Rails bundle install doesn't work 'cause json version error - ruby

I just wanted to convert from ImageMagick v7 to ImageMagick v6.
while doing that, this error was happened.
bundle install doesn't work correctly.
It seems like json version is something wrong.
How do I fix this error?
Environment below
ruby 2.3.1p112 (2016-04-26 revision 54768) [x86_64-darwin17]
Rails -v (couldn't find gem) (becuase bundle install can't work)
json list / json (default: 1.8.3)
multi_json (1.13.1, 1.11.2, 1.11.0)
Bundler version 1.16.4
Mac Mojave 10.14
when I do bundle install on terminal, then I got this error
Fetching gem metadata from https://rubygems.org/........
Fetching gem metadata from https://rubygems.org/.
Resolving dependencies.......
Using rake 12.3.2
Using concurrent-ruby 1.1.4
Using i18n 0.9.5
Fetching json 1.8.6
Installing json 1.8.6 with native extensions
Errno::EPERM: Operation not permitted # chmod_internal -
/Users/***/projects/***/vendor/bundle/ruby/2.3.0/gems/json-1.8.6/tests/test_json.rb
An error occurred while installing json (1.8.6), and Bundler cannot continue.
Make sure that `gem install json -v '1.8.6' --source
'https://rubygems.org/'` succeeds before bundling.
In Gemfile:
rails was resolved to 4.2.6, which depends on
actionmailer was resolved to 4.2.6, which depends on
actionpack was resolved to 4.2.6, which depends on
actionview was resolved to 4.2.6, which depends on
rails-dom-testing was resolved to 1.0.9, which depends on
rails-deprecated_sanitizer was resolved to 1.0.3, which depends on
activesupport was resolved to 4.2.6, which depends on
json
I tried to do like this because error statement says Make sure that
gem install json -v '1.8.6' --source 'https://rubygems.org/' succeeds before bundling
but result shows like this
ERROR: While executing gem ... (Errno::EPERM)
Operation not permitted # chmod_internal - /Users/***/.rbenv/versions/2.3.1/lib/ruby/gems/2.3.0/gems/json-1.8.6/tests/test_json.rb
I can't understand this error statement
Errno::EPERM: Operation not permitted # chmod_internal -
Also, I goggled a lot, then I update commandlinetool follow this
https://howchoo.com/g/m2u0mmuwzda/macos-mojave-fix-invalid-active-developer-path
then, I did this command again,
sudo gem install json -v '1.8.6' --source 'https://rubygems.org/'
then, it's completely succeded like this.
Building native extensions. This could take a while...
Successfully installed json-1.8.6
Parsing documentation for json-1.8.6
Installing ri documentation for json-1.8.6
Done installing documentation for json after 1 seconds
1 gem installed
But, if I do bundle install, still doesn't work: they show same error.

My recommendation is if possible to start fresh. Maybe your rbenv was not installed correctly, try reinstalling it, I suggest using brew install rbenv https://github.com/rbenv/rbenv#homebrew-on-macos
Make sure to add the eval "$(rbenv init -)" to your ~/.bash_profile then open a new terminal.
Navigate to the project directory and install the Ruby version you need: rbenv install 2.3.1
You can make sure you are using that version by issuing rbenv use 2.3.1 and ruby --version.
Now install bundler for that Ruby version, I suggest 1.17.3 for now (the latest before 2.0.1) gem install bundler -v '1.17.3'.
You should be ready to bundle install.
The most common scenario I see for a message Installing ... with native extensions to result in errors is usually due to the lack of binaries, header files and C related code to build that native extension, in your case the issue is due to permissions, hence why I am suggesting some fresh installation.

