I know this is an old question, but after a week of struggle I thought that I should publish my conclusions.
I have successfully edited makefiles for this so that they can compile on Ubuntu 12.04 x64.
You can completely remove the -soname option, this does not seem to be necessary.
As already mentioned: all "m32" change to "m64".
You can replace "$ ROOTSYS / libs" with "$ ROOTLIBS"
and with the make file TwoPad reorder the library order (in LIBS + = (.....)), so -lTwoPad is NOT the last in the list, but for VisuSLitrani make -lPhysMore is the last in its group.
As far as I know, errors saying "set but not used" can be ignored.
If any of this still does not work, contact me and I can send you my makefiles.
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