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Re: [scipion-users] problem installing scipion3
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From: <pc...@cn...> - 2020-10-29 18:45:39
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<div dir='auto'>I don't see any suspicious value.<div dir="auto"><br></div><div dir="auto">I understand, apart from not understanding the location of localrec, all seems to work?</div></div><div class="gmail_extra"><br><div class="gmail_quote">El 29 oct. 2020 17:47, "Moustafa, Ibrahim M." <ri...@ps...> escribió:<br type="attribution" /><blockquote class="quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> Many thanks David! downgrading numpy to version 1.18.4 solved the issue. Now Scipion3 can launch the gui.</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> <br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> 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.</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> <br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> The output of scipion3 printenv is shown below. If it needs edit please let me know!</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> <br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> Scipion v3.0.5 () devel <div>export CUDA_BIN="/opt/debian10/cuda/10.1.243/bin"</div> <div>export CUDA_LIB="/opt/debian10/cuda/10.1.243/lib64"</div> <div>export EMAN2_HOME="/usr/local/scipion/software/em/eman-2.31"</div> <div>export EMFACILITIES_HOME="/usr/local/scipion"</div> <div>export EM_ROOT="software/em"</div> <div>export LOCSCALE_HOME="/usr/local/scipion/software/em/locscale-0.1"</div> <div>export MAXIT_HOME="/usr/local/scipion/software/em/maxit-10.1"</div> <div>export OPENCV="False"</div> <div>export RELION_HOME="/usr/local/scipion/software/em/relion-3.1.0"</div> <div>export SCIPION_CONFIG="/usr/local/scipion/config/scipion.conf"</div> <div>export SCIPION_CWD="/home/ria2"</div> <div>export SCIPION_DOMAIN="pwem"</div> <div>export SCIPION_FONT_NAME="Helvetica"</div> <div>export SCIPION_HOME="/usr/local/scipion"</div> <div>export SCIPION_HOSTS="/usr/local/scipion/config/hosts.conf"</div> <div>export SCIPION_LOCAL_CONFIG="/home/ria2/.config/scipion/scipion.conf"</div> <div>export SCIPION_LOG="/storage/ria2/ScipionUserData/logs/scipion.log"</div> <div>export SCIPION_LOGO="scipion_logo.gif"</div> <div>export SCIPION_LOGS="/storage/ria2/ScipionUserData/logs"</div> <div>export SCIPION_NOTES_ARGS=""</div> <div>export SCIPION_NOTES_FILE="notes.txt"</div> <div>export SCIPION_NOTES_PROGRAM=""</div> <div>export SCIPION_NOTIFY="False"</div> <div>export SCIPION_PLUGIN_REPO_URL="http://scipion.i2pc.es/getplugins/"</div> export SCIPION_PROTOCOLS="/usr/local/scipion/config/protocols.conf"<br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> export SCIPION_SOFTWARE="/usr/local/scipion/software" <div>export SCIPION_SUPPORT_EMAIL="scipion@cnb.csic.es"</div> <div>export SCIPION_TESTS="/usr/local/scipion/data/tests"</div> <div>export SCIPION_TESTS_CMD="scipion3 tests"</div> <div>export SCIPION_TESTS_OUTPUT="/usr/local/scipion/Tests"</div> <div>export SCIPION_TMP="/storage/ria2/ScipionUserData/tmp"</div> <div>export SCIPION_URL="http://scipion.cnb.csic.es/downloads/scipion"</div> <div>export SCIPION_URL_SOFTWARE="http://scipion.cnb.csic.es/downloads/scipion/software"</div> <div>export SCIPION_URL_TESTDATA="http://scipion.cnb.csic.es/downloads/scipion/data/tests"</div> <div>export SCIPION_USER_DATA="/storage/ria2/ScipionUserData"</div> <div>export SCIPION_VERSION="v3.0.5 () devel"</div> <div>export WIZARD_MASK_COLOR="[0.125, 0.909, 0.972]"</div> <div>export XMIPP2_HOME="/usr/local/scipion/software/em/Xmipp-2.4-src"</div> export XMIPP_HOME="/usr/local/scipion/software/em/xmipp"<br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> <br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> Thanks,</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> Ibrahim</div> <div></div> <hr