Vagrant: "Configure Remote Ruby Interpreter" fails with "Can't create Ruby SDK - Communication Error"

Hello,

would it be possible to check how it goes in RubyMine 2019.2 Beta2? If the problem persists there could you please share your Vagrantfile so that I can check your setup as well?

Hello,

I will give it a shot on 2019.2 Beta2 and get back to you.

Hello again,

I tried adding the remote SDK again, this time on RubyMine 2019.2 Beta2.

RubyMine 2019.2 EAP
Build #RM-192.5728.47, built on July 16, 2019
RubyMine EAP User
Expiration date: August 15, 2019
Runtime version: 11.0.3+12-b304.10 amd64
VM: OpenJDK 64-Bit Server VM by JetBrains s.r.o
Linux 4.15.0-54-generic
GC: ParNew, ConcurrentMarkSweep
Memory: 725M
Cores: 4
Registry: ide.editor.tabs.open.at.the.end=true, debugger.watches.in.variables=false, ide.balloon.shadow.size=0
Non-Bundled Plugins: com.alayouni.ansiHighlight, com.vladsch.idea.multimarkdown

I still get an error, but the message/behavior has changed:

* when I try to browse through the directory structure I get "permission denied" at /usr/local. I have verified that the directory is accessible by the vagrant user.
* if I manually enter the path to the ruby command (/usr/local/rbenv/shims/ruby), then I get the error "Could not get RubyGems environment for Remote" (see screenshot), and the path mentioned looks strange (path of the Vagrantfile + absolute path within the VM)

My Vagrantfile (project name redacted):

Vagrant.configure('2') do |config|
  config.vm.box = 'centos/7'

  ssh_port = 22
  config.ssh.guest_port = ssh_port

  IP_ADDRESS = '192.168.56.145'
  config.vm.network "private_network", ip: IP_ADDRESS

  PROJECT_NAME = 'redacted'
  HOST_PORT = ENV.fetch("HOST_PORT", 3000).to_i

  config.vm.provider 'virtualbox' do |vb|
    # Customize the amount of memory on the VM:
    vb.customize ['modifyvm', :id, '--memory', '4048', '--cpus', '2', '--ioapic', 'on']
    # For Symbolic link
    vb.customize ["setextradata", :id, "VBoxInternal2/SharedFoldersEnableSymlinksCreate/v-root", "1"]
  end

  config.vm.synced_folder ".", "/vagrant", disabled: true
  config.vm.synced_folder(".", "/home/vagrant/redacted", type: "nfs")

  config.vm.network(:forwarded_port, guest: 3000, host: HOST_PORT)
end

Thanks, and kind regards

Tor

Have you installed rbenv manually there? Which mode did you use (which way of installing)?

I think it was installed manually there sometime in the past by the person who originally created this VM (I "inherited" the VM)

I've installed rbenv there and ruby 2.5.5, after that I managed to add a Vagrant SDK by specifying the path to the rbenv executable

vagrant@rails-dev-box:~$ which rbenv
/home/vagrant/.rbenv/bin/rbenv

I think I found the cause of the "permission error": There was a broken symlink inside /usr/local (bundle -> /root/vendor/bundle_export). This seems like a bug in the logic that parses the directory listing (in Rubymine). I believe a broken link should not make the whole directory become listed as "Permission Denied".

[vagrant@localhost local]$ ls -la .
total 0
drwxr-xr-x. 13 root root    158  4月 19 09:41 .
drwxr-xr-x. 13 root root    155  1月 29 06:12 ..
drwxr-xr-x.  2 root root     23  4月 19 09:42 bin
lrwxrwxrwx.  1 root root     26  4月 19 09:41 bundle -> /root/vendor/bundle_export
drwxr-xr-x.  2 root root      6  4月 11  2018 etc
drwxr-xr-x.  2 root root      6  4月 11  2018 games
drwxr-xr-x.  2 root root      6  4月 11  2018 include
drwxr-xr-x.  2 root root      6  4月 11  2018 lib
drwxr-xr-x.  2 root root      6  4月 11  2018 lib64
drwxr-xr-x.  2 root root      6  4月 11  2018 libexec
drwxr-sr-x. 12 root vagrant 278  2月  5 19:57 rbenv
drwxr-xr-x.  2 root root      6  4月 11  2018 sbin
drwxr-xr-x.  5 root root     49  1月 29 06:12 share
drwxr-xr-x.  2 root root      6  4月 11  2018 src

However, my main issue remains. I tried pointing RM to /usr/local/rbenv/bin/rbenv instead, but that gives me the error "No Rubies installed". 

Any way to get more specific error messages?

Could you please provide the output for `which rbenv`, `rbenv versions` and also share your idea.log (Help - Show log in)?

