Last updated on 2021-06-28 15:51:18 CEST.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.9.16 | 20.26 | 908.78 | 929.04 | OK | |
| r-devel-linux-x86_64-debian-gcc | 0.9.16 | 15.39 | 400.55 | 415.94 | WARN | |
| r-devel-linux-x86_64-fedora-clang | 0.9.16 | 657.17 | WARN | |||
| r-devel-linux-x86_64-fedora-gcc | 0.9.16 | 511.63 | WARN | |||
| r-devel-windows-x86_64 | 0.9.16 | 26.00 | 489.00 | 515.00 | OK | |
| r-devel-windows-x86_64-gcc10-UCRT | 0.9.16 | OK | ||||
| r-patched-linux-x86_64 | 0.9.16 | 22.89 | 486.03 | 508.92 | WARN | |
| r-patched-solaris-x86 | 0.9.16 | 289.50 | ERROR | |||
| r-release-linux-x86_64 | 0.9.16 | 15.20 | 533.28 | 548.48 | OK | |
| r-release-macos-arm64 | 0.9.16 | OK | ||||
| r-release-macos-x86_64 | 0.9.16 | OK | ||||
| r-release-windows-ix86+x86_64 | 0.9.16 | 33.00 | 525.00 | 558.00 | OK | |
| r-oldrel-macos-x86_64 | 0.9.16 | OK | ||||
| r-oldrel-windows-ix86+x86_64 | 0.9.16 | 34.00 | 466.00 | 500.00 | OK |
Version: 0.9.16
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘constraints.Rmd’ using rmarkdown
Loading required package: OpenMx
Warning: In model 'sharedModel' 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)
Warning: In model 'sharedModel' 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)
Loading required package: ggplot2
--- finished re-building ‘constraints.Rmd’
--- re-building ‘forests.Rmd’ using rmarkdown
Floating point exception
--- re-building ‘getting-started.Rmd’ using rmarkdown
--- finished re-building ‘getting-started.Rmd’
--- re-building ‘score-based-tests.Rmd’ using rmarkdown
--- finished re-building ‘score-based-tests.Rmd’
--- re-building ‘semforest-focus.Rmd’ using rmarkdown
--- finished re-building ‘semforest-focus.Rmd’
SUMMARY: processing the following file failed:
‘forests.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavors: r-devel-linux-x86_64-debian-gcc, r-patched-linux-x86_64
Version: 0.9.16
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘constraints.Rmd’ using rmarkdown
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)
Warning: In model 'sharedModel' 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)
Loading required package: ggplot2
--- finished re-building ‘constraints.Rmd’
sh: line 1: 3892441 Floating point exception(core dumped) R_LIBS=/tmp/RtmppysAik/RLIBS_39ca4f4cef15f1 R_ENVIRON_USER='' R_LIBS_USER='NULL' R_LIBS_SITE='NULL' '/data/gannet/ripley/R/R-clang/bin/R' --vanilla --no-echo > '/tmp/RtmppysAik/working_dir/RtmpVM1Sbx/file3b454b6ee0ee69' 2>&1 < '/tmp/RtmppysAik/working_dir/RtmpVM1Sbx/file3b454b643da1cf'
--- re-building ‘forests.Rmd’ using rmarkdown
--- re-building ‘getting-started.Rmd’ using rmarkdown
--- finished re-building ‘getting-started.Rmd’
--- re-building ‘score-based-tests.Rmd’ using rmarkdown
--- finished re-building ‘score-based-tests.Rmd’
--- re-building ‘semforest-focus.Rmd’ using rmarkdown
--- finished re-building ‘semforest-focus.Rmd’
SUMMARY: processing the following file failed:
‘forests.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.9.16
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘constraints.Rmd’ using rmarkdown
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)
Warning: In model 'sharedModel' 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)
Warning: In model 'sharedModel' 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)
Warning: In model 'sharedModel' 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)
Loading required package: ggplot2
--- finished re-building ‘constraints.Rmd’
sh: line 1: 1955123 Floating point exception(core dumped) '/data/gannet/ripley/R/R-devel/bin/R' --vanilla --no-echo > '/tmp/RtmpV2krrH/working_dir/RtmpQ2P8cM/file1dc2913485ca1a' 2>&1 < '/tmp/RtmpV2krrH/working_dir/RtmpQ2P8cM/file1dc2912b1f1e6b'
--- re-building ‘forests.Rmd’ using rmarkdown
--- re-building ‘getting-started.Rmd’ using rmarkdown
--- finished re-building ‘getting-started.Rmd’
--- re-building ‘score-based-tests.Rmd’ using rmarkdown
--- finished re-building ‘score-based-tests.Rmd’
--- re-building ‘semforest-focus.Rmd’ using rmarkdown
--- finished re-building ‘semforest-focus.Rmd’
SUMMARY: processing the following file failed:
‘forests.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.9.16
Check: tests
Result: ERROR
Running ‘invariance.R’ [0m/180m]
Running ‘lavaan.R’
Running the tests in ‘tests/invariance.R’ failed.
Complete output:
> #
> # testing invariance
> #
>
> # simulation:
> # factor structure holds over SES but not over age
> # both SES and age predict a mean difference in cognitive outcome
>
> set.seed(123)
>
> require("semtree")
Loading required package: semtree
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)
> require("lavaan")
Loading required package: lavaan
This is lavaan 0.6-9
lavaan is FREE software! Please report any bugs.
