CRAN Package Check Results for Package umx

Last updated on 2017-05-23 11:53:21.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 1.7.5 6.94 137.63 144.57 OK
r-devel-linux-x86_64-debian-gcc 1.7.5 6.25 135.70 141.96 OK
r-devel-linux-x86_64-fedora-clang 1.7.5 283.02 OK --no-tests --no-stop-on-test-error
r-devel-linux-x86_64-fedora-gcc 1.7.5 269.10 OK --no-tests --no-stop-on-test-error
r-devel-windows-ix86+x86_64 1.7.5 30.00 234.00 264.00 OK
r-patched-linux-x86_64 1.7.5 6.67 136.54 143.21 OK
r-patched-solaris-sparc 1.7.5 1265.20 ERROR
r-patched-solaris-x86 1.7.5 274.10 ERROR --no-stop-on-test-error
r-release-linux-x86_64 1.7.5 6.39 135.90 142.30 OK
r-release-windows-ix86+x86_64 1.7.5 19.00 297.00 316.00 OK
r-release-osx-x86_64 1.7.5 ERROR
r-oldrel-windows-ix86+x86_64 1.7.5 30.00 274.00 304.00 OK
r-oldrel-osx-x86_64 1.7.5 OK

Check Details

Version: 1.7.5
Check: examples
Result: ERROR
    Running examples in ‘umx-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: loadings.MxModel
    > ### Title: loadings.MxModel
    > ### Aliases: loadings.MxModel
    >
    > ### ** Examples
    >
    > myVars <- c("mpg", "disp", "hp", "wt", "qsec")
    > m1 = umxEFA(name = "test", factors = 2, data = mtcars[, myVars])
    umxEFA is beta-only, and not ready for prime time
    Vars I will scale are:mpg , disp , hp , wt , qsec ,
    2 latent variables were created:F1, F2.
    ManifestVars set to: mpg, disp, hp, wt, qsec.
    Running test with 19 parameters
    Warning: 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)
    $loadings
    
    Loadings:
     F1 F2
    mpg 0.858 0.366
    disp -0.873 -0.389
    hp -0.667 -0.673
    wt -1.027 -0.106
    qsec 0.174 0.914
    
     F1 F2
    SS loadings 3.027 1.585
    Proportion Var 0.605 0.317
    Cumulative Var 0.605 0.922
    
    $rotmat
     [,1] [,2]
    [1,] 0.9196708 0.3926902
    [2,] -0.3926902 0.9196708
    
    ?umxSummary showEstimates='raw|std', digits, report= 'html', filter= 'NS' & more
    Running Saturated test with 20 parameters
    Warning: In model 'Saturated test' Optimizer returned a non-zero status code 10. Starting values are not feasible. Consider mxTryHard()
    Error: The job for model 'Saturated test' exited abnormally with the error message: fit is not finite (0: The continuous part of the model implied covariance (loc2) is not positive definite in data 'Saturated test.data' row 16. Detail:
    covariance = matrix(c( # 5x5
     1, 0, 0, 0, 0
    , -1.29736, 0.281657, 0, 0, 0
    , -1.43775, 0.278197, 0.334659, 0, 0
    , -1.3218, 0.223294, -0.143361, 0.141975, 0
    , 0.91373, -0.202747, -0.732047, 0.348551, 0.303857), byrow=TRUE, nrow=5, ncol=5)
    
    )
    Execution halted
Flavor: r-patched-solaris-sparc

Version: 1.7.5
Check: tests
Result: ERROR
     Running ‘testthat.R’ [110s/107s]
    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())
     For an overview type '?umx'
    
     Attaching package: 'umx'
    
