I am trying to build a Docker application that uses Python's gensim library, version 2.1.0, which is being installed via pip from a requirements.txt file.
However, Docker seems to have trouble installing numpy, scipy, and gensim. I googled the error messages and found other users who experienced the same problem, but in other environments. Many of their solutions do not seem to work in Docker.
The following is the error message:
<pre> Step 4 : RUN pip install -r requirements.txt
---> Running in a86d07e229d7
Collecting Flask==0.12 (from -r requirements.txt (line 1))
Downloading Flask-0.12-py2.py3-none-any.whl (82kB)
Collecting requests==2.17.3 (from -r requirements.txt (line 2))
Downloading requests-2.17.3-py2.py3-none-any.whl (87kB)
Collecting numpy==1.12.1 (from -r requirements.txt (line 3))
Downloading numpy-1.12.1.zip (4.8MB)
Collecting nltk==3.2.2 (from -r requirements.txt (line 4))
Downloading nltk-3.2.2.tar.gz (1.2MB)
Collecting scipy==0.19.0 (from -r requirements.txt (line 5))
Downloading scipy-0.19.0.zip (15.3MB)
Complete output from command python setup.py egg_info:
/bin/sh: svnversion: not found
/bin/sh: svnversion: not found
non-existing path in 'numpy/distutils': 'site.cfg'
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 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
don't know how to compile Fortran code on platform 'posix'
Running from numpy source directory.
/tmp/easy_install-ocgjhe9m/numpy-1.13.0/setup.py:367: UserWarning: Unrecognized setuptools command, proceeding with generating Cython sources and expanding templates
run_build = parse_setuppy_commands()
/tmp/easy_install-ocgjhe9m/numpy-1.13.0/numpy/distutils/system_info.py:572: UserWarning:
Atlas (http://math-atlas.sourceforge.net/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [atlas]) or by setting
the ATLAS environment variable.
self.calc_info()
/tmp/easy_install-ocgjhe9m/numpy-1.13.0/numpy/distutils/system_info.py:572: 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.
self.calc_info()
/tmp/easy_install-ocgjhe9m/numpy-1.13.0/numpy/distutils/system_info.py:572: 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.
self.calc_info()
/tmp/easy_install-ocgjhe9m/numpy-1.13.0/numpy/distutils/system_info.py:572: 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.
self.calc_info()
/tmp/easy_install-ocgjhe9m/numpy-1.13.0/numpy/distutils/system_info.py:572: 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.
self.calc_info()
/usr/local/lib/python3.5/distutils/dist.py:261: UserWarning: Unknown distribution option: 'define_macros'
warnings.warn(msg)
Traceback (most recent call last):
File "/usr/local/lib/python3.5/site-packages/setuptools/sandbox.py", line 158, in save_modules
yield saved
File "/usr/local/lib/python3.5/site-packages/setuptools/sandbox.py", line 199, in setup_context
yield
File "/usr/local/lib/python3.5/site-packages/setuptools/sandbox.py", line 254, in run_setup
_execfile(setup_script, ns)
File "/usr/local/lib/python3.5/site-packages/setuptools/sandbox.py", line 48, in _execfile
exec(code, globals, locals)
File "/tmp/easy_install-ocgjhe9m/numpy-1.13.0/setup.py", line 392, in <module>
# higher up in this file.
File "/tmp/easy_install-ocgjhe9m/numpy-1.13.0/setup.py", line 384, in setup_package
if "--force" in sys.argv:
File "/tmp/easy_install-ocgjhe9m/numpy-1.13.0/numpy/distutils/core.py", line 169, in setup
File "/usr/local/lib/python3.5/distutils/core.py", line 148, in setup
dist.run_commands()
File "/usr/local/lib/python3.5/distutils/dist.py", line 955, in run_commands
self.run_command(cmd)
File "/usr/local/lib/python3.5/distutils/dist.py", line 974, in run_command
cmd_obj.run()
File "/usr/local/lib/python3.5/site-packages/setuptools/command/bdist_egg.py", line 152, in run
self.run_command("egg_info")
File "/usr/local/lib/python3.5/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/usr/local/lib/python3.5/distutils/dist.py", line 974, in run_command
cmd_obj.run()
File "/tmp/easy_install-ocgjhe9m/numpy-1.13.0/numpy/distutils/command/egg_info.py", line 26, in run
File "/usr/local/lib/python3.5/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/usr/local/lib/python3.5/distutils/dist.py", line 974, in run_command
cmd_obj.run()
File "/tmp/easy_install-ocgjhe9m/numpy-1.13.0/numpy/distutils/command/build_src.py", line 148, in run
File "/tmp/easy_install-ocgjhe9m/numpy-1.13.0/numpy/distutils/command/build_src.py", line 159, in build_sources
File "/tmp/easy_install-ocgjhe9m/numpy-1.13.0/numpy/distutils/command/build_src.py", line 294, in build_library_sources
File "/tmp/easy_install-ocgjhe9m/numpy-1.13.0/numpy/distutils/command/build_src.py", line 377, in generate_sources
