Error in YAML when knitting RMarkdown document - Scanner error - r

Question

I'm trying to knit an RMD file in RStudio but I get the following error
Error in yaml::yaml.load(string, ...) : Scanner error: while scanning a plain scalar at line 31, column 5 found a tab character
that violate intendation at line 34, column 1 Calls: ...
parse_yaml_front_matter -> yaml_load_utf8 -> Execution
halted
The header of the rmd file is as following:
> ---
> title: "Homework 4"
> author: NAME OF THE AUTHOR, Fall 2018
> date: Due Friday, September 30, 11:59pm
> subparagraph: yes
> output:
> pdf_document:
> number_sections: true header-includes:
> - \setcounter{secnumdepth}{1}
> - \pagenumbering{gobble}
> - \sloppy
> - \hypersetup{ breaklinks=true,
> pdftitle={\#title},
> pdfauthor={\#author},
> colorlinks=true,
> breaklinks=true,
> urlcolor= blue,
> linkcolor= blue,
> citecolor=blue,
> bookmarksopen=false,
> pdftoolbar=false,
> pdfmenubar=false
> }
> - \usepackage{titlesec}
> - \renewcommand{\thesection}{\arabic{section}.}
> - \usepackage{mathpazo}
> - \usepackage{etoolbox}
> - \usepackage{geometry}
> - \usepackage{graphicx}
> - \newcommand{\protectbracket}[1]{#1}
> - \makeatletter
> \protectbracket{\preto\Gin#extensions{svg,}}
> \DeclareGraphicsRule{.svg}{pdf}{.pdf}{\noexpand\Gin#base.pdf} \makeatother
> - \geometry{verbose,tmargin=1in,bmargin=1in,lmargin=1in,rmargin=1in}
> - \usepackage[most]{tcolorbox}
> - \definecolor{block-gray}{gray}{0.85}
> - \newtcolorbox{darkquote}{colback=block-gray,grow to right by=-10mm,grow to left by=-10mm, boxrule=0pt,boxsep=0pt,breakable}
> - \renewenvironment{quote}{\begin{darkquote}}{\end{darkquote}\ignorespacesafterend}
> ---
Any ideas what is causing this? The error is pointing to character "n" in line 31 which I am not sure how to fix it. any help or suggestion is highly appreciated.
I have tried this with both RStudio installed on both mac and PC.

Answer 1

Assuming those > at the beginning of the line are left-overs from copy and paste (they for sure should not be in the file), you have a YAML document that starts like:
---
title: "Homework 4"
author: NAME OF THE AUTHOR, Fall 2018
date: Due Friday, September 30, 11:59pm
subparagraph: yes
output:
pdf_document:
number_sections: true header-includes:
- \setcounter{secnumdepth}{1}
and that is invalid as you you cannot have both a mapping as value for the key pdf_document as well as a sequence (less indented in addition).
That, probably combined with the combination of the inline colon-space and end-of-line-colon on one line, confuses that parser
You probably want to change that to something beginning with:
---
title: "Homework 4"
author: NAME OF THE AUTHOR, Fall 2018
date: Due Friday, September 30, 11:59pm
subparagraph: yes
output:
pdf_document:
number_sections: true
header-includes:
- \setcounter{secnumdepth}{1}