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Re: [scipion-users] Installation problems (WSL)
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From: Pablo C. <pc...@cn...> - 2019-08-14 08:54:36
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This is starting to ring a bell....I've searched my emails but couldn't find anything, but may be is related to some ssh library missing? I might not be able to explain it but I think python installation requires some ssl libraries (optionally) that latter on will be critical for installing other packages. Could you please have a look at the python installation log files at: <scipion_home>/software/log/python_* May be there is something there that could give us a hint? On 14/8/19 10:37, Viktor Bengtsson wrote: > > 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, > 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* > > strong>Madrid Scipion <http://scipion.i2pc.es> team > > > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users -- Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* |
