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Support for Psych 5 #437

Closed
dorianmariecom opened this issue Dec 5, 2022 · 11 comments
Closed

Support for Psych 5 #437

dorianmariecom opened this issue Dec 5, 2022 · 11 comments

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@dorianmariecom
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I'm getting this output when upgrading psych from 4 to 5:

Gem::Ext::BuildError: ERROR: Failed to build gem native extension.
494 |  
495 | current directory: /usr/local/bundle/gems/skylight-5.3.4/ext
496 | /usr/local/bin/ruby -I /usr/local/lib/ruby/3.1.0 -r
497 | ./siteconf20221205-17-o7zxoa.rb extconf.rb
498 | musl libc (x86_64)
499 | Version 1.2.3
500 | Dynamic Program Loader
501 | Usage: /lib/ld-musl-x86_64.so.1 [options] [--] pathname
502 | *** extconf.rb failed ***
503 | Could not create Makefile due to some reason, probably lack of necessary
504 | libraries and/or headers.  Check the mkmf.log file for more details.  You may
505 | need configuration options.
506 |  
507 | Provided configuration options:
508 | --with-opt-dir
509 | --without-opt-dir
510 | --with-opt-include
511 | --without-opt-include=${opt-dir}/include
512 | --with-opt-lib
513 | --without-opt-lib=${opt-dir}/lib
514 | --with-make-prog
515 | --without-make-prog
516 | --srcdir=.
517 | --curdir
518 | --ruby=/usr/local/bin/$(RUBY_BASE_NAME)
519 | /usr/local/lib/ruby/3.1.0/psych.rb:455:in `parse_stream': undefined method
520 | `parse' for #<Psych::Parser:0x00007f870c732950
521 | @handler=#<Psych::Handlers::DocumentStream:0x00007f870c732b58 @stack=[],
522 | @last=nil, @root=nil, @start_line=nil, @start_column=nil, @end_line=nil,
523 | @end_column=nil, @block=#<Proc:0x00007f870c7329c8
524 | /usr/local/lib/ruby/3.1.0/psych.rb:399>>, @external_encoding=0> (NoMethodError)
525 |  
526 | parser.parse yaml, filename
527 | ^^^^^^
528 | from /usr/local/lib/ruby/3.1.0/psych.rb:399:in `parse'
529 | from /usr/local/lib/ruby/3.1.0/psych.rb:324:in `safe_load'
530 | from /usr/local/lib/ruby/3.1.0/psych.rb:370:in `load'
531 | from /usr/local/lib/ruby/3.1.0/psych.rb:671:in `block in load_file'
532 | from /usr/local/lib/ruby/3.1.0/psych.rb:670:in `open'
533 | from /usr/local/lib/ruby/3.1.0/psych.rb:670:in `load_file'
534 | from extconf.rb:121:in `<main>'
535 | I, [2022-12-05T09:14:41.592907 #3150]  INFO -- :
536 | SKYLIGHT_HDR_PATH=/usr/local/bundle/gems/skylight-5.3.4/ext;
537 | SKYLIGHT_LIB_PATH=/usr/local/bundle/gems/skylight-5.3.4/lib/skylight/native/x86_64-linux-musl
538
@dorianmariecom dorianmariecom mentioned this issue Dec 5, 2022
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@zvkemp
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zvkemp commented Dec 7, 2022

Hi @dorianmariefr!

I don't believe this is an issue with either Skylight nor Psych 5 (your backtrace appears to be pointing to the vendored Psych for ruby 3.1, which is v4). Parser#parse is a natively-implemented function, so I'm guessing something went wrong when Psych was compiled when you installed ruby, and the mostly likely issue is a missing libyaml (or yaml-dev, or your operating system's equivalent).

Ruby should load psych from a gem if it is installed; if it's only in your Gemfile it may not have been installed yet when Skylight's extconf.rb ran. Try a gem install psych -v 5.0.0 (noting any errors about missing native libs) first and bundle again.

@dorianmariecom
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@zvkemp The build and the tests work fine before upgrading to psych 5.

I have libyaml-dev installed (it was generating a yaml.h not found error before)

I set up a debugging session on GitHub Actions and was able to successfully install psych 5

$ sudo gem install psych
Building native extensions. This could take a while...
Successfully installed psych-5.0.1
Parsing documentation for psych-5.0.1
Installing ri documentation for psych-5.0.1
Done installing documentation for psych after 1 seconds
1 gem installed

I was also able to successfully install skylight with sudo gem install skylight.

