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TravisWheelerLab / NINJA

Nearly Infinite Neighbor Joining Application
MIT License
5 stars 7 forks source link

Does not compile on OSX - conda recipe #27

Closed Juke34 closed 4 years ago

Juke34 commented 4 years ago

I tried to make a Conda recipe, it compiles well on Linux, but I got into trouble on OSX, see here: https://github.com/bioconda/bioconda-recipes/pull/20135 and here https://circleci.com/gh/bioconda/bioconda-recipes/93537?utm_campaign=vcs-integration-link&utm_medium=referral&utm_source=github-checks-link

Could you help?

jebrosen commented 4 years ago

@glesica Is there a plan/policy for macOS support? OpenMP makes things a bit tricky because the compiler that comes with macOS does not support it - you have to get a compiler via brew, conda, etc.

If the only other barrier is clock_gettime and related functions, it should be fairly easy to fix and I am looking into it now.

Juke34 commented 4 years ago

Tools using OpenMP compile on OSX with conda. We use llvm-openmp for it.

glesica commented 4 years ago

I'm able to build it with GCC on a Mac. Installing OMP manually would be a another great option. We'll take a look at this before we do the 1.0.0 release.

jebrosen commented 4 years ago

It's easy to remove clock_gettime: https://github.com/TravisWheelerLab/NINJA/compare/cluster...jebrosen:cluster-no-gettime

It only appears in two places, neither important: TreeBuilderManager.cpp in the develop and cluster branches only - not in the avx branch - and not used by default anyway, and in ClusterManager.cpp where values are calculated but not used.

Juke34 commented 4 years ago

Did you have time to work on it?

traviswheeler commented 4 years ago

Apologies for the slow response on this. We've been clearing the decks on other projects, and are now turning some attention to this. Hard to give any exact timeline, but expect to see movement here shortly.