[R-pkg-devel] [CRAN-pretest-archived] CRAN submission gwsem 2.0.3

[Duncan Murdoch]

On 13/06/2020 1:29 p.m., Joshua N Pritikin wrote:
> 
> I'm trying to include vignettes that take much too long for CRAN check.
> 
> At the beginning of the Rmarkdown vignette, I use
> 
>    is_CRAN <- !identical(Sys.getenv("NOT_CRAN"), "true")
>    if (is_CRAN) q()
> 
> And then I use
> 
>    export NOT_CRAN=true
> 
> when I build locally. But CRAN check still complains,

You shouldn't call q() from a vignette.  Since you're using Rmarkdown, 
you can use a variable for the eval chunk option, e.g. put this in your 
setup chunk:

knitr::opts_chunk$set(eval = !is_CRAN)

Duncan Murdoch

> 
> On Mon, Jun 08, 2020 at 04:24:43PM +0200, ligges using statistik.tu-dortmund.de wrote:
>> Flavor: r-devel-linux-x86_64-debian-gcc
>> Check: re-building of vignette outputs, Result: WARNING
>>    Error(s) in re-building vignettes:
>>      ...
>>    --- re-building 'GeneEnvironmentInteraction.Rmd' using rmarkdown
>>    --- re-building 'OneFactorModel.Rmd' using rmarkdown
>>    --- re-building 'PostGWASprocessing.Rmd' using rmarkdown
>>    --- re-building 'ResidualsModel.Rmd' using rmarkdown
>>    --- re-building 'StandardGWAS.Rmd' using rmarkdown
>>    --- re-building 'TwoFactorModel.Rmd' using rmarkdown
>>    --- re-building 'UserSpecifiedGWASModels.Rmd' using rmarkdown
>>    --- re-building 'growth.Rmd' using rmarkdown
>>    Error: Vignette re-building failed.
>>    Execution halted
> 
> What's the correct way to avoid CRAN complaints?
>