     The following object is masked from 'package:stats':
    
     loadings
    
     >
     > test_check("umx")
     Running One Factor with 10 parameters
    
    
     | |x1 |x2 |x3 |x4 |x5 |
     |:--|:----|:-----|:----|:-----|:--|
     |x1 |. |. |0.01 |. |. |
     |x2 |. |. |0.01 |-0.01 |. |
     |x3 |0.01 |0.01 |. |. |. |
     |x4 |. |-0.01 |. |. |. |
     |x5 |. |. |. |. |. |
     [1] "nb: You can zoom in on bad values with, e.g. suppress = .01, which will hide values smaller than this. Use digits = to round"
     'log Lik.' 27287.23 (df=4)
    
    
     | | a1|c1 | e1|
     |:---|----:|:--|----:|
     |wt1 | 0.87|. | 0.49|
     'log Lik.' -11985.57 (df=4)
    
    
     | | a1| c1| e1|
     |:---|----:|----:|----:|
     |ht1 | 0.92| 0.14| 0.36|
     Running m1 with 38 parameters
     Running by_bracket1 with 38 parameters
     Running bylabel with 38 parameters
     Running m1 with 26 parameters
     Running by_bracket with 26 parameters
     Running bylabel with 26 parameters
     Running One Factor with 15 parameters
     Running Saturated One Factor with 20 parameters
     Error: The job for model 'Saturated One Factor' exited abnormally with the error message: fit is not finite (0: The continuous part of the model implied covariance (loc2) is not positive definite in data 'Saturated One Factor.data' row 111. Detail:
     covariance = matrix(c( # 5x5
     0.198544, 0, 0, 0, 0
     , 0.334825, 0.0902381, 0, 0, 0
     , 0.452996, 0.110338, 0.0654995, 0, 0
     , 0.618772, 0.16006, 0.0707545, 0.0681816, 0
     , 0.758898, 0.207326, 0.0838464, 0.0645905, 0.0554296), byrow=TRUE, nrow=5, ncol=5)
    
     )
     In addition: Warning messages:
     1: In model 'One Factor' 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)
     2: In model 'm1' 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)
     3: In model 'by_bracket1' 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)
     4: In model 'bylabel' 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)
     5: In model 'm1' 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)
     6: In model 'by_bracket' 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)
     7: In model 'bylabel' 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)
     8: In model 'One Factor' 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)
     9: In model 'Saturated One Factor' Optimizer returned a non-zero status code 10. Starting values are not feasible. Consider mxTryHard()
     testthat results ================================================================
     OK: 10 SKIPPED: 0 FAILED: 0
     Execution halted
Flavor: r-patched-solaris-sparc

Version: 1.7.5
Flags: --no-stop-on-test-error
Check: examples
Result: ERROR
    Running examples in ‘umx-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: confint.MxModel
    > ### Title: Get confidence intervals from an MxModel
    > ### Aliases: confint.MxModel
    >
    > ### ** Examples
    >
    > require(umx)
    > data(demoOneFactor)
    > latents = c("G")
    > manifests = names(demoOneFactor)
    > m1 <- umxRAM("One Factor", data = mxData(cov(demoOneFactor), type = "cov", numObs = 500),
    + umxPath(from = latents, to = manifests),
    + umxPath(var = manifests),
    + umxPath(var = latents, fixedAt = 1.0)
    + )
    A latent variable 'G' was created.
    ManifestVars set to: x1, x2, x3, x4, x5.
    Running One Factor with 10 parameters
    Warning: In model 'One Factor' 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)
    ?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"
    > m2 = confint(m1, "all") # default: CIs added, but user prompted to set run = TRUE
    Some CIs have been requested, but have not yet been run. Add 'run = TRUE' to your confint() call to run them.
    To store the model run capture it from confint like this:
    m1 = confint(m1, run = TRUE)
    > m2 = confint(m2, run = TRUE) # CIs run and reported
    Running One Factor with 10 parameters
    
     *** caught segfault ***
    address fc11e4a0, cause 'memory not mapped'
    
    Traceback:
     1: runHelper(model, frontendStart, intervals, silent, suppressWarnings, unsafe, checkpoint, useSocket, onlyFrontend, useOptimizer)
     2: mxRun(object, intervals = TRUE)
     3: confint.MxModel(m2, run = TRUE)
     4: confint(m2, run = TRUE)
    An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86

Version: 1.7.5
Flags: --no-stop-on-test-error
Check: tests
Result: ERROR
     Running ‘testthat.R’ [14s/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())
     For an overview type '?umx'
    
