Re: [scipion-users] problem installing scipion3

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Hi David,

 I appreciate your help.  I tried what you suggested, removed xmipp and used 'scipion3 installb xmippSrc -j 8' with 'OPENCV=False option. It compiled with no error.
I re-installed  scipion-em-localrec 'scipion installp -p scipion-em-localrec' and I still get the following error:

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 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')

No idea why it could not build in the site-packages directory (which I own)!

Now if I run: 'scipion3 inspect localrec' I get the following:
Scipion v3.0.5 () devel
Plugin: localrec
   >>> constants:  loaded
   >>> convert:  loaded
   >>> protocols:  loaded
   >>> wizards:  missing
   >>> viewers:  loaded
   >>> tests:  loaded

I also still not able to run Scipion3, I get the following error:
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 262, in main
    ProjectManagerWindow().show()
  File "/usr/local/scipion/pip/pyworkflow/gui/project/project.py", line 391, in __init__
    ProjectBaseWindow.__init__(self, title, minsize=(750, 500),
  File "/usr/local/scipion/pip/pyworkflow/gui/project/base.py", line 53, in __init__
    Window.__init__(self, title, masterWindow, weight=weight,
  File "/usr/local/scipion/pip/pyworkflow/gui/gui.py", line 261, in __init__
    pw.Config.getDomain()._discoverGUIPlugins()
  File "/usr/local/scipion/pip/pyworkflow/plugin.py", line 107, in _discoverGUIPlugins
    entry_point.load()
  File "/usr/local/scipion/pip/pkg_resources/__init__.py", line 2446, in load
    self.require(*args, **kwargs)
  File "/usr/local/scipion/pip/pkg_resources/__init__.py", line 2469, in require
    items = working_set.resolve(reqs, env, installer, extras=self.extras)
  File "/usr/local/scipion/pip/pkg_resources/__init__.py", line 775, in resolve
    raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.ContextualVersionConflict: (numpy 1.19.2 (/usr/local/scipion/pip), Requirement.parse('numpy<=1.18.4'), {'scipion-pyworkflow'})
Error at main: (numpy 1.19.2 (/usr/local/scipion/pip), Requirement.parse('numpy<=1.18.4'), {'scipion-pyworkflow'})

  Any suggestion to get this fixed is appreciated!

  Thanks,
 Ibrahim

________________________________
From: David Maluenda <dma...@cn...>
Sent: Wednesday, October 28, 2020 2:32 PM
To: Mailing list for Scipion users <sci...@li...>
Subject: Re: [scipion-users] problem installing scipion3

Hi,

The error depicted above sounds me. I think it's raised when the xmipp plugin version is not sync with the xmipp software version. Please, try to remove software/em/xmipp and run 'scipion3 installb xmippSrc -j 8'

Hope it helps.

Regards,

_____
Dr. David Maluenda Niubó
(+34) 619.029.310 - dma...@ub...<mailto:dma...@ub...>
Wavefront Engineering Group
Applied Physics (UB)

El mié., 28 oct. 2020 17:25, Moustafa, Ibrahim M. <ri...@ps...<mailto:ri...@ps...>> escribió:
Running "scipion3 inspect localrec" gives the following error:

Scipion v3.0.5 () devel

 >>> WARNING: Image library not found!
  > Please install Xmipp to get full functionality.
(Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window)

Plugin: localrec
   >>> constants:  loaded
   >>> convert:  loaded
   >>> protocols:  loaded
   >>> wizards:  missing
   >>> viewers:  loaded
   >>> tests:  error -> Traceback (most recent call last):
  File "/usr/local/scipion/pip/scipion/install/inspect-plugins.py", line 74, in getSubmodule
    m = importlib.import_module('%s.%s' % (name, subname))
  File "/usr/local/miniconda/envs/.scipion3env/lib/python3.8/importlib/__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 1014, in _gcd_import
  File "<frozen importlib._bootstrap>", line 991, in _find_and_load
  File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 671, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 783, in exec_module
  File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed
  File "/usr/local/scipion/pip/localrec/tests/__init__.py", line 27, in <module>
from .test_protocol_localized_reconstruction import (TestLocalizedReconsBase,
  File "/usr/local/scipion/pip/localrec/tests/test_protocol_localized_reconstruction.py", line 37, in <module>
    from xmipp3.protocols import XmippProtCreateMask3D
  File "/usr/local/scipion/pip/xmipp3/protocols/__init__.py", line 50, in <module>
    from .protocol_ctf_micrographs import XmippProtCTFMicrographs
  File "/usr/local/scipion/pip/xmipp3/protocols/protocol_ctf_micrographs.py", line 44, in <module>
    from xmipp3.base import isMdEmpty
ImportError: cannot import name 'isMdEmpty' from 'xmipp3.base' (/usr/local/scipion/pip/xmipp3/base.py)

Ibrahim
________________________________
From: Pablo Conesa <pc...@cn...<mailto:pc...@cn...>>
Sent: Wednesday, October 28, 2020 2:23 AM
To: sci...@li...<mailto:sci...@li...> <sci...@li...<mailto:sci...@li...>>
Subject: Re: [scipion-users] problem installing scipion3

Despite the error, it seems localrec is installed.

What about:

./scipion3 inspect localrec

On 27/10/20 19:12, Moustafa, Ibrahim M. wrote:
scipion-em-localrec 3.0.1
--
Pablo Conesa - Madrid Scipion<https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fscipion.i2pc.es%2F&data=04%7C01%7Cria2%40psu.edu%7Ca624d41b3c8641fb802b08d87b6fe722%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C1%7C637395067844599235%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=%2B7iKfpsv7zLReOANbRzG1IUSaNvs5lD%2B3%2Fr%2F9K04M5Y%3D&reserved=0> team
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Re: [scipion-users] problem installing scipion3

Image processing framework to integrate EM software packages.

Re: [scipion-users] problem installing scipion3