* using log directory ‘/data/gannet/ripley/R/packages/tests-devel/robustlmm.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 ‘robustlmm/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘robustlmm’ version ‘3.3-1’
* 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 ‘robustlmm’ can be installed ... [100s/251s] OK
See 'https://www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-fedora-gcc/robustlmm-00install.html' for details.
* used C compiler: ‘gcc (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’
* used C++ compiler: ‘g++ (GCC) 14.2.1 20240912 (Red Hat 14.2.1-3)’
* 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 ... [6s/16s] OK
* checking whether the package can be loaded with stated dependencies ... [6s/18s] OK
* checking whether the package can be unloaded cleanly ... [6s/17s] OK
* checking whether the namespace can be loaded with stated dependencies ... [5s/14s] OK
* checking whether the namespace can be unloaded cleanly ... [8s/24s] OK
* checking loading without being on the library search path ... [6s/17s] OK
* checking whether startup messages can be suppressed ... [6s/20s] 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 ... [55s/148s] 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [29s/77s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... [143s/378s] ERROR
Running ‘DAS-scale.R’
Running ‘DASvar-fallback.R’ [8s/23s]
Running ‘PsiFunction.R’ [13s/41s]
Running ‘asymptoticEfficiency.R’ [7s/21s]
Running ‘compare-methods.R’ [17s/48s]
Comparing ‘compare-methods.Rout’ to ‘compare-methods.Rout.save’ ...191,199d190
< Warning messages:
< 1: In optwrap(optimizer, devfun, getStart(start, rho$pp), lower = rho$lower, :
< convergence code -2 from nloptwrap: NLOPT_INVALID_ARGS: Invalid arguments (e.g. lower bounds are bigger than upper bounds, an unknown algorithm was specified, etcetera).
< 2: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
< Model failed to converge with max|grad| = 0.494878 (tol = 0.002, component 1)
< 3: In optwrap(optimizer, devfun, getStart(start, rho$pp), lower = rho$lower, :
< convergence code -2 from nloptwrap: NLOPT_INVALID_ARGS: Invalid arguments (e.g. lower bounds are bigger than upper bounds, an unknown algorithm was specified, etcetera).
< 4: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
< Model failed to converge with max|grad| = 0.494878 (tol = 0.002, component 1)
203a195
> boundary (singular) fit: see help('isSingular')
240a233
> boundary (singular) fit: see help('isSingular')
302,310d294
< Warning messages:
< 1: In optwrap(optimizer, devfun, getStart(start, rho$pp), lower = rho$lower, :
< convergence code -2 from nloptwrap: NLOPT_INVALID_ARGS: Invalid arguments (e.g. lower bounds are bigger than upper bounds, an unknown algorithm was specified, etcetera).
< 2: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
< Model failed to converge with max|grad| = 1.75912 (tol = 0.002, component 1)
< 3: In optwrap(optimizer, devfun, getStart(start, rho$pp), lower = rho$lower, :
< convergence code -2 from nloptwrap: NLOPT_INVALID_ARGS: Invalid arguments (e.g. lower bounds are bigger than upper bounds, an unknown algorithm was specified, etcetera).
< 4: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
< Model failed to converge with max|grad| = 1.75912 (tol = 0.002, component 1)
355c339
< 4.436e-01 4.436e-01 1.241e-01 2.030e-01 -1.084e-06 -2.536e-01 -8.075e-01
---
> 4.436e-01 4.436e-01 1.241e-01 2.030e-01 -1.094e-06 -2.536e-01 -8.075e-01
406c390
< 0.450838 0.450838 0.128411 0.205546 0.000502 -0.256535 -0.815539 0.490628
---
> 0.450838 0.450838 0.128411 0.205545 0.000502 -0.256535 -0.815539 0.490628
412c396
< 0.559398 -0.265494 0.499107 -0.034026 -0.023533 -0.794300
---
> 0.559397 -0.265494 0.499107 -0.034026 -0.023533 -0.794300
441,449d424
< Warning messages:
< 1: In optwrap(optimizer, devfun, getStart(start, rho$pp), lower = rho$lower, :
< convergence code -2 from nloptwrap: NLOPT_INVALID_ARGS: Invalid arguments (e.g. lower bounds are bigger than upper bounds, an unknown algorithm was specified, etcetera).
