From 2cd57785847562b0364ce35adf069ba1deb7a946 Mon Sep 17 00:00:00 2001
From: Christophe Dervieux <christophe.dervieux@gmail.com>
Date: Thu, 11 Dec 2025 11:31:23 +0100
Subject: [PATCH 1/4] rticles::rjournal_article() is now defunct

Remove ressources which will help reduce package size and allow cran release
---
 DESCRIPTION                                   |   2 +-
 NAMESPACE                                     |   1 -
 R/rjournal_article.R                          | 165 +--------
 .../rjournal/resources/RJwrapper.tex          | 170 ---------
 .../templates/rjournal/resources/template.tex |  33 --
 .../templates/rjournal/skeleton/RJournal.sty  | 343 ------------------
 .../rjournal/skeleton/RJreferences.bib        |  18 -
 .../templates/rjournal/skeleton/Rlogo-5.png   | Bin 10704 -> 0 bytes
 .../templates/rjournal/skeleton/skeleton.Rmd  |  82 -----
 .../templates/rjournal/template.yaml          |   5 -
 man/rjournal_article.Rd                       |  67 +---
 11 files changed, 7 insertions(+), 879 deletions(-)
 delete mode 100644 inst/rmarkdown/templates/rjournal/resources/RJwrapper.tex
 delete mode 100644 inst/rmarkdown/templates/rjournal/resources/template.tex
 delete mode 100644 inst/rmarkdown/templates/rjournal/skeleton/RJournal.sty
 delete mode 100644 inst/rmarkdown/templates/rjournal/skeleton/RJreferences.bib
 delete mode 100644 inst/rmarkdown/templates/rjournal/skeleton/Rlogo-5.png
 delete mode 100644 inst/rmarkdown/templates/rjournal/skeleton/skeleton.Rmd
 delete mode 100644 inst/rmarkdown/templates/rjournal/template.yaml

diff --git a/DESCRIPTION b/DESCRIPTION
index 742a80e9d..2bb97be6e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -108,5 +108,5 @@ Config/Needs/website: magick, pdftools, gifski, tidyverse/tidytemplate,
 Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3
 SystemRequirements: GNU make
diff --git a/NAMESPACE b/NAMESPACE
index 8929ca591..cffebc18a 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -37,7 +37,6 @@ export(peerj_article)
 export(pihph_article)
 export(plos_article)
 export(pnas_article)
-export(rjournal_article)
 export(rsos_article)
 export(rss_article)
 export(sage_article)
diff --git a/R/rjournal_article.R b/R/rjournal_article.R
index be76521aa..1ce50e824 100644
--- a/R/rjournal_article.R
+++ b/R/rjournal_article.R
@@ -3,169 +3,12 @@
 #' @description
 #' `r lifecycle::badge('deprecated')`
 #'
-#' This function is now deprecated in favor of the [**rjtools**](https://rjournal.github.io/rjtools/) package
-#' which is now officialy recommanded by R Journal <https://rjournal.github.io/submissions.html>. See below for document
+#' This function is now defunct in favor of the [**rjtools**](https://rjournal.github.io/rjtools/) package
+#' which is now officialy recommanded by R Journal <https://rjournal.github.io/submissions.html>.
 #'
-#' @details # About this format and the R Journal requirements
-#'
-#' Format for creating R Journal articles. Adapted from
-#' <https://journal.r-project.org/submissions.html>.
-#'
-#' This file is only a basic article template. For full details of _The R
-#' Journal_ style and information on how to prepare your article for submission,
-#' see the [Instructions for Authors](https://journal.r-project.org/share/author-guide.pdf)
-#'
-
-#'
-#' `rticles::rjournal_article` will help you build the correct files requirements:
-#'
-#' - A R file will be generated automatically using `knitr::purl` - see
-#' https://bookdown.org/yihui/rmarkdown-cookbook/purl.html for more information.
-#' - A tex file will be generated from this Rmd file and correctly included in
-#' `RJwapper.tex` as expected to build `RJwrapper.pdf`.
-#' - All figure files will be kept in the default rmarkdown `*_files` folder. This
-#' happens because `keep_tex = TRUE` by default in `rticles::rjournal_article`
-#' - Only the bib filename is to be modified. An example bib file is included in the
-#' template (`RJreferences.bib`) and you will have to name your bib file as the
-#' tex, R, and pdf files.
-#'
-#' # About YAML header fields
-#'
-#' This section documents some of the YAML fields that can be used with this
-#' formats.
-#'
-#' ## The `author` field in the YAML header
-#'
-#' | FIELD  | TYPE | DESCRIPTION |
-#' | ------ | ---- | ----------- |
-#' | `name` | *required* | name and surname of the author |
-#' | `affiliation` | *required* | name of the author's affiliation |
-#' | `address` | *required* | at least one address line for the affiliation |
-#' | `url` | *optional* | an additional url for the author or the main affiliation |
-#' | `orcid` | *optional* | the authors ORCID if available |
-#' | `email` | *required* | the author's e-mail address |
-#' | `affiliation2` | *optional* | name of the author's 2nd affiliation |
-#' | `address2` | *optional* | address lines belonging to the author's 2nd affiliation |
-#'
-#' *Please note: Only one `url`, `orcid` and `email` can be provided per author.*
-#'
-#' ## Other YAML fields
-#'
-#' | FIELD | TYPE | DESCRIPTION |
-#' | ----- | ---- | ----------- |
-#' | `bibliography` | *with default* | the BibTeX file with the reference entries |
-#'
-#' @inheritParams rmarkdown::pdf_document
-#' @param ... Arguments to [rmarkdown::pdf_document()].
-#' @export
+#' @internal
 rjournal_article <- function(..., keep_tex = TRUE, citation_package = "natbib") {
 
