[R-pkg-devel] Warning about ggplot although no ggplot is used anywhere in the package

Riko Kelter r|ko@ke|ter @end|ng |rom un|-@|egen@de
Fri Sep 23 12:10:31 CEST 2022 

Dear Duncan,

thanks for the info! This sounds quite reasonable because I used the 
winbuilder service provided at https://win-builder.r-project.org which I 
used for running tests on the current version of R-devel this warning 
occurred. It seems possible that some ggplot version 3.3.4 is cached 
there and this might be the reason why the warning is generated.

On all other systems except this service for Windows binaries no warning 
was generated. I will resubmit the package to CRAN again and see if the 
warning is generated. If so, I will reply to the CRAN maintainer and see 
what happens.

In any case, I will reply again here to inform you of the results.

Kind regards,

Riko

Am 23.09.22 um 11:47 schrieb Duncan Murdoch:
> I installed your tarball, and I do see element_line being called while 
> loading it, though I don't get the warning.
>
> The call I see is from ggplot2::theme_grey, which is called 
> (eventually) from .onLoad in the stan package.
>
> I'm using the CRAN version of ggplot2, which is version 3.3.6. Your 
> error message indicates that you (or winbuilder?) are using 3.4.0.  It 
> doesn't really make sense that ggplot2 would have this error in its 
> theme_grey function in 3.4.0 (it doesn't in the current Github 
> version), so I would guess that something has resulted in you using 
> functions from a mix of package versions.
>
> There was a discussion recently on the R-devel list about the fact 
> that the methods package caches versions of code from other packages, 
> and this causes problems when those other packages change their 
> requirements.  See 
> https://stat.ethz.ch/pipermail/r-devel/2022-September/081971.html .  
> So I'd guess ggplot2 3.4.0 was installed on the bad machine long 
> enough for some parts of it to be cached, but now it is back to 3.3.6.
>
> I didn't see anywhere in that discussion that you could do something 
> to fix or work around this issue.  Probably the problem will go away 
> when all involved machines finally install ggplot2 3.4.0, but before 
> that, I don't see anything you can do to fix it.
>
> Duncan Murdoch
>
>
>
>
> On 23/09/2022 2:59 a.m., Riko Kelter wrote:
>> Hello again,
>>
>> thanks for the help. Here is a link to download the .tar.gz package:
>> https://uni-siegen.sciebo.de/s/Z9BKwutIPGMieGh
>> I followed the advice to scan the examples, source code and vignettes 
>> with the trace function for occurrences of the element_line call.
>>
>> Results: Only when loading either the fbst package (which also loads 
>> rstanarm) or loading rstanarm any appearance of element_line is 
>> noticed by the tracer (see below). This is regardless of whether a 
>> size option is specified or not.
>> As mentioned earlier as a potential solution, rstanarm loads 
>> bayesplot and indeed two functions in bayesplot make use of the size 
>> option in ggplot2::element_line(). However, I do not use these 
>> functions but they are loaded when using library(rstanarm) I guess. I 
>> see no way to load rstanarm then. Any suggestions?
>>> trace(ggplot2::element_line)
>>
>>> library(fbst)
>>
>> Lade nötiges Paket: cubature
>> Lade nötiges Paket: ks
>>
>> Warnung: Paket ‘ks’ wurde unter R Version 4.0.5 erstellt
>> Lade nötiges Paket: viridis
>> Lade nötiges Paket: viridisLite
>>
>> Lade nötiges Paket: rstanarm
>>
>> Lade nötiges Paket: Rcpp
>> Registered S3 methods overwritten by 'htmltools':
>>
>> method from print.html
>> tools:rstudio
>> print.shiny.tag
>>
>> tools:rstudio
>> print.shiny.tag.list
>>
>> tools:rstudio
>>
>> Registered S3 method overwritten by 'htmlwidgets':
>>
>> method from print.htmlwidget tools:rstudio
>> trace: element_line
>>
>> trace: element_line
>>
>> trace: element_line
>> trace: element_line
>>
>> trace: element_line
>>
>> trace: element_line
>>
>> trace: element_line
>>
>> This is rstanarm version 2.21.3
>> -
>>
>> See https://mc-stan.org/rstanarm/articles/priors for changes to 
>> default priors!
>> -
>>
>> Default priors may change, so it's safest to specify priors, even if 
>> equivalent to
>> the defaults.
>> - For execution on a local, multicore CPU with excess RAM we recommend
>>
>> calling
>> options(mc.cores = parallel::detectCores())
>>
>> Kind regards,
>> Riko
>>
>> On Sep. 22 2022, at 5:05 pm, Alexandre Courtiol 
>> <alexandre.courtiol using gmail.com> wrote:
>>> Hi Riko,
>>> That element_line() is called while loading is not a problem, this 
>>> is probably just the loading of the NAMESPACE from rstanarm.
>>>
>>> There is nothing wrong with this function.
>>> The problem is only when it is used with the argument `size = ` 
>>> within it.
