General Questions • [Software] Error in APT

Hello Jeremy!

You were right about .git dependency
root@debian:/# apt policy git etckeeper
git:
Installed: 1:2.39.2-1.1
Candidate: 1:2.39.2-1.1
Version table:
*** 1:2.39.2-1.1 500
500 http://deb.debian.org/debian bookworm/main amd64 Packages
100 /var/lib/dpkg/status
etckeeper:
Installed: 1.18.20-1
Candidate: 1.18.20-1
Version table:
*** 1.18.20-1 500
500 http://deb.debian.org/debian bookworm/main amd64 Packages
100 /var/lib/dpkg/status


I tried the fix in the link, it turned out there were a lot of empty files, and the git check resulted in some errors.

root@debian:/etc/.git# find . -type f -empty -delete -print
./objects/87/2f66e0f76c92dabf0899c32130aa2f8a2f2182
./objects/a7/75a70b90c09ba64ffb1c20153e3c2917617c25
./objects/b3/eaf9e771481e00b287c3f923bf86be73380d57
./objects/bf/7676e159f16be87964668404c13aaabcd81ca1
./objects/bf/bfeb0483e1e22f68a0f8183ce36e16984b06da
./objects/2f/fa9957a39c863baf38f5f076c51ad2e5b33ed1
./objects/96/8080284af8dee385d539ef58aac321077cf2b4
./objects/45/10b78444adad1a279dd7a47f0a072944515987
./objects/45/2aeb25bbc63cd2ee0bc1209c697f6b6a691de9
./objects/e1/618999ef17bd76151daecbbc86469e18a5dc0e
./objects/65/56e2d694d367dd860578d0c6aa1c41d0b5e7b7
./objects/0c/4651be6c52d9d41a6334357bb4454dd44bb094
./objects/8a/578aea57d22c7a2a9f6ff7f4fa9d7edf03a832
./objects/62/ebaac5808217b8566e51e60aeece7e82f1ffdd
./objects/90/762476bbcaea47b9eb59ad1a0e800f5c663acb
./objects/a5/78634f391db8268784bf4e226b158a5b120bff
./objects/c2/67c0c984f43043416c72bf8d0176eff6c65a1f
./objects/c9/1eb777a97ccf06d381fa4a58b00852529bc6d1
./objects/73/384c0a219a30ea2d69f93e19f8c14f785fa9ba
./objects/34/a2efede89bb2c50034a8befbcab71f95b80282
./objects/1c/9dc59cd9791a0607120b50411e503055b0751c

root@debian:/etc/.git# git fsck --full
Checking object directories: 100% (256/256), done.
Checking objects: 100% (2692/2692), done.
error: refs/heads/master: invalid sha1 pointer c267c0c984f43043416c72bf8d0176eff6c65a1f
error: HEAD: invalid sha1 pointer c267c0c984f43043416c72bf8d0176eff6c65a1f
notice: No default references
error: bfbfeb0483e1e22f68a0f8183ce36e16984b06da: invalid sha1 pointer in cache-tree
error: 90762476bbcaea47b9eb59ad1a0e800f5c663acb: invalid sha1 pointer in cache-tree
error: c91eb777a97ccf06d381fa4a58b00852529bc6d1: invalid sha1 pointer in cache-tree
error: bf7676e159f16be87964668404c13aaabcd81ca1: invalid sha1 pointer in cache-tree
missing blob 968080284af8dee385d539ef58aac321077cf2b4
missing blob e1618999ef17bd76151daecbbc86469e18a5dc0e
missing blob 34a2efede89bb2c50034a8befbcab71f95b80282
missing blob 0c4651be6c52d9d41a6334357bb4454dd44bb094
missing blob b3eaf9e771481e00b287c3f923bf86be73380d57
missing blob 8a578aea57d22c7a2a9f6ff7f4fa9d7edf03a832
missing blob 2ffa9957a39c863baf38f5f076c51ad2e5b33ed1
Verifying commits in commit graph: 100% (1/1), done.