-  lifecycle::deprecate_warn("0.25", "rjournal_article()", "rjtools::rjournal_pdf_article()", details = "See official recommandation at https://rjournal.github.io/submissions.html")
-  rmarkdown::pandoc_available("2.2", TRUE)
-
-  base <- pdf_document_format(
-    "rjournal",
-    highlight = NULL, citation_package = citation_package,
-    keep_tex = keep_tex, ...
-  )
-
-  # Render will generate tex file, post-knit hook gerenates the R file,
-  # post-process hook generates appropriate RJwrapper.tex and
-  # use pandoc to build pdf from that
-  base$pandoc$to <- "latex"
-  base$pandoc$ext <- ".tex"
-
-  # Generates R file expected by R journal requirement.
-  # We do that in the post-knit hook do access input file path.
-  pk <- base$post_knit
-  output_R <- NULL
-  base$post_knit <- function(metadata, input_file, runtime, ...) {
-    # run post_knit it exists
-    if (is.function(pk)) pk(metadata, input_file, runtime, ...)
-
-    # purl the Rmd file to R code per requirement
-    temp_R <- tempfile(fileext = ".R")
-    output_R <<- knitr::purl(input_file, temp_R, documentation = 1, quiet = TRUE)
-    # Add magic comment about '"do not edit" (rstudio/rstudio#2082)
-    xfun::write_utf8(c(
-      "# Generated by `rjournal_article()` using `knitr::purl()`: do not edit by hand",
-      sprintf("# Please edit %s to modify this file", input_file),
-      "",
-      xfun::read_utf8(output_R)
-    ), output_R)
-
-    NULL
-  }
-
-  base$post_processor <- function(metadata, utf8_input, output_file, clean, verbose) {
-    filename <- basename(output_file)
-    # underscores in the filename will be problematic in \input{filename};
-    # pandoc will escape underscores but it should not, i.e., should be
-    # \input{foo_bar} instead of \input{foo\_bar}
-    if (filename != (filename2 <- gsub("_", "-", filename))) {
-      file.rename(filename, filename2)
-      filename <- filename2
-    }
-
-    # Copy purl-ed R file with the correct name
-    dest_file <- xfun::with_ext(filename, "R")
-    our_file <- TRUE
-    if (file.exists(dest_file)) {
-      # we check this file is generated by us
-      # otherwise we leave it as is and warn
-      current_r <- xfun::read_utf8(dest_file)
-      our_file <- grepl("Generated.*rjournal_article.*do not edit by hand", current_r[1])
-      if (!our_file) {
-        warning(
-          sprintf("R file with name '%s' already exists.", dest_file),
-          "\nIt will not be overwritten by the one generated",
-          " during rendering using `knitr::purl()`.",
-          "\nRemove the existing file to obtain the generated one.",
-          call. = FALSE
-        )
-      }
-    }
-    if (our_file) {
-      # we only overwrite if it is our file
-      file.copy(output_R, xfun::with_ext(filename, "R"), overwrite = TRUE)
-    }
-    unlink(output_R)
-
-    # post process TEX file
-    temp_tex <- xfun::read_utf8(filename)
-    temp_tex <- post_process_authors(temp_tex)
-    xfun::write_utf8(temp_tex, filename)
-
-    # check bibliography name
-    bib_filename <- metadata$bibliography
-    if (length(bib_filename) == 1 &&
-      xfun::sans_ext(bib_filename) != xfun::sans_ext(filename)) {
-      msg <- paste0(
-        "Per R journal requirement, bibliography file and tex file should",
-        " have the same name. Currently, you have a bib file ", bib_filename,
-        " and a tex file ", filename, ". Don't forget to rename and change",
-        " the bibliography field in the YAML header."
-      )
-      warning(msg, call. = FALSE)
-    }
-
-    # Create RJwrapper.tex per R Journal requirement
-    m <- list(filename = xfun::sans_ext(filename))
-    h <- get_list_element(metadata, c("output", "rticles::rjournal_article", "includes", "in_header"))
-    h <- c(h, if (length(preamble <- unlist(metadata[c("preamble", "header-includes")]))) {
-      f <- tempfile(fileext = ".tex")
-      on.exit(unlink(f), add = TRUE)
-      xfun::write_utf8(preamble, f)
-      f
-    })
-    t <- find_resource("rjournal", "RJwrapper.tex")
-    template_pandoc(m, t, "RJwrapper.tex", h, verbose)
-
-    tinytex::latexmk("RJwrapper.tex", base$pandoc$latex_engine, clean = clean)
-  }
-
-  # Mostly copied from knitr::render_sweave
-  base$knitr$opts_chunk$comment <- "#>"
+  lifecycle::deprecate_stop("0.25", "rjournal_article()", "rjtools::rjournal_pdf_article()", details = "See official recommandation at https://rjournal.github.io/submissions.html")
 
