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Re: [scipion-users] problem installing scipion3
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From: David M. <dma...@cn...> - 2020-10-29 10:49:35
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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, <http://ucm.es/> *_____Dr. David Maluenda Niubó* dma...@cn... - (+34) 619 029 310 CSIC - Centro Nacional de Biotecnología <http://www.cnb.csic.es> BioComputing Unit <http://biocomputingunit.es/> This email message and any documents attached to it may contain confidential or legally protected material and are intended solely for the use of the individual or organization to whom they are addressed. We remind you that if you are not the intended recipient of this email message or the person responsible for processing it, then you are not authorized to read, save, modify, send, copy or disclose any of its contents. If you have received this email message by mistake, we kindly ask you to inform the sender of this and to eliminate both the message and any attachments it carries from your account. Thank you for your collaboration. On Thu, Oct 29, 2020 at 11:16 AM Pablo Conesa <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-3.0.1Traceback (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...> <dma...@cn...> > *Sent:* Wednesday, October 28, 2020 2:32 PM > *To:* Mailing list for Scipion users <sci...@li...> > <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... > Wavefront Engineering Group > Applied Physics (UB) > > El mié., 28 oct. 2020 17:25, Moustafa, Ibrahim M. <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...> > *Sent:* Wednesday, October 28, 2020 2:23 AM > *To:* sci...@li... < > 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* > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > <https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fscipion-users&data=04%7C01%7Cria2%40psu.edu%7Ca624d41b3c8641fb802b08d87b6fe722%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C1%7C637395067844599235%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=ubjyOXExNvy2Ac3v4k9WZCPZaQu4%2Fy8xrXb5U5DqKUw%3D&reserved=0> > > > > _______________________________________________ > scipion-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/scipion-users > > -- > Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team* > _______________________________________________ > scipion-users mailing list > sci...@li... > https://lists.sourceforge.net/lists/listinfo/scipion-users > |
