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I am writing a Python application. It requires a certain version of Python, and some third party dependencies that are available on PyPI. It also depends on a private Python library that I have in a private Git repository. I'd like to depend on a specific Git tag. I need to be able to spin up this environment both on a local machine (where I have SSH access to the git repository) and on a CI server (where I have HTTPS access to the git repository using a username and password). I'm struggling to set up my Pipfile in a way that will work for both cases.
I tried to specify the URL dependency with the SSH URL and then on the CI machine where I only have HTTPS access, tried to first install the library via https directly into the virtual environment. The trouble is that the entire URL (including the protocol) is stored in the Pipfile.lock (and the entire URL is checked by pip when comparing the existing installation to the new one).
pipenv install the dependency from ssh:
$ pipenv install -e git+ssh://git#git.domain.com/my-private-lib#v0.1#egg=my-private-lib
of course if I try to just sync on the CI machine, it will fail:
$ git clone my-project
$ cd my-project
$ pipenv sync
# Warning: Your dependencies could not be resolved.
trying to install using https before running pipenv:
$ git clone my-project
$ cd my-project
$ virtualenv venv
$ source venv/bin/activate
$ pip install my-private-repo # git+https://my_user:my_token#git.domain.com/my-private-lib#v0.1
$ deactivate
$ pipenv sync
But this still will tell me that it can't reach ssh://git#git.domain...
I appreciate that the point of pipenv is to specify concrete dependencies with concrete sources. In my case, the source is slightly different between two machines. Is there any way around this? Perhaps a way to turn off exact URL checking and just check the git hash?
After updating gcloud I get this warning, but how do I do it(Should I remove Docker)?
WARNING: There are older versions of Google Cloud Platform tools on your system PATH.
Please remove the following to avoid accidentally invoking these old tools:
/Applications/Docker.app/Contents/Resources/bin/kubectl
I have this in my .zshrc:
# The next line updates PATH for the Google Cloud SDK.
if [ -f '/Users/<NAME>/google-cloud-sdk/path.zsh.inc' ]; then source '/Users/<NAME>/google-cloud-sdk/path.zsh.inc'; fi
# The next line enables shell command completion for gcloud.
if [ -f '/Users/<NAME>/google-cloud-sdk/completion.zsh.inc' ]; then source '/Users/<NAME>/google-cloud-sdk/completion.zsh.inc'; fi
[ -f ~/.fzf.zsh ] && source ~/.fzf.zsh
This happens because docker-for-mac installs a bin for kubectl, and gcloud-sdk also installs another bin with gcloud components install kubectl.
My recommendation is to uninstall kubectl as component from gcloud, overwrite the symlink from docker-for-mac, and only use the homebrew installed bin.
Try this commands:
gcloud components remove kubectl
brew install kubernetes-cli
brew link --overwrite kubernetes-cli
TLDR
/usr/local/bin/kubectl is a link installed by Docker: ls -l /usr/local/bin/kubectl => /usr/local/bin/kubectl -> /Applications/Docker.app/Contents/Resources/bin/kubectl. Removing the link has no side effects and solves the conflict:
rm /usr/local/bin/kubectl
Justification
The conflict is with the Docker-provided version of kubectl so it makes sense to check what Docker docs have to say about it. https://docs.docker.com/desktop/kubernetes/#use-the-kubectl-command
Extract:
If you installed kubectl using Homebrew, or by some other method, and experience conflicts, remove /usr/local/bin/kubectl.
Here is my case you can refer to. After running gcloud components update, I got this warning:
WARNING: There are older versions of Google Cloud Platform tools on your system PATH.
Please remove the following to avoid accidentally invoking these old tools:
/usr/local/Cellar/kubernetes-cli/1.10.2/bin/kubectl
I check this tool using brew list
☁ issue [master] brew list
coreutils gdbm git-lfs icu4c kops kubectx libpng mtr openssl python#2 sqlite tree wxmac
erlang geoip git-redate jpeg kube-ps1 kubernetes-cli libtiff node pcre readline telnet watchman
After reading the doc. I decided to uninstall kubernetes-cli and its dependencies kops, kube-ps1, and kubectx to avoid the conflicts.
