Error homebrew core is a shallow clone

Bug report

• [* ] ran brew update and can still reproduce the problem?
• [* ] ran brew doctor, fixed all issues and can still reproduce the problem?
• [* ] ran brew config and brew doctor and included their output with your issue?

What you were trying to do (and why)

I tried to run brew update and brew upgrade as usual to update the packages on my machine. Instead, I got the error below informing me that homebrow-core is a shallow clone (that’s a good thing right?) and that I should unshallow it. Seemed a bit odd to me, as I thought the point of a shallow clone was to save a bunch of disk space, but I ran the command anyway. After running the suggested command to unshallow, the error remains on subsequent tries. So perhaps the issue is unrelated to the «shallowness» of the repo.

What happened (include command output)

Command output

$ brew update

Error: homebrew-core is a shallow clone. To brew update first run:

git -C "/usr/local/Homebrew/Library/Taps/homebrew/homebrew-core" fetch --unshallow
$ git -C "/usr/local/Homebrew/Library/Taps/homebrew/homebrew-core" fetch --unshallow

remote: Enumerating objects: 848801, done.

remote: Counting objects: 100% (848798/848798), done.

remote: Compressing objects: 100% (272589/272589), done.

remote: Total 843685 (delta 574218), reused 837687 (delta 568229), pack-reused 0

Receiving objects: 100% (843685/843685), 331.47 MiB | 10.81 MiB/s, done.

Resolving deltas: 100% (574218/574218), completed with 4347 local objects.

From https://github.com/Homebrew/homebrew-core

55b17bad99..536b616fc3 master     -> origin/master
$ brew upgrade

Error: homebrew-cask is a shallow clone. To brew update first run:

git -C "/usr/local/Homebrew/Library/Taps/homebrew/homebrew-cask" fetch --unshallow
  

What you expected to happen

Brew update and upgrade to update and upgrade, respectively.

Step-by-step reproduction instructions (by running brew commands)

Output of brew config and brew doctor commands

Brew Config:

HOMEBREW_VERSION: 2.6.0-68-g5ad9496
ORIGIN: https://github.com/Homebrew/brew
HEAD: 5ad949672f1fd9ce900e1196a0ad2c020f869480
Last commit: 26 hours ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: 55b17bad998d4b72411754fe69d68b7f3b4d1292
Core tap last commit: 25 hours ago
Core tap branch: master
HOMEBREW_PREFIX: /usr/local
HOMEBREW_CASK_OPTS: []
HOMEBREW_EDITOR: nvim
HOMEBREW_MAKE_JOBS: 12
Homebrew Ruby: 2.6.3 => /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/bin/ruby
CPU: dodeca-core 64-bit kabylake
Clang: 12.0 build 1200
Git: 2.24.3 => /Applications/Xcode.app/Contents/Developer/usr/bin/git
Curl: 7.64.1 => /usr/bin/curl
macOS: 11.0.1-x86_64
CLT: 12.2.0.0.1.1604076827
Xcode: 12.2

Brew Doctor:

Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry or file an issue; just ignore this. Thanks!

Warning: Some installed kegs have no formulae!
This means they were either deleted or installed with `brew diy`.
You should find replacements for the following formulae:
  python@2

Warning: Unbrewed header files were found in /usr/local/include.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.

Unexpected header files:
  /usr/local/include/python2.7/greenlet/greenlet.h
  /usr/local/include/python3.7m/greenlet/greenlet.h
  /usr/local/include/python3.8/greenlet/greenlet.h

Warning: You have unlinked kegs in your Cellar.
Leaving kegs unlinked can lead to build-trouble and cause brews that depend on
those kegs to fail to run properly once built. Run `brew link` on these:
  python@2

Warning: Homebrew's sbin was not found in your PATH but you have installed
formulae that put executables in /usr/local/sbin.
Consider setting the PATH for example like so:
  echo 'set -g fish_user_paths "/usr/local/sbin" $fish_user_paths' >> ~/.config/fish/config.fish

A new version of Homebrew is available, and you may encounter this error if it has not been updated. Fortunately, you can fix this error by following a couple of easy steps. First, you must uninstall any Homebrew packages you have installed. Then, run the git command to un-shallow them. This procedure may take a long time.

This error message will occur when attempting to upgrade a clone. The GitHub servers are under enormous computational burdens when updating a shallow clone. They must dynamically compute the delta between the current state and the latest commit. This computation is performed on a local Git client instead of GitHub’s servers. Adding rate-limiting to such a CI system will make Homebrew operations slow and inefficient.

This is a problem with GitHub’s rate-limit. It requires massive computational effort to update a shallow clone, which will negatively affect other users. This restriction is necessary to prevent GitHub from spending massive amounts of money on a single operation. Another issue with this policy is that it will force developers to use a local Git client to perform updates.

To fix this problem, you should revert to the previous version of the homebrew project. This version is an old version, and you must use it to revert back to it. You should consider updating these versions as a last resort if you want to fix this issue. You can also try to run a brew update command from GitHub. This might take a few minutes, but it will be worth the wait.

If you are trying to use this version of Homebrew, you must revert it to the original version. This is an expensive operation. This error occurs when your homebrew-core is a shallow copy. To fix this, you should revert your homebrew project to the original version. Then, run the brew update command. The process will take a few minutes.

If you are a developer, you should consider updating your clone manually. GitHub will make these updates, but they’ll take a long time. You should avoid cloning the same version twice. The more often you update your clone, the better. Just revert it to the original version. Otherwise, you’ll encounter this error again.

