Homebrew-core: Upgrading to Ruby 2.4.1_1 breaks gem command.

Created on 27 Mar 2017 · 27Comments · Source: Homebrew/homebrew-core

[x] Ran brew update and retried your prior step?
[x] Ran brew doctor, fixed as many issues as possible and retried your prior step?
[x] Confirmed this is a problem with specific formulae and not Homebrew/brew? If it's a general Homebrew/brew problem please file this issue at https://github.com/Homebrew/brew/issues/new

After upgrading Ruby to latest 2.4.1_1 formula, gem command no longer works and gives the following error:

/usr/local/Cellar/ruby/2.4.1_1/lib/ruby/2.4.0/yaml.rb:5:in `<top (required)>':
It seems your ruby installation is missing psych (for YAML output).
To eliminate this warning, please install libyaml and reinstall your ruby.
/usr/local/lib/ruby/site_ruby/2.4.0/rubygems/core_ext/kernel_require.rb:55:in `require': dlopen(/usr/local/lib/ruby/gems/2.4.0/gems/psych-2.2.4/lib/psych.bundle, 9): Library not loaded: /usr/local/opt/ruby/lib/libruby.2.4.0.dylib (LoadError)
  Referenced from: /usr/local/lib/ruby/gems/2.4.0/gems/psych-2.2.4/lib/psych.bundle
  Reason: image not found - /usr/local/lib/ruby/gems/2.4.0/gems/psych-2.2.4/lib/psych.bundle
    from /usr/local/lib/ruby/site_ruby/2.4.0/rubygems/core_ext/kernel_require.rb:55:in `require'
    from /usr/local/lib/ruby/gems/2.4.0/gems/psych-2.2.4/lib/psych.rb:8:in `<top (required)>'
    from /usr/local/lib/ruby/site_ruby/2.4.0/rubygems/core_ext/kernel_require.rb:55:in `require'
    from /usr/local/lib/ruby/site_ruby/2.4.0/rubygems/core_ext/kernel_require.rb:55:in `require'
    from /usr/local/Cellar/ruby/2.4.1_1/lib/ruby/2.4.0/yaml.rb:6:in `<top (required)>'
    from /usr/local/lib/ruby/site_ruby/2.4.0/rubygems/core_ext/kernel_require.rb:55:in `require'
    from /usr/local/lib/ruby/site_ruby/2.4.0/rubygems/core_ext/kernel_require.rb:55:in `require'
    from /usr/local/lib/ruby/site_ruby/2.4.0/rubygems.rb:700:in `load_yaml'
    from /usr/local/lib/ruby/site_ruby/2.4.0/rubygems/config_file.rb:340:in `load_file'
    from /usr/local/lib/ruby/site_ruby/2.4.0/rubygems/config_file.rb:202:in `initialize'
    from /usr/local/lib/ruby/site_ruby/2.4.0/rubygems/gem_runner.rb:75:in `new'
    from /usr/local/lib/ruby/site_ruby/2.4.0/rubygems/gem_runner.rb:75:in `do_configuration'
    from /usr/local/lib/ruby/site_ruby/2.4.0/rubygems/gem_runner.rb:40:in `run'
    from /usr/local/bin/gem:21:in `<main>'

I tried both

brew reinstall -s libyaml

and

brew reinstall -s ruby

but none of them resolved the issue.

Could anyone help me fix this?
Many thanks.

Source

dawoonchung

Most helpful comment

Oh hey! That solved it! So both:

rm -rf /usr/local/lib/ruby/gems/2.4.0/gems/psych-2.2.4

and

rm -rf /usr/local/lib/ruby/gems/2.4.0/extensions/x86_64-darwin-16/2.4.0/psych-2.2.4

seems to do the trick! Thanks!!

dawoonchung on 27 Mar 2017

👍17 🎉6

All 27 comments

maybe

rm -rf /usr/local/lib/ruby/site_ruby/
brew uninstall ruby
brew install ruby
gem install psych

ilovezfs on 27 Mar 2017

@ilovezfs Thanks for the suggestion, but it still didn't resolve the issue, throwing the same error.

dawoonchung on 27 Mar 2017

what command are you running

ilovezfs on 27 Mar 2017

I followed your steps for removing and installing Ruby, and I tried any gem command – just gem, gem update, gem update --system, gem install psych, and so on, but none of them works.