☁ issue [master] brew uninstall kops kube-ps1 kubectx
Uninstalling /usr/local/Cellar/kops/1.9.0... (5 files, 129.8MB)
Uninstalling /usr/local/Cellar/kube-ps1/0.6.0... (6 files, 29.0KB)
Uninstalling /usr/local/Cellar/kubectx/0.5.0... (12 files, 27.8KB)
☁ issue [master] brew uninstall kubernetes-cli
Uninstalling /usr/local/Cellar/kubernetes-cli/1.10.2... (178 files, 52.8MB)
☁ issue [master] gcloud components update
All components are up to date.
This warning is gone.
I just went into the Docker file's bin folder and moved the kubectl to the trash.
Do echo $PATH and check which folder takes precedence. In my case it is like .../Users/myname/google-cloud-sdk/bin:/usr/local/bin:/usr/bin:.... Here the kubectl in gcloud is actually before the kubectl from Docker Desktop (which is in /usr/local/bin/kubectl) so there is no problem. If this is also your case you don't need to do anything.
Of course, if you want to completely remove confusion you can just delete the link /usr/local/bin/kubectl -> /Applications/Docker.app/Contents/Resources/bin/kubectl, or rename it.
Update:
In the recent docker desktop releases they actually provided another link /usr/local/bin/kubectl.docker -> /Applications/Docker.app/Contents/Resources/bin/kubectl to differentiate it from other kubectl so it is not a bad idea to just simply delete the link /usr/local/bin/kubectl -> /Applications/Docker.app/Contents/Resources/bin/kubectl
After the latest updates to gcloud and docker I'm unable to access images on my google container repository. Locally when I run: gcloud auth configure-docker as per the instructions after updating gcloud, I get the following message:
WARNING: `docker-credential-gcloud` not in system PATH.
gcloud's Docker credential helper can be configured but it will not work until this is corrected.
gcloud credential helpers already registered correctly.
Running which docker-credential-gcloud returns docker-credential-gcloud not found.
I have no other gcloud-related path issues and for the life of me can't figure out how to install/add docker-credential-gcloud to path. Here's what I have installed (shown via gcloud version):
Google Cloud SDK 197.0.0
beta 2017.09.15
bq 2.0.31
container-builder-local
core 2018.04.06
docker-credential-gcr
gsutil 4.30
I also have Docker CE Version 18.03.0-ce-mac60 (23751).
Here's my $PATH:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin
I also ran source /usr/local/Caskroom/google-cloud-sdk/latest/google-cloud-sdk/path.zsh.inc on original gcloud install.
Notice: All docker-credential-gcr below can be replaced with docker-credential-gcloud. I think it is just different versions of gcloud, I might be wrong.
I used Homebrew Cask to install gcloud too. I installed docker-credential-gcr with
$ gcloud components install docker-credential-gcr
And then like you said, which docker-credential-gcr doesn't gave you anything.
So I ran which gcloud to find there is a symlink to gcloud in /usr/local/bin. This symlink is created by Homebrew when you installed gcloud at first place. Now docker-credential-gcr wasn't installed by Homebrew but by gcloud itself, so there isn't a symlink.
I called readlink /usr/local/bin/gcloud and found out gcloud is installed in /usr/local/Caskroom/google-cloud-sdk/latest/google-cloud-sdk/bin/.
Then:
$ ls /usr/local/Caskroom/google-cloud-sdk/latest/google-cloud-sdk/bin
There you should see docker-credential-gcr listed there.
I simply linked it to /usr/local/bin:
$ ln -s \
/usr/local/Caskroom/google-cloud-sdk/latest/google-cloud-sdk/bin/docker-credential-gcr \
/usr/local/bin/
Then run:
$ docker-credential-gcr configure-docker
It should succeed.
Just had the same issue on Windows, running Docker with Linux containers, Docker engine v19.03.8. Using docker compose. I do not use gcloud for my dockerfiles...
