$ sudo python setup.py build
Gives me the following:
Partial import of sklearn during the build process.
Generating cython files
Cythonizing sources
sklearn
Processing sklearn/_isotonic.pyx
Traceback (most recent call last):
File "/home/scikit-learn/build_tools/cythonize.py", line 198, in <module>
main(root_dir_arg)
File "/home/ascikit-learn/build_tools/cythonize.py", line 190, in main
check_and_cythonize(root_dir)
File "/home/scikit-learn/build_tools/cythonize.py", line 182, in check_and_cythonize
cythonize_if_unchanged(cur_dir, cython_file, gen_file, hashes)
File "/home/scikit-learn/build_tools/cythonize.py", line 156, in cythonize_if_unchanged
cythonize(full_cython_path, full_gen_file_path)
File "/home/scikit-learn/build_tools/cythonize.py", line 61, in cythonize
raise Exception('Building scikit-learn requires Cython >= 0.21')
Exception: Building scikit-learn requires Cython >= 0.21
Traceback (most recent call last):
File "setup.py", line 297, in <module>
setup_package()
File "setup.py", line 280, in setup_package
generate_cython()
File "setup.py", line 185, in generate_cython
raise RuntimeError("Running cythonize failed!")
RuntimeError: Running cythonize failed!
While cython is installed:
Processing ./Cython-0.24-cp27-cp27mu-manylinux1_x86_64.whl
Installing collected packages: Cython
Found existing installation: Cython 0.24
Uninstalling Cython-0.24:
Successfully uninstalled Cython-0.24
Successfully installed Cython-0.24
Related
I have created a python app in my namecheap cpanel. I uploaded by server files in that and also UI files in public_html. However, I was getting Internal Server Error 500. Then I contacted their customer service. They told me install joblib through terminal. I installed it. Then they said in my root folder a file named "stderr.log" it said numpy is missing. So I tried to install numpy. But it shows the following error. Even customer service person failed to provide a solution. When I try pip install numpy, it shows the following large error. Please help.
Building wheels for collected packages: numpy
Building wheel for numpy (pyproject.toml) ... error
error: subprocess-exited-with-error
× Building wheel for numpy (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [61 lines of output]
Running from numpy source directory.
setup.py:67: DeprecationWarning:
`numpy.distutils` is deprecated since NumPy 1.23.0, as a result
of the deprecation of `distutils` itself. It will be removed for
Python >= 3.12. For older Python versions it will remain present.
It is recommended to use `setuptools < 60.0` for those Python versions.
For more details, see:
https://numpy.org/devdocs/reference/distutils_status_migration.html
import numpy.distutils.command.sdist
Traceback (most recent call last):
File "/opt/alt/python39/lib64/python3.9/runpy.py", line 197, in _run_module_as_main
return _run_code(code, main_globals, None,
File "/opt/alt/python39/lib64/python3.9/runpy.py", line 87, in _run_code
exec(code, run_globals)
File "/tmp/pip-build-env-r6jq5if_/overlay/lib64/python3.9/site-packages/cython.py", line 16, in <module>
from Cython.Compiler.Main import main
File "/tmp/pip-build-env-r6jq5if_/overlay/lib64/python3.9/site-packages/Cython/Compiler/Main.py", line 28, in <module>
from .Scanning import PyrexScanner, FileSourceDescriptor
ImportError: /tmp/pip-build-env-r6jq5if_/overlay/lib64/python3.9/site-packages/Cython/Compiler/Scanning.cpython-39-x86_64-linux-gnu.so: failed to map segment from shared object: Operation not permitted
Processing numpy/random/_bounded_integers.pxd.in
Processing numpy/random/_pcg64.pyx
Traceback (most recent call last):
File "/tmp/pip-install-q0hfnoqk/numpy_6a92dfb088184f0aaac1f9f1f3acc80e/tools/cythonize.py", line 205, in <module>
main()
File "/tmp/pip-install-q0hfnoqk/numpy_6a92dfb088184f0aaac1f9f1f3acc80e/tools/cythonize.py", line 201, in main
find_process_files(root_dir)
File "/tmp/pip-install-q0hfnoqk/numpy_6a92dfb088184f0aaac1f9f1f3acc80e/tools/cythonize.py", line 192, in find_process_files
process(root_dir, fromfile, tofile, function, hash_db)
File "/tmp/pip-install-q0hfnoqk/numpy_6a92dfb088184f0aaac1f9f1f3acc80e/tools/cythonize.py", line 158, in process
processor_function(fromfile, tofile)
File "/tmp/pip-install-q0hfnoqk/numpy_6a92dfb088184f0aaac1f9f1f3acc80e/tools/cythonize.py", line 47, in process_pyx
subprocess.check_call(
File "/opt/alt/python39/lib64/python3.9/subprocess.py", line 373, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['/home/nahiuzfc/virtualenv/classify_image/3.9/bin/python3.9_bin', '-m', 'cython', '-3', '--fast-fail', '-o', '_pcg64.c', '_pcg64.pyx']' returned non-zeroexit status 1.
