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

2019-01-08 Thread Iñaki Ucar 
On Tue, 8 Jan 2019 at 08:39, Sebastian Meyer  wrote:
>
> 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)
> }

And to add this automatically to your NAMESPACE with roxygen2, you may
use the following:

#' @rawNamespace if(getRversion() >= "3.6.0") {
#'   S3method(pkg::gen, cls)
#' } else {
#'   export(gen.cls)
#' }

See, e.g., https://github.com/r-quantities/errors/blob/master/R/misc.R#L243

Iñaki

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

2019-01-07 Thread Sebastian Meyer 
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:
> 
> 
> 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
> :
> 
> 
> 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
> 
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[R-pkg-devel] troubleshooting hard-to-reproduce errors

2019-01-07 Thread 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:


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
:


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

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