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unfortunately not all --(very few)-- packages or packagers, to be more to the point, go to the trouble of giving you a target 'uninstall' (in some cases 'deinstall')....
so if make uninstall doesn't work you have to do it by hand
a trick i use sometimes is to run make install again and carefully examine the output
(if it's comphensible) to find all the files to remove or at least get some clue
another trick if you think you might want to wack something later is to do -prefix=/opt/someplace/unique
when you configure it so at least you can find some of it (not all of it) in one folder later for whacking.
but that doesn't help now huh ?
and yes checkinstall is a very cool tool for compiled systems so you can still use a package manager
to uninstall stuff.
And if the program was run by any user, it will often create a .DIRECTORY in your home directory. If you installed say Return to Castle Wolfenstein then the directory would be .wolf. These often do not uninstall automatically, and don't show up when you make, so check your user's home directory if you want a true uninstallation. Use la -la to find it.
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