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Hi,
yes it has been deprecated for some time. You should check the overlay README to see if you need to update how you use the overlay. Upstream has split sage into several smaller packages and what used to be "sage" is currently "sagemath-standard". It is quite possible that the modularisation will be rolled back at some point in the future :( and will have to merge things again.
"emerge -va sage" - command is not working? is it depracated step of installing?
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