Railsでnokogiriのインストールができなくて困っています。

Question

###　native extension を利用する gem のインストールに失敗する

Railsでアプリ開発をしようともい、Railsのインストールを試みる。すると下記のようなエラーコードが出てきました。自分なりに呼んだのですがどうも**nokogiri**のインストールでつまずいている模様。解決の可能性だけでも浮かんだ方がいましたら返答お願いしたいです。

ドットインストールでずっと勉強していたため、環境はWin10上にVagrantでCentOSを載せています。

エラーコード

ERROR:  Error installing rails:
        ERROR: Failed to build gem native extension.

エラー全文

[vagrant@localhost ~]$ gem install rails -v 5.1.3 --no-document
Fetching actionpack-5.1.3.gem
Fetching rack-test-0.6.3.gem
Fetching actionview-5.1.3.gem
Fetching activesupport-5.1.3.gem
Fetching i18n-0.9.5.gem
Fetching actioncable-5.1.3.gem
Fetching rails-5.1.3.gem
Fetching railties-5.1.3.gem
Fetching activejob-5.1.3.gem
Fetching actionmailer-5.1.3.gem
Fetching arel-8.0.0.gem
Fetching activemodel-5.1.3.gem
Fetching activerecord-5.1.3.gem
Fetching websocket-driver-0.6.5.gem
Successfully installed i18n-0.9.5
Successfully installed activesupport-5.1.3
Building native extensions. This could take a while...
ERROR:  Error installing rails:
        ERROR: Failed to build gem native extension.

    current directory: /home/vagrant/.rbenv/versions/2.6.5/lib/ruby/gems/2.6.0/gems/nokogiri-1.10.5/ext/nokogiri
/home/vagrant/.rbenv/versions/2.6.5/bin/ruby -I /home/vagrant/.rbenv/versions/2.6.5/lib/ruby/site_ruby/2.6.0 -r ./siteconf20191006-28714-1175yzn.rb extconf.rb
checking if the C compiler accepts ... yes
Building nokogiri using packaged libraries.
Using mini_portile version 2.4.0
checking for gzdopen() in -lz... yes
checking for iconv... yes
************************************************************************
IMPORTANT NOTICE:

Building Nokogiri with a packaged version of libxml2-2.9.10
with the following patches applied:
        - 0001-Revert-Do-not-URI-escape-in-server-side-includes.patch
        - 0002-Remove-script-macro-support.patch
        - 0003-Update-entities-to-remove-handling-of-ssi.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 libxml2-2.9.10.tar.gz into tmp/x86_64-pc-linux-gnu/ports/libxml2/2.9.10... OK
Running git apply with /home/vagrant/.rbenv/versions/2.6.5/lib/ruby/gems/2.6.0/gems/nokogiri-1.10.5/patches/libxml2/0001-Revert-Do-not-URI-escape-in-server-side-includes.patch... OK
Running git apply with /home/vagrant/.rbenv/versions/2.6.5/lib/ruby/gems/2.6.0/gems/nokogiri-1.10.5/patches/libxml2/0002-Remove-script-macro-support.patch... OK
Running git apply with /home/vagrant/.rbenv/versions/2.6.5/lib/ruby/gems/2.6.0/gems/nokogiri-1.10.5/patches/libxml2/0003-Update-entities-to-remove-handling-of-ssi.patch... OK
Running 'configure' for libxml2 2.9.10... ERROR, review '/home/vagrant/.rbenv/versions/2.6.5/lib/ruby/gems/2.6.0/gems/nokogiri-1.10.5/ext/nokogiri/tmp/x86_64-pc-linux-gnu/ports/libxml2/2.9.10/configure.log' to see what happened. Last lines are:
========================================================================
configure: WARNING: you should use --build, --host, --target
checking whether to enable maintainer-specific portions of Makefiles... yes
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... configure: error: newly created file is older than distributed files!
Check your system clock
========================================================================
*** 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=/home/vagrant/.rbenv/versions/2.6.5/bin/$(RUBY_BASE_NAME)
        --help
        --clean
        --use-system-libraries
        --enable-static
        --disable-static
        --with-zlib-dir
        --without-zlib-dir
        --with-zlib-include
        --without-zlib-include=${zlib-dir}/include
        --with-zlib-lib
        --without-zlib-lib=${zlib-dir}/lib
        --enable-cross-build
        --disable-cross-build
/home/vagrant/.rbenv/versions/2.6.5/lib/ruby/gems/2.6.0/gems/mini_portile2-2.4.0/lib/mini_portile2/mini_portile.rb:402:in `block in execute': Failed to complete configure task (RuntimeError)
        from /home/vagrant/.rbenv/versions/2.6.5/lib/ruby/gems/2.6.0/gems/mini_portile2-2.4.0/lib/mini_portile2/mini_portile.rb:373:in `chdir'
        from /home/vagrant/.rbenv/versions/2.6.5/lib/ruby/gems/2.6.0/gems/mini_portile2-2.4.0/lib/mini_portile2/mini_portile.rb:373:in `execute'
        from /home/vagrant/.rbenv/versions/2.6.5/lib/ruby/gems/2.6.0/gems/mini_portile2-2.4.0/lib/mini_portile2/mini_portile.rb:110:in `configure'
        from /home/vagrant/.rbenv/versions/2.6.5/lib/ruby/gems/2.6.0/gems/mini_portile2-2.4.0/lib/mini_portile2/mini_portile.rb:153:in `cook'
        from extconf.rb:365:in `block (2 levels) in process_recipe'
        from extconf.rb:257:in `block in chdir_for_build'
        from extconf.rb:256:in `chdir'
        from extconf.rb:256:in `chdir_for_build'
        from extconf.rb:364:in `block in process_recipe'
        from extconf.rb:262:in `tap'
        from extconf.rb:262:in `process_recipe'
        from extconf.rb:557:in `<main>'

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

  /home/vagrant/.rbenv/versions/2.6.5/lib/ruby/gems/2.6.0/extensions/x86_64-linux/2.6.0-static/nokogiri-1.10.5/mkmf.log

extconf failed, exit code 1

Gem files will remain installed in /home/vagrant/.rbenv/versions/2.6.5/lib/ruby/gems/2.6.0/gems/nokogiri-1.10.5 for inspection.
Results logged to /home/vagrant/.rbenv/versions/2.6.5/lib/ruby/gems/2.6.0/extensions/x86_64-linux/2.6.0-static/nokogiri-1.10.5/gem_make.out

試したこと

Rubyの再インストール、
gemのアップデート
gccのアップデート

###　エラーの解読
エラーコードに書いてある、

    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

は一通り試しました。

gem install nokogiri -- --use-system-libraries

では↓を実行しなさいと言われたので

 gem install pkg-config -v "~> 1.1"

を実行、このGemのインストールはできたものの、再度nokogiriのインストールをしても初期のエラーと変わらず...
最後の bundle install はそもそもGemFileが存在しないため実行できませんでした。

Comments

[kazto]

/home/vagrant/.rbenv/versions/2.6.5/lib/ruby/gems/2.6.0/extensions/x86_64-linux/2.6.0-static/nokogiri-1.10.5/mkmf.log
の内容を追記お願いします。

[Laugh]

