Whenever I pull from my remote, I get the following error about compression. When I run the manual compression, I get the same:
$ git gc
error: Could not read 3813783126d41a3200b35b6681357c213352ab31
fatal: bad tree object 3813783126d41a3200b35b6681357c213352ab31
error: failed to run repack
Does anyone know, what to do about that?
From cat-file I get this:
$ git cat-file -t 3813783126d41a3200b35b6681357c213352ab31
error: unable to find 3813783126d41a3200b35b6681357c213352ab31
fatal: git cat-file 3813783126d41a3200b35b6681357c213352ab31: bad file
And from git fsck I get this ( don't know if it's actually related):
$ git fsck
error: inflate: data stream error (invalid distance too far back)
error: corrupt loose object '45ba4ceb93bc812ef20a6630bb27e9e0b33a012a'
fatal: loose object 45ba4ceb93bc812ef20a6630bb27e9e0b33a012a (stored in .git/objects/45/ba4ceb93bc812ef20a6630bb27e9e0b33a012a) is corrupted
Can anyone help me decipher this?
I had the same problem (don't know why).
This fix requires access to an uncorrupted remote copy of the repository, and will keep your locally working copy intact.
But it has some drawbacks:
You will lose the record of any commits that were not pushed, and will have to recommit them.
You will lose any stashes.
The fix
Execute these commands from the parent directory above your repo (replace 'foo' with the name of your project folder):
Create a backup of the corrupt directory:
cp -R foo foo-backup
Make a new clone of the remote repository to a new directory:
git clone git#www.mydomain.de:foo foo-newclone
Delete the corrupt .git subdirectory:
rm -rf foo/.git
Move the newly cloned .git subdirectory into foo:
mv foo-newclone/.git foo
Delete the rest of the temporary new clone:
rm -rf foo-newclone
On Windows you will need to use:
copy instead of cp -R
rmdir /S instead of rm -rf
move instead of mv
Now foo has its original .git subdirectory back, but all the local changes are still there. git status, commit, pull, push, etc. work again as they should.
Your best bet is probably to simply re-clone from the remote repository (i.e., GitHub or other). Unfortunately you will lose any unpushed commits and stashed changes, however your working copy should remain intact.
First make a backup copy of your local files. Then do this from the root of your working tree:
rm -fr .git
git init
git remote add origin [your-git-remote-url]
git fetch
git reset --mixed origin/master
git branch --set-upstream-to=origin/master master
Then commit any changed files as necessary.
Working on a VM, in my notebook, battery died, got this error;
error: object file .git/objects/ce/theRef is empty error: object
file .git/objects/ce/theRef is empty fatal: loose object theRef
(stored in .git/objects/ce/theRef) is corrupt
I managed to get the repo working again with only 2 commands and without losing my work (modified files/uncommitted changes)
find .git/objects/ -size 0 -exec rm -f {} \;
git fetch origin
After that I ran a git status, the repo was fine and there were my changes (waiting to be committed, do it now..).
git version 1.9.1
Remember to backup all changes you remember, just in case this solution doesn't works and a more radical approach is needed.
Looks like you have a corrupt tree object. You will need to get that object from someone else. Hopefully they will have an uncorrupted version.
You could actually reconstruct it if you can't find a valid version from someone else by guessing at what files should be there. You may want to see if the dates & times of the objects match up to it. Those could be the related blobs. You could infer the structure of the tree object from those objects.
Take a look at Scott Chacon's Git Screencasts regarding git internals. This will show you how git works under the hood and how to go about doing this detective work if you are really stuck and can't get that object from someone else.
My computer crashed while I was writing a commit message. After rebooting, the working tree was as I had left it and I was able to successfully commit my changes.
However, when I tried to run git status I got
error: object file .git/objects/xx/12345 is empty
fatal: loose object xx12345 (stored in .git/objects/xx/12345 is corrupt
Unlike most of the other answers, I wasn't trying to recover any data. I just needed Git to stop complaining about the empty object file.
Overview
The "object file" is Git's hashed representation of a real file that you care about. Git thinks it should have a hashed version of some/file.whatever stored in .git/object/xx/12345, and fixing the error turned out to be mostly a matter of figuring out which file the "loose object" was supposed to represent.
Details
Possible options seemed to be
Delete the empty file
Get the file into a state acceptable to Git
Approach 1: Remove the object file
The first thing I tried was just moving the object file
mv .git/objects/xx/12345 ..
That didn't work - Git began complaining about a broken link. On to Approach 2.
Approach 2: Fix the file
Linus Torvalds has a great writeup of how to recover an object file that solved the problem for me. Key steps are summarized here.
$> # Find out which file the blob object refers to
$> git fsck
broken link from tree 2d9263c6d23595e7cb2a21e5ebbb53655278dff8
to blob xx12345
missing blob xx12345
$> git ls-tree 2d926
...
10064 blob xx12345 your_file.whatever
This tells you what file the empty object is supposed to be a hash of. Now you can repair it.
$> git hash-object -w path/to/your_file.whatever
After doing this I checked .git/objects/xx/12345, it was no longer empty, and Git stopped complaining.
Try
git stash
This worked for me. It stashes anything you haven't committed and that got around the problem.
A garbage collection fixed my problem:
git gc --aggressive --prune=now
It takes a while to complete, but every loose object and/or corrupted index was fixed.
simply running a git prune fixed this issue for me
I encountered this once my system crashed. What I did is this:
(Please note your corrupt commits are lost, but changes are retained. You might have to recreate those commits at the end of this procedure)
Backup your code.
Go to your working directory and delete the .git folder.
Now clone the remote in another location and copy the .git folder in it.
Paste it in your working directory.
Commit as you wanted.
I just experienced this - my machine crashed whilst writing to the Git repo, and it became corrupted. I fixed it as follows.
I started with looking at how many commits I had not pushed to the remote repo, thus:
gitk &
If you don't use this tool it is very handy - available on all operating systems as far as I know. This indicated that my remote was missing two commits. I therefore clicked on the label indicating the latest remote commit (usually this will be /remotes/origin/master) to get the hash (the hash is 40 chars long, but for brevity I am using 10 here - this usually works anyway).
Here it is:
14c0fcc9b3
I then click on the following commit (i.e. the first one that the remote does not have) and get the hash there:
04d44c3298
I then use both of these to make a patch for this commit:
git diff 14c0fcc9b3 04d44c3298 > 1.patch
I then did likewise with the other missing commit, i.e. I used the hash of the commit before and the hash of the commit itself:
git diff 04d44c3298 fc1d4b0df7 > 2.patch
I then moved to a new directory, cloned the repo from the remote:
git clone git#github.com:username/repo.git
I then moved the patch files into the new folder, and applied them and committed them with their exact commit messages (these can be pasted from git log or the gitk window):
patch -p1 < 1.patch
git commit
patch -p1 < 2.patch
git commit
This restored things for me (and note there's probably a faster way to do it for a large number of commits). However I was keen to see if the tree in the corrupted repo can be repaired, and the answer is it can. With a repaired repo available as above, run this command in the broken folder:
git fsck
You will get something like this:
error: object file .git/objects/ca/539ed815fefdbbbfae6e8d0c0b3dbbe093390d is empty
error: unable to find ca539ed815fefdbbbfae6e8d0c0b3dbbe093390d
error: sha1 mismatch ca539ed815fefdbbbfae6e8d0c0b3dbbe093390d
To do the repair, I would do this in the broken folder:
rm .git/objects/ca/539ed815fefdbbbfae6e8d0c0b3dbbe093390d
cp ../good-repo/.git/objects/ca/539ed815fefdbbbfae6e8d0c0b3dbbe093390d .git/objects/ca/539ed815fefdbbbfae6e8d0c0b3dbbe093390d
i.e. remove the corrupted file and replace it with a good one. You may have to do this several times. Finally there will be a point where you can run fsck without errors. You will probably have "dangling commit" and "dangling blob" lines in the report, these are a consequence of your rebases and amends in this folder, and are OK. The garbage collector will remove them in due course.
Thus (at least in my case) a corrupted tree does not mean unpushed commits are lost.
