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Re: [scipion-users] problem installing scipion3
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From: Moustafa, I. M. <ri...@ps...> - 2020-10-27 18:46:10
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That is what I get:
Scipion v3.0.5 () devel
Package Version
------------------- ---------
appdirs 1.4.4
bibtexparser 1.2.0
biopython 1.76
brotlipy 0.7.0
certifi 2020.6.20
cffi 1.14.3
chardet 3.0.4
configparser 5.0.0
cryptography 3.1.1
cycler 0.10.0
distlib 0.3.1
emtable 0.0.7
filelock 3.0.12
future 0.18.2
idna 2.10
importlib-metadata 2.0.0
joblib 0.17.0
kiwisolver 1.2.0
littleutils 0.2.2
matplotlib 3.2.2
mrcfile 1.1.2
numpy 1.19.2
opencv-python 4.4.0.44
outdated 0.2.0
peppercorn 0.6
Pillow 7.1.2
pip 20.2.4
plotter 1.3.17
psutil 5.7.0
pycparser 2.20
pyOpenSSL 19.1.0
pyparsing 2.4.7
PySocks 1.7.1
python-dateutil 2.8.1
requests 2.23.0
scikit-learn 0.22.1
scipion-app 3.0.5
scipion-em 3.0.4
scipion-em-eman2 3.1.1
scipion-em-localrec 3.0.1
scipion-em-locscale 3.0.2
scipion-em-relion 3.0.0b3
scipion-em-tomo 3.0.6
scipion-em-xmipp 20.7.1
scipion-em-xmipp2 3.0.0
scipion-installer 1.0.9
scipion-pyworkflow 3.0.5
scipy 1.5.3
SCons 4.0.1
setuptools 50.3.2
six 1.15.0
urllib3 1.25.11
virtualenv 20.0.35
wheel 0.35.1zipp 3.3.1
Ibrahim
________________________________
From: Pablo Conesa <pc...@cn...>
Sent: Tuesday, October 27, 2020 1:26 PM
To: sci...@li... <sci...@li...>
Subject: Re: [scipion-users] problem installing scipion3
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...><mailto:pc...@cn...>
Sent: Tuesday, October 27, 2020 4:55 AM
To: sci...@li...<mailto:sci...@li...> <sci...@li...><mailto: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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