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"An error occurred while installing sqlite3 (1.3.13), and Bundler cannot continue"

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I am trying to run a bundle install, but when I do, I am getting an error message that says, "An error occurred while installing sqlite3 (1.3.13), and Bundler cannot continue." I tried running gem install sqlite3 -v '1.3.13', but am getting an error with that as well.

Here is my Gemfile:

source 'https://rubygems.org'

git_source(:github) do |repo_name|
  repo_name = "#{repo_name}/#{repo_name}" unless repo_name.include?("/")
  "https://github.com/#{repo_name}.git"
end


# Bundle edge Rails instead: gem 'rails', github: 'rails/rails'
gem 'rails', '~> 5.1.1'
# Use Puma as the app server
gem 'puma', '~> 3.7'
# Use SCSS for stylesheets
gem 'sass-rails', '~> 5.0'
# Use Uglifier as compressor for JavaScript assets
gem 'uglifier', '>= 1.3.0'
# See https://github.com/rails/execjs#readme for more supported runtimes
# gem 'therubyracer', platforms: :ruby

# Use CoffeeScript for .coffee assets and views
gem 'coffee-rails', '~> 4.2'
# Turbolinks makes navigating your web application faster. Read more: https://github.com/turbolinks/turbolinks
gem 'turbolinks', '~> 5'
# Build JSON APIs with ease. Read more: https://github.com/rails/jbuilder
gem 'jbuilder', '~> 2.5'
# Use Redis adapter to run Action Cable in production
# gem 'redis', '~> 3.0'
# Use ActiveModel has_secure_password
# gem 'bcrypt', '~> 3.1.7'

# Use Capistrano for deployment
# gem 'capistrano-rails', group: :development

group :development, :test do
  # Call 'byebug' anywhere in the code to stop execution and get a debugger console
  gem 'byebug', platforms: [:mri, :mingw, :x64_mingw]
  # Use sqlite3 as the database for Active Record
    gem 'sqlite3'
end

group :development do
  # Access an IRB console on exception pages or by using <%= console %> anywhere in the code.
  gem 'web-console', '>= 3.3.0'
end

group :production do 
    gem 'pg' 
end

# Windows does not include zoneinfo files, so bundle the tzinfo-data gem
gem 'tzinfo-data', platforms: [:mingw, :mswin, :x64_mingw, :jruby]

gem 'jquery-rails'

gem 'devise'

Here is the error I get when I try to run bundle install:

Kelly@LAPTOP /c/Sites/my_app (master)
$ bundle install
Fetching gem metadata from https://rubygems.org/.............
Fetching version metadata from https://rubygems.org/...
Fetching dependency metadata from https://rubygems.org/..
Resolving dependencies..................
Using rake 12.0.0
Using concurrent-ruby 1.0.5 (java)
Using i18n 0.8.4
Using minitest 5.10.2
Using thread_safe 0.3.6 (java)
Using builder 3.2.3
Using erubi 1.6.0
Using nokogiri 1.8.0 (java)
Using rack 2.0.3
Using nio4r 2.1.0 (java)
Using websocket-extensions 0.1.2
Using mime-types-data 3.2016.0521
Using arel 8.0.0
Using bundler 1.15.1
Using method_source 0.8.2
Using thor 0.19.4
Using puma 3.9.1 (java)
Using sass 3.4.24
Using tilt 2.0.7
Using execjs 2.7.0
Using coffee-script-source 1.12.2
Using turbolinks-source 5.0.3
Using multi_json 1.12.1
Fetching sqlite3 1.3.13
Installing sqlite3 1.3.13 with native extensions
C:/jruby-9.1.8.0/lib/ruby/stdlib/rubygems/ext/ext_conf_builder.rb:56: warning: Tempfile#unlink or delete called on open file; ignoring
Fetching bindex 0.5.0
Installing bindex 0.5.0 with native extensions
C:/jruby-9.1.8.0/lib/ruby/stdlib/rubygems/ext/ext_conf_builder.rb:56: warning: Tempfile#unlink or delete called on open file; ignoring
Using bcrypt 3.1.11 (java)
Using orm_adapter 0.5.0
Using tzinfo 1.2.3
Using loofah 2.0.3
Using rack-test 0.6.3
Using sprockets 3.7.1
Using warden 1.2.7
Using websocket-driver 0.6.5 (java)
Using mime-types 3.1
Using uglifier 3.2.0
Using coffee-script 2.4.1
Using turbolinks 5.0.1
Gem::Ext::BuildError: ERROR: Failed to build gem native extension.