< 2: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
< Model failed to converge with max|grad| = 1.09789 (tol = 0.002, component 1)
< 3: In optwrap(optimizer, devfun, getStart(start, rho$pp), lower = rho$lower, :
< convergence code -2 from nloptwrap: NLOPT_INVALID_ARGS: Invalid arguments (e.g. lower bounds are bigger than upper bounds, an unknown algorithm was specified, etcetera).
< 4: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
< Model failed to converge with max|grad| = 1.09789 (tol = 0.002, component 1)
Running ‘expectations.R’
Running ‘fitDatasets.R’ [50s/142s]
Running ‘genericFunctions.R’ [8s/17s]
Running ‘getME.R’ [8s/16s]
Comparing ‘getME.Rout’ to ‘getME.Rout.save’ ... OK
Running ‘multipleGroupingFactorsTestData.R’
Running ‘offset.R’ [8s/21s]
Running ‘psi-rho-funs.R’ [6s/12s]
Running ‘rlmerMod.R’
Running ‘simulationStudies.R’ [7s/15s]
Running ‘subset.R’
Running ‘tau.R’
Running ‘testMatrices.R’
Running ‘weights.R’ [8s/13s]
Running the tests in ‘tests/weights.R’ failed.
Complete output:
> require(robustlmm)
Loading required package: robustlmm
Loading required package: lme4
Loading required package: Matrix
>
> checkEquality <- function(cW, rW, tolerance = 1e-8) {
+ stopifnot(
+ all.equal(
+ coef(cW),
+ coef(rW),
+ tolerance = tolerance,
+ check.attributes = FALSE
+ ),
+ all.equal(
+ fixef(cW),
+ fixef(rW),
+ tolerance = tolerance,
+ check.attributes = FALSE
+ ),
+ all.equal(
+ ranef(cW) ,
+ ranef(rW),
+ tolerance = 100 * tolerance,
+ check.attributes = FALSE
+ ),
+ all.equal(
+ fitted(cW) ,
+ fitted(rW),
+ tolerance = tolerance,
+ check.attributes = FALSE
+ ),
+ all.equal(
+ predict(cW) ,
+ predict(rW),
+ tolerance = tolerance,
+ check.attributes = FALSE
+ ),
+ all.equal(
+ coef(summary(cW)) ,
+ coef(summary(rW)),
+ tolerance = 100 * tolerance,
+ check.attributes = FALSE
+ )
+ )
+ }
>
> testBattery <- function(formula, data, tolerance) {
+ nobs <- nrow(data)
+
+ test <- function(weights) {
+ cW <- lmer(formula, data, weights = weights)
+ rW <-
+ rlmer(
+ formula,
+ data,
+ weights = weights,
+ rho.e = cPsi,
+ rho.b = cPsi,
+ init = lmerNoFit
+ )
+ checkEquality(cW, rW, tolerance)
+ }
+
+ test(rep(2, nobs))
+ test(rep(0.5, nobs))
+
+ set.seed(133)
+ test(runif(nobs))
+ test(rexp(nobs))
+ }
>
> testBattery(Yield ~ 1 | Batch, Dyestuff, 1e-8)
Error in checkEquality(cW, rW, tolerance) :
coef(cW) and coef(rW) are not equal:
Component "Batch": Component "(Intercept)": Mean relative difference: 0.002937986
Calls: testBattery -> test -> checkEquality -> stopifnot
In addition: Warning messages:
1: In optwrap(optimizer, devfun, getStart(start, rho$pp), lower = rho$lower, :
convergence code -2 from nloptwrap: NLOPT_INVALID_ARGS: Invalid arguments (e.g. lower bounds are bigger than upper bounds, an unknown algorithm was specified, etcetera).