DT1001 dockerpycreds.errors.InitializationError:
docker-credential-gcloud not installed or not available in PATH
Option 1: Edit the docker configuration file and remove all gcloud entries from there.
Windows c:/Users/<your account>/.docker/config.json
Linux & MacOS ~/.docker/config.json
Option 2: Go to Troubleshoot -> Reset to factory defaults.
After this my docker compose was creating containers and running the images without any issues.
On MacOS
Step 1：
Install gcloud and docker-credential-gcr,
following this tutorial
Step 2:
$ ln -s /usr/local/google-cloud-sdk/bin/docker-credential-gcr /usr/local/bin/docker-credential-gcloud
Step 3:
$ rm -rf ~/.docker
Step 4:
$ docker-compose build --pull
Finished!
Never found a way to directly resolve the docker-credential-gcloud issue, but the following got me up and running again. WARNING: the following will delete all your existing docker images and install a bunch of gcloud utilities:
gcloud components install docker-credential-gcr,
Restart the terminal completely
docker-credential-gcr configure-docker.
screen ~/Library/Containers/com.docker.docker/Data/com.docker.driver.amd64-linux/tty
umount /var/lib/docker/overlay2
rm -rf /var/lib/docker
Restart the terminal completely.
The new version of google-cloud-sdk has only docker-credential-gcr but not docker-credential-gcloud anymore. On the other hand one of my python packages always requested docker-credential-gcloud.
The solution was to symlink docker-credential-gcloud to docker-credential-gcr:
ln -s /path/to/google-cloud-sdk/bin/docker-credential-gcr /usr/local/bin/docker-credential-gcloud
ls -l /usr/local/bin | grep docker should now print:
...
docker-credential-gcloud -> /path/to/google-cloud-sdk/bin/docker-credential-gcr
...
Usually, this error indicates that your $PATH variable has been clobbered by a package or program you have recently installed so that the Google Cloud SDK can't be found.
$PATH is altered by many programs when they install by altering ~/.profile, ~/.bash_profile or ~/.bashrc or their non-bash equivalents. With a bad $PATH, Google Cloud SDK is configured in docker but can't be seen as executables so we get this error. This assumes you have used the Google Cloud SDK in the past, but if gcloud is configured with your docker then you probably have. Don't reinstall gcloud or disable it, you already have it on your system and that is fine.
The solution then is to fix your $PATH, not to install anything.
echo $PATH
This should be a pretty long : delimited list of directories that your files are in. Do you see a google-cloud-sdk/bin in the string? Is the string way too short given all the trouble you've gotten into in your life on this computer? You use NVM but it is missing? Use Homebrew but it is missing? Try brew from the command line, does it work?
If the answer is "no" to any of the above, inspect the files above to see if there are any new entries at the bottom of each that might have broken things. Did you just install anything new?
Something is clobbering your $PATH and you need to figure out what that is. For me it is usually something to do with Anaconda Python via the conda init command. For you it might be nvm or something else. Figure out what it is and fix the problem. Don't start over with a new $PATH and install the same stuff over again or disable gcloud authentication.
It really seems to be something with the Homebrew Cask. I uninstalled the cask and then reinstalled the Google Cloud SDK by manually downloading the tar ball and running the packaged install script as described there.
Now docker-credential-gcloud is in my path:
$ which docker-credential-gcloud
/Users/moritz/google-cloud-sdk/bin/docker-credential-gcloud
I can't figure out what Google is trying to achieve here. On Linux there is docker-credential-gcloud and on Windows there is docker-credential-gcr.exe, and then there is docker-credential-gcloud.cmd which calls gcloud auth docker-helper. This is kind of a nightmare if you're trying to write portable build scripts or gradle rules because not everything seems capable of finding and calling docker-credential-gcloud.cmd when you exec docker-credential-gcloud... it might work from the dos prompt, but in general doesn't work.
