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Rstudio has a community version for free:

https://www.rstudio.com/products/rstudio/#Desktop

But mentions the license is AGPL v3.

Does this effect the licensing or IP rights of code written on the platform or is it referring to extending the IDE itself?

The paid version commercial license seems to be talking about extending the platform itself making me think the second option, but I could be wrong.

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This is covered in the GNU faq:

the copyright on the editors and tools does not cover the code you write. Using them does not place any restrictions, legally, on the license you use for your code.

The licensing aspects only apply to extending the IDE itself.

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