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What are some alternatives to make for linux/freebsd?
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Linux definitely takes the win when it comes to hardware and architectural support. Linux works on many different platforms, while FreeBSD does not. So if you're concerned about compatibility, there's a better chance that Linux will work for you than FreeBSD.
I like SCons. It is constructed in such a way that every build script (a SConstruct file) is also a syntactically valid Python program. So, you can build arbitrary Python logic into your build script if you need to.
It's also much faster than make and calculates many kinds of dependencies automatically.
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