rails sqiteエラー

Question

前提・実現したいこと

ここに質問の内容を詳しく書いてください。
rails new として　bundle installとすると以下のエラーが出ました。

発生している問題・エラーメッセージ

Fetching sqlite3 1.3.13
Installing sqlite3 1.3.13 with native extensions
Gem::Ext::BuildError: ERROR: Failed to build gem native extension.

    current directory: /root/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/sqlite3-1.3.13/ext/sqlite3
/root/.rbenv/versions/2.5.1/bin/ruby -r ./siteconf20180827-5900-1rwgmgb.rb extconf.rb
checking for sqlite3.h... no
sqlite3.h is missing. Try 'brew install sqlite3',
'yum install sqlite-devel' or 'apt-get install libsqlite3-dev'
and check your shared library search path (the
location where your sqlite3 shared library is located).
*** 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=/root/.rbenv/versions/2.5.1/bin/$(RUBY_BASE_NAME)
        --with-sqlite3-config
        --without-sqlite3-config
        --with-pkg-config
        --without-pkg-config
        --with-sqlite3-dir
        --without-sqlite3-dir
        --with-sqlite3-include
        --without-sqlite3-include=${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:

  /root/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/extensions/x86_64-linux/2.5.0-static/sqlite3-1.3.13/mkmf.log

extconf failed, exit code 1

Gem files will remain installed in /root/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/sqlite3-1.3.13 for inspection.
Results logged to /root/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/extensions/x86_64-linux/2.5.0-static/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' --source 'https://rubygems.org/'` succeeds before bundling.

In Gemfile:
  sqlite3
[root@localhost myapp]# gem install sqlite3 -v '1.3.13' --source 'https://rubygems.org/'
Building native extensions. This could take a while...
ERROR:  Error installing sqlite3:
        ERROR: Failed to build gem native extension.

    current directory: /root/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/sqlite3-1.3.13/ext/sqlite3
/root/.rbenv/versions/2.5.1/bin/ruby -r ./siteconf20180827-5973-1exzsuo.rb extconf.rb
checking for sqlite3.h... no
sqlite3.h is missing. Try 'brew install sqlite3',
'yum install sqlite-devel' or 'apt-get install libsqlite3-dev'
and check your shared library search path (the
location where your sqlite3 shared library is located).
*** 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=/root/.rbenv/versions/2.5.1/bin/$(RUBY_BASE_NAME)
        --with-sqlite3-config
        --without-sqlite3-config
        --with-pkg-config
        --without-pkg-config
        --with-sqlite3-dir
        --without-sqlite3-dir
        --with-sqlite3-include
        --without-sqlite3-include=${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:

  /root/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/extensions/x86_64-linux/2.5.0-static/sqlite3-1.3.13/mkmf.log

extconf failed, exit code 1

Gem files will remain installed in /root/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/sqlite3-1.3.13 for inspection.
Results logged to /root/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/extensions/x86_64-linux/2.5.0-static/sqlite3-1.3.13/gem_make.out

該当のソースコード

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

ruby '2.5.1'

# Bundle edge Rails instead: gem 'rails', github: 'rails/rails'
gem 'rails', '~> 5.2.1'
# Use sqlite3 as the database for Active Record
gem 'sqlite3'
# Use Puma as the app server
gem 'puma', '~> 3.11'
# 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 'mini_racer', 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', '~> 4.0'
# Use ActiveModel has_secure_password
# gem 'bcrypt', '~> 3.1.7'

# Use ActiveStorage variant
# gem 'mini_magick', '~> 4.8'

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

# Reduces boot times through caching; required in config/boot.rb
gem 'bootsnap', '>= 1.1.0', require: false

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]
end

group :development do
  # Access an interactive console on exception pages or by calling 'console' anywhere in the code.
  gem 'web-console', '>= 3.3.0'
  gem 'listen', '>= 3.0.5', '< 3.2'
  # Spring speeds up development by keeping your application running in the background. Read more: https://github.com/rails/spring
  gem 'spring'
  gem 'spring-watcher-listen', '~> 2.0.0'
end

group :test do
  # Adds support for Capybara system testing and selenium driver
  gem 'capybara', '>= 2.15'
  gem 'selenium-webdriver'
  # Easy installation and use of chromedriver to run system tests with Chrome
  gem 'chromedriver-helper'
end

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

試したこと

前にMySQLをdb指定していたのでその名残のようなものなのでは、と思いましたがよく分からないので質問させていただきました。

補足情報（FW/ツールのバージョンなど）

Vagrant 1.8.6・CentOS 6.10
rbenv 1.1.1-39-g59785f6
ruby 2.5.1p57

Answer 1

エラーメッセージで、

    current directory: /root/.rbenv/versions/2.5.1/lib/ruby/gems/2.5.0/gems/sqlite3-1.3.13/ext/sqlite3
/root/.rbenv/versions/2.5.1/bin/ruby -r ./siteconf20180827-5900-1rwgmgb.rb extconf.rb
checking for sqlite3.h... no
sqlite3.h is missing. Try 'brew install sqlite3',
'yum install sqlite-devel' or 'apt-get install libsqlite3-dev'
and check your shared library search path (the
location where your sqlite3 shared library is located).

とありますが、checking for sqlite3.h... noとsqlite3.h is missing.というのはsqlite3のライブラリをビルドしようとした際にsqlite3.hというヘッダファイルが見つからなかったためにエラーになっている、という情報です。
続く文言は、どれかを試せ（OSごとによって対処法が違うので）ということで、CentOSであれば、

yum install sqlite-devel

またはsudoで権限をつけて、

sudo yum install sqlite-devel

を試してから、もう一度bundle installしてみるとよいかと思います（brewはmacOS、apt-getは主にdebian系だと思います）。