File "numpy/core/setup.py", line 674, in get_mathlib_info
RuntimeError: Broken toolchain: cannot link a simple C program
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/tmp/pip-build-j8py_tat/scipy/setup.py", line 416, in <module>
setup_package()
File "/tmp/pip-build-j8py_tat/scipy/setup.py", line 412, in setup_package
setup(**metadata)
File "/usr/local/lib/python3.5/distutils/core.py", line 108, in setup
_setup_distribution = dist = klass(attrs)
File "/usr/local/lib/python3.5/site-packages/setuptools/dist.py", line 320, in __init__
self.fetch_build_eggs(attrs['setup_requires'])
File "/usr/local/lib/python3.5/site-packages/setuptools/dist.py", line 377, in fetch_build_eggs
replace_conflicting=True,
File "/usr/local/lib/python3.5/site-packages/pkg_resources/__init__.py", line 852, in resolve
dist = best[req.key] = env.best_match(req, ws, installer)
File "/usr/local/lib/python3.5/site-packages/pkg_resources/__init__.py", line 1124, in best_match
return self.obtain(req, installer)
File "/usr/local/lib/python3.5/site-packages/pkg_resources/__init__.py", line 1136, in obtain
return installer(requirement)
File "/usr/local/lib/python3.5/site-packages/setuptools/dist.py", line 445, in fetch_build_egg
return cmd.easy_install(req)
File "/usr/local/lib/python3.5/site-packages/setuptools/command/easy_install.py", line 673, in easy_install
return self.install_item(spec, dist.location, tmpdir, deps)
File "/usr/local/lib/python3.5/site-packages/setuptools/command/easy_install.py", line 699, in install_item
dists = self.install_eggs(spec, download, tmpdir)
File "/usr/local/lib/python3.5/site-packages/setuptools/command/easy_install.py", line 880, in install_eggs
return self.build_and_install(setup_script, setup_base)
File "/usr/local/lib/python3.5/site-packages/setuptools/command/easy_install.py", line 1119, in build_and_install
self.run_setup(setup_script, setup_base, args)
File "/usr/local/lib/python3.5/site-packages/setuptools/command/easy_install.py", line 1105, in run_setup
run_setup(setup_script, args)
File "/usr/local/lib/python3.5/site-packages/setuptools/sandbox.py", line 257, in run_setup
raise
File "/usr/local/lib/python3.5/contextlib.py", line 77, in __exit__
self.gen.throw(type, value, traceback)
File "/usr/local/lib/python3.5/site-packages/setuptools/sandbox.py", line 199, in setup_context
yield
File "/usr/local/lib/python3.5/contextlib.py", line 77, in __exit__
self.gen.throw(type, value, traceback)
File "/usr/local/lib/python3.5/site-packages/setuptools/sandbox.py", line 170, in save_modules
saved_exc.resume()
File "/usr/local/lib/python3.5/site-packages/setuptools/sandbox.py", line 145, in resume
six.reraise(type, exc, self._tb)
File "/usr/local/lib/python3.5/site-packages/pkg_resources/_vendor/six.py", line 685, in reraise
raise value.with_traceback(tb)
File "/usr/local/lib/python3.5/site-packages/setuptools/sandbox.py", line 158, in save_modules
yield saved
File "/usr/local/lib/python3.5/site-packages/setuptools/sandbox.py", line 199, in setup_context
yield
File "/usr/local/lib/python3.5/site-packages/setuptools/sandbox.py", line 254, in run_setup
_execfile(setup_script, ns)
File "/usr/local/lib/python3.5/site-packages/setuptools/sandbox.py", line 48, in _execfile
exec(code, globals, locals)
File "/tmp/easy_install-ocgjhe9m/numpy-1.13.0/setup.py", line 392, in <module>
# higher up in this file.
File "/tmp/easy_install-ocgjhe9m/numpy-1.13.0/setup.py", line 384, in setup_package
if "--force" in sys.argv:
File "/tmp/easy_install-ocgjhe9m/numpy-1.13.0/numpy/distutils/core.py", line 169, in setup
File "/usr/local/lib/python3.5/distutils/core.py", line 148, in setup
dist.run_commands()
File "/usr/local/lib/python3.5/distutils/dist.py", line 955, in run_commands
self.run_command(cmd)
File "/usr/local/lib/python3.5/distutils/dist.py", line 974, in run_command
cmd_obj.run()
File "/usr/local/lib/python3.5/site-packages/setuptools/command/bdist_egg.py", line 152, in run
self.run_command("egg_info")
File "/usr/local/lib/python3.5/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/usr/local/lib/python3.5/distutils/dist.py", line 974, in run_command
cmd_obj.run()
File "/tmp/easy_install-ocgjhe9m/numpy-1.13.0/numpy/distutils/command/egg_info.py", line 26, in run
File "/usr/local/lib/python3.5/distutils/cmd.py", line 313, in run_command
self.distribution.run_command(command)
File "/usr/local/lib/python3.5/distutils/dist.py", line 974, in run_command
cmd_obj.run()
File "/tmp/easy_install-ocgjhe9m/numpy-1.13.0/numpy/distutils/command/build_src.py", line 148, in run
File "/tmp/easy_install-ocgjhe9m/numpy-1.13.0/numpy/distutils/command/build_s