current directory:
C:/jruby-9.1.8.0/lib/ruby/gems/shared/gems/sqlite3-1.3.13/ext/sqlite3
C:/jruby-9.1.8.0/bin/jruby.exe -r ./siteconf20170707-17112-s04bux.rb extconf.rb
checking for sqlite3.h... RuntimeError: The compiler failed to generate an
executable file.
You have to install development tools first.

                 try_do at C:/jruby-9.1.8.0/lib/ruby/stdlib/mkmf.rb:456
                try_cpp at C:/jruby-9.1.8.0/lib/ruby/stdlib/mkmf.rb:587
   block in find_header at C:/jruby-9.1.8.0/lib/ruby/stdlib/mkmf.rb:1144
  block in checking_for at C:/jruby-9.1.8.0/lib/ruby/stdlib/mkmf.rb:942
      block in postpone at C:/jruby-9.1.8.0/lib/ruby/stdlib/mkmf.rb:350
                   open at C:/jruby-9.1.8.0/lib/ruby/stdlib/mkmf.rb:320
      block in postpone at C:/jruby-9.1.8.0/lib/ruby/stdlib/mkmf.rb:350
                   open at C:/jruby-9.1.8.0/lib/ruby/stdlib/mkmf.rb:320
               postpone at C:/jruby-9.1.8.0/lib/ruby/stdlib/mkmf.rb:346
           checking_for at C:/jruby-9.1.8.0/lib/ruby/stdlib/mkmf.rb:941
            find_header at C:/jruby-9.1.8.0/lib/ruby/stdlib/mkmf.rb:1143
                 <main> at extconf.rb:50
*** 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=C:/jruby-9.1.8.0/bin/jruby
        --with-sqlite3-config
        --without-sqlite3-config
        --with-pkg-config
        --without-pkg-config
        --with-sqlite3-dir
        --without-sqlite3-dir
        --with-sqlite3-include
        --without-sqlite3-include=${sqlite3-dir}/include
        --with-sqlite3-lib
        --without-sqlite3-lib=${sqlite3-dir}/lib

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

C:/jruby-9.1.8.0/lib/ruby/gems/shared/extensions/universal-java-1.8/2.3.0/sqlite3-1.3.13/mkmf.log

extconf failed, exit code 1

Gem files will remain installed in
C:/jruby-9.1.8.0/lib/ruby/gems/shared/gems/sqlite3-1.3.13 for inspection.
Results logged to
C:/jruby-9.1.8.0/lib/ruby/gems/shared/extensions/universal-java-1.8/2.3.0/sqlite3-1.3.13/gem_make.out

An error occurred while installing sqlite3 (1.3.13), and Bundler cannot
continue.
Make sure that `gem install sqlite3 -v '1.3.13'` succeeds before bundling.

In Gemfile:
  sqlite3

Here is the error I get when I try to run gem install sqlite -v '1.3.13':

Kelly@LAPTOP /c/Sites/my_app (master)
$ gem install sqlite3 -v '1.3.13'
Building native extensions.  This could take a while...
C:/jruby-9.1.8.0/lib/ruby/stdlib/rubygems/ext/ext_conf_builder.rb:56: warning: Tempfile#unlink or delete called on open file; ignoring
ERROR:  Error installing sqlite3:
        ERROR: Failed to build gem native extension.

    current directory: C:/jruby-9.1.8.0/lib/ruby/gems/shared/gems/sqlite3-1.3.13/ext/sqlite3
C:/jruby-9.1.8.0/bin/jruby.exe -r ./siteconf20170707-17048-ojikan.rb extconf.rb
checking for sqlite3.h... RuntimeError: The compiler failed to generate an executable file.
You have to install development tools first.

                 try_do at C:/jruby-9.1.8.0/lib/ruby/stdlib/mkmf.rb:456
                try_cpp at C:/jruby-9.1.8.0/lib/ruby/stdlib/mkmf.rb:587
   block in find_header at C:/jruby-9.1.8.0/lib/ruby/stdlib/mkmf.rb:1144
  block in checking_for at C:/jruby-9.1.8.0/lib/ruby/stdlib/mkmf.rb:942
      block in postpone at C:/jruby-9.1.8.0/lib/ruby/stdlib/mkmf.rb:350
                   open at C:/jruby-9.1.8.0/lib/ruby/stdlib/mkmf.rb:320
      block in postpone at C:/jruby-9.1.8.0/lib/ruby/stdlib/mkmf.rb:350
                   open at C:/jruby-9.1.8.0/lib/ruby/stdlib/mkmf.rb:320
               postpone at C:/jruby-9.1.8.0/lib/ruby/stdlib/mkmf.rb:346
           checking_for at C:/jruby-9.1.8.0/lib/ruby/stdlib/mkmf.rb:941
            find_header at C:/jruby-9.1.8.0/lib/ruby/stdlib/mkmf.rb:1143
                 <main> at extconf.rb:50
*** 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=C:/jruby-9.1.8.0/bin/jruby
        --with-sqlite3-config
        --without-sqlite3-config
        --with-pkg-config
        --without-pkg-config
        --with-sqlite3-dir
        --without-sqlite3-dir
        --with-sqlite3-include
        --without-sqlite3-include=${sqlite3-dir}/include
        --with-sqlite3-lib
        --without-sqlite3-lib=${sqlite3-dir}/lib

