simo simo - 2 months ago 64
Git Question

how to fix GIT error: object file is empty?

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

Answer

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 <nathanvan@gmail.com> 1347306977 -0400  commit: up to p. 24, including correcting spelling of my name
9f0abf890b113a287e10d56b66dbab66adc1662d af9fc0c5939eee40f6be2ed66381d74ec2be895f Nathan VanHoudnos <nathanvan@gmail.com> 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.