I'm trying to compile a fresh install and I get this error.
Anyone seen this before?
build/src/release/linux/2.6/64/x86/gcc/4.5/static/libcore.3.a(ContextIndependentGeometricSolEnergy.o): In function `core::scoring::geometric_solvation::ContextIndependentGeometricSolEnergy::residue_pair_energy_ext(core::conformation::Residue const&, core::conformation::Residue const&, core::scoring::ResPairMinimizationData const&, core::pose::Pose const&, core::scoring::ScoreFunction const&, core::scoring::EMapVector&) const':
ContextIndependentGeometricSolEnergy.cc:(.text+0x4c5): undefined reference to `core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(unsigned long const&, core::conformation::Residue const&, unsigned long const&, core::conformation::Residue const&, core::pose::Pose const&, double&, bool, core::scoring::hbonds::HBondDerivs&) const'
build/src/release/linux/2.6/64/x86/gcc/4.5/static/libcore.3.a(GeometricSolEnergy.o):GeometricSolEnergy.cc:(.text+0x31d): more undefined references to `core::scoring::geometric_solvation::GeometricSolEnergyEvaluator::get_atom_atom_geometric_solvation_for_acceptor(unsigned long const&, core::conformation::Residue const&, unsigned long const&, core::conformation::Residue const&, core::pose::Pose const&, double&, bool, core::scoring::hbonds::HBondDerivs&) const' follow
collect2: ld returned 1 exit status
I haven't seen that particular error before, but I will say I've seen the compiler trip over itself before, and that might be what's happening here.
First try recompiling (just re-issue the same scons command you used the first time). The second time through might work better - you should know whether it works or not quickly.
If that doesn't work, try clearing out the old compile and redoing things. Delete the contents of the rosetta_source/build/ directory (or Rosetta/main/source/build/ directory if you're compiling a weekly release) and re-issue the scons command. The thought is that one of the output files from earlier in the build process is corrupted, and by clearing out the build directory you'll regenerate it, hopefully in a working state this time.