Right now, the PR is being held up due to hyperref not playing nicely with \MakeUppercase. So, using any chapter heading, e.g. # Chapter, is getting a nice ol' error of:

! Undefined control sequence.
\MakeUppercase ...ppercaseUnsupportedInPdfStrings 

Error: Failed to compile _main.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See _main.log for more info.
Please delete _main.Rmd after you finish debugging the error.

So, the solution I opted to go for here is to modify the .cls file.

That is, going from:

\MakeUppercase{}

to

\texorpdfstring{\MakeUppercase{text}}{}

Useful links:

• Chosen solution: suggested using \texorpdfstring{\MakeUppercase{text}}{}
  • https://tex.stackexchange.com/questions/199374/makeuppercase-in-section-and-chapter-with-hyperref-cause-trouble
  • https://latex.org/forum/viewtopic.php?p=59321#p59321
• Attempted solution: Do a global modification of each definition.
  • https://tex.stackexchange.com/a/442011/53878
  • Need to figure out the allowed tex commands. Potential ask a new question?

\makeatletter
\renewcommand{\section}{\@ifstar{\@sSection}{\@Section}}
\newcommand{\@sSection}[2][]{%
  \oldsection*{\texorpdfstring{\MakeUppercase{#2}}{#2}}}
\newcommand{\@Section}[2][]{%
  \def\shortsec{#1}%
  \ifx\shortsec\empty%
    \oldsection{\texorpdfstring{\MakeUppercase{#2}}{#2}}
  \else%
    \oldsection[\texorpdfstring{\MakeUppercase{#1}}{#1}]{\texorpdfstring{\MakeUppercase{#2}}{#2}}
  \fi}
\makeatother

• Attempted solution: Suggested using the package textcase to override \MakeUppercase with \MakeTextUppercase; however, it didn't work even when placed within the .cls
  • https://tex.stackexchange.com/questions/46525/preventing-makeuppercase-from-affecting-mathematics
• More details on the problem
  • https://texfaq.org/FAQ-casechange

Note: Not all instances were changed. Only instances that dealt with a hyperref.

Still not where it needs to be...

! Undefined control sequence.
\listtablename ...tablename \else \texorpdfstring 
                                                  {\MakeUppercase {\thesis@l...
l.97 \listoftables