I don't know Autotools, but I find the CMake workflow to be tolerable. Can someone who knows both provide a comparison?
The problem autotools tries to solve is building your software on a wide array of operating systems and configurations. A very attractive alternative approach taken by most, including CMake[1], is to have a big giant database of systems and what each system can do at which version. Thus, if you want to use a library such as, say, Qt, CMake has a Qt module that looks for Qt libraries, checks their versions, and reports that back to you. These databases of system versions and what is available at each version are necessarily always outdated.
Autotools instead gives you tools to write tests. Do you need this library? Which functions do you need from this library? What should those functions do?
When you're running a ./configure script, that's what autotools is doing. It's checking to see what kind of C library you have, what kind of Unix tools are available, how do those Unix tools behave. It is not going to trust version strings or software names. Perhaps the OS reports that it's Debian but in fact it's some derivative of Debian that changed some things around. If you were relying on CMake's hypothetical database of Debian features, it would fail on this not-quite-Debian system.
Over time, these tests get shared around and become part of the core autotools libraries, which is the other problem: autotools is now checking for the absence of certain features that have not really been missing in any system since 1995.
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[1] CMake can perform autoconf-like feature checks too, but this is not as common as relying on its databases of systems and features.
I use CMake everyday and for me it's not a database but a set of modules. Each of this module will look for a particular thing. Some modules are better written than other but they all allow you to bypass them. Of course on obscure systems it will fail. That's why they are called obscure. But on systems following more or less the good practice, there will be no problem at all. On the others, you need to pass the specific path, but it will be true with autoconf too... no magic here...
Also in the doc, it is stated that if you rely on a specific flag/option/function then you need to test for it, and CMake gives you the tool to do it. That's a good practice everyone should follow.
But I agree, it's not always done. Like Autoconf, I guess it really depends on how well the developer understand the tool, and how much time he is ready to spend on it.
There's no magic, it's a complicated problem, with only complicated solutions. CMake is more attractive to me, because it allows me to do simple stuff easily, but more complicated operations are also possible.
I didn't really mean a literal database. I meant stuff like this:
https://github.com/Kitware/CMake/blob/master/Modules/FindQt4...
This is pretty typical CMake. It's encoding that for a particular version of Qt, add a few more compilation flags. It's a "knowledge base" of Qt versions encoded as a CMake module.
The autoconf way would be to try to link a minimal program to Qt, and if it fails, try to see if adding more libraries makes the linking succeed.
Or this, for example:
https://github.com/Kitware/CMake/blob/master/Modules/FindOpe...
It is trying to account for two popular compilers on Windows but not with Cygwin. It's the whole chain of "if Windows, if cygwin, if mingw, if msvc" what I called a "database" above.
Doesn't clang work on Windows these days? What will this knowledge base do now? Shouldn't clang work almost like mingw? But because it misses the "if mingw" branch, code that probably would have worked for clang will be skipped over.
I agree that this is more problematic with less common, more buggy libs where the API keep changing, but in this case it's quite easy to check for specific files, specific functions, ...
All this assumptions have huge consequences in terms of velocity and ease of use.
But I get your point.
My counter-argument is that more flexibility is left to the developer to assume stuff. These assumptions make things easier in most cases. In corner cases, then you need to provide explicit values to the module so he can find what you need.