Resolving the Flexdashboard Error with Pandoc: A Step-by-Step Guide

Understanding the flexdashboard Error with Pandoc

In recent months, RStudio has introduced a new package called flexdashboard which provides an easy-to-use interface for creating interactive dashboards. One of the features of flexdashboard is its ability to include custom CSS styles in the dashboard. However, this feature can sometimes cause issues, as we will see in this article.

Installing Pandoc

To create a flexdashboard, we first need to install pandoc, which is a command-line tool for converting R Markdown documents into various formats, including HTML and PDF documents. When installing pandoc using the install.packages() function in R, it’s not uncommon to encounter an error like the one described in the question.

# Installing Pandoc

> install.packages("pandoc")
Warning in install.packages :
  package ‘pandoc’ is not available (for R version 3.4.1)

The flexdashboard Error with Pandoc

The error message we see when trying to create a flexdashboard is quite generic and doesn’t provide much information about the cause of the problem. However, by examining the stacktrace more closely, we can see that the issue lies in the pandoc package.

# The Error Message

> pandoc: Could not fetch https://bootswatch.com/4/litera/bootstrap.css
HttpExceptionRequest Request {
  host                 = "bootswatch.com"
  port                 = 443
  secure               = True
  requestHeaders       = []
  path                 = "/4/litera/bootstrap.css"
  queryString          = ""
  method               = "GET"
  proxy                = Nothing
  rawBody              = False
  redirectCount        = 10
  responseTimeout      = ResponseTimeoutDefault
  requestVersion       = HTTP/1.1
}
 (InternalException (HandshakeFailed Error_EOF))
Error: pandoc document conversion failed with error 67
In addition: There were 13 warnings (use warnings() to see them)
Execution halted

The error message is quite cryptic, but it can be broken down into several parts.

The first part of the stacktrace mentions a HttpExceptionRequest object. This object represents an HTTP request that failed. In this case, the request was made to fetch a CSS file from bootswatch.com.
The specific error mentioned is InternalException (HandshakeFailed Error_EOF). This suggests that there was a problem with the network connection or the server responding.
Finally, we see an Error: pandoc document conversion failed with error 67 message. This suggests that there was an issue with converting the R Markdown document to HTML.

Possible Causes

There are several possible causes for this error.

1. Network Connection Issues

One of the most common issues is a problem with your network connection. If you’re behind a proxy or have a slow internet connection, it can cause problems when making requests to external websites like bootswatch.com.

2. Server Errors

Another possible cause is a server error on the part of bootswatch.com. This could be due to a variety of reasons such as maintenance issues, high traffic, or even security measures.

3. Pandoc Version Issues

It’s also worth noting that there might be an issue with the version of pandoc being used. If you’re using an outdated version, it may not be compatible with newer versions of RStudio and its packages.

Solution

To solve this problem, we need to try a few different approaches.

1. Check Your Network Connection

First, let’s check your network connection to make sure it’s stable and working correctly. You can do this by running the following command in R:

# Check Network Connection

> system("ping -c 3 bootswatch.com")

This will attempt to ping bootswatch.com three times. If you don’t see any responses, there might be a problem with your network connection.

2. Clear Cache and Cookies

Next, let’s try clearing the cache and cookies for pandoc. You can do this by running the following code:

# Clear Cache and Cookies

> options(pandoc_cache_size = "off")
>
> # Try creating a flexdashboard again

This will clear the cache and cookies for pandoc, which may help resolve any issues with fetching external resources.

3. Update Pandoc Version

Finally, let’s try updating the version of pandoc being used. You can do this by running the following code:

# Update Pandoc Version

> update.packages()

This will attempt to update pandoc to the latest version available.

Conclusion

In conclusion, the flexdashboard error with pandoc is a common issue that can be caused by a variety of factors. By checking your network connection, clearing cache and cookies, and updating pandoc, you should be able to resolve this problem and create a successful flexdashboard.

Additional Tips and Tricks

Here are some additional tips and tricks for working with flexdashboards and pandoc:

Use the --no-clean Option: If you’re experiencing issues with fetching external resources, try using the --no-clean option when creating your flexdashboard. This will prevent pandoc from cleaning up any temporary files.

# Use --no-clean Option

> pandoc -r rmarkdown::flexdashboard --
  -o flex.html
  --no-clean

Specify a Custom CSS File: If you’re experiencing issues with fetching external CSS resources, try specifying a custom CSS file using the css option.

# Specify Custom CSS File

> pandoc -r rmarkdown::flexdashboard --
  -o flex.html
  --css-url="custom.css"

Use the --no-colors Option: If you’re experiencing issues with colors in your flexdashboard, try using the --no-colors option. This will prevent pandoc from using colors in its output.

# Use --no-colors Option

> pandoc -r rmarkdown::flexdashboard --
  -o flex.html
  --no-colors

By following these tips and tricks, you should be able to create a successful flexdashboard with pandoc.

Last modified on 2024-11-04