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Error when running pypi2nix command: scipy #440

Open jdagilliland opened 4 years ago

jdagilliland commented 4 years ago

Description

I couldn't create an env with scipy, even though I was able to do with numpy. I can tell from this template that you want me to paste in at least parts of the error message I got, and it was seriously massive, but here indeed it is. I hope it helps:

% pypi2nix --version
2.0.4
% pypi2nix -e scipy
  ERROR: Command errored out with exit status 1:
   command: /nix/store/jwabyfhz3h2864i4mns3l64a71nc7rwl-python3-3.7.7-env/bin/python3.7 /nix/store/jwabyfhz3h2864i4mns3l64a71nc7rwl-python3-3.7.7-env/lib/python3.7/site-packages/pip install --ignore-installed --no-user --prefix /tmp/tmpb5uu1d8f/pip-build-env-3c7xedym/overlay --no-warn-script-location --no-binary :all: --only-binary :none: -i https://pypi.org/simple -- wheel setuptools 'Cython>=0.29.13' 'numpy==1.13.3; python_version=='"'"'3.5'"'"' and platform_system!='"'"'AIX'"'"'' 'numpy==1.13.3; python_version=='"'"'3.6'"'"' and platform_system!='"'"'AIX'"'"'' 'numpy==1.14.5; python_version=='"'"'3.7'"'"' and platform_system!='"'"'AIX'"'"'' 'numpy==1.17.3; python_version>='"'"'3.8'"'"' and platform_system!='"'"'AIX'"'"'' 'numpy==1.16.0; python_version=='"'"'3.5'"'"' and platform_system=='"'"'AIX'"'"'' 'numpy==1.16.0; python_version=='"'"'3.6'"'"' and platform_system=='"'"'AIX'"'"'' 'numpy==1.16.0; python_version=='"'"'3.7'"'"' and platform_system=='"'"'AIX'"'"'' 'numpy==1.17.3; python_version>='"'"'3.8'"'"' and platform_system=='"'"'AIX'"'"'' 'pybind11>=2.4.0'
       cwd: None
  Complete output (119 lines):
  Ignoring numpy: markers 'python_version == "3.5" and platform_system != "AIX"' don't match your environment
  Ignoring numpy: markers 'python_version == "3.6" and platform_system != "AIX"' don't match your environment
  Ignoring numpy: markers 'python_version >= "3.8" and platform_system != "AIX"' don't match your environment
  Ignoring numpy: markers 'python_version == "3.5" and platform_system == "AIX"' don't match your environment
  Ignoring numpy: markers 'python_version == "3.6" and platform_system == "AIX"' don't match your environment
  Ignoring numpy: markers 'python_version == "3.7" and platform_system == "AIX"' don't match your environment
  Ignoring numpy: markers 'python_version >= "3.8" and platform_system == "AIX"' don't match your environment
  Collecting wheel
    Downloading wheel-0.34.2.tar.gz (58 kB)
  Collecting setuptools
    Downloading setuptools-46.1.3.zip (862 kB)
  Collecting Cython>=0.29.13
    Downloading Cython-0.29.16.tar.gz (2.1 MB)
  Collecting numpy==1.14.5
    Downloading numpy-1.14.5.zip (4.9 MB)
  Collecting pybind11>=2.4.0
    Downloading pybind11-2.5.0.tar.gz (139 kB)
  Skipping wheel build for wheel, due to binaries being disabled for it.
  Skipping wheel build for setuptools, due to binaries being disabled for it.
  Skipping wheel build for Cython, due to binaries being disabled for it.
  Skipping wheel build for numpy, due to binaries being disabled for it.
  Skipping wheel build for pybind11, due to binaries being disabled for it.
  Installing collected packages: wheel, setuptools, Cython, numpy, pybind11
      Running setup.py install for wheel: started
      Running setup.py install for wheel: finished with status 'done'
      Running setup.py install for setuptools: started
      Running setup.py install for setuptools: finished with status 'done'
      Running setup.py install for Cython: started
      Running setup.py install for Cython: still running...
      Running setup.py install for Cython: finished with status 'done'
      Running setup.py install for numpy: started
      Running setup.py install for numpy: still running...
      Running setup.py install for numpy: still running...
      Running setup.py install for numpy: still running...
      Running setup.py install for numpy: finished with status 'done'
      Running setup.py install for pybind11: started
      Running setup.py install for pybind11: finished with status 'error'
