I have a repo for which git annex fsck --all goes through without any complaints, and git fsck produces
Checking object directories: 100% (256/256), done.
error in tree 97abf6de76c0c56593f78d2f55b4c60d04345281: gitmodulesSymlink: .gitmodules is a symbolic link
Checking objects: 100% (998477/998477), done.
Checking connectivity: 998477, done.
dangling tree f9a2b542f57770c135631de1ae590475fc0caa54
but running git annex repair --force,
repair Running git fsck ...
Unpacking all pack files.
Unpacking objects: 100% (998477/998477), 64.95 MiB | 359.00 KiB/s, done.
Initialized empty Git repository in /tmp/tmprepoqPmkhi/.git/
Trying to recover missing objects from remote A.
fatal: '[a path I censored]' does not appear to be a git repository
fatal: Could not read from remote repository.
Please make sure you have the correct access rights
and the repository exists.
Trying to recover missing objects from remote B.
Unpacking all pack files.
Unpacking objects: 100% (923941/923941), 63.54 MiB | 367.00 KiB/s, done.
[A couple of other cases of remotes not available.]
failed
git-annex: repair: 1 failed
Is the failure likely related to the gitmodulesSymlink error? If so, what could I do about it? If not, how do I figure out what's going on?
Regarding the .gitmodules complaint: The repo has a subfolder with its own .git and .gitmodules, and although nothing in there is commited into the main repo now, I did in the past accidentally, temporarily commit the subfolder/.gitmodules into the main repo.
I don't actually find anything wrong with the repo, the only reason I'm running repair on it is because a remote of it is missing some files, although it claims to be all synced up.
This is on version 8.20200226. I would be happy to try on a more recent one, if there's a way to do so on Ubuntu without compiling from source.
I don't think your problem is related to the "git fsck" error. Also, it doesn't look like the failure of "git annex repair" is related to the "git fsck" error either. What does "git status" say in the repo that is missing files?
git statuson the repo that's missing files (and has old versions of some other files, I just noticed) shows nothing remarkable: Some staged modifications, some other unstaged ones, and some untracked files, but they don't include the missing and/or out-of-date ones.This is not the kind of problem that
git-annex repaircan fix. The problems it fixes are all where one clone of a repo has gotten some object files corrupted by eg disk problems, but other clones still have good copies of those object files.The reason
git-annex repairreports it failed is because it sees thatgit fsckis reporting a problem and the things it's tried to do didn't fix it.Are the "missing files" missing in that their annexed content is not present, or missing in that there is no annex symlink at all? In the former case, you need
git annex fsckon those files, orgit-annex get. In the latter case, ifgit statusdoesn't show a missing file as deleted, that would be a very strange problem with git.