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how to fix GIT error: object file is empty?

Posted by: admin April 4, 2020 Leave a comment

Questions:

When I try to commit changes, I get this error:

error: object file .git/objects/31/65329bb680e30595f242b7c4d8406ca63eeab0 is empty
fatal: loose object 3165329bb680e30595f242b7c4d8406ca63eeab0 (stored in .git/objects/31/65329bb680e30595f242b7c4d8406ca63eeab0) is corrupt

Any idea how to solve this error ?

EDIT

I tried git fsck I’ve got:

error: object file .git/objects/03/dfd60a4809a3ba7023cbf098eb322d08630b71 is empty
fatal: loose object 03dfd60a4809a3ba7023cbf098eb322d08630b71 (stored in .git/objects/03/dfd60a4809a3ba7023cbf098eb322d08630b71) is corrupt
How to&Answers:

I had a similar problem. My laptop ran out of battery during a git operation. Boo.

I didn’t have any backups. (N.B. Ubuntu One is not a backup solution for git; it will helpfully overwrite your sane repository with your corrupted one.)

To the git wizards, if this was a bad way to fix it, please leave a comment. It did, however, work for me… at least temporarily.

Step 1: Make a backup of .git (in fact I do this in between every step that changes something, but with a new copy-to name, e.g. .git-old-1, .git-old-2, etc.):

cp -a .git .git-old

Step 2: Run git fsck --full

[email protected]:~/workspace/mcmc-chapter$ git fsck --full
error: object file .git/objects/8b/61d0135d3195966b443f6c73fb68466264c68e is empty
fatal: loose object 8b61d0135d3195966b443f6c73fb68466264c68e (stored in .git/objects/8b/61d0135d3195966b443f6c73fb68466264c68e) is corrupt

Step 3: Remove the empty file. I figured what the heck; its blank anyway.

[email protected]:~/workspace/mcmc-chapter$ rm .git/objects/8b/61d0135d3195966b443f6c73fb68466264c68e 
rm: remove write-protected regular empty file `.git/objects/8b/61d0135d3195966b443f6c73fb68466264c68e'? y

Step 3: Run git fsck again. Continue deleting the empty files. You can also cd into the .git directory and run find . -type f -empty -delete -print to remove all empty files. Eventually git started telling me it was actually doing something with the object directories:

[email protected]:~/workspace/mcmc-chapter$ git fsck --full
Checking object directories: 100% (256/256), done.
error: object file .git/objects/e0/cbccee33aea970f4887194047141f79a363636 is empty
fatal: loose object e0cbccee33aea970f4887194047141f79a363636 (stored in .git/objects/e0/cbccee33aea970f4887194047141f79a363636) is corrupt

Step 4: After deleting all of the empty files, I eventually came to git fsck actually running:

[email protected]:~/workspace/mcmc-chapter$ git fsck --full
Checking object directories: 100% (256/256), done.
error: HEAD: invalid sha1 pointer af9fc0c5939eee40f6be2ed66381d74ec2be895f
error: refs/heads/master does not point to a valid object!
error: refs/heads/master.u1conflict does not point to a valid object!
error: 0e31469d372551bb2f51a186fa32795e39f94d5c: invalid sha1 pointer in cache-tree
dangling blob 03511c9868b5dbac4ef1343956776ac508c7c2a2
missing blob 8b61d0135d3195966b443f6c73fb68466264c68e
missing blob e89896b1282fbae6cf046bf21b62dd275aaa32f4
dangling blob dd09f7f1f033632b7ef90876d6802f5b5fede79a
missing blob caab8e3d18f2b8c8947f79af7885cdeeeae192fd
missing blob e4cf65ddf80338d50ecd4abcf1caf1de3127c229

Step 5: Try git reflog. Fail because my HEAD is broken.

[email protected]:~/workspace/mcmc-chapter$ git reflog
fatal: bad object HEAD

Step 6: Google. Find this. Manually get the last two lines of the reflog:

[email protected]:~/workspace/mcmc-chapter$ tail -n 2 .git/logs/refs/heads/master
f2d4c4868ec7719317a8fce9dc18c4f2e00ede04 9f0abf890b113a287e10d56b66dbab66adc1662d Nathan VanHoudnos <[email protected]> 1347306977 -0400  commit: up to p. 24, including correcting spelling of my name
9f0abf890b113a287e10d56b66dbab66adc1662d af9fc0c5939eee40f6be2ed66381d74ec2be895f Nathan VanHoudnos <[email protected]> 1347358589 -0400  commit: fixed up to page 28