But when I installed ruby with rvm, and I do a bundle or gem install skylight I get:

current directory: /home/runner/.rvm/gems/ruby-3.1.2/gems/skylight-5.3.4/ext
/home/runner/.rvm/rubies/ruby-3.1.2/bin/ruby -I /home/runner/.rvm/rubies/ruby-3.1.2/lib/ruby/3.1.0 -r ./siteconf20221209-18715-82d0sn.rb extconf.rb
*** extconf.rb failed ***
Could not create Makefile due to some reason, probably lack of necessary
libraries and/or headers.  Check the mkmf.log file for more details.  You may
need configuration options.

Provided configuration options:
        --with-opt-dir
        --without-opt-dir
        --with-opt-include
        --without-opt-include=${opt-dir}/include
        --with-opt-lib
        --without-opt-lib=${opt-dir}/lib
        --with-make-prog
        --without-make-prog
        --srcdir=.
        --curdir
        --ruby=/home/runner/.rvm/rubies/ruby-3.1.2/bin/$(RUBY_BASE_NAME)
/home/runner/.rvm/rubies/ruby-3.1.2/lib/ruby/3.1.0/psych.rb:455:in `parse_stream': undefined method `parse' for #<Psych::Parser:0x00007f01e5023c38 @handler=#<Psych::Handlers::DocumentStream:0x00007f01e5023da0 @stack=[], @last=nil, @root=nil, @start_line=nil, @start_column=nil, @end_line=nil, @end_column=nil, @block=#<Proc:0x00007f01e5023cb0 /home/runner/.rvm/rubies/ruby-3.1.2/lib/ruby/3.1.0/psych.rb:399>>, @external_encoding=0> (NoMethodError)

      parser.parse yaml, filename
            ^^^^^^
        from /home/runner/.rvm/rubies/ruby-3.1.2/lib/ruby/3.1.0/psych.rb:399:in `parse'
        from /home/runner/.rvm/rubies/ruby-3.1.2/lib/ruby/3.1.0/psych.rb:324:in `safe_load'
        from /home/runner/.rvm/rubies/ruby-3.1.2/lib/ruby/3.1.0/psych.rb:370:in `load'
        from /home/runner/.rvm/rubies/ruby-3.1.2/lib/ruby/3.1.0/psych.rb:671:in `block in load_file'
        from /home/runner/.rvm/rubies/ruby-3.1.2/lib/ruby/3.1.0/psych.rb:670:in `open'
        from /home/runner/.rvm/rubies/ruby-3.1.2/lib/ruby/3.1.0/psych.rb:670:in `load_file'
        from extconf.rb:121:in `<main>'
I, [2022-12-09T07:07:04.525750 #18724]  INFO -- : SKYLIGHT_HDR_PATH=/home/runner/.rvm/gems/ruby-3.1.2/gems/skylight-5.3.4/ext; SKYLIGHT_LIB_PATH=/home/runner/.rvm/gems/ruby-3.1.2/gems/skylight-5.3.4/lib/skylight/native/x86_64-linux

extconf failed, exit code 1

I tried removing psych from our Gemfile, removing the < 6 version constraint, upgrading to psych 5.0.1, moving gem "psych" to the top of the Gemfile, but nothing worked

@zvkemp
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zvkemp commented Dec 13, 2022

The issue must be related to bundler not running with your Gemfile context, but so far I am unable to reproduce the issue. The error arises in a public method in /home/runner/.rvm/rubies/ruby-3.1.2/lib/ruby/3.1.0/psych.rb:399; if you installed libyaml after installing ruby, I suggest you remove Ruby 3.1.2 and re-install it.

If you have a Dockerfile or another way to reproduce the error, I would be happy to take a look, but since this isn't really a Skylight issue (we're only calling public methods on built-in Ruby classes), there's nothing for us to fix here.

@zvkemp zvkemp closed this as completed Jan 7, 2023
@dorianmariecom
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We didn't figure it out, we solved this by removing psych from our explicit dependencies as it's not needed by our app

@krainboltgreene
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So this exact error happens in my app (Rails 7.0, Skylight 5.3). I'm using the main branch of rails' Dockerfile which is has a FROM of ruby:3.1.2.20-slim.