I reverted the .git-old directory and run the git fsck --full command again:

root@debian:/etc/.git# git fsck --full
error: object file ./objects/0c/4651be6c52d9d41a6334357bb4454dd44bb094 is empty
error: unable to mmap ./objects/0c/4651be6c52d9d41a6334357bb4454dd44bb094: No such file or directory
error: 0c4651be6c52d9d41a6334357bb4454dd44bb094: object corrupt or missing: ./objects/0c/4651be6c52d9d41a6334357bb4454dd44bb094
error: object file ./objects/1c/9dc59cd9791a0607120b50411e503055b0751c is empty
error: unable to mmap ./objects/1c/9dc59cd9791a0607120b50411e503055b0751c: No such file or directory
error: 1c9dc59cd9791a0607120b50411e503055b0751c: object corrupt or missing: ./objects/1c/9dc59cd9791a0607120b50411e503055b0751c
error: object file ./objects/2f/fa9957a39c863baf38f5f076c51ad2e5b33ed1 is empty
error: unable to mmap ./objects/2f/fa9957a39c863baf38f5f076c51ad2e5b33ed1: No such file or directory
error: 2ffa9957a39c863baf38f5f076c51ad2e5b33ed1: object corrupt or missing: ./objects/2f/fa9957a39c863baf38f5f076c51ad2e5b33ed1
error: object file ./objects/34/a2efede89bb2c50034a8befbcab71f95b80282 is empty
error: unable to mmap ./objects/34/a2efede89bb2c50034a8befbcab71f95b80282: No such file or directory
error: 34a2efede89bb2c50034a8befbcab71f95b80282: object corrupt or missing: ./objects/34/a2efede89bb2c50034a8befbcab71f95b80282
error: object file ./objects/45/10b78444adad1a279dd7a47f0a072944515987 is empty
error: unable to mmap ./objects/45/10b78444adad1a279dd7a47f0a072944515987: No such file or directory
error: 4510b78444adad1a279dd7a47f0a072944515987: object corrupt or missing: ./objects/45/10b78444adad1a279dd7a47f0a072944515987
error: object file ./objects/45/2aeb25bbc63cd2ee0bc1209c697f6b6a691de9 is empty
error: unable to mmap ./objects/45/2aeb25bbc63cd2ee0bc1209c697f6b6a691de9: No such file or directory
error: 452aeb25bbc63cd2ee0bc1209c697f6b6a691de9: object corrupt or missing: ./objects/45/2aeb25bbc63cd2ee0bc1209c697f6b6a691de9
error: object file ./objects/62/ebaac5808217b8566e51e60aeece7e82f1ffdd is empty
error: unable to mmap ./objects/62/ebaac5808217b8566e51e60aeece7e82f1ffdd: No such file or directory
error: 62ebaac5808217b8566e51e60aeece7e82f1ffdd: object corrupt or missing: ./objects/62/ebaac5808217b8566e51e60aeece7e82f1ffdd
error: object file ./objects/65/56e2d694d367dd860578d0c6aa1c41d0b5e7b7 is empty
error: unable to mmap ./objects/65/56e2d694d367dd860578d0c6aa1c41d0b5e7b7: No such file or directory
error: 6556e2d694d367dd860578d0c6aa1c41d0b5e7b7: object corrupt or missing: ./objects/65/56e2d694d367dd860578d0c6aa1c41d0b5e7b7
error: object file ./objects/73/384c0a219a30ea2d69f93e19f8c14f785fa9ba is empty
error: unable to mmap ./objects/73/384c0a219a30ea2d69f93e19f8c14f785fa9ba: No such file or directory
error: 73384c0a219a30ea2d69f93e19f8c14f785fa9ba: object corrupt or missing: ./objects/73/384c0a219a30ea2d69f93e19f8c14f785fa9ba
error: object file ./objects/87/2f66e0f76c92dabf0899c32130aa2f8a2f2182 is empty
error: unable to mmap ./objects/87/2f66e0f76c92dabf0899c32130aa2f8a2f2182: No such file or directory
error: 872f66e0f76c92dabf0899c32130aa2f8a2f2182: object corrupt or missing: ./objects/87/2f66e0f76c92dabf0899c32130aa2f8a2f2182
error: object file ./objects/8a/578aea57d22c7a2a9f6ff7f4fa9d7edf03a832 is empty
error: unable to mmap ./objects/8a/578aea57d22c7a2a9f6ff7f4fa9d7edf03a832: No such file or directory
error: 8a578aea57d22c7a2a9f6ff7f4fa9d7edf03a832: object corrupt or missing: ./objects/8a/578aea57d22c7a2a9f6ff7f4fa9d7edf03a832
