Broken references in Virtualenvs

Question

I recently installed a bunch of dotfiles on my Mac along with some other applications (I changed to iTerm instead of Terminal, and Sublime as my default text editor) but ever since, all my virtual environments have stopped working, although their folders inside .virtualenvs are still there and they give the following error whenever I try to run anything in them:

dyld: Library not loaded: @executable_path/../.Python
  Referenced from: /Users/[user]/.virtualenvs/modclass/bin/python
  Reason: image not found
Trace/BPT trap: 5

I have removed all the files related to dotfiles and have restored my .bash_profile to what it was before, but the problem persists. Is there any way to diagnose the problem or solve it in an easy way (e.g. not requiring to create all the virtualenvs all over again)?

Solution 1

I found the solution to the problem here, so all credit goes to the author.

The gist is that when you create a virtualenv, many symlinks are created to the Homebrew installed Python.

Here is one example:

$ ls -la ~/.virtualenvs/my-virtual-env
...
lrwxr-xr-x  1 ryan staff   78 Jun 25 13:21 .Python -> /usr/local/Cellar/python/2.7.7/Frameworks/Python.framework/Versions/2.7/Python
...

When you upgrade Python using Homebrew and then run brew cleanup, the symlinks in the virtualenv point to paths that no longer exist (because Homebrew deleted them).

The symlinks needs to point to the newly installed Python:

lrwxr-xr-x  1 ryan staff   78 Jun 25 13:21 .Python -> /usr/local/Cellar/python/2.7.8_1/Frameworks/Python.framework/Versions/2.7/Python

The solution is to remove the symlinks in the virtualenv and then recreate them:

find ~/.virtualenvs/my-virtual-env/ -type l -delete
virtualenv ~/.virtualenvs/my-virtual-env

It's probably best to check what links will be deleted first before deleting them:

find ~/.virtualenvs/my-virtual-env/ -type l

In my opinion, it's even better to only delete broken symlinks. You can do this using GNU find:

gfind ~/.virtualenvs/my-virtual-env/ -type l -xtype l -delete

You can install GNU find with Homebrew if you don't already have it:

brew install findutils

Notice that by default, GNU programs installed with Homebrew tend to be prefixed with the letter g. This is to avoid shadowing the find binary that ships with OS X.

Solution 2

After trying a few things, this worked for me:

go to your virtualenv directory (but don't run workon):

cd ~/.virtualenv/name_of_broken_venv

Now delete these files:

rm -rf .Python bin/python* lib/python2.7/* include/python2.7

Then to rebuild your venv, run:

virtualenv .
workon name_of_broken_venv
pip freeze

You should now see a list of your installed packages again.

Solution 3

This occurred when I updated to Mac OS X Mavericks from Snow Leopard. I had to re-install brew beforehand too. Hopefully you ran the freeze command for your project with pip.

To resolve, you have to update the paths that the virtual environment points to.

• Install a version of python with brew:

brew install python

• Re-install virtualenvwrapper.

pip install --upgrade virtualenvwrapper

• Removed the old virtual environment:

rmvirtualenv old_project

• Create a new virtual environment:

mkvirtualenv new_project

• Work on new virtual environment

workon new_project

• Use pip to install the requirements for the new project.

pip install -r requirements.txt

This should leave the project as it was before.

Solution 4

A update version @Chris Wedgwood's answer for keeping site-packages (keeping packages installed)

cd ~/.virtualenv/name_of_broken_venv


mv lib/python2.7/site-packages ./    
rm -rf .Python bin lib include
virtualenv .
rm -rf lib/python2.7/site-packages
mv ./site-packages lib/python2.7/

Solution 5

It appears the proper way to resolve this issue is to run

 pip install --upgrade virtualenv

after you have upgraded python with Homebrew.

This should be a general procedure for any formula that installs something like python, which has it's own package management system. When you install brew install python, you install python and pip and easy_install and virtualenv and so on. So, if those tools can be self-updated, it's best to try to do so before looking to Homebrew as the source of problems.

View more solutions

Comments

[unutbu]

Possibly related: debugfix.com/2011/11/dyld-library-loaded-executable_path-pyt‌​hon

[oxtay]

Thank you for the comment, @unubtu. This certainly is helpful. But I am also not able to make any new virtualenvs. My rmvirtualenv still works but when trying to run mkvirtualenv, I get the following error: -bash: /usr/local/bin/virtualenv: /usr/local/Cellar/python/2.7.6/Frameworks/Python.framework/V‌​ersions/2.7/Resour: bad interpreter: No such file or directory So, it seems a problem with my python paths but I can't see where the problem is, since I can run python and it seems fine.

[oxtay]

[update] I may have found the problem but I am not sure and I am actually not sure how to fix it. It seems that all virtualenv commands are working now in theory, but since there is a problem with python, they don't do anything. So the real problem is with brew's python. And I have a suspicion that the reason is because of a name change in python directories. For some reason, all these commands are looking for python in folder /usr/local/Cellar/python/2.7.6 but the folder's name is actually /usr/local/Cellar/python/2.7.6_1.