I am installing the libyaml-dev from aptitude, so I don't think it's that.

@shanlalit
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shanlalit commented Sep 10, 2023 •
edited
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IMO this ticket on ruby core might shad some light on the root cause. If you have both Psych 4 and 5 this issues appears. After reading this ticket I have removed Psych 5, now bundle is not giving any errors and Skylight is installed correctly.

https://ml.ruby-lang.org/mailman3/hyperkitty/list/[email protected]/thread/MX4LNG2YYMEMREMW4I7VV2FQFD5GGEZT/

@kg-currenxie
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kg-currenxie commented Nov 11, 2023 •
edited
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Same issue here.

Gemfile.lock

GIT
  remote: https://github.com/bullet-train-co/magic_test.git
  revision: 0242eadd9bed7e789f3e0a3210b98ac71b78a063
  tag: v0.1.0
  specs:
    magic_test (0.1.0)
      capybara (>= 3.0)
      pry
      pry-stack_explorer
      rails (>= 5.0)

GEM
  remote: https://rubygems.org/
  specs:
    actioncable (7.1.0)
      actionpack (= 7.1.0)
      activesupport (= 7.1.0)
      nio4r (~> 2.0)
      websocket-driver (>= 0.6.1)
      zeitwerk (~> 2.6)
    actionmailbox (7.1.0)
      actionpack (= 7.1.0)
      activejob (= 7.1.0)
      activerecord (= 7.1.0)
      activestorage (= 7.1.0)
      activesupport (= 7.1.0)
      mail (>= 2.7.1)
      net-imap
      net-pop
      net-smtp
    actionmailer (7.1.0)
      actionpack (= 7.1.0)
      actionview (= 7.1.0)
      activejob (= 7.1.0)
      activesupport (= 7.1.0)
      mail (~> 2.5, >= 2.5.4)
      net-imap
      net-pop
      net-smtp
      rails-dom-testing (~> 2.2)
    actionpack (7.1.0)
      actionview (= 7.1.0)
      activesupport (= 7.1.0)
      nokogiri (>= 1.8.5)
      rack (>= 2.2.4)
      rack-session (>= 1.0.1)
      rack-test (>= 0.6.3)
      rails-dom-testing (~> 2.2)
      rails-html-sanitizer (~> 1.6)
    actiontext (7.1.0)
      actionpack (= 7.1.0)
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      globalid (>= 0.6.0)
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    actionview (7.1.0)
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      builder (~> 3.1)
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    premailer-rails (1.12.0)
      actionmailer (>= 3)
      net-smtp
      premailer (~> 1.7, >= 1.7.9)
    propshaft (0.8.0)
      actionpack (>= 7.0.0)
      activesupport (>= 7.0.0)
      rack
      railties (>= 7.0.0)
    pry (0.14.2)
      coderay (~> 1.1)
      method_source (~> 1.0)
    pry-stack_explorer (0.6.1)
      binding_of_caller (~> 1.0)
      pry (~> 0.13)
    psych (5.1.1.1)
      stringio
    public_suffix (5.0.3)
    puma (6.4.0)
      nio4r (~> 2.0)
    pundit (2.3.0)
      activesupport (>= 3.0.0)
    pundit-matchers (3.1.2)
      rspec-core (~> 3.12)
      rspec-expectations (~> 3.12)
      rspec-mocks (~> 3.12)
      rspec-support (~> 3.12)
    raabro (1.4.0)
    racc (1.7.3)
    rack (3.0.8)
    rack-session (2.0.0)
      rack (>= 3.0.0)
    rack-test (2.1.0)
      rack (>= 1.3)
    rackup (2.1.0)
      rack (>= 3)
      webrick (~> 1.8)
    rails (7.1.0)
      actioncable (= 7.1.0)
      actionmailbox (= 7.1.0)
      actionmailer (= 7.1.0)
      actionpack (= 7.1.0)
      actiontext (= 7.1.0)
      actionview (= 7.1.0)
      activejob (= 7.1.0)
      activemodel (= 7.1.0)
      activerecord (= 7.1.0)
      activestorage (= 7.1.0)
      activesupport (= 7.1.0)
      bundler (>= 1.15.0)
      railties (= 7.1.0)
    rails-dom-testing (2.2.0)
      activesupport (>= 5.0.0)
      minitest
      nokogiri (>= 1.6)
    rails-html-sanitizer (1.6.0)
      loofah (~> 2.21)
      nokogiri (~> 1.14)
    rails-i18n (7.0.8)
      i18n (>= 0.7, < 2)
      railties (>= 6.0.0, < 8)
    rails-patterns (0.11.0)
      actionpack (>= 4.2.6)
      activerecord (>= 4.2.6)
      ruby2_keywords
      virtus
    rails_live_reload (0.3.4)
      listen
      nio4r
      railties
      websocket-driver
    railties (7.1.0)
      actionpack (= 7.1.0)
      activesupport (= 7.1.0)
      irb
      rackup (>= 1.0.0)
      rake (>= 12.2)
