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bschilder avatar bschilder commented on June 17, 2024

See here for details:
https://github.com/omerwe/polyfun/blob/master/polyfun.yml

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bschilder avatar bschilder commented on June 17, 2024

bgen is the only other package that's new, but when i try to install it, it can't be installed in my current echoR env. But i can confirm that the echolocatoR implementation of PolyFun ran all the way through without it:

...
...
ERROR: Could not build wheels for bgen, which is required to install pyproject.toml-based projects

https://github.com/RajLabMSSM/echolocatoR/blob/master/inst/conda/echoR.yml

I think this is because the only place i see bgen being used is a step within finemapper.py where it imports genotype files. echolocatoR doesn't currently use this particular script (just the subscripts used by finemapper.py)

@omerwe let me know if this sounds right to you.

Conda output

⋊> ~/Desktop pip install bgen==1.2.10                                                                          (echoR) 17:52:24
Collecting bgen==1.2.10
  Downloading bgen-1.2.10.tar.gz (664 kB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 665.0/665.0 KB 10.1 MB/s eta 0:00:00
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... done
Requirement already satisfied: numpy in /opt/anaconda3/envs/echoR/lib/python3.9/site-packages (from bgen==1.2.10) (1.21.5)
Building wheels for collected packages: bgen
  Building wheel for bgen (pyproject.toml) ... error
  error: subprocess-exited-with-error
  
  × Building wheel for bgen (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [80 lines of output]
      running bdist_wheel
      running build
      running build_py
      creating build
      creating build/lib.macosx-10.9-x86_64-3.9
      creating build/lib.macosx-10.9-x86_64-3.9/bgen
      copying src/bgen/index.py -> build/lib.macosx-10.9-x86_64-3.9/bgen
      copying src/bgen/__init__.py -> build/lib.macosx-10.9-x86_64-3.9/bgen
      running build_ext
      building 'bgen.reader' extension
      creating build/temp.macosx-10.9-x86_64-3.9
      creating build/temp.macosx-10.9-x86_64-3.9/src
      creating build/temp.macosx-10.9-x86_64-3.9/src/bgen
      clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -fwrapv -O2 -Wall -fPIC -O2 -isystem /opt/anaconda3/envs/echoR/include -fPIC -O2 -isystem /opt/anaconda3/envs/echoR/include -Isrc/ -Isrc/zstd/lib -I/opt/anaconda3/envs/echoR/include/python3.9 -c src/bgen.cpp -o build/temp.macosx-10.9-x86_64-3.9/src/bgen.o -std=c++11 -I/usr/include -stdlib=libc++ -mmacosx-version-min=10.9 -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -mavx
      In file included from src/bgen.cpp:2:
      In file included from src/bgen.h:8:
      In file included from src/header.h:11:
      In file included from src/utils.h:5:
      /opt/anaconda3/envs/echoR/bin/../include/c++/v1/cmath:321:9: error: no member named 'signbit' in the global namespace
      using ::signbit;
            ~~^
      /opt/anaconda3/envs/echoR/bin/../include/c++/v1/cmath:322:9: error: no member named 'fpclassify' in the global namespace
      using ::fpclassify;
            ~~^
      /opt/anaconda3/envs/echoR/bin/../include/c++/v1/cmath:323:9: error: no member named 'isfinite' in the global namespace; did you mean 'finite'?
      using ::isfinite;
            ~~^
      /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/math.h:752:12: note: 'finite' declared here
      extern int finite(double)
                 ^
      In file included from src/bgen.cpp:2:
      In file included from src/bgen.h:8:
      In file included from src/header.h:11:
      In file included from src/utils.h:5:
      /opt/anaconda3/envs/echoR/bin/../include/c++/v1/cmath:324:9: error: no member named 'isinf' in the global namespace
      using ::isinf;
            ~~^
      /opt/anaconda3/envs/echoR/bin/../include/c++/v1/cmath:325:9: error: no member named 'isnan' in the global namespace
      using ::isnan;
            ~~^
      /opt/anaconda3/envs/echoR/bin/../include/c++/v1/cmath:326:9: error: no member named 'isnormal' in the global namespace
      using ::isnormal;
            ~~^
      /opt/anaconda3/envs/echoR/bin/../include/c++/v1/cmath:327:7: error: no member named 'isgreater' in the global namespace; did you mean '::std::greater'?
      using ::isgreater;
            ^~
      /opt/anaconda3/envs/echoR/bin/../include/c++/v1/functional:742:29: note: '::std::greater' declared here
      struct _LIBCPP_TEMPLATE_VIS greater : binary_function<_Tp, _Tp, bool>
                                  ^
      In file included from src/bgen.cpp:2:
      In file included from src/bgen.h:8:
      In file included from src/header.h:11:
      In file included from src/utils.h:5:
      /opt/anaconda3/envs/echoR/bin/../include/c++/v1/cmath:328:7: error: no member named 'isgreaterequal' in the global namespace; did you mean '::std::greater_equal'?
      using ::isgreaterequal;
            ^~
      /opt/anaconda3/envs/echoR/bin/../include/c++/v1/functional:771:29: note: '::std::greater_equal' declared here
      struct _LIBCPP_TEMPLATE_VIS greater_equal : binary_function<_Tp, _Tp, bool>
                                  ^
      In file included from src/bgen.cpp:2:
      In file included from src/bgen.h:8:
      In file included from src/header.h:11:
      In file included from src/utils.h:5:
      /opt/anaconda3/envs/echoR/bin/../include/c++/v1/cmath:329:9: error: no member named 'isless' in the global namespace
      using ::isless;
            ~~^
      /opt/anaconda3/envs/echoR/bin/../include/c++/v1/cmath:330:9: error: no member named 'islessequal' in the global namespace
      using ::islessequal;
            ~~^
      /opt/anaconda3/envs/echoR/bin/../include/c++/v1/cmath:331:9: error: no member named 'islessgreater' in the global namespace
      using ::islessgreater;
            ~~^
      /opt/anaconda3/envs/echoR/bin/../include/c++/v1/cmath:332:9: error: no member named 'isunordered' in the global namespace
      using ::isunordered;
            ~~^
      /opt/anaconda3/envs/echoR/bin/../include/c++/v1/cmath:333:9: error: no member named 'isunordered' in the global namespace
      using ::isunordered;
            ~~^
      13 errors generated.
      error: command '/opt/anaconda3/envs/echoR/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 bgen
Failed to build bgen
ERROR: Could not build wheels for bgen, which is required to install pyproject.toml-based projects

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bschilder avatar bschilder commented on June 17, 2024

bgen is also available on anaconda.org. Do none of these versions work for your purposes @omerwe?
https://anaconda.org/conda-forge/bgen/files?page=2

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omerwe avatar omerwe commented on June 17, 2024

Hi, we just had a discussion about this in the PolyFun GitHub issues: omerwe/polyfun#86

As you can see there, there are two different python packages called bgen, and the one on conda-forge is not the one that PolyFun uses. Just yesterday I updated the yml file to demand a specific version of the bgen package rather than the newest version, following reports that the newest version isn't supported on MacOS (omerwe/polyfun#89). So if you tried before yesterday, please git pull the latest PolyFun code and try again. If you still run into any issues, please let me know and I'll try to look into it.

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bschilder avatar bschilder commented on June 17, 2024

Thanks so much for clarifying, @omerwe! That all makes sense. I'll let you know implementing finemapper.py goes.

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