2: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
Model failed to converge with max|grad| = 2.53309 (tol = 0.002, component 1)
3: In optwrap(optimizer, devfun, getStart(start, rho$pp), lower = rho$lower, :
convergence code -2 from nloptwrap: NLOPT_INVALID_ARGS: Invalid arguments (e.g. lower bounds are bigger than upper bounds, an unknown algorithm was specified, etcetera).
4: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
Model failed to converge with max|grad| = 2.53309 (tol = 0.002, component 1)
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... [45s/106s] ERROR
Error(s) in re-building vignettes:
--- re-building ‘rlmer.Rnw’ using Sweave
Loading required package: robustlmm
Loading required package: lme4
Loading required package: Matrix
Warning in eval(expr, .GlobalEnv) :
Current dir: /data/gannet/ripley/R/packages/tests-devel/robustlmm.Rcheck/robustlmm/ has contents: CITATION, DESCRIPTION, INDEX, Meta, NAMESPACE, R, doc, help, html, libs, simulationStudy
Warning in eval(expr, .GlobalEnv) :
doc dir: /data/gannet/ripley/R/packages/tests-devel/robustlmm.Rcheck/robustlmm/doc has contents: Penicillin.R, ggplot.theme.R, index.html, plots.R, rlmer.R, rlmer.Rnw, rlmer.pdf, simulationStudies.R, simulationStudies.Rnw, simulationStudies.pdf, sleepstudy.R
Warning in eval(expr, .GlobalEnv) :
Filename: /data/gannet/ripley/R/packages/tests-devel/robustlmm.Rcheck/robustlmm/doc/Penicillin.R
Warning in optwrap(optimizer, devfun, getStart(start, rho$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$checkConv, :
Model failed to converge with max|grad| = 0.957735 (tol = 0.002, component 1)
Warning in optwrap(optimizer, devfun, getStart(start, rho$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$checkConv, :
Model failed to converge with max|grad| = 0.957735 (tol = 0.002, component 1)
Loading required package: ggplot2
Warning in optwrap(optimizer, devfun, getStart(start, rho$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$checkConv, :
Model failed to converge with max|grad| = 1.09789 (tol = 0.002, component 1)
Warning in compare(fmUncontam, fm, rfm, rfm2, rfm3, show.rho.functions = FALSE) :
Comparison for objects not fitted to the same dataset
Loading required package: reshape2
--- finished re-building ‘rlmer.Rnw’
--- re-building ‘simulationStudies.Rnw’ using Sweave
Loading required package: ggplot2
Loading required package: robustlmm
Loading required package: lme4
Loading required package: Matrix
Warning in optwrap(optimizer, devfun, getStart(start, rho$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$checkConv, :
Model failed to converge with max|grad| = 0.621439 (tol = 0.002, component 1)
Error: processing vignette 'simulationStudies.Rnw' failed with diagnostics:
chunk 4 (label = source-sensitivity-curves-code)
Error in stopOnFailingFit(fit, "The processed results differed from the stored results:\n", :
Error calling function 'fitDatasets_lmer'. The processed results differed from the stored results:
Component “sigmaâ€: Mean relative difference: 0.02178941Component “thetasâ€: Mean relative difference: 0.1724754Component “bâ€: Mean relative difference: 0.05208771Component “convergedâ€: Mean absolute difference: 2
And some warnings were issued:
list(message = "convergence code -2 from nloptwrap: NLOPT_INVALID_ARGS: Invalid arguments (e.g. lower bounds are bigger than upper bounds, an unknown algorithm was specified, etcetera).", call = optwrap(optimizer, devfun, getStart(start, rho$pp), lower = rho$lower, control = control, adj = FALSE, verbose = verbose, ...))
And some warnings were issued:
list(message = "Model failed to converge with max|grad| = 0.776441 (tol = 0.002, component 1)", call = checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, lbound = environment(devfun)$lower))
--- failed re-building ‘simulationStudies.Rnw’
SUMMARY: processing the following file failed:
‘simulationStudies.Rnw’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... [10s/21s] 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