Since it seems with your configure,
./configure --with-apxs2=/app/apache2/bin/apxs --without-pear --
with-config-file-path=/app/ini --with-mysql=/usr/local/mysql
that you're not building only for mysql extension and not for
PDO/mysql, you will see in your config.log,
dyld: Library not loaded: /usr/local/mysql/lib/mysql/libmysqlclient.15.dylib
Referenced from: /Users/jpons/app/src/php-5.2.3/./conftest
Reason: image not found
Add before your configure step,
setenv LDFLAGS "-bind_at_load -L/usr/local/mysql/lib/mysql -lmysqlclient"
setenv CPPFLAGS "-I/usr/local/mysql/include/mysql"
And try it again.
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