I wanted to use WSL2 Ubuntu to run some scientific programs on my PC (Phenix package). It used to work previously on wsl but after recent update to wsl2 one of the programs written in Python has some problems:
Traceback (most recent call last):
File "/mnt/f/cryoEM/phenix-1.18rc4-3812/build/../modules/phenix/wxGUI2/command_line/main.py", line 23, in <module>
run(sys.argv[1:])
File "/mnt/f/cryoEM/phenix-1.18rc4-3812/build/../modules/phenix/wxGUI2/command_line/main.py", line 16, in run
from wxGUI2 import App
File "/mnt/f/cryoEM/phenix-1.18rc4-3812/modules/phenix/wxGUI2/App.py", line 7, in <module>
from SimpleXMLRPCServer import SimpleXMLRPCServer
File "/mnt/f/cryoEM/phenix-1.18rc4-3812/conda_base/lib/python2.7/SimpleXMLRPCServer.py", line 105, in <module>
import BaseHTTPServer
File "/mnt/f/cryoEM/phenix-1.18rc4-3812/conda_base/lib/python2.7/BaseHTTPServer.py", line 102, in <module>
class HTTPServer(SocketServer.TCPServer):
AttributeError: 'module' object has no attribute 'TCPServer'
I have checked all the packages (BaseHTTPServer, SocketServer) and everything seems to be fine. Using python provided with the package and importing modules separately also works without errors. My previous computer also with WSL2 was running this software package without any issues. I believe that there is something missing on the wsl2 Ubuntu level but cannot guess what it is. Do you have any suggestions what I could try to do? Thanks!
Related
While importing openai's universe, i get these errors:
Traceback (most recent call last):
File "/Users/calvin/Desktop/universe-test/main.py", line 2, in <module>
import universe
File "/Users/calvin/universe/universe/__init__.py", line 22, in <module>
from universe import error, envs
File "/Users/calvin/universe/universe/envs/__init__.py", line 1, in <module>
import universe.envs.vnc_env
File "/Users/calvin/universe/universe/envs/vnc_env.py", line 11, in <module>
from universe.envs import diagnostics
File "/Users/calvin/universe/universe/envs/diagnostics.py", line 94
async = self.qr_pool.apply_async(self.method, (self._last_img, time.time(), available_at))
^
SyntaxError: invalid syntax
I've tried downloading a different version of gym, reinstalling universe, and nothing works. I have python 3.8.5 64-bit. My operating system is macOS Catalina 10.15.6. Any ideas?
async is now a special keyword, and as such, can't be used as a variable name.
That library appears to be made for Python pre-3.5. I believe your only options are:
Use a older version of Python 3 (async was intrduced in 3.5).
Edit the local copy of the library file to change the name to something else.
Check to see if there are any updates/forks to the library that fix that issue.
I have multiple Python versions installed with pyenv on Ubuntu 16.04. I create virtual environments to work with projects using different versions with pipenv. However, for Python 3.5.x only I get errors like this when I try to edit a file with Vim 8 (installed via the PPA) in an activated virtualenv:
"test.py" 49L, 1434C
Error detected while processing function jedi#init_python[4]..<SNR>48_init_python[27]..jedi#setup_python_imports:
line 25:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/home/user/.local/share/virtualenvs/test-AYf6DmHL/lib/python3.5/imp.py", line 19, in <module>
from importlib._bootstrap import _ERR_MSG, _exec, _load, _builtin_from_name
File "/home/user/.local/share/virtualenvs/test-AYf6DmHL/lib/python3.5/importlib/__init__.py", line 57, in <module>
import types
File "/home/user/.local/share/virtualenvs/test-AYf6DmHL/lib/python3.5/types.py", line 166, in <module>
import functools as _functools
File "/home/user/.local/share/virtualenvs/test-AYf6DmHL/lib/python3.5/functools.py", line 23, in <module>
from weakref import WeakKeyDictionary
File "/home/user/.local/share/virtualenvs/test-AYf6DmHL/lib/python3.5/weakref.py", line 12, in <module>
from _weakref import (
ImportError: cannot import name '_remove_dead_weakref'
The issue seems to affect all python related Vim plugins. With other Python versions (e.g. 3.6.x, 3.7.x) this does not occur. What may be causing this issue?
