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.court...@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.kel...@uni-siegen.de > (mailto:riko.kel...@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.court...@gmail.com > > (mailto:alexandre.court...@gmail.com)> > > Sent: 22 September 2022 14:06 > > To: Kelter, Riko > > Cc: r-package-devel@r-project.org (mailto:r-package-devel@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.court...@gmail.com (mailto:alexandre.court...@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.dun...@gmail.com > > > (mailto:murdoch.dun...@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@r-project.org (mailto:R-package-devel@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]] ______________________________________________ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