‘‘‘
"gcc -o conftest -I/home/vagrant/.rbenv/versions/2.6.5/include/ruby-2.6.0/x86_64-linux -I/home/vagrant/.rbenv/versions/2.6.5/include/ruby-2.6.0/ruby/backward -I/home/vagrant/.rbenv/versions/2.6.5/include/ruby-2.6.0 -I. -I/home/vagrant/.rbenv/versions/2.6.5/include -O3 -ggdb3 -Wall -Wextra -Wdeclaration-after-statement -Wdeprecated-declarations -Wimplicit-function-declaration -Wimplicit-int -Wpointer-arith -Wwrite-strings -Wmissing-noreturn -Wno-cast-function-type -Wno-constant-logical-operand -Wno-long-long -Wno-missing-field-initializers -Wno-overlength-strings -Wno-packed-bitfield-compat -Wno-parentheses-equality -Wno-self-assign -Wno-tautological-compare -Wno-unused-parameter -Wno-unused-value -Wunused-variable conftest.c -L. -L/home/vagrant/.rbenv/versions/2.6.5/lib -Wl,-rpath,/home/vagrant/.rbenv/versions/2.6.5/lib -L. -L/home/vagrant/.rbenv/versions/2.6.5/lib -fstack-protector -rdynamic -Wl,-export-dynamic -Wl,-rpath,/home/vagrant/.rbenv/versions/2.6.5/lib -L/home/vagrant/.rbenv/versions/2.6.5/lib -lruby-static -lpthread -lrt -lrt -lrt -ldl -lcrypt -lm -lm -lc "
checked program was:
/* begin */
1: #include "ruby.h"
2:
3: int main(int argc, char **argv)
4: {
5: return 0;
6: }
/* end */

"gcc -I/home/vagrant/.rbenv/versions/2.6.5/include/ruby-2.6.0/x86_64-linux -I/home/vagrant/.rbenv/versions/2.6.5/include/ruby-2.6.0/ruby/backward -I/home/vagrant/.rbenv/versions/2.6.5/include/ruby-2.6.0 -I. -I/home/vagrant/.rbenv/versions/2.6.5/include -O3 -ggdb3 -Wall -Wextra -Wdeclaration-after-statement -Wdeprecated-declarations -Wimplicit-function-declaration -Wimplicit-int -Wpointer-arith -Wwrite-strings -Wmissing-noreturn -Wno-cast-function-type -Wno-constant-logical-operand -Wno-long-long -Wno-missing-field-initializers -Wno-overlength-strings -Wno-packed-bitfield-compat -Wno-parentheses-equality -Wno-self-assign -Wno-tautological-compare -Wno-unused-parameter -Wno-unused-value -Wunused-variable -Werror -c conftest.c"
checked program was:
/* begin */
1: #include "ruby.h"
2:
3: int main() {return 0;}
/* end */

have_library: checking for gzdopen() in -lz... -------------------- yes

"gcc -o conftest -I/home/vagrant/.rbenv/versions/2.6.5/include/ruby-2.6.0/x86_64-linux -I/home/vagrant/.rbenv/versions/2.6.5/include/ruby-2.6.0/ruby/backward -I/home/vagrant/.rbenv/versions/2.6.5/include/ruby-2.6.0 -I. -I/home/vagrant/.rbenv/versions/2.6.5/include -O3 -ggdb3 -Wall -Wextra -Wdeclaration-after-statement -Wdeprecated-declarations -Wimplicit-function-declaration -Wimplicit-int -Wpointer-arith -Wwrite-strings -Wmissing-noreturn -Wno-cast-function-type -Wno-constant-logical-operand -Wno-long-long -Wno-missing-field-initializers -Wno-overlength-strings -Wno-packed-bitfield-compat -Wno-parentheses-equality -Wno-self-assign -Wno-tautological-compare -Wno-unused-parameter -Wno-unused-value -Wunused-variable -g -DXP_UNIX -O3 -Wall -Wcast-qual -Wwrite-strings -Wmissing-noreturn -Winline conftest.c -L. -L/home/vagrant/.rbenv/versions/2.6.5/lib -Wl,-rpath,/home/vagrant/.rbenv/versions/2.6.5/lib -L. -L/home/vagrant/.rbenv/versions/2.6.5/lib -fstack-protector -rdynamic -Wl,-export-dynamic -Wl,-rpath,/home/vagrant/.rbenv/versions/2.6.5/lib -L/home/vagrant/.rbenv/versions/2.6.5/lib -lruby-static -lpthread -lrt -lrt -lrt -ldl -lcrypt -lm -lz -lm -lc "
checked program was:
/* begin */
1: #include "ruby.h"
2:
3: #include <zlib.h>
4:
5: /*top*/
6: extern int t(void);
7: int main(int argc, char **argv)
8: {
9: if (argc > 1000000) {
10: int (* volatile tp)(void)=(int (*)(void))&t;
11: printf("%d", (*tp)());
12: }
13:
14: return 0;
15: }
16: int t(void) { void ((*volatile p)()); p = (void ((*)()))gzdopen; return !p; }
/* end */

