Just to confirm I had email confirmation that the change was merged into master, so post-update I tested again anyway and all works fine.
Thanks for sorting this so quickly.
@aryetis that's the joy of open source projects. Many projects we use come from upstream so when things break it's often nothing we've done and issues and fixes need to be done upstream.
Just for reference this is the repo for desmume and you can see in the recent commit history some changes were made to the makefile and those may have broken the compilation: