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

[Riko Kelter]

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
>
>


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