How can I fix the Git error "object file ... is empty"?

Question

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 

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 can I solve this error?

Answer 1

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 folder .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.):

cd ~/workspace/mcmc-chapter cp -a .git .git-old 

Step 2: Run git fsck --full

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; it's blank anyway.

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:

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:

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.

git reflog  fatal: bad object HEAD 

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

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:

git show 9f0abf890b113a287e10d56b66dbab66adc1662d  commit 9f0abf890b113a287e10d56b66dbab66adc1662d Author: Nathan VanHoudnos <nathanvan@XXXXXX> 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.

git update-ref HEAD 9f0abf890b113a287e10d56b66dbab66adc1662d 

Which didn't complain.

Step 9: See what fsck says:

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 repository.

rm .git/index 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...

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:

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")   git commit -a -m "recovering from the git fiasco"  [master 7922876] recovering from the git fiasco  3 files changed, 12 insertions(+), 94 deletions(-)  git add tex/sept2012_code/example-code-testing.R 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