      ERROR: Command errored out with exit status 1:
       command: /nix/store/jwabyfhz3h2864i4mns3l64a71nc7rwl-python3-3.7.7-env/bin/python3.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/tmpb5uu1d8f/pip-install-diy6tpkd/pybind11/setup.py'"'"'; __file__='"'"'/tmp/tmpb5uu1d8f/pip-install-diy6tpkd/pybind11/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/tmpb5uu1d8f/pip-record-i5bdjpsf/install-record.txt --single-version-externally-managed --prefix /tmp/tmpb5uu1d8f/pip-build-env-3c7xedym/overlay --compile --install-headers /nix/store/jwabyfhz3h2864i4mns3l64a71nc7rwl-python3-3.7.7-env/include/site/python3.7/pybind11
           cwd: /tmp/tmpb5uu1d8f/pip-install-diy6tpkd/pybind11/
      Complete output (74 lines):
      running install
      running build
      running build_py
      creating build
      creating build/lib
      creating build/lib/pybind11
      copying pybind11/_version.py -> build/lib/pybind11
      copying pybind11/__main__.py -> build/lib/pybind11
      copying pybind11/__init__.py -> build/lib/pybind11
      creating build/lib/pybind11/include
      creating build/lib/pybind11/include/pybind11
      creating build/lib/pybind11/include/pybind11/detail
      copying include/pybind11/detail/class.h -> build/lib/pybind11/include/pybind11/detail
      copying include/pybind11/detail/common.h -> build/lib/pybind11/include/pybind11/detail
      copying include/pybind11/detail/descr.h -> build/lib/pybind11/include/pybind11/detail
      copying include/pybind11/detail/init.h -> build/lib/pybind11/include/pybind11/detail
      copying include/pybind11/detail/internals.h -> build/lib/pybind11/include/pybind11/detail
      copying include/pybind11/detail/typeid.h -> build/lib/pybind11/include/pybind11/detail
      copying include/pybind11/attr.h -> build/lib/pybind11/include/pybind11
      copying include/pybind11/buffer_info.h -> build/lib/pybind11/include/pybind11
      copying include/pybind11/cast.h -> build/lib/pybind11/include/pybind11
      copying include/pybind11/chrono.h -> build/lib/pybind11/include/pybind11
      copying include/pybind11/common.h -> build/lib/pybind11/include/pybind11
      copying include/pybind11/complex.h -> build/lib/pybind11/include/pybind11
      copying include/pybind11/eigen.h -> build/lib/pybind11/include/pybind11
      copying include/pybind11/embed.h -> build/lib/pybind11/include/pybind11
      copying include/pybind11/eval.h -> build/lib/pybind11/include/pybind11
      copying include/pybind11/functional.h -> build/lib/pybind11/include/pybind11
      copying include/pybind11/iostream.h -> build/lib/pybind11/include/pybind11
      copying include/pybind11/numpy.h -> build/lib/pybind11/include/pybind11
      copying include/pybind11/operators.h -> build/lib/pybind11/include/pybind11
      copying include/pybind11/options.h -> build/lib/pybind11/include/pybind11
      copying include/pybind11/pybind11.h -> build/lib/pybind11/include/pybind11
      copying include/pybind11/pytypes.h -> build/lib/pybind11/include/pybind11
      copying include/pybind11/stl.h -> build/lib/pybind11/include/pybind11
      copying include/pybind11/stl_bind.h -> build/lib/pybind11/include/pybind11
      running install_lib
      creating /tmp/tmpb5uu1d8f/pip-build-env-3c7xedym/overlay/lib/python3.7/site-packages/pybind11
      creating /tmp/tmpb5uu1d8f/pip-build-env-3c7xedym/overlay/lib/python3.7/site-packages/pybind11/include
      creating /tmp/tmpb5uu1d8f/pip-build-env-3c7xedym/overlay/lib/python3.7/site-packages/pybind11/include/pybind11
      copying build/lib/pybind11/include/pybind11/cast.h -> /tmp/tmpb5uu1d8f/pip-build-env-3c7xedym/overlay/lib/python3.7/site-packages/pybind11/include/pybind11
      copying build/lib/pybind11/include/pybind11/operators.h -> /tmp/tmpb5uu1d8f/pip-build-env-3c7xedym/overlay/lib/python3.7/site-packages/pybind11/include/pybind11
      copying build/lib/pybind11/include/pybind11/complex.h -> /tmp/tmpb5uu1d8f/pip-build-env-3c7xedym/overlay/lib/python3.7/site-packages/pybind11/include/pybind11
      copying build/lib/pybind11/include/pybind11/eigen.h -> /tmp/tmpb5uu1d8f/pip-build-env-3c7xedym/overlay/lib/python3.7/site-packages/pybind11/include/pybind11
