Error building native extensions when running bundle install

[arielj]

I just cloned the project, setup Virtualbox 7 and Vagrant following the instructions.

I cloned my rails fork and sshd into the virtual machine.

When I run bundle install, it fails to install the gems with this error related to psych's native extensions:

vagrant@rails-dev-box:/vagrant/rails$ bundle install
Following files may not be writable, so sudo is needed:
  /usr/local/bin
  /var/lib/gems/3.0.0
  /var/lib/gems/3.0.0/bin
  /var/lib/gems/3.0.0/build_info
  /var/lib/gems/3.0.0/cache
  /var/lib/gems/3.0.0/doc
  /var/lib/gems/3.0.0/extensions
  /var/lib/gems/3.0.0/gems
  /var/lib/gems/3.0.0/plugins
  /var/lib/gems/3.0.0/specifications
Fetching gem metadata from https://rubygems.org/.........
Using rake 13.0.6
Using base64 0.1.1
Using concurrent-ruby 1.1.10
Using connection_pool 2.3.0
Using ruby2_keywords 0.0.5
Using minitest 5.19.0
Using mutex_m 0.1.2
Using bigdecimal 3.1.4
Using builder 3.2.4
Using racc 1.6.2
Using crass 1.0.6
Using rack 3.0.8
Using nio4r 2.5.9
Using websocket-extensions 0.1.5
Using zeitwerk 2.6.6
Using timeout 0.4.0
Using marcel 1.0.2
Using mini_mime 1.1.2
Using date 3.3.3
Using public_suffix 5.0.1
Using amq-protocol 2.3.2
Using ast 2.4.2
Using aws-eventstream 1.2.0
Using aws-partitions 1.691.0
Using jmespath 1.6.2
Using faraday-em_http 1.0.0
Using faraday-em_synchrony 1.0.0
Using faraday-excon 1.1.0
Using faraday-httpclient 1.0.1
Using multipart-post 2.2.3
Using faraday-net_http 1.0.1
Using faraday-net_http_persistent 1.2.0
Using faraday-patron 1.0.0
Using faraday-rack 1.0.0
Using faraday-retry 1.0.3
Using beaneater 1.1.3
Using dante 0.2.0
Using bcrypt 3.1.18
Using benchmark-ips 2.10.0
Using bindex 0.8.1
Using msgpack 1.7.0
Using bundler 2.3.22
Using rbtree 0.4.6
Using set 1.0.3
Using matrix 0.4.2
Using regexp_parser 2.6.2
Using cgi 0.3.6
Using rexml 3.2.5
Using io-console 0.6.0
Using webrick 1.8.1
Using thor 1.2.2
Using dalli 3.2.3
Using declarative 0.0.20
Using digest-crc 0.6.4
Using event_emitter 0.2.6
Using execjs 2.8.1
Using ffi 1.15.5
Using raabro 1.4.0
Using jwt 2.6.0
Using memoist 0.16.2
Using multi_json 1.15.0
Using os 1.1.4
Using httpclient 2.8.3
Using trailblazer-option 0.1.2
Using uber 0.1.0
Using retriable 3.1.2
Using google-cloud-errors 1.3.0
Using hashdiff 1.0.1
Using mini_magick 4.12.0
Using json 2.6.3
Using libxml-ruby 4.0.0
Using rb-fsevent 0.11.2
Using mixlib-cli 2.1.8
Using tomlrb 2.0.3
Using path_expander 1.1.1
Using mono_logger 1.1.1
Using mysql2 0.5.4
Using parallel 1.22.1
Using pg 1.5.3
Using stringio 3.0.7
Using rainbow 3.1.1
Using redcarpet 3.2.3
Using erubi 1.12.0
Using ruby-progressbar 1.13.0
Using unicode-display_width 2.4.2
Using rubyzip 2.3.2
Using websocket 1.2.9
Using sigdump 0.2.4
Using sqlite3 1.6.3 (x86_64-linux)
Using stackprof 0.2.23
Using trilogy 2.5.0
Using drb 2.1.1
Using i18n 1.12.0
Using tzinfo 2.0.5
Using net-http-persistent 4.0.1
Using chef-utils 18.1.29
Using minitest-server 1.0.7
Using minitest-ci 3.4.0
Using minitest-retry 0.2.2
Using redis-client 0.12.0
Using sucker_punch 3.1.0
Using nokogiri 1.15.2 (x86_64-linux)
Using rack-session 2.0.0
Using rack-test 2.1.0
Using websocket-driver 0.7.5