I second #Danilo Cabello's recommendation to start fresh if you can. I just have a few other trouble-shooting ideas:
The fact that your bundle is installing gems in /vendor/bundle means that at some point, you must have specified the path with bundle install --path vendor/bundle as #mogbee alludes to. That path flag will load files associated with your gems into vendor/bundle instead of your system gem location. You might have done that if you're trying to keep the project's gems separate from any other project, but if not, you will need to update your bundler's gem path.
To do this, first, check for any issues by running bundle doctor. If no issues are found, check your bundle configuration with bundle env. Make sure that your RubyGems Gem Home and Gem Path are routed through .rbenv, so they should match and look like /Users/***/.rbenv/versions/2.3.1/lib/ruby/gems/2.3.0. If they don't match, run the rbenv-doctor command below which should make sure your rbenv installation exported the path properly.
If the output of bundle env tells you that you're actually running an older version of bundler (older than 1.16.4), I would definitely update, and would recommend version 1.17.3 as #Danilo Cabello did.
Second, I would run this rbenv-doctor curl command to check the status of your rbenv install: curl -fsSL https://github.com/rbenv/rbenv-installer/raw/master/bin/rbenv-doctor | bash (https://github.com/rbenv/rbenv-installer#rbenv-doctor).
Third, depending on the output of ls -l within your project folder, you may also want to recursively change owner/group for your ~/.rbenv folder to make sure everything is owned by you and not root (https://superuser.com/questions/260925/how-can-i-make-chown-work-recursively/260939#260939)

Related

Issues serving Jekyll to localhost, eventmachine 1.2.7 has an error when installing

Not sure what to do to specifically fix this problem, googled and nothing solved my question. When I try to:
bundle exec jekyll serve
I get told:
Could not find eventmachine-1.2.7 in any of the sources
Run `bundle install` to install missing gems.
Then I:
bundle install
Only to get this:
Installing eventmachine 1.2.7 with native extensions
Gem::Ext::BuildError: ERROR: Failed to build gem native extension.
current directory: /private/var/folders/7f/2c2swwc1153899dmr8781_x40000gn/T/bundler20201130-34411-1lzt2fceventmachine-1.2.7/gems/eventmachine-1.2.7/ext
/System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/bin/ruby -I /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/2.6.0 -r
./siteconf20201130-34411-pd54nh.rb extconf.rb
mkmf.rb can't find header files for ruby at /System/Library/Frameworks/Ruby.framework/Versions/2.6/usr/lib/ruby/include/ruby.h
You might have to install separate package for the ruby development
environment, ruby-dev or ruby-devel for example.
extconf failed, exit code 1
Gem files will remain installed in /var/folders/7f/2c2swwc1153899dmr8781_x40000gn/T/bundler20201130-34411-1lzt2fceventmachine-1.2.7/gems/eventmachine-1.2.7 for
inspection.
Results logged to
/var/folders/7f/2c2swwc1153899dmr8781_x40000gn/T/bundler20201130-34411-1lzt2fceventmachine-1.2.7/extensions/universal-darwin-20/2.6.0/eventmachine-1.2.7/gem_make.out
An error occurred while installing eventmachine (1.2.7), and Bundler cannot continue.
Make sure that `gem install eventmachine -v '1.2.7' --source 'https://rubygems.org/'` succeeds before bundling.
In Gemfile:
minima was resolved to 2.5.1, which depends on
jekyll-feed was resolved to 0.13.0, which depends on
jekyll was resolved to 4.0.0, which depends on
em-websocket was resolved to 0.5.1, which depends on
eventmachine
Where am I going wrong here? Just updated to macOS 11.0.1, this is my first time trying to serve jekyll since the update. Thanks y'all!
Just try:
gem install eventmachine -v '1.2.7' -- --with-cppflags=-I/usr/local/opt/openssl/include
I had the same problem on Big Sur and this solution worked perfectly:
How to fix Jekyll after upgrading to MacOS 11 (Big Sur)
Download XCODE 12 beta from here and copy it to the Applications folder.
Then follow these steps to install rbenv.
git clone https://github.com/rbenv/rbenv.git ~/.rbenv
cd ~/.rbenv && src/configure && make -C src
Add ~/.rbenv/bin to your $PATH for access to the rbenv command-line utility. see: https://github.com/rbenv/rbenv#basic-github-checkout
xcode-select --switch /Applications/Xcode-beta.app/Contents/Developer
Now in your Jekyll project's root, you should be able to run bundle install and it should install all missing dependencies and should work now.
I didn't have to build ruby or install XCode. While Jekyll requires Ruby 2.4.0 or higher and Big Sur comes with 2.6.3, I followed Jekyll's instructions to install the latest version of Ruby.
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
brew install ruby
Add Ruby to your shell configuration in .bash_profile.
PATH="/usr/local/opt/ruby/bin:$PATH"
export PATH
Install bundler. I had to upgrade to Jekyll 4.2 from 4.0, and install webrick which is no longer a default gem with Ruby 3.0. If Jekyll is installed globally, then install it, webrick, and any other gems, like jekyll-paginate, too.
gem install --user-install bundler jekyll
Add the gems path to your shell configuration in .bash_profile, replacing X.X with with first two digits of the Ruby version.
PATH="$HOME/.gem/ruby/X.X.0/bin:$PATH"
export PATH

