'Pandoc cannot find image path referenced in external HTML file pulled into R Markdown, despite using here() package

I am producing an HTML document through R Markdown, which uses a few external HTML documents for headers and footers. I am also using the here() package to allow relative paths throughout my project. However, when using YAML to include the external HTML through R code, the relative paths within those files do not work.

This is the YAML header of the R Markdown code:

---
title: "Test"
output:
  html_document:
    includes:
      in_header: !expr "here::here('FORMATTING','favicon.html')"
---

The file 'favicon.html' has the following code:

<link rel="icon" type="image/png" href="favicon.ico"/>

My folder structure is:

Main
│   └──.here
├──SCRIPTS
│   └──test_code.Rmd
├──FORMATTING
│   └──favicon.html
│   └──favicon.ico

When I run the script using 'Knit' button in RStudio, I get the following error:

File favicon.ico not found in resource path
Error: pandoc document conversion failed with error 99

It seems that pandoc can find the HTML files just fine using there R code, but then it seems to want an absolute file path for the actual image.

How can I ensure pandoc finds the images without having to resort to absolute paths?

htmlrr-markdownpandoc


Solution 1:[1]

I habe exactly the same problem. The solution proposed by Modern_ibex (<link rel="icon" type="image/png" href=".\..\FORMATTING\favicon.ico"/> ) does not work for me.

My favicon.html and logo.png are stored in folder "Data". In favicon.html: "<link rel="shortcut icon" href="Data/logo.png" />"

project.Rproj
|
|___ Data (- favicon.html
|          - logo.png)
|
|___ Scripts
           |__ Rmds (- my file.rmd)
           |
           |__ ...

My rmd file is stored in "Scripts/Rmds". My YAML looks like:

title: "Analysis"
author: "me"
date: "`r format(Sys.time(), '%d. %B %Y')`"
output:
  html_document:
    includes:
      in_header: !expr here::here("Data/favicon.html")

when running I get an error message: File Data/logo.png not found in resource path Error: pandoc document conversion failed with error 99 So favicon.html is read but the href is not interpreted. I tried divers href in favicon.html with ~ or . or .. or / or \ or r code but no results.

thanks in advance for help!

Solution 2:[2]

My solution:

In .Rmd YAML:

title: "Analysis"
author: "me"
date: "`r format(Sys.time(), '%d. %B %Y')`"
output:
  html_document:
    includes:
      in_header: !expr here::here("Data/favicon.html")

In favicon.html:

<link rel="shortcut icon" href="../../Data/logo.png" />

File structure:

project.Rproj
|
|___ Data (- favicon.html
|          - logo.png)
|
|___ Scripts
           |__ Rmds (- my file.rmd)
           |
           |__ ...

Sources

This article follows the attribution requirements of Stack Overflow and is licensed under CC BY-SA 3.0.

Source: Stack Overflow

Solution Source
Solution 1 Claire
Solution 2 Zach Jensz

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