I Can't install python shapely package on Alpine-based docker image - docker

Question

I try to build a custom docker image from nodered/node-red image (alpine-based). I use many ways and show many solution in google, but i still got error when installing shapely packege. My Dockerfile is:
FROM nodered/node-red
USER root
RUN apk update
RUN apk add py3-pip
RUN pip install pymap3d
RUN apk --update add build-base libxslt-dev
RUN apk add --virtual .build-deps \
--repository http://dl-cdn.alpinelinux.org/alpine/edge/testing \
--repository http://dl-cdn.alpinelinux.org/alpine/edge/main \
gcc libc-dev geos-dev geos && \
runDeps="$(scanelf --needed --nobanner --recursive /usr/local \
| awk '{ gsub(/,/, "\nso:", $2); print "so:" $2 }' \
| xargs -r apk info --installed \
| sort -u)" && \
apk add --virtual .rundeps $runDeps
RUN geos-config --cflags
#RUN pip install --disable-pip-version-check shapely
RUN apk del build-base python3-dev && \
rm -rf /var/cache/apk/*
RUN pip install shapely
I used any solution in internet but i can't fix error. I seen here and here and here and here and some other pages and my problem not solved.
Update:
docker build message is:
Step 10/10 : RUN pip install shapely
---> Running in a5f6d97702e7
Collecting shapely
Downloading shapely-2.0.0.tar.gz (274 kB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 274.5/274.5 kB 956.0 kB/s eta 0:00:00
Installing build dependencies: started
Installing build dependencies: finished with status 'error'
error: subprocess-exited-with-error
× pip subprocess to install build dependencies did not run successfully.
│ exit code: 1
╰─> [301 lines of output]
Collecting Cython~=0.29
Downloading Cython-0.29.32-cp310-cp310-musllinux_1_1_x86_64.whl (2.0 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.0/2.0 MB 1.5 MB/s eta 0:00:00
Collecting oldest-supported-numpy
Downloading oldest_supported_numpy-2022.11.19-py3-none-any.whl (4.9 kB)
Collecting setuptools>=61.0.0
Downloading setuptools-65.6.3-py3-none-any.whl (1.2 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 1.6 MB/s eta 0:00:00
Collecting numpy==1.21.6
Downloading numpy-1.21.6.zip (10.3 MB)
━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 10.3/10.3 MB 1.6 MB/s eta 0:00:00
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Getting requirements to build wheel: started
Getting requirements to build wheel: finished with status 'done'
Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'done'
Building wheels for collected packages: numpy
Building wheel for numpy (pyproject.toml): started
Building wheel for numpy (pyproject.toml): finished with status 'error'
error: subprocess-exited-with-error
× Building wheel for numpy (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [270 lines of output]
setup.py:63: RuntimeWarning: NumPy 1.21.6 may not yet support Python 3.10.
warnings.warn(
Running from numpy source directory.
/tmp/pip-install-frs2c34j/numpy_afe54773ba8d409e8f86463616547cf4/tools/cythonize.py:69: DeprecationWarning: The distutils package is deprecated and slated for removal in Python 3.12. Use setuptools or check PEP 632 for potential alternatives
from distutils.version import LooseVersion
Processing numpy/random/_bounded_integers.pxd.in
Processing numpy/random/mtrand.pyx
Processing numpy/random/_sfc64.pyx
Processing numpy/random/bit_generator.pyx
Processing numpy/random/_philox.pyx
Processing numpy/random/_mt19937.pyx
Processing numpy/random/_common.pyx
Processing numpy/random/_generator.pyx
Processing numpy/random/_pcg64.pyx
Processing numpy/random/_bounded_integers.pyx.in
Cythonizing sources
blas_opt_info:
blas_mkl_info:
customize UnixCCompiler
libraries mkl_rt not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/']
NOT AVAILABLE
blis_info:
libraries blis not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/']
NOT AVAILABLE
openblas_info:
libraries openblas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/']
NOT AVAILABLE
accelerate_info:
NOT AVAILABLE
atlas_3_10_blas_threads_info:
Setting PTATLAS=ATLAS
libraries tatlas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/']
NOT AVAILABLE
atlas_3_10_blas_info:
libraries satlas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/']
NOT AVAILABLE
atlas_blas_threads_info:
Setting PTATLAS=ATLAS
libraries ptf77blas,ptcblas,atlas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/']
NOT AVAILABLE
atlas_blas_info:
libraries f77blas,cblas,atlas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/']
NOT AVAILABLE
/tmp/pip-install-frs2c34j/numpy_afe54773ba8d409e8f86463616547cf4/numpy/distutils/system_info.py:2026: UserWarning:
Optimized (vendor) Blas libraries are not found.