Some time has passed where I was a bit too busy to deal with this issue, but I'm back and would really like to get this to work. I have removed my RM folder (~/.Rubymine2019.2) and any .idea folders, and created a new project.I can now add the remote interpreter without seeing any errors, but the gems in the VM does not show up in the list, even if I click the synchronize button.

[vagrant@localhost <redacted>]$ bundle env
## Environment

```
Bundler 1.17.3
Platforms ruby, x86_64-linux
Ruby 2.5.3p105 (2018-10-18 revision 65156) [x86_64-linux]
Full Path /usr/local/bin/ruby
Config Dir /usr/local/etc
RubyGems 3.0.4
Gem Home /usr/local/lib/ruby/gems/2.5.0
Gem Path /home/vagrant/.gem/ruby/2.5.0:/usr/local/lib/ruby/gems/2.5.0
User Path /home/vagrant/.gem/ruby/2.5.0
Bin Dir /usr/local/bin
Tools 
Git 1.8.3.1
RVM not installed
rbenv not installed
chruby not installed
```

## Bundler Build Metadata

```
Built At 2019-06-14
Git SHA d7089abb6
Released Version false
```

## Bundler settings


with
Set for your local app (/home/vagrant/<redacted>/.bundle/config): [:itamae]


## Gemfile

### Gemfile

```ruby
source 'https://rubygems.org'
git_source(:github) { |repo| "https://github.com/#{repo}.git" }

ruby '~> 2.5.0'


<full gemfile contents abbreviated>

GEM
remote: https://rubygems.org/
remote: file:///tmp/<redacted>/gems/
specs:
actioncable (5.2.3)
<full list abbreviated by me>

PLATFORMS
  ruby

DEPENDENCIES
<full list abbreviated by me>


RUBY VERSION
   ruby 2.5.5p157

BUNDLED WITH
   1.17.3

> Could you please provide the output for `which rbenv`, `rbenv versions` and also share your idea.log (Help - Show log in)?

I am not currently using rbenv. Ruby is installed as follows:

mkdir -p ~/src
pushd ~/src
  rm -Rf ruby-2.5.3*
  wget https://cache.ruby-lang.org/pub/ruby/2.5/ruby-2.5.3.tar.gz
  tar zxf ruby-2.5.3.tar.gz
  cd ruby-2.5.3
  ./configure --disable-install-rdoc
  make
  sudo make install
popd
sudo gem update --system --no-document
sudo gem update -f rdoc --no-document
sudo gem update -f rake --no-document
sudo gem update -f bundler --no-document

OS: Centos 7 (in a Vagrant box)

Vagrantfile

# -*- mode: ruby -*-
# vi: set ft=ruby :

# All Vagrant configuration is done below. The "2" in Vagrant.configure
# configures the configuration version (we support older styles for
# backwards compatibility). Please don't change it unless you know what
# you're doing.
Vagrant.configure("2") do |config|
  HOST_PORT = ENV.fetch("HOST_PORT", 3000).to_i

  # The most common configuration options are documented and commented below.
  # For a complete reference, please see the online documentation at
  # https://docs.vagrantup.com.

  # Every Vagrant development environment requires a box. You can search for
  # boxes at https://vagrantcloud.com/search.
  config.vm.box = "centos/7"

  # Disable automatic box update checking. If you disable this, then
  # boxes will only be checked for updates when the user runs
  # `vagrant box outdated`. This is not recommended.
  # config.vm.box_check_update = false

  # Create a forwarded port mapping which allows access to a specific port
  # within the machine from a port on the host machine. In the example below,
  # accessing "localhost:8080" will access port 80 on the guest machine.
  # NOTE: This will enable public access to the opened port
  config.vm.network(:forwarded_port, guest: 3000, host: HOST_PORT)

