gyp info it worked if it ends with ok
gyp info using node-gyp@1.0.1
gyp info using node@0.10.38 | linux | ia32
gyp info chdir ldapjs/node_modules/buffertools
gyp ERR! clean error
gyp ERR! stack Error: EACCES, unlink 'build/Makefile'
gyp ERR! System Linux 4.9.75-30.el6.x86_64
gyp ERR! command "/home/dev/cal/vfcore/cerberus/cerb-node/node_modules/../../bin/node" "/home/dev/cal/vfcore/cerberus/vendor/node/deps/npm/node_modules/node-gyp/bin/node-gyp" "rebuild" "--directory=ldapjs/node_modules/buffertools" "--nodedir=/home/dev/cal/vfcore/cerberus/cerb-node/node_modules/../../vendor/node" "--arch" "ia32"
gyp ERR! cwd /home/dev/cal/vfcore/cerberus/cerb-node/node_modules/ldapjs/node_modules/buffertools
gyp ERR! node -v v0.10.38
gyp ERR! node-gyp -v v1.0.1
gyp ERR! not ok
make[3]: *** [ldapjs] Error 1

Solution

You probably - like me - built with root user before and now are not. Just make a backup of unsaved changes if any, then clean the repo (rm -fr of affected directory, then fresh checkout and/or submodule updates), and retry.