Two hints: use absolute paths for -O and -T. I'm not sure this advice is accurate, but I know absolute paths are ok, and your reported error sounds like path confusion. redirect stderr also. That's missing. in the directory that's trouble $TOOLDIR/bin/nbmake-i386 cleandir $TOOLDIR/bin/nbmake-i386 dependall and see what happens. Also, see pkgsrc/sysutils/etcmanage and read thoroughly BUILD-NetBSD, which has comments. It's a little crufty, but it is at least a helpful example.
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