Re: [scipion-users] problem installing scipion3

[Pablo C. <pc...@cn...>]

One more thing! Do you have write permissions in 
/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages ?

On 27/10/20 7:18, pc...@cn... wrote:
> What gives you:
>
> ls -l 
> /usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_ 
>                                             em_
>
> El 26 oct. 2020 17:57, "Moustafa, Ibrahim M." <ri...@ps...> escribió:
>
>     Hi Pablo,
>
>       Thanks for your reply.
>
>     I tried your suggestions and I got the following error:
>
>     ==================================================================================
>     Scipion v3.0.5 () devel
>     Building scipion-em-localrec ...
>     /usr/local/miniconda/envs/.scipion3env/bin/python -m pip install
>     scipion-em-localrec==3.0.1
>     Collecting scipion-em-localrec==3.0.1
>       Using cached scipion_em_localrec-3.0.1-py3-none-any.whl (530 kB)
>     Installing collected packages: scipion-em-localrec
>     Successfully installed scipion-em-localrec-3.0.1
>     Traceback (most recent call last):
>       File "/usr/local/scipion/pip/scipion/__main__.py", line 453, in
>     <module>
>         main()
>       File "/usr/local/scipion/pip/scipion/__main__.py", line 296, in main
>         installPluginMethods()
>       File "/usr/local/scipion/pip/scipion/install/install_plugin.py",
>     line 229, in installPluginMethod                       s
>         installed = plugin.installPipModule(version=pluginVersion)
>       File "/usr/local/scipion/pip/scipion/install/plugin_funcs.py",
>     line 152, in installPipModule
>         environment.execute()
>       File "/usr/local/scipion/pip/scipion/install/funcs.py", line
>     748, in execute
>         self._executeTargets(targetList)
>       File "/usr/local/scipion/pip/scipion/install/funcs.py", line
>     690, in _executeTargets
>         tgt.execute()
>       File "/usr/local/scipion/pip/scipion/install/funcs.py", line
>     220, in execute
>         command.execute()
>       File "/usr/local/scipion/pip/scipion/install/funcs.py", line
>     160, in execute
>         assert glob(t), ("target '%s' not built (after "
>     AssertionError: target
>     '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_
>     em_localrec*' not built (after running
>     '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip in stall
>     scipion-em-localrec==3.0.1')
>     Error at main: target
>     '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_e
>     m_localrec*' not built (after running
>     '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip ins tall
>     scipion-em-localrec==3.0.1')
>
>     ==================================================================================
>
>     Any idea to fix this?
>
>       Thanks for help.
>     Ibrahim
>     ------------------------------------------------------------------------
>     *From:* pc...@cn... <pc...@cn...>
>     *Sent:* Saturday, October 24, 2020 11:56 PM
>     *To:* Mailing list for Scipion users
>     <sci...@li...>
>     *Cc:* Carnegie, Mike Scott <mz...@ps...>
>     *Subject:* Re: [scipion-users] problem installing scipion3
>     Hi, I'm sorry about you poor experience installing the plugin
>
>     Can you try:
>
>     scipion3 python -m pip uninstall scipion-em-localrec
>
>     And then:
>
>     scipion3 installs -p scipion-em-localrec
>
>     ?
>     Then we can also check what is wrong with bumpy.
>
>     All the best, Pablo.
>
>     El 24 oct. 2020 2:12, "Moustafa, Ibrahim M." <ri...@ps...> escribió:
>
>         Dear All,
>
>           We are having so much trouble installing Scipion 3. We
>         thought it went through installation but then it complained
>         about xmipp because of conflict between numpy-1.19.1
>         (installed with OpenCV) and numpy-1.18.4 (installed from pip).
>         None of the plugins seem to be properly installed when we
>         tried, although it showed "Successfully Finished' in the log!
>
>         Trying to install localrec-em showed the following error:
>
>         ===========================================================================================
>         >scipion3 installp -p scipion-em-localrec
>         /usr/local/miniconda/envs/.scipion3env/bin/python -m pip
>         install scipion-em-localrec==3.0.1
>         Collecting scipion-em-localrec==3.0.1
>           Using cached scipion_em_localrec-3.0.1-py3-none-any.whl (530 kB)
>         Installing collected packages: scipion-em-localrec
>         Successfully installed scipion-em-localrec-3.0.1
>         WARNING: Target directory
>         /usr/local/scipion/pip/scipion_em_localrec-3.0.1.dist-info
>         already exists. Specify --upgrade to force replacement.
>         WARNING: Target directory /usr/local/scipion/pip/localrec
>         already exists. Specify --upgrade to force replacement.
>         Traceback (most recent call last):
>           File "/usr/local/scipion/pip/scipion/__main__.py", line 453,
>         in <module>
>             main()
>           File "/usr/local/scipion/pip/scipion/__main__.py", line 296,
>         in main
>             installPluginMethods()
>           File
>         "/usr/local/scipion/pip/scipion/install/install_plugin.py",
>         line 229, in installPluginMethods
>             installed = plugin.installPipModule(version=pluginVersion)
>           File
>         "/usr/local/scipion/pip/scipion/install/plugin_funcs.py", line
>         152, in installPipModule
>             environment.execute()
>           File "/usr/local/scipion/pip/scipion/install/funcs.py", line
>         748, in execute
>             self._executeTargets(targetList)
>           File "/usr/local/scipion/pip/scipion/install/funcs.py", line
>         690, in _executeTargets
>             tgt.execute()
>           File "/usr/local/scipion/pip/scipion/install/funcs.py", line
>         220, in execute
>             command.execute()
>           File "/usr/local/scipion/pip/scipion/install/funcs.py", line
>         160, in execute
>             assert glob(t), ("target '%s' not built (after "
>         AssertionError: target
>         '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em_localrec*'
>         not built (after running
>         '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip
>         install scipion-em-localrec==3.0.1')
>         Error at main: target
>         '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em_localrec*'
>         not built (after running
>         '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip
>         install scipion-em-localrec==3.0.1')
>         ==================================================================================
>
>             Not sure what we are doing wrong! It would be appreciated
>         if someone can share a "clear" protocol of how to properly
>         install Scipion 3 along with plugins. We are mostly interested in
>         localrec plugin.
>
>         P.S. we are using py3.8 from miniconda
>
>            Appreciate your help,
>               Ibrahim
>
>         Ibrahim M.Moustafa, Ph.D.
>         Pennsylvania State University
>         Biochemistry & Molecular Biology Dept.
>         Millennium Science Complex
>         University Park
>         State College, PA16802
>
>         Phone: (814) 863 5940
>         Fax:      (814) 865 7927
>
>
>
>
>
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-- 
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*