Update: It seems that when I run Vim inside a 3.5.x virtualenv, the Vim's interpreter's sys.path gets updated somehow. For example, this is the output of :py3 import sys; print(sys.path) inside a 3.6.0 virtualenv:
['/usr/lib/python35.zip', '/usr/lib/python3.5', '/usr/lib/python3.5/plat-x86_64-linux-gnu', '/usr/lib/python3.5/lib-dynload', '/usr/local/lib/python3.5
/dist-packages', '/usr/lib/python3/dist-packages', '_vim_path_']
And this is for 3.5.3:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/home/testuser/.local/share/virtualenvs/venv-3.5-8feRiT5s/lib/python3.5/imp.py", line 19, in <module>
from importlib._bootstrap import _ERR_MSG, _exec, _load, _builtin_from_name
File "/home/testuser/.local/share/virtualenvs/venv-3.5-8feRiT5s/lib/python3.5/importlib/__init__.py", line 57, in <module>
import types
File "/home/testuser/.local/share/virtualenvs/venv-3.5-8feRiT5s/lib/python3.5/types.py", line 166, in <module>
import functools as _functools
File "/home/testuser/.local/share/virtualenvs/venv-3.5-8feRiT5s/lib/python3.5/functools.py", line 23, in <module>
from weakref import WeakKeyDictionary
File "/home/testuser/.local/share/virtualenvs/venv-3.5-8feRiT5s/lib/python3.5/weakref.py", line 12, in <module>
from _weakref import (
ImportError: cannot import name '_remove_dead_weakref'
['/must>not&exist', '/home/testuser/.local/share/virtualenvs/venv-3.5-8feRiT5s/lib/python35.zip', '/home/testuser/.local/share/virtualenvs/venv-3.5-8feRiT5s/li
b/python3.5', '/home/testuser/.local/share/virtualenvs/venv-3.5-8feRiT5s/lib/python3.5/plat-x86_64-linux-gnu', '/home/testuser/.local/share/virtualenvs/venv-3.
5-8feRiT5s/lib/python3.5/lib-dynload', '/home/testuser/.pyenv/versions/3.5.7/lib/python3.5', '/home/testuser/.local/share/virtualenvs/venv-3.5-8feRiT5s/lib/pyt
hon3.5/site-packages']
The issue can be reproduced in a ubuntu:16.04 docker container.
Debian Bug report logs - #852163: python3.5-minimal wont configure demonstrates that this error (for Python 3.5 and Python 3.6) is due to another incompatible installation of Python in /usr/local.
Some further digging with another user in #debian who was experiencing this
problem indicated that it was related to a locally installed
/usr/local/bin/python3.5. The stdlib in /usr/lib/python3.5 is picked up by the
/usr/local/bin/python3.5 but is not compatible with it, resulting in the
stacktrace shown.
Removing /usr/local/bin/python3* and all traces of that installation from
/usr/local/lib (plus other associated tools) solved this problem for the user
I was helping in #debian.
-- Stuart Prescott (link)
The problem is caused by the system installed python, which conflicts with personally installed python.
It could be the case that other python versions are interfering here. Do you have a PYTHONPATH set?
echo $PYTHONPATH
If it is set you could try to unset it. It's usually not needed when using virtual environments.
Try running python with sudo. I think the python which comes with OS needs to run with admin privilege.
I am currently trying to run a python script on a GCE virtual machine. However, I keep getting an error when using 'import cv2':
Traceback (most recent call last):
File "train.py", line 12, in <module> from deeplab.datasets import DataSetTrain, DataSetVal
File "/jet/prs/workspace/FYP-Project/Pytorch-Deeplab-master/deeplab/datasets.py", line 10, in <module>
import cv2
File "/jet/prs/workspace/lib/python3.6/site-packages/cv2/__init__.py", line 3, in <module>
from .cv2 import *
ImportError: libgthread-2.0.so.0: cannot open shared object file: No such file or directory
The problem with this is that I have checked that the directory the file being referenced is present. I have installed and reinstalled cv2, however nothing seems to be working. None of the other modules that i installed using pip have this issue, it seems to only occur with cv2.
