CRAN Package Check Results for Package OpenMx

Last updated on 2021-02-27 23:50:45 CET.

Additional issues

clang-UBSAN M1mac rchk

Check Details

Version: 2.18.1
Check: installed package size
Result: NOTE
     installed size is 218.8Mb
     sub-directories of 1Mb or more:
     R 2.5Mb
     libs 208.6Mb
     models 4.7Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-patched-solaris-x86, r-release-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.18.1
Check: Rd cross-references
Result: NOTE
    Undeclared packages ‘ifaTools’, ‘umx’ in Rd xrefs
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 2.18.1
Check: examples
Result: ERROR
    Running examples in ‘OpenMx-Ex.R’ failed
    The error most likely occurred in:
    
    > ### Name: mxModelAverage
    > ### Title: Information-Theoretic Model-Averaging and Multimodel Inference
    > ### Aliases: mxModelAverage omxAkaikeWeights omxAICWeights
    >
    > ### ** Examples
    >
    > require(OpenMx)
    > data(demoOneFactor)
    > factorModel1 <- mxModel(
    + "OneFactor1",
    + mxMatrix(
    + "Full", 5, 1, values=0.8,
    + labels=paste("a",1:5,sep=""),
    + free=TRUE, name="A"),
    + mxMatrix(
    + "Full", 5, 1, values=1,
    + labels=paste("u",1:5,sep=""),
    + free=TRUE, name="Udiag"),
    + mxMatrix(
    + "Symm", 1, 1, values=1,
    + free=FALSE, name="L"),
    + mxAlgebra(vec2diag(Udiag),name="U"),
    + mxAlgebra(A %*% L %*% t(A) + U, name="R"),
    + mxExpectationNormal(
    + covariance = "R",
    + dimnames = names(demoOneFactor)),
    + mxFitFunctionML(),
    + mxData(cov(demoOneFactor), type="cov", numObs=500))
    > factorFit1 <- mxRun(factorModel1)
    Running OneFactor1 with 10 parameters
    Error: C stack usage 271029396 is too close to the limit
    Error: The job for model 'OneFactor1' exited abnormally with the error message: User interrupt
    Execution halted
Flavor: r-patched-solaris-x86

Version: 2.18.1
Check: tests
Result: ERROR
     Running ‘testthat.R’ [52s/83s]
    Running the tests in ‘tests/testthat.R’ failed.
    Complete output:
     > library(testthat)
     > library(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)
     >
     > test_check("OpenMx")
     Error: C stack usage 279221396 is too close to the limit
    
     *** caught segfault ***
     address 0, cause 'memory not mapped'
    
     Traceback:
     1: runHelper(model, frontendStart, intervals, silent, suppressWarnings, unsafe, checkpoint, useSocket, onlyFrontend, useOptimizer, beginMessage)
     2: mxRun(m1)
     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, child_env(env), wrap = wrap)
     15: FUN(X[[i]], ...)
     16: lapply(test_paths, test_one_file, env = env, wrap = wrap)
     17: force(code)
     18: doWithOneRestart(return(expr), restart)
     19: withOneRestart(expr, restarts[[1L]])
     20: withRestarts(testthat_abort_reporter = function() NULL, force(code))
     21: with_reporter(reporters$multi, lapply(test_paths, test_one_file, env = env, wrap = wrap))
     22: test_files(test_dir = test_dir, test_package = test_package, test_paths = test_paths, load_helpers = load_helpers, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap, load_package = load_package)
     23: test_files(test_dir = path, test_paths = test_paths, test_package = package, reporter = reporter, load_helpers = load_helpers, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap, load_package = load_package, parallel = parallel)
     24: test_dir("testthat", package = package, reporter = reporter, ..., load_package = "installed")
     25: test_check("OpenMx")
     An irrecoverable exception occurred. R is aborting now ...
Flavor: r-patched-solaris-x86

Version: 2.18.1
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘Rmpi’
Flavors: r-release-macos-x86_64, r-oldrel-macos-x86_64

Version: 2.18.1
Check: running tests for arch ‘i386’
Result: ERROR
     Running 'testthat.R' [115s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(OpenMx)
     >
     > test_check("OpenMx")
     [1] 1 33 34 40 54 55 81 83 97 104 105 111 113 135 142 145 160 161 188
     [20] 193 196 209 212 230 241 261
     == Skipped tests ===============================================================
     * .Platform$OS.type == "windows" && .Platform$r_arch == "i386" is TRUE (1)
     * On CRAN (3)
     * empty test (1)
     * imxHasOpenMP() is not TRUE (1)
    
     == Warnings ====================================================================
     -- Warning (test-cor.R:31:1): (code run outside of `test_that()`) --------------
     In model 'Both' 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)
     Backtrace:
     1. OpenMx::mxRun(mg) test-cor.R:31:0
     2. OpenMx:::runHelper(...)
     3. OpenMx:::processErrorConditions(model, unsafe, suppressWarnings)
     4. OpenMx:::npsolWarnings(...)
     -- Warning (test-discrete.R:85:3): Normal --------------------------------------
     In model 'One Factor' 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).
     Backtrace:
     1. OpenMx::mxRun(factorModel) test-discrete.R:85:2
     2. OpenMx:::runHelper(...)
     3. OpenMx:::processErrorConditions(model, unsafe, suppressWarnings)
     4. OpenMx:::npsolWarnings(...)
    
     == Failed tests ================================================================
     -- Failure (test-discrete.R:203:3): mediation ----------------------------------
     fit$Discrete$values not equivalent to c(zif, size, prob).
     2/3 mismatches (average diff: 0.0892)
     [1] 0.360 - 0.3 == 0.0596
     [2] 0.619 - 0.5 == 0.1187
    
     [ FAIL 1 | WARN 2 | SKIP 6 | PASS 623 ]
     Error: Test failures
     Execution halted
Flavor: r-oldrel-windows-ix86+x86_64