nokogiri gem installation error
Finally, the problem was caused by nokogiri itself by shipping it's own libxml2 that's incompatible with some systems.
So to install nokogiri I had to tell it that it should use the system libraries.
I installed it manually by:
gem install nokogiri -v 1.6.2.1 -- --use-system-libraries
And it worked well. Other answers didn't solve it.
2020 April 6th Update:
macOS Catalina 10.15
gem install nokogiri -- --use-system-libraries=true --with-xml2-include=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.15.sdk/usr/include/libxml2/
macOS Mojave 10.14
gem install nokogiri -- --use-system-libraries=true --with-xml2-include=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include/libxml2/
macOS High Sierra 10.13
gem install nokogiri -- --use-system-libraries=true --with-xml2-include=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.13.sdk/usr/include/libxml2/
macOS Sierra 10.12:
gem install nokogiri -- --use-system-libraries=true --with-xml2-include=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.12.sdk/usr/include/libxml2/
OS X El Capitan 10.11
gem install nokogiri -- --use-system-libraries=true --with-xml2-include=/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk/usr/include/libxml2/
Consider to add sudo if you don't have permission.
For some reason Apple’s Yosemite version of OSX does not have a system accessible installation of libxml2. Nokogiri requires this in order to compile and luckily Xcode has a version of libxml2 bundled with it — we just need to specify it when installing the gem. It’s important to get Nokogiri installed correctly because as of right now Rails 4.2.1.rc4 automatically attempts to install it and you will feel pain.
Checkout this post for more info.
I ran into this same problem, because of an unlisted build dependency. When I found the tmp directory in question:
find ~/.rbenv/ -name patch.log
It said:
sh: patch: command not found
Fixed that with a simple:
sudo yum install -y patch
On OSX Yosemite, I did xcode-select --install in a terminal. After which, bundle worked fine with that gem.