There are many people with similar issues and I've been one of them in the past on other machines and none of the solutions out there appear to work -- I also appear to have different error than others who have similar problems:
Building native extensions. This could take a while...
ERROR: Error installing therubyracer:
ERROR: Failed to build gem native extension.
/Users/username/.rvm/rubies/ruby-2.0.0-p353/bin/ruby -r ./siteconf20150412-25981-y7cvt6.rb extconf.rb
checking for main() in -lpthread... yes
checking for main() in -lobjc... yes
creating Makefile
make "DESTDIR=" clean
make "DESTDIR="
compiling accessor.cc
clang: warning: argument unused during compilation: '-rdynamic'
In file included from accessor.cc:1:
In file included from ./rr.h:6:
In file included from /Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/vector:265:
In file included from /Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__bit_reference:15:
In file included from /Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/algorithm:628:
In file included from /Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/memory:604:
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/iterator:341:10: fatal error: '__debug' file not found
#include <__debug>
^
1 error generated.
make: *** [accessor.o] Error 1
make failed, exit code 2
Gem files will remain installed in /Users/ecnalyr/.rvm/gems/ruby-2.0.0-p353@canopy/gems/therubyracer-0.12.2 for inspection.
Results logged to /Users/ecnalyr/.rvm/gems/ruby-2.0.0-p353@canopy/extensions/x86_64-darwin-14/2.0.0/therubyracer-0.12.2/gem_make.out
When running:
gem install therubyracer -v '0.12.2'
or simply
bundle install
with therubyracer included in my gemfile.
I'm running Yosemite 10.10.3, Ruby 2.0.0-p353, I have uninstalled everything and tried the gem install libv8 -- --with-system-v8 solution that comes up frequently with these kind of problems, but have found no resolution.
I was able to solve this by re-installing Command Line Tools for XCode 6.2 (instead of those for XCode 6.3).
There's more discussion in Stack Overflow 29529455.