      copying build/lib/pybind11/include/pybind11/attr.h -> /tmp/tmpb5uu1d8f/pip-build-env-3c7xedym/overlay/lib/python3.7/site-packages/pybind11/include/pybind11
      copying build/lib/pybind11/include/pybind11/stl.h -> /tmp/tmpb5uu1d8f/pip-build-env-3c7xedym/overlay/lib/python3.7/site-packages/pybind11/include/pybind11
      copying build/lib/pybind11/include/pybind11/pytypes.h -> /tmp/tmpb5uu1d8f/pip-build-env-3c7xedym/overlay/lib/python3.7/site-packages/pybind11/include/pybind11
      copying build/lib/pybind11/include/pybind11/chrono.h -> /tmp/tmpb5uu1d8f/pip-build-env-3c7xedym/overlay/lib/python3.7/site-packages/pybind11/include/pybind11
      copying build/lib/pybind11/include/pybind11/options.h -> /tmp/tmpb5uu1d8f/pip-build-env-3c7xedym/overlay/lib/python3.7/site-packages/pybind11/include/pybind11
      copying build/lib/pybind11/include/pybind11/eval.h -> /tmp/tmpb5uu1d8f/pip-build-env-3c7xedym/overlay/lib/python3.7/site-packages/pybind11/include/pybind11
      copying build/lib/pybind11/include/pybind11/numpy.h -> /tmp/tmpb5uu1d8f/pip-build-env-3c7xedym/overlay/lib/python3.7/site-packages/pybind11/include/pybind11
      copying build/lib/pybind11/include/pybind11/stl_bind.h -> /tmp/tmpb5uu1d8f/pip-build-env-3c7xedym/overlay/lib/python3.7/site-packages/pybind11/include/pybind11
      copying build/lib/pybind11/include/pybind11/common.h -> /tmp/tmpb5uu1d8f/pip-build-env-3c7xedym/overlay/lib/python3.7/site-packages/pybind11/include/pybind11
      copying build/lib/pybind11/include/pybind11/iostream.h -> /tmp/tmpb5uu1d8f/pip-build-env-3c7xedym/overlay/lib/python3.7/site-packages/pybind11/include/pybind11
      copying build/lib/pybind11/include/pybind11/functional.h -> /tmp/tmpb5uu1d8f/pip-build-env-3c7xedym/overlay/lib/python3.7/site-packages/pybind11/include/pybind11
      creating /tmp/tmpb5uu1d8f/pip-build-env-3c7xedym/overlay/lib/python3.7/site-packages/pybind11/include/pybind11/detail
      copying build/lib/pybind11/include/pybind11/detail/internals.h -> /tmp/tmpb5uu1d8f/pip-build-env-3c7xedym/overlay/lib/python3.7/site-packages/pybind11/include/pybind11/detail
      copying build/lib/pybind11/include/pybind11/detail/init.h -> /tmp/tmpb5uu1d8f/pip-build-env-3c7xedym/overlay/lib/python3.7/site-packages/pybind11/include/pybind11/detail
      copying build/lib/pybind11/include/pybind11/detail/typeid.h -> /tmp/tmpb5uu1d8f/pip-build-env-3c7xedym/overlay/lib/python3.7/site-packages/pybind11/include/pybind11/detail
      copying build/lib/pybind11/include/pybind11/detail/descr.h -> /tmp/tmpb5uu1d8f/pip-build-env-3c7xedym/overlay/lib/python3.7/site-packages/pybind11/include/pybind11/detail
      copying build/lib/pybind11/include/pybind11/detail/class.h -> /tmp/tmpb5uu1d8f/pip-build-env-3c7xedym/overlay/lib/python3.7/site-packages/pybind11/include/pybind11/detail
      copying build/lib/pybind11/include/pybind11/detail/common.h -> /tmp/tmpb5uu1d8f/pip-build-env-3c7xedym/overlay/lib/python3.7/site-packages/pybind11/include/pybind11/detail
      copying build/lib/pybind11/include/pybind11/buffer_info.h -> /tmp/tmpb5uu1d8f/pip-build-env-3c7xedym/overlay/lib/python3.7/site-packages/pybind11/include/pybind11
      copying build/lib/pybind11/include/pybind11/pybind11.h -> /tmp/tmpb5uu1d8f/pip-build-env-3c7xedym/overlay/lib/python3.7/site-packages/pybind11/include/pybind11
      copying build/lib/pybind11/include/pybind11/embed.h -> /tmp/tmpb5uu1d8f/pip-build-env-3c7xedym/overlay/lib/python3.7/site-packages/pybind11/include/pybind11
      copying build/lib/pybind11/_version.py -> /tmp/tmpb5uu1d8f/pip-build-env-3c7xedym/overlay/lib/python3.7/site-packages/pybind11
      copying build/lib/pybind11/__main__.py -> /tmp/tmpb5uu1d8f/pip-build-env-3c7xedym/overlay/lib/python3.7/site-packages/pybind11
      copying build/lib/pybind11/__init__.py -> /tmp/tmpb5uu1d8f/pip-build-env-3c7xedym/overlay/lib/python3.7/site-packages/pybind11
      byte-compiling /tmp/tmpb5uu1d8f/pip-build-env-3c7xedym/overlay/lib/python3.7/site-packages/pybind11/_version.py to _version.cpython-37.pyc