Step 7: Note that from Step 6 we learned that the HEAD is currently pointing to the very last commit. So let’s try to just look at the parent commit:

[email protected]:~/workspace/mcmc-chapter$ git show 9f0abf890b113a287e10d56b66dbab66adc1662d
commit 9f0abf890b113a287e10d56b66dbab66adc1662d
Author: Nathan VanHoudnos <[email protected]>
Date:   Mon Sep 10 15:56:17 2012 -0400

    up to p. 24, including correcting spelling of my name

diff --git a/tex/MCMC-in-IRT.tex b/tex/MCMC-in-IRT.tex
index 86e67a1..b860686 100644
--- a/tex/MCMC-in-IRT.tex
+++ b/tex/MCMC-in-IRT.tex

It worked!

Step 8: So now we need to point HEAD to 9f0abf890b113a287e10d56b66dbab66adc1662d.

[email protected]:~/workspace/mcmc-chapter$ git update-ref HEAD 9f0abf890b113a287e10d56b66dbab66adc1662d

Which didn’t complain.

Step 9: See what fsck says:

[email protected]:~/workspace/mcmc-chapter$ git fsck --full
Checking object directories: 100% (256/256), done.
error: refs/heads/master.u1conflict does not point to a valid object!
error: 0e31469d372551bb2f51a186fa32795e39f94d5c: invalid sha1 pointer in cache-tree
dangling blob 03511c9868b5dbac4ef1343956776ac508c7c2a2
missing blob 8b61d0135d3195966b443f6c73fb68466264c68e
missing blob e89896b1282fbae6cf046bf21b62dd275aaa32f4
dangling blob dd09f7f1f033632b7ef90876d6802f5b5fede79a
missing blob caab8e3d18f2b8c8947f79af7885cdeeeae192fd
missing blob e4cf65ddf80338d50ecd4abcf1caf1de3127c229

Step 10: The invalid sha1 pointer in cache-tree seemed like it was from a (now outdated) index file (source). So I killed it and reset the repo.

[email protected]:~/workspace/mcmc-chapter$ rm .git/index
[email protected]:~/workspace/mcmc-chapter$ git reset
Unstaged changes after reset:
M   tex/MCMC-in-IRT.tex
M   tex/recipe-example/build-example-plots.R
M   tex/recipe-example/build-failure-plots.R

Step 11: Looking at the fsck again…

[email protected]:~/workspace/mcmc-chapter$ git fsck --full
Checking object directories: 100% (256/256), done.
error: refs/heads/master.u1conflict does not point to a valid object!
dangling blob 03511c9868b5dbac4ef1343956776ac508c7c2a2
dangling blob dd09f7f1f033632b7ef90876d6802f5b5fede79a

The dangling blobs are not errors. I’m not concerned with master.u1conflict, and now that it is working I don’t want to touch it anymore!

Step 12: Catching up with my local edits:

[email protected]:~/workspace/mcmc-chapter$ git status
# On branch master
# Changes not staged for commit:
#   (use "git add <file>..." to update what will be committed)
#   (use "git checkout -- <file>..." to discard changes in working directory)
#
#   modified:   tex/MCMC-in-IRT.tex
#   modified:   tex/recipe-example/build-example-plots.R
#   modified:   tex/recipe-example/build-failure-plots.R
#
< ... snip ... >
no changes added to commit (use "git add" and/or "git commit -a")


[email protected]:~/workspace/mcmc-chapter$ git commit -a -m "recovering from the git fiasco"
[master 7922876] recovering from the git fiasco
 3 files changed, 12 insertions(+), 94 deletions(-)

[email protected]:~/workspace/mcmc-chapter$ git add tex/sept2012_code/example-code-testing.R
[email protected]:~/workspace/mcmc-chapter$ git commit -a -m "adding in the example code"
[master 385c023] adding in the example code
 1 file changed, 331 insertions(+)
 create mode 100644 tex/sept2012_code/example-code-testing.R

So hopefully that can be of some use to people in the future. I’m glad it worked.

Answer:

The git object files have gone corrupt (as pointed out in other answers as well). This can happen during machine crashes, etc.

I had the same thing. After reading the other top answers here I found the quickest way to fix the broken git repository with the following commands (execute in the git working directory that contains the .git folder):

(Be sure to back up your git repository folder first!)

find .git/objects/ -type f -empty | xargs rm
git fetch -p
git fsck --full

This will first remove any empty object files that cause corruption of the repository as a whole, and then fetch down the missing objects (as well as latest changes) from the remote repository, and then do a full object store check. Which, at this point, should succeed without any errors (there may be still some warnings though!)