      thor (~> 1.0, >= 1.2.2)
      zeitwerk (~> 2.6)
    rainbow (3.1.1)
    rake (13.1.0)
    ransack (4.0.0)
      activerecord (>= 6.1.5)
      activesupport (>= 6.1.5)
      i18n
    rb-fsevent (0.11.2)
    rb-inotify (0.10.1)
      ffi (~> 1.0)
    rdoc (6.6.0)
      psych (>= 4.0.0)
    redis (5.0.8)
      redis-client (>= 0.17.0)
    redis-client (0.18.0)
      connection_pool
    regexp_parser (2.8.2)
    reline (0.4.0)
      io-console (~> 0.5)
    request_store (1.5.1)
      rack (>= 1.4)
    responders (3.1.1)
      actionpack (>= 5.2)
      railties (>= 5.2)
    rexml (3.2.6)
    rotp (6.3.0)
    rqrcode (2.2.0)
      chunky_png (~> 1.0)
      rqrcode_core (~> 1.0)
    rqrcode_core (1.2.0)
    rspec (3.12.0)
      rspec-core (~> 3.12.0)
      rspec-expectations (~> 3.12.0)
      rspec-mocks (~> 3.12.0)
    rspec-core (3.12.2)
      rspec-support (~> 3.12.0)
    rspec-expectations (3.12.3)
      diff-lcs (>= 1.2.0, < 2.0)
      rspec-support (~> 3.12.0)
    rspec-mocks (3.12.6)
      diff-lcs (>= 1.2.0, < 2.0)
      rspec-support (~> 3.12.0)
    rspec-rails (6.0.1)
      actionpack (>= 6.1)
      activesupport (>= 6.1)
      railties (>= 6.1)
      rspec-core (~> 3.11)
      rspec-expectations (~> 3.11)
      rspec-mocks (~> 3.11)
      rspec-support (~> 3.11)
    rspec-support (3.12.1)
    rspec_junit_formatter (0.6.0)
      rspec-core (>= 2, < 4, != 2.12.0)
    rubocop (1.57.2)
      json (~> 2.3)
      language_server-protocol (>= 3.17.0)
      parallel (~> 1.10)
      parser (>= 3.2.2.4)
      rainbow (>= 2.2.2, < 4.0)
      regexp_parser (>= 1.8, < 3.0)
      rexml (>= 3.2.5, < 4.0)
      rubocop-ast (>= 1.28.1, < 2.0)
      ruby-progressbar (~> 1.7)
      unicode-display_width (>= 2.4.0, < 3.0)
    rubocop-ast (1.30.0)
      parser (>= 3.2.1.0)
    rubocop-daemon (0.3.2)
      rubocop
    rubocop-packaging (0.5.2)
      rubocop (>= 1.33, < 2.0)
    rubocop-performance (1.19.1)
      rubocop (>= 1.7.0, < 2.0)
      rubocop-ast (>= 0.4.0)
    rubocop-rails (2.19.1)
      activesupport (>= 4.2.0)
      rack (>= 1.1)
      rubocop (>= 1.33.0, < 2.0)
    ruby-next-core (0.15.3)
    ruby-progressbar (1.13.0)
    ruby-vips (2.2.0)
      ffi (~> 1.12)
    ruby2_keywords (0.0.5)
    ruby_parser (3.20.3)
      sexp_processor (~> 4.16)
    rubyzip (2.3.2)
    selenium-webdriver (4.14.0)
      rexml (~> 3.2, >= 3.2.5)
      rubyzip (>= 1.2.2, < 3.0)
      websocket (~> 1.0)
    sexp_processor (4.17.0)
    shellany (0.0.1)
    skylight (6.0.1)
      activesupport (>= 5.2.0)
    smart_properties (1.17.0)
    solid_cache (0.1.0)
      rails (>= 7)
    sshkit (1.21.5)
      net-scp (>= 1.1.2)
      net-ssh (>= 2.8.0)
    stimulus-rails (1.2.1)
      railties (>= 6.0.0)
    stringio (3.0.9)
    super_diff (0.10.0)
      attr_extras (>= 6.2.4)
      diff-lcs
      patience_diff
    tailwindcss-rails (2.0.27-arm64-darwin)
      railties (>= 6.0.0)
    tailwindcss-rails (2.0.27-x86_64-linux)
      railties (>= 6.0.0)
    telephone_number (1.4.20)
    terminal-table (3.0.2)
      unicode-display_width (>= 1.1.1, < 3)
    thor (1.3.0)
    thread_safe (0.3.6)
    timeout (0.4.1)
    ttfunk (1.7.0)
    turbo-rails (1.4.0)
      actionpack (>= 6.0.0)
      activejob (>= 6.0.0)
      railties (>= 6.0.0)
    tzinfo (2.0.6)
      concurrent-ruby (~> 1.0)
    unaccent (0.4.0)
    unicode-display_width (2.5.0)
    uniform_notifier (1.16.0)
    unread (0.12.0)
      activerecord (>= 3)
    view_component (2.82.0)
      activesupport (>= 5.2.0, < 8.0)
      concurrent-ruby (~> 1.0)
      method_source (~> 1.0)
    view_component-contrib (0.1.3)
      ruby-next-core (>= 0.12.0)
      view_component
    virtus (2.0.0)
      axiom-types (~> 0.1)
      coercible (~> 1.0)
      descendants_tracker (~> 0.0, >= 0.0.3)
    warden (1.2.9)
      rack (>= 2.0.9)
    web-console (4.2.1)
      actionview (>= 6.0.0)
      activemodel (>= 6.0.0)
      bindex (>= 0.4.0)
      railties (>= 6.0.0)
    webrick (1.8.1)
    websocket (1.2.10)
    websocket-driver (0.7.6)
      websocket-extensions (>= 0.1.0)
    websocket-extensions (0.1.5)
    xpath (3.2.0)
      nokogiri (~> 1.8)
    zeitwerk (2.6.12)