The solution offered by Felipe Pereira (above) in addition to Stephan's comment to that answer with the name of the branch I was on when the objects got corrupted is what worked for me.
find .git/objects/ -size 0 -exec rm -f {} \;
git fetch origin
git symbolic-ref HEAD refs/heads/${BRANCH_NAME}
The answer of user1055643 is missing the last step:
rm -fr .git
git init
git remote add origin your-git-remote-url
git fetch
git reset --hard origin/master
git branch --set-upstream-to=origin/master master
Runnning git stash; git stash pop fixed my problem
I followed many of the other steps here; Linus' description of how to look at the git tree/objects and find what's missing was especially helpful. git-git recover corrupted blob
But in the end, for me, I had loose/corrupt tree objects caused by a partial disk failure, and tree objects are not so easily recovered/not covered by that doc.
In the end, I moved the conflicting objects/<ha>/<hash> out of the way, and used git unpack-objects with a pack file from a reasonably up to date clone. It was able to restore the missing tree objects.
Still left me with a lot of dangling blobs, which can be a side effect of unpacking previously archived stuff, and addressed in other questions here
I was getting a corrupt loose object error as well.
./objects/x/x
I successfully fixed it by going into the directory of the corrupt object. I saw that the users assigned to that object was not my git user's. I don't know how it happened, but I ran a chown git:git on that file and then it worked again.
This may be a potential fix for some peoples' issues but not necessary all of them.
To me this happened due to a power failure while doing a git push.
The messages looked like this:
$ git status
error: object file .git/objects/c2/38824eb3fb602edc2c49fccb535f9e53951c74 is empty
error: object file .git/objects/c2/38824eb3fb602edc2c49fccb535f9e53951c74 is empty
fatal: loose object c238824eb3fb602edc2c49fccb535f9e53951c74 (stored in .git/objects/c2/38824eb3fb602edc2c49fccb535f9e53951c74) is corrupt
I tried things like git fsck but that didn't help.
Since the crash happened during a git push, it obviously happened during rewrite on the client side which happens after the server is updated. I looked around and figured that c2388 in my case was a commit object, because it was referred to by entries in .git/refs. So I knew that I would be able to find c2388 when I look at the history (through a web interface or second clone).
On the second clone I did a git log -n 2 c2388 to identify the predecessor of c2388. Then I manually modified .git/refs/heads/master and .git/refs/remotes/origin/master to be the predecessor of c2388 instead of c2388.
Then I could do a git fetch.
The git fetch failed a few times for conflicts on empty objects. I removed each of these empty objects until git fetch succeeded. That has healed the repository.
We just had the case here. It happened that the problem was the ownership of the corrupt file was root instead of our normal user. This was caused by a commit done on the server after someone has done a "sudo su --".
First, identify your corrupt file with:
$> git fsck --full
You should receive a answer like this one:
fatal: loose object 11b25a9d10b4144711bf616590e171a76a35c1f9 (stored in .git/objects/11/b25a9d10b4144711bf616590e171a76a35c1f9) is corrupt
Go in the folder where the corrupt file is and do a:
$> ls -la
Check the ownership of the corrupt file. If that's different, just go back to the root of your repo and do a:
$> sudo chown -R YOURCORRECTUSER:www-data .git/
Hope it helps!
I solved this way:
I decided to simply copy the uncorrupted object file from the backup's clone to my original repository. This worked just as well. (By the way: If you can't find the object in .git/objects/ by its name, it probably has been [packed][pack] to conserve space.)
I got this error after my (Windows) machine decided to reboot itself.
Thankfully my remote repository was up to date, so I just did a fresh Git clone...
This seems to be an issue with Dropbox or symlinking folders out of Dropbox for me. Probably the same for any of the other similar services. When I go to git push I'd get the Corrupt loose object error. For me, on macOS Big Sur, the fix was simply to make a recursive copy of the repo to a directory outside of Dropbox. I believe this caused Dropbox to pull the live files for the broken dynamic references. After the copy I was immediately able to git push without error.
I have had the same issue before.
I simply get passed it by removing the object file from the .git/objects directory.
For this error below.
