Trouble installing cypari2 on M1 Mac

[liammulh]

Hello,

I'm having trouble installing cypari2 on a new-ish Mac using the Poetry package manager. Any help would be greatly appreciated!

System Info

• macOS Monterey Version 12.4
• MacBook Air (M1, 2020)

What I'm Trying to Do

Command I'm Issuing and Resultant Error

(backscope-xBHlVOM6-py3.10) liam@ratbook backscope % poetry add cypari2
Using version ^2.1.2 for cypari2

Updating dependencies
Resolving dependencies... (0.1s)

Writing lock file

Package operations: 1 install, 0 updates, 0 removals

  • Installing cypari2 (2.1.2): Failed

  EnvCommandError

  Command ['/Users/liam/Library/Caches/pypoetry/virtualenvs/backscope-xBHlVOM6-py3.10/bin/pip', 'install', '--no-deps', 'file:///Users/liam/Library/Caches/pypoetry/artifacts/0a/70/e5/c27a295638f41052766b4dc4bee01122a4788154100ad59cefa22105d0/cypari2-2.1.2.tar.gz'] errored with the following return code 1, and output: 
  Processing /Users/liam/Library/Caches/pypoetry/artifacts/0a/70/e5/c27a295638f41052766b4dc4bee01122a4788154100ad59cefa22105d0/cypari2-2.1.2.tar.gz
    Preparing metadata (setup.py): started
    Preparing metadata (setup.py): finished with status 'done'
  Building wheels for collected packages: cypari2
    Building wheel for cypari2 (setup.py): started
    Building wheel for cypari2 (setup.py): finished with status 'error'
    error: subprocess-exited-with-error
    
    × python setup.py bdist_wheel did not run successfully.
    │ exit code: 1
    ╰─> [46 lines of output]
        running bdist_wheel
        running build
        running build_py
        creating build
        creating build/lib.macosx-10.9-universal2-cpython-310
        creating build/lib.macosx-10.9-universal2-cpython-310/cypari2
        copying cypari2/__init__.py -> build/lib.macosx-10.9-universal2-cpython-310/cypari2
        copying cypari2/types.pxd -> build/lib.macosx-10.9-universal2-cpython-310/cypari2
        copying cypari2/gen.pxd -> build/lib.macosx-10.9-universal2-cpython-310/cypari2
        copying cypari2/convert.pxd -> build/lib.macosx-10.9-universal2-cpython-310/cypari2
        copying cypari2/auto_paridecl.pxd -> build/lib.macosx-10.9-universal2-cpython-310/cypari2
        copying cypari2/stack.pxd -> build/lib.macosx-10.9-universal2-cpython-310/cypari2
        copying cypari2/string_utils.pxd -> build/lib.macosx-10.9-universal2-cpython-310/cypari2
        copying cypari2/paridecl.pxd -> build/lib.macosx-10.9-universal2-cpython-310/cypari2
        copying cypari2/handle_error.pxd -> build/lib.macosx-10.9-universal2-cpython-310/cypari2
        copying cypari2/pari_instance.pxd -> build/lib.macosx-10.9-universal2-cpython-310/cypari2
        copying cypari2/paripriv.pxd -> build/lib.macosx-10.9-universal2-cpython-310/cypari2
        copying cypari2/closure.pxd -> build/lib.macosx-10.9-universal2-cpython-310/cypari2
        copying cypari2/cypari.h -> build/lib.macosx-10.9-universal2-cpython-310/cypari2
        running build_ext
        Compiling cypari2/closure.pyx because it changed.
        Compiling cypari2/convert.pyx because it changed.
        Compiling cypari2/gen.pyx because it changed.
        Compiling cypari2/handle_error.pyx because it changed.
        Compiling cypari2/pari_instance.pyx because it changed.
        Compiling cypari2/stack.pyx because it changed.
        Compiling cypari2/string_utils.pyx because it changed.
        [1/7] Cythonizing cypari2/closure.pyx
        [2/7] Cythonizing cypari2/convert.pyx
        [3/7] Cythonizing cypari2/gen.pyx
        [4/7] Cythonizing cypari2/handle_error.pyx
        [5/7] Cythonizing cypari2/pari_instance.pyx
        [6/7] Cythonizing cypari2/stack.pyx
        [7/7] Cythonizing cypari2/string_utils.pyx
        building 'cypari2.closure' extension
        creating build/temp.macosx-10.9-universal2-cpython-310
        creating build/temp.macosx-10.9-universal2-cpython-310/cypari2
        clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I./cypari2 -I/Users/liam/Library/Caches/pypoetry/virtualenvs/backscope-xBHlVOM6-py3.10/lib/python3.10/site-packages/cysignals -I/opt/homebrew/include -I/Users/liam/Library/Caches/pypoetry/virtualenvs/backscope-xBHlVOM6-py3.10/include -I/Library/Frameworks/Python.framework/Versions/3.10/include/python3.10 -c cypari2/closure.c -o build/temp.macosx-10.9-universal2-cpython-310/cypari2/closure.o
        clang -bundle -undefined dynamic_lookup -arch arm64 -arch x86_64 -g build/temp.macosx-10.9-universal2-cpython-310/cypari2/closure.o -L/opt/homebrew/lib -lgmp -lpari -o build/lib.macosx-10.9-universal2-cpython-310/cypari2/closure.cpython-310-darwin.so
        ld: warning: dylib (/opt/homebrew/lib/libgmp.dylib) was built for newer macOS version (12.0) than being linked (11.0)
        ld: warning: dylib (/opt/homebrew/lib/libpari.dylib) was built for newer macOS version (12.0) than being linked (11.0)
        ld: warning: ignoring file /opt/homebrew/lib/libgmp.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
        ld: warning: ignoring file /opt/homebrew/lib/libpari.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
        ld: illegal thread local variable reference to regular symbol _avma for architecture x86_64
        clang: error: linker command failed with exit code 1 (use -v to see invocation)
        error: command '/usr/bin/clang' failed with exit code 1
        [end of output]
    