  # Create a forwarded port mapping which allows access to a specific port
  # within the machine from a port on the host machine and only allow access
  # via 127.0.0.1 to disable public access
  # config.vm.network "forwarded_port", guest: 80, host: 8080, host_ip: "127.0.0.1"

  # Create a private network, which allows host-only access to the machine
  # using a specific IP.
  # config.vm.network "private_network", ip: "192.168.33.10"

  # Create a public network, which generally matched to bridged network.
  # Bridged networks make the machine appear as another physical device on
  # your network.
  # config.vm.network "public_network"

  # Share an additional folder to the guest VM. The first argument is
  # the path on the host to the actual folder. The second argument is
  # the path on the guest to mount the folder. And the optional third
  # argument is a set of non-required options.
  # config.vm.synced_folder "../data", "/vagrant_data"
config.vm.synced_folder ".", "/vagrant", disabled: true
config.vm.synced_folder ".", "/home/vagrant/<redacted>"

  # Provider-specific configuration so you can fine-tune various
  # backing providers for Vagrant. These expose provider-specific options.
  # Example for VirtualBox:
  #
  # config.vm.provider "virtualbox" do |vb|
  #   # Display the VirtualBox GUI when booting the machine
  #   vb.gui = true
  #
  #   # Customize the amount of memory on the VM:
  #   vb.memory = "1024"
  # end
  #
  # View the documentation for the provider you are using for more
  # information on available options.
  config.vm.provider "virtualbox" do |vb|
    vb.memory = "2048"
  end

  # Enable provisioning with a shell script. Additional provisioners such as
  # Puppet, Chef, Ansible, Salt, and Docker are also available. Please see the
  # documentation for more information about their specific syntax and use.
  # config.vm.provision "shell", inline: <<-SHELL
  #   apt-get update
  #   apt-get install -y apache2
  # SHELL
end

Below is the log from opening Rubymine, going to settings, selecting the remote interpreter and clicking the synchronize button:

2019-08-29 13:26:31,956 [ 0] INFO - #com.intellij.idea.Main - ------------------------------------------------------ IDE STARTED ------------------------------------------------------ 
2019-08-29 13:26:32,099 [ 143] INFO - #com.intellij.idea.Main - JNA library (64-bit) loaded in 97 ms 
2019-08-29 13:26:32,174 [ 218] INFO - #com.intellij.idea.Main - IDE: RubyMine (build #RM-192.6262.57, 20 Aug 2019 22:16) 
2019-08-29 13:26:32,174 [ 218] INFO - #com.intellij.idea.Main - OS: Linux (4.15.0-58-generic, amd64) 
2019-08-29 13:26:32,174 [ 218] INFO - #com.intellij.idea.Main - JRE: 11.0.3+12-b304.39 (JetBrains s.r.o) 
2019-08-29 13:26:32,174 [ 218] INFO - #com.intellij.idea.Main - JVM: 11.0.3+12-b304.39 (OpenJDK 64-Bit Server VM) 
2019-08-29 13:26:32,175 [ 219] INFO - #com.intellij.idea.Main - JVM Args: -Xms128m -Xmx1967m -XX:ReservedCodeCacheSize=240m -XX:+UseConcMarkSweepGC -XX:SoftRefLRUPolicyMSPerMB=50 -ea -XX:CICompilerCount=2 -Dsun.io.useCanonPrefixCache=false -Djava.net.preferIPv4Stack=true -Djdk.http.auth.tunneling.disabledSchemes="" -XX:+HeapDumpOnOutOfMemoryError -XX:-OmitStackTraceInFastThrow -Djdk.attach.allowAttachSelf -Dkotlinx.coroutines.debug=off -Dawt.useSystemAAFontSettings=lcd -Dsun.java2d.renderer=sun.java2d.marlin.MarlinRenderingEngine -Dsun.tools.attach.tmp.only=true -XX:ErrorFile=/home/tor/java_error_in_RUBYMINE_%p.log -XX:HeapDumpPath=/home/tor/java_error_in_RUBYMINE.hprof -Didea.paths.selector=RubyMine2019.2 -Djb.vmOptionsFile=/home/tor/.RubyMine2019.2/config/rubymine64.vmoptions -Didea.platform.prefix=Ruby 
2019-08-29 13:26:32,175 [ 219] INFO - #com.intellij.idea.Main - charsets: JNU=UTF-8 file=UTF-8 
2019-08-29 13:26:34,509 [ 2553] INFO - tellij.diagnostic.LoadingPhase - Reached SPLASH loading phase 
2019-08-29 13:26:34,515 [ 2559] INFO - plication.impl.ApplicationImpl - CPU cores: 4; ForkJoinPool.commonPool: java.util.concurrent.ForkJoinPool@2cbbba96[Running, parallelism = 3, size = 0, active = 0, running = 0, steals = 0, tasks = 0, submissions = 0]; factory: com.intellij.concurrency.IdeaForkJoinWorkerThreadFactory@335b611b 
2019-08-29 13:26:34,642 [ 2686] INFO - .intellij.idea.IdeaApplication - WM detected: Compiz 
