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I don't think so. The same, incorrect -B arguments will still be there.This seems to be an automake problem:
/newdisk/programs/mipsel-gccmaincvs/gcc/gcj -B/newdisk/programs/mipsel-gccmaincvs/gcc/ -B/home/test35/mipsel-linux/bin/ -B/home/test35/mipsel-linux/lib/
The later two -B flags are incorrect, because they point to the installation directory when building libjava. The AM_PROG_GCJ macro is attaching these to $(GCJ). It should be instead passing the equivalent locations in the _build_ directory.
Try
http://gcc.gnu.org/ml/gcc-patches/2004-09/msg00357.html
It should fix it.
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