If you get this warning on your local machine one of these steps might help:

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Rebuilt the gem with the newer library

gem install --no-rdoc --no-ri nokogiri -- --with-xml2-include=/opt/local/include/libxml2 --with-xml2-lib=/opt/local/lib

If you still get the error, try to uninstall all nokogiri versions with

gem uninstall nokogiri

and install nokogiri again.

Fixing the issue on servers

However, on our servers this probably will not work. On the server, gems are stored in the ../shared/bundle/ruby/:version/gems directory (relative to the current app directory).
If you do gem install in the current app directory, bundler will have no knowledge of this.

What you want to do instead is

bundle pristine nokogiri

and restart the application servers (e.g. b cap <environment> passenger:restart)

This should install the right nokogiri version and make the warning go away.