      byte-compiling /tmp/tmpb5uu1d8f/pip-build-env-3c7xedym/overlay/lib/python3.7/site-packages/pybind11/__main__.py to __main__.cpython-37.pyc
      byte-compiling /tmp/tmpb5uu1d8f/pip-build-env-3c7xedym/overlay/lib/python3.7/site-packages/pybind11/__init__.py to __init__.cpython-37.pyc
      running install_headers
      creating /nix/store/jwabyfhz3h2864i4mns3l64a71nc7rwl-python3-3.7.7-env/include/site
      error: could not create '/nix/store/jwabyfhz3h2864i4mns3l64a71nc7rwl-python3-3.7.7-env/include/site': Read-only file system
      ----------------------------------------
  ERROR: Command errored out with exit status 1: /nix/store/jwabyfhz3h2864i4mns3l64a71nc7rwl-python3-3.7.7-env/bin/python3.7 -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/tmpb5uu1d8f/pip-install-diy6tpkd/pybind11/setup.py'"'"'; __file__='"'"'/tmp/tmpb5uu1d8f/pip-install-diy6tpkd/pybind11/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/tmpb5uu1d8f/pip-record-i5bdjpsf/install-record.txt --single-version-externally-managed --prefix /tmp/tmpb5uu1d8f/pip-build-env-3c7xedym/overlay --compile --install-headers /nix/store/jwabyfhz3h2864i4mns3l64a71nc7rwl-python3-3.7.7-env/include/site/python3.7/pybind11 Check the logs for full command output.
  WARNING: You are using pip version 20.0.dev0; however, version 20.0.2 is available.
  You should consider upgrading via the 'pip install --upgrade pip' command.
  ----------------------------------------
ERROR: Command errored out with exit status 1: /nix/store/jwabyfhz3h2864i4mns3l64a71nc7rwl-python3-3.7.7-env/bin/python3.7 /nix/store/jwabyfhz3h2864i4mns3l64a71nc7rwl-python3-3.7.7-env/lib/python3.7/site-packages/pip install --ignore-installed --no-user --prefix /tmp/tmpb5uu1d8f/pip-build-env-3c7xedym/overlay --no-warn-script-location --no-binary :all: --only-binary :none: -i https://pypi.org/simple -- wheel setuptools 'Cython>=0.29.13' 'numpy==1.13.3; python_version=='"'"'3.5'"'"' and platform_system!='"'"'AIX'"'"'' 'numpy==1.13.3; python_version=='"'"'3.6'"'"' and platform_system!='"'"'AIX'"'"'' 'numpy==1.14.5; python_version=='"'"'3.7'"'"' and platform_system!='"'"'AIX'"'"'' 'numpy==1.17.3; python_version>='"'"'3.8'"'"' and platform_system!='"'"'AIX'"'"'' 'numpy==1.16.0; python_version=='"'"'3.5'"'"' and platform_system=='"'"'AIX'"'"'' 'numpy==1.16.0; python_version=='"'"'3.6'"'"' and platform_system=='"'"'AIX'"'"'' 'numpy==1.16.0; python_version=='"'"'3.7'"'"' and platform_system=='"'"'AIX'"'"'' 'numpy==1.17.3; python_version>='"'"'3.8'"'"' and platform_system=='"'"'AIX'"'"'' 'pybind11>=2.4.0' Check the logs for full command output.
WARNING: You are using pip version 20.0.dev0; however, version 20.0.2 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
Collecting scipy
  Downloading scipy-1.4.1.tar.gz (24.6 MB)
  Saved /tmp/tmpb5uu1d8f/download/scipy-1.4.1.tar.gz
  Installing build dependencies: started
  Installing build dependencies: still running...
  Installing build dependencies: still running...
  Installing build dependencies: still running...
  Installing build dependencies: still running...
  Installing build dependencies: finished with status 'error'
jdagilliland commented 4 years ago

Like I said, though, I was able to work it with numpy:

% nix-shell requirements.nix -A interpreter
<output elided for brevity...>
$ head -n 5 requirements.nix                                                                          
# generated using pypi2nix tool (version: 2.0.4)                                        
# See more at: https://github.com/nix-community/pypi2nix                                
#
# COMMAND:
#   pypi2nix -e numpy
$ python     
Python 3.7.7 (default, Mar 10 2020, 06:34:06)                                           
[GCC 9.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.                  
>>> import numpy as np
>>> np.array([1,2,3])
array([1, 2, 3])
placeybordeaux commented 4 years ago

Interestingly installing pybind11 by it's self seems to work fine. I am also experiencing this problem, scipy is certainly not an unused library so it'd be really nice to see this fixed.