Cannot build Hyphy on a Mac OSX

[bouzidnm]

I've been trying to compile Hyphy using the provided instructions to install PoMo. cmake ./ fails with the error:

"Try OpenMP C flag = [ ] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Failed -- Try OpenMP C flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Failed -- Try OpenMP C flag = [/openmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Failed ... Could NOT find OpenMP (missing: OpenMP_C_FLAGS OpenMP_CXX_FLAGS)"

I've installed a bunch of new OpenMP compatible compilers, including gcc, clang-omp, hoping it would solve the problem. It did not. All other dependencies are installed. When I try to proceed and run make MP2 It fails with the following errors:

"make[3]: * [CMakeFiles/HYPHYMP.dir/src/core/_hyExecutionContext.cpp.o] Error 1 make[2]: * [CMakeFiles/HYPHYMP.dir/all] Error 2 make[1]: * [CMakeFiles/MP2.dir/rule] Error 2 make: * [MP2] Error 2"

Not sure if this is a problem with the Mac OSX or with the Makefile.

[dschrempf]

Hello,

thank you for your interest in PoMo. I am sorry, but I cannot help you with issues about compiling HyPhy on a Mac. Maybe @Nicola De Maio can help you with this.

If you do not succeed in compiling HyPhy, but you would like to use PoMo on your data set, I urge you to try our new version. It is reversible, suitable for larger data sets and implemented into IQ-TREE because IQ-TREE comes with tree search algorithms.

Please check out the code from https://github.com/Cibiv/IQ-TREE/tree/PoMo

Instructions for compilation for all operating systems can be found at http://www.cibiv.at/software/iqtree/doc/Compilation-Guide/

There is not much information about PoMo in the manual yet. However, you can check out PoMo-specific help with running `iqtree --help' (if you compiled using the PoMo branch).

A command line example: iqtree -s YourData.cf

I hope this helps, Dominik

On Thu, Mar 03 2016, N. M. Bouzid wrote:

I've been trying to compile Hyphy using the provided installation instructions to install PoMo. cmake ./ fails with the error:

"Try OpenMP C flag = [ ] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Failed -- Try OpenMP C flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Failed -- Try OpenMP C flag = [/openmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Failed ... Could NOT find OpenMP (missing: OpenMP_C_FLAGS OpenMP_CXX_FLAGS)"

I've installed a bunch of new OpenMP compatible compilers, including gcc, clang-omp, hoping it would solve the problem. It did not. All other dependencies are installed. When I try to proceed and run make MP2 It fails with the following errors:

"make[3]: * [CMakeFiles/HYPHYMP.dir/src/core/ _hyExecutionContext.cpp.o] Error 1 make[2]: * [CMakeFiles/HYPHYMP.dir/all] Error 2 make[1]: * [CMakeFiles/MP2.dir/rule] Error 2 make: * [MP2] Error 2"

Not sure if this is a problem with the Mac OSX or with the Makefile.

Reply to this email directly or view it on GitHub.*

[NicolaDM]

Dear Dominik and bouzidnm, This seems to be a problem of the old HyPhy versions with the new mac OS, see https://github.com/veg/hyphy/issues/192. Might be worth checking if PoMo works with newer HyPhy versions.

Nicola

[NicolaDM]

Dear bouzidnm, I will try to fix the issue with HyPhy. In the meanwhile, if you don't have access to a linux machine or an older mac OS, there are 2 alternative implementations of PoMo that you can use: (i) the one on IQTree that Dominik mentioned, which is very fast; (ii) The very general (but slower) one on BEAST2 that you can find here https://bitbucket.org/nicofmay/pomo-beast/overview or that can you can install via BEAUti.

Best wishes, Nicola