PS. This answer suggests you have a remote copy of your git repository
somewhere (e.g. on GitHub) and the broken repository is the local repository that is tied to the remote repository which is still in tact. If that is not the case, then do not attempt to fix it the way I recommend.

Answer:

I solved this removing the various empty files that git fsck was detecting, and then running a simple git pull.

I find it disappointing that now that even filesystems implement journaling and other “transactional” techniques to keep the fs sane, git can get to a corrupted state (and not be able to recover by itself) because of a power failure or space on device.

Answer:

This error happens to me when I am pushing my commit and my computer hangs.
This is how I’ve fix it.


Steps to fix

git status

show the empty/corrupt object file

rm .git/objects/08/3834cb34d155e67a8930604d57d3d302d7ec12

remove it

git status

I got fatal: bad object HEAD message

rm .git/index

I remove the index for the reset

git reset

fatal: Could not parse object ‘HEAD’.

git status
git pull

just to check whats happening

tail -n 2 .git/logs/refs/heads/MY-CURRENT-BRANCH

prints the last 2 lines tail -n 2 of log branch to show my last 2 commit hash

git update-ref HEAD 7221fa02cb627470db163826da4265609aba47b2

I pick the last commit hash

git status

shows all my file as deleted because i removed the .git/index file

git reset

continue to the reset

git status

verify my fix


Note: The steps starts when I landed on this question and used the answers as reference.

Answer:

I just had the same issue : after pulling the distant repository, when I did a git status I got :
“error: object file (…) is empty”
“fatal: loose object (…) is corrupted”

The way I resolved this was to :

  1. git stash
  2. removing git file in error (not sure that is necessary)
  3. git stash clear

I dont know exactly what things happened, but that instructions seemed to make everything clean.

Answer:

Because I have to reboot my VM regularly, so somehow this problem happens to me very often. After few times of it, I realized I cannot repeat the process described by @Nathan-Vanhoudnos every time this happens, though it always works. Then I figured out the following faster solution.

Step 1

Move your entire repo to another folder.

mv current_repo temp_repo

Step 2

Clone the repo from origin again.

git clone source_to_current_repo.git

Step 3

Remove Everything under the new repo except the .git folder.

Step 4

Move Everything from the temp_repo to the new repo except the .git folder.

Step 5

Remove the temp_repo, and we are done.

After few times, I’m sure you can do this procedures very quickly.

Answer:

  1. mv your folder app to make backup, i.e. mv app_folder app_folder_bk (it is like a git stash)
  2. git clone your_repository
  3. Finally,. Open a merge tool (I use meld diff viewer linux or Winmerge Windows) and copy the changes from right(app_folder_bk) to left( new app_folder) (it is like a git stash apply).

That’s all. Maybe it is not the best way, but I think it is so practical .

Answer:

In my case, this error occurred because I was typing the commit message and my notebook turned off.

I did these steps to fix the error:

  • git checkout -b backup-branch # Create a backup branch
  • git reset --hard HEAD~4 # Reset to the commit where everything works well. In my case, I had to back 4 commits in the head, that is until my head be at the point before I was typing the commit message. Before doing this step, copy the hash of the commits you will reset, in my case I copied the hash of the 4 last commits
  • git cherry-pick <commit-hash> # Cherry pick the reseted commits (in my case are 4 commits, so I did this step 4 times) from the old branch to the new branch.
  • git push origin backup-branch # Push the new branch to be sure everything works well
  • git branch -D your-branch # Delete the branch locally (‘your-branch’ is the branch with problem)
  • git push origin :your-branch # Delete the branch from remote
  • git branch -m backup-branch your-branch # Rename the backup branch to have the name of the branch that had the problem
  • git push origin your-branch # Push the new branch
  • git push origin :backup-branch # Delete the backup branch from remote

Answer:

git stash
git checkout master
cd .git/ && find . -type f -empty -delete
git branch your-branch-name -D
git checkout -b your-branch-name
git stash pop

resolve my problem

Answer:

Here is a really simple and quick way to deal with this problem IF you have a local repo with all the branches and commits you need, and if you’re OK with creating a new repo (or deleting the server’s repo and making a new one in it’s place):

  1. Create a new empty repo on the server (or delete the old repo and create a new one in its place)
  2. Change the remote URL of your local copy to point to the remote URL of the new repo.
  3. Push all branches from your local repo to the new server repo.