2019-08-29 13:26:34,971 [ 3015] INFO - llij.ide.plugins.PluginManager - Plugin 'Configuration Script' can't be loaded because: Plugin does not include any module dependency tags in its plugin.xml therefore is assumed legacy and can be loaded only in IntelliJ IDEA 
2019-08-29 13:26:34,971 [ 3015] INFO - llij.ide.plugins.PluginManager - Plugin 'Native Debug for IntelliJ' can't be loaded because: Plugin does not include any module dependency tags in its plugin.xml therefore is assumed legacy and can be loaded only in IntelliJ IDEA 
2019-08-29 13:26:35,043 [ 3087] INFO - llij.ide.plugins.PluginManager - Loaded bundled plugins: CSS (192.6262.57), CoffeeScript (192.6262.57), Database Tools and SQL (192.6262.57), Docker (192.6262.57), EditorConfig (192.6262.57), Gherkin (192.6262.57), Git (192.6262.57), HTML Tools (192.6262.57), HTTP Client (192.6262.57), Haml (192.6262.57), IDE Settings Sync (192.6262.57), IDEA CORE (192.6262.57), IntelliLang (192.6262.57), JavaScript Debugger (192.6262.57), JavaScript Intention Power Pack (192.6262.57), JavaScript and TypeScript (192.6262.57), Less (192.6262.57), Markdown (192.6262.57), Performance Testing (192.6262.57), Puppet (192.6262.57), Remote Hosts Access (192.6262.57), Ruby CSS Support Integration (192.6262.57), Ruby Code Coverage (192.6262.57), Ruby Cucumber support (192.6262.57), Ruby Database Support Integration (192.6262.57), Ruby Docker (192.6262.57), Ruby Haml Support Integration (192.6262.57), Ruby I18n Support Integration (192.6262.57), Ruby JavaScript Debugger Integration (192.6262.57), Ruby Performance Testing (192.6262.57), Ruby Puppet Support Integration (192.6262.57), Ruby Remote SDK Support (192.6262.57), Ruby Slim Support Integration (192.6262.57), Ruby UML Support Integration (192.6262.57), SSH Remote Run (192.6262.57), Sass (192.6262.57), Settings Repository (192.6262.57), Shell Script (192.6262.57), Slim (192.6262.57), Stylus (192.6262.57), Task Management (192.6262.57), Terminal (192.6262.57), TextMate bundles (192.6262.57), Time Tracking (192.6262.57), UML (192.6262.57), Vagrant (192.6262.57), YAML (192.6262.57), tslint (192.6262.57) 
2019-08-29 13:26:35,043 [ 3087] INFO - llij.ide.plugins.PluginManager - Disabled plugins: Configuration Script (192.6262.57), GitHub (192.6262.57), Mercurial (192.6262.57), Native Debug for IntelliJ (192.6262.57), Perforce (192.6262.57), Subversion (192.6262.57) 
2019-08-29 13:26:35,446 [ 3490] INFO - cloudConfig.CloudConfigManager - === Start: JBA_NOT_CONNECTED === 
2019-08-29 13:26:35,495 [ 3539] INFO - tellij.diagnostic.LoadingPhase - Reached CONFIGURATION_STORE_INITIALIZED loading phase 
2019-08-29 13:26:35,614 [ 3658] INFO - ellij.util.io.PagedFileStorage - lower=100; upper=500; buffer=10; max=1914 
2019-08-29 13:26:35,713 [ 3757] INFO - pl.local.NativeFileWatcherImpl - Starting file watcher: /home/tor/local/rubymine/bin/fsnotifier64 
2019-08-29 13:26:35,742 [ 3786] INFO - pl.local.NativeFileWatcherImpl - Native file watcher is operational. 
2019-08-29 13:26:36,708 [ 4752] INFO - til.net.ssl.CertificateManager - Default SSL context initialized 
2019-08-29 13:26:36,755 [ 4799] INFO - tellij.ide.SystemHealthMonitor - restored ignored PIPE handler 
2019-08-29 13:26:36,777 [ 4821] INFO - rains.ide.BuiltInServerManager - built-in server started, port 63342 
2019-08-29 13:26:37,130 [ 5174] INFO - il.indexing.FileBasedIndexImpl - File index extensions iterated:153 
2019-08-29 13:26:37,521 [ 5565] WARN - com.intellij.util.xmlb.Binding - no accessors for class org.jetbrains.plugins.ruby.version.management.system.RubySystemData 
2019-08-29 13:26:37,844 [ 5888] INFO - pl$FileIndexDataInitialization - Initialization done:867 
2019-08-29 13:26:37,995 [ 6039] INFO - exImpl$StubIndexInitialization - Initialization done:150 
2019-08-29 13:26:38,164 [ 6208] INFO - j.ide.ui.OptionsTopHitProvider - 40 ms spent to cache options in application 
