Menu
▾
▴
Re: [scipion-users] problem installing scipion3
|
From: <pc...@cn...> - 2020-10-27 06:25:08
|
<div dir='auto'>What gives you:<div dir="auto"><br></div><div dir="auto">ls -l <span style="font-family: calibri, arial, helvetica, sans-serif; font-size: 16px;">/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_ em_</span></div></div><div class="gmail_extra"><br><div class="gmail_quote">El 26 oct. 2020 17:57, "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 )"> Hi Pablo,</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 for your reply.</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 tried your suggestions and I got 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 )"> ==================================================================================</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> Scipion v3.0.5 () devel <div>Building scipion-em-localrec ...</div> <div>/usr/local/miniconda/envs/.scipion3env/bin/python -m pip install scipion-em-localrec==3.0.1</div> <div>Collecting scipion-em-localrec==3.0.1</div> <div> Using cached scipion_em_localrec-3.0.1-py3-none-any.whl (530 kB)</div> <div>Installing collected packages: scipion-em-localrec</div> <div>Successfully installed scipion-em-localrec-3.0.1</div> <div>Traceback (most recent call last):</div> <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 296, in main</div> <div> installPluginMethods()</div> <div> File "/usr/local/scipion/pip/scipion/install/install_plugin.py", line 229, in installPluginMethod s</div> <div> installed = plugin.installPipModule(version=pluginVersion)</div> <div> File "/usr/local/scipion/pip/scipion/install/plugin_funcs.py", line 152, in installPipModule</div> <div> environment.execute()</div> <div> File "/usr/local/scipion/pip/scipion/install/funcs.py", line 748, in execute</div> <div> self._executeTargets(targetList)</div> <div> File "/usr/local/scipion/pip/scipion/install/funcs.py", line 690, in _executeTargets</div> <div> tgt.execute()</div> <div> File "/usr/local/scipion/pip/scipion/install/funcs.py", line 220, in execute</div> <div> command.execute()</div> <div> File "/usr/local/scipion/pip/scipion/install/funcs.py", line 160, in execute</div> <div> assert glob(t), ("target '%s' not built (after "</div> <div>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 in stall scipion-em-localrec==3.0.1')</div> <div>Error at main: target '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_e m_localrec*' not built (after running '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip ins tall scipion-em-localrec==3.0.1')</div> <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 )"> Any idea to fix this?</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 for help.</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> pconesa@cnb.csic.es <pconesa@cnb.csic.es><br /> <b>Sent:</b> Saturday, October 24, 2020 11:56 PM<br /> <b>To:</b> Mailing list for Scipion users <scipion-users@lists.sourceforge.net><br /> <b>Cc:</b> Carnegie, Mike Scott <mzc5001@psu.edu><br /> <b>Subject:</b> Re: [scipion-users] problem installing scipion3</font> <div> </div> </div> <div> <div dir="auto"> <div>Hi, I'm sorry about you poor experience installing the plugin <div dir="auto"><br /> </div> <div dir="auto">Can you try:</div> <div dir="auto"><br /> </div> <div dir="auto">scipion3 python -m pip uninstall scipion-em-localrec</div> <div dir="auto"><br /> </div> <div dir="auto">And then:</div> <div dir="auto"><br /> </div> <div dir="auto">scipion3 installs -p scipion-em-localrec</div> <br /> <div dir="auto">?</div> <div dir="auto">Then we can also check what is wrong with bumpy.</div> <div dir="auto"><br /> </div> <div dir="auto">All the best, Pablo.</div> <div><br /> <div>El 24 oct. 2020 2:12, "Moustafa, Ibrahim M." <ria2@psu.edu> escribió:<br type="attribution" /> <blockquote style="margin:0 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 )"> Dear All,</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 )"> We are having so much trouble installing Scipion 3. We thought it went through installation but then it complained about xmipp because of conflict between numpy-1.19.1 (installed with OpenCV) and numpy-1.18.4 (installed from pip). None of the plugins seem to be properly installed when we tried, although it showed "Successfully Finished' in the log!