When comparing Autotools vs Tup, the Slant community recommends Tup for most people. In the question“What are the best open-source build systems for C/C++?” Tup is ranked 4th while Autotools is ranked 16th. The most important reason people chose Tup is:
It is very fast.
Ranked in these QuestionsQuestion Ranking
Pro Based on standard tools
It's a standard tool built over standard tools.
It's a well established build system that is ubiquitous in the open source world.
Pro make distcheck
Build your project, run the tests, create a release tarball, unpack it with read-only sources, build it and run the tests. This should be the minimum standard for every build system, yet it seems hard to reach.
Pro Basic API for building anything: ./configure; make
The skills you learn for building one language still work when you build something else, even down to creating books for print from emacs org-mode.
It is very fast.
It will automatically clean-up old files.
Not bound to C/C++.
Tup supports writing build definitions using Lua or Tupfiles.
Pro Cross platform
Supports Linux, OSX, and Windows.
Con Autotools is far too complicated
It seems to add far too much complexity to projects. The build system has a tendency to be more complex than the actual projects that it's being used to build.
Autoconf is dependent on Perl.
Con Poor documentation
In spite of its many years of existence, the available documentation leaves much to be desired.
Con Variants not working on Windows
The solution for having different build configuration (think Release/Debug) is broken on Windows.
Con Cannot incrementally modify or delete files
Cannot incrementally modify files (e.g. LaTeX PDF, VISing and LIGHTing Quake maps, which takes the same BSP file as input and output), and will not delete files (e.g. rm build/*.o).