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

  C:/jruby-9.1.8.0/lib/ruby/gems/shared/extensions/universal-java-1.8/2.3.0/sqlite3-1.3.13/mkmf.log

extconf failed, exit code 1

Gem files will remain installed in C:/jruby-9.1.8.0/lib/ruby/gems/shared/gems/sqlite3-1.3.13 for inspection.
Results logged to C:/jruby-9.1.8.0/lib/ruby/gems/shared/extensions/universal-java-1.8/2.3.0/sqlite3-1.3.13/gem_make.out

Any help is appreciated as I cannot move forward until I run a successful bundle install and I've tried researching for days and cannot figure out how to fix this.

Updated 7/9/17: Here is my updated Gemfile where I am still not able to run bundle install nor bundle update:

source 'https://rubygems.org'

git_source(:github) do |repo_name|
  repo_name = "#{repo_name}/#{repo_name}" unless repo_name.include?("/")
  "https://github.com/#{repo_name}.git"
end


# Bundle edge Rails instead: gem 'rails', github: 'rails/rails'
gem 'rails', '~> 5.1.1'
# Use Puma as the app server
gem 'puma', '~> 3.7'
# Use SCSS for stylesheets
gem 'sass-rails', '~> 5.0'
# Use Uglifier as compressor for JavaScript assets
gem 'uglifier', '>= 1.3.0'
# See https://github.com/rails/execjs#readme for more supported runtimes
# gem 'therubyracer', platforms: :ruby

# Use CoffeeScript for .coffee assets and views
gem 'coffee-rails', '~> 4.2'
# Turbolinks makes navigating your web application faster. Read more: https://github.com/turbolinks/turbolinks
gem 'turbolinks', '~> 5'
# Build JSON APIs with ease. Read more: https://github.com/rails/jbuilder
gem 'jbuilder', '~> 2.5'
# Use Redis adapter to run Action Cable in production
# gem 'redis', '~> 3.0'
# Use ActiveModel has_secure_password
# gem 'bcrypt', '~> 3.1.7'

# Use Capistrano for deployment
# gem 'capistrano-rails', group: :development

group :development, :test do
  # Call 'byebug' anywhere in the code to stop execution and get a debugger console
  gem 'byebug', platforms: [:mri, :mingw, :x64_mingw]
  # Use sqlite3 as the database for Active Record
    gem 'sqlite3', platform: :ruby
    gem 'jdbc-sqlite3', platform: :jruby
    gem 'activerecord-jdbc-adapter', platform: :jruby
end

group :development do
  # Access an IRB console on exception pages or by using <%= console %> anywhere in the code.
  gem 'web-console', '>= 3.3.0'
end

group :production do 
    gem 'pg' 
end

# Windows does not include zoneinfo files, so bundle the tzinfo-data gem
gem 'tzinfo-data', platforms: [:mingw, :mswin, :x64_mingw, :jruby]

gem 'jquery-rails'

gem 'activerecord-jdbcsqlite3-adapter', '~> 1.3', '>= 1.3.23'

Updated 7/10/17: After removing gem 'activerecord-jdbcsqlite3-adapter', '~> 1.3', '>= 1.3.23', I tried bundle install again and this time, I got a different error:

Kelly@LAPTOP /c/Sites/my_app (master)
$ bundle install
The dependency sqlite3 (>= 0) will be unused by any of the platforms Bundler is installing for. Bundler is installing for x86-mingw32, java but the dependency is only for ruby. To add those platforms to the bundle, run `bundle lock --add-platform ruby`.
Fetching gem metadata from https://rubygems.org/...........
Fetching version metadata from https://rubygems.org/...
Fetching dependency metadata from https://rubygems.org/..
Resolving dependencies........................
Using rake 12.0.0
Using concurrent-ruby 1.0.5 (java)
Using i18n 0.8.4
Using minitest 5.10.2
Using thread_safe 0.3.6 (java)
Using builder 3.2.3
Using erubi 1.6.0
Using nokogiri 1.8.0 (java)
Using rack 2.0.3
Using nio4r 2.1.0 (java)
Using websocket-extensions 0.1.2
Using mime-types-data 3.2016.0521
Using arel 8.0.0
Using bundler 1.15.1
Using method_source 0.8.2
Using thor 0.19.4
Using puma 3.9.1 (java)
Using sass 3.4.24
Using tilt 2.0.7
Using execjs 2.7.0
Using coffee-script-source 1.12.2
Using turbolinks-source 5.0.3
Using multi_json 1.12.1
Using jdbc-sqlite3 3.15.1
Fetching bindex 0.5.0
Installing bindex 0.5.0 with native extensions
C:/jruby-9.1.8.0/lib/ruby/stdlib/rubygems/ext/ext_conf_builder.rb:56: warning: Tempfile#unlink or delete called on open file; ignoring
Using tzinfo 1.2.3
Using loofah 2.0.3
Using rack-test 0.6.3
Using sprockets 3.7.1
Using websocket-driver 0.6.5 (java)
Using mime-types 3.1
Using uglifier 3.2.0
Using coffee-script 2.4.1
Using turbolinks 5.0.1
Gem::Ext::BuildError: ERROR: Failed to build gem native extension.

current directory:
C:/jruby-9.1.8.0/lib/ruby/gems/shared/gems/bindex-0.5.0/ext/bindex
C:/jruby-9.1.8.0/bin/jruby.exe -r ./siteconf20170710-21728-1asiecp.rb extconf.rb

current directory:
C:/jruby-9.1.8.0/lib/ruby/gems/shared/gems/bindex-0.5.0/ext/bindex
make "DESTDIR=" clean
'make' is not recognized as an internal or external command,
operable program or batch file.

current directory:
C:/jruby-9.1.8.0/lib/ruby/gems/shared/gems/bindex-0.5.0/ext/bindex
make "DESTDIR="
'make' is not recognized as an internal or external command,
operable program or batch file.

make failed, exit code 1

Gem files will remain installed in
C:/jruby-9.1.8.0/lib/ruby/gems/shared/gems/bindex-0.5.0 for inspection.
Results logged to
C:/jruby-9.1.8.0/lib/ruby/gems/shared/extensions/universal-java-1.8/2.3.0/bindex-0.5.0/gem_make.out

An error occurred while installing bindex (0.5.0), and Bundler cannot continue.
Make sure that `gem install bindex -v '0.5.0'` succeeds before bundling.

In Gemfile:
  web-console was resolved to 3.5.1, which depends on
    bindex
ruby-on-rails sqlite rubygems bundle-install
Original Q&A
3

There are 3 best solutions below

13
MarsAtomic On

The gem activerecord-jdbcsqlite3-adapter is not yet compatible with Rails 5. I was able to successfully use JRuby with Rails 4.1.3, from a couple of years ago. The team working on JDBC adapters operates on an open source basis, which general means they work for free, so you get what you get.

You have two choices:

1) Uninstall JRuby and use Rails 5 with an MRI-based interpreter; or

2) Use JRuby with an older version of Rails, like 4.2.9 or lower.

My suggestion is to stick with option 1, since you don't have to do anything special at all -- MRI is the normal Ruby interpreter. You also never explained your reasons for choosing JRuby, which makes me suspect a bit of an XY Problem. If you go with option 2, please review your reasons for selecting JRuby and make sure you know both what you're doing and why you're doing it.

1
Eric Andrews On

There has been a perfect answer. Check out the article "An error occurred while installing sqlite3 (1.3.7), and Bundler cannot continue Cannot create rails app" in stackoverflow.

I quote the following solution

It's failing because you are missing a dependency. You can get it by running sudo apt-get install libsqlite3-dev

0
Ahmedakhtar11 On

This is a very common problem when running a Rails App.

The answer is at this link: https://github.com/sparklemotion/sqlite3-ruby/issues/224

or this Youtube video: https://www.youtube.com/watch?v=G-B_KUFNkQQ&t=556s

Instructions:

Step 1: Open your Gemfile

Step 2: Find where it says:

gem 'sqlite3'

and change this to:

gem 'sqlite3', git: "https://github.com/larskanis/sqlite3-ruby", branch: "add-gemspec"

(Run "bundle install" if the server still doesn't run.)

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