Question: Problems installing CONTRAfold
0
gravatar for Thomas Bradley
2.5 years ago by
UEA,Norwich,UK
Thomas Bradley90 wrote:

Hello,

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?

Thanks!

ADD COMMENTlink written 2.5 years ago by Thomas Bradley90
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