Last updated on 2020-08-07 01:49:54 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 2.17.4 | 1242.71 | 351.76 | 1594.47 | OK | |
| r-devel-linux-x86_64-debian-gcc | 2.17.4 | 1042.95 | 288.06 | 1331.01 | OK | |
| r-devel-linux-x86_64-fedora-clang | 2.17.4 | 2190.58 | NOTE | |||
| r-devel-linux-x86_64-fedora-gcc | 2.17.4 | 2162.99 | OK | |||
| r-devel-windows-ix86+x86_64 | 2.17.4 | 2616.00 | 510.00 | 3126.00 | NOTE | |
| r-patched-linux-x86_64 | 2.17.4 | 1105.66 | 372.60 | 1478.26 | OK | |
| r-patched-solaris-x86 | 2.17.4 | 1530.00 | ERROR | |||
| r-release-linux-x86_64 | 2.17.4 | 1084.64 | 375.95 | 1460.59 | OK | |
| r-release-macos-x86_64 | 2.17.4 | NOTE | ||||
| r-release-windows-ix86+x86_64 | 2.17.4 | 2555.00 | 650.00 | 3205.00 | NOTE | |
| r-oldrel-macos-x86_64 | 2.17.4 | NOTE | ||||
| r-oldrel-windows-ix86+x86_64 | 2.17.4 | 1797.00 | 434.00 | 2231.00 | NOTE |
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-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-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
*** caught segfault ***
address 0, cause 'memory not mapped'
Flavor: r-patched-solaris-x86
Version: 2.17.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [66s/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] 1.1e+18 - 0 == 1.1e+18
── 11. Failure: (unknown) (@test-ifa-drm1.R#89) ───────────────────────────────
m2$output$status$code not equivalent to 0.
1/1 mismatches
[1] 6 - 0 == 6
── 12. Failure: (unknown) (@test-ifa-drm1.R#92) ───────────────────────────────
`a` not equivalent to `b`.
1/1 mismatches
[1] 212 - 10 == 202
── 13. Failure: (unknown) (@test-ifa-drm1.R#93) ───────────────────────────────
`a` not equivalent to `b`.
1/1 mismatches
[1] 334 - 33 == 301
── 14. Failure: (unknown) (@test-ifa-drm1.R#94) ───────────────────────────────
`a` not equivalent to `b`.
1/1 mismatches
[1] 936 - 59 == 877
── 15. Failure: (unknown) (@test-ifa-drm1.R#99) ───────────────────────────────
`a` not equivalent to `b`.
1/1 mismatches
[1] 27195 - 6216 == 20979
── 16. Failure: (unknown) (@test-ifa-drm1.R#100) ──────────────────────────────
`a` not equivalent to `b`.
1/1 mismatches
[1] 27235 - 6256 == 20979
── 17. Failure: (unknown) (@test-ifa-drm1.R#101) ──────────────────────────────
`a` not equivalent to `b`.
1/1 mismatches
[1] 27319 - 6341 == 20979
── 18. Failure: (unknown) (@test-ifa-drm1.R#120) ──────────────────────────────
`a` not equivalent to `b`.
1/1 mismatches
[1] 24045 - 6382 == 17662
── 19. Failure: (unknown) (@test-ifa-drm1.R#121) ──────────────────────────────
`a` not equivalent to `b`.
1/1 mismatches
[1] 24065 - 6402 == 17662
── 20. Failure: (unknown) (@test-ifa-drm1.R#122) ──────────────────────────────
`a` not equivalent to `b`.
1/1 mismatches
[1] 24107 - 6444 == 17662
── 21. Failure: (unknown) (@test-ifa-drm1.R#126) ──────────────────────────────
`a` not equivalent to `b`.
1/1 mismatches
[1] 0.313 - 0.988 == -0.675
── 22. Failure: (unknown) (@test-ifa-drm1.R#141) ──────────────────────────────
`a` not equivalent to `b`.
5/5 mismatches (average diff: 5)
[1] -0.627 - 0.678 == -1.306
[2] -21.903 - 0.285 == -22.188
[3] 0.000 - -0.344 == 0.344
[4] 0.000 - -0.103 == 0.103
[5] 0.000 - -1.082 == 1.082
── 23. 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] NaN - 0.667 == NaN
[3] 0 - 0.663 == -0.663
[4] 0 - 0.662 == -0.662
[5] 0 - 0.680 == -0.680
── 24. 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
── 25. 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
── 26. 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
── 27. 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
── 28. 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)
── 29. 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
── 30. 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
── 31. 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
── 32. 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: 434 | SKIPPED: 4 | WARNINGS: 3 | FAILED: 32 ]
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: for non-standard things in the check directory
Result: NOTE
Found the following files/directories:
‘core’
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-macos-x86_64, r-oldrel-macos-x86_64