--------------------

have_iconv?: checking for iconv... -------------------- yes

"gcc -o conftest -I/home/vagrant/.rbenv/versions/2.6.5/include/ruby-2.6.0/x86_64-linux -I/home/vagrant/.rbenv/versions/2.6.5/include/ruby-2.6.0/ruby/backward -I/home/vagrant/.rbenv/versions/2.6.5/include/ruby-2.6.0 -I. -I/home/vagrant/.rbenv/versions/2.6.5/include -O3 -ggdb3 -Wall -Wextra -Wdeclaration-after-statement -Wdeprecated-declarations -Wimplicit-function-declaration -Wimplicit-int -Wpointer-arith -Wwrite-strings -Wmissing-noreturn -Wno-cast-function-type -Wno-constant-logical-operand -Wno-long-long -Wno-missing-field-initializers -Wno-overlength-strings -Wno-packed-bitfield-compat -Wno-parentheses-equality -Wno-self-assign -Wno-tautological-compare -Wno-unused-parameter -Wno-unused-value -Wunused-variable -g -DXP_UNIX -O3 -Wall -Wcast-qual -Wwrite-strings -Wmissing-noreturn -Winline conftest.c -L. -L/home/vagrant/.rbenv/versions/2.6.5/lib -Wl,-rpath,/home/vagrant/.rbenv/versions/2.6.5/lib -L. -L/home/vagrant/.rbenv/versions/2.6.5/lib -fstack-protector -rdynamic -Wl,-export-dynamic -Wl,-rpath,/home/vagrant/.rbenv/versions/2.6.5/lib -L/home/vagrant/.rbenv/versions/2.6.5/lib -lruby-static -lpthread -lrt -lrt -lrt -ldl -lcrypt -lm -lm -lc "
checked program was:
/* begin */
1: #include "ruby.h"
2:
3: #include <stdlib.h>
4: #include <iconv.h>
5:
6: int main(void)
7: {
8: iconv_t cd = iconv_open("", "");
9: iconv(cd, NULL, NULL, NULL, NULL);
10: return EXIT_SUCCESS;
11: }
/* end */
‘‘‘

[kazto]

上記ですべてでしょうか？エラーが見当たりません。

[Laugh]

全てです...

[Laugh]

"gcc -o conftest -I/home/vagrant/.rbenv/versions/2.6.5/include/ruby-2.6.0/x86_64-linux -I/home/vagrant/.rbenv/versions/2.6.5/include/ruby-2.6.0/ruby/backward -I/home/vagrant/.rbenv/versions/2.6.5/include/ruby-2.6.0 -I. -I/home/vagrant/.rbenv/versions/2.6.5/include -O3 -ggdb3 -Wall -Wextra -Wdeclaration-after-statement -Wdeprecated-declarations -Wimplicit-function-declaration -Wimplicit-int -Wpointer-arith -Wwrite-strings -Wmissing-noreturn -Wno-cast-function-type -Wno-constant-logical-operand -Wno-long-long -Wno-missing-field-initializers -Wno-overlength-strings -Wno-packed-bitfield-compat -Wno-parentheses-equality -Wno-self-assign -Wno-tautological-compare -Wno-unused-parameter -Wno-unused-value -Wunused-variable conftest.c -L. -L/home/vagrant/.rbenv/versions/2.6.5/lib -Wl,-rpath,/home/vagrant/.rbenv/versions/2.6.5/lib -L. -L/home/vagrant/.rbenv/versions/2.6.5/lib -fstack-protector -rdynamic -Wl,-export-dynamic -Wl,-rpath,/home/vagrant/.rbenv/versions/2.6.5/lib -L/home/vagrant/.rbenv/versions/2.6.5/lib -lruby-static -lpthread -lrt -lrt -lrt -ldl -lcrypt -lm -lm -lc "
checked program was:
/* begin */
1: #include "ruby.h"
2:
3: int main(int argc, char **argv)
4: {
5: return 0;
6: }
/* end */