When you try to install homebrew-core, you will get an error: “homebrew-core is a shallow cleaver”. If you are a developer, you need to update the clone on GitHub. It is a common mistake, and is not recommended. If you’re a beginner, you should use the GitHub clone.

This error can make it difficult to update your clone of Homebrew. You should try a different version. There are other ways to fix this error. One way is to make it less of a shallow clone. It is important to avoid this error. Using this method will cause your clone to be incompatible with other clones.

This error is caused by an issue with GitHub’s rate-limits. If you’re updating a homebrew-core clone, it will take a few minutes to complete. It’s not a good idea to clone a GitHub clone if you’re not confident in the source code. It’s not a safe practice.

A homebrew-core clone is a shallow clone. Rather, a clone is a clone of an old version. It’s possible to use both versions of a clone and a new one. You can upgrade Homebrew only if you have the correct Macos version.

➜  ~ brew info test 
Error: No available formula with the name "test" 
==> Searching for a previously deleted formula...
Warning: homebrew/core is shallow clone. To get complete history run:
  git -C "$(brew --repo homebrew/core)" fetch --unshallow

Error: No previously deleted formula found.

9 Answers

git -C /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core fetch --unshallow

cd /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core
git pull --unshallow

cd /usr/local/Homebrew/Library/Taps/homebrew/homebrew-cask
git pull --unshallow

cd /usr/local/Homebrew/Library/Taps/homebrew/
rm -rf homebrew-core
git clone https://github.com/Homebrew/homebrew-core.git

for tap in /usr/local/Homebrew/Library/Taps/homebrew/homebrew-{cask,core}; do 
  mv $tap{/,}.git ; 
  echo "gitdir: $tap.git" >$tap/.git ; 
done

git -C "$(brew --repo homebrew/core)" fetch --unshallow

sudo git -C "$(brew --repo homebrew/core)" fetch --unshallow

You do not need to install or configure anything else to use Python 2. As you can see below, there is already Python 2.7.x version on macOS X.

AnalysisMan:/Users/analysisman% python —version
Python 2.7.16

Now let’s install Python 3.x version.

Step 1. Install Homebrew

Homebrew is an essential package for Mac users. Homebrew allows us to install the latest and updated version of popular applications, packages, and developer tools.

Here is a link to how to install Homebrew on macOS.

Step 2. Install Python3 with a brew command

brew install python3
This will take a minute or two.

AnalysisMan:/Users/analysisman% brew install python3
Error:
homebrew-core is a shallow clone.
homebrew-cask is a shallow clone.
To `brew update`, first run:
git -C /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core fetch —unshallow
git -C /usr/local/Homebrew/Library/Taps/homebrew/homebrew-cask fetch —unshallow
This restriction has been made on GitHub’s request because updating shallow
clones is an extremely expensive operation due to the tree layout and traffic of
Homebrew/homebrew-core and Homebrew/homebrew-cask. We don’t do this for you
automatically to avoid repeatedly performing an expensive unshallow operation in
CI systems (which should instead be fixed to not use shallow clones). Sorry for the inconvenience!
Error: [email protected]: no bottle available!
You can try to install from source with e.g.
brew install —build-from-source [email protected]
Please note building from source is unsupported. You will encounter build
failures with some formulae. If you experience any issues please create pull
requests instead of asking for help on Homebrew’s GitHub, Twitter or any other
official channels.

If you see the above error, try out the following command.

AnalysisMan:/Users/analysisman% brew install —build-from-source [email protected]

Error:
homebrew-core is a shallow clone.
homebrew-cask is a shallow clone.
To `brew update`, first run:
git -C /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core fetch —unshallow
git -C /usr/local/Homebrew/Library/Taps/homebrew/homebrew-cask fetch —unshallow
This restriction has been made on GitHub’s request because updating shallow
clones is an extremely expensive operation due to the tree layout and traffic of
Homebrew/homebrew-core and Homebrew/homebrew-cask. We don’t do this for you
automatically to avoid repeatedly performing an expensive unshallow operation in
CI systems (which should instead be fixed to not use shallow clones). Sorry for
the inconvenience!
==> Downloading https://homebrew.bintray.com/bottles/pkg-config-0.29.2_3.catalina.bottle.tar.gz
==> Downloading from https://d29vzk4ow07wi7.cloudfront.net/80f141e695f73bd058fd82e9f539dc67471666ff6800c5e280b5af7d3050f435?response-
######################################################################## 100.0%

… snipped…

> Downloading https://files.pythonhosted.org/packages/cb/5f/ae1eb8bda1cde4952bd12e468ab8a254c345a0189402bf1421457577f4f3/pip-20.3.1
######################################################################## 100.0%
==> Downloading https://www.python.org/ftp/python/3.9.1/Python-3.9.1.tar.xz
######################################################################## 100.0%
Error: Xcode alone is not sufficient on Catalina.
Install the Command Line Tools:
xcode-select —install

If you get an error as below, install the Xcode by ‘xcode-select —install‘.
Error: Xcode alone is not sufficient on Catalina.

Step 3. Make an alias for Python3 or link by symbolic link

Now you have two Python versions. The default Python 2.7.x and the newly installed Python 3.x.
If you want to make the Python 3.x as default. Here are two options.

Option 1) Alias in your Shell

You can alias the commands in most Shells, Since the default shells in macOS (bash in 10.14 and below; zsh in 10.15). You could put alias python=’python3′ in your ~/.bash_profile, and then source ~/.bash_profile in your ~/.bash_profile or ./.zshrc and source ~/.zshrc.

# bash
vi ~/.bash_profile