Cythonizing sources
Traceback (most recent call last):
File "/home/nahiuzfc/virtualenv/classify_image/3.9/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>
main()
File "/home/nahiuzfc/virtualenv/classify_image/3.9/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
File "/home/nahiuzfc/virtualenv/classify_image/3.9/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 251, in build_wheel
return _build_backend().build_wheel(wheel_directory, config_settings,
File "/tmp/pip-build-env-r6jq5if_/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 230, in build_wheel
return self._build_with_temp_dir(['bdist_wheel'], '.whl',
File "/tmp/pip-build-env-r6jq5if_/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 215, in _build_with_temp_dir
self.run_setup()
File "/tmp/pip-build-env-r6jq5if_/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 267, in run_setup
super(_BuildMetaLegacyBackend,
File "/tmp/pip-build-env-r6jq5if_/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 158, in run_setup
exec(compile(code, __file__, 'exec'), locals())
File "setup.py", line 479, in <module>
setup_package()
File "setup.py", line 458, in setup_package
generate_cython()
File "setup.py", line 261, in generate_cython
raise RuntimeError("Running cythonize failed!")
RuntimeError: Running cythonize failed!
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for numpy
Failed to build numpy
ERROR: Could not build wheels for numpy, which is required to install pyproject.toml-based projects
I'm installing this package https://github.com/fuzailpalnak/kaizen, with this command:
pip3 install kaizen-mapping
but I'm getting this error. I've looked up online from many sites have a similar error, which seems to suggest that the root of the error is likely in the python version or in pip. Anyone knows how I can resolve this issue? Thanks!
Preparing metadata (pyproject.toml) ... error
error: subprocess-exited-with-error
× Preparing metadata (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [45 lines of output]
Error in sitecustomize; set PYTHONVERBOSE for traceback:
AssertionError:
Running from numpy source directory.
<string>:470: UserWarning: Unrecognized setuptools command, proceeding with generating Cython sources and expanding templates
Error in sitecustomize; set PYTHONVERBOSE for traceback:
AssertionError:
Processing numpy/random/_bounded_integers.pxd.in
Processing numpy/random/_philox.pyx
Traceback (most recent call last):
File "/private/var/folders/3g/6bwtmr4x4m3dvzm2dwby16q40000gn/T/pip-install-m94k6wqb/numpy/tools/cythonize.py", line 59, in process_pyx
from Cython.Compiler.Version import version as cython_version
ModuleNotFoundError: No module named 'Cython'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/private/var/folders/3g/6bwtmr4x4m3dvzm2dwby16q40000gn/T/pip-install-m94k6wqb/numpy/tools/cythonize.py", line 235, in <module>
main()
File "/private/var/folders/3g/6bwtmr4x4m3dvzm2dwby16q40000gn/T/pip-install-m94k6wqb/numpy/tools/cythonize.py", line 231, in main
find_process_files(root_dir)
File "/private/var/folders/3g/6bwtmr4x4m3dvzm2dwby16q40000gn/T/pip-install-m94k6wqb/numpy/tools/cythonize.py", line 222, in find_process_files
process(root_dir, fromfile, tofile, function, hash_db)
File "/private/var/folders/3g/6bwtmr4x4m3dvzm2dwby16q40000gn/T/pip-install-m94k6wqb/numpy/tools/cythonize.py", line 188, in process
processor_function(fromfile, tofile)
File "/private/var/folders/3g/6bwtmr4x4m3dvzm2dwby16q40000gn/T/pip-install-m94k6wqb/numpy/tools/cythonize.py", line 64, in process_pyx
raise OSError('Cython needs to be installed in Python as a module')
OSError: Cython needs to be installed in Python as a module
Cythonizing sources
Traceback (most recent call last):
File "/opt/homebrew/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 363, in <module>
main()
File "/opt/homebrew/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 345, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
File "/opt/homebrew/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 164, in prepare_metadata_for_build_wheel
return hook(metadata_directory, config_settings)
File "/opt/homebrew/Cellar/python#3.10/3.10.6_2/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/setuptools/build_meta.py", line 188, in prepare_metadata_for_build_wheel
self.run_setup()
File "/opt/homebrew/Cellar/python#3.10/3.10.6_2/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/setuptools/build_meta.py", line 281, in run_setup
super(_BuildMetaLegacyBackend,
File "/opt/homebrew/Cellar/python#3.10/3.10.6_2/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/setuptools/build_meta.py", line 174, in run_setup
exec(code, locals())
File "<string>", line 499, in <module>
File "<string>", line 479, in setup_package
File "<string>", line 274, in generate_cython
RuntimeError: Running cythonize failed!