     Attaching package: 'umx'
    
     The following object is masked from 'package:stats':
    
     loadings
    
     >
     > test_check("umx")
     Running One Factor with 10 parameters
    
    
     | |x1 |x2 |x3 |x4 |x5 |
     |:--|:----|:-----|:----|:-----|:--|
     |x1 |. |. |0.01 |. |. |
     |x2 |. |. |0.01 |-0.01 |. |
     |x3 |0.01 |0.01 |. |. |. |
     |x4 |. |-0.01 |. |. |. |
     |x5 |. |. |. |. |. |
     [1] "nb: You can zoom in on bad values with, e.g. suppress = .01, which will hide values smaller than this. Use digits = to round"
    
     *** caught segfault ***
     address fc11e4a0, cause 'memory not mapped'
    
     Traceback:
     1: runHelper(model, frontendStart, intervals, silent, suppressWarnings, unsafe, checkpoint, useSocket, onlyFrontend, useOptimizer)
     2: mxRun(model)
     3: umxACE(selDVs = "wt", dzData = dzData, mzData = mzData, sep = "", boundDiag = 0)
     4: eval(code, test_env)
     5: eval(code, test_env)
     6: withCallingHandlers(eval(code, test_env), expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error)
     7: doTryCatch(return(expr), name, parentenv, handler)
     8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
     9: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
     10: doTryCatch(return(expr), name, parentenv, handler)
     11: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], parentenv, handlers[[nh]])
     12: tryCatchList(expr, classes, parentenv, handlers)
     13: tryCatch(withCallingHandlers(eval(code, test_env), expectation = handle_expectation, skip = handle_skip, warning = handle_warning, message = handle_message, error = handle_error), error = function(e) {}, skip = function(e) {})
     14: test_code(desc, code, env = parent.frame())
     15: test_that("umxACE works", { data(twinData) mzData <- twinData[twinData$zygosity %in% "MZFF", ] dzData <- twinData[twinData$zygosity %in% "DZFF", ] m1 = umxACE(selDVs = "wt", dzData = dzData, mzData = mzData, sep = "", boundDiag = 0) expect_error({ m1 = umxACE(selDVs = "wt", dzData = dzData, mzData = mzData, sep = "", boundDiag = TRUE) }) m1 = umxACE(selDVs = "ht", dzData = dzData, mzData = mzData, sep = "") expect_lt(as.numeric(logLik(m1)), 5992.784)})
     16: eval(exprs, env)
     17: eval(exprs, env)
     18: source_file(path, new.env(parent = env), chdir = TRUE)
     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) end_context() })
     21: FUN(X[[i]], ...)
     22: lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE)
     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))
     25: test_files(paths, reporter = reporter, env = env, ...)
     26: test_dir(test_path, reporter = reporter, env = env, filter = filter, ...)
     27: with_top_env(env, { test_dir(test_path, reporter = reporter, env = env, filter = filter, ...)})
     28: run_tests(package, test_path, filter, reporter, ...)
     29: test_check("umx")
     An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86

Version: 1.7.5
Check: examples
Result: ERROR
    Running examples in ‘umx-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: logLik.MxModel
    > ### Title: logLik.MxModel
    > ### Aliases: logLik.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-release-osx-x86_64

Version: 1.7.5
Check: tests
Result: ERROR
     Running ‘testthat.R’ [5s/5s]
    Running the tests in ‘tests/testthat.R’ failed.
    Last 13 lines of output:
     Attaching package: 'umx'
    
     The following object is masked from 'package:stats':
    
     loadings
    
     >
     > test_check("umx")
     Running One Factor with 10 parameters
     Error in runHelper(model, frontendStart, intervals, silent, suppressWarnings, :
     c++ exception (unknown reason)
     Calls: test_check ... eval -> eval -> umxRun -> mxRun -> runHelper -> .Call
     testthat results ================================================================
     OK: 0 SKIPPED: 0 FAILED: 0
     Execution halted
Flavor: r-release-osx-x86_64