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merenlab / anvio

An analysis and visualization platform for 'omics data
http://merenlab.org/software/anvio
GNU General Public License v3.0
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[BUG] Failed building wheel for datrie #2215

Closed hmamine closed 5 months ago

hmamine commented 5 months ago

Short description of the problem

I tried to install anvio on macOS and ran into the issue Failed building wheel for date. I appreicate your input.

anvi'o version

clang: error: unsupported argument 'core2' to option '-march=' error: command '/usr/bin/clang' failed with exit code 1 [end of output]

ivagljiva commented 5 months ago

@hmamine , we don't have enough information to help diagnose your problem. What version of anvi'o? What operating system version? What is your architecture (intel or M1/M2 mac)?

In addition, since clang is giving the error, I would ask you to run clang --version and paste the output here.

And finally, I would suggest trying the solutions recommended here: https://anvio.org/install/macos/stable/#issues-with-the-c-compiler

It is a similar problem, so one of those solutions might work.

hmamine commented 5 months ago

@ivagljiva , thank you, I have indicated these below The solution indicated in there could not solve the current issue. I have exported CC and CXX, then run pip. The system is M2 sonoma 14.2 (23C64). ~/Downloads ❯ clang --version 31s  anvio-dev 22:10:53 clang version 16.0.6 Target: x86_64-apple-darwin23.2.0 Thread model: posix InstalledDir: /Users/user/Software/miniforge3/envs/anvio-dev/bin

ivagljiva commented 5 months ago

Hmm, I wonder if the issue has to do with the discrepancy between your computer architecture (M2, which is ARM) and the clang target architecture (which is showing up as x86_64-apple-darwin23.2.0). But if you ran conda config --env --set subdir osx-64 before creating the environment as suggested on the installation page, then I think this is not the problem.

However, I also notice that you are using miniforge rather than miniconda. We only test our installation instructions with miniconda, so the instructions as written may not work for your setup.

ivagljiva commented 5 months ago

The only potential solution I can think of at the moment is to re-install clang and try again.

hmamine commented 5 months ago

Thanks to @mjfos2r, we found a workaround. 😊 There is an open issue for [datrie](https://github.com/pytries/datrie/issues) We changed to [llvm compiler](https://github.com/llvm/llvm-project), then mamba install datrie. Afterward, complete the pip install.

ivagljiva commented 5 months ago

Great! Very glad you solved it :)