style="display:inline-block;width:98%" /> <div dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> David Maluenda <dmaluenda@cnb.csic.es><br /> <b>Sent:</b> Thursday, October 29, 2020 6:48 AM<br /> <b>To:</b> Mailing list for Scipion users <scipion-users@lists.sourceforge.net><br /> <b>Subject:</b> Re: [scipion-users] problem installing scipion3</font> <div> </div> </div> <div> <div dir="ltr"> <div style="font-family:'trebuchet ms' , sans-serif;font-size:small;color:#000000"> The error when launching scipion3 seems a versioning crash for numpy. Try to downgrade numpy by</div> <div style="font-family:'trebuchet ms' , sans-serif;font-size:small;color:#000000"> <br /> </div> <blockquote style="margin:0 0 0 40px;border:none;padding:0px"> <div style="font-size:small;color:rgb( 0 , 0 , 0 )"><font face="monospace">./scipion3 python -m pip install numpy==1.18.4</font></div> </blockquote> <div style="font-family:'trebuchet ms' , sans-serif;font-size:small;color:#000000"> <br /> </div> <div style="font-family:'trebuchet ms' , sans-serif;font-size:small;color:#000000"> Hope it helps,</div> <div style="font-family:'trebuchet ms' , sans-serif;font-size:small;color:#000000"> <br /> </div> <div style="font-family:'trebuchet ms' , sans-serif;font-size:small;color:#000000"> Regards,</div> <div> <div dir="ltr"> <div dir="ltr"> <div> <div dir="ltr"> <div> <div dir="ltr"> <div> <div dir="ltr"> <div> <div dir="ltr"> <div> <div dir="ltr"> <div dir="ltr"> <div dir="ltr"><font color="#888888"></font></div> <div dir="ltr"><font color="#000000" face="trebuchet ms,sans-serif"> <div style="font-size:small;display:inline"><a href="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"></a></div> </font><font color="#000000" face="trebuchet ms,sans-serif"><b>_____<br /> Dr. David Maluenda Niubó</b><br /> </font></div> <div dir="ltr"><font color="#000000" face="trebuchet ms,sans-serif"><a href="mailto:dmaluenda@cnb.csic.es">dmaluenda@cnb.csic.es</a> </font><font color="#000000" face="trebuchet ms,sans-serif">- <font size="1">(+34)</font> 619 029 310</font></div> <div><span style="font-family:'trebuchet ms' , sans-serif"><a href="https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.cnb.csic.es%2F&data=04%7C01%7Cria2%40psu.edu%7C8e9b7c5aa1d54746d3e408d87bf860fc%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637395654004311009%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=6kFNVSCUIjY9yH8KWZdNRtX2stnOT92uoobn3EWhseo%3D&reserved=0"><font color="#0000ff">CSIC - Centro Nacional de Biotecnología</font></a></span></div> <div><span style="font-family:'trebuchet ms' , sans-serif"><font color="#0000ff"><a href="https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbiocomputingunit.es%2F&data=04%7C01%7Cria2%40psu.edu%7C8e9b7c5aa1d54746d3e408d87bf860fc%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637395654004311009%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=4PytI0mGWheRX0qMHZc1runOa3ipTB5axLBZ6bZMwjs%3D&reserved=0">BioComputing Unit</a><br /> </font></span></div> <div><font size="1" color="#cccccc" face="Arial"><br /> 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. 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Thank you for your collaboration.</font></div> <div><font size="1" color="#cccccc" face="Arial"><br /> </font></div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> </div> <br /> </div> <br /> <div> <div dir="ltr">On Thu, Oct 29, 2020 at 11:16 AM Pablo Conesa <<a href="mailto:pconesa@cnb.csic.es">pconesa@cnb.csic.es</a>> wrote:<br /> </div> <blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb( 204 , 204 , 204 );padding-left:1ex"> <div> <p>I think now localrec is installed depite the error message and xmipp looks fixed too.