I am attempting to install a bioinformatics tool called 'CONTRAfold' which is a dependency for another bioinformatics which I want to install called MIRZA.
However, I seem to be having some problem compiling CONTRAfold - when I run make, I return the following error:
In file included from Contrafold.cpp:16: In file included from ./OptimizationWrapper.hpp:12: In file included from ./InnerOptimizationWrapper.hpp:12: In file included from ./LBFGS.hpp:52: ./LBFGS.ipp:110:21: error: use of undeclared identifier 'DoLineSearch' Real step = DoLineSearch(x[k%2], f[k%2], g[k%2], d, ^ this-> ./InnerOptimizationWrapperLBFGS.ipp:84:26: note: in instantiation of member function 'LBFGS<double>::Minimize' requested here return LBFGS<RealT>::Minimize(x0); ^ ./OptimizationWrapper.ipp:127:51: note: in instantiation of member function 'InnerOptimizationWrapperLBFGS<double>::Minimize' requested here cached_f = inner_optimization_wrapper.Minimize(cached_learned_w); ^ Contrafold.cpp:447:30: note: in instantiation of member function 'OptimizationWrapper<double>::Train' requested here optimization_wrapper.Train(units, w, regularization_coefficients); ^ Contrafold.cpp:68:9: note: in instantiation of function template specialization 'RunTrainingMode<double>' requested here RunTrainingMode<double>(options, descriptions); ^ ./LineSearch.hpp:51:10: note: must qualify identifier to find this declaration in dependent base class Real DoLineSearch ^
I have no idea why I am receiving this error, I worry that it could be down to my operating system (OS X El Capitan) and which compiler I am using. When I run the 'gcc --version' command I return the following:
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1 Apple LLVM version 7.3.0 (clang-703.0.31) Target: x86_64-apple-darwin15.6.0 Thread model: posix InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin
I am afraid I don't really have the expertise to know what the problem is here, or how to fix it?
Got any ideas?