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Cannot install pymrmr #487

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MariamSheha opened this issue Mar 15, 2021 · 4 comments
Open

Cannot install pymrmr #487

MariamSheha opened this issue Mar 15, 2021 · 4 comments

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@MariamSheha
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MariamSheha commented Mar 15, 2021 •
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  • PymRMR version:
  • Python version: python 3
  • Operating System: OS X El Capitan "10.11.6"

Description

Describe what you were trying to get done.
Tell us what happened, what went wrong, and what you expected to happen.

What I Did

pip install numpy Cython
pip install pymrmr

Collecting pymrmr
  Using cached pymrmr-0.1.11.tar.gz (69 kB)
Requirement already satisfied: numpy>=1.19.5 in /opt/anaconda3/lib/python3.7/site-packages (from pymrmr) (1.20.1)
Building wheels for collected packages: pymrmr
  Building wheel for pymrmr (setup.py) ... �[?25lerror
  ERROR: Command errored out with exit status 1:
   command: /opt/anaconda3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/wf/m4g31w8s68z88597d_64hbw80000gn/T/pip-install-f7qo02kj/pymrmr_32f3a729caae47319ee9a082199328fe/setup.py'"'"'; __file__='"'"'/private/var/folders/wf/m4g31w8s68z88597d_64hbw80000gn/T/pip-install-f7qo02kj/pymrmr_32f3a729caae47319ee9a082199328fe/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /private/var/folders/wf/m4g31w8s68z88597d_64hbw80000gn/T/pip-wheel-frxhfca6
       cwd: /private/var/folders/wf/m4g31w8s68z88597d_64hbw80000gn/T/pip-install-f7qo02kj/pymrmr_32f3a729caae47319ee9a082199328fe/
  Complete output (38 lines):
  /opt/anaconda3/lib/python3.7/site-packages/setuptools/dist.py:723: UserWarning: Module Cython was already imported from /opt/anaconda3/lib/python3.7/site-packages/Cython/__init__.py, but /private/var/folders/wf/m4g31w8s68z88597d_64hbw80000gn/T/pip-install-f7qo02kj/pymrmr_32f3a729caae47319ee9a082199328fe/.eggs/Cython-3.0a6-py3.7.egg is being added to sys.path
    pkg_resources.working_set.add(dist, replace=True)
  running bdist_wheel
  running build
  running build_py
  package init file 'pymrmr/__init__.py' not found (or not a regular file)
  running egg_info
  writing pymrmr.egg-info/PKG-INFO
  writing dependency_links to pymrmr.egg-info/dependency_links.txt
  writing requirements to pymrmr.egg-info/requires.txt
  writing top-level names to pymrmr.egg-info/top_level.txt
  reading manifest file 'pymrmr.egg-info/SOURCES.txt'
  reading manifest template 'MANIFEST.in'
  warning: no previously-included files matching '__pycache__' found under directory '*'
  warning: no previously-included files matching '*.py[co]' found under directory '*'
  warning: no files found matching '*.jpg' under directory 'docs'
  warning: no files found matching '*.png' under directory 'docs'
  warning: no files found matching '*.gif' under directory 'docs'
  writing manifest file 'pymrmr.egg-info/SOURCES.txt'
  creating build
  creating build/lib.macosx-10.9-x86_64-3.7
  creating build/lib.macosx-10.9-x86_64-3.7/pymrmr
  copying pymrmr/crank.cpp -> build/lib.macosx-10.9-x86_64-3.7/pymrmr
  copying pymrmr/mrmr.cpp -> build/lib.macosx-10.9-x86_64-3.7/pymrmr
  copying pymrmr/nrutil.cpp -> build/lib.macosx-10.9-x86_64-3.7/pymrmr
  copying pymrmr/nrutil.h -> build/lib.macosx-10.9-x86_64-3.7/pymrmr
  copying pymrmr/pbetai.cpp -> build/lib.macosx-10.9-x86_64-3.7/pymrmr
  copying pymrmr/pymrmr.cpp -> build/lib.macosx-10.9-x86_64-3.7/pymrmr
  copying pymrmr/pymrmr.pyx -> build/lib.macosx-10.9-x86_64-3.7/pymrmr
  copying pymrmr/sort2.cpp -> build/lib.macosx-10.9-x86_64-3.7/pymrmr
  running build_ext
  skipping 'pymrmr/pymrmr.cpp' Cython extension (up-to-date)
  building 'pymrmr' extension
  creating build/temp.macosx-10.9-x86_64-3.7
  creating build/temp.macosx-10.9-x86_64-3.7/pymrmr
  gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/opt/anaconda3/include -arch x86_64 -I/opt/anaconda3/include -arch x86_64 -I/opt/anaconda3/lib/python3.7/site-packages/numpy/core/include -I/opt/anaconda3/include/python3.7m -c pymrmr/pymrmr.cpp -o build/temp.macosx-10.9-x86_64-3.7/pymrmr/pymrmr.o -fopenmp -Ofast
  clang: error: unsupported option '-fopenmp'
  error: command 'gcc' failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for pymrmr
nning setup.py clean for pymrmr
Failed to build pymrmr
Installing collected packages: pymrmr
    Running setup.py install for pymrmr ... �[?25lerror
    ERROR: Command errored out with exit status 1:
