkpoint, useSocket, onlyFrontend, useOptimizer)
     2: mxRun(model1)
     3: doTryCatch(return(expr), name, parentenv, handler)
     4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     5: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     6: doTryCatch(return(expr), name, parentenv, handler)
     7: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
     8: tryCatchList(expr, classes, parentenv, handlers)
     9: tryCatch({ if (tryHard == "no") { model1 = mxRun(model1) } else if (tryHard == "mxTryHard") { model1 = mxTryHard(model1) } else if (tryHard == "mxTryHardOrdinal") { model1 = mxTryHardOrdinal(model1) } else if (tryHard == "mxTryHardWideSearch") { model1 = mxTryHardWideSearch(model1) } else { stop("Don't know how to do tryHard = ", omxQuotes(tryHard)) }}, warning = function(w) { message("Warning incurred trying to run model: try mxTryHard on it.") message(w)}, error = function(e) { message("Error incurred trying to run model: try mxTryHard on it.") message(e)})
    10: xmu_safe_run_summary(model, autoRun = autoRun, tryHard = tryHard)
    11: umxACE(selDVs = "gff", sep = "_T", mzData = subset(GFF, zyg_2grp == "MZ"), dzData = subset(GFF, zyg_2grp == "DZ"))
    An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86

Version: 2.9.9
Check: tests
Result: ERROR
     Running ‘testthat.R’ [11s/38s]
    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: xmu_safe_run_summary(newModel, autoRun = autoRun, tryHard = tryHard)
     3: tryCatch({
     if (tryHard == "no") {
     model1 = mxRun(model1)
     }
     else if (tryHard == "mxTryHard") {
     model1 = mxTryHard(model1)
     }
     else if (tryHard == "mxTryHardOrdinal") {
     model1 = mxTryHardOrdinal(model1)
     }
     else if (tryHard == "mxTryHardWideSearch") {
     model1 = mxTryHardWideSearch(model1)
     }
     else {
     stop("Don't know how to do tryHard = ", omxQuotes(tryHard))
     }
     }, warning = function(w) {
     message("Warning incurred trying to run model: try mxTryHard on it.")
     message(w)
     }, error = function(e) {
     message("Error incurred trying to run model: try mxTryHard on it.")
     message(e)
     })
     4: tryCatchList(expr, classes, parentenv, handlers)
     5: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh],
     parentenv, handlers[[nh]])
     6: doTryCatch(return(expr), name, parentenv, handler)
     7: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     9: value[[3L]](cond)
     10: message(w)
     11: withRestarts({
     signalCondition(cond)
     defaultHandler(cond)
     }, muffleMessage = function() NULL)
     12: withOneRestart(expr, restarts[[1L]])
     13: doWithOneRestart(return(expr), restart)
     14: signalCondition(cond)
     15: (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")))
     16: invokeRestart("muffleWarning")
     17: stop(gettextf("no 'restart' '%s' found", as.character(r)), domain = NA)
    
    
     *** caught segfault ***
     address fc167b50, 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: 2.9.9
Check: dependencies in R code
Result: NOTE
    Missing or unexported object: ‘devtools::check_rhub’
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64