These issues originate in a change in how R looks for S3 methods, at least on some of the CRAN machines. To reproduce locally, you currently need to set the environnment variable
_R_S3_METHOD_LOOKUP_BASEENV_AFTER_GLOBALENV_=TRUE See the source code at https://svn.r-project.org/R/trunk/src/main/objects.c To fix method lookup for R >= 3.6.0, you can use delayed S3 method registration along the lines of: if (getRversion() >= "3.6.0") { S3method(pkg::gen, cls) } See the manual at https://cran.r-project.org/doc/manuals/r-devel/R-exts.html#Registering-S3-methods Hope this helps! Cheers, Sebastian Am 08.01.19 um 04:56 schrieb Ben Bolker: > > 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 > ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
