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How to fix "nokogiri" gem releated dependency issues in OSX (El Capitan)

I tried setting up a nice Jekyll-based site (or theme, rather) Indigo on my up-to-date Mac today, and ran into a host of issues. I spent quite some time resolving it all, to the extent I thought this would be valuable for others to get recapped.

My experience setting up "Indigo" Jekyll theme

First, I clone repo. Install Jekyll, NodeJS and Bundler. Do bundle install, and get hit in the face:

An error occurred while installing nokogiri (, and Bundler cannot continue.

Scroll the logs and see:

libxml2 is missing. Please locate mkmf.log to investigate how it is failing.

Run _ find / -name mkmf.log to locate logs hoping to become wiser. Locate logs, read it, and indeed, libxml2 related errors (and a bunch others) are reflected:

package configuration for libxslt is not found
package configuration for libxml-2.0 is not found
package configuration for libiconv is not found

bundle install logs also advice me to: Make sure that "gem install nokogiri -v ''" succeeds before bundling., so I try it:

sudo gem install nokogiri -v ''

Fails similarly. libxml2 is missing.

I start Googling for tips, and realize that I am one in a million experiencing issues installing Nokogiri on OSX.

Find two valueable resources:

I educate myself, and understand I should try to override the system libriaries used during the install. OK, fair enough - I'll install & use sys. libs. for nokogiri:

brew install libxml2 libxslt libiconv

libxml2 and libxslt seem to install fine, but for libiconv I get errors:

Error: No available formula with the name "libiconv"
==> Searching for similarly named formulae...
Error: No similarly named formulae found.
==> Searching taps...
This formula was found in a tap:
To install it, run:
  brew install homebrew/dupes/libiconv

Based on tips in the SO thread linked above, I try to install libiconv from source:

tar xvfz libiconv-1.13.1.tar.gz
cd libiconv-1.13.1
./configure --prefix=/usr/local/Cellar/libiconv/1.13.1
sudo make install


Now I try to install nokogiri with sys. libs:

sudo gem install nokogiri -v '' -- --use-system-libraries --with-xml2-include=/usr/include/libxml2 --with-xml2-lib=/usr/lib ``

and get:

Building native extensions with: '--use-system-libraries --with-xml2-include=/usr/include/libxml2 --with-xml2-lib=/usr/lib'
This could take a while...
ERROR:  While executing gem ... (Errno::EPERM)
    Operation not permitted - /usr/bin/nokogiri

WTF?? Sudo!! I am the lord here! Listen to me computer, like you always do!


I must google. Educate myself. Now I'm starting to be really puzzled. It turns out:

Apparently with OSX el Capitan, there is a new security function that prevents you from modifying system files called Rootless.

(from SO)

Goddamit, more of this BS. Turns out I must reboot my Mac to Recovery mode, and disable this new System Integrity Protection (see SO thread for instructions). So I do.

I retry the command

sudo gem install nokogiri -v '' -- --use-system-libraries --with-xml2-include=/usr/include/libxml2 --with-xml2-lib=/usr/lib

and, guess what:

1 gem installed


Now I can continue to bundle install the remaining deps, and kick off my newly setup Jekyll-based blog with the excellent Indigo theme!

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