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Re: [scipion-users] problem installing scipion3
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From: Pablo C. <pc...@cn...> - 2020-10-27 17:26:55
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ummm,
what does give you:
scipion3 python -m pip list ?
On 27/10/20 17:23, Moustafa, Ibrahim M. wrote:
> I can confirm that I have permission on the environment folder.
> I also checked to see if installation goes to HOME/.local but nothing
> related to scipion there.
>
> Ibrahim
>
>
> ------------------------------------------------------------------------
> *From:* Pablo Conesa <pc...@cn...>
> *Sent:* Tuesday, October 27, 2020 4:55 AM
> *To:* sci...@li...
> <sci...@li...>
> *Subject:* Re: [scipion-users] problem installing scipion3
>
> I meant ls -l
> /usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em*
>
>
> But I can see that environment lacks all scipion packages.
>
>
> I'm guessing you do not have permission on the environment folder and
> all goes to you HOME/.local installation.
>
>
> If I'm right non of the plugins installation should work cause we do
> not expect not having permissions on the environment.
>
>
> Could you please verify this case?
>
>
> ls -l /usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages
>
>
> Will list who owns that folder.
>
>
> On 27/10/20 8:29, Moustafa, Ibrahim M. wrote:
>> ls -l
>> /usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em
>>
>> gives nothing.
>>
>> The following packages exist in
>> ls -l /usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/
>>
>> brotli
>> brotlipy-0.7.0-py3.8.egg-info
>> certifi
>> certifi-2020.6.20-py3.8.egg-info
>> cffi
>> cffi-1.14.3.dist-info
>> _cffi_backend.cpython-38-x86_64-linux-gnu.so
>> chardet
>> chardet-3.0.4.dist-info
>> cryptography
>> cryptography-3.1.1.dist-info
>> _distutils_hack
>> distutils-precedence.pth
>> easy_install.py
>> idna
>> idna-2.10.dist-info
>> OpenSSL
>> pip
>> pip-20.2.4-py3.8.egg-info
>> pkg_resources
>> __pycache__
>> pycparser
>> pycparser-2.20.dist-info
>> pyOpenSSL-19.1.0.dist-info
>> PySocks-1.7.1.dist-info
>> README.txt
>> requests
>> requests-2.24.0.dist-info
>> SConse--(71%)
>> scons-3.1.2-py3.8.egg-info
>> setuptools
>> setuptools-50.3.0.post20201006-py3.8.egg-info
>> six-1.15.0.dist-info
>> six.py
>> sockshandler.py
>> socks.py
>> urllib3
>> urllib3-1.25.11.dist-info
>> wheel
>> wheel-0.35.1-py3.6.egg-info
>>
>> Ibrahim
>> ------------------------------------------------------------------------
>> *From:* pc...@cn... <mailto:pc...@cn...>
>> <pc...@cn...> <mailto:pc...@cn...>
>> *Sent:* Tuesday, October 27, 2020 2:18 AM
>> *To:* Mailing list for Scipion users
>> <sci...@li...>
>> <mailto:sci...@li...>
>> *Subject:* Re: [scipion-users] problem installing scipion3
>> What gives you:
>>
>> ls -l
>> /usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_
>> em_
>>
>> El 26 oct. 2020 17:57, "Moustafa, Ibrahim M." <ri...@ps...>
>> <mailto:ri...@ps...> escribió:
>>
>> Hi Pablo,
>>
>> Thanks for your reply.
>>
>> I tried your suggestions and I got the following error:
>>
>> ==================================================================================
>> Scipion v3.0.5 () devel
>> Building scipion-em-localrec ...
>> /usr/local/miniconda/envs/.scipion3env/bin/python -m pip install
>> scipion-em-localrec==3.0.1
>> Collecting scipion-em-localrec==3.0.1
>> Using cached scipion_em_localrec-3.0.1-py3-none-any.whl (530 kB)
>> Installing collected packages: scipion-em-localrec
>> 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 installPluginMethod s
>> 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 in
>> stall scipion-em-localrec==3.0.1')
>> 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')
>>
>> ==================================================================================
>>
>> Any idea to fix this?
>>
>> Thanks for help.
>> Ibrahim
>> ------------------------------------------------------------------------
>> *From:* pc...@cn... <mailto:pc...@cn...>
>> <pc...@cn...> <mailto:pc...@cn...>
>> *Sent:* Saturday, October 24, 2020 11:56 PM
>> *To:* Mailing list for Scipion users
>> <sci...@li...>
>> <mailto:sci...@li...>
>> *Cc:* Carnegie, Mike Scott <mz...@ps...> <mailto:mz...@ps...>
>> *Subject:* Re: [scipion-users] problem installing scipion3
>> Hi, I'm sorry about you poor experience installing the plugin
>>
>> Can you try:
>>
>> scipion3 python -m pip uninstall scipion-em-localrec
>>
>> And then:
>>
>> scipion3 installs -p scipion-em-localrec
>>
>> ?
>> Then we can also check what is wrong with bumpy.
>>
>> All the best, Pablo.
>>
>> El 24 oct. 2020 2:12, "Moustafa, Ibrahim M." <ri...@ps...>
>> <mailto:ri...@ps...> escribió:
>>
>> Dear All,
>>
>> 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!
>>
>> Trying to install localrec-em showed the following error:
>>
>> ===========================================================================================
>> >scipion3 installp -p scipion-em-localrec
>> /usr/local/miniconda/envs/.scipion3env/bin/python -m pip
>> install scipion-em-localrec==3.0.1
>> Collecting scipion-em-localrec==3.0.1
>> Using cached scipion_em_localrec-3.0.1-py3-none-any.whl
>> (530 kB)
>> Installing collected packages: scipion-em-localrec
>> Successfully installed scipion-em-localrec-3.0.1
>> WARNING: Target directory
>> /usr/local/scipion/pip/scipion_em_localrec-3.0.1.dist-info
>> already exists. Specify --upgrade to force replacement.
>> WARNING: Target directory /usr/local/scipion/pip/localrec
>> already exists. Specify --upgrade to force replacement.
>> 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')
>> ==================================================================================
>>
>> 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
>> localrec plugin.
>>
>> P.S. we are using py3.8 from miniconda
>>
>> Appreciate your help,
>> Ibrahim
>>
>> Ibrahim M.Moustafa, Ph.D.
>> Pennsylvania State University
>> Biochemistry & Molecular Biology Dept.
>> Millennium Science Complex
>> University Park
>> State College, PA16802
>>
>> Phone: (814) 863 5940
>> Fax: (814) 865 7927
>>
>>
>>
>>
>>
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> --
> Pablo Conesa - *Madrid Scipion
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> team*
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--
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