    note: This error originates from a subprocess, and is likely not a problem with pip.
    ERROR: Failed building wheel for cypari2
    Running setup.py clean for cypari2
  Failed to build cypari2
  Installing collected packages: cypari2
    Running setup.py install for cypari2: started
    Running setup.py install for cypari2: finished with status 'error'
    error: subprocess-exited-with-error
    
    × Running setup.py install for cypari2 did not run successfully.
    │ exit code: 1
    ╰─> [34 lines of output]
        running install
        /Users/liam/Library/Caches/pypoetry/virtualenvs/backscope-xBHlVOM6-py3.10/lib/python3.10/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
          warnings.warn(
        running build
        running build_py
        creating build
        creating build/lib.macosx-10.9-universal2-cpython-310
        creating build/lib.macosx-10.9-universal2-cpython-310/cypari2
        copying cypari2/__init__.py -> build/lib.macosx-10.9-universal2-cpython-310/cypari2
        copying cypari2/types.pxd -> build/lib.macosx-10.9-universal2-cpython-310/cypari2
        copying cypari2/gen.pxd -> build/lib.macosx-10.9-universal2-cpython-310/cypari2
        copying cypari2/convert.pxd -> build/lib.macosx-10.9-universal2-cpython-310/cypari2
        copying cypari2/auto_paridecl.pxd -> build/lib.macosx-10.9-universal2-cpython-310/cypari2
        copying cypari2/stack.pxd -> build/lib.macosx-10.9-universal2-cpython-310/cypari2
        copying cypari2/string_utils.pxd -> build/lib.macosx-10.9-universal2-cpython-310/cypari2
        copying cypari2/paridecl.pxd -> build/lib.macosx-10.9-universal2-cpython-310/cypari2
        copying cypari2/handle_error.pxd -> build/lib.macosx-10.9-universal2-cpython-310/cypari2
        copying cypari2/pari_instance.pxd -> build/lib.macosx-10.9-universal2-cpython-310/cypari2
        copying cypari2/paripriv.pxd -> build/lib.macosx-10.9-universal2-cpython-310/cypari2
        copying cypari2/closure.pxd -> build/lib.macosx-10.9-universal2-cpython-310/cypari2
        copying cypari2/cypari.h -> build/lib.macosx-10.9-universal2-cpython-310/cypari2
        running build_ext
        building 'cypari2.closure' extension
        creating build/temp.macosx-10.9-universal2-cpython-310
        creating build/temp.macosx-10.9-universal2-cpython-310/cypari2
        clang -Wno-unused-result -Wsign-compare -Wunreachable-code -fno-common -dynamic -DNDEBUG -g -fwrapv -O3 -Wall -arch arm64 -arch x86_64 -g -I./cypari2 -I/Users/liam/Library/Caches/pypoetry/virtualenvs/backscope-xBHlVOM6-py3.10/lib/python3.10/site-packages/cysignals -I/opt/homebrew/include -I/Users/liam/Library/Caches/pypoetry/virtualenvs/backscope-xBHlVOM6-py3.10/include -I/Library/Frameworks/Python.framework/Versions/3.10/include/python3.10 -c cypari2/closure.c -o build/temp.macosx-10.9-universal2-cpython-310/cypari2/closure.o
        clang -bundle -undefined dynamic_lookup -arch arm64 -arch x86_64 -g build/temp.macosx-10.9-universal2-cpython-310/cypari2/closure.o -L/opt/homebrew/lib -lgmp -lpari -o build/lib.macosx-10.9-universal2-cpython-310/cypari2/closure.cpython-310-darwin.so
