I am upgrading the brew package to 1.2 and get this problem: ``` ./configure --with-capnp=/bio/linuxbrew/opt/capnp --with-protobuf=/bio/linuxbrew/opt/protobuf configure: WARNING: unrecognized options: --with-capnp checking for protoc... yes checking for capnp... yes checking whether the C++ compiler works... yes <snip> config.status: creating Makefile configure: WARNING: unrecognized options: --with-capnp ``` However, I think it has created the Makefile just fine, and it compiles.