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Finding includes and libraries during software compile

I have been using Debian for five or so years now and have basically learned most of Linux on Debian, hence I post my question to this list. When I compile software such as PHP with imap, Exim with Mysql, or PHP with Openldap, I find that often the libraries or includes are not found even though I have the CPPFLAGS and LDFLAGS set and even though I have DIR defined in the configure option and even though I have added the correct paths to ld.so.conf and run ldconfig. Often it requires much tweaking of things to get the configure/make to find the libraries and includes. Can anyone give insight into why this is the case in general? I assume it's not Debian specific problem. Can anyone shed light on this issue?
Craig Jackson

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