</p> <p><br /> </p> <p>Could you please send the output of:</p> <p><br /> </p> <p>scipion3 printenv</p> <p><br /> </p> <p><br /> </p> <div>On 29/10/20 4:18, Moustafa, Ibrahim M. wrote:<br /> </div> <blockquote> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> Hi David,</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> <br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> 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. </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> I re-installed scipion-em-localrec 'scipion installp -p scipion-em-localrec' and I still get the following error:</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> <br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> <pre style="margin:4px 0px;padding:8px;font-size:12px;line-height:1.50001;white-space:pre-wrap;border-radius:4px;color:rgb( 209 , 210 , 211 );text-align:left;font-family:'monaco' , 'menlo' , 'consolas' , 'courier new' , monospace"><span style="color:rgb( 0 , 0 , 0 )">Successfully installed scipion-em-localrec-3.0.1</span> <span style="color:rgb( 0 , 0 , 0 )">Traceback (most recent call last):</span> <span style="color:rgb( 0 , 0 , 0 )"> File "/usr/local/scipion/pip/scipion/__main__.py", line 453, in <module></span> <span style="color:rgb( 0 , 0 , 0 )"> main()</span> <span style="color:rgb( 0 , 0 , 0 )"> File "/usr/local/scipion/pip/scipion/__main__.py", line 296, in main</span> <span style="color:rgb( 0 , 0 , 0 )"> installPluginMethods()</span> <span style="color:rgb( 0 , 0 , 0 )"> File "/usr/local/scipion/pip/scipion/install/install_plugin.py", line 229, in installPluginMethods</span> <span style="color:rgb( 0 , 0 , 0 )"> installed = plugin.installPipModule(version=pluginVersion)</span> <span style="color:rgb( 0 , 0 , 0 )"> File "/usr/local/scipion/pip/scipion/install/plugin_funcs.py", line 152, in installPipModule</span> <span style="color:rgb( 0 , 0 , 0 )"> environment.execute()</span> <span style="color:rgb( 0 , 0 , 0 )"> File "/usr/local/scipion/pip/scipion/install/funcs.py", line 748, in execute</span> <span style="color:rgb( 0 , 0 , 0 )"> self._executeTargets(targetList)</span> <span style="color:rgb( 0 , 0 , 0 )"> File "/usr/local/scipion/pip/scipion/install/funcs.py", line 690, in _executeTargets</span> <span style="color:rgb( 0 , 0 , 0 )"> tgt.execute()</span> <span style="color:rgb( 0 , 0 , 0 )">File "/usr/local/scipion/pip/scipion/install/funcs.py", line 220, in execute</span> <span style="color:rgb( 0 , 0 , 0 )"> command.execute()</span> <span style="color:rgb( 0 , 0 , 0 )"> File "/usr/local/scipion/pip/scipion/install/funcs.py", line 160, in execute</span> <span style="color:rgb( 0 , 0 , 0 )"> assert glob(t), ("target '%s' not built (after "</span> <span style="color:rgb( 0 , 0 , 0 )">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')</span> <span style="color:rgb( 0 , 0 , 0 )">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')</span></pre> <br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> No idea why it could not build in the site-packages directory (which I own)!</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> <br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> Now if I run: 'scipion3 inspect localrec' I get the following: </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> Scipion v3.0.5 () devel <div>Plugin: localrec</div> <div> >>> constants: loaded</div> <div> >>> convert: loaded</div> <div> >>> protocols: loaded</div> <div> >>> wizards: missing</div> <div> >>> viewers: loaded</div> <div> >>> tests: loaded</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> <br /> </div> I also still not able to run Scipion3, I get the following error:</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> Traceback (most recent call last): <div> File "/usr/local/scipion/pip/scipion/__main__.py", line 453, in <module></div> <div> main()</div> <div> File "/usr/local/scipion/pip/scipion/__main__.py", line 262, in main</div> <div> ProjectManagerWindow().show()</div> <div> File "/usr/local/scipion/pip/pyworkflow/gui/project/project.py", line 391, in __init__</div> <div> ProjectBaseWindow.__init__(self, title, minsize=(750, 500),</div> <div> File "/usr/local/scipion/pip/pyworkflow/gui/project/base.py", line 53, in __init__</div> <div> Window.