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.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
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