After upgrading to macOS Mojave gem update is failing - macos

Question

Building native extensions. This could take a while...
ERROR: Error installing libxml-ruby:
ERROR: Failed to build gem native extension.
current directory: /Library/Ruby/Gems/2.3.0/gems/libxml-ruby-3.1.0/ext/libxml
/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/bin/ruby -r ./siteconf20180926-80978-eoqfjh.rb extconf.rb
checking for libxml/xmlversion.h in /opt/include/libxml2,/opt/local/include/libxml2,/usr/local/include/libxml2,/usr/include/libxml2... no
*** extconf.rb failed ***
Could not create Makefile due to some reason, probably lack of necessary
libraries and/or headers. Check the mkmf.log file for more details. You may
need configuration options.
Provided configuration options:
--with-opt-dir
--without-opt-dir
--with-opt-include
--without-opt-include=${opt-dir}/include
--with-opt-lib
--without-opt-lib=${opt-dir}/lib
--with-make-prog
--without-make-prog
--srcdir=.
--curdir
--ruby=/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/bin/$(RUBY_BASE_NAME)
--with-xml2-config
--without-xml2-config
--with-xml2-dir
--without-xml2-dir
--with-xml2-include
--without-xml2-include=${xml2-dir}/include
--with-xml2-lib
--without-xml2-lib=${xml2-dir}/lib
extconf failure: need libxml2.
Install the library or try one of the following options to extconf.rb:
--with-xml2-config=/path/to/xml2-config
--with-xml2-dir=/path/to/libxml2
--with-xml2-lib=/path/to/libxml2/lib
--with-xml2-include=/path/to/libxml2/include
To see why this extension failed to compile, please check the mkmf.log which can be found here:
/Library/Ruby/Gems/2.3.0/extensions/universal-darwin-18/2.3.0/libxml-ruby-3.1.0/mkmf.log
extconf failed, exit code 1
Gem files will remain installed in /Library/Ruby/Gems/2.3.0/gems/libxml-ruby-3.1.0 for inspection.
Results logged to /Library/Ruby/Gems/2.3.0/extensions/universal-darwin-18/2.3.0/libxml-ruby-3.1.0/gem_make.out
Updating nokogiri
Building native extensions. This could take a while...
ERROR: While executing gem ... (Gem::FilePermissionError)
You don't have write permissions for the /usr/bin directory.

Answer 1

The error is due to macOS Mojave has stopped placing the standard header files in /usr/include, keeping them only inside the XCode directory.
You can verify this by running ls /usr/include and most likely this directory does not exist anymore. On contrary, the usual trick by running xcode-select --install will not solve the problem.
The fix is to run legacy installer provided by Apple that will install the header files to /usr/include
sudo installer -pkg /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg -target /

Answer 2

If you are using homebrew, the recommended approach is to tell pkg-config where it can find the libxml2 library:
brew reinstall libxml2
export PKG_CONFIG_PATH="/usr/local/opt/libxml2/lib/pkgconfig"

Answer 3

Also, you may have outdated bundle config, which is in the way. Run bundle config build.nokogiri --use-system-libraries and it'll give you a warning and show what config you currently have. I was following all guides and reinstalled all gems and even ruby a few times only to find out that config was set to use a path that doesn't exist anymore.