2019-08-29 13:26:38,320 [ 6364] INFO - tellij.diagnostic.LoadingPhase - Reached FRAME_SHOWN loading phase 
2019-08-29 13:26:39,039 [ 7083] INFO - penapi.wm.impl.GlobalMenuLinux - Appeared dbus-service 'com.canonical.AppMenu.Registrar' 
2019-08-29 13:26:39,416 [ 7460] INFO - penapi.wm.impl.GlobalMenuLinux - created instance of GlobalMenuLinux for xid=0x3200026 
2019-08-29 13:26:39,515 [ 7559] INFO - penapi.wm.impl.GlobalMenuLinux - new window info: xid=0x3200026 menuPath='/com/canonical/menu/0x3200026' registrar=0x0x7fc260ba7de0 server=0x0x7fc24038e3e0 menuroot=0x0x7fc254016740 
2019-08-29 13:26:40,629 [ 8673] INFO - pl.projectlevelman.NewMappings - VCS Root: [Git] - [/home/tor/work/nacl/<redacted>/repos/<redacted>] 
2019-08-29 13:26:41,061 [ 9105] INFO - com.intellij.ide.ui.UISettings - Loaded: fontSize=12, fontScale=1.0; restored: fontSize=12, fontScale=1.0 
2019-08-29 13:26:41,083 [ 9127] WARN - s.impl.EditorColorsManagerImpl - Cannot find scheme: VibrantInk from plugin: com.intellij.database 
2019-08-29 13:26:41,083 [ 9127] WARN - s.impl.EditorColorsManagerImpl - Cannot find scheme: WarmNeon from plugin: com.intellij.database 
2019-08-29 13:26:41,083 [ 9127] WARN - s.impl.EditorColorsManagerImpl - Cannot find scheme: High сontrast from plugin: com.intellij.database 
2019-08-29 13:26:41,927 [ 9971] INFO - j.ide.script.IdeStartupScripts - 0 startup script(s) found 
2019-08-29 13:26:42,267 [ 10311] INFO - rojectCodeStyleSettingsManager - Initialized from default code style settings. 
2019-08-29 13:26:43,785 [ 11829] INFO - PerformancePlugin - Performance Plugin is in silent mode 
2019-08-29 13:26:44,132 [ 12176] INFO - pl.ProjectRootManagerComponent - project roots have changed 
2019-08-29 13:26:44,390 [ 12434] INFO - .diagnostic.PerformanceWatcher - Pushing JS language level to 6 libraries took 350ms; general responsiveness: ok; EDT responsiveness: ok 
2019-08-29 13:26:44,401 [ 12445] INFO - .diagnostic.PerformanceWatcher - Pushing JS language level to 6 libraries took 9ms; general responsiveness: ok; EDT responsiveness: ok 
2019-08-29 13:26:44,543 [ 12587] INFO - llij.database.util.SqlDialects - SQL dialects initialized in 25 ms 
2019-08-29 13:26:45,361 [ 13405] INFO - .diagnostic.PerformanceWatcher - Pushing properties took 885ms; general responsiveness: ok; EDT responsiveness: ok 
2019-08-29 13:26:46,866 [ 14910] INFO - ge.ExternalProjectsDataStorage - Load external projects data in 8 millis (read time: 7) 
2019-08-29 13:26:47,062 [ 15106] INFO - j.ide.ui.OptionsTopHitProvider - 749 ms spent to cache options in project 
2019-08-29 13:26:47,082 [ 15126] INFO - .diagnostic.PerformanceWatcher - Post-startup activities under progress took 2927ms; general responsiveness: ok; EDT responsiveness: 0/2 sluggish, 1/2 very slow 
2019-08-29 13:26:47,980 [ 16024] INFO - cloudConfig.CloudConfigManager - === Start.updateInitStatus === 
2019-08-29 13:26:47,986 [ 16030] INFO - cloudConfig.CloudConfigManager - === StatusBar.update create === 
2019-08-29 13:26:47,987 [ 16031] INFO - cloudConfig.CloudConfigManager - === calculateInitStatus === 
2019-08-29 13:26:48,215 [ 16259] INFO - .diagnostic.PerformanceWatcher - Indexable file iteration took 2852ms; general responsiveness: ok; EDT responsiveness: 0/3 sluggish, 3/3 very slow 
2019-08-29 13:26:48,223 [ 16267] INFO - indexing.UnindexedFilesUpdater - Unindexed files update started: 23 files to update 
2019-08-29 13:26:48,994 [ 17038] INFO - .cloudConfig.CloudConfigClient - === Get cloud config URL: https://cloudconfig.jetbrains.com/cloudconfig/files === 
2019-08-29 13:26:49,664 [ 17708] INFO - tartup.impl.StartupManagerImpl - /home/tor/work/nacl/<redacted>/repos/<redacted>/.idea case-sensitivity: expected=true actual=true 
2019-08-29 13:26:49,675 [ 17719] INFO - tellij.diagnostic.LoadingPhase - Reached PROJECT_OPENED loading phase 
