CRAN Package Check Results for Package OpenMx

Last updated on 2020-07-02 12:49:31 CEST.

Flavor Version Tinstall Tcheck Ttotal Status Flags
r-devel-linux-x86_64-debian-clang 2.17.4 1234.42 353.08 1587.50 OK
r-devel-linux-x86_64-debian-gcc 2.17.4 1049.01 290.25 1339.26 OK
r-devel-linux-x86_64-fedora-clang 2.17.4 2362.81 NOTE
r-devel-linux-x86_64-fedora-gcc 2.17.4 2149.46 OK
r-devel-windows-ix86+x86_64 2.17.4 2553.00 653.00 3206.00 NOTE
r-patched-linux-x86_64 2.17.4 1096.95 368.82 1465.77 OK
r-patched-solaris-x86 2.17.4 1532.50 ERROR
r-release-linux-x86_64 2.17.4 1098.36 377.60 1475.96 OK
r-release-osx-x86_64 2.17.4 NOTE
r-release-windows-ix86+x86_64 2.17.4 1909.00 502.00 2411.00 NOTE
r-oldrel-osx-x86_64 2.17.4 NOTE
r-oldrel-windows-ix86+x86_64 2.17.4 2279.00 561.00 2840.00 NOTE

Additional issues

rchk

Check Details

Version: 2.17.4
Check: installed package size
Result: NOTE
     installed size is 220.5Mb
     sub-directories of 1Mb or more:
     R 2.5Mb
     libs 210.4Mb
     models 4.7Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-patched-solaris-x86, r-release-osx-x86_64, r-release-windows-ix86+x86_64, r-oldrel-osx-x86_64, r-oldrel-windows-ix86+x86_64

Version: 2.17.4
Check: Rd cross-references
Result: NOTE
    Undeclared packages ‘ifaTools’, ‘umx’ in Rd xrefs
Flavor: r-devel-linux-x86_64-fedora-clang

Version: 2.17.4
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 270767252 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: 2.17.4
Check: tests
Result: ERROR
     Running ‘testthat.R’ [63s/73s]
    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-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)
    
     Error: C stack usage 279221396 is too close to the limit
     ── 2. Error: (unknown) (@test-cor.R#29) ───────────────────────────────────────
     The job for model 'L' exited abnormally with the error message: User interrupt
     Backtrace:
     1. OpenMx::mxRun(fl)
     2. OpenMx:::runHelper(...)
     3. OpenMx:::processErrorConditions(model, unsafe, suppressWarnings)
    
     Error: C stack usage 279221396 is too close to the limit
     ── 3. Error: (unknown) (@test-gendata-multilevel.R#34) ────────────────────────
     The job for model 'yield' exited abnormally with the error message: User interrupt
     Backtrace:
     1. OpenMx::mxRun(yield, silent = TRUE)
     2. OpenMx:::runHelper(...)
     3. OpenMx:::processErrorConditions(model, unsafe, suppressWarnings)
    
     ── 4. Failure: (unknown) (@test-ifa-drm1.R#50) ────────────────────────────────
     `a` not equivalent to `b`.
     1/1 mismatches
     [1] 10000 - 5000 == 5000
    
     ── 5. Failure: (unknown) (@test-ifa-drm1.R#51) ────────────────────────────────
     `a` not equivalent to `b`.
     3/5 mismatches (average diff: 27.1)
     [3] 0.138 - 0.0688 == 0.0688
     [4] 14.316 - 7.1582 == 7.1582
     [5] 148.317 - 74.1583 == 74.1583
    
     ── 6. Failure: (unknown) (@test-ifa-drm1.R#57) ────────────────────────────────
     `a` not equivalent to `b`.
     20/20 mismatches (average diff: 250)
     [1] 163 - 326 == -163
     [2] 337 - 674 == -337
     [3] 119 - 238 == -119
     [4] 381 - 762 == -381
     [5] 221 - 442 == -221
     [6] 279 - 558 == -279
     [7] 228 - 456 == -228
     [8] 272 - 544 == -272
     [9] 289 - 578 == -289
     ...
    