After a ton of fooling around with .bat scripts, cygwin scripts, .cmd scripts and so forth, I found the best solution was to go into the gcloud installation and just copy docker-credential-gcr.exe docker-credential-gcloud.exe ... not a very satisfying solution, but is the only thing I found that would do the trick.
I got the issue when I tried to SSH from Google Cloud Build into an Engine VM Instance, so I had
steps:
- name: 'gcr.io/cloud-builders/gcloud'
args: ['compute', 'ssh',
'--project', '$PROJECT_ID',
'--zone', 'asia-southeast1-b',
'--strict-host-key-checking=no',
'username#instance-1',
'--command' ,'sh start.sh'
My start.sh
#!/bin/sh
echo "Started: $(date --iso-8601=seconds)"
docker pull gcr.io/aaa/bbbc/cccc
echo "Finished: $(date --iso-8601=seconds)"
The issue was How to set PATH when running a ssh command?
https://unix.stackexchange.com/questions/332532/how-to-set-path-when-running-a-ssh-command
So I just faced the same problem where I am trying to pull an image from GCR to an GCP instance and want to share my solution.
I ran gcloud auth configure-docker and got the warning:
WARNING: `docker-credential-gcloud\` not in system PATH.
gcloud's Docker credential helper can be configured but it will not work until this is corrected.
I applied the accepted answer for this thread and ran gcloud components install docker-credential-gcr and got a long error:
ERROR: (gcloud.components.install) You cannot perform this action because this Cloud SDK installation is managed by an external package manager.
Please consider using a separate installation of the Cloud SDK created through the default mechanism described at: https://cloud.google.com/sdk/
When no solution was working, I uninstalled the Google provided google-cloud-sdk package that was installed via snap and instlled with distro specifice package manager, for me that is apt-get as instructed in the Installing Google Cloud SDK: Installation options page and re-ran the gcloud auth configure-docker and this time it solved my problem.
In my case the problem was due to how WSL 1 works with Docker on Windows. At first I only installed and initialized gcloud in WSL Ubuntu, not in Windows. However as Docker daemon is actually run by Windows, you need to install gcloud for Windows as well (and don't forget to run all of the inits and authorizations there).
On Windows 10/11, you need to ensure that C:\Users\USERNAME\AppData\Local\Google\Cloud SDK\google-cloud-sdk\bin\ is added to your system $PATH environment variable. It may not have been added if the Google Cloud SDK was not able to add it during GCloud installation. So add it manually like this:
Windows Task Bar ➔ Press the search icon 🔍 or the search bar
Type "environment" ➔ and click on "Edit the System Environment Variables" (ensure that you have Administrator access)
At the bottom of the dialog, click the Environment Variables... button
System Variables ➔ click Path ➔ Edit... ➔ New ➔ paste in C:\Users\USERNAME\AppData\Local\Google\Cloud SDK\google-cloud-sdk\bin\ (replace "USERNAME" with your username)
Close and restart any open Command Prompt windows.
Then verify on the Git Bash for Windows console:
Optional: Note that the AppData folder is hidden by default, so you may want to unhide AppData first, to see its contents.
Restart the Git Bash Terminal window
echo $PATH ➔ This should print a long string that contains: :/c/Users/USERNAME/AppData/Local/Google/Cloud SDK/google-cloud-sdk/bin
where docker-credential-gcloud ➔ This should print C:\Users\USERNAME\AppData\Local\Google\Cloud SDK\google-cloud-sdk\bin\docker-credential-gcloud.cmd
I have a Homebrew installation in $HOME/brew, and historically it has worked well. Unfortunately, over time Homebrew has become less and less tolerant of installations outside of /usr/local. Various formulae make hard assumptions about the installation prefix, and do not work properly (i.e., were not tested) with a non-standard prefix. The brew doctor command even goes so far as to warn about this now:
Warning: Your Homebrew is not installed to /usr/local
You can install Homebrew anywhere you want, but some brews may only build
correctly if you install in /usr/local. Sorry!
