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The patent grant applied to any use of the software including in proprietary software. It's not much of a permissive license if you can't actually use it permissively due to patents. OIN is based around Linux specifically which is a lot different and even somewhat harmful.
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the larger reason, imo that OIN is problematic is because it legitimizes the view that software patents are somehow acceptable and should be a thing. we should be looking to abolish software patents in all forms.
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Copyright very narrowly avoided being a potentially even more serious issue in the US with the whole Java API case. Definitely not completely resolved since it wasn't determined that APIs aren't copyrightable and fair use has to be decided on a case-by-case basis.
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