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

[jasonperrone]

Have you been stuck on this since July 2022, or did you get past it?

[DavidRawk-Blake]

I'm trapped by this as well. ASDF seems to have the same problem

[caged]

I was setting up a clean machine on MacOS Ventura 13.0 and ran into this issue.
Running brew install libyaml allowed the rbenv install to complete without error.

[kurko]

This didn't fix it for me, despite uninstalling it, unlinking and relinking and all the incantations possible.

[sekitaka]

It works for me!

[arg]

Got this issue on Ubuntu 22.04 while installing Ruby 3.2.0 as well. Fixed by installing libyaml:

sudo apt install libyaml-dev

[arknamal]

ty. worked for me on same ubuntu. I m bcz we are ;)

[nikolaz90]

thanks you :)

[mralaminahamed]

thank you. this is work for me.

[aecordova]

this worked for me!!! :)

[stratigos]

Also found this on SO: https://stackoverflow.com/questions/77082389/ubuntu-unable-to-locate-package-libyaml - to confirm for us Ubuntu folks.

[rafaelfranca]

I get this no matter which version of Ruby I try to install using debian. libyaml-dev is already installed, but I can't install any Ruby version because I get the "It seems your ruby installation is missing psych (for YAML output)" error.

Here is the log

https://gist.github.com/rafaelfranca/91250c4079cb483c9cc6796c6356cd82

[HLFH]

@rafaelfranca Try this script to clean gems? https://gist.github.com/IanVaughan/2902499

[kurko]

Getting this suddenly for all versions as well, but on Mac M2 13.1. Currently installed versions show this,

incompatible library version - /Users/alex/.gem/ruby/2.7.0/gems/psych-5.0.2/lib/psych.bundle (LoadError)
/Users/alex/.rbenv/versions/2.7.1/lib/ruby/2.7.0/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.

and I can't rbenv install any version

[lunohodov]

Make sure your environment meets the requirements as suggested in the wiki. Then, depending on your system, pass the libyaml path to the installation process.

For me, on an M2 Ventura 13.2.1, with a Homebrew-installed asdf (ruby-build under the hood):

~ % brew reinstall libyaml
~ % gem install psych -- --with-libyaml-dir=$(brew --prefix libyaml)
~ % export RUBY_CONFIGURE_OPTS=--with-libyaml-dir=$(brew --prefix libyaml)
~ % asdf install ruby latest

[mislav]

@lunohodov Thanks! With the latest version of ruby-build, manually linking to Homebrew's libyaml isn't necessary anymore, since ruby-build will automatically pass --with-libyaml-dir=$(brew --prefix libyaml) if libyaml was found. 🚀

[QMiqTx6DHn1bA9yaNaAbsD3CLG8gTmd4]

@mislav Any ideas why/what could cause the error?

/Users/username/.rubies/2.7.7/lib/ruby/2.7.0/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

Full log attached - 1.log

---

Seemingly it happened already after the Ruby 2.7.7 was successfully installed. Having checked the installation I don't see any issues with YAML/Psych & smoke test code below runs perfectly. 🤷‍♂️

$ ruby -e "require 'psych'; require 'yaml'; puts YAML.dump('abc')"
--- abc

[mislav]

I can't spot anything that went wrong in your installation, and I'm puzzled by the error since it looks like Ruby had linked to Homebrew libyaml successfully and that psych worked. Note, however, that Ruby 2.7 is becoming EOL end of this month.

@hsbt: any ideas?

[hsbt]

installing default gems from ext:   /Users/username/.rubies/2.7.7/lib/ruby/gems/2.7.0 (build_info, cache, doc, extensions, gems, specifications)
6048   │                                     bigdecimal 2.0.0
(snip)
6058   │                                     psych 3.1.0

Installation is successful. This user may use GEM_HOME and mixed psych binary of several versions.

[cwatson-im]

Thanks! I had the same issue in this subthread, and unset GEM_HOME fixed it for me.

[nkokkos]

My solution:

I use Rocky Linux 8 ( forked from centos) and I tried to install ruby 3.2.2 using:

rbenv install 3.2.2

So, I got this message:

Leaving directory '/tmp/ruby-build.20230427112055.48112.QYerKI/ruby-3.2.2'
Generating RDoc documentation
/tmp/ruby-build.20230427112055.48112.QYerKI/ruby-3.2.2/lib/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.

How I resolved it:

as root, I installed libyaml + libyaml-devel:

yum install libyaml

But you have to enable powertools repo to install source version libyaml-devel:

yum --enablerepo=powertools install libyaml-devel

After installing both, at my root prompt I typed;

ldconfig -vvv

Finally, I logged in as normal user and installed ruby version 3.2.2:

rbenv install 3.2.2

It worked for me.

[geanttechnology]

it worked for me as well. Rocky Linux 8 needs libyaml-devel to compile ruby 3.2.2. Thanks

[amruali]

Worked for me, Thanks Nick.

[initseis]

For Mac M1 with Monterey I could install Ruby 2.3.1 and 3.2.1 with Rosetta following these tutorials:

• https://soffes.com/blog/homebrew-on-apple-silicon
• https://soffes.com/blog/ruby-on-apple-silicon

[npickens]

Oof, this was frustrating. A simple 3.1.2 to 3.2.1 Ruby upgrade on CentOS Stream 9 turned into an hours-long event because of this issue. Key thing ended up being enabling crb rather than powertools on CentOS:

dnf config-manager --set-enabled crb
yum install -y libyaml-devel

I think the above should do it, but if not, here's everything that I did:

# These might not be necessary
yum install -y dnf-plugins-core
yum install -y epel-release

dnf config-manager --set-enabled crb
yum install -y libtool libyaml-devel

# Get location of psych gem and manually delete it (cannot gem uninstall because it's a default gem)
gem info psych
rm -rf <directory where psych is installed>
gem install psych

rbenv install <desired version>