As such, I would now like to migrate my Homebrew installation over to /usr/local. However, I am loath to simply mv all the files, as I suspect this will cause problems. I could not find any instructions on the Homebrew site or here on migrating an existing installation to a new prefix. Of course, I could uninstall Homebrew and then reinstall it, but I would prefer not to rebuild all my kegs.
Is there any existing script or documented practice for performing such a migration?
Or is this impossible due to hardcoded absolute paths in linked binaries?
The modern way to do this is with homebrew-bundle.
brew tap Homebrew/bundle
brew bundle dump # Creates 'Brewfile' in the current directory
# later ...
brew bundle # Installs packages listed in 'Brewfile'
I just wrote a script to achieve the goal to migrate homebrew packages to a new system, which also applies for your case (named backup-homebrew.sh):
#!/bin/bash
echo '#!/bin/bash'
echo ''
echo 'failed_items=""'
echo 'function install_package() {'
echo 'echo EXECUTING: brew install $1 $2'
echo 'brew install $1 $2'
echo '[ $? -ne 0 ] && $failed_items="$failed_items $1" # package failed to install.'
echo '}'
brew tap | while read tap; do echo "brew tap $tap"; done
brew list --formula | while read item;
do
echo "install_package $item '$(brew info $item | /usr/bin/grep 'Built from source with:' | /usr/bin/sed 's/^[ \t]*Built from source with:/ /g; s/\,/ /g')'"
done
echo '[ ! -z $failed_items ] && echo The following items were failed to install: && echo $failed_items'
You should first run this script on your original system to generate a restore script:
./backup-homebrew.sh >restore-homebrew.sh && chmod +x restore-homebrew.sh
Then, after installing Homebrew on your new system (in your case the same system), simply run restore-homebrew.sh to install all those packages you have on your original system.
The benefits of this script over the one given by #ctrueden is that this script also tries to back up the installation options you used when you installed the packages.
A more detailed description is in my blog.
As suggested by Peter Eisentraut, I indeed ended up migrating my Homebrew installation by reinstalling it. You can script things a bit to retap all your extra taps, and reinstall all your previously installed kegs, without too much manual work:
#!/bin/sh
# save list of kegs for later reinstallation
brew list > kegs.txt
# back up old Homebrew installation
mv $HOME/brew $HOME/old-brew
# install Homebrew into /usr/local
ruby -e "$(curl -fsSL https://raw.github.com/mxcl/homebrew/go)"
# retap all the taps
# NB: It is not enough to move the tap repos to their new location,
# because Homebrew will not automatically recognize the new formulae.
# There might be a configuration file we could edit, but rather than
# risk an incomplete data structure, let's just retap everything.
for tapDir in $HOME/old-brew/Library/Taps/*
do (
cd $tapDir
tap=$(git remote -v | \
grep '(fetch)' | \
sed 's/.*github.com\///' | \
sed 's/ (fetch)//')
/usr/local/bin/brew tap $tap
) done
# reinstall all the kegs
/usr/local/bin/brew install $(cat kegs.txt)
# much later... ;-)
rm -rf kegs.txt $HOME/old-brew
Of course, customized Homebrew installations will have additional wrinkles. For example, if you have committed changes to any of your Homebrew-related Git repos, you may want to import that work before reinstalling your kegs or blowing away your old installation:
cd /usr/local
for f in $(find . -name '.git')
do (
repoDir=$(dirname $f)
cd $f/..
git remote add old-brew-$f $(dirname $HOME/old-brew/$f/..)
git fetch old-brew-$f
) done
Note that I only tested the second snippet above very lightly, as I personally have not customized my Homebrew in such a way.
Another aspect of Homebrew not addressed by this approach is custom flags using during your original installation. For example, to install wine you need to install various dependencies with the --universal flag, and the script above will not reinstall them with such flags enabled. See #xuhdev's answer for a solution that does so.
Or is this impossible due to hardcoded absolute paths in linked binaries?
Indeed. You'll need to reinstall everything from scratch.
Trying to update Homebrew with brew update I got the following error
error: The following untracked working tree files would be overwrittenby merge:
Library/Formula/argp-standalone.rb
Library/Formula/cocot.rb
Please move or remove them before you can merge.