[oxtay]

Since I am a novice, I don't know how risky it is to manually change the name from 2.7.6_1 to 2.7.6 and see what happens.

[unutbu]

You should be able to rename 2.7.6_1 to 2.7.6. If worse came to worst, you could rename it back.

[oxtay]

Yup. I actually went ahead and tried it. That actually made me notice another problem. The problem wasn't the name, but rather it seemed it was broken links, somehow caused in brew. I tried a bunch of things and the problem seems to be gone now. What seems to have worked was uninstalling Python in homebrew all together and installing it again and then running brew unlink python && brew link python followed by brew linkapps. Although I think the second part wasn't even necessary since I had tried it before to no avail. Thanks again for the help!

[Patrick Williams]

Broken links didn't work for me, unfortunately. I was able to work around the 'bad interpreter' problem by @oxtay's solution, by making a new directory (mkdir) called /usr/local/Cellar/python/2.7.6 and copying (cp -r) all of the files from /usr/local/Cellar/python/2.7.9 into that folder. I was too nervous to just rename the folder!

[Robert Brisita]

This worked for an issue with setuptools, specifically: Warning: cannot find svn location for setuptools==0.6c12dev-r88846

[oxtay]

This was a while ago and I believe I eventually did something along these lines, but since I hadn't run 'pip freeze > requirements.txt' back then, it wasn't the most efficient solution. Lesson learned.

[2Toad]

+1 gfind was perfect, since I had a lot of unbroken symlinks (e.g., nodeenv) that I didn't want to delete

[Ryan]

FWIW, I just tried this approach after upgrading to El Capitan and re-installing homebrew, and my package list was not preserved.

[RafazZ]

I guess it is because this solution is not obsolete -- I have just tried it and it fixed my issue. Also, I think if you don't have symlinks, you won't see the error described here, so this comment becomes not a solution but a distraction -- Just because you have a newer version, doesn't mean everybody does. That's my guess why the downvote :)

[sds]

@RafazZ: I hope it is now better. However, I wonder why it is still a symlink for you. And yes, I do get that error because the virtualenv python is linked against the stock python libs.

[RafazZ]

I think the default behaviour is still to create symlinks and you need an --always-copy argument to override it. At least that what I got from the User Guide

[sds]

@RafazZ: I never used --always-copy and I have regular files :-(

[vdboor]

Another way to remove broken symlinks is using the standard find: find -L ~/.virtualenvs/my-virtual-env/ -type l | xargs rm

[christang]

I applied this solution, followed by running: virtualenv . in my broken virtual environment. The updated version of virtualenv then recreated the necessary dependencies and I was good to go. This process was more self-managed and robust than the accepted answer for me.

[Harry Moreno]

with pipenv you can remove by doing pipenv --rm and recreate, pipenv shell,pipenv install

[Aseem]

I deleted my entire virtualenv dir. now i cannot remove symlinks. Non of the solutions mentioned on this page work for me on mac. i still get same error "image not found . Abort trap: 6"

[deed02392]

These steps didn't quite work for me: pip3 freeze dyld: lazy symbol binding failed: Symbol not found: __Py_UnixMain

[Bohumir Zamecnik]

Just to add, if the env was with Python 2, run it with argument: virtualenv ~/.virtualenvs/foo -p python2, otherwise it will use Python 3.

[Francisco Peters]

If you're complementing another user's answers you should leave a comment for them so they can edit! Nice contribution.

[Tyler Smith]

He doesn't have enough reputation points to comment on an answer.

[Harish Prasanna]

This is beyond perfection. Helps migrate python version while retaining all the packages. If you are following this, do not execute @Chris Wedgewood's instructions.

[user2233949]

Thank you very much. Deleting the symlinks and recreating the virtualenv did the trick. Well done

[dhanshreeA]

Thank you so much for this answer! Another very hacky solution that I tried was to unlink brew from the upgraded version of Python, and reinstalling the previous version.

[Handfeger]

you also can use pipenv --rm in the folder of your env and then pipenv install --dev

[lukik]

This also worked to fix broken links after installing Python 3.7 on a system that had Python3.6

[David Buck]

Welcome to SO. Though we thank you for your answer, it would be better if it provided additional value on top of the other answers. In this case, your answer does not provide additional value, since another user already posted that solution. If a previous answer was helpful to you, you should vote it up once you have enough reputation

[scubabuddha]

In 2020, this is still the answer.

[cybertoast]

If you get errors related to virtualenvwrapper.sh: There was a problem running the initialization hooks you will need to pip install virtualenv virtualenvwrapper or pip3 install virtualenv virtualenvwrapper just to get everything back in sync.

[Ran Halprin]

This didn't work for me, but Robert Brisita's suggestion of reinstalling virtualenvwrapper did