-  set_sweave_hooks(base)
 }
diff --git a/inst/rmarkdown/templates/rjournal/resources/RJwrapper.tex b/inst/rmarkdown/templates/rjournal/resources/RJwrapper.tex
deleted file mode 100644
index f96e6bb6b..000000000
--- a/inst/rmarkdown/templates/rjournal/resources/RJwrapper.tex
+++ /dev/null
@@ -1,170 +0,0 @@
-\documentclass[a4paper]{report}
-\usepackage[utf8]{inputenc}
-\usepackage[T1]{fontenc}
-\usepackage{RJournal}
-\usepackage{amsmath,amssymb,array}
-\usepackage{booktabs}
-
-$if(highlighting-macros)$
-% Pandoc syntax highlighting
-$highlighting-macros$
-$endif$
-
-% tightlist command for lists without linebreak
-\providecommand{\tightlist}{%
-  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
-
-$if(tables)$
-% From pandoc table feature
-\usepackage{longtable,booktabs,array}
-$if(pandoc3821)$\newcounter{none} % for unnumbered tables
-$endif$
-$if(multirow)$
-\usepackage{multirow}
-$endif$
-\usepackage{calc} % for calculating minipage widths
-% Correct order of tables after \paragraph or \subparagraph
-\usepackage{etoolbox}
-\makeatletter
-\patchcmd\longtable{\par}{\if@noskipsec\mbox{}\fi\par}{}{}
-\makeatother
-% Allow footnotes in longtable head/foot
-\IfFileExists{footnotehyper.sty}{\usepackage{footnotehyper}}{\usepackage{footnote}}
-\makesavenoteenv{longtable}
-$endif$
-
-% Add imagehandling
-$-- Only needed for pandoc 3.2.1 and above requiring graphics for new command.
-$if(graphics)$$if(pandoc321)$
-% Custom command from Pandoc 3.2.1 to scale images if necessary
-\usepackage{graphicx}
-\makeatletter
-\newsavebox\pandoc@box
-\newcommand*\pandocbounded[1]{% scales image to fit in text height/width
-  \sbox\pandoc@box{#1}%
-  \Gscale@div\@tempa{\textheight}{\dimexpr\ht\pandoc@box+\dp\pandoc@box\relax}%
-  \Gscale@div\@tempb{\linewidth}{\wd\pandoc@box}%
-  \ifdim\@tempb\p@<\@tempa\p@\let\@tempa\@tempb\fi% select the smaller of both
-  \ifdim\@tempa\p@<\p@\scalebox{\@tempa}{\usebox\pandoc@box}%
-  \else\usebox{\pandoc@box}%
-  \fi%
-}
-\makeatother
-$endif$$endif$
-
-$if(csl-refs)$
-% Pandoc citation processing
-$if(pandoc318)$
-%From Pandoc 3.1.8
-% definitions for citeproc citations
-\NewDocumentCommand\citeproctext{}{}
-\NewDocumentCommand\citeproc{mm}{%
-  \begingroup\def\citeproctext{#2}\cite{#1}\endgroup}
-\makeatletter
- % allow citations to break across lines
- \let\@cite@ofmt\@firstofone
- % avoid brackets around text for \cite:
- \def\@biblabel#1{}
- \def\@cite#1#2{{#1\if@tempswa , #2\fi}}
-\makeatother
-\newlength{\cslhangindent}
-\setlength{\cslhangindent}{1.5em}
-\newlength{\csllabelwidth}
-\setlength{\csllabelwidth}{3em}
-\newenvironment{CSLReferences}[2] % #1 hanging-indent, #2 entry-spacing
- {\begin{list}{}{%
-  \setlength{\itemindent}{0pt}
-  \setlength{\leftmargin}{0pt}
-  \setlength{\parsep}{0pt}
-  % turn on hanging indent if param 1 is 1
-  \ifodd #1
-   \setlength{\leftmargin}{\cslhangindent}
-   \setlength{\itemindent}{-1\cslhangindent}
-  \fi
-  % set entry spacing
-  \setlength{\itemsep}{#2\baselineskip}}}
- {\end{list}}
-$else$$if(pandoc317)$
-% definitions for citeproc citations
-\NewDocumentCommand\citeproctext{}{}
-\NewDocumentCommand\citeproc{mm}{%
-  \begingroup\def\citeproctext{#2}\cite{#1}\endgroup}
-% avoid brackets around text for \cite:
-\makeatletter
- \def\@biblabel#1{}
- \def\@cite#1#2{{#1\if@tempswa , #2\fi}}
-\makeatother
-\newlength{\cslhangindent}
-\setlength{\cslhangindent}{1.5em}
-\newlength{\csllabelwidth}
-\setlength{\csllabelwidth}{3em}
-\newlength{\cslentryspacing}
-\setlength{\cslentryspacing}{0em}
-\usepackage{enumitem}
-\newlist{CSLReferences}{itemize}{1}
-\setlist[CSLReferences]{label={},
-  leftmargin=\cslhangindent,
-  itemindent=-1\cslhangindent,
-  parsep=\parskip,
-  itemsep=\cslentryspacing}
-$else$
-\newlength{\cslhangindent}
-\setlength{\cslhangindent}{1.5em}
-\newlength{\csllabelwidth}
-\setlength{\csllabelwidth}{3em}
-\newlength{\cslentryspacingunit} % times entry-spacing
-\setlength{\cslentryspacingunit}{\parskip}
-% for Pandoc 2.8 to 2.10.1
-\newenvironment{cslreferences}%
-  {$if(csl-hanging-indent)$\setlength{\parindent}{0pt}%
-  \everypar{\setlength{\hangindent}{\cslhangindent}}\ignorespaces$endif$}%
-  {\par}
-% For Pandoc 2.11+
-\newenvironment{CSLReferences}[2] % #1 hanging-ident, #2 entry spacing
- {% don't indent paragraphs
-  \setlength{\parindent}{0pt}
-  % turn on hanging indent if param 1 is 1
-  \ifodd #1
-  \let\oldpar\par
-  \def\par{\hangindent=\cslhangindent\oldpar}
-  \fi
-  % set entry spacing
-  \setlength{\parskip}{#2\cslentryspacingunit}
- }%
- {}
-$endif$$endif$
-\usepackage{calc}
-\newcommand{\CSLBlock}[1]{#1\hfill\break}
-\newcommand{\CSLLeftMargin}[1]{\parbox[t]{\csllabelwidth}{#1}}
-\newcommand{\CSLRightInline}[1]{\parbox[t]{\linewidth - \csllabelwidth}{#1}\break}
-\newcommand{\CSLIndent}[1]{\hspace{\cslhangindent}#1}
-$endif$
-
-$for(header-includes)$
-$header-includes$
-$endfor$
-
-\begin{document}
-
-$for(include-before)$
-$include-before$
-
-$endfor$
-
-%% do not edit, for illustration only
-\sectionhead{Contributed research article}
-\volume{XX}
-\volnumber{YY}
-\year{20ZZ}
-\month{AAAA}
-
-\begin{article}
-  \input{$filename$}
-\end{article}
-
-$for(include-after)$
-$include-after$
-
-$endfor$
-
-\end{document}
diff --git a/inst/rmarkdown/templates/rjournal/resources/template.tex b/inst/rmarkdown/templates/rjournal/resources/template.tex
deleted file mode 100644
index 49e42eb0a..000000000
--- a/inst/rmarkdown/templates/rjournal/resources/template.tex
+++ /dev/null
@@ -1,33 +0,0 @@
-% !TeX root = RJwrapper.tex
-\title{$title$}
-\author{by $for(author)$$author.name$$sep$, $endfor$}
-
-\maketitle
-
-$if(abstract)$
-\abstract{%
-$abstract$
-}
-$endif$
-
-$body$
-
-$if(bibliography)$
-\bibliography{$for(bibliography)$$bibliography$$sep$,$endfor$}
-$endif$
-
-$for(author)$
-\address{%
-$author.name$\\
-$author.affiliation$\\%
-$for(author.address)$$author.address$$sep$\\ $endfor$\\
-$if(author.affiliation2)$
-$author.affiliation2$\\%
-$for(author.address2)$$author.address2$$sep$\\ $endfor$\\
-$endif$%
-$if(author.url)$$author.url$\\$endif$%