dawoonchung on 27 Mar 2017

looks fine here starting from clean install: https://gist.github.com/ilovezfs/48a77d39c08220f34d9e8ead7d51656b

so not sure what to tell you

ilovezfs on 27 Mar 2017

Strange. I tried with [email protected], and it is working without any problem. But as soon as I upgrade it to 2.4.1, the problem pops up again.

dawoonchung on 27 Mar 2017

what's output for brew config and brew doctor

ilovezfs on 27 Mar 2017

dorapen@~$ brew config
HOMEBREW_VERSION: 1.1.11
ORIGIN: https://github.com/Homebrew/brew
HEAD: 394f9fa0aaa5854aa52bc589708a079665dcf462
Last commit: 3 weeks ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: e360ded5f8533c30e58a095b2263965af8d50988
Core tap last commit: 17 minutes ago
HOMEBREW_PREFIX: /usr/local
HOMEBREW_REPOSITORY: /usr/local/Homebrew
HOMEBREW_CELLAR: /usr/local/Cellar
HOMEBREW_BOTTLE_DOMAIN: https://homebrew.bintray.com
CPU: octa-core 64-bit haswell
Homebrew Ruby: 2.0.0-p648
Clang: 8.0 build 800
Git: 2.12.2 => /usr/local/bin/git
Perl: /usr/local/bin/perl => /usr/local/Cellar/perl/5.24.1/bin/perl
Python: /usr/local/bin/python => /usr/local/Cellar/python/2.7.13/Frameworks/Python.framework/Versions/2.7/bin/python2.7
Ruby: /usr/local/bin/ruby => /usr/local/Cellar/ruby/2.4.1_1/bin/ruby
Java: 1.8.0_121, 1.8.0_112, 1.7.0_80
macOS: 10.12.3-x86_64
Xcode: 8.2.1
CLT: 8.2.0.0.1.1480973914
X11: 2.7.11 => /opt/X11

dorapen@~$ brew doctor
Your system is ready to brew.

dawoonchung on 27 Mar 2017

Im having the exact same problem.
All i did was brew update && brew upgrade and now gem is not working anymore.

I tried to reinstall both libyaml and ruby, but the error stays the same.

I checked if psych is there on my system. Everything seems to be there.

But /usr/local/opt/ruby/lib/libruby.2.4.0.dylib from the error message is not there.
How can i get this dylib?

Bufallo on 27 Mar 2017

@xu-cheng Any ideas here? I notice you may have done some related work on this in adfcc5a078c962ad1c687396da9096b2d4df916e.

ilovezfs on 27 Mar 2017

Please try rm -rf /usr/local/lib/ruby/gems/2.4.0/gems/psych-2.2.4.

It is most likely a different version of psych is installed by users. However, that version is incorrectly linked to wrong lib file, which should be caused by the incorrect abi_version in https://github.com/Homebrew/homebrew-core/pull/11474

xu-cheng on 27 Mar 2017

@dorapen @Bufallo please give that a try.

ilovezfs on 27 Mar 2017

@ilovezfs @xu-cheng Nope, it didn't resolve the issue. I tried to reinstall ruby after deleting psych, both with brew reinstall ruby and brew reinstall -s ruby but neither worked. Also reinstalling libyaml didn't work.

dawoonchung on 27 Mar 2017

This time following psych was referenced:

Referenced from: /usr/local/lib/ruby/gems/2.4.0/extensions/x86_64-darwin-16/2.4.0/psych-2.2.4/psych.bundle

dawoonchung on 27 Mar 2017

@dorpen What is the error message? Is it a different gem reporting the error?

A dramatical solution would be:

rm -rf /usr/local/lib/ruby
brew reinstall ruby

However, this would remove all installed rubygems.

xu-cheng on 27 Mar 2017

👍1

@dorapen Oh, you could remove that file as well.