__init__(self, title, masterWindow, weight=weight,</div> <div> File "/usr/local/scipion/pip/pyworkflow/gui/gui.py", line 261, in __init__</div> <div> pw.Config.getDomain()._discoverGUIPlugins()</div> <div> File "/usr/local/scipion/pip/pyworkflow/plugin.py", line 107, in _discoverGUIPlugins</div> <div> entry_point.load()</div> <div> File "/usr/local/scipion/pip/pkg_resources/__init__.py", line 2446, in load</div> <div> self.require(*args, **kwargs)</div> <div> File "/usr/local/scipion/pip/pkg_resources/__init__.py", line 2469, in require</div> <div> items = working_set.resolve(reqs, env, installer, extras=self.extras)</div> <div> File "/usr/local/scipion/pip/pkg_resources/__init__.py", line 775, in resolve</div> <div> raise VersionConflict(dist, req).with_context(dependent_req)</div> <div>pkg_resources.ContextualVersionConflict: (numpy 1.19.2 (/usr/local/scipion/pip), Requirement.parse('numpy<=1.18.4'), {'scipion-pyworkflow'})</div> <div>Error at main: (numpy 1.19.2 (/usr/local/scipion/pip), Requirement.parse('numpy<=1.18.4'), {'scipion-pyworkflow'})</div> <br /> <br /> Any suggestion to get this fixed is appreciated!</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> <br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> Thanks,</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> Ibrahim<br /> <br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> <br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> <br /> </div> <hr style="display:inline-block;width:98%" /> <div dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> David Maluenda <a href="mailto:dmaluenda@cnb.csic.es"><dmaluenda@cnb.csic.es></a><br /> <b>Sent:</b> Wednesday, October 28, 2020 2:32 PM<br /> <b>To:</b> Mailing list for Scipion users <a href="mailto:scipion-users@lists.sourceforge.net"> <scipion-users@lists.sourceforge.net></a><br /> <b>Subject:</b> Re: [scipion-users] problem installing scipion3</font> <div> </div> </div> <div> <div dir="auto">Hi, <div dir="auto"><br /> </div> <div dir="auto">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'</div> <div dir="auto"><br /> </div> <div dir="auto"><br /> </div> <div dir="auto">Hope it helps.</div> <div dir="auto"><br /> </div> <div dir="auto">Regards,<br /> <br /> <div dir="auto">_____<br /> Dr. David Maluenda Niubó<br /> (+34) 619.029.310 - <a href="mailto:dmaluenda@ub.edu">dmaluenda@ub.edu</a><br /> Wavefront Engineering Group<br /> Applied Physics (UB)</div> </div> </div> <br /> <div> <div dir="ltr">El mié., 28 oct. 2020 17:25, Moustafa, Ibrahim M. <<a href="mailto:ria2@psu.edu">ria2@psu.edu</a>> escribió:<br /> </div> <blockquote style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb( 204 , 204 , 204 );padding-left:1ex"> <div dir="ltr"> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> Running "scipion3 inspect localrec" gives the following error:</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> <br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> Scipion v3.0.5 () devel <div><br /> </div> <div> >>> WARNING: Image library not found!</div> <div> > Please install Xmipp to get full functionality.</div> <div>(Configuration->Plugins->scipion-em-xmipp -> expand, in Scipion plugin manager window)</div> <div><br /> </div> <div><br /> </div> <div>Plugin: localrec</div> <div> >>> constants: loaded</div> <div> >>> convert: loaded</div> <div> >>> protocols: loaded</div> <div> >>> wizards: missing</div> <div> >>> viewers: loaded</div> <div> >>> tests: error -> Traceback (most recent call last):</div> <div> File "/usr/local/scipion/pip/scipion/install/inspect-plugins.py", line 74, in getSubmodule</div> <div> m = importlib.import_module('%s.