Last updated on 2020-08-07 01:50:23 CEST.
| Package | FAIL | ERROR | NOTE | OK |
|---|---|---|---|---|
| gwsem | 1 | 6 | 5 | |
| ifaTools | 1 | 11 | ||
| OpenMx | 1 | 6 | 5 | |
| pcFactorStan | 1 | 2 | 9 | |
| rpf | 1 | 3 | 8 |
Current CRAN status: ERROR: 1, NOTE: 6, OK: 5
Version: 2.0.5
Check: installed package size
Result: NOTE
installed size is 14.2Mb
sub-directories of 1Mb or more:
libs 12.5Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-devel-windows-ix86+x86_64, r-release-macos-x86_64, r-release-windows-ix86+x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64
Version: 2.0.5
Check: tests
Result: ERROR
Running ‘testthat.R’ [13s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(gwsem)
Loading required package: 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("gwsem")
Error: C stack usage 273650804 is too close to the limit
── 1. Error: (unknown) (@test-covariate.R#36) ─────────────────────────────────
This model has 5 matrices, but the backend has returned 0 values
Backtrace:
1. gwsem::GWAS(...)
2. OpenMx::mxRun(model)
3. OpenMx:::runHelper(...)
4. OpenMx:::updateModelMatrices(model, flatModel, output$matrices)
Error: C stack usage 273650804 is too close to the limit
── 2. Error: (unknown) (@test-formats.R#24) ───────────────────────────────────
This model has 4 matrices, but the backend has returned 0 values
Backtrace:
1. gwsem::GWAS(...)
2. OpenMx::mxRun(model)
3. OpenMx:::runHelper(...)
4. OpenMx:::updateModelMatrices(model, flatModel, output$matrices)
Error: C stack usage 273650804 is too close to the limit
── 3. Error: gxe data roundtrip (@test-gxe.R#36) ──────────────────────────────
This model has 7 matrices, but the backend has returned 0 values
Backtrace:
1. gwsem::GWAS(...)
2. OpenMx::mxRun(model)
3. OpenMx:::runHelper(...)
4. OpenMx:::updateModelMatrices(model, flatModel, output$matrices)
── 4. Error: (unknown) (@test-model.R#75) ─────────────────────────────────────
incompatible dimensions
Backtrace:
1. testthat::expect_equal(cor(ml$P, pgen$P), 1, tolerance = 0.001)
4. stats::cor(ml$P, pgen$P)
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 16 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 4 ]
1. Error: (unknown) (@test-covariate.R#36)
2. Error: (unknown) (@test-formats.R#24)
3. Error: gxe data roundtrip (@test-gxe.R#36)
4. Error: (unknown) (@test-model.R#75)
Error: testthat unit tests failed
Execution halted
Flavor: r-patched-solaris-x86
Current CRAN status: ERROR: 1, OK: 11
Version: 0.21
Check: examples
Result: ERROR
Running examples in ‘ifaTools-Ex.R’ failed
The error most likely occurred in:
> ### Name: univariatePrior
> ### Title: Univariate priors commonly used in IFA models
> ### Aliases: univariatePrior
>
> ### ** Examples
>
> model <- univariatePrior("logit-norm", "x1", -1)
> model$priorParam$values[1,1] <- -.6
> model <- mxRun(model)
Running univariatePrior with 1 parameter
Error: C stack usage 308581524 is too close to the limit
Error: The job for model 'univariatePrior' exited abnormally with the error message: User interrupt
Execution halted
Flavor: r-patched-solaris-x86
Version: 0.21
Check: tests
Result: ERROR
Running ‘testthat.R’ [310s/205s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> # NOTE: This will not test an uninstalled package.
> library(testthat)
> test_check('ifaTools')
Loading required package: ifaTools
Loading required package: shiny
Loading required package: ggplot2
Loading required package: reshape2
Loading required package: rpf
Loading required package: parallel
Loading required package: OpenMx
To take full advantage of multiple cores, use:
mxOption(key='Number of Threads', value=parallel::detectCores()) #now
Sys.setenv(OMP_NUM_THREADS=parallel::detectCores()) #before library(OpenMx)
Welcome to ifaTools!
Use itemModelExplorer() to explore item models.
Use modelBuilder() to build an IFA model.
── 1. Failure: addExploratoryFactors (@test-addExploratoryFactor.R#84) ────────
m1p$output$fit not equal to 33454.39.