xu-cheng on 27 Mar 2017

@xu-cheng Here's the error message:

dorapen@~$ gem
/usr/local/Cellar/ruby/2.4.1_1/lib/ruby/2.4.0/yaml.rb:5:in `<top (required)>':
It seems your ruby installation is missing psych (for YAML output).
To eliminate this warning, please install libyaml and reinstall your ruby.
/usr/local/Cellar/ruby/2.4.1_1/lib/ruby/2.4.0/rubygems/core_ext/kernel_require.rb:55:in `require': dlopen(/usr/local/lib/ruby/gems/2.4.0/extensions/x86_64-darwin-16/2.4.0/psych-2.2.4/psych.bundle, 9): Library not loaded: /usr/local/opt/ruby/lib/libruby.2.4.0.dylib (LoadError)
  Referenced from: /usr/local/lib/ruby/gems/2.4.0/extensions/x86_64-darwin-16/2.4.0/psych-2.2.4/psych.bundle
  Reason: image not found - /usr/local/lib/ruby/gems/2.4.0/extensions/x86_64-darwin-16/2.4.0/psych-2.2.4/psych.bundle
    from /usr/local/Cellar/ruby/2.4.1_1/lib/ruby/2.4.0/rubygems/core_ext/kernel_require.rb:55:in `require'
    from /usr/local/Cellar/ruby/2.4.1_1/lib/ruby/2.4.0/psych.rb:8:in `<top (required)>'
    from /usr/local/Cellar/ruby/2.4.1_1/lib/ruby/2.4.0/rubygems/core_ext/kernel_require.rb:55:in `require'
    from /usr/local/Cellar/ruby/2.4.1_1/lib/ruby/2.4.0/rubygems/core_ext/kernel_require.rb:55:in `require'
    from /usr/local/Cellar/ruby/2.4.1_1/lib/ruby/2.4.0/yaml.rb:6:in `<top (required)>'
    from /usr/local/Cellar/ruby/2.4.1_1/lib/ruby/2.4.0/rubygems/core_ext/kernel_require.rb:55:in `require'
    from /usr/local/Cellar/ruby/2.4.1_1/lib/ruby/2.4.0/rubygems/core_ext/kernel_require.rb:55:in `require'
    from /usr/local/Cellar/ruby/2.4.1_1/lib/ruby/2.4.0/rubygems.rb:700:in `load_yaml'
    from /usr/local/Cellar/ruby/2.4.1_1/lib/ruby/2.4.0/rubygems/config_file.rb:340:in `load_file'
    from /usr/local/Cellar/ruby/2.4.1_1/lib/ruby/2.4.0/rubygems/config_file.rb:202:in `initialize'
    from /usr/local/Cellar/ruby/2.4.1_1/lib/ruby/2.4.0/rubygems/gem_runner.rb:75:in `new'
    from /usr/local/Cellar/ruby/2.4.1_1/lib/ruby/2.4.0/rubygems/gem_runner.rb:75:in `do_configuration'
    from /usr/local/Cellar/ruby/2.4.1_1/lib/ruby/2.4.0/rubygems/gem_runner.rb:40:in `run'
    from /usr/local/bin/gem:21:in `<main>'

dawoonchung on 27 Mar 2017

Oh hey! That solved it! So both:

rm -rf /usr/local/lib/ruby/gems/2.4.0/gems/psych-2.2.4

and

rm -rf /usr/local/lib/ruby/gems/2.4.0/extensions/x86_64-darwin-16/2.4.0/psych-2.2.4

seems to do the trick! Thanks!!

dawoonchung on 27 Mar 2017

👍17 🎉6

@Bufallo does that take care of it for you too?

ilovezfs on 27 Mar 2017

Yes!
After removing the psych gem wir rm -rf the gem command is working again.

Bufallo on 27 Mar 2017

Perfect. Thanks for the speedy help here @xu-cheng. It's much appreciated.

ilovezfs on 27 Mar 2017

Many thanks to you both for the support, @ilovezfs and @xu-cheng!

dawoonchung on 27 Mar 2017

👍2

Thank you so much for the solution. :)

kud on 29 Mar 2017

Worked for me too!

rm -rf /usr/local/lib/ruby/gems/
brew uninstall ruby --ignore-dependencies
brew install ruby

AndreTheHunter on 1 Apr 2017

👍3 😄1

Thanks so much for this!!!

joneslm1 on 4 Apr 2017

@dorapen's solution above worked, thank you so much!

irliao on 8 Apr 2017

I've been dealing with the same error and @dorapen's solution worked for me:

rm -rf /usr/local/lib/ruby/gems/2.4.0/gems/psych-2.2.4
rm -rf /usr/local/lib/ruby/gems/2.4.0/extensions/x86_64-darwin-16/2.4.0/psych-2.2.4

Thank you!!!

huebs on 12 Apr 2017

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