-$if(author.orcid)$\textit{ORCiD: \href{https://orcid.org/$author.orcid$}{$author.orcid$}}\\$endif$%
-$if(author.email)$$author.email$$endif$%
-}
-
-$endfor$
diff --git a/inst/rmarkdown/templates/rjournal/skeleton/RJournal.sty b/inst/rmarkdown/templates/rjournal/skeleton/RJournal.sty
deleted file mode 100644
index 160054510..000000000
--- a/inst/rmarkdown/templates/rjournal/skeleton/RJournal.sty
+++ /dev/null
@@ -1,343 +0,0 @@
-% Package `RJournal' to use with LaTeX2e
-% Copyright (C) 2010 by the R Foundation
-% Copyright (C) 2013 by the R Journal
-%
-% Originally written by Kurt Hornik and Friedrich Leisch with subsequent 
-% edits by the editorial board
-%
-% CAUTION:
-% Do not modify this style file. Any changes to this file will be reset when your
-% article is submitted.
-% If you must modify the style or add LaTeX packages to the article, these 
-% should be specified in RJwrapper.tex
-
-\NeedsTeXFormat{LaTeX2e}[1995/12/01]
-\ProvidesPackage{RJournal}[2022/06/27 v0.14 RJournal package]
-
-\RequirePackage{tikz}
-
-% Overall page layout, fonts etc -----------------------------------------------
-
-% Issues of of \emph{The R Journal} are created from the standard \LaTeX{}
-% document class \pkg{report}. 
-
-\RequirePackage{geometry}
-\geometry{a4paper, 
-   textwidth=14cm, top=1cm, bottom=1cm,
-   includehead,includefoot,centering,
-   footskip=1.5cm}
-\raggedbottom
-
-\RequirePackage{fancyhdr}
-\fancyhead{}
-\fancyheadoffset{2cm} 
-\fancyhead[L]{\textsc{\RJ@sectionhead}}
-\fancyhead[R]{\thepage}
-\fancyfoot{}
-\fancyfoot[L]{The R Journal Vol. \RJ@volume/\RJ@number, \RJ@month~\RJ@year}
-\fancyfoot[R]{ISSN 2073-4859}
-\pagestyle{fancy}
-
-% We use the following fonts (all with T1 encoding):
-% 
-%   rm   & palatino
-%   tt   & inconsolata
-%   sf   & helvetica
-%   math & palatino
-
-\RequirePackage{microtype}
-
-\RequirePackage[scaled=0.92]{helvet}
-\RequirePackage{palatino,mathpazo}
-\RequirePackage[scaled=1.02]{inconsolata}
-\RequirePackage[T1]{fontenc}
-
-\RequirePackage[hyphens]{url}
-\RequirePackage[pagebackref]{hyperref}
-\renewcommand{\backref}[1]{[p#1]}
-
-% Dark blue colour for all links
-\RequirePackage{color}
-\definecolor{link}{rgb}{0.45,0.51,0.67}
-\hypersetup{
-  colorlinks,%
-  citecolor=link,%
-  filecolor=link,%
-  linkcolor=link,%
-  urlcolor=link
-}
-
-% Give the text a little room to breath
-\setlength{\parskip}{3pt}
-\RequirePackage{setspace}
-\setstretch{1.05}
-
-% Issue and article metadata ---------------------------------------------------
-
-% Basic front matter information about the issue: volume, number, and
-% date.
-
-\newcommand{\volume}[1]{\def\RJ@volume{#1}}
-\newcommand{\volnumber}[1]{\def\RJ@number{#1}}
-\renewcommand{\month}[1]{\def\RJ@month{#1}}
-\renewcommand{\year}[1]{\def\RJ@year{#1}}
-
-
-% Individual articles correspond to
-% chapters, and are contained in |article| environments.  This makes it
-% easy to have figures counted within articles and hence hyperlinked
-% correctly.
-
-% An article has an author, a title, and optionally a subtitle.  We use
-% the obvious commands for specifying these. Articles will be put in certain
-% journal sections, named by \sectionhead.
-
-\newcommand  {\sectionhead}  [1]{\def\RJ@sectionhead{#1}}
-\renewcommand{\author}       [1]{\def\RJ@author{#1}}
-\renewcommand{\title}        [1]{\def\RJ@title{#1}}
-\newcommand  {\subtitle}     [1]{\def\RJ@subtitle{#1}}
-
-% Control appearance of titles: make slightly smaller than usual, and 
-% suppress section numbering. See http://tex.stackexchange.com/questions/69749
-% for why we don't use \setcounter{secnumdepth}{-1} 
-
-\usepackage[medium]{titlesec}
-\usepackage{titletoc}
-\titleformat{\section}   {\normalfont\large\bfseries}{\arabic{section}}{1em}{}
-\titleformat{\subsection}{\normalfont\normalsize\bfseries}{}{0em}{}
-\titlecontents{chapter}   [0em]{}{}{}{\titlerule*[1em]{.}\contentspage}
-
-% Article layout ---------------------------------------------------------------
-
-% Environment |article| clears the article header information at its beginning. 
-% We use |\FloatBarrier| from the placeins package to keep floats within
-% the article.
-\RequirePackage{placeins}
-\newenvironment{article}{\author{}\title{}\subtitle{}\FloatBarrier}{\FloatBarrier}
-
-% Refereed articles should have an abstract, so we redefine |\abstract| to
-% give the desired style
-
-\renewcommand{\abstract}[1]{%
-\setstretch{1}%
-\noindent%
-\small%
-\textbf{Abstract} #1 
-}
-
-% The real work is done by a redefined version of |\maketitle|.  Note
-% that even though we do not want chapters (articles) numbered, we
-% need to increment the chapter counter, so that figures get correct
-% labelling.
-
-\renewcommand{\maketitle}{%
-\noindent
-  \chapter{\RJ@title}\refstepcounter{chapter}
-  \ifx\empty\RJ@subtitle
-  \else
-    \noindent\textbf{\RJ@subtitle}
-    \par\nobreak\addvspace{\baselineskip}
-  \fi
-  \ifx\empty\RJ@author
-  \else
-    \noindent\textit{\RJ@author}
-    \par\nobreak\addvspace{\baselineskip}
-  \fi
-  \@afterindentfalse\@nobreaktrue\@afterheading
-}
-
-% Now for some ugly redefinitions.  We do not want articles to start a
-% new page. (Actually, we do, but this is handled via explicit
-% \newpage
-%
-% The name@of@eq is a hack to get hyperlinks to equations to work
-% within each article, even though there may be multiple eq.(1)
-%    \begin{macrocode}
-\renewcommand\chapter{\secdef\RJ@chapter\@schapter}
-\providecommand{\nohyphens}{%
-  \hyphenpenalty=10000\exhyphenpenalty=10000\relax}
-\newcommand{\RJ@chapter}{%
-  \edef\name@of@eq{equation.\@arabic{\c@chapter}}%
-  \renewcommand{\@seccntformat}[1]{}%
-  \@startsection{chapter}{0}{0mm}{%
-    -2\baselineskip \@plus -\baselineskip \@minus -.2ex}{\p@}{%
-    \phantomsection\normalfont\huge\bfseries\raggedright}}
-
-% Book reviews should appear as sections in the text and in the pdf bookmarks,
-% however we wish them to appear as chapters in the TOC. Thus we define an
-% alternative to |\maketitle| for reviews.
-\newcommand{\review}[1]{
