I'm using rmarkdown, and after knitting a document I always receive this warning (the document knits normal, though).

Output created: XY.pdf
Warning message:
LaTeX Warning: Command \@footnotemark  has changed.
               Check if current package is valid. 

I've learned the issue might be related to the "footmisc" package and the order of package loading. Therefore, I assume a package clash whatsoever. Since there are several answers for similar warnings, but none of them including \@footnotemark, allow me to post the relevant part of my YAML header here. What should I possibly change?

    fig_caption: yes
    keep_tex: yes
    # toc: yes
    toc_depth: 3
    # number_sections: true
lang: en
subparagraph: yes
fontsize: 12pt
link-citations: yes
linkcolor: blue
- \usepackage{setspace}
- \usepackage[hang,flushmargin]{footmisc}
- \usepackage{fancyhdr}
- \usepackage{pdflscape}
- \usepackage{dcolumn}
# - \usepackage[english]{babel}
- \usepackage{rotating, graphicx}
- \usepackage{floatpag}
- \usepackage{caption}
- \usepackage[export]{adjustbox}
- \usepackage{icomma}
- \usepackage{tabularx}
- \usepackage{lipsum}
- \usepackage{csquotes}
- \usepackage{amsmath,amssymb}
- \usepackage{amsfonts}
- \usepackage{mathtools,extarrows}
# - \usepackage[sf,bf]{titlesec}
- \usepackage[labelfont=bf]{caption}
- \usepackage{scrextend}
- \usepackage{graphicx}
- \usepackage{subfig}
- \usepackage{dcolumn}
- \usepackage{changepage}
# - \usepackage{siunitx}
# - \documentclass[english, article]
- \usepackage{placeins}

- \pagestyle{fancy}
- \fancyhf{} % sets both header and footer to nothing
- \renewcommand{\headrulewidth}{0pt}
- \fancyhead[LE,RO]{\textsf{\thepage}}
- \fancyfoot[CE,CO]{}
- \fancyhead[LO,RE]{\textsf{\textit{\footnotesize{author$\text{:}$ title}}}}
- \newcommand{\blandscape}{\begin{landscape}}
- \newcommand{\elandscape}{\end{landscape}}
- \floatpagestyle{empty}
- \setlength{\columnsep}{18pt}
- \setlength{\parskip}{0cm}
- \setlength{\parindent}{1em}
- \setlength{\headheight}{14.5pt}
- \captionsetup{justification=raggedright, singlelinecheck=false}
# nocite: | 
#  @knitr, @rmarkdown, @RStudio, @R
urlcolor: blue
# documentclass: article
- a4paper
- twoside
# - english


Edit: And this would be the compiled LaTeX code:

% Options for packages loaded elsewhere
\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
  \usepackage{textcomp} % provide euro and other symbols
\else % if luatex or xetex
% Use upquote if available, for straight quotes in verbatim environments
\IfFileExists{microtype.sty}{% use microtype if available
  \UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts
\@ifundefined{KOMAClassName}{% if non-KOMA class
  }{% else
    \setlength{\parskip}{6pt plus 2pt minus 1pt}}
}{% if KOMA class
\IfFileExists{xurl.sty}{\usepackage{xurl}}{} % add URL line breaks if available
  pdfcreator={LaTeX via pandoc}}
\urlstyle{same} % disable monospaced font for URLs
% Scale images if necessary, so that they will not overflow the page
% margins by default, and it is still possible to overwrite the defaults
% using explicit options in \includegraphics[width, height, ...]{}
% Set default figure placement to htbp
\setlength{\emergencystretch}{3em} % prevent overfull lines
\setcounter{secnumdepth}{-\maxdimen} % remove section numbering
\usepackage{rotating, graphicx}
\fancyhf{} % sets both header and footer to nothing
\fancyhead[LO,RE]{\textsf{\textit{\footnotesize{author$\text{:}$ title}}}}
\captionsetup{justification=raggedright, singlelinecheck=false}
  % Load polyglossia as late as possible: uses bidi with RTL langages (e.g. Hebrew, Arabic)




  • Could you please make your code compilable? – leandriis Jan 7 '20 at 10:37
  • 2
    Note that not many here are using markdown or r-markdown to generate LaTeX/PDF. So it would be useful to have the generated latex code posted as that is easier for us to debug than markdown setups. (I'm guessing this is what @leandriis is asking for in their comment above) – daleif Jan 7 '20 at 11:17
  • 2
    @daleif I understand, thx for the suggestion, updated. – jay.sf Jan 7 '20 at 11:23
  • 2
    MWE that still reproduced the warning: \documentclass{article} \usepackage{hyperref} \usepackage[hang,flushmargin]{footmisc} \usepackage{scrextend} \begin{document} test \end{document}. You can get rid of the warning in the above MWE by loading hyperref last, which is, according to its documentation, generally (with a few exceptions) the correct order. – leandriis Jan 7 '20 at 12:07
  • 3
    As mentioned we mostly handles LaTeX stuff, so we cannot help debugging markdown compilers. So you probably have to find someone who knows about this markdown conversion route. – daleif Jan 7 '20 at 12:41

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