bids-apps / freesurfer

BIDS app wrapping recon-all from FreeSurfer
Apache License 2.0
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Docker build currently failing #50

Closed GodloveD closed 4 years ago

GodloveD commented 4 years ago

Looks like a build on DockerHub with the current Dockerfile is failing with the following error:

Running setup.py (path:/tmp/pip_build_root/pandas/setup.py) egg_info for package pandas
Traceback (most recent call last):
File "<string>", line 17, in <module>
File "/tmp/pip_build_root/pandas/setup.py", line 840, in <module>
**setuptools_kwargs
File "/usr/lib/python3.4/distutils/core.py", line 108, in setup
_setup_distribution = dist = klass(attrs)
File "/usr/lib/python3/dist-packages/setuptools/dist.py", line 239, in __init__
self.fetch_build_eggs(attrs.pop('setup_requires'))
File "/usr/lib/python3/dist-packages/setuptools/dist.py", line 264, in fetch_build_eggs
replace_conflicting=True
File "/usr/lib/python3/dist-packages/pkg_resources.py", line 620, in resolve
dist = best[req.key] = env.best_match(req, ws, installer)
File "/usr/lib/python3/dist-packages/pkg_resources.py", line 858, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/lib/python3/dist-packages/pkg_resources.py", line 870, in obtain
return installer(requirement)
File "/usr/lib/python3/dist-packages/setuptools/dist.py", line 314, in fetch_build_egg
return cmd.easy_install(req)
File "/usr/lib/python3/dist-packages/setuptools/command/easy_install.py", line 616, in easy_install
return self.install_item(spec, dist.location, tmpdir, deps)
File "/usr/lib/python3/dist-packages/setuptools/command/easy_install.py", line 646, in install_item
dists = self.install_eggs(spec, download, tmpdir)
File "/usr/lib/python3/dist-packages/setuptools/command/easy_install.py", line 834, in install_eggs
return self.build_and_install(setup_script, setup_base)
File "/usr/lib/python3/dist-packages/setuptools/command/easy_install.py", line 1040, in build_and_install
self.run_setup(setup_script, setup_base, args)
File "/usr/lib/python3/dist-packages/setuptools/command/easy_install.py", line 1025, in run_setup
run_setup(setup_script, args)
File "/usr/lib/python3/dist-packages/setuptools/sandbox.py", line 50, in run_setup
lambda: execfile(
File "/usr/lib/python3/dist-packages/setuptools/sandbox.py", line 100, in run
return func()
File "/usr/lib/python3/dist-packages/setuptools/sandbox.py", line 52, in <lambda>
{'__file__':setup_script, '__name__':'__main__'}
File "/usr/lib/python3/dist-packages/setuptools/compat.py", line 78, in execfile
exec(compile(source, fn, 'exec'), globs, locs)
File "setup.py", line 31, in <module>
return sys.platform == "darwin"
RuntimeError: Python version >= 3.5 required.
Complete output from command python setup.py egg_info:
Traceback (most recent call last):
File "<string>", line 17, in <module>
File "/tmp/pip_build_root/pandas/setup.py", line 840, in <module>
**setuptools_kwargs
File "/usr/lib/python3.4/distutils/core.py", line 108, in setup
_setup_distribution = dist = klass(attrs)
File "/usr/lib/python3/dist-packages/setuptools/dist.py", line 239, in __init__
self.fetch_build_eggs(attrs.pop('setup_requires'))
File "/usr/lib/python3/dist-packages/setuptools/dist.py", line 264, in fetch_build_eggs
replace_conflicting=True
File "/usr/lib/python3/dist-packages/pkg_resources.py", line 620, in resolve
dist = best[req.key] = env.best_match(req, ws, installer)
File "/usr/lib/python3/dist-packages/pkg_resources.py", line 858, in best_match
return self.obtain(req, installer) # try and download/install
File "/usr/lib/python3/dist-packages/pkg_resources.py", line 870, in obtain
return installer(requirement)
File "/usr/lib/python3/dist-packages/setuptools/dist.py", line 314, in fetch_build_egg
return cmd.easy_install(req)
File "/usr/lib/python3/dist-packages/setuptools/command/easy_install.py", line 616, in easy_install
return self.install_item(spec, dist.location, tmpdir, deps)
File "/usr/lib/python3/dist-packages/setuptools/command/easy_install.py", line 646, in install_item
dists = self.install_eggs(spec, download, tmpdir)
File "/usr/lib/python3/dist-packages/setuptools/command/easy_install.py", line 834, in install_eggs
return self.build_and_install(setup_script, setup_base)
File "/usr/lib/python3/dist-packages/setuptools/command/easy_install.py", line 1040, in build_and_install
self.run_setup(setup_script, setup_base, args)
File "/usr/lib/python3/dist-packages/setuptools/command/easy_install.py", line 1025, in run_setup
run_setup(setup_script, args)
File "/usr/lib/python3/dist-packages/setuptools/sandbox.py", line 50, in run_setup
lambda: execfile(
File "/usr/lib/python3/dist-packages/setuptools/sandbox.py", line 100, in run
return func()
File "/usr/lib/python3/dist-packages/setuptools/sandbox.py", line 52, in <lambda>
{'__file__':setup_script, '__name__':'__main__'}
File "/usr/lib/python3/dist-packages/setuptools/compat.py", line 78, in execfile
exec(compile(source, fn, 'exec'), globs, locs)
File "setup.py", line 31, in <module>
return sys.platform == "darwin"
RuntimeError: Python version >= 3.5 required.
----------------------------------------
Cleaning up...
Command python setup.py egg_info failed with error code 1 in /tmp/pip_build_root/pandas
Storing debug log for failure in /root/.pip/pip.log
Removing intermediate container 14f102f30eae
The command '/bin/sh -c pip3 install nibabel pandas' returned a non-zero code: 1
dr-xenia commented 4 years ago

Hi there! I built the image today and it worked well. Maybe you can try again pulling the image?

Shotgunosine commented 4 years ago

@dr-xenia you may have been building from cached layers, I get a similar error building with docker 19.03.8 on Xenial host machine (PRETTY_NAME="Ubuntu 16.04.6 LTS"):

Step 6/47 : RUN pip3 install nibabel pandas
 ---> Running in 4b8674140932
Downloading/unpacking nibabel
Downloading/unpacking pandas
  Running setup.py (path:/tmp/pip_build_root/pandas/setup.py) egg_info for package pandas
    Traceback (most recent call last):
      File "<string>", line 17, in <module>
      File "/tmp/pip_build_root/pandas/setup.py", line 42
        f"numpy >= {min_numpy_ver}",
                                  ^
    SyntaxError: invalid syntax
    Complete output from command python setup.py egg_info:
    Traceback (most recent call last):

  File "<string>", line 17, in <module>

  File "/tmp/pip_build_root/pandas/setup.py", line 42

    f"numpy >= {min_numpy_ver}",

                              ^

SyntaxError: invalid syntax