Git submodule head reference is not a tree error

Question

I have a project with a submodule that is pointing to an invalid commit  the submodule commit remained local and when I try to fetch it from another repo I get     git submodule update fatal  reference is not a tree  2d7cfbd09fc96c04c4c41148d44ed7778add6b43 Unable to checkout  2d7cfbd09fc96c04c4c41148d44ed7778add6b43  in submodule path  mysubmodule    I know what the submodule HEAD should be  is there any way I can change this locally  without pushing from the repo that does have commit 2d7cfbd09fc96c04c4c41148d44ed7778add6b43    I m not sure if I m being clear    here s a similar situation I found

User · Answer

This may also happen when you have a submodule pointing to a repository that was rebased and the given commit is  gone   While the commit may still be in the remote repository  it is not in a branch  If you can t create a new branch  e g  not your repository   you re stuck with having to update the super project to point to a new commit  Alternatively you can push one of your copies of the submodules elsewhere and then update the super-project to point to that repository instead

User · Answer

In my case  none of answer above solve the problem even thoungh they are good answers  So I post my solution  in my case there are two git clients  client A and B     go to submodule s dir   cd sub  checkout to master   git checkout master  rebase to a commit code which both client can see go back to the parent s dir  commit to master change to the other client  do rebase again  finally it works fine now  Maybe lose a couple of commits but it works  FYI  don t try to remove your submodule  it will remain  git modules there and cannot readd this submodule again  unless reactive local one

User · Answer

I got this error when I did     git submodule update --init --depth 1   but the commit in the parent project was pointing at an earlier commit     Deleting the submodule folder and running     git submodule update --init   did NOT solve the problem  I deleted the repo and tried again without the depth flag and it worked   This error happens in Ubuntu 16 04 git 2 7 4  but not on Ubuntu 18 04 git 2 17  TODO find exact fixing commit or version

User · Answer

Just stumbled upon this problem  and none of these solutions worked for me  What turned out to be the solution for my issue is actually much simpler  upgrade Git  Mine was 1 7 1  and after I upgraded it to 2 16 1  latest   the problem went away without a trace  Guess I m leaving it here  hope it helps someone

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To sync the git repo with the submodule s head  in case that is really what you want  I found that removing the submodule and then readding it avoids the tinkering with the history  Unfortunately removing a submodule requires hacking rather than being a single git command  but doable   Steps I followed to remove the submodule  inspired by https   gist github com kyleturner 1563153    Run git rm --cached  Delete the relevant lines from the  gitmodules file  Delete the relevant section from  git config  Delete the now untracked submodule files  Remove directory  git modules    Again  this can be useful if all you want is to point at the submodule s head again  and you haven t complicated things by needing to keep the local copy of the submodule intact  It assumes you have the submodule  right  as its own repo  wherever the origin of it is  and you just want to get back to properly including it as a submodule    Note  always make a full copy of your project before engaging in these kinds of manipulation or any git command beyond simple commit or push  I d advise that with all other answers as well  and as a general git guideline

User · Answer

This error can mean that a commit is missing in the submodule   That is  the repository  A  has a submodule  B    A wants to load B so that it is pointing to a certain commit  in B    If that commit is somehow missing  you ll get that error   Once possible cause  the reference to the commit was pushed in A  but the actual commit was not pushed from B   So I d start there   Less likely  there s a permissions problem  and the commit cannot be pulled  possible if you re using git ssh    Make sure the submodule paths look ok in  git config and  gitmodules   One last thing to try - inside the submodule directory  git reset HEAD --hard