1/1 mismatches
[1] 66904 - 33454 == 33450
── 2. Failure: addExploratoryFactors (@test-addExploratoryFactor.R#96) ────────
m2p$output$fit not equal to 33338.99.
1/1 mismatches
[1] 66233 - 33339 == 32894
Error: C stack usage 308581524 is too close to the limit
── 3. Error: univariatePrior (@test-prior.R#24) ───────────────────────────────
The job for model 'univariatePrior' exited abnormally with the error message: User interrupt
Backtrace:
1. ifaTools:::checkAnalyticDeriv(...)
2. OpenMx::mxRun(...)
3. OpenMx:::runHelper(...)
4. OpenMx:::processErrorConditions(model, unsafe, suppressWarnings)
Error: C stack usage 308581524 is too close to the limit
── 4. Error: uniquenessPrior (@test-prior.R#54) ───────────────────────────────
The job for model 'test' exited abnormally with the error message: User interrupt
Backtrace:
1. ifaTools:::checkAnalyticDeriv(omxAssignFirstParameters(m1))
2. OpenMx::mxRun(...)
3. OpenMx:::runHelper(...)
4. OpenMx:::processErrorConditions(model, unsafe, suppressWarnings)
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 0 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 4 ]
1. Failure: addExploratoryFactors (@test-addExploratoryFactor.R#84)
2. Failure: addExploratoryFactors (@test-addExploratoryFactor.R#96)
3. Error: univariatePrior (@test-prior.R#24)
4. Error: uniquenessPrior (@test-prior.R#54)
Error: testthat unit tests failed
Execution halted
Flavor: r-patched-solaris-x86
Version: 0.21
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘pritikin-schmidt.Rnw’ using knitr
Quitting from lines 1347-1404 (pritikin-schmidt.Rnw)
Error: processing vignette 'pritikin-schmidt.Rnw' failed with diagnostics:
Fit not achieved
--- failed re-building ‘pritikin-schmidt.Rnw’
SUMMARY: processing the following file failed:
‘pritikin-schmidt.Rnw’
Error: Vignette re-building failed.
Execution halted
Flavor: r-patched-solaris-x86
Current CRAN status: ERROR: 1, NOTE: 6, OK: 5
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
Current CRAN status: FAIL: 1, ERROR: 2, NOTE: 9
Version: 1.5.1
Check: for GNU extensions in Makefiles
Result: NOTE
GNU make is a SystemRequirements.
Flavors: r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-patched-linux-x86_64, r-patched-solaris-x86, r-release-linux-x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64
Version: 1.5.1
Check: installed package size
Result: NOTE
installed size is 172.8Mb
sub-directories of 1Mb or more:
doc 2.9Mb
libs 169.3Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-patched-solaris-x86, r-release-macos-x86_64, r-oldrel-macos-x86_64, r-oldrel-windows-ix86+x86_64
Version: 1.5.1
Check: whether package can be installed
Result: ERROR
Installation failed.
Flavors: r-devel-windows-ix86+x86_64, r-release-windows-ix86+x86_64
Version: 1.5.1
Check: foreign function calls
Result: FAIL
Flavor: r-release-macos-x86_64
Current CRAN status: ERROR: 1, NOTE: 3, OK: 8
Version: 1.0.4
Check: installed package size
Result: NOTE
installed size is 22.7Mb
sub-directories of 1Mb or more:
libs 21.7Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-release-macos-x86_64, r-oldrel-macos-x86_64
Version: 1.0.4
Check: tests
Result: ERROR
Running ‘testthat.R’ [15s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
> library(testthat)
> library(rpf)
Loading required package: parallel
>
> test_check("rpf")
── 1. Failure: EAPscores (@test-weightColumn.R#40) ────────────────────────────
grp1$score[, 1] not equal to grp2$score[, 1].
754/1000 mismatches (average diff: 3.02)
[1] -0.554 - -1.725 == 1.1711
[2] -0.554 - 0.000 == -0.5540
[3] -0.554 - 0.978 == -1.5324
[4] -0.719 - 4.044 == -4.7627
[5] -0.719 - 5.019 == -5.7373
[6] -0.719 - -1.207 == 0.4885
[7] -0.719 - 0.000 == -0.7188
[8] -0.719 - -0.718 == -0.0005
[9] -0.719 - 0.000 == -0.7188
...
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 401 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
1. Failure: EAPscores (@test-weightColumn.R#40)
Error: testthat unit tests failed
Execution halted
Flavor: r-patched-solaris-x86