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I know nothing about smalltalk, but I had a problem and asked a question on gnu-smalltalk mailing list. I was advised to check the value of Directory systemKernel. Well, it contains ${D}, so it's definitely invalid. If I receive more help from the list, I post it here. And BTW gnu-smalltalk-3.0.2 was released on 7th of March.
Well, it seems that the solution is to use econf instead of ./configure and `make DESTDIR="${D}" install` instead of the lines used for install in current ebuild.
I have just uploaded latest version of gnu-smalltalk 3.0.2. This bug should fixed there, please test. Notice how econf can't be used, since it is apparently broken, so ./configure is still being used. Thanks for reporting this problem,