Couldn't install gem - extconf.rb failed - ruby

Question

I upgraded the macos to Mojave and reinstalled xcode, xcode CLT, ruby, etc. Then when I tried:
gem install nokogiri
I got the following error (installing other gems gave similar error):
ERROR: Failed to build gem native extension.
current directory: /usr/local/lib/ruby/gems/2.5.0/gems/nokogiri-1.8.5/ext/nokogiri
/usr/local/opt/ruby/bin/ruby -r ./siteconf20181209-20884-etfc5r.rb extconf.rb
checking if the C compiler accepts ... *** 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.
I checked the mkmf.log, which contains the following:
"clang -o conftest -I/usr/local/Cellar/ruby/2.5.3_1/include/ruby-2.5.0/x86_64-darwin18 -I/usr/local/Cellar/ruby/2.5.3_1/include/ruby-2.5.0/ruby/backward -I/usr/local/Cellar/ruby/2.5.3_1/include/ruby-2.5.0 -I. -I/usr/local/opt/libyaml/include -I/usr/local/opt/openssl/include -I/usr/local/opt/readline/include -D_XOPEN_SOURCE -D_DARWIN_C_SOURCE -D_DARWIN_UNLIMITED_SELECT -D_REENTRANT -O3 -ggdb3 -Wall -Wextra -Wno-unused-parameter -Wno-parentheses -Wno-long-long -Wno-missing-field-initializers -Wno-tautological-compare -Wno-parentheses-equality -Wno-constant-logical-operand -Wno-self-assign -Wunused-variable -Wimplicit-int -Wpointer-arith -Wwrite-strings -Wdeclaration-after-statement -Wshorten-64-to-32 -Wimplicit-function-declaration -Wdivision-by-zero -Wdeprecated-declarations -Wextra-tokens -fno-common -pipe conftest.c -L. -L/usr/local/Cellar/ruby/2.5.3_1/lib -L/usr/local/opt/libyaml/lib -L/usr/local/opt/openssl/lib -L/usr/local/opt/readline/lib -L. -fstack-protector -L/usr/local/lib -L/usr/local/opt/libyaml/lib -L/usr/local/opt/openssl/lib -L/usr/local/opt/readline/lib -lruby.2.5.3 -lpthread -ldl -lobjc "
In file included from conftest.c:1:
In file included from /usr/local/Cellar/ruby/2.5.3_1/include/ruby-2.5.0/ruby.h:33:
In file included from /usr/local/Cellar/ruby/2.5.3_1/include/ruby-2.5.0/ruby/ruby.h:29:
The text went on like this for a while. I also cd to the nokogiri folder and directly run extconf.rb, and got the following error:
checking if the C compiler accepts ... *** 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
--with-opt-include
... (skipped similar content for brevity and continued below)
usr/local/Cellar/ruby/2.5.3_1/lib/ruby/2.5.0/mkmf.rb:456:in 'try_do': The compiler failed to generate an executable file. (RuntimeError)
You have to install development tools first.
I tried to install xcode. I also installed the header and acknowledged the license. I at first thought it has to do with GCC, but the mkmf file showed that the problem is with Clang.
Hope someone can help.

Answer 1

I had to run the following cryptic commands to get nokogiri installed. Basically this entails getting my C compiler working in mac osx Mojave, after having everything working fine in a previous OS (Yosemite I think it was...)
This is an (somewhat) obvious step when upgrading osx:
xcode-select --install
I also had to do this, which I never would've known how to do without google and this post
sudo installer -pkg /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg -target /
Finally, I had to agree to the xcode license (found I had to do this via the makefile logs when install of nokogiri failed...)
sudo xcodebuild -licence
It'll prompt you to eventually type "agree"
Finally, continuing with bundle works as expected for a new rails project that includes nokogiri. Success!