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Fix the “fatal: refusing to merge unrelated histories” Git Error

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Learn how to fix the “fatal: refusing to merge unrelated histories” Git error. Our Server Management Support team is here to answer your queries and concerns.

Fix the “fatal: refusing to merge unrelated histories” Git Error

Fix the “fatal: refusing to merge unrelated histories” Git ErrorIf you are having trouble with the following Git error message, you have come to the right place.

fatal: refusing to merge unrelated histories

This error occurs when merging two Git repositories or branches that don’t share a common commit history. Git sees them as entirely separate and is unwilling to combine their histories without extra guidance. Since there’s no shared starting point between them, Git cannot figure out how to merge them.

Like other fatal errors in development environments, like the SQL Server fatal error 615, this Git issue halts your progress until it’s resolved correctly.

Key Impacts of the Error

Here’s how this error can affect our development workflow:

  • Prevents successful merges, halting progress.
  • If not handled carefully, changes might be lost during reconciliation.
  • Requires extra commands or manual conflict resolution.
  • It can be puzzling for new contributors.
  • Troubleshooting can divert focus from core development tasks.
  • Poorly managed merges may lead to broken or inconsistent project states.

Errors like these can be critical in scenarios involving production environments or live servers. That’s why robust server management services are essential—they help prevent such errors from impacting system performance and uptime.

Common Causes and How to Fix Them

1. Incompatibility Between Local and Remote Repositories

Local and remote have diverged without being synced.

Click here for the Solution.

To resolve this issue, follow these steps:

  1. First, open a terminal and go to the local repository directory.
  2. Then, check which branch we are currently on. We can switch if needed.
    git checkout main
  3. Then, run this command:
    git pull origin main –allow-unrelated-histories

    This command pushes Git to merge changes from the remote repository into the local branch, even if they do not share a common history.

If there are any conflicts, Git will notify us. In this case, we can open the conflicted files, fix the issue, and mark them as resolved.

git add conflicted-file

Then commit the changes.

commit -m "Merged unrelated histories"

Finally, push the merged changes with this command:

git push origin main

 

2. Merging Two Independent Repositories

Attempting to merge repositories with no shared commits.

Click here for the Solution.
  1. First, add the second repository as a remote if it hasn’t already been done:
    git remote add other-repo other-repo-url
  2. Then, fetch changes from the other repository:
    git fetch other-repo
  3. Now, run this command to merge with the –allow-unrelated-histories flag:
    git merge other-repo/main –allow-unrelated-histories

    This command will merge the main branch of the second repository into the current branch, allowing for unrelated histories.

  4. Finally, resolve conflicts if they pop up, then commit and push as needed.

3. Corrupted `.git` Directory

The `.git` directory is damaged or missing files.

Click here for the Solution.
  • First, remove the corrupted .git directory:
    rm -rf .git
  • Then, reinitialize the repository with this command:
    git init
  • Now, re-add the remote repository:
    git remote add origin repository-url
  • Then, fetch changes from the remote repository:
    git fetch origin
  • Finally, merge changes as needed:
    git pull origin main –allow-unrelated-histories

 

Corruption issues aren’t limited to Git. An error like “Allowed memory size exhausted” in cPanel can occur in web hosting environments if the system isn’t well-monitored or configured.

4. Pulling into a Newly Initialized Repository

A new local repo is trying to pull from a remote with existing history.

Click here for the Solution.
  1. First, go to the new local repository directory and pull changes with this command:
    git pull origin main –allow-unrelated-histories
  2. Resolve any conflicts if they pop up, commit, and push as needed.

5. Merging Diverged Branches

Branches have no common ancestor.

Click here for the Solution.
  1. First, create an empty commit to connect histories:
    git commit --allow-empty -m "Merge unrelated histories"
  2. Then, merge as seen below:
    git merge branch-name --allow-unrelated-histories
  3. Resolve any conflicts if they pop up, commit, and push as needed.

6. Accidental Repository Initialization

The developer initialized a new repo instead of cloning an existing one.

Click here for the Solution.

In this case, clone the existing repository instead of initializing a new one:

git clone repository-url

Then, go to the cloned directory and start working with it. Ensure all history is intact.

Prevention Tips

Here are some tips to avoid this error in the future:

  • Always clone when collaborating on a shared project.
  • Regularly pull from remotes to prevent divergence.
  • Make sure all team members understand the Git workflow.
  • Use `–force` only when vital.
  • Use Git Flow or trunk-based development to structure work cleanly.
  • Create backups of important branches before merging.

[Need assistance with a different issue? Our team is available 24/7.]

Conclusion

The “fatal: refusing to merge unrelated histories” error is manageable once we find the root cause.

In brief, our Support Experts demonstrated how to fix the “fatal: refusing to merge unrelated histories” Git error.

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