error: object file ./objects/90/762476bbcaea47b9eb59ad1a0e800f5c663acb is empty
error: unable to mmap ./objects/90/762476bbcaea47b9eb59ad1a0e800f5c663acb: No such file or directory
error: 90762476bbcaea47b9eb59ad1a0e800f5c663acb: object corrupt or missing: ./objects/90/762476bbcaea47b9eb59ad1a0e800f5c663acb
error: object file ./objects/96/8080284af8dee385d539ef58aac321077cf2b4 is empty
error: unable to mmap ./objects/96/8080284af8dee385d539ef58aac321077cf2b4: No such file or directory
error: 968080284af8dee385d539ef58aac321077cf2b4: object corrupt or missing: ./objects/96/8080284af8dee385d539ef58aac321077cf2b4
error: object file ./objects/a5/78634f391db8268784bf4e226b158a5b120bff is empty
error: unable to mmap ./objects/a5/78634f391db8268784bf4e226b158a5b120bff: No such file or directory
error: a578634f391db8268784bf4e226b158a5b120bff: object corrupt or missing: ./objects/a5/78634f391db8268784bf4e226b158a5b120bff
error: object file ./objects/a7/75a70b90c09ba64ffb1c20153e3c2917617c25 is empty
error: unable to mmap ./objects/a7/75a70b90c09ba64ffb1c20153e3c2917617c25: No such file or directory
error: a775a70b90c09ba64ffb1c20153e3c2917617c25: object corrupt or missing: ./objects/a7/75a70b90c09ba64ffb1c20153e3c2917617c25
error: object file ./objects/b3/eaf9e771481e00b287c3f923bf86be73380d57 is empty
error: unable to mmap ./objects/b3/eaf9e771481e00b287c3f923bf86be73380d57: No such file or directory
error: b3eaf9e771481e00b287c3f923bf86be73380d57: object corrupt or missing: ./objects/b3/eaf9e771481e00b287c3f923bf86be73380d57
error: object file ./objects/bf/7676e159f16be87964668404c13aaabcd81ca1 is empty
error: unable to mmap ./objects/bf/7676e159f16be87964668404c13aaabcd81ca1: No such file or directory
error: bf7676e159f16be87964668404c13aaabcd81ca1: object corrupt or missing: ./objects/bf/7676e159f16be87964668404c13aaabcd81ca1
error: object file ./objects/bf/bfeb0483e1e22f68a0f8183ce36e16984b06da is empty
error: unable to mmap ./objects/bf/bfeb0483e1e22f68a0f8183ce36e16984b06da: No such file or directory
error: bfbfeb0483e1e22f68a0f8183ce36e16984b06da: object corrupt or missing: ./objects/bf/bfeb0483e1e22f68a0f8183ce36e16984b06da
error: object file ./objects/c2/67c0c984f43043416c72bf8d0176eff6c65a1f is empty
error: unable to mmap ./objects/c2/67c0c984f43043416c72bf8d0176eff6c65a1f: No such file or directory
error: c267c0c984f43043416c72bf8d0176eff6c65a1f: object corrupt or missing: ./objects/c2/67c0c984f43043416c72bf8d0176eff6c65a1f
error: object file ./objects/c9/1eb777a97ccf06d381fa4a58b00852529bc6d1 is empty
error: unable to mmap ./objects/c9/1eb777a97ccf06d381fa4a58b00852529bc6d1: No such file or directory
error: c91eb777a97ccf06d381fa4a58b00852529bc6d1: object corrupt or missing: ./objects/c9/1eb777a97ccf06d381fa4a58b00852529bc6d1
error: object file ./objects/e1/618999ef17bd76151daecbbc86469e18a5dc0e is empty
error: unable to mmap ./objects/e1/618999ef17bd76151daecbbc86469e18a5dc0e: No such file or directory
error: e1618999ef17bd76151daecbbc86469e18a5dc0e: object corrupt or missing: ./objects/e1/618999ef17bd76151daecbbc86469e18a5dc0e
Checking object directories: 100% (256/256), done.
Checking objects: 100% (2692/2692), done.
error: object file ./objects/c2/67c0c984f43043416c72bf8d0176eff6c65a1f is empty
error: object file ./objects/c2/67c0c984f43043416c72bf8d0176eff6c65a1f is empty
fatal: loose object c267c0c984f43043416c72bf8d0176eff6c65a1f (stored in ./objects/c2/67c0c984f43043416c72bf8d0176eff6c65a1f) is corrupt

