You could use the --init flag to specify an initial cache file. For example,

# javaCache.cmake

SET(JNI_H FALSE CACHE BOOL "" FORCE)
SET(Java_JAVA_EXECUTABLE FALSE CACHE BOOL "" FORCE)
SET(Java_JAVAC_EXECUTABLE FALSE CACHE BOOL "" FORCE)

./bootstrap --init=/full/path/to/javaCache.cmake


HTH,
David


On Fri, Jan 14, 2011 at 11:50 AM, Brian Lewis <br...@monetra.com> wrote:
> When the cmake bootstrap sets some variables to NOTFOUND, what is the
> correct way to fix them? To edit CMakeCache.txt?
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