Configuration files and log files installation with automake

The GNU Build System does not use obj/ directories, so the autotools are not designed to support that.

However I can think of two ways to work around this.

As an installer, you can build any package out of its source directory by typing

mkdir builddir
cd builddir
../path-to-sourcedir/configure
make

Then any output file will be created in the builddir/ directory. This compilation scheme makes it possible to compile source code out stored in a readonly directory (this made more sense back in the years where the FSF was distributing CDs with uncompressed source code), or to compile the same source with differents settings (or even for different architectures).

As a packager, the only way you could force your package to build everything in obj/ is to put your Makefile.am in obj/, and declare all your build rules there. This would mean a obj/Makefile.am looking like:

bin_PROGRAMS = foo bar
foo_SOURCES = ../src/foo/main.c ../src/foo/help.c ../src/foo/list.c
bar_SOURCES = ../src/bar/bar.c 

etc. I remember that 10 years ago, POSE, the Palm OS Emulator, was using a setup like the above. I don't recommend it as it's not really maintainable. It's really better to stick with the philosophy of the tools, and use a build systems that work like the other GNU packages.

For an introduction to the GNU Build System, I recommend reading the introduction of the Automake manual: http://www.gnu.org/software/automake/manual/automake.html#GNU-Build-System

Especially the Use-Cases section. If you don't care about these use cases, I think your best course is NOT to use Automake, and build your own Makefiles. Otherwise you will keep trying to force Automake doing something it is not designed for, and you'll quickly hate it.

EDIT 2013-08-26: Note that an Automake project using a subdirectory named using obj/ is not portable to BSD make.

Two issues in your configure.ac file. First, the syntax of your AM_INIT_AUTOMAKE invocation is 10 year old, I suspect you copied it from a very old tutorial (hint: the Automake manual has a tutorialish introduction). You've already passed the package and version to AC_INIT, there is no need to repeat that in AM_INIT_AUTOMAKE. Second, the list of files passed to AC_CONFIG_OUTPUT should be a space-separated list given as first argument.

In other words, your configure.ac should look like

AC_PREREQ([2.63])
AC_INIT([app], [0.1], [your@email])
AM_INIT_AUTOMAKE([-Wall])
AC_CONFIG_SRCDIR([src/main.h])
AC_CONFIG_HEADERS([config.h])
AC_PROG_CC
AC_CONFIG_FILES([Makefile src/Makefile])
AC_OUTPUT

Note there is no coma on the AC_CONFIG_FILES line.

The -Wall option will cause automake to output more warnings (this really is an automake option, not a gcc option), it's probably safer if you discover these tools.

This should fix your configure problem. Then I suspect you'll probably have to split your app_LDADD line into app_CPPFLAGS and app_LDFLAGS.