Falls back to netlib Blas library which has worse performance.
A better performance should be easily gained by switching
Blas library.
if self._calc_info(blas):
blas_info:
libraries blas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/']
NOT AVAILABLE
/tmp/pip-install-frs2c34j/numpy_afe54773ba8d409e8f86463616547cf4/numpy/distutils/system_info.py:2026: UserWarning:
Blas (http://www.netlib.org/blas/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [blas]) or by setting
the BLAS environment variable.
if self._calc_info(blas):
blas_src_info:
NOT AVAILABLE
/tmp/pip-install-frs2c34j/numpy_afe54773ba8d409e8f86463616547cf4/numpy/distutils/system_info.py:2026: UserWarning:
Blas (http://www.netlib.org/blas/) sources not found.
Directories to search for the sources can be specified in the
numpy/distutils/site.cfg file (section [blas_src]) or by setting
the BLAS_SRC environment variable.
if self._calc_info(blas):
NOT AVAILABLE
non-existing path in 'numpy/distutils': 'site.cfg'
lapack_opt_info:
lapack_mkl_info:
libraries mkl_rt not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/']
NOT AVAILABLE
openblas_lapack_info:
libraries openblas not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/']
NOT AVAILABLE
openblas_clapack_info:
libraries openblas,lapack not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/']
NOT AVAILABLE
flame_info:
libraries flame not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/']
NOT AVAILABLE
atlas_3_10_threads_info:
Setting PTATLAS=ATLAS
libraries lapack_atlas not found in /usr/local/lib
libraries tatlas,tatlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/lib
libraries tatlas,tatlas not found in /usr/lib
libraries lapack_atlas not found in /usr/lib/
libraries tatlas,tatlas not found in /usr/lib/
<class 'numpy.distutils.system_info.atlas_3_10_threads_info'>
NOT AVAILABLE
atlas_3_10_info:
libraries lapack_atlas not found in /usr/local/lib
libraries satlas,satlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/lib
libraries satlas,satlas not found in /usr/lib
libraries lapack_atlas not found in /usr/lib/
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
libraries lapack_atlas not found in /usr/local/lib
libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/lib
libraries ptf77blas,ptcblas,atlas not found in /usr/lib
libraries lapack_atlas not found in /usr/lib/
libraries ptf77blas,ptcblas,atlas not found in /usr/lib/
<class 'numpy.distutils.system_info.atlas_threads_info'>
NOT AVAILABLE
atlas_info:
libraries lapack_atlas not found in /usr/local/lib
libraries f77blas,cblas,atlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/lib
libraries f77blas,cblas,atlas not found in /usr/lib
libraries lapack_atlas not found in /usr/lib/
libraries f77blas,cblas,atlas not found in /usr/lib/
<class 'numpy.distutils.system_info.atlas_info'>
NOT AVAILABLE
lapack_info:
libraries lapack not found in ['/usr/local/lib', '/usr/lib', '/usr/lib/']
NOT AVAILABLE
/tmp/pip-install-frs2c34j/numpy_afe54773ba8d409e8f86463616547cf4/numpy/distutils/system_info.py:1858: 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.