-  \pdfbookmark[1]{#1}{#1}
-  \section*{#1}
-  \addtocontents{toc}{\protect\contentsline{chapter}{#1}{\thepage}{#1.1}}
-}
-
-% We want bibliographies as starred sections within articles.
-% 
-\RequirePackage[sectionbib,round]{natbib}
-\bibliographystyle{abbrvnat}
-
-% Equations, figures and tables are counted within articles, but we do
-% not show the article number. For equations it becomes a bit messy to avoid
-% having hyperref getting it wrong. 
-
-% \numberwithin{equation}{chapter}
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-    The \raisebox{-8pt}{\includegraphics[height=77pt]{Rlogo-5}}\hspace{10pt}
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diff --git a/inst/rmarkdown/templates/rjournal/skeleton/RJreferences.bib b/inst/rmarkdown/templates/rjournal/skeleton/RJreferences.bib
deleted file mode 100644
index f5d901444..000000000
--- a/inst/rmarkdown/templates/rjournal/skeleton/RJreferences.bib
+++ /dev/null
@@ -1,18 +0,0 @@
-@Manual{R,
-  title = {R: A Language and Environment for Statistical Computing},
-  author = {{R Core Team}},
-  organization = {R Foundation for Statistical Computing},
-  address = {Vienna, Austria},
-  year = {2012},
-  note = {{ISBN} 3-900051-07-0},
-  url = {http://www.R-project.org/},
-}
-
-@article{ihaka:1996,
-  Author = {Ihaka, Ross and Gentleman, Robert},
-	Journal = {Journal of Computational and Graphical Statistics},
-	Number = 3,
-	Pages = {299--314},
-	Title = {R: A Language for Data Analysis and Graphics},
-	Volume = 5,
-	Year = 1996}
diff --git a/inst/rmarkdown/templates/rjournal/skeleton/Rlogo-5.png b/inst/rmarkdown/templates/rjournal/skeleton/Rlogo-5.png
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diff --git a/inst/rmarkdown/templates/rjournal/skeleton/skeleton.Rmd b/inst/rmarkdown/templates/rjournal/skeleton/skeleton.Rmd
deleted file mode 100644
index 55258e638..000000000
--- a/inst/rmarkdown/templates/rjournal/skeleton/skeleton.Rmd
+++ /dev/null
@@ -1,82 +0,0 @@
----
-title: Capitalized Title Here
-author:
-  # see ?rjournal_article for more information
-  - name: Author One
-    affiliation: Affiliation
-    address:
-    - line 1
-    - line 2
-    url: https://journal.r-project.org
-    orcid: 0000-0002-9079-593X
-    email:  author1@work
-  - name: Author Two
-    url: https://journal.r-project.org
-    email: author2@work
-    orcid: 0000-0002-9079-593X
-    affiliation: Affiliation 1
-    address:
-    - line 1 affiliation 1
-    - line 2 affiliation 1
-    affiliation2: Affiliation 2
-    address2:
-    - line 1 affiliation 2
-    - line 2 affiliation 2
-  - name: Author Three
-    url: https://journal.r-project.org
-    email: author3@work
-    affiliation: Affiliation
-    address:
-    - line 1 affiliation
-    - line 2 affiliation
-abstract: >
-  An abstract of less than 150 words.
-preamble: |
-  % Any extra LaTeX you need in the preamble
-  
-# per R journal requirement, the bib filename should be the same as the output 
-# tex file. Don't forget to rename the bib file and change this example value.
-bibliography: RJreferences.bib
-
-output: rticles::rjournal_article
----
-
-## Introduction
-
-Introductory section which may include references in parentheses
-[@R], or cite a reference such as @R in the text.
-
-## Section title in sentence case
-
-This section may contain a figure such as Figure \ref{fig:Rlogo}.
-
-```{r, Rlogo, echo=FALSE, fig.cap='The logo of R.', out.width='2in', fig.align='center', fig.pos='htbp'}
-knitr::include_graphics('Rlogo-5.png')
-```
-
-## Another section
-
-There will likely be several sections, perhaps including code snippets, such as:
-
-```{r}
-x <- 1:10
-plot(x)
-```
-
-## Summary
-
-This file is only a basic article template. For full details of _The R Journal_ style and information on how to prepare your article for submission, see the [Instructions for Authors](https://journal.r-project.org/share/author-guide.pdf).
-
-### About this format and the R Journal requirements
-
-`rticles::rjournal_article` will help you build the correct files requirements: 
-
-* A R file will be generated automatically using `knitr::purl` - see
-https://bookdown.org/yihui/rmarkdown-cookbook/purl.html for more information.
-* A tex file will be generated from this Rmd file and correctly included in
-`RJwapper.tex` as expected to build `RJwrapper.pdf`.
-* All figure files will be kept in the default rmarkdown `*_files` folder. This
-happens because `keep_tex = TRUE` by default in `rticles::rjournal_article`
-* Only the bib filename is to modifed. An example bib file is included in the
-template (`RJreferences.bib`) and you will have to name your bib file as the
-tex, R, and pdf files.
diff --git a/inst/rmarkdown/templates/rjournal/template.yaml b/inst/rmarkdown/templates/rjournal/template.yaml
deleted file mode 100644
index 570a3c351..000000000
--- a/inst/rmarkdown/templates/rjournal/template.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-name: R Journal Submission
-description: >
- Template for creating articles for the R journal.
-create_dir: true
-
diff --git a/man/rjournal_article.Rd b/man/rjournal_article.Rd
index d509cab28..018f8d12e 100644
--- a/man/rjournal_article.Rd
+++ b/man/rjournal_article.Rd
@@ -6,72 +6,9 @@
 \usage{
 rjournal_article(..., keep_tex = TRUE, citation_package = "natbib")
 }
-\arguments{
-\item{...}{Arguments to \code{\link[rmarkdown:pdf_document]{rmarkdown::pdf_document()}}.}
-
-\item{keep_tex}{Keep the intermediate tex file used in the conversion to PDF.
-Note that this argument does not control whether to keep the auxiliary
-files (e.g., \file{.aux}) generated by LaTeX when compiling \file{.tex} to
-\file{.pdf}. To keep these files, you may set \code{options(tinytex.clean =
-FALSE)}.}
-
-\item{citation_package}{The LaTeX package to process citations, \code{natbib}
-or \code{biblatex}. Use \code{default} if neither package is to be used,
-which means citations will be processed via the command
-\command{pandoc-citeproc}.}
-}
 \description{
 \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}}
 