Aborting
Updating e088818..5909e2c
Error: Failed while executing git pull origin refs/heads/master:refs/remotes/origin/master
I found a blog post by someone who experienced a similar problem after having installed Mountain Lion (which I did this week too). He explains how he removed the files referred to in the error message
I removed these files:
$ cd $(brew --prefix)
$ rm cocot.rb
However, removing these files didn't help with the brew update. Instead I had to manually update brew through git:
$ cd $(brew --prefix)
$ git fetch origin
$ git reset --hard origin/master
$ brew update
Already up-to-date.
Assuming those instructions are correct (which I maybe shouldn't assume), I tried to follow these instructions and do
$ cd $(brew --prefix)
$ rm cocot.rb
However, it said 'file doesn't exist' when I tried to rm cocot.rb
One thing I'm not sure about is the cd $(brew --prefix) Are those the exact words I type or do I have to replace prefix with something? the cd was successful, so I'm assuming it was correct -- it moved me into /usr/local, but there was no file to remove. Contents of /usr/local are
Cellar clamXav git mysql var Library doc heroku mysql-5.5.15-osx10.6-x86_64 README.md etc include rvm bin foreman lib share
At any rate, do you know how I can fix the 'brew update'
Update: After removing the files according to favoretti's instructions and trying chown -R <your_username> $(brew --prefix)/.git, I got the following error running brew update
error: The following untracked working tree files would be overwritten by merge:
Library/Aliases/gperftools
Library/Aliases/hashdeep
Library/Aliases/htop
Library/Aliases/nodejs
Library/Aliases/ocio
Library/Aliases/oiio
Library/Aliases/pgrep
Library/Aliases/pkill
Library/Aliases/qt4
Library/Aliases/twolame
Library/Aliases/wxwidgets
Library/Contributions/cmds/brew-aspell-dictionaries
Library/Contributions/cmds/brew-beer.rb
Library/Contributions/cmds/brew-dirty.rb
Library/Contributions/cmds/brew-graph
Library/Contributions/cmds/brew-grep
Library/Contributions/cmds/brew-leaves.rb
Library/Contributions/cmds/brew-linkapps.rb
Library/Contributions/cmds/brew-ls-taps.rb
Library/Contributions/cmds/brew-man
Library/Contributions/cmds/brew-md5-to-sha1
Library/Contributions/cmds/brew-mirror-check.rb
Library/Contributions/cmds/brew-pull.rb
Library/Contributions/cmds/brew-readall.rb
Library/Contributions/cmds/brew-server
Library/Contributions/cmds/brew-services.rb
Library/Contributions/cmds/brew-switch.rb
Library/Contributions/cmds/brew-test-bot.rb
Library/Contributions/cmds/brew-tests.rb
Library/Contributions/cmds/brew-unpack.rb
Library/Contributions/cmds/brew-which.rb
Library/Contributions/cmds/git
Library/Contributions/cmds/svn
Library/ENV/4.3/apr-1-config
Library/ENV/4.3/bsdmake
Library/ENV/4.3/c++
Library/ENV/4.3/c89
Library/ENV/4.3/c99
Library/ENV/4.3/cc
Library/ENV/4.3/clang
Library/ENV/4.3/clang++
Library/ENV/4.3/cpp
Library/ENV/4.3/g++
Library/ENV/4.3/gcc
Library/ENV/4.3/git
Library/ENV/4.3/i686-apple-darwin11-llvm-g++-4.2
Library/ENV/4.3/i686-apple-darwin11-llvm-gcc-4.2
Library/ENV/4.3/ld
Library/ENV/4.3/llvm-g++
Library/ENV/4.3/llvm-g++-4.2
Library/ENV/4.3/llvm-gcc
Library/ENV/4.3/llvm-gcc-4.2
