We have a mapping file that is used to preserve the mapping from one build to the next, which is checked into our source control.
Recently we found that one of our developers was getting a "Warning :method is not being kept, but is being remapped".
From investigating this, the original build was done with java 1.6.0_29.
This particular developer was using java 1.6.0_24.
I have taken the build tree and have reproduced this warning, i.e. checking out the build tree, along with the mapping, and build this with 0_29 doesn't generate this warning. However taking this build and just swapping to 0_24, generate this warning.
So it appears that using a mapping file with different versions of the jdk can causes mapping conflicts (well at least warnings), although the code that is being built and the map file are unchanged.
Note this was happening with both v4.6 and v4.7.
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