title: Boost no longer works with Homebrew on Mac El Capitan
body: <p>I just updated from Yosemite to El Capitan and it has broken one of my C++ programs which was relying on Boost. Whenever I try to compile, I get these errors:</p>
  
  <pre><code>fatal error: 'boost/timer/timer.hpp' file not found
  #include &lt;boost/timer/timer.hpp&gt;
  
  fatal error: 'boost/program_options.hpp' file not found
  #include "boost/program_options.hpp"
  </code></pre>
  
  <p>I've been compiling it with the correct flags and it worked perfectly before:</p>
  
  <pre><code>-lboost_timer-mt \
  -lboost_program_options-mt \
  </code></pre>
  
  <p>I've followed the home-brew instructions to chown /usr/local, run brew doctor and brew update, even brew reinstall boost. I've also checked and timer.hpp is present in /usr/local/include/boost.</p>
  
  <p><strong>Update</strong> Ran: clang++ -E -x c++ - -v &lt; /dev/null</p>
  
  <pre><code>Apple LLVM version 7.0.0 (clang-700.0.72) Target: x86_64-apple-darwin15.0.0 Thread model: posix  "/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/clang"
      -cc1 -triple x86_64-apple-macosx10.11.0 -Wdeprecated-objc-isa-usage -Werror=deprecated-objc-isa-usage -E -disable-free -disable-llvm-verifier -main-file-name - -mrelocation-model pic -pic-level 2 -mthread-model posix -mdisable-fp-elim -masm-verbose -munwind-tables -target-cpu core2 -target-linker-version 253.2 -v -dwarf-column-info -resource-dir /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/7.0.0
      -isysroot /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk
      -stdlib=libc++ -fdeprecated-macro -fdebug-compilation-dir /usr/local/lib -ferror-limit 19 -fmessage-length 272 -stack-protector 1 -mstackrealign -fblocks -fobjc-runtime=macosx-10.11.0
      -fencode-extended-block-signature -fcxx-exceptions -fexceptions -fmax-type-align=16 -fdiagnostics-show-option -fcolor-diagnostics -o - -x c++ - clang -cc1 version 7.0.0 based upon LLVM 3.7.0svn default target x86_64-apple-darwin15.0.0 ignoring nonexistent directory "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk/usr/include/c++/v1" ignoring nonexistent directory "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk/usr/local/include" ignoring nonexistent directory "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk/Library/Frameworks"
      #include "..." search starts here:
      #include &lt;...&gt; search starts here:  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1 /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/7.0.0/include /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk/usr/include /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk/System/Library/Frameworks (framework directory) End of search list.
      # 1 "&lt;stdin&gt;"
      # 1 "&lt;built-in&gt;" 1
      # 1 "&lt;built-in&gt;" 3
      # 332 "&lt;built-in&gt;" 3
      # 1 "&lt;command line&gt;" 1
      # 1 "&lt;built-in&gt;" 2
      # 1 "&lt;stdin&gt;" 2
  </code></pre>