"gcc -I/home/vagrant/.rbenv/versions/2.6.5/include/ruby-2.6.0/x86_64-linux -I/home/vagrant/.rbenv/versions/2.6.5/include/ruby-2.6.0/ruby/backward -I/home/vagrant/.rbenv/versions/2.6.5/include/ruby-2.6.0 -I. -I/home/vagrant/.rbenv/versions/2.6.5/include -O3 -ggdb3 -Wall -Wextra -Wdeclaration-after-statement -Wdeprecated-declarations -Wimplicit-function-declaration -Wimplicit-int -Wpointer-arith -Wwrite-strings -Wmissing-noreturn -Wno-cast-function-type -Wno-constant-logical-operand -Wno-long-long -Wno-missing-field-initializers -Wno-overlength-strings -Wno-packed-bitfield-compat -Wno-parentheses-equality -Wno-self-assign -Wno-tautological-compare -Wno-unused-parameter -Wno-unused-value -Wunused-variable -Werror -c conftest.c"
checked program was:
/* begin */
1: #include "ruby.h"
2:
3: int main() {return 0;}
/* end */

have_library: checking for gzdopen() in -lz... -------------------- yes

"gcc -o conftest -I/home/vagrant/.rbenv/versions/2.6.5/include/ruby-2.6.0/x86_64-linux -I/home/vagrant/.rbenv/versions/2.6.5/include/ruby-2.6.0/ruby/backward -I/home/vagrant/.rbenv/versions/2.6.5/include/ruby-2.6.0 -I. -I/home/vagrant/.rbenv/versions/2.6.5/include -O3 -ggdb3 -Wall -Wextra -Wdeclaration-after-statement -Wdeprecated-declarations -Wimplicit-function-declaration -Wimplicit-int -Wpointer-arith -Wwrite-strings -Wmissing-noreturn -Wno-cast-function-type -Wno-constant-logical-operand -Wno-long-long -Wno-missing-field-initializers -Wno-overlength-strings -Wno-packed-bitfield-compat -Wno-parentheses-equality -Wno-self-assign -Wno-tautological-compare -Wno-unused-parameter -Wno-unused-value -Wunused-variable -g -DXP_UNIX -O3 -Wall -Wcast-qual -Wwrite-strings -Wmissing-noreturn -Winline conftest.c -L. -L/home/vagrant/.rbenv/versions/2.6.5/lib -Wl,-rpath,/home/vagrant/.rbenv/versions/2.6.5/lib -L. -L/home/vagrant/.rbenv/versions/2.6.5/lib -fstack-protector -rdynamic -Wl,-export-dynamic -Wl,-rpath,/home/vagrant/.rbenv/versions/2.6.5/lib -L/home/vagrant/.rbenv/versions/2.6.5/lib -lruby-static -lpthread -lrt -lrt -lrt -ldl -lcrypt -lm -lz -lm -lc "
checked program was:
/* begin */
1: #include "ruby.h"
2:
3: #include <zlib.h>
4:
5: /*top*/
6: extern int t(void);
7: int main(int argc, char **argv)
8: {
9: if (argc > 1000000) {
10: int (* volatile tp)(void)=(int (*)(void))&t;
11: printf("%d", (*tp)());
12: }
13:
14: return 0;
15: }
16: int t(void) { void ((*volatile p)()); p = (void ((*)()))gzdopen; return !p; }
/* end */

