Re: [scipion-users] problem installing scipion3

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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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Re: [scipion-users] problem installing scipion3

Image processing framework to integrate EM software packages.

Re: [scipion-users] problem installing scipion3