Nokogiri seems to be the source of many problems on my Mac and after upgrading to macOS Sierra, I wasn’t very surprised to have problem.

Problem

You may get an error similar to:

ERROR: Error installing nokogiri:
ERROR: Failed to build gem native extension.
/System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/bin/ruby extconf.rb
Using pkg-config version 1.1.7
checking if the C compiler accepts ... yes
checking if the C compiler accepts -Wno-error=unused-command-line-argument-hard-error-in-future... no
Building nokogiri using packaged libraries.
Using mini_portile version 2.1.0
checking for iconv.h... yes
checking for gzdopen() in -lz... yes
checking for iconv... yes
************************************************************************
IMPORTANT NOTICE:
Building Nokogiri with a packaged version of libxml2-2.9.4.

Suggesting using system libraries with:

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

Which leads to other less than helpful suggestions.

Solution

It seems after the macOS upgrade and moving to Xcode 8.0, command line tools were not installed.

I was able to get Nokogiri installed by first installing the Xcode command line tools:

xcode-select --install

Then install Nokogiri using the system libraries:

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

I hope this helps someone trying to solve a problem that seems should have been solved better by now.