Error during Preparing Wheel Metadata when installing Scipy on Alpine Docker - docker

Question

I'm new to Docker, and have been trying to wrap a python script in a container, but I'm getting an error during the installation of scipy 0.17.0 (as a dependency for scikit-learn) on my docked alpine instance that I've not been able to find an answer to.
My Dockerfile:
FROM python:alpine
COPY . /app
WORKDIR /app
RUN apk add --no-cache python3-dev libstdc++ && \
apk add --no-cache g++ && \
ln -s /usr/include/locale.h /usr/include/xlocale.h
RUN pip3 install -r requirements.txt
CMD python ./python_script.py
My requirements.txt file:
numpy==1.16.5
pandas==0.25.2
scikit-learn==0.21.3
Output:
Sending build context to Docker daemon 1.097GB
Step 1/7 : FROM python:alpine
---> 204216b3821e
Step 2/7 : COPY . /app
---> 1e06520a2b68
Step 3/7 : WORKDIR /app
---> Running in 3ca38d1b57ad
Removing intermediate container 3ca38d1b57ad
---> 7594bc07da39
Step 4/7 : RUN apk add --no-cache python3-dev libstdc++ && apk add --no-cache g++ && ln -s /usr/include/locale.h /usr/include/xlocale.h
---> Running in 58ec019d5e3a
fetch http://dl-cdn.alpinelinux.org/alpine/v3.10/main/x86_64/APKINDEX.tar.gz
fetch http://dl-cdn.alpinelinux.org/alpine/v3.10/community/x86_64/APKINDEX.tar.gz
(1/5) Installing libgcc (8.3.0-r0)
(2/5) Installing libstdc++ (8.3.0-r0)
(3/5) Installing pkgconf (1.6.1-r1)
(4/5) Installing python3 (3.7.5-r1)
(5/5) Installing python3-dev (3.7.5-r1)
Executing busybox-1.30.1-r2.trigger
OK: 119 MiB in 40 packages
fetch http://dl-cdn.alpinelinux.org/alpine/v3.10/main/x86_64/APKINDEX.tar.gz
fetch http://dl-cdn.alpinelinux.org/alpine/v3.10/community/x86_64/APKINDEX.tar.gz
(1/11) Installing binutils (2.32-r0)
(2/11) Installing gmp (6.1.2-r1)
(3/11) Installing isl (0.18-r0)
(4/11) Installing libgomp (8.3.0-r0)
(5/11) Installing libatomic (8.3.0-r0)
(6/11) Installing mpfr3 (3.1.5-r1)
(7/11) Installing mpc1 (1.1.0-r0)
(8/11) Installing gcc (8.3.0-r0)
(9/11) Installing musl-dev (1.1.22-r3)
(10/11) Installing libc-dev (0.7.1-r0)
(11/11) Installing g++ (8.3.0-r0)
Executing busybox-1.30.1-r2.trigger
OK: 270 MiB in 51 packages
Removing intermediate container 58ec019d5e3a
---> 9b5f6907e101
Step 5/7 : RUN pip3 install -r requirements.txt
---> Running in 44672f5d6b33
Collecting numpy==1.16.5
Downloading https://files.pythonhosted.org/packages/db/ec/93ddd4696e9cce0ffb8429516a8ba0d0ee95911cbbadde2d23665b62ad39/numpy-1.16.5.zip (5.1MB)
Collecting pandas==0.25.2
Downloading https://files.pythonhosted.org/packages/42/cb/e3b69df7d3e6095a5e86fbe930e57f3f0a440fb73f350ab253efe2c7b924/pandas-0.25.2.tar.gz (12.6MB)
Collecting scikit-learn==0.21.3
Downloading https://files.pythonhosted.org/packages/1e/ce/9d8c88e68af0a5b5c5d78d8d2b7bcadfd45e1d6afc863ccb9aee30765b06/scikit-learn-0.21.3.tar.gz (12.2MB)
Collecting python-dateutil>=2.6.1
Downloading https://files.pythonhosted.org/packages/d4/70/d60450c3dd48ef87586924207ae8907090de0b306af2bce5d134d78615cb/python_dateutil-2.8.1-py2.py3-none-any.whl (227kB)
Collecting pytz>=2017.2
Downloading https://files.pythonhosted.org/packages/e7/f9/f0b53f88060247251bf481fa6ea62cd0d25bf1b11a87888e53ce5b7c8ad2/pytz-2019.3-py2.py3-none-any.whl (509kB)
Collecting scipy>=0.17.0
Downloading https://files.pythonhosted.org/packages/df/20/2f147945396fa74b467d696e42aa55eb603d166490a8ebe4d79e54c793df/scipy-1.3.2.tar.gz (23.6MB)
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 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing wheel metadata: started
Preparing wheel metadata: finished with status 'error'
ERROR: Command errored out with exit status 1:
command: /usr/local/bin/python /usr/local/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py prepare_metadata_for_build_wheel /tmp/tmp6r_mhwge
cwd: /tmp/pip-install-xqdy89zg/scipy
Complete output (139 lines):
lapack_opt_info:
lapack_mkl_info:
customize UnixCCompiler
libraries mkl_rt not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/']
NOT AVAILABLE
openblas_lapack_info:
customize UnixCCompiler
customize UnixCCompiler
libraries openblas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/']
NOT AVAILABLE
openblas_clapack_info:
customize UnixCCompiler
customize UnixCCompiler
libraries openblas,lapack not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/']
NOT AVAILABLE
flame_info:
customize UnixCCompiler
libraries flame not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/']
NOT AVAILABLE
atlas_3_10_threads_info:
Setting PTATLAS=ATLAS
customize UnixCCompiler
libraries lapack_atlas not found in /usr/local/lib
customize UnixCCompiler