--------------------

have_iconv?: checking for iconv... -------------------- yes

"gcc -o conftest -I/home/vagrant/.rbenv/versions/2.6.5/include/ruby-2.6.0/x86_64-linux -I/home/vagrant/.rbenv/versions/2.6.5/include/ruby-2.6.0/ruby/backward -I/home/vagrant/.rbenv/versions/2.6.5/include/ruby-2.6.0 -I. -I/home/vagrant/.rbenv/versions/2.6.5/include -O3 -ggdb3 -Wall -Wextra -Wdeclaration-after-statement -Wdeprecated-declarations -Wimplicit-function-declaration -Wimplicit-int -Wpointer-arith -Wwrite-strings -Wmissing-noreturn -Wno-cast-function-type -Wno-constant-logical-operand -Wno-long-long -Wno-missing-field-initializers -Wno-overlength-strings -Wno-packed-bitfield-compat -Wno-parentheses-equality -Wno-self-assign -Wno-tautological-compare -Wno-unused-parameter -Wno-unused-value -Wunused-variable -g -DXP_UNIX -O3 -Wall -Wcast-qual -Wwrite-strings -Wmissing-noreturn -Winline conftest.c -L. -L/home/vagrant/.rbenv/versions/2.6.5/lib -Wl,-rpath,/home/vagrant/.rbenv/versions/2.6.5/lib -L. -L/home/vagrant/.rbenv/versions/2.6.5/lib -fstack-protector -rdynamic -Wl,-export-dynamic -Wl,-rpath,/home/vagrant/.rbenv/versions/2.6.5/lib -L/home/vagrant/.rbenv/versions/2.6.5/lib -lruby-static -lpthread -lrt -lrt -lrt -ldl -lcrypt -lm -lm -lc "
checked program was:
/* begin */
1: #include "ruby.h"
2:
3: #include <stdlib.h>
4: #include <iconv.h>
5:
6: int main(void)
7: {
8: iconv_t cd = iconv_open("", "");
9: iconv(cd, NULL, NULL, NULL, NULL);
10: return EXIT_SUCCESS;
11: }
/* end */

--------------------

cyberduck を更新し忘れていたかもしれないので更新して再度追記いたします。

Answer 1

エラー内容は見ないで回答しますが、だいたいCentOSのgem install時にハマるパターンは決まっているので、こちらをお試しください。

CentOSにおけるgem install時のエラーの解決の流れ

• (1) 必要とされているdevelパッケージをyumコマンドでインストールする
• (2) gem installを試す
• (3) エラーが出たら、(1)(2)を繰り返す

(1) nokogiriが必要とするパッケージをインストールする

※CentOSではnative extension系のエラーはdevelパッケージをインストールとだいたい解決します。
どのdevelパッケージが必要なのかはエラーメッセージなどから判断したり、
「CentOS nokogiri devel」とかで検索すると分かる場合があります。

nokogoriの場合は「libxml2-devel」「libxslt-devel」のはずです。

$ sudo yum install -y libxml2-devel libxslt-devel

(2) gem installを試す

$ gem install rails -v 5.1.3 --no-document

Comments

[Laugh]

libxml2-devel,libxslt-devel　はインストールできましたが変わらず同じエラーメッセージが出てきました...

[mingos]

なるほど、ではまた別の問題ということですね。
ちなみにCentOS7ですか？

[Laugh]

今解決いたしました！
develパッケージをインストールした後、
＄ gem install nokogiri -- --use-system-libraries
でnokogiriだけインストールした後にRailsをインストールしたら何の引っ掛かりもなくできました！
ありがとうございます！

[mingos]

解決したようで安心しました！

Answer 2

エラーメッセージに、

checking whether build environment is sane... configure: error: newly created file is older than distributed files!

Check your system clock

とあります。時計がずれているとSSL通信の障害となるなど何かとトラブルになりますので、仮想マシン内の時計が正しいかも確認してみてください。