2019-08-29 13:26:49,696 [ 17740] INFO - #git4idea.commands.GitHandler - [.] git version 
2019-08-29 13:26:49,704 [ 17748] INFO - #git4idea.commands.GitHandler - git version 2.7.4 
2019-08-29 13:26:49,712 [ 17756] INFO - ea.config.GitExecutableManager - Git version for /usr/bin/git : 2.7.4 
2019-08-29 13:26:49,977 [ 18021] INFO - Json.PackageJsonUpdateNotifier - processPackageJsonFiles [file:///home/tor/work/nacl/<redacted>/repos/<redacted>/package.json] 
2019-08-29 13:26:50,181 [ 18225] INFO - cloudConfig.CloudConfigManager - === calculateInitStatus.value: JBA_NOT_CONNECTED === 
2019-08-29 13:26:50,908 [ 18952] INFO - son.PackageVersionRangeMatcher - Matching 6 done in 437 ms 
2019-08-29 13:26:51,330 [ 19374] INFO - .diagnostic.PerformanceWatcher - Unindexed files update took 3107ms; general responsiveness: ok; EDT responsiveness: ok 
2019-08-29 13:26:51,549 [ 19593] INFO - ment.rvm.LocalRvmPathsSettings - RVM installation wasn't detected. 
2019-08-29 13:26:51,550 [ 19594] INFO - .diagnostic.PerformanceWatcher - Pushing properties took 91ms; general responsiveness: ok; EDT responsiveness: ok 
2019-08-29 13:26:51,564 [ 19608] INFO - tor.impl.FileEditorManagerImpl - Project opening took 11684 ms 
2019-08-29 13:26:51,568 [ 19612] INFO - .diagnostic.PerformanceWatcher - Indexable file iteration took 18ms; general responsiveness: ok; EDT responsiveness: ok 
2019-08-29 13:26:51,568 [ 19612] INFO - indexing.UnindexedFilesUpdater - Unindexed files update started: 1 files to update 
2019-08-29 13:26:51,736 [ 19780] INFO - cloudConfig.CloudConfigManager - === End.updateInitStatus === 
2019-08-29 13:26:53,466 [ 21510] INFO - .diagnostic.PerformanceWatcher - Unindexed files update took 1898ms; general responsiveness: ok; EDT responsiveness: ok 
2019-08-29 13:26:54,219 [ 22263] INFO - .script.IdeScriptEngineManager - javax.script.ScriptEngineManager initialized in 795 ms 
2019-08-29 13:26:54,697 [ 22741] INFO - ings.impl.UpdateCheckerService - channel: release 
2019-08-29 13:26:54,951 [ 22995] INFO - tellij.diagnostic.LoadingPhase - Reached INDEXING_FINISHED loading phase 
2019-08-29 13:26:55,021 [ 23065] INFO - cloudConfig.CloudConfigManager - === StatusBar.start another widget: com.intellij.cloudConfig.StatusBarInfoManager$InfoComponent@3f495e41 === 
2019-08-29 13:26:57,419 [ 25463] INFO - pl.ProjectRootManagerComponent - project roots have changed 
2019-08-29 13:26:57,613 [ 25657] INFO - .diagnostic.PerformanceWatcher - Pushing JS language level to 6 libraries took 3ms; general responsiveness: ok; EDT responsiveness: ok 
2019-08-29 13:26:57,645 [ 25689] INFO - .diagnostic.PerformanceWatcher - Pushing properties took 83ms; general responsiveness: ok; EDT responsiveness: ok 
2019-08-29 13:26:57,657 [ 25701] INFO - .diagnostic.PerformanceWatcher - Indexable file iteration took 11ms; general responsiveness: ok; EDT responsiveness: ok 
2019-08-29 13:26:57,738 [ 25782] INFO - e.GemRequirementsChangeWatcher - Initial scan started 
2019-08-29 13:26:58,460 [ 26504] INFO - e.GemRequirementsChangeWatcher - Initial scan took: 722 ms 
2019-08-29 13:27:29,014 [ 57058] INFO - byRemoteInterpreterManagerImpl - Uploading helpers for Remote: ruby-2.5.3-p105: ver.2.5.3p105 ( revision 65156) p105 (vagrant:///home/tor/work/nacl/<redacted>/repos/<redacted>/usr/local/bin/ruby) at Thread[AWT-EventQueue-0 2019.2.1#RM-192.6262.57 RubyMine, eap:false, os:Linux 4.15.0-58-generic, java-version:JetBrains s.r.o 11.0.3+12-b304.39 2019.2.1#RM-192.6262.57 RubyMine, eap:false, os:Linux 4.15.0-58-generic, java-version:JetBrains s.r.o 11.0.3+12-b304.39,6,Idea Thread Group] 
2019-08-29 13:27:31,486 [ 59530] INFO - port.random.BouncyCastleRandom - Generating random seed from SecureRandom. 
2019-08-29 13:27:31,607 [ 59651] WARN - om.intellij.ssh.impl.sshj.sshj - Unsupported options in config: [HashKnownHosts=no, compression.s2c=zlib,none] 
