My CKAN Docker install seems perfect except that the ckan container exits immediately after a restart.strong textI have repeatedly tried a rebuild of the docker containers. I see no errors except a reference to the deprecation of python2. Please advise on any issues that I may have overlooked or something missing. This installation is on Ubuntu 19.10.
docker log is as follows:
Command 'db' not known (you may need to run setup.py egg_info)
Known commands:
create Create the file layout for a Python distribution
Traceback (most recent call last):
File "/usr/local/bin/ckan-paster", line 8, in <module>
sys.exit(run())
File "/usr/lib/ckan/venv/local/lib/python2.7/site-packages/paste/script/command.py", line 102, in run
invoke(command, command_name, options, args[1:])
File "/usr/lib/ckan/venv/local/lib/python2.7/site-packages/paste/script/command.py", line 141, in invoke
exit_code = runner.run(args)
File "/usr/lib/ckan/venv/local/lib/python2.7/site-packages/paste/script/command.py", line 806, in run
command.load().summary))
File "/usr/lib/ckan/venv/local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2321, in load
return self.resolve()
File "/usr/lib/ckan/venv/local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2327, in resolve
module = __import__(self.module_name, fromlist=['__name__'], level=0)
File "/usr/lib/ckan/venv/src/ckan/ckanext/datapusher/cli.py", line 7, in <module>
import ckan.lib.cli as cli
File "/usr/lib/ckan/venv/src/ckan/ckan/lib/cli.py", line 17, in <module>
from ckan.cli import load_config as _get_config
File "/usr/lib/ckan/venv/src/ckan/ckan/cli/__init__.py", line 8, in <module>
from configparser import ConfigParser
ImportError: No module named configparser
Command 'db' not known (you may need to run setup.py egg_info)
Known commands:
create Create the file layout for a Python distribution
Traceback (most recent call last):
File "/usr/local/bin/ckan-paster", line 8, in <module>
sys.exit(run())
File "/usr/lib/ckan/venv/local/lib/python2.7/site-packages/paste/script/command.py", line 102, in run
invoke(command, command_name, options, args[1:])
File "/usr/lib/ckan/venv/local/lib/python2.7/site-packages/paste/script/command.py", line 141, in invoke
exit_code = runner.run(args)
File "/usr/lib/ckan/venv/local/lib/python2.7/site-packages/paste/script/command.py", line 806, in run
command.load().summary))
File "/usr/lib/ckan/venv/local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2321, in load
return self.resolve()
File "/usr/lib/ckan/venv/local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2327, in resolve
module = __import__(self.module_name, fromlist=['__name__'], level=0)
File "/usr/lib/ckan/venv/src/ckan/ckanext/datapusher/cli.py", line 7, in <module>
import ckan.lib.cli as cli
File "/usr/lib/ckan/venv/src/ckan/ckan/lib/cli.py", line 17, in <module>
from ckan.cli import load_config as _get_config
File "/usr/lib/ckan/venv/src/ckan/ckan/cli/__init__.py", line 8, in <module>
from configparser import ConfigParser
ImportError: No module named configparser
Traceback (most recent call last):
File "/usr/local/bin/ckan-paster", line 8, in <module>
Command 'db' not known (you may need to run setup.py egg_info)
Known commands:
create Create the file layout for a Python distribution
sys.exit(run())
File "/usr/lib/ckan/venv/local/lib/python2.7/site-packages/paste/script/command.py", line 102, in run
invoke(command, command_name, options, args[1:])
File "/usr/lib/ckan/venv/local/lib/python2.7/site-packages/paste/script/command.py", line 141, in invoke
exit_code = runner.run(args)
File "/usr/lib/ckan/venv/local/lib/python2.7/site-packages/paste/script/command.py", line 806, in run
command.load().summary))
File "/usr/lib/ckan/venv/local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2321, in load
return self.resolve()
File "/usr/lib/ckan/venv/local/lib/python2.7/site-packages/pkg_resources/__init__.py", line 2327, in resolve
module = __import__(self.module_name, fromlist=['__name__'], level=0)
File "/usr/lib/ckan/venv/src/ckan/ckanext/datapusher/cli.py", line 7, in <module>
import ckan.lib.cli as cli
File "/usr/lib/ckan/venv/src/ckan/ckan/lib/cli.py", line 17, in <module>
from ckan.cli import load_config as _get_config
File "/usr/lib/ckan/venv/src/ckan/ckan/cli/__init__.py", line 8, in <module>
from configparser import ConfigParser
ImportError: No module named configparser
You are using python 2.7 but importing configparser, which is Python 3 module. Check which version you are pooling from the Docker, I think you need 2.8.x tag as the latest stable.