Library/ENV/4.3/make
Library/ENV/4.3/mig
Library/ENV/4.3/sed
Library/ENV/4.3/svn
Library/ENV/4.3/xcrun
Library/ENV/libsuperenv.rb
Library/ENV/pkgconfig/leopard/libcrypto.pc
Library/ENV/pkgconfig/leopard/libcurl.pc
Library/ENV/pkgconfig/mountain_lion/libcurl.pc
Library/ENV/pkgconfig/mountain_lion/libexslt.pc
Library/ENV/pkgconfig/mountain_lion/libxml-2.0.pc
Library/ENV/pkgconfig/mountain_lion/libxslt.pc
Library/Formula/abcl.rb
Library/Formula/abcmidi.rb
Library/Formula/aiccu.rb
Library/Formula/akka.rb
Library/Formula/alac.rb
Library/Formula/alure.rb
Library/Formula/appledoc.rb
Library/Formula/arangodb.rb
Library/Formula/argp-standalone.rb
Library/Formula/argtable.rb
Library/Formula/autopano-sift-c.rb
Library/Formula/avian.rb
Library/Formula/avidemux.rb
Library/Formula/avro-cpp.rb
Library/Formula/aws-cloudsearch.rb
Library/Formula/aws-sns-cli.rb
Library/Formula/backupninja.rb
Library/Formula/bact.rb
Library/Formula/bam.rb
Library/Formula/basex.rb
Library/Formula/berkeley-db4.rb
Library/Formula/bind.rb
Library/Formula/blazeblogger.rb
Library/Formula/bochs.rb
Library/Formula/boost149.rb
Library/Formula/bsdconv.rb
Library/Formula/bsdmake.rb
Library/Formula/buildapp.rb
Library/Formula/bup.rb
Library/Formula/byacc.rb
Library/Formula/cadubi.rb
Library/Formula/camellia.rb
Library/Formula/casperjs.rb
Library/Formula/ccextractor.rb
Library/Formula/cconv.rb
Library/Formula/cdo.rb
Library/Formula/cdpr.rb
Library/Formula/cgvg.rb
Library/Formula/checkstyle.rb
Library/Formula/chordii.rb
Library/Formula/chruby.rb
Library/Formula/cifer.rb
Library/Formula/clhep.rb
Library/Formula/cntlm.rb
Library/Formula/cocot.rb
Library/Formula/cogl.rb
Library/Formula/collada-dom.rb
Library/Formula/crash.rb
Library/Formula/crossroads.rb
Library/Formula/crosstool-ng.rb
Library/Formula/css-crush.rb
Library/Formula/csync.rb
Library/Formula/ctemplate.rb
Library/Formula/curlftpfs.rb
Library/Formula/cutter.rb
Library/Formula/cvsutils.rb
Library/Formula/darkstat.rb
Library/Formula/darner.rb
Library/Formula/dart.rb
Library/Formula/dasm.rb
Library/Formula/debianutils.rb
Library/Formula/dfc.rb
Library/Formula/dgtal.rb
Library/Formula/dhcping.rb
Library/Formula/di.rb
Library/Formula/dmtx-utils.rb
Library/Formula/drip.rb
Library/Formula/dsniff.rb
Library/Fo
Aborting
Updating e088818..c1fbc29
Error: Failed while executing git pull origin refs/heads/master:refs/remotes/origin/master
You need to do the following:
cd $(brew --prefix)
rm Library/Formula/argp-standalone.rb
rm Library/Formula/cocot.rb
And then do the
git fetch origin
git reset --hard origin/master
brew update
Basically, to explain a bit more:
cd $(brew --prefix)
tells cd to change the directory to whatever brew --prefix will output.
If you try executing brew --prefix command you should see something in lines of:
brew --prefix
/usr/local
So the command would be in this case an equivalent of cd /usr/local.
Newer brew versions have formulae under its installation prefix and Library/Formula/, so that's where you need to look for those outdated/changed files.
Note, that if you changed those formulae yourself for a particular reason (like pinning a version) this action will revert them back to default ones and may produce unwanted effects.
