So, my experience is the total opposite, but it is probably because you only want to compile for your one computer whereas I am constantly trying to compile for twenty platform / architecture combinations with sometimes arbitrary toolchain requirements (like "must use clang" or "must use a compile newer than X" or "must generate object files capable of being used on this older version of the operating system"). I have _never_ had a hard time compiling something when it uses autoconf: I had to learn how autocons works and what its expectations about the world are, but they are actually mostly correct... libtool, on the other hand, causes me issues sometimes, but I have largely figured those out over the years.

But when people use CMake? Ugh. I am in for a world of hurt, and probably so many custom assumptions about how to interface with the compiler and the operating system that not only is cross compilation probably off the table, but compiling it at all for one of my target platforms is likely not going to work :/. I pretty much always end up having to just throw away your build system entirely and start over from scratch just to even test the project for my target. OMG: a bunch of projects like using tools like Meson... the entire Meson 0.52.x line entirely broke the ability to cross compile to targets like Android on macOS as it incorrectly detected stuff about the target linker using the host compiler, and as it is largely a black box the only real way to deal with this is to avoid 0.52.x forever (I filed an issue about this right as 0.52 came out but they failed to fix this serious regression until 0.53).

And in languages other than C++? Ha ha ha omg they are all so horrible :(. I have been fighting for a month now trying to get a Rust library compiled to a static archive so I can link it into my project, and have nothing but a long list of bugs filed with upstream and workarounds for their broken build system to show for it, as in the end I finally decided it just wasn't worth dealing with anymore: bindgen passes the wrong target to clang for iOS (with no way to work around it as the person doing the compile, and often this happens in some deep dependency which makes overriding that really hard, as the build system believes it should be in charge of building dependencies), buildcc incorrectly mixes up HOST_CC and TARGET_CC when you are doing a cross compile to a target (such as CentOS 6) from a host (such as Ubuntu bionic) that shares a triple, the MinGW build not only tries to link against some entirely-wrong set of libraries that comes with Rust (they just last month shipped a broken fix for this that works in cases where you aren't passing a custom sysroot... but if you are doing MinGW seriously you have a custom sysroot so you can be compatible with MSYS2) but it also embeds into the archives parts of the target's standard libraries (which is just crazy: they apparently do this for MinGW, musl, and one other target), and I can't yet for the life of me get it to generate reproducible builds even for simpler packages (which is normally trivial with C++--yes, even with autoconf--I need to spend more time looking into this problem and filing issues about it, though).