The message "Unable to revert mtime: /usr/local/share/fonts" comes from libfontconfig1, and has nothing to do with emacs per se. See https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=909728
Submitter: if you're still seeing this, you might want to talk to the fontconfig folks. Maintainer: depending on what submitter has to say, you can probably either close this or reassign it.