#TedPennings noted in comments that this worked for him, but his sequence was:
chown everything to my_username:admin, ie, sudo chown -R ted:admin $(brew --prefix)
run the two git commands above,git fetch origin and git reset --hard origin/master
cd $(brew --prefix)
git reset --hard HEAD
brew update
This is caused by an old bug in the update code that has long since been fixed. However, the nature of the bug requires that you do the following:
cd $(brew --repository)
git reset --hard FETCH_HEAD
If brew doctor still complains about uncommitted modifications, also run this command:
cd $(brew --repository)
git clean -fd
$ cd $(brew --prefix)
$ git clean -fd
$ git reset --hard
$ sudo chown -R `whoami` `brew --prefix`
$ brew update
Note: steps 2&3 worked for me since I did step 5 before 4 before I got the error. The brew update before changing the owner of the folder caused the whole problem.
I had a similar issue where my brew package library got downloaded as a root user and then I was not able to run brew update as git would complain about not able to merge the file.
Solution was to do :-
sudo chown -R <user> /usr/local/Library
Resetting the brew repository should be the most efficient way if you don't mind to discard potential modifications on formulas you might have been applied:
$ cd `brew --prefix`
$ git fetch origin
$ git reset --hard origin/master
$ brew cleanup --force
$ brew update
I was able to fix this on my machine by adding admin group write (and setgid bit) permission at these paths:
sudo chmod -R g+ws /usr/local /Library/Caches/Homebrew
The s sets the group id on execution so that the write permissions aren't lost the next time a different admin user updates or upgrades Homebrew.
This answer is somewhat incomplete because when I try to do brew cleanup --force there is a permissions issue when Homebrew tries to remove content in /usr/local/Cellar/. (Unfortunately I'm not able to investigate this further at the moment.)
Another option is to just use git stash.
The brew update command performs a git pull, so if there are any changed files (or even file attributes, which happened to me when I changed permissions in the directory recursively) you have to somehow fix the conflicts. Using git stash is one way; it takes any changes and puts them aside so you effectively revert to the last updated repo version. The Homebrew 'location' is by default /usr/local and it installs as a git repository. You can look for a .git folder to see for yourself. I'm writing a homebrew uninstall script to be posted on my GitHub profile soon with more info.
sudo chown -R USER /usr/local/bin
note - for USER use command whom i.e. your username
sudo brew doctor
This approach may be simpler than some. It involves:
fixing a git issue so you can delegate management of changes to it again.
no manual moves of files or directories.
no manual adjustments of file or directory permissions.
Steps (with notes for those who want explanations):
cd $(brew --repository) // see Note 1 below
git remote add brew https://github.com/Homebrew/brew // see Note 2 below
git pull brew master // promising fast-forward report!
brew update // see Note 3 below
Overview:
From what I can tell, the actual cause of this issue is a change in the repo url. It's now brew and was brew.git. (Full up-to-date url: https://github.com/Homebrew/brew)
Note 1: This first command takes you from anywhere in your file structure to the correct directory. The directory structure is different for me than what others show above (Mac OS 10.11.16), but with this command, those differences should not matter.
Note 2: This second command adds the correct remote url to a new alias; I did so just in case this approach didn't accomplish what I wanted and I needed the previous address again. Since the new remote worked, I'll invite someone else to comment on simply changing the url aliased by origin. I'll happily update the answer to reflect what worked for you.
Note 3: This forth command has exactly the desired result: it reports a large number of updates, including the particularly nice report of "==> Migrated HOMEBREW_REPOSITORY to /usr/local/Homebrew!" (emphasis theirs).
This post helped me after updating to El Capitan. In my case, chown wasn't working ("zsh: command not found: chown"), so step 1 was adding this line to my .zshrc:
export PATH="$PATH:/usr/sbin"
I'd already tried several of the more popular answers above, so I'm pretty sure that git status was coming up clean by the time I pasted in the critical command from the blog post:
sudo chown $(whoami):admin /usr/local && sudo chown -R $(whoami):admin /usr/local
This should work.
1. cd `brew --prefix`
2. git fetch origin
3. git reset --hard origin/master
4. sudo brew update