R Markdown YAML "Scanner error: mapping values..."

Question

I have noticed this issue when knitting all file types (html, pdf, word). To make sure there's not an issue specific to my program, I went ahead and ran the default .rmd file you get when you create a new markdown. In each case, it does knit correctly, but I always see this at the end. I have searched online and here but cannot seem to find an explanation

Error in yaml::yaml.load(string, ...) : 
  Scanner error: mapping values are not allowed in this context at line 6, column 19
Error in yaml::yaml.load(string, ...) : 
  Scanner error: mapping values are not allowed in this context at line 6, column 19
Error in yaml::yaml.load(string, ...) : 
  Scanner error: mapping values are not allowed in this context at line 4, column 22

Here is my default YAML

---
title: "Untitled"
author: "Scott Jackson"
date: "April 20, 2017"
output: word_document
---

Line 4, column 22 is the space between the 7 and " I'm not sure where Line 6, column 19 is, but that line is the dashes at the bottom

Any ideas?

Thank you.

Amandaamandi

I can only guess. There might be some spaces in any of those lines that dont belong there? – Bullshit

Do you get this error running the default markdown file (if you do use markdown)? – Amandaamandi

No. As I said, I think I had this error once when I had unnecessary spaces in my YAML. – Bullshit

I get this error whenever I open a new RStudio session. – Asuncionasunder

I had this because of a space in my style file. – Albie

I had this because I wasn't wrapping by title with quotation marks. That worked fine until I added a colon in the title. Then I started getting that error, which was solved by putting the document title between quotes. – Chocolate

I also receive this same error. I wrote: title:"Untitled" without space between title: and "Untitled". I fix this error when i wrote title: "Untitled" with space. – Geochemistry

Answer 1

I get this error when trying to add a table of contents to the YAML:

title: "STAC2020 Data Analysis"
date: "July 16, 2020"
output: html_notebook:
  toc: true

However, if I put html_notebook: on to a separate line then I don't get the error:

title: "STAC2020 Data Analysis"
date: "July 16, 2020"
output:
  html_notebook:
    toc: true

I do not know why this formatting makes a difference, but it allowed my document to knit and with a table of contents.

Handel

frustrating because the "wrong" example you posted is basically lifted straight from the RMarkdown cheat sheet – Male

Answer 2

I realize this question has gone unanswered for awhile, but maybe someone can still benefit. I had the same error message and I realized I had an extra header command in my yaml. I can't reproduce your exact error, but I get the same message with different line/column references with:

---
title: "Untitled"
author: "Scott Jackson"
date: "April 20, 2017"
output: output: word_document
---

Error in yaml::yaml.load(string, ...) : 
  Scanner error: mapping values are not allowed in this context at line 4, column 15
Calls: <Anonymous> ... parse_yaml_front_matter -> yaml_load_utf8 -> <Anonymous>
Execution halted

Line 4 column 15 seems to refer to the second colon after the second "output".

Bioclimatology

Yet another example of a thoroughly unhelpful and misleading error message! It seems to mean "Something wrong with your YAML, but don't know what". – Trawler

Answer 3

I received this error when there was an indentation in the wrong place:

For example, the indentation before header-includes as seen in the example code below caused the error

---
title: "This is a title"
author: "Author Name"
   header-includes:
.
.
.
---

When you remove the indentation, the following code below did not produce the error:

---
title: "This is a title"
author: "Author Name"
header-includes:
.
.
.
---

Admix

Answer 4

Similarly to Tim Ewers I also got this error when I added a TOC to the YAML:

title: "My title"
date: "April 1, 2020"
output:
  pdf_document: default 
    toc: true
  html_document: paged

However, the solution I found was to remove "default", this allowed me to knit the document without an error:

title: "My title"
date: "April 1, 2020"
output:
  pdf_document:
    toc: true
  html_document: paged

Phantom

Answer 5

I know this is a 5 year old question but I just got this same error as I was missing a colon

---
title: ''
output: 
  pdf_document
    includes: 
      before_body: before_body.tex
---

should have been

---
title: ''
output: 
  pdf_document:
    includes: 
      before_body: before_body.tex
---

and while that doesn't strictly answer the example given, I hope it will help future sufferers of this error message.

Fishback

Answer 6

I guess this error happens on your content instead of your yaml block. Because there is no extra content display so I will give a minimal example.

> library(yaml)
> library(magrittr)
> "
+ ---
+ title: 'This is a title'
+ output: github_document
+ ---
+ 
+ some content
+ " %>% 
+     yaml.load()
$title
[1] "This is a title"

$output
[1] "github_document"

It works well. And here is another example.

> "
+ ---
+ title: 'This is a title'
+ output: github_document
+ ---
+ 
+ some content
+ some content: some content
+ " %>% 
+     yaml.load()
Error in yaml.load(.) : 
  Scanner error: mapping values are not allowed in this context at line 8, column 13

The errors happens at line 8. Because there is a key-value pair not at yaml block. yaml.load is not enough smart for me. The temporal solution for me is just extract all lines above the second ---.

> text <- "
+ ---
+ title: 'This is a title'
+ output: github_document
+ ---
+ 
+ some content
+ some content: some content
+ "
> library(xfun)
> read_lines(text,n_max = 5) %>% 
+     yaml.load()
$title
[1] "This is a title"

$output
[1] "github_document"

Wetmore

Answer 7

I also got the error when I had a colon in my title--

Failed

title: Bad: Title
output: html_document

Fixed

title: Good Title
output: html_document

Orient

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