nokogiriのインストールでnokogiriをコンパイル出来なく、エラーが出まくる

前提・実現したいこと

railsで既存のアプリをcloneして、bundle installを行いたいのですが、nokogiriのインストール（おそらくコンパイル段階）でエラーが発生し、gemをインストール出来ません。

この原因を探り、エラーを取り除きたいです。

仮想環境上でvagrantを立ててやっています。
boxはbento/amazonlinux-2です。

rubyは2.4.1
railsは5.1.6
rubyはインストール済みです。

解決策をご存知の方がいれば　教えていただきたいです。

発生している問題・エラーメッセージ

$ bundle install --path vendor/bundle

をすると、

Fetching nokogiri 1.8.4
Installing nokogiri 1.8.4 with native extensions
Gem::Ext::BuildError: ERROR: Failed to build gem native extension.

    current directory: /var/www/cryptospells/vendor/bundle/ruby/2.4.0/gems/nokogiri-1.8.4/ext/nokogiri
/home/vagrant/.rbenv/versions/2.4.1/bin/ruby -r ./siteconf20190804-23564-1r2lh07.rb extconf.rb
checking if the C compiler accepts ... yes
Building nokogiri using packaged libraries.
Using mini_portile version 2.3.0
checking for gzdopen() in -lz... yes
checking for iconv... yes
************************************************************************
IMPORTANT NOTICE:

Building Nokogiri with a packaged version of libxml2-2.9.8
with the following patches applied:
	- 0001-Revert-Do-not-URI-escape-in-server-side-includes.patch

Team Nokogiri will keep on doing their best to provide security
updates in a timely manner, but if this is a concern for you and want
to use the system library instead; abort this installation process and
reinstall nokogiri as follows:

    gem install nokogiri -- --use-system-libraries
        [--with-xml2-config=/path/to/xml2-config]
        [--with-xslt-config=/path/to/xslt-config]

If you are using Bundler, tell it to use the option:

    bundle config build.nokogiri --use-system-libraries
    bundle install

Note, however, that nokogiri is not fully compatible with arbitrary
versions of libxml2 provided by OS/package vendors.
************************************************************************
Extracting libxml2-2.9.8.tar.gz into tmp/x86_64-pc-linux-gnu/ports/libxml2/2.9.8... OK
Running git apply with /var/www/cryptospells/vendor/bundle/ruby/2.4.0/gems/nokogiri-1.8.4/patches/libxml2/0001-Revert-Do-not-URI-escape-in-server-side-includes.patch... OK
Running 'configure' for libxml2 2.9.8... OK
Running 'compile' for libxml2 2.9.8... OK
Running 'install' for libxml2 2.9.8... OK
Activating libxml2 2.9.8 (from /var/www/cryptospells/vendor/bundle/ruby/2.4.0/gems/nokogiri-1.8.4/ports/x86_64-pc-linux-gnu/libxml2/2.9.8)...
************************************************************************
IMPORTANT NOTICE:

Building Nokogiri with a packaged version of libxslt-1.1.32.

Team Nokogiri will keep on doing their best to provide security
updates in a timely manner, but if this is a concern for you and want
to use the system library instead; abort this installation process and
reinstall nokogiri as follows:

    gem install nokogiri -- --use-system-libraries
        [--with-xml2-config=/path/to/xml2-config]
        [--with-xslt-config=/path/to/xslt-config]

If you are using Bundler, tell it to use the option:

    bundle config build.nokogiri --use-system-libraries
    bundle install
************************************************************************
Extracting libxslt-1.1.32.tar.gz into tmp/x86_64-pc-linux-gnu/ports/libxslt/1.1.32... OK
Running 'configure' for libxslt 1.1.32... OK
Running 'compile' for libxslt 1.1.32... OK
Running 'install' for libxslt 1.1.32... OK
Activating libxslt 1.1.32 (from /var/www/cryptospells/vendor/bundle/ruby/2.4.0/gems/nokogiri-1.8.4/ports/x86_64-pc-linux-gnu/libxslt/1.1.32)...
checking for -llzma... yes
checking for xmlParseDoc() in libxml/parser.h... yes
checking for xsltParseStylesheetDoc() in libxslt/xslt.h... yes
checking for exsltFuncRegister() in libexslt/exslt.h... yes
checking for xmlHasFeature()... yes
checking for xmlFirstElementChild()... yes
checking for xmlRelaxNGSetParserStructuredErrors()... yes
checking for xmlRelaxNGSetParserStructuredErrors()... yes
checking for xmlRelaxNGSetValidStructuredErrors()... yes
checking for xmlSchemaSetValidStructuredErrors()... yes
checking for xmlSchemaSetParserStructuredErrors()... yes
creating Makefile

current directory: /var/www/cryptospells/vendor/bundle/ruby/2.4.0/gems/nokogiri-1.8.4/ext/nokogiri
make "DESTDIR=" clean