Using net-protocol 0.2.1
Using addressable 2.8.1
Using aws-sigv4 1.5.2
Using faraday-multipart 1.0.4
Using backburner 1.6.0
Using bootsnap 1.15.0
Using sorted_set 1.0.3
Using crack 0.4.5
Using reline 0.3.2
Using rackup 2.1.0
Using representable 3.2.0
Using ruby-vips 2.1.4
Using kramdown 2.4.0
Using rb-inotify 0.10.1
Using parser 3.2.1.1
Using puma 6.3.0
Using rack-cache 1.14.0
Using sinatra 1.0
Using sprockets 4.2.0
Using terser 1.1.13
Using mixlib-config 3.0.27
Using rouge 4.1.0
Using queue_classic 4.0.0
Using activesupport 7.1.0.alpha from source at `.`
Using loofah 2.21.3
Using net-imap 0.3.6
Using net-pop 0.1.2
Using net-smtp 0.3.3
Using aws-sdk-core 3.168.4
Using faraday 1.10.2
Using bunny 2.20.2
Using xpath 3.2.0
Using irb 1.6.2
Using et-orbi 1.2.7
Using image_processing 1.12.2
Using kramdown-parser-gfm 1.1.0
Using listen 3.8.0
Using mixlib-shellout 3.2.7
Using minitest-bisect 1.6.0
Using redis 5.0.5
Using rubocop-ast 1.28.0
Using selenium-webdriver 4.11.0
Using serverengine 2.0.7
Using sidekiq 7.0.3
Using w3c_validators 1.3.7
Using webmock 3.18.1
Using websocket-client-simple 0.3.0 from https://github.com/matthewd/websocket-client-simple.git (at close-race@e161305)
Using rails-dom-testing 2.2.0
Using rails-html-sanitizer 1.6.0
Using globalid 1.1.0
Using activemodel 7.1.0.alpha from source at `.`
Installing psych 5.1.0 with native extensions
Using mail 2.8.0.1
Using aws-sdk-kms 1.61.0
Using aws-sdk-sns 1.57.0
Using faraday_middleware 1.2.0
Using capybara 3.39.2
Using debug 1.7.1
Using delayed_job 4.1.11
Using fugit 1.8.0
Using signet 0.17.0
Using google-cloud-env 1.6.0
Using mdl 0.12.0
Using redis-namespace 1.10.0
Using rubocop 1.48.1
Using sneakers 2.11.0
Using actionview 7.1.0.alpha from source at `.`
Using activejob 7.1.0.alpha from source at `.`
Using activerecord 7.1.0.alpha from source at `.`
Using aws-sdk-s3 1.117.2
Using azure-storage-common 2.0.4
Using rufus-scheduler 3.8.2
Using googleauth 1.3.0
Using google-cloud-core 1.6.0
Using actionpack 7.1.0.alpha from source at `.`
Using azure-storage-blob 2.0.3
Using delayed_job_active_record 4.1.7
Using google-apis-core 0.9.4
Using jbuilder 2.11.5
Using resque 2.4.0
Using rubocop-md 1.2.0
Using rubocop-minitest 0.29.0
Using rubocop-packaging 0.5.2
Using rubocop-performance 1.16.0
Using rubocop-rails 2.18.0
Using actioncable 7.1.0.alpha from source at `.`
Using activestorage 7.1.0.alpha from source at `.`
Using actionmailer 7.1.0.alpha from source at `.`
Using railties 7.1.0.alpha from source at `.` and installing its executables
Using google-apis-iamcredentials_v1 0.16.0
Using google-apis-storage_v1 0.19.0
Using resque-scheduler 4.7.0
Using sprockets-rails 3.4.2
Using actionmailbox 7.1.0.alpha from source at `.`
Using actiontext 7.1.0.alpha from source at `.`
Using cssbundling-rails 1.1.2
Using dartsass-rails 0.4.1
Using importmap-rails 1.1.5
Using jsbundling-rails 1.1.1
Using propshaft 0.6.4
Using stimulus-rails 1.2.1
Using tailwindcss-rails 2.0.21 (x86_64-linux)
Using turbo-rails 1.3.2
Using web-console 4.2.0
Using google-cloud-storage 1.44.0
Using rails 7.1.0.alpha from source at `.`
Gem::Ext::BuildError: ERROR: Failed to build gem native extension.