gem install bson_ext issues

I am running genghisapp - the gem for Mongo management. When I run it it gives me a warning that the native BSON extension was not loaded and suggest I run gem install bson_ext.
I have recently installed rbenv and have my gems such as genghisapp installed in ~/.gem which is on my path and loads fine.
My first attempt was to run gem install bson_ext but after restarting mongo/shell had no effect - the message is still there.
I then suspected this was not a genghisapp message but a Mongo one so thought I might need to install this as sudo. However this resulted in breaking my rbenv install due to permissions being now set to root/whatever because I was still using the local rbenv gem.
What is the proper way to solve this? Should I find the OSX gem and call its full path to install or do I need to specify something else?
The issue is because a) the version of mongo and bson_ext must match and b) there must not be any other bson_ext version installed.
The comments on this issue helped me solved the issue.
Run: gem list | grep -w 'bson\|bson_ext\|mongo' which will print out all the versions. It should look like:
bson (1.9.2)
bson_ext (1.9.2)
mongo (1.9.2)
And not like:
bson (2.3.0, 1.10.2, 1.9.2)
bson_ext (1.10.2, 1.9.2)
mongo (1.10.2, 1.9.2)
If so, (de)install versions as necessary.

Bundler installing gem that's already installed

I believe I'm misunderstanding the way bundler works, but from the bundle install documentation it seems to indicate bundler will use locally installed system gems.
...
--system: Install to the system location ($BUNDLE_PATH or $GEM_HOME) even if the bundle was previously installed somewhere else for this application
...
The --system option is the default. Pass it to switch back after using the --path option as described below.
I'm not using rbenv/rvm or any other Ruby version manager. I'm using ChefDK as my primary development environment, which ships with Ruby and a bunch of preinstalled gems.
The full contents of the Gemfile, there is no Gemfile.lock yet.
source 'https://rubygems.org'
gem 'nokogiri', '1.6.3.1'
Local nokogiri installed
$ gem list --local | grep nokogiri
nokogiri (1.6.6.2, 1.6.3.1, 1.5.5)
System Gem location has nokogiri 1.6.3.1 installed
$ echo $GEM_HOME
/Users/arthur/.chefdk/gem/ruby/2.1.0
$ find /Users/arthur/.chefdk/gem/ruby/2.1.0 | grep nokogiri | grep 1.6.3.1
/Users/arthur/.chefdk/gem/ruby/2.1.0/cache/nokogiri-1.6.3.1.gem
/Users/arthur/.chefdk/gem/ruby/2.1.0/extensions/x86_64-darwin-12/2.1.0/nokogiri-1.6.3.1
/Users/arthur/.chefdk/gem/ruby/2.1.0/extensions/x86_64-darwin-12/2.1.0/nokogiri-1.6.3.1/mkmf.log
/Users/arthur/.chefdk/gem/ruby/2.1.0/gems/nokogiri-1.6.3.1
/Users/arthur/.chefdk/gem/ruby/2.1.0/gems/nokogiri-1.6.3.1/.autotest
/Users/arthur/.chefdk/gem/ruby/2.1.0/gems/nokogiri-1.6.3.1/.editorconfig
...
However, when I run a bundle install, it tries to install and compile libxml2 for nokogiri.
$ bundle install
Fetching gem metadata from https://rubygems.org/.........
Resolving dependencies...
Using mini_portile 0.6.0
Building nokogiri using packaged libraries.
Building libxml2-2.8.0 for nokogiri with the following patches applied:
- 0001-Fix-parser-local-buffers-size-problems.patch
- 0002-Fix-entities-local-buffers-size-problems.patch
- 0003-Fix-an-error-in-previous-commit.patch
- 0004-Fix-potential-out-of-bound-access.patch
- 0005-Detect-excessive-entities-expansion-upon-replacement.patch
- 0006-Do-not-fetch-external-parsed-entities.patch
