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Re: [scipion-users] Installation problems (WSL)
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From: Viktor B. <vik...@mm...> - 2019-08-14 08:37:31
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When I import Queue I get the result <module 'Queue' from '/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/Queue/__init__.pyc'> I also tried the “from pip._internal” line from the traceback posted previously, and got the same error as before. So either the problem is having Queue as a module installed along with the rest, or there is something else. There seems to be something strange going on with urllib3. Thank you for all the patience, Viktor From: Pablo Conesa <pc...@cn...> Sent: den 14 augusti 2019 08:54 To: sci...@li... Subject: Re: [scipion-users] Installation problems (WSL) I guess changes of this (https://github.com/python-zk/kazoo/issues/239) being your case are low, but just in case? On 13/8/19 15:51, Viktor Bengtsson wrote: Thanks for the suggestion. Unfortunately I get the same error: /mnt/e/Linux_programs/scipion$ scipion python -m pip install requests Scipion v2.0 (2019-04-23) Diocletian >>>>> python "-m" "pip" "install" "requests" Traceback (most recent call last): File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/runpy.py", line 174, in _run_module_as_main "__main__", fname, loader, pkg_name) File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/runpy.py", line 72, in _run_code exec code in run_globals File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/__main__.py", line 16, in <module> from pip._internal import main as _main # isort:skip # noqa File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_internal/__init__.py", line 19, in <module> from pip._vendor.urllib3.exceptions import DependencyWarning File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/__init__.py", line 8, in <module> from .connectionpool import ( File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/connectionpool.py", line 44, in <module> from .util.queue import LifoQueue File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/util/queue.py", line 7, in <module> import Queue as _unused_module_Queue # noqa: F401 File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/util/Queue.py", line 10, in <module> class LifoQueue(queue.Queue): AttributeError: 'module' object has no attribute 'Queue' Kind regards, Viktor From: Pablo Conesa <pc...@cn...><mailto:pc...@cn...> Sent: den 13 augusti 2019 14:40 To: sci...@li...<mailto:sci...@li...> Subject: Re: [scipion-users] Installation problems (WSL) What if you do: scipion python -m pip install requests On 13/8/19 13:18, Viktor Bengtsson wrote: Hi, I tried what you suggested, but nothing seems to work. All packages installed prior to requests seem to install properly, so I wonder if there is something in particular related to that package that causes an error. Alternatively, is there some workaround to install that package into site-packages without using pip included with the installation of Scipion? Kind regards, Viktor From: Lugmayr, Wolfgang <w.l...@uk...><mailto:w.l...@uk...> Sent: den 12 augusti 2019 16:47 To: Mailing list for Scipion users <sci...@li...><mailto:sci...@li...> Subject: Re: [scipion-users] Installation problems (WSL) hi, maybe your os python is mixed up with the scipion one: can you check the following environment variables and test to set the scipion path first? LD_LIBRARY_PATH /whereever.../scipion/software/lib PYTHONPATH /whereever.../scipion/software/lib cheers, wolfgang ________________________________ From: "Viktor Bengtsson" <vik...@mm...<mailto:vik...@mm...>> To: "Mailing list for Scipion users" <sci...@li...<mailto:sci...@li...>> Sent: Monday, 12 August, 2019 14:49:20 Subject: [scipion-users] Installation problems (WSL) Dear all, Before summer I could use Scipion without problem. However, after vacation (and possibly some change in environment) it would not start at all. Unfortunately I did not save the error message before trying to reinstall, and reinstallation does not seem to work at all. The initial attempt was made on Ubuntu 16.04 installed through WSL on my work computer. I also tried installing on Ubuntu 18.04 installed on WSL on my home computer (where I have not used WSL at all previously, so no prior python installation). In all cases there have been a number of problems compiling python packages, and I can’t start Scipion. I followed the instructions found at https://scipion-em.github.io/docs/docs/scipion-modes/how-to-install<https://scipion-em.github.io/docs/docs/scipion-modes/how-to-install>, both for “From Binaries” and “Sources from GitHub”. The attached log files should include all input and all output. Does anyone know what might be the problem? Kind regards, Viktor Bengtsson PhD student Stockholm University PS. The final error I get when attempting to install from sources is : /mnt/e/Linux_programs/scipion/scipion/software/bin/python /mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip install requests==2.18.4 Traceback (most recent call last): File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/runpy.py", line 174, in _run_module_as_main "__main__", fname, loader, pkg_name) File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/runpy.py", line 72, in _run_code exec code in run_globals File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/__main__.py", line 16, in <module> from pip._internal import main as _main # isort:skip # noqa File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_internal/__init__.py", line 19, in <module> from pip._vendor.urllib3.exceptions import DependencyWarning File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/__init__.py", line 7, in <module> from .connectionpool import ( File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/connectionpool.py", line 45, in <module> from .util.queue import LifoQueue File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/util/queue.py", line 7, in <module> import Queue as _unused_module_Queue # noqa: F401 File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip/_vendor/urllib3/util/Queue.py", line 10, in <module> class LifoQueue(queue.Queue): AttributeError: 'module' object has no attribute 'Queue' Error: target '/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/requests' not built (after running '/mnt/e/Linux_programs/scipion/scipion/software/bin/python /mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/pip install requests==2.18.4') The original error (that reoccurred after installing from binaries) is: user@WORKCOMPUTER:/mnt/e/Linux_programs/scipion/scipion$ scipion Scipion v2.0 (2019-04-23) Diocletian >>>>> python /mnt/e/Linux_programs/scipion/scipion/pyworkflow/apps/pw_manager.py Traceback (most recent call last): File "/mnt/e/Linux_programs/scipion/scipion/pyworkflow/apps/pw_manager.py", line 32, in <module> from pyworkflow.gui.project import ProjectManagerWindow File "/mnt/e/Linux_programs/scipion/scipion/pyworkflow/gui/__init__.py", line 27, in <module> from gui import * File "/mnt/e/Linux_programs/scipion/scipion/pyworkflow/gui/gui.py", line 29, in <module> import Tkinter as tk File "/mnt/e/Linux_programs/scipion/scipion/software/lib/python2.7/site-packages/Tkinter/__init__.py", line 6, in <module> from Tkinter import (_cnfmerge, _default_root, _flatten, ImportError: cannot import name _cnfmerge _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users sers">https://lists.sourceforge.net/lists/listinfo/scipion-users _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users > ot;Times New Roman",serif;color:windowtext;mso-fareast-language:SV">> _______________________________________________ scipion-users mailing list sci...@li...<mailto:sci...@li...> https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - Madrid Scipion<http://scipion.i2pc.es> team ablo Conesa - Madrid Scipion<http://scipion.i2pc.es> team -- Pablo Conesa - Madrid Scipion<http://scipion.i2pc.es> team ablo Conesa - Madrid Scipion<http://scipion.i2pc.es> team |
