How to fix Git error: object file is empty?
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
nathanvan@nathanvan-N61Jq:~/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.
nathanvan@nathanvan-N61Jq:~/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:
nathanvan@nathanvan-N61Jq:~/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:
nathanvan@nathanvan-N61Jq:~/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.
nathanvan@nathanvan-N61Jq:~/workspace/mcmc-chapter$ git reflog
fatal: bad object HEAD
Step 6: Google. Find this. Manually get the last two lines of the reflog:
nathanvan@nathanvan-N61Jq:~/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:
nathanvan@nathanvan-N61Jq:~/workspace/mcmc-chapter$ 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.
nathanvan@nathanvan-N61Jq:~/workspace/mcmc-chapter$ git update-ref HEAD 9f0abf890b113a287e10d56b66dbab66adc1662d
Which didn't complain.
Step 9: See what fsck says:
nathanvan@nathanvan-N61Jq:~/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.
nathanvan@nathanvan-N61Jq:~/workspace/mcmc-chapter$ rm .git/index
nathanvan@nathanvan-N61Jq:~/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...
nathanvan@nathanvan-N61Jq:~/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:
nathanvan@nathanvan-N61Jq:~/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")
nathanvan@nathanvan-N61Jq:~/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(-)
nathanvan@nathanvan-N61Jq:~/workspace/mcmc-chapter$ git add tex/sept2012_code/example-code-testing.R
nathanvan@nathanvan-N61Jq:~/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.
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.
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.