How can I get CMake to find my alternative Boost installation?

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You should have a look at FindBoost.cmake script, which handles Boost detection and setting up all Boost variables. It typically resides in /usr/share/cmake-2.6/Modules/. In it, you will find documentation. For instance:

# These last three variables are available also as environment variables:
#
#   BOOST_ROOT or BOOSTROOT      The preferred installation prefix for searching for
#                                Boost.  Set this if the module has problems finding
#                                the proper Boost installation.
#

In contrast to BOOST_ROOT, the variables you are referring to are actually variables that are set by the FindBoost module. Note that you don’t have to (and probably also don’t want to) edit your CMake project configuration to set BOOST_ROOT. Instead, you should use the environment variable, e.g. calling

# BOOST_ROOT=/usr/local/... ccmake .

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