# Error "fatal: not a git repository" after auto packing 4 messages from 2014-08-11 to 2014-08-12. Participants: Luke Campagnola, Duy Nguyen, Dennis Kaarsemaker. Thread: https://gitlist.dev/t/37332 ## Luke Campagnola, 2014-08-11 22:56 Subject: Error "fatal: not a git repository" after auto packing Message-ID: URL: https://gitlist.dev/e/CACZXET_qPzBtqJLXBbou%2BiZ_Muj%3DVqCBe5qMADN72VScsuHRVQ%40mail.gmail.com ``` Greetings, I have been working happily with git for a couple of years, and ran into a mysterious issue today: after running a git-pull during which I saw the message "Auto packing the repository for optimum performance". I now receive the error "Fatal: not a git repository" when running any git commands, and a little investigation revealed that my .git/refs directory has gone missing, presumably because the refs were all combined into .git/packed-refs. To restore access to the repository, all I needed was to `mkdir .git/refs`. Is this a known bug? It seems like either git should tolerate the absence of a .git/refs directory, or the auto packer should not remove it. I am using git 1.9.1 on kubuntu 14.04. The surrounding console output follows: raven:/home/luke/vispy (transform-cache)$ git commit -a [transform-cache 15a0fe3] Optimizations for grid_large 6 files changed, 91 insertions(+), 52 deletions(-) raven:/home/luke/vispy (transform-cache)$ git push lcampagn transform-cache Counting objects: 114, done. Delta compression using up to 4 threads. Compressing objects: 100% (31/31), done. Writing objects: 100% (31/31), 4.00 KiB | 0 bytes/s, done. Total 31 (delta 25), reused 0 (delta 0) To git@github.com:lcampagn/vispy.git 24b37a6..15a0fe3 transform-cache -> transform-cache raven:/home/luke/vispy (transform-cache)$ git fetch vispy remote: Counting objects: 78, done. remote: Compressing objects: 100% (78/78), done. remote: Total 78 (delta 34), reused 0 (delta 0) Unpacking objects: 100% (78/78), done. From https://github.com/vispy/vispy ec740af..fd8aa37 master -> vispy/master Auto packing the repository for optimum performance. You may also run "git gc" manually. See "git help gc" for more information. Counting objects: 5349, done. Delta compression using up to 4 threads. Compressing objects: 100% (5315/5315), done. Writing objects: 100% (5349/5349), done. Total 5349 (delta 3977), reused 0 (delta 0) Removing duplicate objects: 100% (256/256), done. raven:/home/luke/vispy (transform-cache)$ git checkout master Switched to branch 'master' Deleted 103 .pyc files Deleted 11 empty directories raven:/home/luke/vispy$ git pull vispy master fatal: Not a git repository (or any of the parent directories): .git raven:/home/luke/vispy$ git status fatal: Not a git repository (or any of the parent directories): .git raven:/home/luke/vispy$ ls -al .git total 288 drwxr-xr-x 6 luke luke 4096 Aug 11 17:09 . drwxr-xr-x 9 luke luke 4096 Aug 11 09:25 .. -rw-r--r-- 1 luke luke 601 Aug 11 12:22 COMMIT_EDITMSG -rw-rw-r-- 1 luke luke 1088 Aug 11 09:21 config -rw-r--r-- 1 luke luke 73 Mar 2 08:41 description -rw-r--r-- 1 luke luke 323 Aug 11 16:56 FETCH_HEAD -rw-r--r-- 1 luke luke 337 Mar 3 10:18 GIT_COLA_MSG -rw-r--r-- 1 luke luke 193478 Aug 11 11:14 gitk.cache -rw-rw-r-- 1 luke luke 23 Aug 11 17:09 HEAD drwxr-xr-x 2 luke luke 4096 Mar 8 07:30 hooks -rw-rw-r-- 1 luke luke 31104 Aug 11 17:09 index drwxr-xr-x 2 luke luke 4096 Aug 11 16:57 info drwxr-xr-x 3 luke luke 4096 Aug 11 16:56 logs drwxr-xr-x 105 luke luke 4096 Aug 11 16:57 objects -rw-rw-r-- 1 luke luke 41 Aug 11 09:25 ORIG_HEAD -rw-rw-r-- 1 luke luke 8210 Aug 11 16:56 packed-refs ``` ## Duy Nguyen, 2014-08-12 15:41 Subject: Re: Error "fatal: not a git repository" after auto packing Message-ID: URL: https://gitlist.dev/e/CACsJy8A576_OxXNKpsar5DiJ3Z%3DYsG4DURxL_JceknhRxBjB%2Bg%40mail.gmail.com In-Reply-To: ``` On Tue, Aug 12, 2014 at 5:56 AM, Luke Campagnola wrote: > Greetings, > > I have been working happily with git for a couple of years, and ran > into a mysterious issue today: after running a git-pull during which I > saw the message "Auto packing the repository for optimum performance". > I now receive the error "Fatal: not a git repository" when running any > git commands, and a little investigation revealed that my .git/refs > directory has gone missing, presumably because the refs were all > combined into .git/packed-refs. To restore access to the repository, > all I needed was to `mkdir .git/refs`. Is this a known bug? Not to me. > It seems > like either git should tolerate the absence of a .git/refs directory, > or the auto packer should not remove it. I tried to clone from vispy.git, running 'git gc' manually and 'pack-refs' (which should be in charge of removing empty dirs with v1.9.1. Things worked fine. Looked at refs.c:try_remove_empty_parents() as well. Still could not find any bug there.. So no good news. I don't suppose that if you run "git gc" again, it would remove $GIT_DIR/refs one more time? -- Duy ``` ## Dennis Kaarsemaker, 2014-08-12 16:11 Subject: Re: Error "fatal: not a git repository" after auto packing Message-ID: <1407859882.17965.1.camel@spirit> URL: https://gitlist.dev/e/1407859882.17965.1.camel%40spirit In-Reply-To: ``` On ma, 2014-08-11 at 18:56 -0400, Luke Campagnola wrote: > > raven:/home/luke/vispy (transform-cache)$ git checkout master > Switched to branch 'master' > Deleted 103 .pyc files > Deleted 11 empty directories This looks like you have a local post-checkout hook that deletes empty directories. Fix that hook to not do anything in .git and it should be fine. -- Dennis Kaarsemaker www.kaarsemaker.net ``` ## Luke Campagnola, 2014-08-12 16:16 Subject: Re: Error "fatal: not a git repository" after auto packing Message-ID: URL: https://gitlist.dev/e/CACZXET-O0SZnJp_LWg_v8ZFfkUXbYtS-j96UYmMkDtbv%2BNZM5w%40mail.gmail.com In-Reply-To: <1407859882.17965.1.camel@spirit> ``` On Tue, Aug 12, 2014 at 12:11 PM, Dennis Kaarsemaker wrote: > On ma, 2014-08-11 at 18:56 -0400, Luke Campagnola wrote: >> >> raven:/home/luke/vispy (transform-cache)$ git checkout master >> Switched to branch 'master' >> Deleted 103 .pyc files >> Deleted 11 empty directories > > This looks like you have a local post-checkout hook that deletes empty > directories. Fix that hook to not do anything in .git and it should be > fine. Of course you are correct. Sorry for the noise. ```