Homebrew Cannot Update, Doctor, Unlink, etc.

[stonemirror]

Bug reports:

I ran a brew update yesterday unproblematically. Today, no matter what I try to do, I'm getting the following response:

Error: Could not symlink bin/easy_install
Target /usr/local/bin/easy_install
is a symlink belonging to python. You can unlink it:
  brew unlink python

To force the link and overwrite all conflicting files:
  brew link --overwrite python3

To list all files that would be deleted:
  brew link --overwrite --dry-run python3

Executing any of the brew link or brew unlink commands results in the same error. Removing the symlink and rerunning the command gives the same error; the symlink file reappears after any such attempt. I get the same error in response to a brew doctor command. I'm kind of at a loss here.

I also attempted the following:

chown -R $USER:admin /usr/local
cd /usr/local
git reset --hard origin/master
brew update

which, again, resulted in the same error.

I've made no changes since yesterday except that I upgraded my copy of Xcode (and the Xcode command line tools), so I'm guessing that's what might be responsible somehow. Any suggestions as to how I might produce better information on what's going on here would be welcome...

[zmwangx]

Latest update. If you update to the latest version of brew it should probably heal itself now. Make sure you run brew update TWICE.

---

Caution: This workaround may not be up-to-date!

---

Before anything else, to update brew to the latest (assuming brew is installed to /usr/local):

cd /usr/local; git fetch; git reset --hard origin/master

---

Please AN OLD COMMAND THAT'S NO LONGER NEEDED and that should probably get you back on your feet again. Sorry.

Note: Please run the above command with caution. It's probably best to take a look at what's inside /usr/local/Library/LinkedKegs first and make sure they're nothing but a bunch of symlinks.

---

There's a brief explanation of what happened below.

[stonemirror]

Thanks, but I'm receiving the same error:

<<mcfate::local>> $ AN OLD COMMAND THAT'S NO LONGER NEEDED
<<mcfate::local>> $ brew update
Error: Could not symlink bin/easy_install
Target /usr/local/bin/easy_install
is a symlink belonging to python. You can unlink it:
  brew unlink python

To force the link and overwrite all conflicting files:
  brew link --overwrite python3

To list all files that would be deleted:
  brew link --overwrite --dry-run python3
<<mcfate::local>> $

[zmwangx]

Please attach --debug to brew update.

[enriquefernandez]

I was having a similar issue and just run AN OLD COMMAND THAT'S NO LONGER NEEDED

What is that supposed to do?
Do I need to "refix" that somehow?

I don't think I've updated Xcode, so I don't really know why this happened...

[stonemirror]

I've posted a gist of the debug output here...

[zmwangx]

@enriquefernandez

First, did that fix the problem for you?

---

We're migrating /usr/local/Library/LinkedKegs to /usr/local/var/homebrew/linked (and /usr/local/Library/PinnedKegs to /usr/local/var/homebrew/pinned for that matter) and unfortunately there were bugs in migration code that had done damage that may be hard to remedy within brew without a lot of complication.

AN OLD COMMAND THAT'S NO LONGER NEEDED

What is that supposed to do?

Blow away the old directory that somehow failed to migrate.

Do I need to "refix" that somehow?

You may need to brew unlink $(brew ls); brew link $(brew ls) to restore keg links into /usr/local/var/homebrew/linked (ignore the keg-only warnings).

[zmwangx]

@stonemirror Could you try cd /usr/local; git fetch; git reset --hard origin/master?

[publicarray]

@zmwangx thanks that worked. It did fail on rake and python for some reason. I fixed it by reinstalling them.

[stonemirror]

Okay, I seem to be getting closer to something that's working; I got an Already up-to-date response from brew update and I'm running a brew upgrade now, which seems to be working. I think I may have to uninstall and reinstall python3, but that's do-able.

[zmwangx]

@publicarray Those appear to be conflicting files from multiple formulae. For instance, in OP's case, python3 is trying to link its bin/easy_install while it should only have bin/easy_install-3.5, so I'm not exactly sure what's going on. Maybe not the latest version; or maybe it was built with some not heavily-tested options.

[enriquefernandez]

It partially solved my issues. Brew commands now work and I can update and install new things.

When running brew unlink $(brew ls); brew link $(brew ls) I'm getting errors about homebrew not being able to create symlinks.

Example:

Error: Could not symlink lib/pkgconfig/eigen3.pc
Target /usr/local/lib/pkgconfig/eigen3.pc
already exists. You may want to remove it:
  rm '/usr/local/lib/pkgconfig/eigen3.pc'

To force the link and overwrite all conflicting files:
  brew link --overwrite eigen

To list all files that would be deleted:
  brew link --overwrite --dry-run eigen

After running brew link --overwrite --dry-run eigen now I'm getting the same with gfortran:

Error: Could not symlink bin/gfortran
Target /usr/local/bin/gfortran
is a symlink belonging to gcc. You can unlink it:
  brew unlink gcc

To force the link and overwrite all conflicting files:
  brew link --overwrite gfortran

To list all files that would be deleted:
  brew link --overwrite --dry-run gfortran

Got one more error with ghostcript that was solved in the same way: brew link --overwrite ghostscript

After that, brew link $(brew ls) completed successfully, and it seems like everything is working normally now.

Thanks!

[zmwangx]

@stonemirror Good to hear, let us know if you're hitting other errors (other than conflicting links, which usually means you either have stale links that you could safely remove, or for some reason you have conflicting files from multiple formulae, which you should try to resolve by reinstalling the formula at question first).

[zmwangx]

@enriquefernandez Yeah unfortunately you have to resolve them one at a time, each time followed by a rerun of brew link $(brew ls).

brew list | xargs -n1 brew link might help ease the process (you only need to run that once), but you'll need to pick out the errors from a stream of output and resolve them.

[enriquefernandez]

Solved! (sorry, updated my previous comment before seeing your reply)

[zmwangx]

@enriquefernandez As for gfortran in particular, it's a stale formula you have and you should probably just brew uninstall --force gfortran. It's now provided as part of gcc.

[zmwangx]

@enriquefernandez Glad to hear.

[stonemirror]

Yeah, I've uninstalled and reinstalled python3 after my science/opencv upgrade failed, and rerun the brew upgrade --all. Seems to be working again, or at least the problems at this point seem to be OpenCV's, not Homebrew's... 😆

I'll close this, thanks for the help, @zmwangx!

[zmwangx]

Let's leave this open for a while actually for visibility.

[MikeMcQuaid]

#992 or similar will hopefully address this case a bit better.

[zmwangx]

Edited title to uncouple from Xcode update.

[ashfurrow]

Running brew update twice fixed it for me (was seeing this on CI), thanks @zmwangx for adding that solution to the top of the discussion 👍

[zmwangx]

Affected folks have probably sought (and hopefully found) help already. Closing.