Re: [scipion-users] problem installing scipion3

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Many thanks David! downgrading numpy to version 1.18.4 solved the issue. Now Scipion3 can launch the gui.

Pablo: I see localrec indicated as installed plugin in the plugins manager. Still puzzled why it did not build in the site-packages under .scipionenv directory! Not sure if that affects localrec or it can still work properly.

The output of scipion3 printenv is shown below. If it needs edit please let me know!

Scipion v3.0.5 () devel
export CUDA_BIN="/opt/debian10/cuda/10.1.243/bin"
export CUDA_LIB="/opt/debian10/cuda/10.1.243/lib64"
export EMAN2_HOME="/usr/local/scipion/software/em/eman-2.31"
export EMFACILITIES_HOME="/usr/local/scipion"
export EM_ROOT="software/em"
export LOCSCALE_HOME="/usr/local/scipion/software/em/locscale-0.1"
export MAXIT_HOME="/usr/local/scipion/software/em/maxit-10.1"
export OPENCV="False"
export RELION_HOME="/usr/local/scipion/software/em/relion-3.1.0"
export SCIPION_CONFIG="/usr/local/scipion/config/scipion.conf"
export SCIPION_CWD="/home/ria2"
export SCIPION_DOMAIN="pwem"
export SCIPION_FONT_NAME="Helvetica"
export SCIPION_HOME="/usr/local/scipion"
export SCIPION_HOSTS="/usr/local/scipion/config/hosts.conf"
export SCIPION_LOCAL_CONFIG="/home/ria2/.config/scipion/scipion.conf"
export SCIPION_LOG="/storage/ria2/ScipionUserData/logs/scipion.log"
export SCIPION_LOGO="scipion_logo.gif"
export SCIPION_LOGS="/storage/ria2/ScipionUserData/logs"
export SCIPION_NOTES_ARGS=""
export SCIPION_NOTES_FILE="notes.txt"
export SCIPION_NOTES_PROGRAM=""
export SCIPION_NOTIFY="False"
export SCIPION_PLUGIN_REPO_URL="http://scipion.i2pc.es/getplugins/"
export SCIPION_PROTOCOLS="/usr/local/scipion/config/protocols.conf"
export SCIPION_SOFTWARE="/usr/local/scipion/software"
export SCIPION_SUPPORT_EMAIL="sc...@cn..."
export SCIPION_TESTS="/usr/local/scipion/data/tests"
export SCIPION_TESTS_CMD="scipion3 tests"
export SCIPION_TESTS_OUTPUT="/usr/local/scipion/Tests"
export SCIPION_TMP="/storage/ria2/ScipionUserData/tmp"
export SCIPION_URL="http://scipion.cnb.csic.es/downloads/scipion"
export SCIPION_URL_SOFTWARE="http://scipion.cnb.csic.es/downloads/scipion/software"
export SCIPION_URL_TESTDATA="http://scipion.cnb.csic.es/downloads/scipion/data/tests"
export SCIPION_USER_DATA="/storage/ria2/ScipionUserData"
export SCIPION_VERSION="v3.0.5 () devel"
export WIZARD_MASK_COLOR="[0.125, 0.909, 0.972]"
export XMIPP2_HOME="/usr/local/scipion/software/em/Xmipp-2.4-src"
export XMIPP_HOME="/usr/local/scipion/software/em/xmipp"

 Thanks,
Ibrahim
________________________________
From: David Maluenda <dma...@cn...>
Sent: Thursday, October 29, 2020 6:48 AM
To: Mailing list for Scipion users <sci...@li...>
Subject: Re: [scipion-users] problem installing scipion3

The error when launching scipion3 seems a versioning crash for numpy. Try to downgrade numpy by

./scipion3 python -m pip install numpy==1.18.4

Hope it helps,

Regards,
<https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fucm.es%2F&data=04%7C01%7Cria2%40psu.edu%7C8e9b7c5aa1d54746d3e408d87bf860fc%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637395654004301017%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=85csE4HN%2BamymeYf96qZGBrQ9Lpe2TdyNiWtvzMyy7U%3D&reserved=0>
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Dr. David Maluenda Niubó
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On Thu, Oct 29, 2020 at 11:16 AM Pablo Conesa <pc...@cn...<mailto:pc...@cn...>> wrote:

I think  now localrec is installed depite the error message and xmipp looks fixed too.

Could you please send the output of:

scipion3 printenv

On 29/10/20 4:18, Moustafa, Ibrahim M. wrote:
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...><mailto:dma...@cn...>
Sent: Wednesday, October 28, 2020 2:32 PM
To: Mailing list for Scipion users <sci...@li...><mailto: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
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Re: [scipion-users] problem installing scipion3

Image processing framework to integrate EM software packages.

Re: [scipion-users] problem installing scipion3