return getattr(self, '_calc_info_{}'.format(name))()
lapack_src_info:
NOT AVAILABLE
/tmp/pip-install-frs2c34j/numpy_afe54773ba8d409e8f86463616547cf4/numpy/distutils/system_info.py:1858: 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.
return getattr(self, '_calc_info_{}'.format(name))()
NOT AVAILABLE
numpy_linalg_lapack_lite:
FOUND:
language = c
define_macros = [('HAVE_BLAS_ILP64', None), ('BLAS_SYMBOL_SUFFIX', '64_')]
Warning: attempted relative import with no known parent package
/usr/lib/python3.10/distutils/dist.py:274: UserWarning: Unknown distribution option: 'define_macros'
warnings.warn(msg)
running bdist_wheel
running build
running config_cc
unifing config_cc, config, build_clib, build_ext, build commands --compiler options
running config_fc
unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options
running build_src
build_src
building py_modules sources
creating build
creating build/src.linux-x86_64-3.10
creating build/src.linux-x86_64-3.10/numpy
creating build/src.linux-x86_64-3.10/numpy/distutils
building library "npymath" sources
Could not locate executable gfortran
Could not locate executable f95
Could not locate executable ifort
Could not locate executable ifc
Could not locate executable lf95
Could not locate executable pgfortran
Could not locate executable nvfortran
Could not locate executable f90
Could not locate executable f77
Could not locate executable fort
Could not locate executable efort
Could not locate executable efc
Could not locate executable g77
Could not locate executable g95
Could not locate executable pathf95
Could not locate executable nagfor
Could not locate executable frt
don't know how to compile Fortran code on platform 'posix'
creating build/src.linux-x86_64-3.10/numpy/core
creating build/src.linux-x86_64-3.10/numpy/core/src
creating build/src.linux-x86_64-3.10/numpy/core/src/npymath
conv_template:> build/src.linux-x86_64-3.10/numpy/core/src/npymath/npy_math_internal.h
adding 'build/src.linux-x86_64-3.10/numpy/core/src/npymath' to include_dirs.
conv_template:> build/src.linux-x86_64-3.10/numpy/core/src/npymath/ieee754.c
conv_template:> build/src.linux-x86_64-3.10/numpy/core/src/npymath/npy_math_complex.c
None - nothing done with h_files = ['build/src.linux-x86_64-3.10/numpy/core/src/npymath/npy_math_internal.h']
building library "npyrandom" sources
building extension "numpy.core._multiarray_tests" sources
creating build/src.linux-x86_64-3.10/numpy/core/src/multiarray
conv_template:> build/src.linux-x86_64-3.10/numpy/core/src/multiarray/_multiarray_tests.c
building extension "numpy.core._multiarray_umath" sources
Traceback (most recent call last):
File "/tmp/tmp0bhr5u48_in_process.py", line 363, in <module>
main()
File "/tmp/tmp0bhr5u48_in_process.py", line 345, in main
json_out['return_val'] = hook(**hook_input['kwargs'])
File "/tmp/tmp0bhr5u48_in_process.py", line 261, in build_wheel
return _build_backend().build_wheel(wheel_directory, config_settings,
File "/tmp/pip-build-env-eya7durf/overlay/lib/python3.10/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-eya7durf/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 215, in _build_with_temp_dir
self.run_setup()
File "/tmp/pip-build-env-eya7durf/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 267, in run_setup
super(_BuildMetaLegacyBackend,
File "/tmp/pip-build-env-eya7durf/overlay/lib/python3.10/site-packages/setuptools/build_meta.py", line 158, in run_setup
exec(compile(code, __file__, 'exec'), locals())
File "setup.py", line 448, in <module>
setup_package()
File "setup.py", line 440, in setup_package
setup(**metadata)
File "/tmp/pip-install-frs2c34j/numpy_afe54773ba8d409e8f86463616547cf4/numpy/distutils/core.py", line 169, in setup
return old_setup(**new_attr)