$ git fsck
error: inflate: data stream error (invalid distance too far back)
error: corrupt loose object '45ba4ceb93bc812ef20a6630bb27e9e0b33a012a'
fatal: loose object 45ba4ceb93bc812ef20a6630bb27e9e0b33a012a (stored in .git/objects/45/ba4ceb93bc812ef20a6630bb27e9e0b33a012a) is corrupted
Solution:
Go to your top directory and unhide the .git folder
On windows, you can do this by running this command on cmd: attrib +s +h .git
Then go to .git/objects folder
As mentioned on the error message above (stored in .git/objects/45/ba4ceb93bc812ef20a6630bb27e9e0b33a012a) is corrupted
you can see that the object is found on a director called "45". Therefore, go to the directory .git/objects/45/
Finally find the object named ba4ceb93bc812ef20a6630bb27e9e0b33a012a and delete it.
Now, you can go ahead and check with git status or git add . your change and proceed.
I had this same problem in my bare remote git repo. After much troubleshooting, I figured out one of my coworkers had made a commit in which some files in .git/objects had permissions of 440 (r--r-----) instead of 444 (r--r--r--). After asking the coworker to change the permissions with "chmod 444 -R objects" inside the bare git repo, the problem was fixed.
I just had a problem like this. My particular problem was caused by a system crash that corrupted the most recent commit (and hence also the master branch). I hadn't pushed, and wanted to re-make that commit. In my particular case, I was able to deal with it like this:
Make a backup of .git/: rsync -a .git/ git-bak/
Check .git/logs/HEAD, and find the last line with a valid commit ID. For me, this was the second most recent commit. This was good, because I still had the working directory versions of the file, and so the every version I wanted.
Make a branch at that commit: git branch temp <commit-id>
re-do the broken commit with the files in the working directory.
git reset master temp to move the master branch to the new commit you made in step 2.
git checkout master and check that it looks right with git log.
git branch -d temp.
git fsck --full, and it should now be safe to delete any corrupted objects that fsck finds.
If it all looks good, try pushing. If that works,
That worked for for me. I suspect that this is a reasonably common scenario, since the most recent commit is the most likely one to be corrupted, but if you lose one further back, you can probably still use a method like this, with careful use of git cherrypick, and the reflog in .git/logs/HEAD.
When I had this issue I backed up my recent changes (as I knew what I had changed) then deleted that file it was complaining about in .git/location. Then I did a git pull. Take care though, this might not work for you.
Create a backup and clone the repository into a fresh directory
cp -R foo foo-backup
git clone git#url:foo foo-new
(optional) If you are working on a different branch than master, switch it.
cd foo-new
git checkout -b branch-name origin/branch-name
Sync changes excluding the .git directory
rsync -aP --exclude=.git foo-backup/ foo-new
This problem usually occures when using various git clients with different versions on the same git checkout. Think of:
Command line
IDE build-in git
Inside docker / vm container
GIT gui tool
Make sure you push with the same client that created the commits.
What I did not to lose other unpushed branches:
A reference to the broken object should be in refs/heads/<current_branch>. If you go to .git\logs\refs\heads\<current_branch> you can see that the last commit has the exactly same value. I copied the one from the previous commit to the first file and it solved the problem.
I had a similar issue on a Windows 10 computer with onedrive backing up my documents folder where I have my git repositories.
Looking at the object in the git object directory I did not see a green checkmark but the blue sync icon for that file. All other object files appeared to have the green checkmark. Playing around, trying things, I tried selecting the option always keep this folder on this device but got an error: error 0x80071129 the tag present in the reparse point buffer is invalid.
This link (https://answers.microsoft.com/en-us/msoffice/forum/all/error-0x80071129-the-tag-present-in-the-reparse/b8011cee-98c5-4c33-ba99-d0eec7c535a0) suggests to run chkdsk /r /f as an admin to fix the issue (have to reboot computer). I did that and it fixed my issue.
Have the same issue after my linux mint crash, and I press power button to shutdown my laptop, that's why my .git is corrupt
find .git/objects/ -empty -delete
After that, I get error fatal: Bad object head. I just Reinitialized my git
git init
And fetch from remote repo
git fetch
To check your git, use
git status
And it's work again. I don't lose my local changes, so I can commit without rewriting code
I had the exact same error and managed to get my repo back without losing my changes.
