CRAN Package Check Results for Package OpenMx

Last updated on 2020-09-24 04:57:25 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.18.1 1247.09 428.93 1676.02 OK
r-devel-linux-x86_64-debian-gcc 2.18.1 1051.87 344.70 1396.57 OK
r-devel-linux-x86_64-fedora-clang 2.18.1 2335.26 NOTE
r-devel-linux-x86_64-fedora-gcc 2.18.1 2306.27 OK
r-devel-windows-ix86+x86_64 2.18.1 2500.00 714.00 3214.00 NOTE
r-patched-linux-x86_64 2.18.1 1094.91 435.56 1530.47 OK
r-patched-solaris-x86 2.18.1 1523.50 ERROR
r-release-linux-x86_64 2.18.1 1119.31 436.27 1555.58 OK
r-release-macos-x86_64 2.18.1 NOTE
r-release-windows-ix86+x86_64 2.18.1 2128.00 755.00 2883.00 NOTE
r-oldrel-macos-x86_64 2.18.1 NOTE
r-oldrel-windows-ix86+x86_64 2.18.1 1778.00 521.00 2299.00 ERROR

Additional issues

clang-UBSAN rchk

Check Details

Version: 2.18.1
Check: installed package size
Result: NOTE
     installed size is 222.4Mb
     sub-directories of 1Mb or more:
     R 2.5Mb
     libs 212.2Mb
     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 271094932 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’ [54s/88s]
    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
     ── 1. Error: (unknown) (@test-DataErrorDetection.R#57) ────────────────────────
     The job for model 'untitled17' exited abnormally with the error message: User interrupt
     Backtrace:
     1. OpenMx::mxRun(model)
     2. OpenMx:::runHelper(...)
     3. OpenMx:::processErrorConditions(model, unsafe, suppressWarnings)
    
     Error: C stack usage 279221396 is too close to the limit
     ── 2. Error: (unknown) (@test-GREML_Error_Detection.R#75) ─────────────────────
     The job for model 'GREMLtest' exited abnormally with the error message: User interrupt
     Backtrace:
     1. OpenMx::omxCheckWarning(...)
     7. OpenMx::mxRun(testmod, suppressWarnings = TRUE)
     8. OpenMx:::runHelper(...)
     9. OpenMx:::processErrorConditions(model, unsafe, suppressWarnings)
    
     ── 3. Error: (unknown) (@test-LegacyMultipleGroupWLS.R#67) ────────────────────
     The job for model 'group' exited abnormally with the error message: Non-conformable matrices 'auto1.expCov[1]' 0x0 and 'auto1.expCov[2]' 2x2 in matrix multiply
     Backtrace:
     1. OpenMx::mxAutoStart(autGroup)
     2. OpenMx::mxRun(omxBuildAutoStartModel(model, type), silent = TRUE)
     3. OpenMx:::runHelper(...)
     4. OpenMx:::processErrorConditions(model, unsafe, suppressWarnings)
    
    
     *** 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, new.env(parent = env), chdir = TRUE, wrap = wrap)
     15: force(code)
     16: doWithOneRestart(return(expr), restart)
     17: withOneRestart(expr, restarts[[1L]])
     18: withRestarts(testthat_abort_reporter = function() NULL, force(code))
     19: 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() })
     20: FUN(X[[i]], ...)
     21: lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
     22: force(code)
     23: doWithOneRestart(return(expr), restart)
     24: withOneRestart(expr, restarts[[1L]])
     25: withRestarts(testthat_abort_reporter = function() NULL, force(code))
     26: with_reporter(reporter = current_reporter, results <- lapply(paths, test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap))
     27: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning, wrap = wrap)
     28: 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)
     29: 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)
     30: 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' [92s]
    Running the tests in 'tests/testthat.R' failed.
    Complete output:
     > library(testthat)
     > library(OpenMx)
     >
     > test_check("OpenMx")
     -- 1. Failure: mediation (@test-discrete.R#203) -------------------------------
     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
    
     [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
     == testthat results ===========================================================
     [ OK: 623 | SKIPPED: 6 | WARNINGS: 2 | FAILED: 1 ]
     1. Failure: mediation (@test-discrete.R#203)
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-oldrel-windows-ix86+x86_64