Appendix D — Extra: Merge conflicts in Git

Normally Git is very good at synchronizing and merging changes between a local repository and its remote repository. However, sometimes, when it encounters a problem it doesn’t know how to fix, it stops merging the two histories and lets you manually fix the problem. This is called a “merge conflict” and it is when one or more files have changes that conflict with one another.

An example would be when you make a change to some code on your work computer, then on another day are working on the code on your home computer and make a slightly different edit to the same code. Normally, if you keep your repository synchronized, this wouldn’t be a problem. But sometimes you forget to synchronize, so when you do, Git may detect a conflict on the same lines in a file between the histories of the local and remote repositories. At this point, Git stops and gives you control to resolve it.

Let’s force a conflict to happen. In your LearningR RStudio R Project, open up the Git interface and make sure that you don’t see docs/learning.qmd anywhere in the list and that you’ve pushed and pulled already with your GitHub repository. Then, open up docs/learning.qmd and add the text # Here's an example of a conflict to the very first line. In the Git interface, add and commit this change but don’t push the changes!

Then, go to your GitHub repository and open up the docs/learning.qmd file. Click the “Edit” button, as you learned previously in the session. In the first line of the file, add the text # When a conflict happens. Write a simple commit message and commit the change.

Now, go back to your RStudio project, open the Git interface and click “Pull”. You can try to push first, but when there are differences between your local and remote repository, Git will prevent you from pushing to GitHub until you first pull. Once you pull, Git will detect if a file conflict exists and halt it’s “merging” process.

What you should see is something like the below text (it may be slightly different):

<<<<<<< HEAD
# Here's an example of a conflict
=======
# When a conflict happens
>>>>>>> ad3fsd45bsdd23lda2304

The text on the top between <<<<<<< HEAD and ======= are the changes found on your local repository. The text on the bottom between ======= and >>>>>>> ad3fsd45bsdd23lda2304 are the changes found on your remote (GitHub) repository. HEAD is the term to mean where your files are currently at. Think of HEAD as meaning the “top” of the history. The long string with numbers and letters (like ad3fsd45bsdd23lda2304) represents the ID for the commit (the “commit hash”) and, in this case, comes from main (or sometimes called master) branch of the origin remote. The concept and use of branches is a powerful feature of Git, but due to time we won’t be covering them. You only need to know that every Git repository starts with the default main (or master) branch.

At this point, you decide what to keep and what to remove by deleting text within the docs/learning.qmd script in RStudio. You’ll need to also delete the lines with the <<<<<<< HEAD, =======, and >>>>>>> ad3fsd45bsdd23lda2304 (or something that looks similar).

After deciding what to keep and removing all the left over merge conflict tags, open up the Git interface in RStudio. The files listed in the staging area will show the conflict file with a yellow/orange “U”. To resolve the merge conflict, stage the file with the merge conflict. This will change the colour to blue. Next you commit the changes in the Git interface, without writing a commit message (this is not necessary when resolving merge conflicts). Push the changes to GitHub, then open up the Git repository in GitHub, refresh the browser, and view that the changes have taken place.

D.1 🧑‍💻 Exercise: Dealing with merge conflicts

Time: ~10 minutes.

Throughout this course you hopefully won’t encounter many merge conflicts, including during the group project. Regardless, here is some practice to deal with them.

  1. In your GitHub LearningR repository, edit the README.md file by replacing one word with a random word (e.g. “blahblah”). Commit the change.
  2. Go to your RStudio LearningR.Rproj project and, without pulling from GitHub, replace the same word you did on the GitHub version of the README.md file, but instead use a different random word (e.g. “ticktock” instead of “blahblah” from above). Add to the staging and commit the change with RStudio’s Git interface using or with the Palette (, then type “commit”).
  3. While in RStudio’s Git interface, pull the changes from GitHub. There should be a warning about merge conflicts. Now you can practice dealing with and fixing merge conflicts. Add the changes to the staging after you fixed them and click the commit button (you don’t need to type out a commit message).
  4. Push the changes up to GitHub and view them there to make sure they have been synchronized (you may need to refresh the browser).
Sticky/hat up!

When you’re ready to continue, place the sticky/paper hat on your computer to indicate this to the instructor 👒 🎩

D.2 Summary

  • When there are differences in changes to the same lines in a file, a merge conflict occurs that you must deal with manually.
    • Decide on which text to keep between the tags: <<<<<<< HEAD, =======, and >>>>>>> origin/main (the last name may sometimes look different), and remove tags.