PLATFORMS
  arm64-darwin-22
  x86_64-linux

DEPENDENCIES
  active_decorator (= 1.4.1)
  active_flag (= 1.6.0)
  active_storage_validations (= 1.0.3)
  acts-as-taggable-on (= 10.0.0)
  annotate (= 3.2.0)
  aws-sdk-s3 (= 1.136.0)
  bootsnap (= 1.16.0)
  brakeman (= 6.0.1)
  bugsnag (= 6.26.0)
  bullet (= 7.1.2)
  countries (= 5.7.0)
  database_cleaner (= 2.0.2)
  debug (= 1.8.0)
  devise (= 4.8.1)
  devise-two-factor (= 5.0.0)
  factory_bot_rails (= 6.2.0)
  faker (= 3.2.0)
  fasterer (= 0.10.1)
  good_job (= 3.20.0)
  guard (= 2.18.0)
  guard-brakeman (= 0.8.6)
  guard-bundler (= 3.0.1)
  guard-fasterer (= 0.1.0)
  guard-pow (= 2.0.0)
  guard-rspec (= 4.7.3)
  hiredis (= 0.6.3)
  httparty (= 0.21.0)
  i18n-tasks (= 1.0.12)
  image_processing (= 1.12.2)
  imgproxy (= 2.1.0)
  importmap-rails (= 1.2.3)
  kamal (= 1.0)
  kredis (= 1.3.0.1)
  letter_opener (= 1.8.1)
  magic_test!
  matrix (= 0.4.2)
  meilisearch-rails (= 0.10.1)
  mina (= 1.2.4)
  money-rails (= 1.15.0)
  motor-admin (= 0.4.11)
  pagy (= 6.0.4)
  pg (= 1.4.6)
  pgreset (= 0.4)
  prawn (= 2.4)
  prawn-table (= 0.2.2)
  premailer-rails (= 1.12.0)
  propshaft (= 0.8.0)
  puma (= 6.4.0)
  pundit (= 2.3.0)
  pundit-matchers (= 3.1.2)
  rails (= 7.1.0)
  rails-patterns (= 0.11.0)
  rails_live_reload (= 0.3.4)
  ransack (= 4.0.0)
  rqrcode (= 2.2.0)
  rspec-rails (= 6.0.1)
  rspec_junit_formatter (= 0.6.0)
  rubocop (= 1.57.2)
  rubocop-daemon (= 0.3.2)
  rubocop-packaging (= 0.5.2)
  rubocop-performance (= 1.19.1)
  rubocop-rails (= 2.19.1)
  ruby-progressbar (= 1.13.0)
  selenium-webdriver (= 4.14.0)
  skylight (= 6.0.1)
  solid_cache (= 0.1.0)
  stimulus-rails (= 1.2.1)
  super_diff (= 0.10.0)
  tailwindcss-rails (= 2.0.27)
  telephone_number (= 1.4.20)
  turbo-rails (= 1.4.0)
  tzinfo-data (= 1.2023.3)
  unread (= 0.12.0)
  view_component (= 2.82.0)
  view_component-contrib (= 0.1.3)
  web-console (= 4.2.1)

