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(Solution)
I experienced a similar problem trying to configure tomcat to work with apache. I saw the error above when running:
./configure --with-apxs=<PATH-to-APACHE>/bin/apxs
The problem was that the apache had originally been installed to /usr/local/apache_2.0.61_new_install and later been moved to /usr/local/apache_2.0.61
apxs is not very clever about working out why apxs isn't working, it tries to run it, throws the output away to /dev/null and if it doesn't work, it claims it can't find it.
In my case, the problem was that apache had been moved since it was installed, but there could be any number of errors causing the problem. I can think of 20 and I'm sure you can too, for example permission problems, bad path to perl, not set executable, libraries missing, etc. Run <PATH-to-APXS>/apxs -q PREFIX manually, and inspect the error message to find out yourself.
Presuming that you see the same error I did (which will report that it can't find a path to the original install location):
The /usr/local/apache_2.0.61/bin and /conf directories had been amended to pick up the new directory (otherwise apache would not have started) - but /build and /include also needed to be edited so that all the files pointed to the current install directory.
apxs -q PREFIX then returned the correct /usr/local/apache_2.0.61 directory and I was able to run the configure script.
Of course, it fell over with a missing dependency, but that's a different story.
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