CRAN Package Check Results for Package semtree

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

Check Details

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