We ran into a problem this time with distribution of our linux build for ROOT. It seems prefix cannot be used, so we must set the ROOTSYS env var for our build. make install no longer seems to work unless prefix is used, so we are left to prune the resulting ROOT build directories on our own.
set ROOTSYS to the same directory as the source was checked out into. cd into the root directory and then run configure:
./configure linux --disable-cern --enable-mysql --enable-xrootd --with-python-incdir=/afs/slac/g/glast/ground/GLAST_EXT/rh9_gcc32/python/2.5.1/include/python2.5 --with-python-libdir=/afs/slac/g/glast/ground/GLAST_EXT/rh9_gcc32/python/2.5.1/lib/python2.5/config --enable-mathcore --enable-mathmore --enable-reflex --enable-cintex --enable-roofit --with-oracle-incdir=/usr/oracle/rdbms/public --with-oracle-libdir=/usr/oracle/lib --enable-minuit2 --enable-unuran --enable-table --enable-explicitlink
and then just copied the useful directories to another location