> #
> lambda <- list()
> age <- c(0,0,1,1) # 0=young, 1 =old
> ses <- c(0,1,0,1) # 0=low, 1=high
> lambda[[1]] <- c(1,0.9,0.8,0.8)
> lambda[[2]] <- c(1,0.9,0.8,0.8)
> lambda[[3]] <- c(1,0.4,0.2,0.9)
> lambda[[4]] <- c(1,0.4,0.2,0.9)
> cogmean <- 80-age*30 + ses*20
> cogsd <- 1
> errsd <- 1
>
> Nsub <- 200 # persons per agexSES group
>
> cbind(age,ses,cogmean)
age ses cogmean
[1,] 0 0 80
[2,] 0 1 100
[3,] 1 0 50
[4,] 1 1 70
>
> # simulate data from 4 groups
> data <- c()
> for (i in 1:4) {
+ cogsim <- rnorm(n = Nsub,mean = cogmean[i],cogsd)
+ scores <- as.matrix(t(outer(lambda[[i]],cogsim))) + rnorm(Nsub*4,0,errsd)
+ data <- rbind(data,scores)
+ }
> data <- data.frame(data)
> names(data) <- paste0("x",1:4)
>
> fulldata <- cbind(data, age=factor(rep(age,each=Nsub)),ses=factor(rep(ses,each=Nsub)))
> #
> model<-"
+ ! regressions
+ F=~1.0*x1
+ F=~l2*x2
+ F=~l3*x3
+ F=~l4*x4
+ ! residuals, variances and covariances
+ x1 ~~ VAR_x1*x1
+ x2 ~~ VAR_x2*x2
+ x3 ~~ VAR_x3*x3
+ x4 ~~ VAR_x4*x4
+ F ~~ 1.0*F
+ ! means
+ F~1
+ x1~0*1;
+ x2~0*1;
+ x3~0*1;
+ x4~0*1;
+ ";
> result<-lavaan(model, data=data, fixed.x=FALSE, missing="FIML");
Warning message:
In lav_object_post_check(object) :
lavaan WARNING: some estimated ov variances are negative
>
> manifests<-c("x1","x2","x3","x4")
> latents<-c("F")
> model <- mxModel("Unnamed_Model",
+ type="RAM",
+ manifestVars = manifests,
+ latentVars = latents,
+ mxPath(from="F",to=c("x1","x2","x3","x4"), free=c(FALSE,TRUE,TRUE,TRUE),
+ value=c(1.0,1.0,1.0,1.0) , arrows=1, label=c("F__x1","l2","l3","l4") ),
+ mxPath(from="one",to=c("F"), free=c(TRUE), value=c(1.0) , arrows=1, label=c("const__F") ),
+ mxPath(from="one",to=c("x2","x3","x4"), free=c(TRUE,TRUE,TRUE), value=c(1.0,1.0,1.0) , arrows=1, label=c("const__x2","const__x3","const__x4") ),
+ mxPath(from="x1",to=c("x1"), free=c(TRUE), value=c(1.0) , arrows=2, label=c("VAR_x1") ),
+ mxPath(from="x2",to=c("x2"), free=c(TRUE), value=c(1.0) , arrows=2, label=c("VAR_x2") ),
+ mxPath(from="x3",to=c("x3"), free=c(TRUE), value=c(1.0) , arrows=2, label=c("VAR_x3") ),
+ mxPath(from="x4",to=c("x4"), free=c(TRUE), value=c(1.0) , arrows=2, label=c("VAR_x4") ),
+ mxPath(from="F",to=c("F"), free=c(FALSE), value=c(1.0) , arrows=2, label=c("VAR_F") ),
+ mxPath(from="one",to=c("x1"), free=F, value=0, arrows=1),
+ mxData(data[1:50,], type = "raw")
+ );
>
> result <- mxRun(model)
Running Unnamed_Model with 11 parameters
*** caught segfault ***
address e46, cause 'memory not mapped'
Flavor: r-patched-solaris-x86
Version: 0.9.16
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
Terminated
Warning: elapsed-time limit of 1 hours reached for sub-process
--- re-building ‘constraints.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Loading required package: OpenMx
To take full advantage of multiple cores, use:
mxOption(key='Number of Threads', value=parallel::detectCores()) #now
Sys.setenv(OMP_NUM_THREADS=parallel::detectCores()) #before library(OpenMx)
*** caught segfault ***
address 7, cause 'memory not mapped'
--- re-building ‘forests.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Error: C stack usage 315659412 is too close to the limit
Quitting from lines 40-53 (forests.Rmd)
Error: processing vignette 'forests.Rmd' failed with diagnostics:
The job for model 'Simple Model' exited abnormally with the error message: User interrupt
--- failed re-building ‘forests.Rmd’
--- re-building ‘getting-started.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Error: C stack usage 315135124 is too close to the limit
Quitting from lines 110-111 (getting-started.Rmd)
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
non-numeric argument to mathematical function
--- failed re-building ‘getting-started.Rmd’
--- re-building ‘score-based-tests.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Error: C stack usage 314872980 is too close to the limit
Quitting from lines 44-58 (score-based-tests.Rmd)
Error: processing vignette 'score-based-tests.Rmd' failed with diagnostics:
The job for model 'Simple Model' exited abnormally with the error message: User interrupt
--- failed re-building ‘score-based-tests.Rmd’
--- re-building ‘semforest-focus.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
Pandoc (>= 1.12.3) not available. Falling back to R Markdown v1.
Error: C stack usage 250713236 is too close to the limit
Quitting from lines 29-61 (semforest-focus.Rmd)
Error: processing vignette 'semforest-focus.Rmd' failed with diagnostics:
The job for model 'Bivariate_Model' exited abnormally with the error message: User interrupt
--- failed re-building ‘semforest-focus.Rmd’
SUMMARY: processing the following files failed:
‘constraints.Rmd’ ‘forests.Rmd’ ‘getting-started.Rmd’
‘score-based-tests.Rmd’ ‘semforest-focus.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-patched-solaris-x86