-This function is now deprecated in favor of the \href{https://rjournal.github.io/rjtools/}{\strong{rjtools}} package
-which is now officialy recommanded by R Journal \url{https://rjournal.github.io/submissions.html}. See below for document
-}
-\section{About this format and the R Journal requirements}{
-Format for creating R Journal articles. Adapted from
-\url{https://journal.r-project.org/submissions.html}.
-
-This file is only a basic article template. For full details of \emph{The R
-Journal} style and information on how to prepare your article for submission,
-see the \href{https://journal.r-project.org/share/author-guide.pdf}{Instructions for Authors}
-
-\code{rticles::rjournal_article} will help you build the correct files requirements:
-\itemize{
-\item A R file will be generated automatically using \code{knitr::purl} - see
-https://bookdown.org/yihui/rmarkdown-cookbook/purl.html for more information.
-\item A tex file will be generated from this Rmd file and correctly included in
-\code{RJwapper.tex} as expected to build \code{RJwrapper.pdf}.
-\item All figure files will be kept in the default rmarkdown \verb{*_files} folder. This
-happens because \code{keep_tex = TRUE} by default in \code{rticles::rjournal_article}
-\item Only the bib filename is to be modified. An example bib file is included in the
-template (\code{RJreferences.bib}) and you will have to name your bib file as the
-tex, R, and pdf files.
-}
-}
-
-\section{About YAML header fields}{
-This section documents some of the YAML fields that can be used with this
-formats.
-\subsection{The \code{author} field in the YAML header}{\tabular{lll}{
-   FIELD \tab TYPE \tab DESCRIPTION \cr
-   \code{name} \tab \emph{required} \tab name and surname of the author \cr
-   \code{affiliation} \tab \emph{required} \tab name of the author's affiliation \cr
-   \code{address} \tab \emph{required} \tab at least one address line for the affiliation \cr
-   \code{url} \tab \emph{optional} \tab an additional url for the author or the main affiliation \cr
-   \code{orcid} \tab \emph{optional} \tab the authors ORCID if available \cr
-   \code{email} \tab \emph{required} \tab the author's e-mail address \cr
-   \code{affiliation2} \tab \emph{optional} \tab name of the author's 2nd affiliation \cr
-   \code{address2} \tab \emph{optional} \tab address lines belonging to the author's 2nd affiliation \cr
+This function is now defunct in favor of the \href{https://rjournal.github.io/rjtools/}{\strong{rjtools}} package
+which is now officialy recommanded by R Journal \url{https://rjournal.github.io/submissions.html}.
 }
-
-
-\emph{Please note: Only one \code{url}, \code{orcid} and \code{email} can be provided per author.}
-}
-
-\subsection{Other YAML fields}{\tabular{lll}{
-   FIELD \tab TYPE \tab DESCRIPTION \cr
-   \code{bibliography} \tab \emph{with default} \tab the BibTeX file with the reference entries \cr
-}
-
-}
-}
-

