Gem and Bundler are different package manager and has different package under its folder

jekyll build use Gem package bundle exec jekyll build use Bundler package

The file "/usr/include/iconv.h" is missing in your build environment, when install nokogiri

• In OSX 10.9+, you may need to run xcode-select --install to install xCode command tools to allow you to install libiconv.
• if you want the newest version, go through the following steps
• install a newer version of libiconv by brew install libiconv
• then link your new iconv libs using brew link libiconv
• then install your gem using gem install nokogiri -- --with-iconv-dir=/usr/local/Cellar/libiconv/1.14