2019-08-29 13:27:31,688 [ 59732] INFO - z.sshj.transport.TransportImpl - Client identity string: SSH-2.0-SSHJ_0.27.0 
2019-08-29 13:27:31,697 [ 59741] INFO - z.sshj.transport.TransportImpl - Server identity string: SSH-2.0-OpenSSH_7.4 
2019-08-29 13:27:31,973 [ 60017] INFO - y.remote.RubySshRemoteTransfer - Uploading helpers 
2019-08-29 13:27:31,990 [ 60034] INFO - #com.intellij.ssh.RSyncUtil - rsync version: rsync version 3.1.1 protocol version 31 
2019-08-29 13:27:32,649 [ 60693] WARN - ution.process.OSProcessHandler - Process has been already terminated: /usr/bin/rsync -zarv -e "ssh -p 2222 -i /home/tor/work/nacl/<redacted>/repos/<redacted>/.vagrant/machines/default/virtualbox/private_key" --log-file=null /home/tor/local/RubyMine-2019.2/rb vagrant@127.0.0.1:/home/vagrant/.rubymine_helpers/ 
2019-08-29 13:27:32,679 [ 60723] WARN - byRemoteInterpreterManagerImpl - Remote Host Identification has changed 
com.intellij.ssh.SshRemoteHostIdentificationHasChangedException: Remote Host Identification has changed
at com.intellij.ssh.RSyncUtil$2.onTextAvailable(RSyncUtil.java:213)
at jdk.internal.reflect.GeneratedMethodAccessor108.invoke(Unknown Source)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.base/java.lang.reflect.Method.invoke(Method.java:566)
at com.intellij.execution.process.ProcessHandler$2.invoke(ProcessHandler.java:214)
at com.sun.proxy.$Proxy24.onTextAvailable(Unknown Source)
at com.intellij.execution.process.ProcessHandler.notifyTextAvailable(ProcessHandler.java:188)
at com.intellij.execution.process.BaseOSProcessHandler$SimpleOutputReader.onTextAvailable(BaseOSProcessHandler.java:179)
at com.intellij.util.io.BaseOutputReader.sendText(BaseOutputReader.java:211)
at com.intellij.util.io.BaseOutputReader.processInput(BaseOutputReader.java:195)
at com.intellij.util.io.BaseOutputReader.readAvailableBlocking(BaseOutputReader.java:149)
at com.intellij.util.io.BaseDataReader.readAvailable(BaseDataReader.java:77)
at com.intellij.util.io.BaseDataReader.doRun(BaseDataReader.java:155)
at com.intellij.util.ConcurrencyUtil.runUnderThreadName(ConcurrencyUtil.java:208)
at com.intellij.util.io.BaseDataReader.lambda$start$0(BaseDataReader.java:61)
at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:515)
at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
at java.base/java.lang.Thread.run(Thread.java:834)
2019-08-29 13:27:33,218 [ 61262] INFO - byRemoteInterpreterManagerImpl - Updating gems for Remote: ruby-2.5.3-p105: ver.2.5.3p105 ( revision 65156) p105 (vagrant:///home/tor/work/nacl/<redacted>/repos/<redacted>/usr/local/bin/ruby) 
2019-08-29 13:27:33,232 [ 61276] INFO - y.remote.RubySshRemoteTransfer - Updating gems' local copy 
2019-08-29 13:27:33,263 [ 61307] INFO - #com.intellij.ssh.RSyncUtil - rsync version: rsync version 3.1.1 protocol version 31 
2019-08-29 13:27:33,293 [ 61337] INFO - #com.intellij.ssh.RSyncUtil - rsync version: rsync version 3.1.1 protocol version 31 
2019-08-29 13:27:33,893 [ 61937] INFO - byRemoteInterpreterManagerImpl - Gems for Remote: ruby-2.5.3-p105: ver.2.5.3p105 ( revision 65156) p105 (vagrant:///home/tor/work/nacl/<redacted>/repos/<redacted>/usr/local/bin/ruby) updated 
2019-08-29 13:27:33,893 [ 61937] INFO - byRemoteInterpreterManagerImpl - Starting roots refresh for Remote: ruby-2.5.3-p105: ver.2.5.3p105 ( revision 65156) p105 (vagrant:///home/tor/work/nacl/<redacted>/repos/<redacted>/usr/local/bin/ruby) (12 roots) 
2019-08-29 13:27:33,926 [ 61970] INFO - byRemoteInterpreterManagerImpl - Roots refreshed for Remote: ruby-2.5.3-p105: ver.2.5.3p105 ( revision 65156) p105 (vagrant:///home/tor/work/nacl/<redacted>/repos/<redacted>/usr/local/bin/ruby) (12 roots); Refreshing gems; 
2019-08-29 13:27:35,338 [ 63382] INFO - pl.ProjectRootManagerComponent - project roots have changed 
