Thanks Ralph! :)
I now have in my test/Makefile.am
AM_DEFAULT_SOURCE_EXT = .f90
TESTS = forward/Example1_Simple/Example1_Simple \
        k_matrix/Example1_Simple/Example1_Simple
check_PROGRAMS = $(TESTS)
AUTOMAKE_OPTIONS=subdir-objects


automake and configure now work but at the end  of running make I get:
Making all in test
make[1]: Entering directory
`/net/orbit272l/home/pub/evemarie/projects/CRTM/autoconf/play/CRTM/test'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory
`/net/orbit272l/home/pub/evemarie/projects/CRTM/autoconf/play/CRTM/test'
make[1]: Entering directory
`/net/orbit272l/home/pub/evemarie/projects/CRTM/autoconf/play/CRTM'
make[1]: Nothing to be done for `all-am'.
make[1]: Leaving directory
`/net/orbit272l/home/pub/evemarie/projects/CRTM/autoconf/play/CRTM'

if I try make test I get
make test
make: Nothing to be done for `test'.

It hasn't created the *.o files either....
I haven't specified test: or all: but in the main Makefile.am I haven't
either and it figures out how to compile what. I thought TESTS would do
that for me??

I am sorry to be so needy.... I am making a powerpoint in parallel
trying to explain what I had to do. Hopefully this can be useful to the
community once I am done....
Thanks,
Cheers,

Eve-Marie

Ralf Wildenhues said the following on 1/27/2011 1:24 PM:
> Hello Eve-Marie,
>
> * Eve-Marie Devaliere wrote on Thu, Jan 27, 2011 at 07:07:51PM CET:
>> AM_DEFAULT_SOURCE_EXT = .f90
>> TESTS = forward/Example1_Simple/Example1_Simple \
>>         k_matrix/Example1_Simple/Example1_Simple
>> check_PROGRAMS = $(TESTS)
>>
>> when I run automake it outputs
>> automake
>> test/Makefile.am: object `Example1_Simple.$(OBJEXT)' created by
>> `k_matrix/Example1_Simple/Example1_Simple.f90' and
>> `forward/Example1_Simple/Example1_Simple.f90'
> Use the 'subdir-objects' Automake option (see 'info Automake Options'
> for how to do that).
>
>> but nothing was created and if I try configure it complains that:
>>
>> config.status: error: cannot find input file: `test/Makefile.in')
> That looks like a followup error: if automake errors out, it won't
> create a Makefile.in file.
>
> Cheers,
> Ralf

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