* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/trouBBlme4SolveR.Rcheck’
* using R Under development (unstable) (2025-02-15 r87726)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
GNU Fortran (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)
* running under: Fedora Linux 40 (Workstation Edition)
* using session charset: UTF-8
* using option ‘--no-stop-on-test-error’
* checking for file ‘trouBBlme4SolveR/DESCRIPTION’ ... OK
* this is package ‘trouBBlme4SolveR’ version ‘0.1.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘trouBBlme4SolveR’ can be installed ... [14s/37s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/trouBBlme4SolveR-00install.html' for details.
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [4s/10s] OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... [4s/11s] OK
* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [18s/53s] OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [4s/13s] ERROR
Running examples in ‘trouBBlme4SolveR-Ex.R’ failed
The error most likely occurred in:
> ### Name: dwmw
> ### Title: Solver for (generalized) linear MM warnings
> ### Aliases: dwmw trouBBlme4SolveR
> ### Keywords: models
>
> ### ** Examples
>
>
> if(requireNamespace("nlme")){
+ library(lme4)
+ data(Orthodont, package = "nlme")
+ Orthodont$nsex <- as.numeric(Orthodont$Sex == "Male")
+ Orthodont$nsexage <- with(Orthodont, nsex*age)
+ ## Without using dwmw, the next model is singular
+ fmo <- lmer(distance ~ age + (age|Subject) + (0+nsex|Subject) +
+ (0 + nsexage|Subject), data = Orthodont)
+ summary(fmo)
+
+ ## Using dwmw, we remove the singularity of the model
+ fmo1 <- dwmw(lmer(distance ~ age + (age|Subject) + (0+nsex|Subject) +
+ (0 + nsexage|Subject), data = Orthodont))
+ summary(fmo1)
+
+ ## It also can be used on the output object
+
+ fmo2 <- dwmw(fmo)
+ summary(fmo2)
+ }
Loading required package: Matrix
Warning in optwrap(optimizer, devfun, getStart(start, rho$pp), lower = rho$lower, :
convergence code -2 from nloptwrap: NLOPT_INVALID_ARGS: Invalid arguments (e.g. lower bounds are bigger than upper bounds, an unknown algorithm was specified, etcetera).
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
unable to evaluate scaled gradient
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
Model failed to converge: degenerate Hessian with 2 negative eigenvalues
Error in dwmw(lmer(distance ~ age + (age | Subject) + (0 + nsex | Subject) + :
Too many iterations!! to get the model distance ~ age + (age | Subject) + (0 + nsex | Subject) + (0 + nsexage | Subject) to converge. Check it!!
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [208s/543s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘introduction.Rnw’ using Sweave
Loading required package: Matrix
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
Model failed to converge with max|grad| = 0.0971375 (tol = 0.002, component 1)
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
Model is nearly unidentifiable: very large eigenvalue
- Rescale variables?;Model is nearly unidentifiable: large eigenvalue ratio
- Rescale variables?
Correlation matrix not shown by default, as p = 16 > 12.
Use print(res$value, correlation=TRUE) or
vcov(res$value) if you need it
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
Model failed to converge with max|grad| = 0.132634 (tol = 0.002, component 1)
boundary (singular) fit: see help('isSingular')
Correlation matrix not shown by default, as p = 16 > 12.
Use print(res$value, correlation=TRUE) or
vcov(res$value) if you need it
Numeric predictors rescaled!!!
The default multilevel model is singular since the between-Day variance for the intercept and the between-SUR.ID variance for the intercepts are zero.
Then, we consider the next model after removing these random effects.
Correlation matrix not shown by default, as p = 16 > 12.
Use print(res$value, correlation=TRUE) or
vcov(res$value) if you need it
Warning in optwrap(optimizer, devfun, getStart(start, rho$pp), lower = rho$lower, :
convergence code -2 from nloptwrap: NLOPT_INVALID_ARGS: Invalid arguments (e.g. lower bounds are bigger than upper bounds, an unknown algorithm was specified, etcetera).
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
unable to evaluate scaled gradient
Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
Model failed to converge: degenerate Hessian with 2 negative eigenvalues
Error: processing vignette 'introduction.Rnw' failed with diagnostics:
chunk 2
Error in dwmw(fmo) :
Too many iterations!! to get the model distance ~ age + (age | Subject) + (0 + nsex | Subject) + (0 + nsexage | Subject) to converge. Check it!!
--- failed re-building ‘introduction.Rnw’
SUMMARY: processing the following file failed:
‘introduction.Rnw’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... [7s/15s] OK
* checking HTML version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 2 ERRORs