The L-BFGS-B library in question is now in Debian as liblbfgsb0 and liblbfgsb-dev.
Removing the relevant source files from scipy/optimize/setup.py and adding lbfgsb to the list of libraries to link to seems to work fine, and the relevant tests still pass. I did - sources = ['lbfgsb.pyf', 'lbfgsb.f', 'linpack.f', 'timer.f'] + sources = ['lbfgsb.pyf'] + libs = lapack.setdefault('libraries', []) + libs.append('lbfgsb') + lapack['libraries'] = libs which obviously is confusing name-wise, but works. With this change, one gets rid of an embedded copy of both lbfgsb and Linpack. See also #811069. Best, Gard