configure fails because AUTOMAKE_OPTIONS = subdir-objects is not set

I'm running an up-to-date Arch Linux. When I first run configure, I get this error:

configure: creating ./config.status
config.status: error: cannot find input file: `Makefile.in'

So I tried running autogen.sh, which resulted in:

automake: warnings are treated as errors
Makefile.am:43: warning: source file 'src/@DRIVER_NAME@.c' is in a subdirectory,
Makefile.am:43: but option 'subdir-objects' is disabled
automake: warning: possible forward-incompatibility.
automake: At least a source file is in a subdirectory, but the 'subdir-objects'
automake: automake option hasn't been enabled. For now, the corresponding output
automake: object file(s) will be placed in the top-level directory. However,
automake: this behaviour will change in future Automake versions: they will
automake: unconditionally cause object files to be placed in the same subdirectory
automake: of the corresponding sources.
automake: You are advised to start using 'subdir-objects' option throughout your
automake: project, to avoid future incompatibilities.
autoreconf: automake failed with exit status: 1

I was able to fix this by adding the line:

AUTOMAKE_OPTIONS = subdir-objects

to Makefile.am. I added it right underneath the ACLOCAL_AMFLAGS line.

After that, running autogen.sh did work (but configure did not work if run first).