        ld: warning: dylib (/opt/homebrew/lib/libgmp.dylib) was built for newer macOS version (12.0) than being linked (11.0)
        ld: warning: dylib (/opt/homebrew/lib/libpari.dylib) was built for newer macOS version (12.0) than being linked (11.0)
        ld: warning: ignoring file /opt/homebrew/lib/libgmp.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
        ld: warning: ignoring file /opt/homebrew/lib/libpari.dylib, building for macOS-x86_64 but attempting to link with file built for macOS-arm64
        ld: illegal thread local variable reference to regular symbol _avma for architecture x86_64
        clang: error: linker command failed with exit code 1 (use -v to see invocation)
        error: command '/usr/bin/clang' failed with exit code 1
        [end of output]
    
    note: This error originates from a subprocess, and is likely not a problem with pip.
  error: legacy-install-failure
  
  × Encountered error while trying to install package.
  ╰─> cypari2
  
  note: This is an issue with the package mentioned above, not pip.
  hint: See above for output from the failure.
  

  at ~/Library/Application Support/pypoetry/venv/lib/python3.10/site-packages/poetry/utils/env.py:1195 in _run
      1191│                 output = subprocess.check_output(
      1192│                     cmd, stderr=subprocess.STDOUT, **kwargs
      1193│                 )
      1194│         except CalledProcessError as e:
    → 1195│             raise EnvCommandError(e, input=input_)
      1196│ 
      1197│         return decode(output)
      1198│ 
      1199│     def execute(self, bin, *args, **kwargs):


Failed to add packages, reverting the pyproject.toml file to its original content.

clang Version

(backscope-xBHlVOM6-py3.10) liam@ratbook backscope % clang --version
Apple clang version 13.0.0 (clang-1300.0.27.3)
Target: arm64-apple-darwin21.5.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin

Where to go from here?

It seems like the error has to do with the .dylib files for GNU multiple precision arithmetic library (a dependency of PARI/GP) and PARI/GP installed via Homebrew being incompatible with what is being linked. If this the case, then I guess this isn't an issue with cypari2 per se, but I'm not sure where else I would ask for help. Again, any advice or directions would be greatly appreciated. Thanks in advance! :)

[videlec]

Indeed, there is an incompatibility with your compiler (clang which comes from your system) and the libraries that cypari2 depends on (libgmp and libpari that are managed by homebrew). I am not familiar with homebrew. Isn't it possible to use it to install a compatible compiler? Or maybe it is already installed but not picked up by the setup.py script. In that case you could try to set up the environment variable CC=/path/to/the/homebrew/compiler Two other possibilities are

• create a conda environment with a c-compiler, libgmp and pari/GP
• compile gmp and PARI/GP with the clang from your system

[liammulh]

I haven't been able to install cypari2 on my Mac yet. I plan on using Docker for my application that uses cypari2. Feel free to close this issue if you don't want it lingering in this repo.