Boost no longer works with Homebrew on Mac El Capitan

Question

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:

fatal error: 'boost/timer/timer.hpp' file not found
#include <boost/timer/timer.hpp>

fatal error: 'boost/program_options.hpp' file not found
#include "boost/program_options.hpp"

I've been compiling it with the correct flags and it worked perfectly before:

-lboost_timer-mt \
-lboost_program_options-mt \

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.

Update Ran: clang++ -E -x c++ - -v < /dev/null

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 <...> 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 "<stdin>"
    # 1 "<built-in>" 1
    # 1 "<built-in>" 3
    # 332 "<built-in>" 3
    # 1 "<command line>" 1
    # 1 "<built-in>" 2
    # 1 "<stdin>" 2

Answer 1

You should install the Xcode Command Line tools with xcode-select --install to get a version of clang that searches /usr/local by default. Otherwise, you're using the versions provided by Xcode proper, which only search the OS X SDK paths. (/usr/bin/gcc and /usr/bin/g++ both invoke clang and are not actually versions of gcc.)