Created attachment 389292 [details, diff] silence LD_FLAG warnings new version works with copied ebuild, but to address bug 480346 you should apply attached patch.
Added the ebuild to the science overlay, with your patch applied [1]. I will remove it from the overlay as soon as the the new version is available in the tree. [1] https://github.com/gentoo-science/sci/pull/291
+*mendeleydesktop-1.12.4 (08 Jan 2015) + + 08 Jan 2015; Justin Lecher <jlec@gentoo.org> -mendeleydesktop-1.11.ebuild, + +mendeleydesktop-1.12.4.ebuild, metadata.xml: + Import version bump from sci overlay and drop old, resolves #480346 & #529230 +