Error when running pypi2nix command: scipy
jdagilliland opened this issue · 2 comments
jdagilliland commented
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
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
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.