I had installed numpy on alpine docker and everything looked good before running numpy:
Traceback (most recent call last):
File "/app/venv/lib/python3.7/site-packages/numpy/core/__init__.py", line 24, in <module>
from . import multiarray
File "/app/venv/lib/python3.7/site-packages/numpy/core/multiarray.py", line 14, in <module>
from . import overrides
File "/app/venv/lib/python3.7/site-packages/numpy/core/overrides.py", line 7, in <module>
from numpy.core._multiarray_umath import (
ImportError: Error loading shared library libcblas.so.3: No such file or directory (needed by /app/venv/lib/python3.7/site-packages/numpy/core/_multiarray_umath.cpython-37m-x86_64-linux-gnu.so)
I found that licblas.so might be in /usr/lib/ as mentioned here: alpine blas
but it wasn't there.
After installing lapack, the missing file libcblas.so.3 appeared in /usr/lib/:
apk add lapack
I had openblas-dev installed from before but that was not sufficient.
Followed through installation tips, but after typing
$ python underactuated/src/double_pendulum/simulate.py
I get
ImportError: dynamic module does not define init function (init_module_py).
If I run python3 I get
ImportError: cannot import name 'FindResource'.
After typing $ python3 -c 'import pydrake; print(pydrake.__file__)' I get /opt/drake/lib/python3.6/site-packages/pydrake/__init__.py
Edit:
Full output of running python3
Traceback (most recent call last):
File "underactuated/src/double_pendulum/simulate.py", line 5, in <module>
from underactuated import FindResource, PlanarSceneGraphVisualizer
ImportError: cannot import name 'FindResource'
And full output of running python (without3):
Traceback (most recent call last):
File "underactuated/src/double_pendulum/simulate.py", line 1, in <module>
from pydrake.all import (AddMultibodyPlantSceneGraph,
File "/opt/drake/lib/python3.6/site-packages/pydrake/__init__.py", line 32, in <module>
from . import common
File "/opt/drake/lib/python3.6/site-packages/pydrake/common/__init__.py", line 3, in <module>
from ._module_py import *
ImportError: dynamic module does not define init function (init_module_py)
Version of python after typing python -V is Python 2.7.15+
The fact that the print test succeeds suggests that drake is installed correctly.
Please post the full output of running simulate.py with python3.
When I try to do the quickstart instructions for NiftyNet installed from PyPI I get the following error when running net_segment:
net_segment inference -c ~/niftynet/extensions/dense_vnet_abdominal_ct/config.ini
WARNING:tensorflow:SimpleITK adapter failed to load, reducing the supported file formats.
Traceback (most recent call last):
File "/usr/local/bin/net_segment", line 11, in <module>
sys.exit(main())
File "/usr/local/lib/python2.7/dist-packages/niftynet/__init__.py", line 51, in main
set_logger()
File "/usr/local/lib/python2.7/dist-packages/niftynet/io/misc_io.py", line 585, in set_logger
tf.logging._logger.handlers = []
AttributeError: 'module' object has no attribute '_logger'
I have tried this on a Linux Mint 18.3 install (this one) as well as an Arch Linux install with SimpleITK.
Here is the same error on Arch Linux with NiftyNet installed from the AUR with SimpleITK installed.
net_segment inference -c ~/niftynet/extensions/dense_vnet_abdominal_ct/config.ini
Traceback (most recent call last):
File "/usr/bin/net_segment", line 11, in <module>
load_entry_point('NiftyNet==0.2.2', 'console_scripts', 'net_segment')()
File "/usr/lib/python3.6/site-packages/niftynet/__init__.py", line 51, in main
set_logger()
File "/usr/lib/python3.6/site-packages/niftynet/io/misc_io.py", line 585, in set_logger
tf.logging._logger.handlers = []
AttributeError: module 'tensorflow.tools.api.generator.api.logging' has no attribute '_logger'
Solved by downgrading TensorFlow to version 1.7.
NiftyNet does not support TF 1.8 yet, as you have discovered.
clang-ctags is producing the following error
$ clang-ctags trace make
Traceback (most recent call last):
File "/usr/local/bin/clang-ctags", line 9, in <module>
import clang.cindex
ImportError: No module named clang.cindex
Or
$ clang-ctags
Traceback (most recent call last):
File "/usr/local/bin/clang-ctags", line 9, in <module>
import clang.cindex
ImportError: No module named clang.cindex
I cannot find anything on the internet and I don't know python either. Can anyone solve this please?
If you are on Ubuntu you can install the Python bindings to Clang with the package
python-clang-3.4 or python-clang-3.5
To install it just run:
sudo apt-get install python-clang-3.4