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Re: [scipion-users] problem installing scipion3
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From: Pablo C. <pc...@cn...> - 2020-10-29 10:16:24
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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...>
> *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
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--
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
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