Frequently asked questions

workflowr version 1.1.1

John Blischak

2018-07-06

Why isn’t my website displaying online?

Occasionally your website may not display (or recent updates will not immediately appear), and you may even receive an email from GitHub with the following message:

The page build failed for the master branch with the following error:

unable to build page. Please try again later.

For information on troubleshooting Jekyll see:

https://help.github.com/articles/troubleshooting-jekyll-builds

If you have any questions you can contact us by replying to this email.

If you’ve followed the setup instructions from the Getting started vignette, and especially if the website displayed in the past, it’s very unlikely that you caused the problem. The hosting is provided by GitHub Pages, and it sometimes is delayed or down. Overall for a free service, it is very reliable. If you wait 5 minutes (or 30 minutes at most), your website will likely be back to normal.

If you are anxious to know if there is a problem and when it will be resolved, you can check the status of the Twitter account GitHub Status for the most up-to-date reports from GitHub. If you suspect that the problem may have been caused by your recent changes to your website (again, this is unlikely), you can view the GitHub help page Troubleshooting GitHub Pages builds.

Can I make my workflowr website private?

Short answer: No, not if you use the default setup that hosts the site on GitHub Pages. For an alternative setup, see the FAQ below that describes an option for securely sharing your workflowr site.

Long answer: Even if you create a private GitHub repository, the website it creates is still public. If you’re not ready to publish your results online, you can always wait and activate GitHub Pages later. In the meantime, you’ll still have a version-controlled, organized set of results for your project. However, the risk that someone that doesn’t have the link to your website is able to find it is very low. Search engines prioritize the results by how many other sites link to a site, so your website will not be high in the results even if you search for very specific terms. Thus if you only share the URL to your results with your close collaborators, and request that they not share it widely, your website is effectively private. That being said, being truly scooped in science is rare (at best) and openly sharing your work will help establish your expertise in the field (and furthermore establishes your priority), so you should consider keeping both your code and website public.

Can I include Shiny apps in my website?

No, at least not in the standard setup. The website is hosted with GitHub pages, which only supports static web pages. Shiny apps are dynamic, i.e. a user can interact with them to change the content. The easiest way to share your Shiny app would be to host it at shinyapps.io and add a link to your app on your workflowr website. Alternatively you could host your workflowr website on your own server, but that would require much more knowledge and resources to accomplish.

Can I change “X” on my website?

Almost certainly yes, but some things are easier to customize than others. The vignette Customize your research website provides some ideas that are simple to implement. Check out the documentation for rmarkdown and Twitter Bootstrap for inspiration.

Why am I not getting the same result with wflow_build() as with the RStudio Knit HTML button?

wflow_build() is designed to have the same functionality as the Knit HTML button in RStudio, namely that it knits the HTML file in a separate R session to avoid any clashes with variables or pacakges in use in the current R session. However, the technical implementations are not identical, and thus informally we have noticed the behavior of the two options occassionally differs. At the moment, we believe that if the file results in an error when using wflow_build(), the file needs to be fixed, regardless of whether the file is able to be built with the RStudio button. If you have a use case that you think should be supported by wflow_build(), please open an Issue and provide a small reproducible example.

Can I share workflowr websites directly with collaborators in a secure fashion?

If your project contains senstive data that prevents you from publicly sharing the results, one alternative option is to self-host your workflowr website using Beaker Browser. This solution was contributed by Josh Johnson. For more details, please read his blog post and the discussion in Issue #59.

Beaker Browser allows website creation, cloning, modification, and publishing locally. After the site is ready, hitting “share” produces a unique Dat project dat:// hyperlink, for example:

dat://adef21aa8bbac5e93b0c20a97c6f57f93150cf4e7f5eb1eb522eb88e682309bc

This dat:// link can then be shared and the site opened all the while being hosted locally on the site producer’s machine. The particular example above is a site, produced in RStudio using workflowr, with placeholder content and R code chunks, compiled as usual.

Security for your site is achieved with site encryption inherent in the Dat protocol (see “Security” on the datproject docs page), as well as the obscurity of the unique link. Beaker Browser saves your individual project sites in the folder ~/Sites.

To create a Beaker Browser version of your workflowr site:

  1. Install Beaker Browser and run it.
  2. Select “New Site” in the three-bar dropdown menu found to the right of the “omnibar” for web link entry, and enter its Title and (optional) a Description of the site. This creates a folder in the Beaker Browser ~/Sites directory named for your Title, for example, “placeholder_workflowr”, and populates the folder with a dat.json file.
  3. In the main Beaker Browser pane, use “Add Files” or “Open Folder” to copy the entire contents of the workflowr docs/ folder to your new Beaker Browser site folder (see Symlink Synchronization, below).
  4. Once copied, the new site is ready to go. Pressing “Share” in the main Beaker Browser pane reveals the unique dat:// link generated for your Beaker Browser site. Sharing this link with anyone running Beaker Browser will allow them to access your workflowr HTML files…directly from your computer.

Instead of having to manually copy your workflowr docs/ directory to your Beaker Browser site directory, you can create a symlink from your workflowr docs/ directory to the Beaker Browser site directory. The line below links the docs/ directory of a hypothetical “workflowr-project” saved in ~/github/ to the hypothetical Beaker placeholder_workflowr subdirectory:

ln -s ~/github/workflowr-project/docs ~/Users/joshua/Sites/placeholder_workflowr

The direct-sharing nature of the above workflow means that the host computer needs to be running for site access. Two alternative recommended by Beaker Browser developer Paul Frazee are hashbase.io and the Beaker Browser subproject dathttpd. While hosting Beaker Browser sites is outside of the scope of this direct sharing paradigm, each of these options has strengths. The former, hashbase.io (free account required), is a web-hosted central location for dat:// -linked content, removing the need for the host computer to be running. The latter dathttpd example is an additional server/self-hosting option that can be used if desired.

Can I create a single HTML or PDF file of one of my workflowr R Markdown files?

Yes! If you’d like to create a single HTML or PDF file to distribute an isolated analysis from your project, you can directly run the rmarkdown function render.

library("rmarkdown")
# Create analysis/file.html
render("analysis/file.Rmd", html_document())
# Create analysis/file.pdf
render("analysis/file.Rmd", pdf_document())

There are two main caveats to this:

  1. Internal links to other HTML pages in your workflowr site will be broken since they are not being distributed with the single file.
  2. An R Markdown file that can be converted to HTML is not guaranteed to be converted to PDF. You’ll need to ensure that you have LaTeX installed on your computer and avoid complicated characters and/or syntax.

How should I pronounce and spell workflowr?

You can say “workflowr + er” or “workflowr + R”, whichever is more natural to you.

Workflowr should be capitalized at the beginning of a sentence, but otherwise the lowercase workflowr should be the preferred option.