I was having trouble getting pip to build the python module lxml against the native libxml2 libraries on Mac OS X v10.11 - “El Capitan.” The problem was that I was missing the header files – in fact the entire /usr/include tree was gone.

The fix is to run xcode-select --install. Apparently you can have the developer tools installed, but not have the “command line developer tools” which include /usr/include. Unfortunately, thanks to the “rootless” feature, this Apple-sanctioned installer is pretty much the only way to get /usr/lib back.