Common Desktop Environment? I have a couple old RISC boxes running it...

;-)

Sorry. Couldn't resist...

Now, seriously, this goes a bit beyond package management by bringing along what seemed to be the specific versions of libraries. The goal is to do reproducible results for scientific data but, in this case, I would prefer not to have the original libraries packed along but having the dependencies flagged in a way that any version-specific bug could be easily pointed out.