Ruby installation is missing Psych. Ruby yaml extension not compiled

[DirtyF]

My setup:

• macOS Mojave with ruby 2.3.7 as the default ruby (/usr/bin/ruby)
• brew install ruby install ruby 2.5.3 (/usr/local/opt/ruby/bin/ruby)
• gems are installed in ~/gems/

gem env

RubyGems Environment:
  - RUBYGEMS VERSION: 2.7.8
  - RUBY VERSION: 2.5.3 (2018-10-18 patchlevel 105) [x86_64-darwin18]
  - INSTALLATION DIRECTORY: /Users/frank/gems
  - USER INSTALLATION DIRECTORY: /Users/frank/.gem/ruby/2.5.0
  - RUBY EXECUTABLE: /usr/local/opt/ruby/bin/ruby
  - EXECUTABLE DIRECTORY: /Users/frank/gems/bin
  - SPEC CACHE DIRECTORY: /Users/frank/.gem/specs
  - SYSTEM CONFIGURATION DIRECTORY: /usr/local/Cellar/ruby/2.5.3_1/etc
  - RUBYGEMS PLATFORMS:
    - ruby
    - x86_64-darwin-18
  - GEM PATHS:
     - /Users/frank/gems
     - /Users/frank/.gem/ruby/2.5.0
     - /usr/local/lib/ruby/gems/2.5.0
     - /usr/local/Cellar/ruby/2.5.3_1/lib/ruby/gems/2.5.0
  - GEM CONFIGURATION:
     - :update_sources => true
     - :verbose => true
     - :backtrace => false
     - :bulk_threshold => 1000
     - "gem" => "--no-document"
  - REMOTE SOURCES:
     - https://rubygems.org/
  - SHELL PATH:
     - /usr/local/opt/llvm@4/bin
     - /Users/frank/.rbenv/shims
     - /Users/frank/.rbenv/bin
     - /Users/frank/gems/bin
     - /usr/local/opt/ruby/bin
     - /usr/local/bin
     - /usr/bin
     - /bin
     - /usr/sbin
     - /sbin
     - ~/bin
     - /Users/frank/.go/bin
     - /usr/local/opt/go/libexec/bin
     - /usr/local/opt/fzf/bin

---

When I run rbenv install 2.6.0-preview3 the following error occurs on macOS Mojave:

/Users/frank/.rbenv/versions/2.6.0-preview3/lib/ruby/2.6.0/yaml.rb:3: warning: It seems your ruby installation is missing psych (for YAML output).
To eliminate this warning, please install libyaml and reinstall your ruby.
The Ruby yaml extension was not compiled.
ERROR: Ruby install aborted due to missing extensions

The Psych gem is installed for ruby 2.5.3:

otool -L ~/gems/gems/psych-3.0.3/lib/psych.bundle
/Users/frank/gems/gems/psych-3.0.3/lib/psych.bundle:
	/usr/local/opt/ruby/lib/libruby.2.5.dylib (compatibility version 2.5.0, current version 2.5.3)
	/usr/local/opt/libyaml/lib/libyaml-0.2.dylib (compatibility version 3.0.0, current version 3.5.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1252.200.5)
	/usr/lib/libobjc.A.dylib (compatibility version 1.0.0, current version 228.0.0)

What is wrong? How do I fix this?

[hsbt]

Your pysch extension(~/gems/gems/psych-3.0.3/lib/psych.bundle) was built by 2.5.x.

[DirtyF]

@hsbt thanks, by uninstalling psych, rbenv installed ruby 2.6.0-preview3 without errors:

Installed ruby-2.6.0-preview3 to /Users/frank/.rbenv/versions/2.6.0-preview3

[taliesinpenbardd]

Same problem here. gem command won't respond to anything :

To eliminate this warning, please install libyaml and reinstall your ruby.
Traceback (most recent call last):
	15: from /usr/local/bin/gem:21:in `<main>'
	14: from /usr/local/Cellar/ruby/2.5.3_1/lib/ruby/2.5.0/rubygems/gem_runner.rb:44:in `run'
	13: from /usr/local/Cellar/ruby/2.5.3_1/lib/ruby/2.5.0/rubygems/gem_runner.rb:79:in `do_configuration'
	12: from /usr/local/Cellar/ruby/2.5.3_1/lib/ruby/2.5.0/rubygems/gem_runner.rb:79:in `new'
	11: from /usr/local/Cellar/ruby/2.5.3_1/lib/ruby/2.5.0/rubygems/config_file.rb:202:in `initialize'
	10: from /usr/local/Cellar/ruby/2.5.3_1/lib/ruby/2.5.0/rubygems/config_file.rb:349:in `load_file'
	 9: from /usr/local/Cellar/ruby/2.5.3_1/lib/ruby/2.5.0/rubygems.rb:729:in `load_yaml'
	 8: from /usr/local/Cellar/ruby/2.5.3_1/lib/ruby/2.5.0/rubygems/core_ext/kernel_require.rb:59:in `require'
	 7: from /usr/local/Cellar/ruby/2.5.3_1/lib/ruby/2.5.0/rubygems/core_ext/kernel_require.rb:59:in `require'
	 6: from /usr/local/Cellar/ruby/2.5.3_1/lib/ruby/2.5.0/yaml.rb:6:in `<top (required)>'
	 5: from /usr/local/Cellar/ruby/2.5.3_1/lib/ruby/2.5.0/rubygems/core_ext/kernel_require.rb:59:in `require'
	 4: from /usr/local/Cellar/ruby/2.5.3_1/lib/ruby/2.5.0/rubygems/core_ext/kernel_require.rb:59:in `require'
	 3: from /Users/lucdlb/.rvm/gems/ruby-2.5.1/gems/psych-3.0.3/lib/psych.rb:13:in `<top (required)>'
	 2: from /Users/lucdlb/.rvm/gems/ruby-2.5.1/gems/psych-3.0.3/lib/psych.rb:16:in `rescue in <top (required)>'
	 1: from /usr/local/Cellar/ruby/2.5.3_1/lib/ruby/2.5.0/rubygems/core_ext/kernel_require.rb:59:in `require'
/usr/local/Cellar/ruby/2.5.3_1/lib/ruby/2.5.0/rubygems/core_ext/kernel_require.rb:59:in `require': incompatible library version - /Users/username/.rvm/gems/ruby-2.5.1/gems/psych-3.0.3/lib/psych.bundle (LoadError)

ruby -v:
ruby 2.5.3p105 (2018-10-18 revision 65156) [x86_64-darwin18]

OS :
Mac OS X Mojave 10.14.1

Any idea how to debug that ?

[DirtyF]

@taliesinpenbardd so you can not run gem unsinstall psych? Maybe try to remove /Users/username/.rvm/gems/ruby-2.5.1/gems/psych-3.0.3/ manually?

[taliesinpenbardd]

@DirtyF I've finally uninstalled RVM, and tried my luck with RBENV. No luck so far, I still can't use the gems I've installed (and reinstalled). I suppose it's a wrong installation location on the system, or perhaps a permissions problem. Still looking, but I guess it's out of the focus of this ticket.
Thanks anyway.

[DirtyF]

@taliesinpenbardd FWIW you can choose to store your gems in your home directory, by adding the following to your shell config file:

export GEM_HOME=$HOME/gems
export PATH=$HOME/gems/bin:$PATH

[taliesinpenbardd]

@DirtyF Thank you very much, it seems to work. (and thank you also, I did discover Jekyll and am gonna use it sometime in the future. 😄 )

[farisarie]

i have a problem when i trying to installing feedkit library and this warning showup I didn't find any solution, do u know what I should do?

/System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0/yaml.rb:3: warning: It seems your ruby installation is missing psych (for YAML output).
To eliminate this warning, please install libyaml and reinstall your ruby.
/Library/Ruby/Site/2.6.0/rubygems/core_ext/kernel_require.rb:85:in `require': dlopen(/Library/Ruby/Gems/2.6.0/gems/psych-4.0.2/lib/psych.bundle, 0x0009): tried: '/Library/Ruby/Gems/2.6.0/gems/psych-4.0.2/lib/psych.bundle' (mach-o file, but is an incompatible architecture (have 'arm64', need 'x86_64')), '/usr/lib/psych.bundle' (no such file) - /Library/Ruby/Gems/2.6.0/gems/psych-4.0.2/lib/psych.bundle (LoadError)

[eertmanhidde]

Running gem uninstall psych from my older ruby version(2.7.2) fixed the issue for me

[askdesigners]

I get this when trying to uninstall
Gem psych-4.0.3 cannot be uninstalled because it is a default gem