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Assuming the submodule s repository does contain a commit you want to use  unlike the commit that is referenced from current state of the super-project   there are two ways to do it   The first requires you to already know the commit from the submodule that you want to use  It works from the    inside  out    by directly adjusting the submodule then updating the super-project  The second works from the    outside  in    by finding the super-project s commit that modified the submodule and then reseting the super-project s index to refer to a different submodule commit   Inside  Out  If you already know which commit you want the submodule to use  cd to the submodule  check out the commit you want  then git add and git commit it back in the super-project   Example     git submodule update fatal  reference is not a tree  e47c0a16d5909d8cb3db47c81896b8b885ae1556 Unable to checkout  e47c0a16d5909d8cb3db47c81896b8b885ae1556  in submodule path  sub    Oops  someone made a super-project commit that refers to an unpublished commit in the submodule sub  Somehow  we already know that we want the submodule to be at commit 5d5a3ee314476701a20f2c6ec4a53f88d651df6c  Go there and check it out directly   Checkout in the Submodule    cd sub   git checkout 5d5a3ee314476701a20f2c6ec4a53f88d651df6c Note  moving to  5d5a3ee314476701a20f2c6ec4a53f88d651df6c  which isn t a local branch If you want to create a new branch from this checkout  you may do so  now or later  by using -b with the checkout command again  Example    git checkout -b  lt new branch name gt  HEAD is now at 5d5a3ee    quux   cd      Since we are checking out a commit  this produces a detached HEAD in the submodule  If you want to make sure that the submodule is using a branch  then use git checkout -b newbranch  lt commit gt  to create and checkout a branch at the commit or checkout the branch that you want  e g  one with the desired commit at the tip    Update the Super-project  A checkout in the submodule is reflected in the super-project as a change to the working tree  So we need to stage the change in the super-project s index and verify the results     git add sub   Check the Results    git submodule update   git diff   git diff --cached diff --git c sub i sub index e47c0a1  5d5a3ee 160000 --- c sub     i sub    -1  1    -Subproject commit e47c0a16d5909d8cb3db47c81896b8b885ae1556  Subproject commit 5d5a3ee314476701a20f2c6ec4a53f88d651df6c   The submodule update was silent because the submodule is already at the specified commit  The first diff shows that the index and worktree are the same  The third diff shows that the only staged change is moving the sub submodule to a different commit   Commit  git commit   This commits the fixed-up submodule entry     Outside  In  If you are not sure which commit you should use from the submodule  you can look at the history in the superproject to guide you  You can also manage the reset directly from the super-project     git submodule update fatal  reference is not a tree  e47c0a16d5909d8cb3db47c81896b8b885ae1556 Unable to checkout  e47c0a16d5909d8cb3db47c81896b8b885ae1556  in submodule path  sub    This is the same situation as above  But this time we will focus on fixing it from the super-project instead of dipping into the submodule   Find the Super-project s Errant Commit    git log --oneline -p -- sub ce5d37c local change in sub diff --git a sub b sub index 5d5a3ee  e47c0a1 160000 --- a sub     b sub    -1  1    -Subproject commit 5d5a3ee314476701a20f2c6ec4a53f88d651df6c  Subproject commit e47c0a16d5909d8cb3db47c81896b8b885ae1556 bca4663 added sub diff --git a sub b sub new file mode 160000 index 0000000  5d5a3ee ---  dev null     b sub    -0 0  1     Subproject commit 5d5a3ee314476701a20f2c6ec4a53f88d651df6c   OK  it looks like it went bad in ce5d37c  so we will restore the submodule from its parent  ce5d37c     Alternatively  you can take the submodule s commit from the patch text  5d5a3ee314476701a20f2c6ec4a53f88d651df6c  and use the above    inside  out    process instead   Checkout in the Super-project    git checkout ce5d37c  -- sub   This reset the submodule entry for sub to what it was at commit ce5d37c  in the super-project   Update the Submodule    git submodule update Submodule path  sub   checked out  5d5a3ee314476701a20f2c6ec4a53f88d651df6c    The submodule update went OK  it indicates a detached HEAD    Check the Results    git diff ce5d37c  -- sub   git diff   git diff --cached diff --git c sub i sub index e47c0a1  5d5a3ee 160000 --- c sub     i sub    -1  1    -Subproject commit e47c0a16d5909d8cb3db47c81896b8b885ae1556  Subproject commit 5d5a3ee314476701a20f2c6ec4a53f88d651df6c   The first diff shows that sub is now the same in ce5d37c   The second diff shows that the index and worktree are the same  The third diff shows the only staged change is moving the sub submodule to a different commit   Commit  git commit   This commits the fixed-up submodule entry

User · Answer

This answer is for users of SourceTree with limited terminal git experience    Open the problematic submodule from within the Git project  super-project    Fetch and ensure  Fetch all tags  is checked   Rebase pull your Git project   This will solve the  reference is not a tree  problem 9 out of ten times  That 1 time it won t  is a terminal fix as described by the top answer

User · Answer

Your submodule history is safely preserved in the submodule git anyway   So  why not just delete the submodule and add it again   Otherwise  did you try manually editing the HEAD or the refs master head within the submodule  git

User · Answer

Your branch may not be up to date  a simple solution but try git fetch

User · Answer

try this   git submodule sync git submodule update

User · Answer

Just to be sure  try updating your git binaries   GitHub for Windows has the version git version 1 8 4 msysgit 0 which in my case was the problem  Updating solved it

User · Answer

Possible cause  This can happens when     Submodule s  have been edited in place Submodule s  committed  which updates the hash of the submodule being pointed to Submodule s  not pushed    e g  something like this happened     cd submodule   emacs my source file    edit some file s    git commit -am  Making some changes but will forget to push     Should have submodule pushed at this point     cd      back to parent repository   git commit -am  updates to parent repository    git push origin master   As a result  the missing commits could not possibly be found by the remote user because they are still on the local disk   Solution  Informa the person who modified the submodule to push  i e     cd submodule   git push

[git] Git submodule head 'reference is not a tree' error

Examples related to git

Examples related to git-submodules