My colleagues and I are preparing a new submission of a package for CRAN (https://github.com/glmmTMB/glmmTMB/tree/master/glmmTMB). We've tested it on all the platforms we have access to: Travis/Linux (devel and release), MacOS (release), Ubuntu 16.04 (release), win-builder (devel and release), without any serious problems.
On CRAN's Debian test machine, we get an ERROR and a WARNING. 1. Can anyone suggest the best way to test/find a platform where we can figure out what's going on? I haven't used R-hub: should I try that? 2. The specific problem is in the "downstream_methods" example: <https://github.com/glmmTMB/glmmTMB/blob/master/glmmTMB/man/downstream_methods.Rd#L65-L67> warp.lm <- glmmTMB(breaks ~ wool * tension, data = warpbreaks) if (require(emmeans)) { emmeans (warp.lm, poly ~ tension | wool) } the error is: Loading required package: emmeans Error in ref_grid(object, ...) : Can't handle an object of class 'glmmTMB' Use help("models", package = "emmeans") for information on supported models. Calls: emmeans -> ref_grid Execution halted I can imagine that this has something to do with environment/method loading. If I run example("downstream_methods", package="glmmTMB") in an R console it works fine (even if glmmTMB isn't loaded). I can reproduce the error if *without loading the glmmTMB package* I run warp.lm <- glmmTMB::glmmTMB(breaks ~ wool * tension, data = warpbreaks) if (require(emmeans)) { emmeans (warp.lm, poly ~ tension | wool) } ... but I don't see why the methods from a package wouldn't be loaded when running its own examples ?? 3. The other problem is in vignette building (see below). Any suggestions for debugging since it doesn't seem to fail locally? The lines indicated suggest some similar kind of method-access problem <https://github.com/glmmTMB/glmmTMB/blob/master/glmmTMB/vignettes/model_evaluation.rmd#L94-L95>: Anova(owls_nb1) ## default type II Anova(owls_nb1,type="III") Any suggestions welcome ... cheers Ben Bolker --- * checking re-building of vignette outputs ... [80s/81s] WARNING Error(s) in re-building vignettes: ... --- re-building ‘covstruct.rmd’ using rmarkdown Attaching package: 'TMB' The following object is masked from 'package:glmmTMB': tmbroot --- 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 ‘model_evaluation.rmd’ using rmarkdown Loading required package: carData lattice theme set by effectsTheme() See ?effectsTheme for details. Loading required package: mvtnorm Loading required package: survival Loading required package: TH.data Loading required package: MASS Attaching package: 'TH.data' The following object is masked from 'package:MASS': geyser Attaching package: 'multcomp' The following object is masked from 'package:emmeans': cld Note that, since v0.1.6.2, DHARMa includes support for glmmTMB, but there are still a few minor limitations associatd with this package. Please see https://github.com/florianhartig/DHARMa/issues/16 for details, in particular if you use this for production. Loading required package: ggplot2 Quitting from lines 94-96 (model_evaluation.rmd) Error: processing vignette 'model_evaluation.rmd' failed with diagnostics: subscript out of bounds --- failed re-building ‘model_evaluation.rmd’ --- re-building ‘sim.rmd’ using rmarkdown --- finished re-building ‘sim.rmd’ --- re-building ‘troubleshooting.rmd’ using rmarkdown --- finished re-building ‘troubleshooting.rmd’ --- re-building ‘glmmTMB.Rnw’ using knitr Loading required package: stats4 Warning in qt((1 - level)/2, df) : NaNs produced --- finished re-building ‘glmmTMB.Rnw’ SUMMARY: processing the following file failed: ‘model_evaluation.rmd’ Error: Vignette re-building failed. Execution halted ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
