Error about nokogiri while capistrano deployment on ubuntu server

Question

While bundle:install phase after deploy:finalize_update,i'm getting an error about nokogiri. It suggests ,

 ** [out :: *******] Make sure that `gem install nokogiri -v '1.6.0'` succeeds before bundling.

So i tried to install nokogiri by myself on server.But it gives following error,

Building native extensions.  This could take a while...
ERROR:  Error installing nokogiri:
    ERROR: Failed to build gem native extension.

    /home/deployer/.rvm/rubies/ruby-2.0.0-p0/bin/ruby extconf.rb
Extracting libxml2-2.8.0.tar.gz into tmp/x86_64-linux-gnu/ports/libxml2/2.8.0... OK
Running 'configure' for libxml2 2.8.0... OK
Running 'compile' for libxml2 2.8.0... ERROR, review 'tmp/x86_64-linux-gnu/ports/libxml2/2.8.0/compile.log' to see what happened.
*** 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/deployer/.rvm/rubies/ruby-2.0.0-p0/bin/ruby
/home/deployer/.rvm/rubies/ruby-2.0.0-p0/lib/ruby/gems/2.0.0/gems/mini_portile-0.5.0/lib/mini_portile.rb:235:in `block in execute': Failed to complete compile task (RuntimeError)
    from /home/deployer/.rvm/rubies/ruby-2.0.0-p0/lib/ruby/gems/2.0.0/gems/mini_portile-0.5.0/lib/mini_portile.rb:227:in `chdir'
    from /home/deployer/.rvm/rubies/ruby-2.0.0-p0/lib/ruby/gems/2.0.0/gems/mini_portile-0.5.0/lib/mini_portile.rb:227:in `execute'
    from /home/deployer/.rvm/rubies/ruby-2.0.0-p0/lib/ruby/gems/2.0.0/gems/mini_portile-0.5.0/lib/mini_portile.rb:61:in `compile'
    from /home/deployer/.rvm/rubies/ruby-2.0.0-p0/lib/ruby/gems/2.0.0/gems/mini_portile-0.5.0/lib/mini_portile.rb:101:in `cook'
    from extconf.rb:101:in `block in <main>'
    from extconf.rb:119:in `call'
    from extconf.rb:119:in `block in <main>'
    from extconf.rb:109:in `tap'
    from extconf.rb:109:in `<main>'


Gem files will remain installed in /home/deployer/.rvm/gems/ruby-2.0.0-p0/gems/nokogiri-1.6.0 for inspection.
Results logged to /home/deployer/.rvm/gems/ruby-2.0.0-p0/gems/nokogiri-1.6.0/ext/nokogiri/gem_make.out

It just started today.Also libxml2 is already installed.

Any idea?

Thanks.

EDIT: I dont require explicitly nokogiri in my gemfile.

Answer 1

I faced the same issue with Nokogiri 1.6.0. The problem, as you can see from the logs, it's caused by a failed compilation of libxml2 that, together with libxslt, is now shipped embedded in the gem and compiled when you install it.

To find out what exactly went wrong with the compilation, have a look at the suggested file compile.log that, in your case, you can find at:

/home/deployer/.rvm/gems/ruby-2.0.0-p0/gems/nokogiri-1.6.0/ext/nokogiri/tmp/x86_64-linux-gnu/ports/libxml2/2.8.0/compile.log

As a workaround (assuming you have libxml2-dev and libxslt-dev installed), you can do:

NOKOGIRI_USE_SYSTEM_LIBRARIES=1 bundle install

I hope it helps.

Answer 2

If you're using Capistrano 3.x you can do the following in your deploy.rb file (or environment specific file i.e. deploy/production.rb)

set :bundle_env_variables, { 'NOKOGIRI_USE_SYSTEM_LIBRARIES' => 1 }

This way you avoid overriding the bundle install task. This will set the given env variables when running bundle install.