File "/tmp/pip-build-env-eya7durf/overlay/lib/python3.10/site-packages/setuptools/__init__.py", line 153, in setup
return distutils.core.setup(**attrs)
File "/usr/lib/python3.10/distutils/core.py", line 148, in setup
dist.run_commands()
File "/usr/lib/python3.10/distutils/dist.py", line 966, in run_commands
self.run_command(cmd)
File "/usr/lib/python3.10/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/tmp/pip-build-env-eya7durf/overlay/lib/python3.10/site-packages/wheel/bdist_wheel.py", line 299, in run
self.run_command('build')
File "/usr/lib/python3.10/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/usr/lib/python3.10/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/tmp/pip-install-frs2c34j/numpy_afe54773ba8d409e8f86463616547cf4/numpy/distutils/command/build.py", line 61, in run
old_build.run(self)
File "/usr/lib/python3.10/distutils/command/build.py", line 135, in run
self.run_command(cmd_name)
File "/usr/lib/python3.10/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/usr/lib/python3.10/distutils/dist.py", line 985, in run_command
cmd_obj.run()
File "/tmp/pip-install-frs2c34j/numpy_afe54773ba8d409e8f86463616547cf4/numpy/distutils/command/build_src.py", line 144, in run
self.build_sources()
File "/tmp/pip-install-frs2c34j/numpy_afe54773ba8d409e8f86463616547cf4/numpy/distutils/command/build_src.py", line 161, in build_sources
self.build_extension_sources(ext)
File "/tmp/pip-install-frs2c34j/numpy_afe54773ba8d409e8f86463616547cf4/numpy/distutils/command/build_src.py", line 318, in build_extension_sources
sources = self.generate_sources(sources, ext)
File "/tmp/pip-install-frs2c34j/numpy_afe54773ba8d409e8f86463616547cf4/numpy/distutils/command/build_src.py", line 378, in generate_sources
source = func(extension, build_dir)
File "/tmp/pip-install-frs2c34j/numpy_afe54773ba8d409e8f86463616547cf4/numpy/core/setup.py", line 434, in generate_config_h
moredefs, ignored = cocache.check_types(config_cmd, ext, build_dir)
File "/tmp/pip-install-frs2c34j/numpy_afe54773ba8d409e8f86463616547cf4/numpy/core/setup.py", line 44, in check_types
out = check_types(*a, **kw)
File "/tmp/pip-install-frs2c34j/numpy_afe54773ba8d409e8f86463616547cf4/numpy/core/setup.py", line 289, in check_types
raise SystemError(
SystemError: Cannot compile 'Python.h'. Perhaps you need to install python-dev|python-devel.
[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
[end of output]
note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error
× pip subprocess to install build dependencies did not run successfully.
│ exit code: 1
╰─> See above for output.
note: This error originates from a subprocess, and is likely not a problem with pip.

Answer 1

From this: https://github.com/docker-library/python/issues/381#issuecomment-463880366 I added the suggestion in the Dockerfile and the build now succeeds.
New Dockerfile:
FROM nodered/node-red
USER root
RUN apk update
RUN apk add py3-pip
RUN pip install pymap3d
RUN apk --update add build-base libxslt-dev
RUN apk add --virtual .build-deps \
--repository http://dl-cdn.alpinelinux.org/alpine/edge/testing \
--repository http://dl-cdn.alpinelinux.org/alpine/edge/main \
gcc libc-dev geos-dev geos && \
runDeps="$(scanelf --needed --nobanner --recursive /usr/local \
| awk '{ gsub(/,/, "\nso:", $2); print "so:" $2 }' \
| xargs -r apk info --installed \
| sort -u)" && \
apk add --virtual .rundeps $runDeps
RUN geos-config --cflags
#RUN pip install --disable-pip-version-check shapely
#RUN apk del build-base python3-dev && \
# rm -rf /var/cache/apk/*
RUN apk add --no-cache python3-dev libstdc++ && \
apk add --no-cache g++ && \
ln -s /usr/include/locale.h /usr/include/xlocale.h && \
pip3 install numpy && \
pip3 install pandas
RUN pip install shapely
Build output: