[scipion-users] problem installing scipion3

[Moustafa, I. M. <ri...@ps...>]

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