- 0007-Enforce-XML_PARSER_EOF-state-handling-through-the-pa.patch
- 0008-Improve-handling-of-xmlStopParser.patch
- 0009-Fix-a-couple-of-return-without-value.patch
- 0010-Keep-non-significant-blanks-node-in-HTML-parser.patch
- 0011-Do-not-fetch-external-parameter-entities.patch
************************************************************************
IMPORTANT! Nokogiri builds and uses a packaged version of libxml2.
...
What am I missing? How can I force bundler to use the already installed nokogiri 1.6.3.1 (that ships with ChefDK)? I'm trying to avoid having nokogiri compile libxml2 because that fails consistently on many different developer/operations workstations and has caused no end of grief. Thanks.
Edit
Thanks to Tim Moore, using bundle env I noticed in the output that bundler had shared gems disabled.
$ bundle env
Bundler 1.7.12
Ruby 2.1.4 (2014-10-27 patchlevel 265) [x86_64-darwin12.0]
Rubygems 2.4.4
GEM_HOME /Users/arthur/.chefdk/gem/ruby/2.1.0
GEM_PATH /Users/arthur/.chefdk/gem/ruby/2.1.0:/opt/chefdk/embedded/lib/ruby/gems/2.1.0
Bundler settings
disable_shared_gems
Set for the current user (/Users/arthur/.bundle/config): "1"
Gemfile
source 'https://rubygems.org'
...
Looking at the ~/.bundle/config, sure enough the global config was set.
---
BUNDLE_DISABLE_SHARED_GEMS: '1'
Once removed, Bundler resolves nokogiri 1.6.3.1 correctly and doesn't try reinstalling it. This setting should not be there by default, by default bundler installs with --system. I must have set this setting many months back and forgot I did.
Try running bundle env to verify that the install location is what you expect.
If not, check whether there is a .bundle/config or ~/.bundle/config file overriding the install path. The output of bundle env will tell you what configuration it is using and how it was determined (i.e., which file it was in or whether it was picked up from an environment variable).
Try removing all contents of gemfile.lock file. Save the file. Run bundle install again.
There are a couple of methods. In gemfile you can specify the path which will force bundle to use from there.
gem "my_gem", :path => "path to gem"
As i see the issue is with the default paths here. Try doing this.
ChefDK doesn't install gems globally, it installs them under /opt/chefdk so they won't interfere with "your" global gems. I suggest you leave ChefDK gems isolated as they should be.
You need to use the proper bundler and gem. If you're using ChefDK, then it includes its own bundler and gem executables. They should be inside the /opt/chefdk directory, I believe under /opt/chefdk/embedded (I don't use chefdk, so I can be 100% sure of that).
To work 100% inside that ruby install, you need to ensure that the chefdk binaries are in your path before the other ruby related binaries. You can verify that with which ruby which gem and which bundle.
All that said, you really SHOULDN'T be messing with the ruby install for chefdk. It's embedded for a reason, so that you don't accidentally mess it up. I'd suggest you stick with the system ruby for your own work, and let Chef handle its ruby.
From Bundler docs:
--path: Specify a different path than the system default ($BUNDLE_PATH or $GEM_HOME). Bundler will remember this value for future installs on
this machine
Your bundler may have cached a --path specified install command.
Try:
bundle install --system
This will tell bundler to use the system installed gems as opposed to downloading new gem copies to a folder specific gem collection.