</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 )"> Trying to install localrec-em showed 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 )"> ===========================================================================================</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> >scipion3 installp -p scipion-em-localrec</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> /usr/local/miniconda/envs/.scipion3env/bin/python -m pip install scipion-em-localrec==3.0.1 <div>Collecting scipion-em-localrec==3.0.1</div> <div> Using cached scipion_em_localrec-3.0.1-py3-none-any.whl (530 kB)</div> <div>Installing collected packages: scipion-em-localrec</div> <div>Successfully installed scipion-em-localrec-3.0.1</div> <div>WARNING: Target directory /usr/local/scipion/pip/scipion_em_localrec-3.0.1.dist-info already exists. Specify --upgrade to force replacement.</div> <div>WARNING: Target directory /usr/local/scipion/pip/localrec already exists. Specify --upgrade to force replacement.</div> <div>Traceback (most recent call last):</div> <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 296, in main</div> <div> installPluginMethods()</div> <div> File "/usr/local/scipion/pip/scipion/install/install_plugin.py", line 229, in installPluginMethods</div> <div> installed = plugin.installPipModule(version=pluginVersion)</div> <div> File "/usr/local/scipion/pip/scipion/install/plugin_funcs.py", line 152, in installPipModule</div> <div> environment.execute()</div> <div> File "/usr/local/scipion/pip/scipion/install/funcs.py", line 748, in execute</div> <div> self._executeTargets(targetList)</div> <div> File "/usr/local/scipion/pip/scipion/install/funcs.py", line 690, in _executeTargets</div> <div> tgt.execute()</div> <div> File "/usr/local/scipion/pip/scipion/install/funcs.py", line 220, in execute</div> <div> command.execute()</div> <div> File "/usr/local/scipion/pip/scipion/install/funcs.py", line 160, in execute</div> <div> assert glob(t), ("target '%s' not built (after "</div> <div>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')</div> 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')<br /> </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> ==================================================================================</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 )"> Not sure what we are doing wrong! It would be appreciated if someone can share a "clear" protocol of how to properly install Scipion 3 along with plugins. We are mostly interested in </div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> localrec plugin.</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 )"> P.S. we are using py3.8 from miniconda</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 )"> Appreciate your help,</div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> Ibrahim</div> <div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> <br /> </div> <div> <div> <div style="font-family:'calibri' , 'arial' , 'helvetica' , sans-serif;font-size:12pt;color:rgb( 0 , 0 , 0 )"> <div style="color:rgb( 34 , 34 , 34 );font-family:'arial' , 'helvetica' , sans-serif;font-size:small;background-color:rgb( 255 , 255 , 255 )"> <span style="font-family:'comic sans ms' , 'chalkboard' , cursive">Ibrahim M.Moustafa, Ph.D.</span><br /> <span style="font-family:'comic sans ms' , 'chalkboard' , cursive">Pennsylvania State University</span><br /> </div> <div style="color:rgb( 34 , 34 , 34 );font-family:'arial' , 'helvetica' , sans-serif;font-size:small;background-color:rgb( 255 , 255 , 255 )"> <span style="font-family:'comic sans ms' , 'chalkboard' , cursive">Biochemistry & Molecular Biology Dept.</span></div> <div style="color:rgb( 34 , 34 , 34 );font-family:'arial' , 'helvetica' , sans-serif;font-size:small;background-color:rgb( 255 , 255 , 255 )"> <span style="font-family:'comic sans ms' , 'chalkboard' , cursive">Millennium Science Complex </span><br /> <span style="font-family:'comic sans ms' , 'chalkboard' , cursive">University Park</span><br /> <span style="font-family:'comic sans ms' , 'chalkboard' , cursive">State College, PA16802</span><br /> <br /> <span style="font-family:'comic sans ms' , 'chalkboard' , cursive">Phone: (814) 863 5940</span><br /> <span style="font-family:'comic sans ms' , 'chalkboard' , cursive">Fax: (814) 865 7927</span></div> <br /> </div> </div> </div> </div> </div> </blockquote> </div> <br /> </div> </div> </div> </div> </div> </blockquote></div><br></div> |