    current directory: /tmp/bundler20230905-29261-na9i1epsych-5.1.0/gems/psych-5.1.0/ext/psych
/usr/bin/ruby3.0 -I /usr/lib/ruby/vendor_ruby -r ./siteconf20230905-29261-ohet3k.rb extconf.rb
checking for yaml.h... no
yaml.h not found
*** 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=/usr/bin/$(RUBY_BASE_NAME)3.0
	--with-libyaml-source-dir
	--without-libyaml-source-dir
	--with-yaml-0.1-config
	--without-yaml-0.1-config
	--with-pkg-config
	--without-pkg-config
	--with-libyaml-dir
	--without-libyaml-dir
	--with-libyaml-include
	--without-libyaml-include=${libyaml-dir}/include
	--with-libyaml-lib
	--without-libyaml-lib=${libyaml-dir}/lib

To see why this extension failed to compile, please check the mkmf.log which can be found here:

  /tmp/bundler20230905-29261-na9i1epsych-5.1.0/extensions/x86_64-linux/3.0.0/psych-5.1.0/mkmf.log

extconf failed, exit code 1

Gem files will remain installed in /tmp/bundler20230905-29261-na9i1epsych-5.1.0/gems/psych-5.1.0 for inspection.
Results logged to /tmp/bundler20230905-29261-na9i1epsych-5.1.0/extensions/x86_64-linux/3.0.0/psych-5.1.0/gem_make.out

  /usr/lib/ruby/vendor_ruby/rubygems/ext/builder.rb:95:in `run'
  /usr/lib/ruby/vendor_ruby/rubygems/ext/ext_conf_builder.rb:47:in `block in build'
  /usr/lib/ruby/3.0.0/tempfile.rb:317:in `open'
  /usr/lib/ruby/vendor_ruby/rubygems/ext/ext_conf_builder.rb:26:in `build'
  /usr/lib/ruby/vendor_ruby/rubygems/ext/builder.rb:164:in `build_extension'
  /usr/lib/ruby/vendor_ruby/rubygems/ext/builder.rb:198:in `block in build_extensions'
  /usr/lib/ruby/vendor_ruby/rubygems/ext/builder.rb:195:in `each'
  /usr/lib/ruby/vendor_ruby/rubygems/ext/builder.rb:195:in `build_extensions'
  /usr/lib/ruby/vendor_ruby/rubygems/installer.rb:851:in `build_extensions'
  /var/lib/gems/3.0.0/gems/bundler-2.3.22/lib/bundler/rubygems_gem_installer.rb:72:in `build_extensions'
  /var/lib/gems/3.0.0/gems/bundler-2.3.22/lib/bundler/rubygems_gem_installer.rb:28:in `install'
  /var/lib/gems/3.0.0/gems/bundler-2.3.22/lib/bundler/source/rubygems.rb:207:in `install'
  /var/lib/gems/3.0.0/gems/bundler-2.3.22/lib/bundler/installer/gem_installer.rb:54:in `install'
  /var/lib/gems/3.0.0/gems/bundler-2.3.22/lib/bundler/installer/gem_installer.rb:16:in `install_from_spec'
  /var/lib/gems/3.0.0/gems/bundler-2.3.22/lib/bundler/installer/parallel_installer.rb:186:in `do_install'
  /var/lib/gems/3.0.0/gems/bundler-2.3.22/lib/bundler/installer/parallel_installer.rb:177:in `block in worker_pool'
  /var/lib/gems/3.0.0/gems/bundler-2.3.22/lib/bundler/worker.rb:62:in `apply_func'
  /var/lib/gems/3.0.0/gems/bundler-2.3.22/lib/bundler/worker.rb:57:in `block in process_queue'
  /var/lib/gems/3.0.0/gems/bundler-2.3.22/lib/bundler/worker.rb:54:in `loop'
  /var/lib/gems/3.0.0/gems/bundler-2.3.22/lib/bundler/worker.rb:54:in `process_queue'
  /var/lib/gems/3.0.0/gems/bundler-2.3.22/lib/bundler/worker.rb:91:in `block (2 levels) in create_threads'

An error occurred while installing psych (5.1.0), and Bundler cannot continue.

In Gemfile:
  sdoc was resolved to 3.0.0.alpha, which depends on
    rdoc was resolved to 6.5.0, which depends on
      psych

I understand it should work out of the box, right? or am I missing some dependency?

EDIT: when I try to check this file /tmp/bundler20230905-29261-na9i1epsych-5.1.0/extensions/x86_64-linux/3.0.0/psych-5.1.0/mkmf.log, it doesn't exist

[arielj]

I had to run apt-get install libyaml and now it's working.

EDIT: I see there's a PR adding libyaml #209 (I didn't need the other dependency so far)

[yahonda]

#211 has been merged to the master branch that should address this issue.

[yahonda]

I'm closing this issue because #211 should have taken care of it. Please let us know if this issue still exists.