bundle install fails on nokogiri

I'm installing some chef dependencies following this website:
https://learnchef.opscode.com/starter-use-cases/multi-node-ec2/
I got to the bundle install part, here's what my Gemfile looks like:
source 'https://rubygems.org'
gem 'berkshelf'
gem 'chef'
gem 'knife-ec2'
I get this error when I try to run
bundle install --path vendor:
Gem::Installer::ExtensionBuildError: ERROR: Failed to build gem native extension.
...
libiconv is missing. please visit http://nokogiri.org/tutorials/installing_nokogiri.html for help with installing dependencies.
...
An error occurred while installing nokogiri (1.6.0), and Bundler cannot continue.
Make sure that `gem install nokogiri -v '1.6.0'` succeeds before bundling.
I went to the nokogiri site and I was able to follow the directions and successfully install nokgiri 1.6.0 with homebrew .9.5:
nokogiri --version
WARNING: Nokogiri was built against LibXML version 2.9.1, but has dynamically loaded 2.8.0
# Nokogiri (1.6.0)
I get the same message when I then try running the bundle install again. I'm told that the bundle installer doesn't care about installs done outside of it. How to I get around this and install these dependencies?
After a little digging, I figured it out. This is specifically for OSX Mountain Lion.
The rbenv bundler needs to know the same paths specified using these switches given by the nokogiri site:
http://nokogiri.org/tutorials/installing_nokogiri.html
This is done using the bundler config command:
bundle config build.nokogiri --with-xml2-include=/usr/local/Cellar/libxml2/2.7.8/include/libxml2 --with-xml2-lib=/usr/local/Cellar/libxml2/2.7.8/lib --with-xslt-dir=/usr/local/Cellar /libxslt/1.1.26 --with-iconv-include=/usr/local/Cellar/libiconv/1.13.1/include --with-iconv-lib=/usr/local/Cellar/libiconv/1.13.1/lib
I still ran into troulbe because the config was only picking up the first line of that config setting. I had to edit $HOME/.bundle/config and take out some newlnes before it would take all of the switches. I hope this will save someone else some time.

Can't install JSON gem

I need to install json because I get this error:
Could not find json-1.4.6 in any of the sources
I ran gem install json and bundle install but I was only able to install json-1.5.1 when I need json-1.4.6
I have gem 'json', '1.4.6' in my gemfile, so I'm not sure what's going on...
UPDATE
I get this error:
Installing json (1.4.6) /System/Library/Frameworks/Ruby.framework/Versions/1.8/usr/lib/ruby/1.8/fileutils.rb:1216:in `chmod': Operation not permitted - /Library/Ruby/Gems/1.8/gems/json-1.4.6/CHANGES (Errno::EPERM)
After checking logs by running $ heroku logs
I found "An error occurred while installing json (1.4.6), and Bundler cannot continue.
Make sure that gem install json -v '1.4.6' succeeds before bundling."
I then removed 2 json entries from the Gemfile.lock and had no further issues.
Why did you run gem install json at all? Bundler takes care of that for you and will ensure that the correct version of each gem is installed (since sometimes dependencies require an older version). Run
gem uninstall json
bundle install
Also ensure you have source 'https://rubygems.org' at the top of your Gemfile.
As for the permissions info, you may have to run gem and bundle commands with sudo.
By the way, I highly recommend taking a look at and using RVM, particularly the gemsets feature. It will make your life infinitely better when developing Ruby apps. If you decide to do so, I'd also suggest trashing all the gems you've install using the system Ruby by running sudo rm -rf /Library/Ruby/Gems/1.8/. It's also important that when using RVM you don't have to use sudo when running gem (or bundle), which is not only safer but less typing too.
Please update your rubygems by executing the following command..
gem update --system
may be it will solve the problem. After updating your gem. Then run the following command to install json
gem install json
Now you can get json gem installed in your system.
Try:
$ sudo apt-get install ruby1.8-dev
If you're using rbenv, try rbenv rehash
I had this problem when trying to build a website with Jekyll.
Turned out I hadn't followed all the instructions at https://jekyllrb.com/docs/installation/ubuntu/
I don't know if it was the missing packages or commands into ~/.bashrc but it fixed the problem in two instances of Ubuntu in WSL
Remove the json entries from the Gemfile.lock file and try to re run bundle install..

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