[R-sig-ME] debugging glmmTMB 1.1.3 on Windows

Mollie Brooks mo|||eebrook@ @end|ng |rom gm@||@com
Fri Mar 4 16:56:10 CET 2022

Dear R-sig-mixed,

The glmmTMB developers and I are preparing a new version of the package. On some Windows systems, we get an error mentioning the `up2date` function which we provide for back compatibility. I can’t replicate it on a Windows laptop that I’m unfamiliar with because I get an different error about "file too big". To progress any further with that laptop, I need to figure out how to add a "/bigobj flag" (https://digitalkarabela.com/mingw-w64-how-to-fix-file-too-big-too-many-sections/ <https://digitalkarabela.com/mingw-w64-how-to-fix-file-too-big-too-many-sections/>), but still the Windows system is unfamiliar to me, so it would be even more helpful if someone with Windows skills could figure out what’s going on with the errors below. We think the way to reproduce them might be using devtools::run_examples()


 https://win-builder.r-project.org/incoming_pretest/glmmTMB_1.1.3_20220303_161208/Windows/00check.log <https://win-builder.r-project.org/incoming_pretest/glmmTMB_1.1.3_20220303_161208/Windows/00check.log>
Status: 3 ERRORs, 1 NOTE

The output states
* checking examples ... [8s] ERROR
Running examples in 'glmmTMB-Ex.R' failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Anova.glmmTMB
> ### Title: Downstream methods
> ### Aliases: Anova.glmmTMB Effect.glmmTMB downstream_methods
> ###   emmeans.glmmTMB
> ### ** Examples
> warp.lm <- glmmTMB(breaks ~ wool * tension, data = warpbreaks)
> salamander1 <- up2date(readRDS(system.file("example_files","salamander1.rds",package="glmmTMB")))
* checking for unstated dependencies in 'tests' ... OK
* checking tests ... [5s] ERROR
  Running 'AAAtest-all.R' [4s]
Running the tests in 'tests/AAAtest-all.R' failed.
Complete output:
  > if (require("testthat")) {
  +     pkg <- "glmmTMB"
  +     require(pkg, character.only=TRUE)
  +     print(sessionInfo())
  +     test_check(pkg, reporter="summary")
  +     print(warnings()) # TODO? catch most of these by expect_warning(..)
  + } else {
  +     warnings("Package 'testthat' not available, cannot run unit tests for package",
  + 	     sQuote(pkg))
  + }
  Loading required package: testthat
  Loading required package: glmmTMB
  R Under development (unstable) (2022-03-02 r81842 ucrt)
  Platform: x86_64-w64-mingw32/x64 (64-bit)
  Running under: Windows Server x64 (build 20348)
  Matrix products: default
  [1] LC_COLLATE=C                 LC_CTYPE=German_Germany.utf8
  [3] LC_MONETARY=C                LC_NUMERIC=C                
  [5] LC_TIME=C                   
  attached base packages:
  [1] stats     graphics  grDevices utils     datasets  methods   base     
  other attached packages:
  [1] glmmTMB_1.1.3  testthat_3.1.3
  loaded via a namespace (and not attached):
   [1] Rcpp_1.0.8          TMB_1.7.22          magrittr_2.0.2     
   [4] splines_4.2.0       MASS_7.3-55         xtable_1.8-4       
   [7] lattice_0.20-45     R6_2.5.1            rlang_1.0.1        
  [10] multcomp_1.4-18     minqa_1.2.4         grid_4.2.0         
  [13] nlme_3.1-155        TH.data_1.1-0       cli_3.2.0          
  [16] coda_0.19-4         emmeans_1.7.2       survival_3.3-1     
  [19] lme4_1.1-28         numDeriv_2016.8-1.1 brio_1.1.3         
  [22] Matrix_1.4-0        nloptr_2.0.0        codetools_0.2-18   
  [25] sandwich_3.0-1      estimability_1.3    compiler_4.2.0     
  [28] boot_1.3-28         mvtnorm_1.1-3       zoo_1.8-9          
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking re-building of vignette outputs ... [64s] ERROR
Error(s) in re-building vignettes:
--- re-building 'covstruct.rmd' using rmarkdown
--- finished re-building 'covstruct.rmd'

--- re-building 'mcmc.rmd' using rmarkdown
--- finished re-building 'mcmc.rmd'

--- re-building 'miscEx.rmd' using rmarkdown
--- finished re-building 'miscEx.rmd'

--- re-building 'parallel.Rmd' using rmarkdown
--- finished re-building 'parallel.Rmd'

--- re-building 'sim.rmd' using rmarkdown
--- finished re-building 'sim.rmd'

--- re-building 'troubleshooting.rmd' using rmarkdown

* checking PDF version of manual ... OK
* checking for detritus in the temp directory ... OK
Status: 3 ERRORs, 1 NOTE

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