2019-08-29 13:27:35,569 [ 63613] INFO - pl.ProjectRootManagerComponent - project roots have changed 
2019-08-29 13:27:35,582 [ 63626] INFO - .diagnostic.PerformanceWatcher - Pushing JS language level to 6 libraries took 58ms; general responsiveness: ok; EDT responsiveness: ok 
2019-08-29 13:27:35,747 [ 63791] INFO - .diagnostic.PerformanceWatcher - Pushing JS language level to 6 libraries took 2ms; general responsiveness: ok; EDT responsiveness: ok 
2019-08-29 13:27:36,023 [ 64067] INFO - .diagnostic.PerformanceWatcher - Pushing properties took 161ms; general responsiveness: ok; EDT responsiveness: ok 
2019-08-29 13:27:36,056 [ 64100] INFO - .channel.direct.SessionChannel - Will request `sftp` subsystem 
2019-08-29 13:27:36,117 [ 64161] INFO - .diagnostic.PerformanceWatcher - Indexable file iteration took 93ms; general responsiveness: ok; EDT responsiveness: ok 
2019-08-29 13:27:36,118 [ 64162] INFO - indexing.UnindexedFilesUpdater - Unindexed files update started: 1 files to update 
2019-08-29 13:27:36,369 [ 64413] INFO - rationStore.ComponentStoreImpl - Saving appProjectJdkTable took 19 ms 
2019-08-29 13:27:36,586 [ 64630] INFO - mponents.impl.stores.StoreUtil - saveProjectsAndApp took 553 ms 
2019-08-29 13:27:36,722 [ 64766] INFO - rationStore.ComponentStoreImpl - Saving appFileTypeManager took 16 ms 
2019-08-29 13:27:36,785 [ 64829] INFO - mponents.impl.stores.StoreUtil - saveProjectsAndApp took 198 ms 
2019-08-29 13:27:36,797 [ 64841] INFO - .diagnostic.PerformanceWatcher - Unindexed files update took 678ms; general responsiveness: ok; EDT responsiveness: ok 
2019-08-29 13:27:44,761 [ 72805] INFO - rationStore.ComponentStoreImpl - Saving appGemManagerSettings took 52 ms 
2019-08-29 13:27:44,917 [ 72961] INFO - rationStore.ComponentStoreImpl - Saving Project '/home/tor/work/nacl/<redacted>/repos/<redacted>' <redacted>XDebuggerManager took 13 ms, editorHistoryManager took 15 ms 
2019-08-29 13:27:44,961 [ 73005] WARN - ext.RubyScriptExecutionContext - Unable to run gem 'spring'. Cannot find 'spring' 
2019-08-29 13:27:45,064 [ 73108] INFO - z.sshj.transport.TransportImpl - Disconnected - BY_APPLICATION 
2019-08-29 13:27:45,074 [ 73118] INFO - stubs.SerializationManagerImpl - START StubSerializationManager SHUTDOWN 
2019-08-29 13:27:45,075 [ 73119] INFO - stubs.SerializationManagerImpl - END StubSerializationManager SHUTDOWN 
2019-08-29 13:27:45,075 [ 73119] INFO - il.indexing.FileBasedIndexImpl - START INDEX SHUTDOWN 
2019-08-29 13:27:45,138 [ 73182] INFO - il.indexing.FileBasedIndexImpl - END INDEX SHUTDOWN 
2019-08-29 13:27:45,141 [ 73185] INFO - org.jetbrains.io.BuiltInServer - web server stopped 
2019-08-29 13:27:45,149 [ 73193] INFO - Types.impl.FileTypeManagerImpl - FileTypeManager: 149 auto-detected files
Elapsed time on auto-detect: 152 ms 
2019-08-29 13:27:45,163 [ 73207] INFO - newvfs.persistent.PersistentFS - VFS dispose started 
2019-08-29 13:27:45,176 [ 73220] INFO - newvfs.persistent.PersistentFS - VFS dispose completed 
2019-08-29 13:27:45,209 [ 73253] INFO - pl.local.NativeFileWatcherImpl - Watcher terminated with exit code 0 
2019-08-29 13:27:45,214 [ 73258] INFO - #com.intellij.idea.Main - ------------------------------------------------------ IDE SHUTDOWN ------------------------------------------------------ 
2019-08-29 13:27:45,217 [ 73261] INFO - org.jetbrains.io.BuiltInServer - web server stopped 

Okay, good news: I notice an error message appearing:

13:32 Remote Host Identification has changed
Check file known_hosts

I tried moving the known_hosts file and now the gems are synced!

I am still curious as to what caused my original problems. Perhaps having multiple Vagrantfiles (I was moving code between two applications)..?

Anyway my problem seems solved for now. I will open a new issue if needed. Thanks for your help so far.