From 9a8d8aeafaf08124db2d8ae3f35483eceb2b18d2 Mon Sep 17 00:00:00 2001
From: Christophe Dervieux <christophe.dervieux@gmail.com>
Date: Thu, 11 Dec 2025 11:43:21 +0100
Subject: [PATCH 2/4] remove from other docs and vignette

---
 R/rjournal_article.R                   | 2 +-
 R/utils.R                              | 2 +-
 man/journals.Rd                        | 2 +-
 man/rjournal_article.Rd                | 1 +
 vignettes/articles/_child_examples.Rmd | 5 -----
 5 files changed, 4 insertions(+), 8 deletions(-)

diff --git a/R/rjournal_article.R b/R/rjournal_article.R
index 1ce50e824..e0721c8b9 100644
--- a/R/rjournal_article.R
+++ b/R/rjournal_article.R
@@ -6,7 +6,7 @@
 #' This function is now defunct in favor of the [**rjtools**](https://rjournal.github.io/rjtools/) package
 #' which is now officialy recommanded by R Journal <https://rjournal.github.io/submissions.html>.
 #'
-#' @internal
+#' @keywords internal
 rjournal_article <- function(..., keep_tex = TRUE, citation_package = "natbib") {
 
   lifecycle::deprecate_stop("0.25", "rjournal_article()", "rjtools::rjournal_pdf_article()", details = "See official recommandation at https://rjournal.github.io/submissions.html")
diff --git a/R/utils.R b/R/utils.R
index 70d6adaa2..684c221b9 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -5,7 +5,7 @@
 #' These names can be useful in two ways:
 #'
 #' * You can add `_article` suffix to get the name of the output format (e.g.,
-#' [rjournal_article()]).
+#' [jss_article()]).
 #'
 #' * You can use the name directly in the `template` argument of
 #' [rmarkdown::draft()].
diff --git a/man/journals.Rd b/man/journals.Rd
index 3e3649cd0..b769bf3dd 100644
--- a/man/journals.Rd
+++ b/man/journals.Rd
@@ -16,7 +16,7 @@ List available journal names in this package.
 These names can be useful in two ways:
 \itemize{
 \item You can add \verb{_article} suffix to get the name of the output format (e.g.,
-\code{\link[=rjournal_article]{rjournal_article()}}).
+\code{\link[=jss_article]{jss_article()}}).
 \item You can use the name directly in the \code{template} argument of
 \code{\link[rmarkdown:draft]{rmarkdown::draft()}}.
 }
diff --git a/man/rjournal_article.Rd b/man/rjournal_article.Rd
index 018f8d12e..edbb01541 100644
--- a/man/rjournal_article.Rd
+++ b/man/rjournal_article.Rd
@@ -12,3 +12,4 @@ rjournal_article(..., keep_tex = TRUE, citation_package = "natbib")
 This function is now defunct in favor of the \href{https://rjournal.github.io/rjtools/}{\strong{rjtools}} package
 which is now officialy recommanded by R Journal \url{https://rjournal.github.io/submissions.html}.
 }
+\keyword{internal}
diff --git a/vignettes/articles/_child_examples.Rmd b/vignettes/articles/_child_examples.Rmd
index 94e6b0ab0..c861f1d4d 100644
--- a/vignettes/articles/_child_examples.Rmd
+++ b/vignettes/articles/_child_examples.Rmd
@@ -64,11 +64,6 @@ for (journal in journals()) {
     path = xfun::with_ext(out_pdf, "gif"),
     delay = 1)
   message("Retrieving built files.")
-  # specific treatment for rjournal name
-  if (journal == "rjournal") {
-    file.rename(out_pdf, out_pdf <- file.path(dirname(out_pdf), "rjournal_article.pdf"))
-    file.rename(out_gif, out_gif <- file.path(dirname(out_gif), "rjournal_article.gif"))
-  }
   file.copy(out_pdf, out_dir)
   file.copy(out_gif, out_dir)
   # clean temp dir

