Question

I am having a strange issue that I can’t seem to resolve. Here is what happend:

I had some log files in a github repository that I didn’t want there. I found this script that removes files completely from git history like so:

    #!/bin/bash
set -o errexit

# Author: David Underhill
# Script to permanently delete files/folders from your git repository.  To use 
# it, cd to your repository's root and then run the script with a list of paths
# you want to delete, e.g., git-delete-history path1 path2

if [ $# -eq 0 ]; then
    exit 0are still
fi

# make sure we're at the root of git repo
if [ ! -d .git ]; then
    echo "Error: must run this script from the root of a git repository"
    exit 1
fi

# remove all paths passed as arguments from the history of the repo
files=$@
git filter-branch --index-filter "git rm -rf --cached --ignore-unmatch $files" HEAD

# remove the temporary history git-filter-branch otherwise leaves behind for a long time
rm -rf .git/refs/original/ && git reflog expire --all &&  git gc --aggressive --prune

I, of course, made a backup first and then tried it. It seemed to work fine. I then did a git push -f and was greeted with the following messages:

error: Unable to append to .git/logs/refs/remotes/origin/master: Permission denied
error: Cannot update the ref 'refs/remotes/origin/master'.

Everything seems to have pushed fine though, because the files seem to be gone from the GitHub repository, if I try and push again I get the same thing:

error: Unable to append to .git/logs/refs/remotes/origin/master: Permission denied
error: Cannot update the ref 'refs/remotes/origin/master'.
Everything up-to-date

EDIT

$ sudo chgrp {user} .git/logs/refs/remotes/origin/master
$ sudo chown {user} .git/logs/refs/remotes/origin/master
$ git push
Everything up-to-date

Thanks!

EDIT

Uh Oh. Problem. I’ve been working on this project all night and just went to commit my changes:

error: Unable to append to .git/logs/refs/heads/master: Permission denied
fatal: cannot update HEAD ref

So I:

sudo chown {user} .git/logs/refs/heads/master
sudo chgrp {user} .git/logs/refs/heads/master

I try the commit again and I get:

error: Unable to append to .git/logs/HEAD: Permission denied
fatal: cannot update HEAD ref

So I:

sudo chown {user} .git/logs/HEAD
sudo chgrp {user} .git/logs/HEAD

And then I try the commit again:

16 files changed, 499 insertions(+), 284 deletions(-)
create mode 100644 logs/DBerrors.xsl
delete mode 100644 logs/emptyPHPerrors.php
create mode 100644 logs/trimXMLerrors.php
rewrite public/codeCore/Classes/php/DatabaseConnection.php (77%)
create mode 100644 public/codeSite/php/init.php
$ git push
Counting objects: 49, done.
Delta compression using up to 2 threads.
Compressing objects: 100% (27/27), done.
Writing objects: 100% (27/27), 7.72 KiB, done.
Total 27 (delta 15), reused 0 (delta 0)
To [e-mail]:IAmCorbin/MooKit.git
59da24e..68b6397  master -> master

Hooray. I jump on http://GitHub.com and check out the repository, and my latest commit is no where to be found. ::scratch head:: So I push again:

Everything up-to-date

Umm…it doesn’t look like it. I’ve never had this issue before, could this be a problem with github? or did I mess something up with my git project?

EDIT

Nevermind, I did a simple:

git push origin master

and it pushed fine.

Answer 1

This looks like you ran git as root locally, thus changing ownership on some of the files tracking the location of the origin branch.

Fix the file ownership, and you should be fine:

# run this from the root of the git working tree
sudo chown -R "${USER:-$(id -un)}" .