RUBY VERSION
   ruby 3.1.4p223

BUNDLED WITH
   2.4.19

While i personally don't have psych in my Gemfile, there's railties -> irb -> rdoc -> psych >= 4.0.0 and the single psych (5.1.1.1) in the lock file. libyaml-dev is installed via apt.

=> gem pristine psych --version 5.1.1.1

Restoring gems to pristine condition...
Building native extensions. This could take a while...
Restored psych-5.1.1.1

=> bundle add psych

Ignoring psych-5.1.1.1 because its extensions are not built. Try: gem pristine psych --version 5.1.1.1
--- ERROR REPORT TEMPLATE -------------------------------------------------------

NoMethodError: undefined method `_native_parse' for #<Psych::Parser:0x00007f53655ff5e0 @handler=#<Psych::Handlers::DocumentStream:0x00007f53655ff8d8 @stack=[], @last=nil, @root=nil, @start_line=nil, @start_column=nil, @end_line=nil, @end_column=nil, @block=#<Proc:0x00007f53655ff658 /var/www/prickkoll.se/staging/shared/vendor/bundle/ruby/3.1.0/gems/psych-5.1.1.1/lib/psych.rb:399>>, @external_encoding=0>

      _native_parse @handler, yaml, path
      ^^^^^^^^^^^^^

@zvkemp
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zvkemp commented Nov 11, 2023

I believe you are encountering this Ruby bug: https://ml.ruby-lang.org/mailman3/hyperkitty/list/[email protected]/message/ZYU7X5A336FDS3BRM37NL47VWJXE3GGP/

It seems you can remove Psych 5 if it is not explicitly required by your Gemfile.lock.

On our side, I will investigate bundling a specific YAML parser (or using a different format during extconf) to avoid the issue entirely.

@zvkemp zvkemp reopened this Nov 11, 2023
@Frexuz
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Frexuz commented Nov 12, 2023

I had to manually remove psych (5.1.1.1) from the lockfile, as nothing else was dependent on it (at some previous point I guess?). It didn't even disappear from the lockfile when specifying psych 4.x in the gemfile 🤷

then then migrating, for some reason i had to completely clean the bundle cache with bundle clean (ssh to the machine), otherwise it still failed with compiling the c-extension 🤷

not sure if there's another way, but at least i could continue, and use skylight now :)

@zvkemp
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zvkemp commented Nov 30, 2023

It seems this issue was fixed in Rubygems 3.4.9 (https://github.com/rubygems/rubygems/blob/master/CHANGELOG.md#349--2023-03-20). gem update --system should update your version of rubygems and allow correct usage of YAML in extconf.

@zvkemp
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zvkemp commented Jan 9, 2024

This issue is now bypassed in v6.0.2 — we no longer require yaml during extconf.

@zvkemp zvkemp closed this as completed Jan 9, 2024
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@shanlalit @Frexuz @krainboltgreene @zvkemp @kg-currenxie @dorianmariecom