current directory: /var/www/cryptospells/vendor/bundle/ruby/2.4.0/gems/nokogiri-1.8.4/ext/nokogiri
make "DESTDIR="
compiling html_document.c
compiling html_element_description.c
compiling html_entity_lookup.c
compiling html_sax_parser_context.c
compiling html_sax_push_parser.c
compiling nokogiri.c
compiling xml_attr.c
compiling xml_attribute_decl.c
compiling xml_cdata.c
compiling xml_comment.c
compiling xml_document.c
compiling xml_document_fragment.c
compiling xml_dtd.c
compiling xml_element_content.c
compiling xml_element_decl.c
compiling xml_encoding_handler.c
compiling xml_entity_decl.c
compiling xml_entity_reference.c
compiling xml_io.c
compiling xml_libxml2_hacks.c
compiling xml_namespace.c
compiling xml_node.c
compiling xml_node_set.c
compiling xml_processing_instruction.c
compiling xml_reader.c
compiling xml_relax_ng.c
compiling xml_sax_parser.c
compiling xml_sax_parser_context.c
compiling xml_sax_push_parser.c
compiling xml_schema.c
compiling xml_syntax_error.c
compiling xml_text.c
compiling xml_xpath_context.c
compiling xslt_stylesheet.c
linking shared-object nokogiri/nokogiri.so
Cleaning files only used during build.
rm -rf /var/www/cryptospells/vendor/bundle/ruby/2.4.0/gems/nokogiri-1.8.4/ext/nokogiri/tmp/x86_64-pc-linux-gnu/ports
rm -rf /var/www/cryptospells/vendor/bundle/ruby/2.4.0/gems/nokogiri-1.8.4/ports

current directory: /var/www/cryptospells/vendor/bundle/ruby/2.4.0/gems/nokogiri-1.8.4/ext/nokogiri
make "DESTDIR=" install
/usr/bin/install -c -m 0755 nokogiri.so ./.gem.20190804-23564-1x4wqub/nokogiri
/usr/bin/install: `./.gem.20190804-23564-1x4wqub/nokogiri/nokogiri.so' のパーミッションを設定します: Operation not permitted
make: *** [install-so] エラー 1

make install failed, exit code 2

Gem files will remain installed in /var/www/cryptospells/vendor/bundle/ruby/2.4.0/gems/nokogiri-1.8.4 for inspection.
Results logged to /var/www/cryptospells/vendor/bundle/ruby/2.4.0/extensions/x86_64-linux/2.4.0-static/nokogiri-1.8.4/gem_make.out

An error occurred while installing nokogiri (1.8.4), and Bundler cannot continue.
Make sure that `gem install nokogiri -v '1.8.4' --source 'https://rubygems.org/'` succeeds before bundling.

In Gemfile:
  rails_admin was resolved to 1.4.2, which depends on
    rails was resolved to 5.1.6, which depends on
      actioncable was resolved to 5.1.6, which depends on
        actionpack was resolved to 5.1.6, which depends on
          actionview was resolved to 5.1.6, which depends on
            rails-dom-testing was resolved to 2.0.3, which depends on
              nokogiri

該当のソースコード

Gemfile
1
2source 'https://rubygems.org'
3
4git_source(:github) do |repo_name|
5  repo_name = "#{repo_name}/#{repo_name}" unless repo_name.include?("/")
6  "https://github.com/#{repo_name}.git"
7end
8
9gem 'devise', '4.5.0'
10gem 'rails_admin'
11gem 'omniauth', '1.6.1'
12gem 'omniauth-twitter', '1.4.0'
13gem 'dotenv-rails', '2.2.1'
14gem 'therubyracer', platforms: :ruby
15gem 'paypal-sdk-rest'
16gem 'whenever'
17gem 'feedjira'
18gem 'httpclient'
19gem 'kaminari'
20gem 'redis'
21gem 'rack-user_agent'
22
23gem  'aws-sdk-rails'
24gem 'aws-record'
25
26gem 'webpacker', github: 'rails/webpacker'
27gem 'activerecord-import', '0.27.0'
28gem 'carrierwave'
29gem 'fog'
30gem 'rmagick'
31gem 'enum_help'
32gem 'sentry-raven'
33
34
35gem 'rails', '~> 5.1.6'
36gem 'puma', '~> 3.7'
37gem 'sass-rails', '~> 5.0'
38gem 'uglifier', '>= 1.3.0'
39gem 'coffee-rails', '~> 4.2'
40gem 'jbuilder', '~> 2.5'
41

試したこと

yumで色々なものをインストールしてみました。

下記は、sudo yum install でインストールしたものです。

  - openssl-devel
  - readline-devel
  - zlib-devel
  - gcc
  - gcc-c++
  - ImageMagick
  - ImageMagick-devel
  - libxml2-devel
  - libcurl
  - libcurl-devel
  - libxslt-devel
  - libxslt

また、エラーメッセージに書かれていた

sample.rb
1
2gem install nokogiri -- --use-system-libraries
3bundle config build.nokogiri --use-system-libraries
4bundle install
5gem install nokogiri -v '1.8.4'などもやりましたがダメでした。
6
7また、最初に、
8gem install bundler
9gem install rails
10
11も行なっています。
12