[R-pkg-devel] troubleshooting hard-to-reproduce errors

[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