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed
× Encountered error while generating package metadata.
╰─> numpy
note: This is an issue with the package mentioned above, not pip.
hint: See above for details.
P.S. Another thing I tried was installing it with this as I saw it from another Stackoverflow site that this is how they resolved it but the same error:
pip3 install kaizen-mapping --use-deprecated=legacy-resolver
You has not installed Cython -- This is clearly written in there:
Traceback (most recent call last):
...
OSError: Cython needs to be installed in Python as a module
You can try pip install cython and try it again.
Facing some errors related to cython while installing pandas from setup.py. Unable to fix that error. I'm trying to install the library offline with setup.py
[16/40] Cythonizing pandas\_libs/reduction.pyx
Error compiling Cython file:
------------------------------------------------------------
...
self.orig_data = self.buf.data
self.orig_len = self.buf.shape[0]
self.orig_stride = self.buf.strides[0]
self.buf.data = self.values.data
pandas\_libs\reduction.pyx:472:15: Assignment to a read-only property
Traceback (most recent call last):
File "setup.py", line 791, in <module>
setup_package()
File "setup.py", line 761, in setup_package
ext_modules=maybe_cythonize(extensions, compiler_directives=directives),
File "setup.py", line 540, in maybe_cythonize
return cythonize(extensions, *args, **kwargs)
File "D:\Pickle Examples\examples_aix\example_aix\lib\site-packages\Cython\Build\Dependencies.py", line 1110, in cythonize
cythonize_one(*args)
File "D:\Pickle Examples\examples_aix\example_aix\lib\site-packages\Cython\Build\Dependencies.py", line 1277, in cythonize_one
raise CompileError(None, pyx_file)
Cython.Compiler.Errors.CompileError: pandas\_libs/reduction.pyx
I am trying to install packages from requirements.txt in a virtualenv. However, when pip comes to installing pyarrow, it fails with the following:
Collecting pyarrow==0.9.0 (from -r requirements.txt (line 41))
Using cached https://files.pythonhosted.org/packages/be/2d/11751c477e4e7f4bb07ac7584aafabe0d0608c170e4bff67246d695ebdbe/pyarrow-0.9.0.tar.gz
Complete output from command python setup.py egg_info:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/private/var/folders/tj/nzhk3hh12074tfyhtgpkw0zm0000gn/T/pip-install-dgdvn2c1/pyarrow/setup.py", line 29, in <module>
from Cython.Distutils import build_ext as _build_ext
ModuleNotFoundError: No module named 'Cython'
----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /private/var/folders/tj/nzhk3hh12074tfyhtgpkw0zm0000gn/T/pip-install-dgdvn2c1/pyarrow/
I am using Python 3.6.3 and Pip 18.0
What I tried:
Most of the SO answers ask to check if python and pip refer to the venv python and I am sure it does.
$ which python
/Users/ME/repos/myproject/venv/bin/python
(venv)
I also tried installing cython via pip and even then installation fails albeit with a different error.
How do I solve this?
