[R-sig-ME] debugging glmmTMB 1.1.3 on Windows
Ben Bolker
bbo|ker @end|ng |rom gm@||@com
Sun Mar 6 02:35:55 CET 2022
I will second this.
I've successfully installed glmmTMB on a Windows 11 virtual machine
(circumventing the /bigobj issue), but haven't been able to reproduce
the errors. Short version:
* relatively trivial code from ?glmmTMB::Anova.glmmTMB (the first
example run)
salamander1 <-
up2date(readRDS(system.file("example_files","salamander1.rds",package="glmmTMB")))
causes an error/makes check fail on CRAN windows platforms (Win-builder
and their checking platforms).
Daniel Luedecke successfully ran checks (i.e. failed to reproduce the
problem) on
R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22000)
glmmTMB 1.1.3 (2022-03-02 [1] Github (ea6c64a))
I failed to reproduce the problem on
version R version 4.1.2 (2021-11-01)
os Windows 10 x64 (build 22000) [really Windows 11]
glmmTMB 1.1.3
Matrix 1.3-4
TMB 1.7.22
and R Under development (unstable) (2022-03-04 r81849 ucrt)
on the same system.
So far we haven't been able to find a Windows platform that
reproduces the problem and that we can play with interactively, and
haven't been able to isolate what the important differences are.
https://github.com/glmmTMB/glmmTMB/issues/787
On 3/4/22 10:56 AM, Mollie Brooks wrote:
> 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()
>
> cheers,
> Mollie
>
>
> 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
>
> locale:
> [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
> * DONE
> Status: 3 ERRORs, 1 NOTE
>
>
> [[alternative HTML version deleted]]
>
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--
Dr. Benjamin Bolker
Professor, Mathematics & Statistics and Biology, McMaster University
Director, School of Computational Science and Engineering
(Acting) Graduate chair, Mathematics & Statistics
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