     ── 7. Failure: (unknown) (@test-ifa-drm1.R#66) ────────────────────────────────
     `a` not equivalent to `b`.
     1/1 mismatches
     [1] 12887 - 6444 == 6444
    
     ── 8. Failure: (unknown) (@test-ifa-drm1.R#67) ────────────────────────────────
     `a` not equivalent to `b`.
     5/5 mismatches (average diff: 337)
     [1] -1024.3 - -256.1 == -768.2
     [2] -66.4 - -16.6 == -49.8
     [3] 85.6 - 21.4 == 64.2
     [4] 206.5 - 51.6 == 154.9
     [5] 863.7 - 215.9 == 647.8
    
     ── 9. Failure: (unknown) (@test-ifa-drm1.R#68) ────────────────────────────────
     `a` not equivalent to `b`.
     5/5 mismatches (average diff: 285)
     [1] 52.5 - 13.1 == 39.4
     [2] 52.5 - 13.1 == 39.4
     [3] 263.8 - 66.0 == 197.9
     [4] 668.4 - 167.1 == 501.3
     [5] 861.7 - 215.4 == 646.3
    
     ── 10. Failure: (unknown) (@test-ifa-drm1.R#88) ───────────────────────────────
     `a` not equivalent to `b`.
     1/1 mismatches
     [1] 6588 - 0 == 6588
    
     ── 11. Failure: (unknown) (@test-ifa-drm1.R#92) ───────────────────────────────
     `a` not equivalent to `b`.
     1/1 mismatches
     [1] 36 - 10 == 26
    
     ── 12. Failure: (unknown) (@test-ifa-drm1.R#93) ───────────────────────────────
     `a` not equivalent to `b`.
     1/1 mismatches
     [1] 69 - 33 == 36
    
     ── 13. Failure: (unknown) (@test-ifa-drm1.R#94) ───────────────────────────────
     `a` not equivalent to `b`.
     1/1 mismatches
     [1] 180 - 59 == 121
    
     ── 14. Failure: (unknown) (@test-ifa-drm1.R#99) ───────────────────────────────
     `a` not equivalent to `b`.
     1/1 mismatches
     [1] 12433 - 6216 == 6216
    
     ── 15. Failure: (unknown) (@test-ifa-drm1.R#100) ──────────────────────────────
     `a` not equivalent to `b`.
     1/1 mismatches
     [1] 12473 - 6256 == 6216
    
     ── 16. Failure: (unknown) (@test-ifa-drm1.R#101) ──────────────────────────────
     `a` not equivalent to `b`.
     1/1 mismatches
     [1] 12557 - 6341 == 6216
    
     ── 17. Failure: (unknown) (@test-ifa-drm1.R#120) ──────────────────────────────
     `a` not equivalent to `b`.
     1/1 mismatches
     [1] 12764 - 6382 == 6382
    
     ── 18. Failure: (unknown) (@test-ifa-drm1.R#121) ──────────────────────────────
     `a` not equivalent to `b`.
     1/1 mismatches
     [1] 12784 - 6402 == 6382
    
     ── 19. Failure: (unknown) (@test-ifa-drm1.R#122) ──────────────────────────────
     `a` not equivalent to `b`.
     1/1 mismatches
     [1] 12827 - 6444 == 6382
    
     ── 20. Failure: (unknown) (@test-ifa-drm1.R#141) ──────────────────────────────
     `a` not equivalent to `b`.
     5/5 mismatches (average diff: 95.4)
     [1] -474 - 0.678 == -475.013
     [2] 0 - 0.285 == -0.285
     [3] 0 - -0.344 == 0.344
     [4] 0 - -0.103 == 0.103
     [5] 0 - -1.082 == 1.082
    
     ── 21. Failure: (unknown) (@test-ifa-drm1.R#142) ──────────────────────────────
     `a` not equivalent to `b`.
     5/5 mismatches (average diff: 0.668)
     [1] NaN - 0.677 == NaN
     [2] 0 - 0.667 == -0.667
     [3] 0 - 0.663 == -0.663
     [4] 0 - 0.662 == -0.662
     [5] 0 - 0.680 == -0.680
    
     ── 22. Error: (unknown) (@test-ifa-drm1.R#143) ────────────────────────────────
     missing value where TRUE/FALSE needed
     Backtrace:
     1. OpenMx::omxCheckCloseEnough(...)
     2. testthat::expect_equivalent(...)
     4. testthat:::compare.numeric(act$val, exp$val, ..., check.attributes = FALSE)
     6. base::all.equal.numeric(...)
    