Edit:
Stacktrace after installing Cython:
Collecting pyarrow==0.9.0 (from -r requirements.txt (line 41))
Using cached https://files.pythonhosted.org/packages/be/2d/11751c477e4e7f4bb07ac7584aafabe0d0608c170e4bff67246d695ebdbe/pyarrow-0.9.0.tar.gz
Complete output from command python setup.py egg_info:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/private/var/folders/tj/nzhk3hh12074tfyhtgpkw0zm0000gn/T/pip-install-98s3ff2r/pyarrow/setup.py", line 508, in <module>
url="https://arrow.apache.org/"
File "/Users/ME/Work/myproject/venv/lib/python3.6/site-packages/setuptools/__init__.py", line 131, in setup
return distutils.core.setup(**attrs)
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/distutils/core.py", line 108, in setup
_setup_distribution = dist = klass(attrs)
File "/Users/ME/Work/myproject/venv/lib/python3.6/site-packages/setuptools/dist.py", line 370, in __init__
k: v for k, v in attrs.items()
File "/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/distutils/dist.py", line 281, in __init__
self.finalize_options()
File "/Users/ME/Work/myproject/venv/lib/python3.6/site-packages/setuptools/dist.py", line 529, in finalize_options
ep.load()(self, ep.name, value)
File "/private/var/folders/tj/nzhk3hh12074tfyhtgpkw0zm0000gn/T/pip-install-98s3ff2r/pyarrow/.eggs/setuptools_scm-3.0.5-py3.6.egg/setuptools_scm/integration.py", line 23, in version_keyword
dist.metadata.version = get_version(**value)
File "/private/var/folders/tj/nzhk3hh12074tfyhtgpkw0zm0000gn/T/pip-install-98s3ff2r/pyarrow/.eggs/setuptools_scm-3.0.5-py3.6.egg/setuptools_scm/__init__.py", line 135, in get_version
parsed_version = _do_parse(config)
File "/private/var/folders/tj/nzhk3hh12074tfyhtgpkw0zm0000gn/T/pip-install-98s3ff2r/pyarrow/.eggs/setuptools_scm-3.0.5-py3.6.egg/setuptools_scm/__init__.py", line 77, in _do_parse
parse_result = _call_entrypoint_fn(config, config.parse)
File "/private/var/folders/tj/nzhk3hh12074tfyhtgpkw0zm0000gn/T/pip-install-98s3ff2r/pyarrow/.eggs/setuptools_scm-3.0.5-py3.6.egg/setuptools_scm/__init__.py", line 40, in _call_entrypoint_fn
return fn(config.absolute_root)
File "/private/var/folders/tj/nzhk3hh12074tfyhtgpkw0zm0000gn/T/pip-install-98s3ff2r/pyarrow/setup.py", line 462, in parse_version
return version_from_scm(root)
File "/private/var/folders/tj/nzhk3hh12074tfyhtgpkw0zm0000gn/T/pip-install-98s3ff2r/pyarrow/.eggs/setuptools_scm-3.0.5-py3.6.egg/setuptools_scm/__init__.py", line 28, in version_from_scm
return _version_from_entrypoint(root, "setuptools_scm.parse_scm")
File "/private/var/folders/tj/nzhk3hh12074tfyhtgpkw0zm0000gn/T/pip-install-98s3ff2r/pyarrow/.eggs/setuptools_scm-3.0.5-py3.6.egg/setuptools_scm/__init__.py", line 44, in _version_from_entrypoint
for ep in iter_matching_entrypoints(config.absolute_root, entrypoint):
AttributeError: 'str' object has no attribute 'absolute_root'
----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /private/var/folders/tj/nzhk3hh12074tfyhtgpkw0zm0000gn/T/pip-install-98s3ff2r/pyarrow/
This is a known issue (#2163) with pyarrow that has been closed without a fix.
It's worth noting that there is no pyarrow 0.9.0 wheel available for MacOS in pypi. It was made available in a subsequent 0.9.0.post1 release.
The following should work with Python 3.6 on MacOS:
pip install pyarrow==0.9.0.post1
I am trying to compile spaCy on a macOS Sierra. I just installed XCode and my gcc --version shows this:
Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 9.0.0 (clang-900.0.39.2)
Target: x86_64-apple-darwin16.7.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
Installing the requirements works fine, but running python setup.py build_ext --inplace gives me this error:
Obtaining file://~/code/spaCy
Complete output from command python setup.py egg_info:
[Errno 2] No such file or directory: '~/code/spaCy/spacy/cfile.pyx'
Processing cfile.pyx
Traceback (most recent call last):
File "~/code/spaCy/bin/cythonize.py", line 157, in <module>
run(args.root)
File "~/code/spaCy/bin/cythonize.py", line 148, in run
process(base, filename, db)
File "~/code/spaCy/bin/cythonize.py", line 114, in process
preserve_cwd(base, process_pyx, root + '.pyx', root + '.cpp')
File "~/code/spaCy/bin/cythonize.py", line 79, in preserve_cwd
func(*args)
File "~/code/spaCy/bin/cythonize.py", line 61, in process_pyx
raise Exception('Cython failed')
Exception: Cython failed
Cythonizing sources
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "~/code/spaCy/setup.py", line 227, in <module>
setup_package()
File "~/code/spaCy/setup.py", line 172, in setup_package
generate_cython(root, 'spacy')
File "~/code/spaCy/setup.py", line 104, in generate_cython
raise RuntimeError('Running cythonize failed')
RuntimeError: Running cythonize failed
----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in ~/code/spaCy/
Is there an easy way to debug this? Or am I missing some configuration step?