This package was found to have dev-libs/boost in RDEPEND, but doesn't install either any binary that links against boost libs nor any files that include boost headers. That means it uses boost header-only libraries at compile time only. The tracker bug contains the emerge --info of the test system.
$ ldd $(find /var/tmp/portage/sci-chemistry/avogadro-1.0.0/image/usr/|grep so$)|grep boost libboost_python-mt-1_41.so.1.41.0 => /usr/lib64/libboost_python-mt-1_41.so.1.41.0 (0x00002b11d1a10000) libboost_python-mt-1_41.so.1.41.0 => /usr/lib64/libboost_python-mt-1_41.so.1.41.0 (0x00002b59ebe51000) It only RDEPENDS on it when build with USE="python"