>>> You need to figure out when that happens.
>>> ++
>>>
>>>
>>>
>>>
>>> On Thu, 22 Sept 2022 at 15:49, Kelter, Riko 
>>> <Riko.Kelter using uni-siegen.de (mailto:Riko.Kelter using uni-siegen.de)> wrote:
>>>> Hello everyone,
>>>>
>>>>
>>>>
>>>> thanks a lot for the help.
>>>>
>>>>
>>>> I tried the approach to use the trace function to identify where 
>>>> the element_line() command is actually used. In fact, the vignette 
>>>> twodimfbst.Rmd is the problem, but weirdly even if I only load the 
>>>> rstanarm package the trace function tells me that the code is used.
>>>>
>>>>
>>>> Thus, it seems that one cannot even load the rstanarm package 
>>>> without getting this warning (see the appended PDF screenshot). In 
>>>> fact, the element_line() is identified by the trace function only 
>>>> if the rstanarm or fbst package are loaded inside the vignette. I 
>>>> also tried to replace rstanarm with rstan instead but the same 
>>>> happens because both packages rely on ggplot2.
>>>>
>>>>
>>>> I also appended the .tar.gz package file so you can check the 
>>>> vignette code yourself if interested.
>>>>
>>>>
>>>> Has anyone an idea how to avoid this warning on R devel when 
>>>> rstanarm is loaded inside a vignette? I currently see no way to 
>>>> solve this except for not using rstanarm which is inconvenient.
>>>>
>>>>
>>>> Kind regards,
>>>> Riko
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> From: Alexandre Courtiol <alexandre.courtiol using gmail.com 
>>>> (mailto:alexandre.courtiol using gmail.com)>
>>>> Sent: 22 September 2022 14:06
>>>> To: Kelter, Riko
>>>> Cc: r-package-devel using r-project.org 
>>>> (mailto:r-package-devel using r-project.org)
>>>> Subject: Re: [R-pkg-devel] Warning about ggplot although no ggplot 
>>>> is used anywhere in the package
>>>>
>>>>
>>>> In rstanarm, the function posterior_vs_prior and pp_validate use 
>>>> bayesplot::grid_lines which is defined as:
>>>>
>>>> function (color = "gray50", size = 0.2)
>>>> {
>>>> theme(panel.grid.major = element_line(color = color, size = size),
>>>> panel.grid.minor = element_line(color = color, size = size *
>>>> 0.5))
>>>> }
>>>>
>>>>
>>>> so bayesplot seems to be the culprit if you use these functions.
>>>>
>>>> On Thu, 22 Sept 2022 at 13:51, Alexandre Courtiol 
>>>> <alexandre.courtiol using gmail.com 
>>>> (mailto:alexandre.courtiol using gmail.com)> wrote:
>>>>> You could trace the ggplot function using 
>>>>> trace(ggplot2::element_line)
>>>>> and then load the package and run your examples.
>>>>> Whenever the function is used in the background, it should tell you.
>>>>> ++
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On Thu, 22 Sept 2022 at 13:40, Duncan Murdoch 
>>>>> <murdoch.duncan using gmail.com (mailto:murdoch.duncan using gmail.com)> wrote:
>>>>>> On 21/09/2022 5:09 p.m., Riko Kelter wrote:
>>>>>>> Hello everyone,
>>>>>>>
>>>>>>> I ran R CMD check --as-cran without any errors. However, when I 
>>>>>>> run a check on the current version of r-devel I obtain the 
>>>>>>> following strange error about some ggplot function:
>>>>>>> * installing *source* package 'fbst' ...
>>>>>>> ** using staged installation
>>>>>>> ** R
>>>>>>> ** inst
>>>>>>> ** byte-compile and prepare package for lazy loading
>>>>>>> Warning message:
>>>>>>> The `size` argument of `element_line()` is deprecated as of 
>>>>>>> ggplot2 3.4.0.
>>>>>>> Please use the `linewidth` argument instead.
>>>>>>> The weird thing is: Although my package fbst depends on the 
>>>>>>> package rstanarm which itself imports ggplot,
>>>>>>> (1) no package code uses ggplot in any form,
>>>>>>> (2) no examples use any ggplot commands and
>>>>>>> (3) no vignette uses any ggplot command.
>>>>>>>
>>>>>>> Logs are available at 
>>>>>>> https://win-builder.r-project.org/CX36AbHDU6Tl/
>>>>>>> I am thankful for any suggestion why this error occurs.
>>>>>>> All the best and kind regards,
>>>>>>> Riko
>>>>>>
>>>>>> Could you provide the source for the package? I can see the 
>>>>>> DESCRIPTION
>>>>>> file at win-builder, but can't install it myself since I don't 
>>>>>> use Windows.
>>>>>>
>>>>>> Duncan Murdoch
>>>>>> ______________________________________________
>>>>>> R-package-devel using r-project.org 
>>>>>> (mailto:R-package-devel using r-project.org) mailing list
>>>>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> -- 
>>>>> Alexandre Courtiol, www.datazoogang.de (http://www.datazoogang.de)
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>>
>>>> -- 
>>>> Alexandre Courtiol, www.datazoogang.de (http://www.datazoogang.de)
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>>
>>> -- 
>>> Alexandre Courtiol, www.datazoogang.de
>>>
>>>
>>
>>
>>     [[alternative HTML version deleted]]
>>
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