I have a source code written in Java that I would like to run on Windows RT / Surface 2. So far the tablet cannot run JVM. Is it possible to use J# to transform at least part of the code to run it under CRL (possibly with rewriting GUI part)? Will it be faster than start from zero?
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I don't believe so. It requires some trickiness to use J# with .Net 4.0 and none of the tricks I've seen will work in a Windows Runtime app. Even if you could compile J# to the .Net Core framework, it probably wouldn't buy you much since you wouldn't have the java namespaces available.
It will probably be faster to convert from Java to C#, with the main difficulty being the differences in library code rather than language based. MSDN has a topic Move from Android to WinRT that may help with that if you are familiar with Android programming.