Guess will have to reinitialize etckeeper! What do you think?
Thanks, have a nice new year!
Celso

Amazing!
You are right! Thanks

Nice! You are most welcome.

Found the file in the path you mentioned, this file is zero bytes, is it safe to delete it?

Hopefully!? Now you've found the offending file, I suggest checking out the link provided to you right near the start of this thread:

What about this?
dev.to: How to fix Git error: object file is empty?

That looks like it will fix your issue here. Note that those instructions include backing up the original git repo, just in case. So worst case scenario, you can roll back to where you are now.

Having said that, assuming that it was etckeeper that created the git repo there (seems incredibly likely to me - but you can check below), then if you don't mind losing your /etc history (it won't wipe any of your actual config files in /etc, just the histroy of changes), then another option might be to reinitialize etckeeper:

Code:

sudo etckeeper uninitsudo etckeeper init

(man etckeeper)

As it seems there is some issue with the git repo, there is chance that that might fail and you may need to resort to a manual fix anyway. Personally, I'd probably do the manual fix, but I wanted to give you all the options that seem relevant.

Don´t know what it does, in this machine Installed a Virtualmin LAMP stack via a Script,
so it migh have installed a lot of stuff, inside virtualmin panel its possible to install debian packages and server modules,
I guess thats where git is necessary.

etckeeper is a pretty awesome tool IMO. It basically stores all changes in /etc in a git repo. It allows you to easily see what config has changed and when. You can also roll back changes if/when required. IIRC it does a daily auto commit (if there are any changes) and (as you've discovered) it also has an apt hook, to commit changes when packages are updated (before if there are uncommitted changes and again afterwards)

I suspect that git was installed as a dependency of etckeeper, but I have no idea what installed that? Perhaps virtualmin - but TBH I doubt it? Whilst I rarely use it myself (I much prefer CLI) I'm quite familiar with Webmin and that doesn't install anything else beyond it's hard dependencies (which should already generally be installed on most systems AFAIK - you need to manually install specific module dependencies if you want to use them). I'm not at all familiar with Virtualmin. Re-reading your post, I suspect that your script probably installed etckeeper but I'm really only guessing.

Bottom line though, if your system is working ok at the moment then even if you destroy all the git history, it's probably not that big a deal. As I've noted above, it's only the changes that it saves, the current config files in /etc will be fine regardless.

My guess is that etckeeper (and git as it's dependency) is installed via Debian package. But it's easy to check:

Code:

apt policy git etckeeper

That should show where both git and etckeeper come from.

As a last word, IMO git is often a vital tool on a server these days and it's not that big, so leaving that installed is a no-brainer IMO. etckeeper is also well worth having IMO, but if it's causing you more headaches than it's helping you avoid, then you could always completely remove it!?

Code:

sudo apt remove etckeeper

Good luck!

Statistics: Posted by cferrarini — 2024-01-07 00:46 — Replies 19 — Views 3256

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