I have been using the zxcvbn, which is a great piece of programming.
Especially, the port python-zxcvbn has been perfect for a small project I am doing.
Despite this, I am trying to invoke python-zxcvbn from Python 3.4 and I get errors like this:
Traceback (most recent call last):
File "entropy.py", line 7, in <module>
from zxcvbn import password_strength
File "/usr/lib/python3.4/site-packages/zxcvbn/__init__.py", line 1, in <module>
from zxcvbn import main
File "/usr/lib/python3.4/site-packages/zxcvbn/main.py", line 3, in <module>
from zxcvbn.matching import omnimatch
File "/usr/lib/python3.4/site-packages/zxcvbn/matching.py", line 89, in <module>
_load_frequency_lists()
File "/usr/lib/python3.4/site-packages/zxcvbn/matching.py", line 67, in _load_frequency_lists
dicts = json.loads(data)
File "/usr/lib/python3.4/json/__init__.py", line 312, in loads
s.__class__.__name__))
TypeError: the JSON object must be str, not 'bytes'
I have tried both installing the library from github, and with pip, with the same result.
To avoid that, I am currently running python2 in the module that uses zxcvbn, but I'd like to have a cleaner version of my project which runs fully with Python 3.4.
Is anyone successfully using python-zxcvbn with Python 3.4?
As answered by unutbu, there is a fork on github by moreati that is compatible with Python 3.4. It worked flawlessly for me.
https://github.com/moreati/python-zxcvbn
I'm a beginner in OpenGL/OpenCL.
I'm trying to execute code from this
example, but there is an error:
Traceback (most recent call last):
File "/home/anka-rybalko/workspace/bla/openGL.py", line 99, in initializeGL
self.initialize_buffers()
File "/home/anka-rybalko/workspace/bla/openGL.py", line 61, in initialize_buffers
self.ctx, self.queue = clinit()
File "/home/anka-rybalko/workspace/bla/openGL.py", line 37, in clinit
+ get_gl_sharing_context_properties())
File "/usr/lib64/python2.7/site-packages/pyopencl-2014.1-py2.7-linux-x86_64.egg/pyopencl/tools.py", line 422, in get_gl_sharing_context_properties
from OpenGL import platform as gl_platform, GLX, WGL
File "/usr/lib/python2.7/site-packages/OpenGL/WGL/__init__.py", line 1, in <module>
from OpenGL.raw.WGL.VERSION.WGL_1_0 import *
File "/usr/lib/python2.7/site-packages/OpenGL/raw/WGL/VERSION/WGL_1_0.py", line 48, in <module>
#_p.types(_cs.c_int,_cs.HDC,ctypes.POINTER(_cs.PIXELFORMATDESCRIPTOR))
File "/usr/lib/python2.7/site-packages/OpenGL/raw/WGL/VERSION/WGL_1_0.py", line 13, in _f
return _p.createFunction( function,_p.PLATFORM.WGL,'WGL_VERSION_WGL_1_0',error_checker=_errors._error_checker)
AttributeError: 'GLXPlatform' object has no attribute 'WGL'
As I understand, WGL is an API for Windows OS and not for Linux. Should I somehow specify my platform before? Or how can I fix this?
Thanks in advance!
The code you are using (PyOpenGL 2014.1) is importing two platform-specific modules (WGL and GLX). PyOpenGL should have raised that error as an ImportError (rather than the AttributeError), but it still would have failed.
PyOpenCL has, in the meantime, worked around the issue in their github repository. If you have git installed (and pip) then this should get you a new version (note: not set up for OpenCL development here, so can't actually test this):
pip install git+https://github.com/pyopencl/pyopencl#egg=pyopencl