     Error: C stack usage 279221364 is too close to the limit
     ── 23. Error: (unknown) (@test-loadDataByCol.R#67) ────────────────────────────
     The job for model 'loadData' exited abnormally with the error message: User interrupt
     Backtrace:
     1. OpenMx::mxRun(model2)
     2. OpenMx:::runHelper(...)
     3. OpenMx:::processErrorConditions(model, unsafe, suppressWarnings)
    
     Error: C stack usage 279221364 is too close to the limit
     ── 24. Error: (unknown) (@test-loadDataByRow.R#66) ────────────────────────────
     The job for model 'loadData' exited abnormally with the error message: User interrupt
     Backtrace:
     1. OpenMx::mxRun(model2)
     2. OpenMx:::runHelper(...)
     3. OpenMx:::processErrorConditions(model, unsafe, suppressWarnings)
    
     Error: C stack usage 279221396 is too close to the limit
     ── 25. Error: (unknown) (@test-mxSE.R#23) ─────────────────────────────────────
     The job for model 'one_is_the_loneliest_number' exited abnormally with the error message: User interrupt
     Backtrace:
     1. OpenMx::mxRun(m1)
     2. OpenMx:::runHelper(...)
     3. OpenMx:::processErrorConditions(model, unsafe, suppressWarnings)
    
     Error: C stack usage 279221396 is too close to the limit
     ── 26. Error: (unknown) (@test-mxsave.R#47) ───────────────────────────────────
     The job for model 'testFish' exited abnormally with the error message: User interrupt
     Backtrace:
     1. OpenMx::mxRun(testModel, checkpoint = TRUE)
     2. OpenMx:::runHelper(...)
     3. OpenMx:::processErrorConditions(model, unsafe, suppressWarnings)
    
     ── 27. Error: (unknown) (@test-naAction.R#16) ─────────────────────────────────
     no 'dimnames' attribute for array
     Backtrace:
     1. OpenMx::mxModel(...)
     3. OpenMx::imxModelBuilder(...)
     4. OpenMx:::listArgumentLISREL(model, lst, remove)
     5. OpenMx:::addEntriesLISREL(model, lst)
     6. OpenMx:::insertAllPathsLISREL(model, paths)
     7. OpenMx:::insertMeansPathLISREL(...)
    
     Error: C stack usage 279221364 is too close to the limit
     ── 28. Error: (unknown) (@test-npdWarningWLS.R#44) ────────────────────────────
     The job for model 'fake' exited abnormally with the error message: User interrupt
     Backtrace:
     1. OpenMx::omxCheckWarning(...)
     7. OpenMx::omxAugmentDataWithWLSSummary(...)
     8. OpenMx::mxRun(fake, silent = silent)
     9. OpenMx:::runHelper(...)
     10. OpenMx:::processErrorConditions(model, unsafe, suppressWarnings)
    
     Error: C stack usage 279221396 is too close to the limit
     ── 29. Error: (unknown) (@test-simplestCI.R#41) ───────────────────────────────
     The job for model 'CIExample' exited abnormally with the error message: User interrupt
     Backtrace:
     1. OpenMx::mxRun(model, silent = TRUE)
     2. OpenMx:::runHelper(...)
     3. OpenMx:::processErrorConditions(model, unsafe, suppressWarnings)
    
     Error: C stack usage 279221364 is too close to the limit
     ── 30. Failure: (unknown) (@test-wls-binary.R#43) ─────────────────────────────
     `mxRun(wlsTest4)` threw an error with unexpected message.
     Expected match: "correlated gradients: [3,1]"
     Actual message: "The job for model 'GWAS' exited abnormally with the error message: User interrupt"
     Backtrace:
     1. testthat::expect_error(...)
     6. OpenMx::mxRun(wlsTest4)
     7. OpenMx:::runHelper(...)
     8. OpenMx:::processErrorConditions(model, unsafe, suppressWarnings)
    
     ══ testthat results ═══════════════════════════════════════════════════════════
     [ OK: 436 | SKIPPED: 4 | WARNINGS: 2 | FAILED: 30 ]
     1. Error: (unknown) (@test-GREML_Error_Detection.R#75)
     2. Error: (unknown) (@test-cor.R#29)
     3. Error: (unknown) (@test-gendata-multilevel.R#34)
     4. Failure: (unknown) (@test-ifa-drm1.R#50)
     5. Failure: (unknown) (@test-ifa-drm1.R#51)
     6. Failure: (unknown) (@test-ifa-drm1.R#57)
     7. Failure: (unknown) (@test-ifa-drm1.R#66)
     8. Failure: (unknown) (@test-ifa-drm1.R#67)
     9. Failure: (unknown) (@test-ifa-drm1.R#68)
     1. ...
    
     Error: testthat unit tests failed
     Execution halted
Flavor: r-patched-solaris-x86

Version: 2.17.4
Check: package dependencies
Result: NOTE
    Package suggested but not available for checking: ‘Rmpi’
Flavors: r-release-osx-x86_64, r-oldrel-osx-x86_64