     command: /opt/anaconda3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/wf/m4g31w8s68z88597d_64hbw80000gn/T/pip-install-f7qo02kj/pymrmr_32f3a729caae47319ee9a082199328fe/setup.py'"'"'; __file__='"'"'/private/var/folders/wf/m4g31w8s68z88597d_64hbw80000gn/T/pip-install-f7qo02kj/pymrmr_32f3a729caae47319ee9a082199328fe/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/wf/m4g31w8s68z88597d_64hbw80000gn/T/pip-record-zrfq3baf/install-record.txt --single-version-externally-managed --compile --install-headers /opt/anaconda3/include/python3.7m/pymrmr
         cwd: /private/var/folders/wf/m4g31w8s68z88597d_64hbw80000gn/T/pip-install-f7qo02kj/pymrmr_32f3a729caae47319ee9a082199328fe/
    Complete output (38 lines):
    /opt/anaconda3/lib/python3.7/site-packages/setuptools/dist.py:723: UserWarning: Module Cython was already imported from /opt/anaconda3/lib/python3.7/site-packages/Cython/__init__.py, but /private/var/folders/wf/m4g31w8s68z88597d_64hbw80000gn/T/pip-install-f7qo02kj/pymrmr_32f3a729caae47319ee9a082199328fe/.eggs/Cython-3.0a6-py3.7.egg is being added to sys.path
      pkg_resources.working_set.add(dist, replace=True)
    running install
    running build
    running build_py
    package init file 'pymrmr/__init__.py' not found (or not a regular file)
    running egg_info
    writing pymrmr.egg-info/PKG-INFO
    writing dependency_links to pymrmr.egg-info/dependency_links.txt
    writing requirements to pymrmr.egg-info/requires.txt
    writing top-level names to pymrmr.egg-info/top_level.txt
    reading manifest file 'pymrmr.egg-info/SOURCES.txt'
    reading manifest template 'MANIFEST.in'
    warning: no previously-included files matching '__pycache__' found under directory '*'
    warning: no previously-included files matching '*.py[co]' found under directory '*'
    warning: no files found matching '*.jpg' under directory 'docs'
    warning: no files found matching '*.png' under directory 'docs'
    warning: no files found matching '*.gif' under directory 'docs'
    writing manifest file 'pymrmr.egg-info/SOURCES.txt'
    creating build
    creating build/lib.macosx-10.9-x86_64-3.7
    creating build/lib.macosx-10.9-x86_64-3.7/pymrmr
    copying pymrmr/crank.cpp -> build/lib.macosx-10.9-x86_64-3.7/pymrmr
    copying pymrmr/mrmr.cpp -> build/lib.macosx-10.9-x86_64-3.7/pymrmr
    copying pymrmr/nrutil.cpp -> build/lib.macosx-10.9-x86_64-3.7/pymrmr
    copying pymrmr/nrutil.h -> build/lib.macosx-10.9-x86_64-3.7/pymrmr
    copying pymrmr/pbetai.cpp -> build/lib.macosx-10.9-x86_64-3.7/pymrmr
    copying pymrmr/pymrmr.cpp -> build/lib.macosx-10.9-x86_64-3.7/pymrmr
    copying pymrmr/pymrmr.pyx -> build/lib.macosx-10.9-x86_64-3.7/pymrmr
    copying pymrmr/sort2.cpp -> build/lib.macosx-10.9-x86_64-3.7/pymrmr
    running build_ext
    skipping 'pymrmr/pymrmr.cpp' Cython extension (up-to-date)
    building 'pymrmr' extension
    creating build/temp.macosx-10.9-x86_64-3.7
    creating build/temp.macosx-10.9-x86_64-3.7/pymrmr
    gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/opt/anaconda3/include -arch x86_64 -I/opt/anaconda3/include -arch x86_64 -I/opt/anaconda3/lib/python3.7/site-packages/numpy/core/include -I/opt/anaconda3/include/python3.7m -c pymrmr/pymrmr.cpp -o build/temp.macosx-10.9-x86_64-3.7/pymrmr/pymrmr.o -fopenmp -Ofast
    clang: error: unsupported option '-fopenmp'
    error: command 'gcc' failed with exit status 1
    ----------------------------------------
ERROR: Command errored out with exit status 1: /opt/anaconda3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/var/folders/wf/m4g31w8s68z88597d_64hbw80000gn/T/pip-install-f7qo02kj/pymrmr_32f3a729caae47319ee9a082199328fe/setup.py'"'"'; __file__='"'"'/private/var/folders/wf/m4g31w8s68z88597d_64hbw80000gn/T/pip-install-f7qo02kj/pymrmr_32f3a729caae47319ee9a082199328fe/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/var/folders/wf/m4g31w8s68z88597d_64hbw80000gn/T/pip-record-zrfq3baf/install-record.txt --single-version-externally-managed --compile --install-headers /opt/anaconda3/include/python3.7m/pymrmr Check the logs for full command output.
�[?25hNote: you may need to restart the kernel to use updated packages.
@JacksonBurns
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This looks like it might just be a problem with OpenMP -- check out this StackOverflow post.

@sunformoon
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@MariamSheha Hi, did you have a chance to fix it? I had the same error on my macOS High Sierra.

@MariamSheha
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MariamSheha commented Sep 26, 2021 via email

@sunformoon
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@MariamSheha , thank you for your reply. I gave up installing this package on my Mac. However,

  1. I successfully installed this package on a Ubuntu 18.04 machine.
  2. On my own Mac, I found this repo working for me. https://github.com/danielhomola/mifs

Hopefully, this helps for you.

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@sunformoon @JacksonBurns @MariamSheha