This preserves all the commit history and branches that you had in your local repo.

If you have collaborators on the repo, then I think in many cases all your collaborators have to do is change the remote URL of their local repo as well, and optionally push any commits they have that the server doesn’t have.

This solution worked for me when I ran into this same problem. I had one collaborator. After I pushed my local repo to the new remote repo, he simply changed his local repo to point to the remote repo URL and everything worked fine.

Answer:

I am assuming you have a remote with all relevant changes already pushed to it. I did not care about local changes and simply wanted to avoid deleting and recloning a large repository. If you do have important local changes you might want to be more careful.

I had the same problem after my laptop crashed.
Probably because it was a large repository I had quite a few corrupt object files, which only appeared one at a time when calling git fsck --full, so I wrote a small shell one-liner to automatically delete one of them:

$ sudo rm `git fsck --full 2>&1 | grep -oE -m 1 ".git/objects/[0-9a-f]{2}/[0-9a-f]*"`

  • 2>&1 redirects the error message to stdout to be able to grep it
  • grep options used:
    • -o only returns the part of a line that actually matches
    • -E enables advanced regexes
    • -m 1 make sure only the first match is returned
    • [0-9a-f]{2} matches any of the characters between 0 and 9 and a and f if two of them occur together
    • [0-9a-f]* matches any number of the characters between 0 and 9 and a and f occuring together

It still only deletes one file at a time, so you might want to call it in a loop like:

$ while true; do sudo rm `git fsck --full 2>&1 | grep -oE -m 1 ".git/objects/[0-9a-f]{2}/[0-9a-f]*"`; done

The problem with this is, that it does not output anything useful anymore so you do not know when it is finished (it should just not do anything useful after some time)

To “fix” this I then just added a call of git fsck --full after each round like so:
$ while true; do sudo rm `git fsck --full 2>&1 | grep -oE -m 1 ".git/objects/[0-9a-f]{2}/[0-9a-f]*"`; git fsck --full; done

It now is approximately half as fast, but it does output it’s “state”.

After this I played around some with the suggestions in this thread and finally got to a point where I could git stash and git stash drop a lot of the broken stuff.

first problem solved

Afterwards I still had the following problem:
unable to resolve reference 'refs/remotes/origin/$branch': reference broken which could be solved by
$ rm \repo.git\refs\remotes\origin\$branch

$ git fetch

I then did a
$ git gc --prune=now

$ git remote prune origin

for good measure and

git reflog expire --stale-fix --all

to get rid of error: HEAD: invalid reflog entry $blubb when running git fsck --full.

Answer:

Let’s go simple.. only case you uploaded source to remote git repo

  1. Backup your .git
  2. check your git

    git fsck --full
    
  3. remove empty object file (all)

    rm .git/objects/8b/61d0135d3195966b443f6c73fb68466264c68e
    
  4. check your git again.

    git fsck --full
    
  5. pull your source from remote git

    git pull origin master
    

Answer:

I encounter the same problem, and I use a very simple way to fix it. I found that those missing files existed on my teammate’s computer.

I copied those files one by one to a git server (9 files total), and that fixed the problem.

Answer:

My colleagues and I have crossed several times with this same problem and to solve it we simply do the steps that I describe below. It is not the most elegant solution that can be found but it works without loss of data.

  1. Rename the current working directory. (old_project for this example).
  2. Clone the repository within a new directory using git clone.
  3. On the command line, change the working directory to the newly created project and switch to the branch you have been working on.
  4. Copy all files and directories within old_project (except the .git directory) to the newly created project directory.
  5. Check your working tree status (note that there are many more changes than you expect) and then commit the changes.

I hope it helps…

Answer:

Here is a way to solve the problem if your public repo on github.com is working, but your local repo is corrupt. Be aware that you will loose all the commits you’ve done in the local repo.

Alright, so I have one repo locally that is giving me this object empty error, and the same repo on github.com, but without this error. So what I simply did was to clone the repo that is working from github, and then copied everything from the corrupt repo (except the .git folder), and paste it the cloned repo that is working.

This may not be a practical solution (since you delete the local commits), however, you maintain the code and a repaired version control.

Remember to back-up before applying this approach.

Answer:

In my case, it wasn’t important for me to keep the local commit history. So if that applies to you too, you can do this as a quick alternative to the solutions above:

You basically just replace the corrupted .git/ directory with a clean one.

