I don't know. IMHO, these problems are not specific to lilypond, and should be fixed by the distributor. Also, we have a packaged script, called
lexer-gcc-3.1.sh
which seems to fix the same problem. Perhaps we have to rename the script. Can you check whether that script does the trick?
As the name of this script induces, it fixes compilation for gcc 3.1 but it not working with gcc >= 3.3.
You're right, that these problems should eventually be fixed by the flex developers, however they have been unable (ignorant) to do so for severel years now, so a working solution distributed with your software would let users of *your* software benefit.
Maybe an automatic patch via "configure" scripts is too much, you should at least distribute a working fix-script for current releases of software needed to build lilypond (and I won't call gcc 3.1 current nowadays).
-- ---> doj / cubic ----> http://cubic.org/~doj -----> http://llg.cubic.org
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