From 3701ee6e440cbf81fa4bcc7a94da62f00c0a2949 Mon Sep 17 00:00:00 2001
From: Christophe Dervieux <christophe.dervieux@gmail.com>
Date: Thu, 11 Dec 2025 11:43:34 +0100
Subject: [PATCH 3/4] Update test

---
 tests/testit/test-formats.R               | 1 -
 tests/testthat/_snaps/rjournal_article.md | 6 +++---
 tests/testthat/test-rjournal_article.R    | 4 ++--
 3 files changed, 5 insertions(+), 6 deletions(-)

diff --git a/tests/testit/test-formats.R b/tests/testit/test-formats.R
index 073b476a3..0b5e3f5c5 100644
--- a/tests/testit/test-formats.R
+++ b/tests/testit/test-formats.R
@@ -72,7 +72,6 @@ test_format("peerj")
 test_format("pihph")
 test_format("plos")
 test_format("pnas")
-test_format("rjournal")
 test_format("rsos")
 test_format("rss")
 test_format("sage")
diff --git a/tests/testthat/_snaps/rjournal_article.md b/tests/testthat/_snaps/rjournal_article.md
index cd17d812f..994522821 100644
--- a/tests/testthat/_snaps/rjournal_article.md
+++ b/tests/testthat/_snaps/rjournal_article.md
@@ -1,10 +1,10 @@
-# rjournal_article() is deprecated
+# rjournal_article() is defunct
 
     Code
       x <- rjournal_article()
     Condition
-      Warning:
-      `rjournal_article()` was deprecated in rticles 0.25.
+      Error:
+      ! `rjournal_article()` was deprecated in rticles 0.25 and is now defunct.
       i Please use `rjtools::rjournal_pdf_article()` instead.
       i See official recommandation at https://rjournal.github.io/submissions.html
 
diff --git a/tests/testthat/test-rjournal_article.R b/tests/testthat/test-rjournal_article.R
index 9f7d2ed6e..c1fb151cb 100644
--- a/tests/testthat/test-rjournal_article.R
+++ b/tests/testthat/test-rjournal_article.R
@@ -1,5 +1,5 @@
-test_that("rjournal_article() is deprecated", {
+test_that("rjournal_article() is defunct", {
   expect_snapshot({
     x <- rjournal_article()
-  })
+  }, error = TRUE)
 })

From 4c9bdebdb71744417895bae1a37fe66686555bea Mon Sep 17 00:00:00 2001
From: Christophe Dervieux <christophe.dervieux@gmail.com>
Date: Thu, 11 Dec 2025 11:46:25 +0100
Subject: [PATCH 4/4] Other removal

---
 R/utils.R                            | 7 -------
 tests/testthat/test-check-template.R | 3 ---
 vignettes/usage.md                   | 3 ---
 3 files changed, 13 deletions(-)

diff --git a/R/utils.R b/R/utils.R
index 684c221b9..5db5f63b8 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -47,13 +47,6 @@ merge_list <- function(x, y) {
 #' @param output Path to save output.
 #' @param in_header Paths to files to include in the header.
 #' @return (Invisibly) The path of the generate file.
-#' @examples
-#' x <- rticles:::template_pandoc(
-#'   list(preamble = "%abc", filename = "wickham"),
-#'   rticles:::find_resource("rjournal", "RJwrapper.tex"),
-#'   tempfile()
-#' )
-#' if (interactive()) file.show(x)
 #' @noRd
 template_pandoc <- function(metadata, template, output,
                             in_header = NULL, verbose = FALSE) {
diff --git a/tests/testthat/test-check-template.R b/tests/testthat/test-check-template.R
index f576f7b88..b802a4ff4 100644
--- a/tests/testthat/test-check-template.R
+++ b/tests/testthat/test-check-template.R
@@ -3,9 +3,6 @@ skip_on_cran()
 
 temp_file <- list.files(pkg_file_template(), recursive = TRUE, pattern = "template.tex$", full.names = TRUE)
 
-# Rjournal template has another name
-temp_file[grep("rjournal", temp_file)] <- pkg_file_template("rjournal", "resources", "RJwrapper.tex")
-
 expect_contains <- function(file, pattern, nb = 1, at_least = NULL, ...) {
   content <- xfun::read_utf8(file)
   matched <- grepl(pattern, content, ...)
diff --git a/vignettes/usage.md b/vignettes/usage.md
index b339e11fd..dabdf3ac7 100644
--- a/vignettes/usage.md
+++ b/vignettes/usage.md
@@ -11,9 +11,6 @@ If you are not using RStudio, you'll also need to install [Pandoc](https://pando
 rmarkdown::draft(
     "MyJSSArticle.Rmd", template = "jss", package = "rticles"
 )
-rmarkdown::draft(
-    "MyRJournalArticle", template = "rjournal", package = "rticles"
-)
 ```
    
    This will create a folder containing a Rmd file using the corresponding output format and all the assets required by this format.