Lets presume the following directory for your project with the corrupted git: projects/corrupt_git/

  1. cp projects/corrupt_git projects/backup – (optional) make a backup
  2. git clone [repo URL] projects/clean_git – so that you get projects/clean_git
  3. rm -rf corrupt_git/.git/ – remove the corrupted .git folder
  4. mv clean_git/.git/ corrupt_git/ – move clean git to corrupt_git/.git
  5. git status in projects/corrupt_git – to make sure it worked

Answer:

I run into this problem a lot with virtual machines.

For me the following works:

cd /path/to/your/project
rm -rf .git

If you want to save yourself some downloads – go in your file explorer and delete all files in the folder that are already committed and leave in your /vendor and /node_modules (I work with composer and npm) folders.

then just create a new repo

git init

add your remote

git remote add origin ssh://[email protected]/YourUsername/repoName.git

and fetch the branch / all of it

git fetch origin somebranch

and check it out

git checkout somebranch

then you should be at the point before the error.

Hope this helps.

Regards.

Answer:

Copy everything (in the folder containing the .git) to a backup, then delete everything and restart. Make sure you have the git remote handy:

git remote -v
 origin [email protected]:rwldrn/idiomatic.js.git (fetch)
 origin [email protected]:rwldrn/idiomatic.js.git (push)

Then

mkdir mygitfolder.backup
cp mygitfolder/* mygitfolder.backup/
cd mygitfolder
rm -r * .git*
git init
git remote add origin [email protected]:rwldrn/idiomatic.js.git

Then merge any new files manually, and try to keep your computer turned on.

Answer:

Had the same problem after checking out master from a clean branch.
After a while I recognized a lot of modified files in master. I don’t know why they have been there, after switching from a clean branch. Anyways, because the modified files made no sense to me, I just stashed them and the error was gone.

git:(master) git stash

Answer:

if you have an OLD backup and is in a hurry:

make a NEW BACKUP of your current, git-broken, project path.

  1. move your .git to trash (never delete)
  2. copy .git from the OLD backup
  3. git pull (will create merge conflicts)
  4. move all your sources (everything you put in git) to trash: ./src (never delete)
  5. .copy all your sources (everything you put in git) from the NEW BACKUP
  6. accept all “merges” at git gui, push and… clap your hands!

Answer:

The twelve step solution covered above helped get me out of a jam as well. Thanks. The key steps were to enter:

git fsck --full

and remove all empty objects

rm .git/objects/...

Then getting the two lines of the flog:

tail -n 2 .git/logs/refs/heads/master

With the returned values

git update-ref HEAD ...

At this point I had no more errors, so I made a backup of my most recent files. Then do a git pull followed by a git push. Copied my backups to my git repository file and did another git push. That got me current.

Answer:

I fixed my git error: object file is empty by:

  1. Saving a copy of all files that I edited since my last successful commit/push,
  2. Removing and re-cloning my repository,
  3. Replacing the old files with my edited files.

Hopes this helps.

Answer:

This also happens to me almost regularly. Haven’t made a protocol when this happens exactly, but I have a suspicion that it occurs whenever my virtual machine exists “unexpectedly”. If I close the VM window (I am using Ubuntu 18.04) and start again, things always(?) work. But if the VM window is still open when my laptop is shut down (Windows host system), then I encounter this problem rather frequently.

As to all the answers given here:

  1. thank you – they are very useful; I usually save a local copy of my code, restore the repo from remote, and move the backup copy back into the local folder.

  2. as the underlying problem is not really a git issue, but rather a VM and/or Linux issue, I wonder if there shouldn’t be a way to cure the reason rather the symptoms? Doesn’t this kind of error indicate that some file system changes are not “applied” in any reasonable time, but only cached? (see for example https://unix.stackexchange.com/questions/464184/are-file-edits-in-linux-directly-saved-into-disk) — to me it appears as if virtual Linux machines don’t fsynch their stuff frequently enough. Whether this is an issue of Oracle’s VirtualBox (which otherwise works very nicely) or of the guest file system, or of some settings, which we all overlook, is beyond my expertise. But I would be happy if someone could shed light on this.

Answer:

Warning: With more experience, I realize that this is the nuclear option and shouldn’t typically be done and doesn’t teach anything. However, on rare occasions for personal projects, I’ve still found it useful, so I’m leaving it up.

If you don’t care about keeping your historical commits, just run

rm -r .git

Then answer yes to anything asking about deleting write-protected files.
Problem solved in under a minute.