science/votca: Partially fix build

Define BOOST_TIMER_ENABLE_DEPRECATED in CXXFLAGS to avoid build failure
with newer versions of Boost library

Poudriere reports filesystem violations in usr/local/share/libint

PR: 274437
Reviewed by: yuri (maintainer)

(cherry picked from commit 744d2334a25046ed65a47331b711194fcce877f3)