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dawoonchung opened this issue Mar 27, 2017 · 27 comments
Closed
3 tasks done

Upgrading to Ruby 2.4.1_1 breaks gem command. #11636

dawoonchung opened this issue Mar 27, 2017 · 27 comments

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@dawoonchung
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dawoonchung commented Mar 27, 2017 •
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  • Ran brew update and retried your prior step?
  • Ran brew doctor, fixed as many issues as possible and retried your prior step?
  • 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.
@dawoonchung dawoonchung changed the title Upgrading to Ruby 2.4.1_1 breaks gem. Upgrading to Ruby 2.4.1_1 breaks gem command. Mar 27, 2017
@ilovezfs
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maybe

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

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

@ilovezfs
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what command are you running

@dawoonchung
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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.

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

so not sure what to tell you

@dawoonchung
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Strange. I tried with ruby@2.3, and it is working without any problem. But as soon as I upgrade it to 2.4.1, the problem pops up again.

@ilovezfs
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what's output for brew config and brew doctor

@dawoonchung
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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.

@Bufallo
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Bufallo commented Mar 27, 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?

@ilovezfs
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@xu-cheng Any ideas here? I notice you may have done some related work on this in adfcc5a.

@xu-cheng
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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 #11474

@ilovezfs
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@dorapen @Bufallo please give that a try.

@ilovezfs ilovezfs added the needs response Needs a response from the issue/PR author label Mar 27, 2017
@BrewTestBot BrewTestBot removed the needs response Needs a response from the issue/PR author label Mar 27, 2017
@ilovezfs ilovezfs added the needs response Needs a response from the issue/PR author label Mar 27, 2017
@dawoonchung
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@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.

@BrewTestBot BrewTestBot removed the needs response Needs a response from the issue/PR author label Mar 27, 2017
@dawoonchung
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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

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

@dawoonchung
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@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
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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!!

@ilovezfs
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ilovezfs commented Mar 27, 2017 •
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@Bufallo does that take care of it for you too?

@Bufallo
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Bufallo commented Mar 27, 2017

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

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

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

@dawoonchung dawoonchung mentioned this issue Mar 27, 2017
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@ilovezfs ilovezfs mentioned this issue Mar 28, 2017
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This was referenced Mar 28, 2017
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@kud
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kud commented Mar 29, 2017

Thank you so much for the solution. :)

@AndreTheHunter
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Worked for me too!

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

@ilovezfs ilovezfs mentioned this issue Apr 3, 2017
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@joneslm1
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joneslm1 commented Apr 4, 2017

Thanks so much for this!!!

@irliao
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irliao commented Apr 8, 2017 •
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@dorapen's solution above worked, thank you so much!

@huebs
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huebs commented Apr 12, 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!!!

@Homebrew Homebrew locked and limited conversation to collaborators Apr 12, 2017
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@kud @dawoonchung @AndreTheHunter @huebs @BrewTestBot @irliao @xu-cheng @ilovezfs @Bufallo @joneslm1