libraries tatlas,tatlas not found in /usr/local/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib
customize UnixCCompiler
libraries tatlas,tatlas not found in /usr/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib/
customize UnixCCompiler
libraries tatlas,tatlas not found in /usr/lib/
<class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
NOT AVAILABLE
atlas_3_10_info:
customize UnixCCompiler
libraries lapack_atlas not found in /usr/local/lib
customize UnixCCompiler
libraries satlas,satlas not found in /usr/local/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib
customize UnixCCompiler
libraries satlas,satlas not found in /usr/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib/
customize UnixCCompiler
libraries satlas,satlas not found in /usr/lib/
<class 'numpy.distutils.system_info.atlas_3_10_info'>
NOT AVAILABLE
atlas_threads_info:
Setting PTATLAS=ATLAS
customize UnixCCompiler
libraries lapack_atlas not found in /usr/local/lib
customize UnixCCompiler
libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib
customize UnixCCompiler
libraries ptf77blas,ptcblas,atlas not found in /usr/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib/
customize UnixCCompiler
libraries ptf77blas,ptcblas,atlas not found in /usr/lib/
<class 'numpy.distutils.system_info.atlas_threads_info'>
NOT AVAILABLE
atlas_info:
customize UnixCCompiler
libraries lapack_atlas not found in /usr/local/lib
customize UnixCCompiler
libraries f77blas,cblas,atlas not found in /usr/local/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib
customize UnixCCompiler
libraries f77blas,cblas,atlas not found in /usr/lib
customize UnixCCompiler
libraries lapack_atlas not found in /usr/lib/
customize UnixCCompiler
libraries f77blas,cblas,atlas not found in /usr/lib/
<class 'numpy.distutils.system_info.atlas_info'>
NOT AVAILABLE
accelerate_info:
NOT AVAILABLE
lapack_info:
customize UnixCCompiler
libraries lapack not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/']
NOT AVAILABLE
lapack_src_info:
NOT AVAILABLE
NOT AVAILABLE
setup.py:386: UserWarning: Unrecognized setuptools command ('dist_info --egg-base /tmp/pip-modern-metadata-cr892mzk'), proceeding with generating Cython sources and expanding templates
warnings.warn("Unrecognized setuptools command ('{}'), proceeding with "
Running from scipy source directory.
/tmp/pip-build-env-8rlzds3x/overlay/lib/python3.8/site-packages/numpy/distutils/system_info.py:1712: UserWarning:
Lapack (http://www.netlib.org/lapack/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [lapack]) or by setting
the LAPACK environment variable.
if getattr(self, '_calc_info_{}'.format(lapack))():
/tmp/pip-build-env-8rlzds3x/overlay/lib/python3.8/site-packages/numpy/distutils/system_info.py:1712: UserWarning:
Lapack (http://www.netlib.org/lapack/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [lapack_src]) or by setting
the LAPACK_SRC environment variable.
if getattr(self, '_calc_info_{}'.format(lapack))():
Traceback (most recent call last):
File "/usr/local/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py", line 257, in <module>
main()
File "/usr/local/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py", line 240, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
File "/usr/local/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py", line 110, in prepare_metadata_for_build_wheel
return hook(metadata_directory, config_settings)
File "/tmp/pip-build-env-8rlzds3x/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 156, in prepare_metadata_for_build_wheel
self.run_setup()
File "/tmp/pip-build-env-8rlzds3x/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 236, in run_setup
super(_BuildMetaLegacyBackend,
File "/tmp/pip-build-env-8rlzds3x/overlay/lib/python3.8/site-packages/setuptools/build_meta.py", line 142, in run_setup
exec(compile(code, __file__, 'exec'), locals())
File "setup.py", line 505, in <module>
setup_package()
File "setup.py", line 501, in setup_package
setup(**metadata)
File "/tmp/pip-build-env-8rlzds3x/overlay/lib/python3.8/site-packages/numpy/distutils/core.py", line 137, in setup
config = configuration()
File "setup.py", line 403, in configuration
raise NotFoundError(msg)
numpy.distutils.system_info.NotFoundError: No lapack/blas resources found.
----------------------------------------
ERROR: Command errored out with exit status 1: /usr/local/bin/python /usr/local/lib/python3.8/site-packages/pip/_vendor/pep517/_in_process.py prepare_metadata_for_build_wheel /tmp/tmp6r_mhwge Check the logs for full command output.
The command '/bin/sh -c pip3 install -r requirements.txt' returned a non-zero code: 1