I do not know if it could work for others as corruption reason can be multiple, but it's worth trying
I:
Made several backups of the corrupt git repository just in case
Cloned the lasted pushed version from the remote repository
Copied all the files from the corrupt .git folder EXCEPT all files related to HEAD, FETCH_HEAD, ORG_HEAD etc ... the most important are the refs, obj, and index
Ended up with a valid history, but corrupt index, applied the solution from this post How to resolve "Error: bad index – Fatal: index file corrupt" when using Git
And my repository was back working ...
To make sure I did not push anything wrong, I cloned again from the remote, checked-out the changes I wanted to save from the restored repository, and comited them fresh.
My eclipse suddenly shut down, and after that for a particular file, there are two files present:
the main file and
a .checkedout version of it.
Now the main file is not checkedout out from my machine, still if anyone else tries to check out the file: it shows it is checked out already.
I have seen from Clearcase explorer too, it is the same there.
Any solution for this?
It depends on the version of ClearCase (client and server, including their OS), and of the type of ClearCase view you are using (snapshot, dynamic, web view)
But in general, if a file is checked out and should not be, you can delete any checked out status associated to your view.
However, please note it will cancel all your checked out files done in this particular view (for that particular Vob), so make sure it won't impact your current work in progress (save it first elsewhere to be safe).
cleartool descr -l vob:\myVob
# get the uuid of the user's view from the description of the vob
cleartool mount \myVob
cd m:\mynewView\myVob
cleartool rmview -force -uuid old_view_uuid
Note: you can also get your view UUID with
cd path/to/my/view
cleartool lsview -l -full -pro -cview
That way, nobody else will see any of your previously checked out file as "checked out".
Note that a .checkedout file is typically the result of a failed checkout for permission issue.
Example:
Unable to rename "M:\myView\myVob\path\to\afile.png" to "M:\myView\myVob\path\to\afile.png.keep": Permission denied.
Checked out version, but could not copy data to "M:\myView\myVob\path\to\afile.png" in view: File exists.
Correct the condition, then uncheckout and re-checkout the element.
Copied checked-out version data to "M:\myView\myVob\path\to\afile.png.checkedout".
Checked out "M:\myView\myVob\path\to\afile.png" from version "\main\myStream\0".
Attached activity:
activity:deliver.stream_myStream.20120426.115512#\myPVob
In our clearcase we are having few folders require same contents.
We use to have symlink to achieve that. But Now our folders are having view private files, so symlink doesn't do any good.
Is copying it again the only mechanism ?
Any other policy or settings which can help to symlink view private file?
Symlinks (OS symlinks, not cleartool symlinks) should be supported, even for private files (they would certainly work in snapshot view anyway: those are based on the native OS).
Otherwise, copy is still a solution to fallback on.
But I am not aware of any dedicated policy on ClearCase for symlinks on private view files.
The is only one policy for versionned symlinks (created by cleartool ln -s, but this isn't your current scenario):
On Linux and UNIX systems, symbolic links are listed as absolute pathnames by default.
To list symbolic links as relative pathnames, set the environment variable CCASE_LS_RELATIVE_SYMLINK_PATH.
The OP Samselvaprabu mentions using Dynamic view drive and i am in windows environment, and reports the following error on symlink creation:
Object Msilist.bat is not a valid symlink target; no symlinks will be created.
Please select only valid symlink targets and retry the operation.
The man page "To create a Vob symlink" mentions the following restrictions:
You can use the cleartool ln -s command to create a VOB symbolic link (symlink) to the following items:
A file or directory (checked in or checked out)
A symbolic link
An eclipsed element (dynamic views only)
A hijacked element (snapshot views only)
The target of the symbolic link must be in the same view as the directory in which the symbolic link is to be created.
If you are in a snapshot view, unloaded elements are not valid symlink targets. Also, the directory in which the symlink is to be created must also be loaded.
My point was:
If cleartool ln -s doesn't work, especially for private file (which are not in ClearCase anyway), use OS symlink (in your case, NTFS symlinks if you are on Windows Vista or more, otherwise simple junction points)
So OS symlinks (native symlinks, not created by cleartool) should work.