%s' % (name, subname))</div> <div> File "/usr/local/miniconda/envs/.scipion3env/lib/python3.8/importlib/__init__.py", line 127, in import_module</div> <div> return _bootstrap._gcd_import(name[level:], package, level)</div> <div> File "<frozen importlib._bootstrap>", line 1014, in _gcd_import</div> <div> File "<frozen importlib._bootstrap>", line 991, in _find_and_load</div> <div> File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked</div> <div> File "<frozen importlib._bootstrap>", line 671, in _load_unlocked</div> <div> File "<frozen importlib._bootstrap_external>", line 783, in exec_module</div> <div> File "<frozen importlib._bootstrap>", line 219, in _call_with_frames_removed</div> File "/usr/local/scipion/pip/localrec/tests/__init__.py", line 27, in <module><br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> from .test_protocol_localized_reconstruction import (TestLocalizedReconsBase, <div> File "/usr/local/scipion/pip/localrec/tests/test_protocol_localized_reconstruction.py", line 37, in <module></div> <div> from xmipp3.protocols import XmippProtCreateMask3D</div> <div> File "/usr/local/scipion/pip/xmipp3/protocols/__init__.py", line 50, in <module></div> <div> from .protocol_ctf_micrographs import XmippProtCTFMicrographs</div> <div> File "/usr/local/scipion/pip/xmipp3/protocols/protocol_ctf_micrographs.py", line 44, in <module></div> <div> from xmipp3.base import isMdEmpty</div> ImportError: cannot import name 'isMdEmpty' from 'xmipp3.base' (/usr/local/scipion/pip/xmipp3/base.py)<br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> <br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> Ibrahim</div> <hr style="display:inline-block;width:98%" /> <div dir="ltr"> <font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Pablo Conesa <<a href="mailto:pconesa@cnb.csic.es">pconesa@cnb.csic.es</a>><br /> <b>Sent:</b> Wednesday, October 28, 2020 2:23 AM<br /> <b>To:</b> <a href="mailto:scipion-users@lists.sourceforge.net"> scipion-users@lists.sourceforge.net</a> <<a href="mailto:scipion-users@lists.sourceforge.net">scipion-users@lists.sourceforge.net</a>><br /> <b>Subject:</b> Re: [scipion-users] problem installing scipion3</font> <div> </div> </div> <div> <p>Despite the error, it seems localrec is installed.</p> <p>What about:</p> <p>./scipion3 inspect localrec</p> <p><br /> </p> <div>On 27/10/20 19:12, Moustafa, Ibrahim M. wrote:<br /> </div> <blockquote>scipion-em-localrec 3.0.1</blockquote> <div>-- <br /> Pablo Conesa - <strong>Madrid <a href="https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fscipion.i2pc.es%2F&data=04%7C01%7Cria2%40psu.edu%7C8e9b7c5aa1d54746d3e408d87bf860fc%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637395654004311009%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=FjnNlurCxbneNXwp7bE3txsqZK8VC2JELVR%2Fvxl2FBc%3D&reserved=0"> Scipion</a> team</strong></div> </div> </div> _______________________________________________<br /> scipion-users mailing list<br /> <a href="mailto:scipion-users@lists.sourceforge.net">scipion-users@lists.sourceforge.net</a><br /> <a href="https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fscipion-users&data=04%7C01%7Cria2%40psu.edu%7C8e9b7c5aa1d54746d3e408d87bf860fc%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637395654004321001%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=ygQiTpaQhhAPZskDNurYuAACI%2BM5mZ%2Fn8g%2FDuBss0yI%3D&reserved=0">https://lists.sourceforge.net/lists/listinfo/scipion-users</a><br /> </blockquote> </div> </div> <br /> <fieldset></fieldset> <br /> <fieldset></fieldset> <pre>_______________________________________________ scipion-users mailing list <a href="mailto:scipion-users@lists.sourceforge.net">scipion-users@lists.sourceforge.net</a> <a href="https://nam01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fscipion-users&data=04%7C01%7Cria2%40psu.edu%7C8e9b7c5aa1d54746d3e408d87bf860fc%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C0%7C637395654004330999%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=cKPih6fvBenoVP0i36Y7FHkkS2zCssv3GhWgehsI8%2BA%3D&reserved=0">https://lists.sourceforge.net/lists/listinfo/scipion-users</a> </pre> </blockquote> <div>-- <br /> Pablo Conesa - 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